protomo2aligner.py --parallel=True --starting_tlt_file=Coarse_Iter_2 --r1_region_x=2226 --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 --r5_mask_width_y=2277 --r1_lowpass_diameter_x=50 --r2_lowpass_diameter_x=25 --r3_lowpass_diameter_x=12.5 --r4_lowpass_diameter_x=6.25 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=50 --r2_lowpass_diameter_y=25 --r3_lowpass_diameter_y=12.5 --r4_lowpass_diameter_y=6.25 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=125 --r2_lowpass_apod_x=63 --r3_lowpass_apod_x=31 --r4_lowpass_apod_x=16 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=125 --r2_lowpass_apod_y=63 --r3_lowpass_apod_y=31 --r4_lowpass_apod_y=16 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=1962 --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=10 --r2_iters=10 --r3_iters=5 --r4_iters=10 --r5_iters=0 --preprocessing=true --azimuth_stability_check=False --azimuth_max_deviation=3 --exclude_images_by_angle_accuracy=0.05 --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 --do_estimation=false --norotations=false --correlation_size_x=160 --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 --translimit=959 --orientation=true --azimuth=true --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true --video_type=html5vid --runname=tiltseries0006 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0006 --tiltseries=6 --sessionname=17mar18a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=1 --expid=3662 --jobtype=protomo node03 Start time: 2017yr03m20d-16hr57m20s Description: coarse_series0006_iter2.tlt not found, using coarse_series0006.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0006.tlt to series0006.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00718866462793 0.00718866462793 } window.highpass.apodization = { 0.0143773292559 0.0143773292559 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 47.6996506649 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 47.6996506649 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.04806 for Iteration #1 of Tilt-Series #6. CCMS(rotations) = 1.60703 for Iteration #1 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6. The scaled sum of CCMS values is #0.05617 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01049 for Iteration #2 of Tilt-Series #6. CCMS(rotations) = 0.21864 for Iteration #2 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6. The scaled sum of CCMS values is #0.00962 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01186 for Iteration #3 of Tilt-Series #6. CCMS(rotations) = 0.21499 for Iteration #3 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6. The scaled sum of CCMS values is #0.01023 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01266 for Iteration #4 of Tilt-Series #6. CCMS(rotations) = 0.15913 for Iteration #4 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6. The scaled sum of CCMS values is #0.00951 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01165 for Iteration #5 of Tilt-Series #6. CCMS(rotations) = 0.24258 for Iteration #5 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6. The scaled sum of CCMS values is #0.01068 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01165 for Iteration #6 of Tilt-Series #6. CCMS(rotations) = 0.11225 for Iteration #6 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6. The scaled sum of CCMS values is #0.00807 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01114 for Iteration #7 of Tilt-Series #6. CCMS(rotations) = 0.33996 for Iteration #7 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6. The scaled sum of CCMS values is #0.01237 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.0138 for Iteration #8 of Tilt-Series #6. CCMS(rotations) = 0.13454 for Iteration #8 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6. The scaled sum of CCMS values is #0.00959 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01412 for Iteration #9 of Tilt-Series #6. CCMS(rotations) = 0.308 for Iteration #9 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6. The scaled sum of CCMS values is #0.01322 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01383 for Iteration #10 of Tilt-Series #6. CCMS(rotations) = 0.13533 for Iteration #10 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6. The scaled sum of CCMS values is #0.00962 for Tilt-Series #6. 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 #6 lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.223875555556 0.223875555556 } map.sampling = 4 window.highpass.diameter = { 0.00359433231397 0.00359433231397 } window.highpass.apodization = { 0.00718866462793 0.00718866462793 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 95.3993013298 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 95.3993013298 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01076 for Iteration #11 of Tilt-Series #6. CCMS(rotations) = 0.29603 for Iteration #11 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6. The scaled sum of CCMS values is #0.0113 for Tilt-Series #6. Creating 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 #6 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00853 for Iteration #12 of Tilt-Series #6. CCMS(rotations) = 0.1502 for Iteration #12 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6. The scaled sum of CCMS values is #0.00727 for Tilt-Series #6. Creating 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 #6 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00802 for Iteration #13 of Tilt-Series #6. CCMS(rotations) = 0.17653 for Iteration #13 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6. The scaled sum of CCMS values is #0.00754 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00844 for Iteration #14 of Tilt-Series #6. CCMS(rotations) = 0.13807 for Iteration #14 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6. The scaled sum of CCMS values is #0.00698 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00827 for Iteration #15 of Tilt-Series #6. CCMS(rotations) = 0.17312 for Iteration #15 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6. The scaled sum of CCMS values is #0.0076 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.0083 for Iteration #16 of Tilt-Series #6. CCMS(rotations) = 0.14401 for Iteration #16 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6. The scaled sum of CCMS values is #0.00703 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00819 for Iteration #17 of Tilt-Series #6. CCMS(rotations) = 0.17604 for Iteration #17 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6. The scaled sum of CCMS values is #0.00762 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00815 for Iteration #18 of Tilt-Series #6. CCMS(rotations) = 0.14396 for Iteration #18 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6. The scaled sum of CCMS values is #0.00695 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00811 for Iteration #19 of Tilt-Series #6. CCMS(rotations) = 0.1787 for Iteration #19 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6. The scaled sum of CCMS values is #0.00763 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00806 for Iteration #20 of Tilt-Series #6. CCMS(rotations) = 0.14311 for Iteration #20 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6. The scaled sum of CCMS values is #0.00689 for Tilt-Series #6. 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 #6 lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.227486451613 0.227486451613 } map.sampling = 2 window.highpass.diameter = { 0.00179716615698 0.00179716615698 } window.highpass.apodization = { 0.00359433231397 0.00359433231397 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 190.79860266 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 190.79860266 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00738 for Iteration #21 of Tilt-Series #6. CCMS(rotations) = 0.11425 for Iteration #21 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6. The scaled sum of CCMS values is #0.00597 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00824 for Iteration #22 of Tilt-Series #6. CCMS(rotations) = 0.16984 for Iteration #22 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6. The scaled sum of CCMS values is #0.00752 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00792 for Iteration #23 of Tilt-Series #6. CCMS(rotations) = 0.10129 for Iteration #23 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6. The scaled sum of CCMS values is #0.00598 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00879 for Iteration #24 of Tilt-Series #6. CCMS(rotations) = 0.20317 for Iteration #24 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6. The scaled sum of CCMS values is #0.00846 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00787 for Iteration #25 of Tilt-Series #6. CCMS(rotations) = 0.14977 for Iteration #25 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6. The scaled sum of CCMS values is #0.00693 for Tilt-Series #6. 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 #6 lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.2203775 0.2203775 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 381.597205319 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 381.597205319 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00916 for Iteration #26 of Tilt-Series #6. CCMS(rotations) = 0.10658 for Iteration #26 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6. The scaled sum of CCMS values is #0.00671 for Tilt-Series #6. Creating 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 #6 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00665 for Iteration #27 of Tilt-Series #6. CCMS(rotations) = 0.18247 for Iteration #27 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6. The scaled sum of CCMS values is #0.00697 for Tilt-Series #6. Creating 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 #6 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00613 for Iteration #28 of Tilt-Series #6. CCMS(rotations) = 0.11086 for Iteration #28 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6. The scaled sum of CCMS values is #0.00528 for Tilt-Series #6. Creating 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 #6 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.0055 for Iteration #29 of Tilt-Series #6. CCMS(rotations) = 0.13438 for Iteration #29 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6. The scaled sum of CCMS values is #0.00544 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00554 for Iteration #30 of Tilt-Series #6. CCMS(rotations) = 0.10615 for Iteration #30 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6. The scaled sum of CCMS values is #0.00489 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00532 for Iteration #31 of Tilt-Series #6. CCMS(rotations) = 0.09907 for Iteration #31 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6. The scaled sum of CCMS values is #0.00464 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.0052 for Iteration #32 of Tilt-Series #6. CCMS(rotations) = 0.14492 for Iteration #32 of Tilt-Series #6. CCMS(scale) = 0.00222 for Iteration #32 of Tilt-Series #6. The scaled sum of CCMS values is #0.00441 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00452 for Iteration #33 of Tilt-Series #6. CCMS(rotations) = 0.11501 for Iteration #33 of Tilt-Series #6. CCMS(scale) = 0.00281 for Iteration #33 of Tilt-Series #6. The scaled sum of CCMS values is #0.00398 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00661 for Iteration #34 of Tilt-Series #6. CCMS(rotations) = 0.18066 for Iteration #34 of Tilt-Series #6. CCMS(scale) = 0.00199 for Iteration #34 of Tilt-Series #6. The scaled sum of CCMS values is #0.00528 for Tilt-Series #6. 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 #6 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00589 for Iteration #35 of Tilt-Series #6. CCMS(rotations) = 0.12441 for Iteration #35 of Tilt-Series #6. CCMS(scale) = 0.00301 for Iteration #35 of Tilt-Series #6. The scaled sum of CCMS values is #0.00462 for Tilt-Series #6. 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 #6! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org and include this log file. If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2017yr03m21d-04hr13m49s