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=tiltseries0007 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0007 --tiltseries=7 --sessionname=17mar18a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=1 --expid=3662 --jobtype=protomo node04 Start time: 2017yr03m20d-18hr22m39s Description: coarse_series0007_iter2.tlt not found, using coarse_series0007.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0007.tlt to series0007.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #7 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 = 47.7004001531 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 = 47.7004001531 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.05845 for Iteration #1 of Tilt-Series #7. CCMS(rotations) = 1.54948 for Iteration #1 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7. The scaled sum of CCMS values is #0.06022 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01659 for Iteration #2 of Tilt-Series #7. CCMS(rotations) = 0.08704 for Iteration #2 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7. The scaled sum of CCMS values is #0.01004 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00849 for Iteration #3 of Tilt-Series #7. CCMS(rotations) = 0.14326 for Iteration #3 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7. The scaled sum of CCMS values is #0.00711 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00586 for Iteration #4 of Tilt-Series #7. CCMS(rotations) = 0.04944 for Iteration #4 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7. The scaled sum of CCMS values is #0.00392 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00572 for Iteration #5 of Tilt-Series #7. CCMS(rotations) = 0.05945 for Iteration #5 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7. The scaled sum of CCMS values is #0.00405 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00755 for Iteration #6 of Tilt-Series #7. CCMS(rotations) = 0.10027 for Iteration #6 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7. The scaled sum of CCMS values is #0.00578 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.006 for Iteration #7 of Tilt-Series #7. CCMS(rotations) = 0.07353 for Iteration #7 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7. The scaled sum of CCMS values is #0.00447 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00642 for Iteration #8 of Tilt-Series #7. CCMS(rotations) = 0.12948 for Iteration #8 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7. The scaled sum of CCMS values is #0.0058 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00624 for Iteration #9 of Tilt-Series #7. CCMS(rotations) = 0.06637 for Iteration #9 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7. The scaled sum of CCMS values is #0.00445 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #7 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00672 for Iteration #10 of Tilt-Series #7. CCMS(rotations) = 0.14214 for Iteration #10 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7. The scaled sum of CCMS values is #0.0062 for Tilt-Series #7. 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 #7 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 = 95.4008003062 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 = 95.4008003062 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.0078 for Iteration #11 of Tilt-Series #7. CCMS(rotations) = 0.13389 for Iteration #11 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7. The scaled sum of CCMS values is #0.00658 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00686 for Iteration #12 of Tilt-Series #7. CCMS(rotations) = 0.22149 for Iteration #12 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7. The scaled sum of CCMS values is #0.00786 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00439 for Iteration #13 of Tilt-Series #7. CCMS(rotations) = 0.19011 for Iteration #13 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7. The scaled sum of CCMS values is #0.006 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00384 for Iteration #14 of Tilt-Series #7. CCMS(rotations) = 0.21553 for Iteration #14 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7. The scaled sum of CCMS values is #0.00623 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00391 for Iteration #15 of Tilt-Series #7. CCMS(rotations) = 0.15918 for Iteration #15 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7. The scaled sum of CCMS values is #0.00514 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00424 for Iteration #16 of Tilt-Series #7. CCMS(rotations) = 0.20703 for Iteration #16 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7. The scaled sum of CCMS values is #0.00626 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #17 of Tilt-Series #7. CCMS(rotations) = 0.174 for Iteration #17 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7. The scaled sum of CCMS values is #0.00526 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00424 for Iteration #18 of Tilt-Series #7. CCMS(rotations) = 0.20945 for Iteration #18 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7. The scaled sum of CCMS values is #0.00631 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00381 for Iteration #19 of Tilt-Series #7. CCMS(rotations) = 0.1522 for Iteration #19 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7. The scaled sum of CCMS values is #0.00495 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #7 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.0039 for Iteration #20 of Tilt-Series #7. CCMS(rotations) = 0.21513 for Iteration #20 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7. The scaled sum of CCMS values is #0.00625 for Tilt-Series #7. 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 #7 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 = 190.801600612 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 = 190.801600612 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00902 for Iteration #21 of Tilt-Series #7. CCMS(rotations) = 0.22576 for Iteration #21 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7. The scaled sum of CCMS values is #0.00903 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #7 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00718 for Iteration #22 of Tilt-Series #7. CCMS(rotations) = 0.16635 for Iteration #22 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7. The scaled sum of CCMS values is #0.00692 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #7 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00512 for Iteration #23 of Tilt-Series #7. CCMS(rotations) = 0.1653 for Iteration #23 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7. The scaled sum of CCMS values is #0.00586 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #7 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.006 for Iteration #24 of Tilt-Series #7. CCMS(rotations) = 0.17642 for Iteration #24 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7. The scaled sum of CCMS values is #0.00653 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #7 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00453 for Iteration #25 of Tilt-Series #7. CCMS(rotations) = 0.18248 for Iteration #25 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7. The scaled sum of CCMS values is #0.00592 for Tilt-Series #7. 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 #7 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 = 381.603201225 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 = 381.603201225 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00692 for Iteration #26 of Tilt-Series #7. CCMS(rotations) = 0.11091 for Iteration #26 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7. The scaled sum of CCMS values is #0.00568 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.0109 for Iteration #27 of Tilt-Series #7. CCMS(rotations) = 0.17001 for Iteration #27 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7. The scaled sum of CCMS values is #0.00885 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01422 for Iteration #28 of Tilt-Series #7. CCMS(rotations) = 0.23954 for Iteration #28 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7. The scaled sum of CCMS values is #0.0119 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01248 for Iteration #29 of Tilt-Series #7. CCMS(rotations) = 0.26843 for Iteration #29 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7. The scaled sum of CCMS values is #0.01161 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00972 for Iteration #30 of Tilt-Series #7. CCMS(rotations) = 0.33013 for Iteration #30 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7. The scaled sum of CCMS values is #0.01146 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #7 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00586 for Iteration #31 of Tilt-Series #7. CCMS(rotations) = 0.16297 for Iteration #31 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7. The scaled sum of CCMS values is #0.00619 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00737 for Iteration #32 of Tilt-Series #7. CCMS(rotations) = 0.17538 for Iteration #32 of Tilt-Series #7. CCMS(scale) = 0.00255 for Iteration #32 of Tilt-Series #7. The scaled sum of CCMS values is #0.00564 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00936 for Iteration #33 of Tilt-Series #7. CCMS(rotations) = 0.12333 for Iteration #33 of Tilt-Series #7. CCMS(scale) = 0.00214 for Iteration #33 of Tilt-Series #7. The scaled sum of CCMS values is #0.00548 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01026 for Iteration #34 of Tilt-Series #7. CCMS(rotations) = 0.25358 for Iteration #34 of Tilt-Series #7. CCMS(scale) = 0.00249 for Iteration #34 of Tilt-Series #7. The scaled sum of CCMS values is #0.00763 for Tilt-Series #7. 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 #7 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #7 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.01107 for Iteration #35 of Tilt-Series #7. CCMS(rotations) = 0.27829 for Iteration #35 of Tilt-Series #7. CCMS(scale) = 0.00379 for Iteration #35 of Tilt-Series #7. The scaled sum of CCMS values is #0.00867 for Tilt-Series #7. 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 #7! 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-06hr36m40s