protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0016_thick300 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3443.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2428 --r1_region_y=1591 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3443.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1591 --r2_region_x=2428 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1722.0 --defocus_ang_positive=90 --r5_mask_width_x=2403 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3443.0 --r3_highpass_apod_x=1722.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=582 --r2_mask_width_y=372 --r5_region_x=2428 --r5_region_y=1591 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=8.64 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=3443.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=1566 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1722.0 --runname=tiltseries0016_thick300 --r1_highpass_diameter_x=3443.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=2403 --r4_mask_width_y=1566 --r5_highpass_apod_y=1722.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1722.0 --r1_highpass_apod_x=1722.0 --r2_highpass_apod_x=1722.0 --sampling=8 --starting_tlt_file=Imod_Coarse --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=16 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=770 --r3_mask_width_x=1189 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3443.0 --r4_highpass_diameter_x=3443.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3443.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1722.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3443.0 --defocus_max=0 --r4_region_y=1591 --r4_region_x=2428 --r5_kernel_y=5 --r3_region_x=2428 --r3_region_y=1591 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=300 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=3443.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1722.0 --r4_highpass_apod_y=1722.0 --azimuth=true --r1_mask_width_y=178 --r1_mask_width_x=278 --jobtype=protomo --from_multirefine=True node37 Start time: 2018yr01m23d-18hr15m41s Description: Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) lowpass = 69.12 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms) window.lowpass.apodization = { 0.20016 0.20016 } align.translimit = 47.125e0 map.sampling = 8 window.highpass.diameter = { 0.010057415045 0.010057415045 } window.highpass.apodization = { 0.020108989547 0.020108989547 } window.mask.apodization = { 10 10 } align.mask.width = { 278 178 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 24.498345799 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 303 198 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 278 178 } reference.body = 24.498345799 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.12783 for Iteration #1 of Tilt-Series #16. CCMS(rotations) = 0.61936 for Iteration #1 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #16. The scaled sum of CCMS values is #0.0763 for iteration 1 of Tilt-Series #16. Alignment quality for Iteration #1 of Tilt-Series #16 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 93.333333%)Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... No Round parameters changed for Iteration #2 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.07873 for Iteration #2 of Tilt-Series #16. CCMS(rotations) = 0.40746 for Iteration #2 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #16. The scaled sum of CCMS values is #0.04751 for iteration 2 of Tilt-Series #16. Alignment quality for Iteration #2 of Tilt-Series #16 (17dec26e): Bad (confidence: 93.333333%)Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... No Round parameters changed for Iteration #3 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01932 for Iteration #3 of Tilt-Series #16. CCMS(rotations) = 0.23119 for Iteration #3 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #16. The scaled sum of CCMS values is #0.01428 for iteration 3 of Tilt-Series #16. Alignment quality for Iteration #3 of Tilt-Series #16 (17dec26e): Good (confidence: 93.333333%)Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... No Round parameters changed for Iteration #4 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00866 for Iteration #4 of Tilt-Series #16. CCMS(rotations) = 0.26421 for Iteration #4 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #16. The scaled sum of CCMS values is #0.00961 for iteration 4 of Tilt-Series #16. Alignment quality for Iteration #4 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00532 for Iteration #5 of Tilt-Series #16. CCMS(rotations) = 0.13844 for Iteration #5 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #16. The scaled sum of CCMS values is #0.00543 for iteration 5 of Tilt-Series #16. Alignment quality for Iteration #5 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00792 for Iteration #6 of Tilt-Series #16. CCMS(rotations) = 0.26297 for Iteration #6 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #16. The scaled sum of CCMS values is #0.00922 for iteration 6 of Tilt-Series #16. Alignment quality for Iteration #6 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #16 (17dec26e): StableCreating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00724 for Iteration #7 of Tilt-Series #16. CCMS(rotations) = 0.1548 for Iteration #7 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #16. The scaled sum of CCMS values is #0.00671 for iteration 7 of Tilt-Series #16. Alignment quality for Iteration #7 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00538 for Iteration #8 of Tilt-Series #16. CCMS(rotations) = 0.22411 for Iteration #8 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #16. The scaled sum of CCMS values is #0.00717 for iteration 8 of Tilt-Series #16. Alignment quality for Iteration #8 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... No Round parameters changed for Iteration #9 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00622 for Iteration #9 of Tilt-Series #16. CCMS(rotations) = 0.16905 for Iteration #9 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #16. The scaled sum of CCMS values is #0.00649 for iteration 9 of Tilt-Series #16. Alignment quality for Iteration #9 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... No Round parameters changed for Iteration #10 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00576 for Iteration #10 of Tilt-Series #16. CCMS(rotations) = 0.21117 for Iteration #10 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #16. The scaled sum of CCMS values is #0.0071 for iteration 10 of Tilt-Series #16. Alignment quality for Iteration #10 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #16 (17dec26e): Very StableCreating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... Beginning Refinement Iteration #11, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) lowpass = 34.56 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms) window.lowpass.apodization = { 0.20132372093 0.20132372093 } align.translimit = 94.25e0 map.sampling = 4 window.highpass.diameter = { 0.00502870752251 0.00502870752251 } window.highpass.apodization = { 0.0100544947735 0.0100544947735 } window.mask.apodization = { 10 10 } align.mask.width = { 582 372 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 48.9966915979 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 607 397 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 582 372 } reference.body = 48.9966915979 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00564 for Iteration #11 of Tilt-Series #16. CCMS(rotations) = 0.1452 for Iteration #11 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #16. The scaled sum of CCMS values is #0.00572 for iteration 11 of Tilt-Series #16. Alignment quality for Iteration #11 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #16 (17dec26e): StableCreating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00469 for Iteration #12 of Tilt-Series #16. CCMS(rotations) = 0.18396 for Iteration #12 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #16. The scaled sum of CCMS values is #0.00602 for iteration 12 of Tilt-Series #16. Alignment quality for Iteration #12 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #16 (17dec26e): Very StableCreating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00466 for Iteration #13 of Tilt-Series #16. CCMS(rotations) = 0.22442 for Iteration #13 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #16. The scaled sum of CCMS values is #0.00682 for iteration 13 of Tilt-Series #16. Alignment quality for Iteration #13 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... No Round parameters changed for Iteration #14 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00485 for Iteration #14 of Tilt-Series #16. CCMS(rotations) = 0.22337 for Iteration #14 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #16. The scaled sum of CCMS values is #0.00689 for iteration 14 of Tilt-Series #16. Alignment quality for Iteration #14 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #15 of Tilt-Series #16. CCMS(rotations) = 0.28055 for Iteration #15 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #16. The scaled sum of CCMS values is #0.0074 for iteration 15 of Tilt-Series #16. Alignment quality for Iteration #15 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... No Round parameters changed for Iteration #16 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00514 for Iteration #16 of Tilt-Series #16. CCMS(rotations) = 0.26754 for Iteration #16 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #16. The scaled sum of CCMS values is #0.00792 for iteration 16 of Tilt-Series #16. Alignment quality for Iteration #16 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... No Round parameters changed for Iteration #17 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00511 for Iteration #17 of Tilt-Series #16. CCMS(rotations) = 0.27892 for Iteration #17 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #16. The scaled sum of CCMS values is #0.00813 for iteration 17 of Tilt-Series #16. Alignment quality for Iteration #17 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... No Round parameters changed for Iteration #18 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00495 for Iteration #18 of Tilt-Series #16. CCMS(rotations) = 0.27082 for Iteration #18 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #16. The scaled sum of CCMS values is #0.00789 for iteration 18 of Tilt-Series #16. Alignment quality for Iteration #18 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00461 for Iteration #19 of Tilt-Series #16. CCMS(rotations) = 0.27426 for Iteration #19 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #16. The scaled sum of CCMS values is #0.00779 for iteration 19 of Tilt-Series #16. Alignment quality for Iteration #19 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00435 for Iteration #20 of Tilt-Series #16. CCMS(rotations) = 0.26584 for Iteration #20 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #16. The scaled sum of CCMS values is #0.00749 for iteration 20 of Tilt-Series #16. Alignment quality for Iteration #20 of Tilt-Series #16 (17dec26e): Excellent (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Beginning Refinement Iteration #21, Round #3 of Tilt-Series #16 (tiltseries0016_thick300) lowpass = 17.28 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms) window.lowpass.apodization = { 0.20132372093 0.20132372093 } align.translimit = 188.5e0 map.sampling = 2 window.highpass.diameter = { 0.00251435376125 0.00251435376125 } window.highpass.apodization = { 0.00502724738676 0.00502724738676 } window.mask.apodization = { 10 10 } align.mask.width = { 1189 770 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 97.9933831959 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1214 795 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1189 770 } reference.body = 97.9933831959 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00407 for Iteration #21 of Tilt-Series #16. CCMS(rotations) = 0.28599 for Iteration #21 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #16. The scaled sum of CCMS values is #0.00776 for iteration 21 of Tilt-Series #16. Alignment quality for Iteration #21 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... No Round parameters changed for Iteration #22 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.0039 for Iteration #22 of Tilt-Series #16. CCMS(rotations) = 0.31138 for Iteration #22 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #16. The scaled sum of CCMS values is #0.00818 for iteration 22 of Tilt-Series #16. Alignment quality for Iteration #22 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... No Round parameters changed for Iteration #23 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00409 for Iteration #23 of Tilt-Series #16. CCMS(rotations) = 0.30876 for Iteration #23 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #16. The scaled sum of CCMS values is #0.00822 for iteration 23 of Tilt-Series #16. Alignment quality for Iteration #23 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... No Round parameters changed for Iteration #24 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00377 for Iteration #24 of Tilt-Series #16. CCMS(rotations) = 0.30268 for Iteration #24 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #16. The scaled sum of CCMS values is #0.00794 for iteration 24 of Tilt-Series #16. Alignment quality for Iteration #24 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... No Round parameters changed for Iteration #25 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00416 for Iteration #25 of Tilt-Series #16. CCMS(rotations) = 0.30077 for Iteration #25 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #16. The scaled sum of CCMS values is #0.00809 for iteration 25 of Tilt-Series #16. Alignment quality for Iteration #25 of Tilt-Series #16 (17dec26e): Very Good (confidence: 93.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Beginning Refinement Iteration #26, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) lowpass = 8.64 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms) window.lowpass.apodization = { 0.196748181818 0.196748181818 } align.translimit = 377.0e0 map.sampling = 1 window.highpass.diameter = { 0.00125717688063 0.00125717688063 } window.highpass.apodization = { 0.00251362369338 0.00251362369338 } window.mask.apodization = { 10 10 } align.mask.width = { 2403 1566 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 195.986766392 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2428 1591 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2403 1566 } reference.body = 195.986766392 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00753 for Iteration #26 of Tilt-Series #16. CCMS(rotations) = 0.37939 for Iteration #26 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #16. The scaled sum of CCMS values is #0.01135 for iteration 26 of Tilt-Series #16. Alignment quality for Iteration #26 of Tilt-Series #16 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #16 (17dec26e): StableCreating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... No Round parameters changed for Iteration #27 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00616 for Iteration #27 of Tilt-Series #16. CCMS(rotations) = 0.43981 for Iteration #27 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #16. The scaled sum of CCMS values is #0.01188 for iteration 27 of Tilt-Series #16. Alignment quality for Iteration #27 of Tilt-Series #16 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #16 (17dec26e): Very StableCreating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... No Round parameters changed for Iteration #28 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00563 for Iteration #28 of Tilt-Series #16. CCMS(rotations) = 0.54462 for Iteration #28 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #16. The scaled sum of CCMS values is #0.01371 for iteration 28 of Tilt-Series #16. Alignment quality for Iteration #28 of Tilt-Series #16 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #16 (17dec26e): StableCreating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... No Round parameters changed for Iteration #29 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00536 for Iteration #29 of Tilt-Series #16. CCMS(rotations) = 0.36851 for Iteration #29 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #16. The scaled sum of CCMS values is #0.01005 for iteration 29 of Tilt-Series #16. Alignment quality for Iteration #29 of Tilt-Series #16 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... No Round parameters changed for Iteration #30 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00387 for Iteration #30 of Tilt-Series #16. CCMS(rotations) = 0.19586 for Iteration #30 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #16. The scaled sum of CCMS values is #0.00585 for iteration 30 of Tilt-Series #16. Alignment quality for Iteration #30 of Tilt-Series #16 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... No Round parameters changed for Iteration #31 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00372 for Iteration #31 of Tilt-Series #16. CCMS(rotations) = 0.18507 for Iteration #31 of Tilt-Series #16. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #16. The scaled sum of CCMS values is #0.00556 for iteration 31 of Tilt-Series #16. Alignment quality for Iteration #31 of Tilt-Series #16 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... No Round parameters changed for Iteration #32 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00305 for Iteration #32 of Tilt-Series #16. CCMS(rotations) = 0.17681 for Iteration #32 of Tilt-Series #16. CCMS(scale) = 0.0009 for Iteration #32 of Tilt-Series #16. The scaled sum of CCMS values is #0.00367 for iteration 32 of Tilt-Series #16. Alignment quality for Iteration #32 of Tilt-Series #16 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... No Round parameters changed for Iteration #33 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00337 for Iteration #33 of Tilt-Series #16. CCMS(rotations) = 0.18593 for Iteration #33 of Tilt-Series #16. CCMS(scale) = 0.00116 for Iteration #33 of Tilt-Series #16. The scaled sum of CCMS values is #0.00399 for iteration 33 of Tilt-Series #16. Alignment quality for Iteration #33 of Tilt-Series #16 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... No Round parameters changed for Iteration #34 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00337 for Iteration #34 of Tilt-Series #16. CCMS(rotations) = 0.17959 for Iteration #34 of Tilt-Series #16. CCMS(scale) = 0.00089 for Iteration #34 of Tilt-Series #16. The scaled sum of CCMS values is #0.00381 for iteration 34 of Tilt-Series #16. Alignment quality for Iteration #34 of Tilt-Series #16 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... No Round parameters changed for Iteration #35 of Tilt-Series #16 (tiltseries0016_thick300) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #16 (tiltseries0016_thick300) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.0043 for Iteration #35 of Tilt-Series #16. CCMS(rotations) = 0.16706 for Iteration #35 of Tilt-Series #16. CCMS(scale) = 0.00128 for Iteration #35 of Tilt-Series #16. The scaled sum of CCMS values is #0.00408 for iteration 35 of Tilt-Series #16. Alignment quality for Iteration #35 of Tilt-Series #16 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #16 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... Finished Refinement for Tilt-Series #16 (tiltseries0016_thick300)! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file. If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2018yr01m24d-02hr18m21s