protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/jbrasch/19mar29h/protomo_alignments/tiltseries0002_thick800 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4834.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2633 --r1_region_y=3083 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4834.0 --r4_lowpass_apod_y=18.0 --r4_lowpass_apod_x=18.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=37.0 --r3_lowpass_apod_y=37.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0002_thick800 --r2_region_y=3083 --r2_region_x=2633 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2417.0 --defocus_ang_positive=90 --r5_mask_width_x=2608 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4834.0 --r3_highpass_apod_x=2417.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=633 --r2_mask_width_y=745 --r5_region_x=2633 --r5_region_y=3083 --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=7.36 --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=4834.0 --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=3058 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=2417.0 --r3_iters=5 --r1_highpass_diameter_x=4834.0 --r2_lowpass_diameter_y=29.44 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.68 --r5_lowpass_diameter_x=3.68 --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=2608 --r4_mask_width_y=3058 --r5_highpass_apod_y=2417.0 --logging=true --DefocusTol=200 --filter=median --sessionname=19mar29h --exclude_images=999999 --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=2417.0 --r1_highpass_apod_x=2417.0 --r2_highpass_apod_x=2417.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=9.0 --r5_lowpass_apod_y=9.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=58.88 --r1_lowpass_diameter_x=58.88 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=2 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1516 --r3_mask_width_x=1291 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4834.0 --r4_highpass_diameter_x=4834.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=147.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4834.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2417.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4834.0 --defocus_max=0 --r4_region_y=3083 --r4_region_x=2633 --r5_kernel_y=5 --r3_region_x=2633 --r3_region_y=3083 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=800 --expid=8799 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=14.72 --r3_lowpass_diameter_x=14.72 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=4834.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=74.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=74.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=301.0 --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=29.44 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=147.0 --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=2.5 --tilt_clip=true --r4_highpass_apod_x=2417.0 --r4_highpass_apod_y=2417.0 --azimuth=true --r1_mask_width_y=360 --r1_mask_width_x=304 --jobtype=protomo --from_multirefine=True node18 Start time: 2019yr05m16d-12hr13m00s Description: Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) lowpass = 58.88 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms) window.lowpass.apodization = { 0.199821496599 0.199821496599 } align.translimit = 37.625e0 map.sampling = 8 window.highpass.diameter = { 0.00607649151841 0.00607649151841 } window.highpass.apodization = { 0.0121529830368 0.0121529830368 } window.mask.apodization = { 10 10 } align.mask.width = { 304 360 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 88.460737923 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 329 385 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 304 360 } reference.body = 88.460737923 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.1373 for Iteration #1 of Tilt-Series #2. CCMS(rotations) = 2.44007 for Iteration #1 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2. The scaled sum of CCMS values is #0.11745 for iteration 1 of Tilt-Series #2. Alignment quality for Iteration #1 of Tilt-Series #2 (19mar29h): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.07959 for Iteration #2 of Tilt-Series #2. CCMS(rotations) = 1.18054 for Iteration #2 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2. The scaled sum of CCMS values is #0.06341 for iteration 2 of Tilt-Series #2. Alignment quality for Iteration #2 of Tilt-Series #2 (19mar29h): Bad (confidence: 100.000000%)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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01547 for Iteration #3 of Tilt-Series #2. CCMS(rotations) = 0.60667 for Iteration #3 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2. The scaled sum of CCMS values is #0.01987 for iteration 3 of Tilt-Series #2. Alignment quality for Iteration #3 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01375 for Iteration #4 of Tilt-Series #2. CCMS(rotations) = 0.35587 for Iteration #4 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2. The scaled sum of CCMS values is #0.01399 for iteration 4 of Tilt-Series #2. Alignment quality for Iteration #4 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01265 for Iteration #5 of Tilt-Series #2. CCMS(rotations) = 0.26169 for Iteration #5 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2. The scaled sum of CCMS values is #0.01156 for iteration 5 of Tilt-Series #2. Alignment quality for Iteration #5 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01057 for Iteration #6 of Tilt-Series #2. CCMS(rotations) = 0.25175 for Iteration #6 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2. The scaled sum of CCMS values is #0.01032 for iteration 6 of Tilt-Series #2. Alignment quality for Iteration #6 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (19mar29h): Rock Solid!Creating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00944 for Iteration #7 of Tilt-Series #2. CCMS(rotations) = 0.2387 for Iteration #7 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2. The scaled sum of CCMS values is #0.00949 for iteration 7 of Tilt-Series #2. Alignment quality for Iteration #7 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00979 for Iteration #8 of Tilt-Series #2. CCMS(rotations) = 0.21901 for Iteration #8 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2. The scaled sum of CCMS values is #0.00928 for iteration 8 of Tilt-Series #2. Alignment quality for Iteration #8 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00903 for Iteration #9 of Tilt-Series #2. CCMS(rotations) = 0.22411 for Iteration #9 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2. The scaled sum of CCMS values is #0.009 for iteration 9 of Tilt-Series #2. Alignment quality for Iteration #9 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00889 for Iteration #10 of Tilt-Series #2. CCMS(rotations) = 0.23113 for Iteration #10 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2. The scaled sum of CCMS values is #0.00907 for iteration 10 of Tilt-Series #2. Alignment quality for Iteration #10 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (19mar29h): Rock Solid!Creating 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 #2 (tiltseries0002_thick800) lowpass = 29.44 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms) window.lowpass.apodization = { 0.198471351351 0.198471351351 } align.translimit = 75.25e0 map.sampling = 4 window.highpass.diameter = { 0.00303824575921 0.00303824575921 } window.highpass.apodization = { 0.00607649151841 0.00607649151841 } window.mask.apodization = { 10 10 } align.mask.width = { 633 745 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 176.921475846 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 658 770 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 633 745 } reference.body = 176.921475846 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00943 for Iteration #11 of Tilt-Series #2. CCMS(rotations) = 0.33696 for Iteration #11 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2. The scaled sum of CCMS values is #0.01145 for iteration 11 of Tilt-Series #2. Alignment quality for Iteration #11 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.01008 for Iteration #12 of Tilt-Series #2. CCMS(rotations) = 0.30937 for Iteration #12 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2. The scaled sum of CCMS values is #0.01123 for iteration 12 of Tilt-Series #2. Alignment quality for Iteration #12 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.0095 for Iteration #13 of Tilt-Series #2. CCMS(rotations) = 0.25658 for Iteration #13 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2. The scaled sum of CCMS values is #0.00988 for iteration 13 of Tilt-Series #2. Alignment quality for Iteration #13 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00929 for Iteration #14 of Tilt-Series #2. CCMS(rotations) = 0.30702 for Iteration #14 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2. The scaled sum of CCMS values is #0.01079 for iteration 14 of Tilt-Series #2. Alignment quality for Iteration #14 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (19mar29h): Very StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00936 for Iteration #15 of Tilt-Series #2. CCMS(rotations) = 0.25698 for Iteration #15 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2. The scaled sum of CCMS values is #0.00982 for iteration 15 of Tilt-Series #2. Alignment quality for Iteration #15 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (19mar29h): Very StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00925 for Iteration #16 of Tilt-Series #2. CCMS(rotations) = 0.29417 for Iteration #16 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2. The scaled sum of CCMS values is #0.01051 for iteration 16 of Tilt-Series #2. Alignment quality for Iteration #16 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.01191 for Iteration #17 of Tilt-Series #2. CCMS(rotations) = 0.22263 for Iteration #17 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2. The scaled sum of CCMS values is #0.01041 for iteration 17 of Tilt-Series #2. Alignment quality for Iteration #17 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00985 for Iteration #18 of Tilt-Series #2. CCMS(rotations) = 0.26991 for Iteration #18 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2. The scaled sum of CCMS values is #0.01033 for iteration 18 of Tilt-Series #2. Alignment quality for Iteration #18 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (19mar29h): Very StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.01098 for Iteration #19 of Tilt-Series #2. CCMS(rotations) = 0.25486 for Iteration #19 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2. The scaled sum of CCMS values is #0.01059 for iteration 19 of Tilt-Series #2. Alignment quality for Iteration #19 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00911 for Iteration #20 of Tilt-Series #2. CCMS(rotations) = 0.25334 for Iteration #20 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2. The scaled sum of CCMS values is #0.00962 for iteration 20 of Tilt-Series #2. Alignment quality for Iteration #20 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) lowpass = 14.72 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms) window.lowpass.apodization = { 0.198471351351 0.198471351351 } align.translimit = 150.5e0 map.sampling = 2 window.highpass.diameter = { 0.0015191228796 0.0015191228796 } window.highpass.apodization = { 0.00303824575921 0.00303824575921 } window.mask.apodization = { 10 10 } align.mask.width = { 1291 1516 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 353.842951692 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1316 1541 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1291 1516 } reference.body = 353.842951692 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00778 for Iteration #21 of Tilt-Series #2. CCMS(rotations) = 0.25938 for Iteration #21 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2. The scaled sum of CCMS values is #0.00908 for iteration 21 of Tilt-Series #2. Alignment quality for Iteration #21 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (19mar29h): Very StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00754 for Iteration #22 of Tilt-Series #2. CCMS(rotations) = 0.26505 for Iteration #22 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2. The scaled sum of CCMS values is #0.00907 for iteration 22 of Tilt-Series #2. Alignment quality for Iteration #22 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00804 for Iteration #23 of Tilt-Series #2. CCMS(rotations) = 0.26368 for Iteration #23 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2. The scaled sum of CCMS values is #0.00929 for iteration 23 of Tilt-Series #2. Alignment quality for Iteration #23 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.01027 for Iteration #24 of Tilt-Series #2. CCMS(rotations) = 0.27778 for Iteration #24 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2. The scaled sum of CCMS values is #0.01069 for iteration 24 of Tilt-Series #2. Alignment quality for Iteration #24 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00978 for Iteration #25 of Tilt-Series #2. CCMS(rotations) = 0.21685 for Iteration #25 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2. The scaled sum of CCMS values is #0.00923 for iteration 25 of Tilt-Series #2. Alignment quality for Iteration #25 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) lowpass = 7.36 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms) window.lowpass.apodization = { 0.203984444444 0.203984444444 } align.translimit = 301.0e0 map.sampling = 1 window.highpass.diameter = { 0.000759561439801 0.000759561439801 } window.highpass.apodization = { 0.0015191228796 0.0015191228796 } window.mask.apodization = { 10 10 } align.mask.width = { 2608 3058 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 707.685903384 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2633 3083 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2608 3058 } reference.body = 707.685903384 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.01208 for Iteration #26 of Tilt-Series #2. CCMS(rotations) = 0.27878 for Iteration #26 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2. The scaled sum of CCMS values is #0.01162 for iteration 26 of Tilt-Series #2. Alignment quality for Iteration #26 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (19mar29h): Very 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.01306 for Iteration #27 of Tilt-Series #2. CCMS(rotations) = 0.36745 for Iteration #27 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2. The scaled sum of CCMS values is #0.01388 for iteration 27 of Tilt-Series #2. Alignment quality for Iteration #27 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01029 for Iteration #28 of Tilt-Series #2. CCMS(rotations) = 0.41138 for Iteration #28 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2. The scaled sum of CCMS values is #0.01337 for iteration 28 of Tilt-Series #2. Alignment quality for Iteration #28 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.0129 for Iteration #29 of Tilt-Series #2. CCMS(rotations) = 0.51618 for Iteration #29 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2. The scaled sum of CCMS values is #0.01677 for iteration 29 of Tilt-Series #2. Alignment quality for Iteration #29 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (19mar29h): Very StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.0136 for Iteration #30 of Tilt-Series #2. CCMS(rotations) = 0.50962 for Iteration #30 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2. The scaled sum of CCMS values is #0.01699 for iteration 30 of Tilt-Series #2. Alignment quality for Iteration #30 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.01029 for Iteration #31 of Tilt-Series #2. CCMS(rotations) = 0.48826 for Iteration #31 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2. The scaled sum of CCMS values is #0.01491 for iteration 31 of Tilt-Series #2. Alignment quality for Iteration #31 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (19mar29h): StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00904 for Iteration #32 of Tilt-Series #2. CCMS(rotations) = 0.47099 for Iteration #32 of Tilt-Series #2. CCMS(scale) = 0.0039 for Iteration #32 of Tilt-Series #2. The scaled sum of CCMS values is #0.01059 for iteration 32 of Tilt-Series #2. Alignment quality for Iteration #32 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (19mar29h): StableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.01139 for Iteration #33 of Tilt-Series #2. CCMS(rotations) = 0.60065 for Iteration #33 of Tilt-Series #2. CCMS(scale) = 0.00596 for Iteration #33 of Tilt-Series #2. The scaled sum of CCMS values is #0.01379 for iteration 33 of Tilt-Series #2. Alignment quality for Iteration #33 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (19mar29h): UnstableCreating 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01392 for Iteration #34 of Tilt-Series #2. CCMS(rotations) = 0.55587 for Iteration #34 of Tilt-Series #2. CCMS(scale) = 0.00675 for Iteration #34 of Tilt-Series #2. The scaled sum of CCMS values is #0.0143 for iteration 34 of Tilt-Series #2. Alignment quality for Iteration #34 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick800) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick800) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.01174 for Iteration #35 of Tilt-Series #2. CCMS(rotations) = 0.71311 for Iteration #35 of Tilt-Series #2. CCMS(scale) = 0.00758 for Iteration #35 of Tilt-Series #2. The scaled sum of CCMS values is #0.01595 for iteration 35 of Tilt-Series #2. Alignment quality for Iteration #35 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (19mar29h): StableCreating 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 #2 (tiltseries0002_thick800)! Did everything blow up and now you're yelling at your computer screen? If so, kindly post your issue on the following Appion-Protomo Google group or email Alex at anoble@nysbc.org explaining the issue and include this log file. https://groups.google.com/forum/#!topic/appion-protomo 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: 2019yr05m18d-08hr25m51s