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=tiltseries0008 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0008 --tiltseries=8 --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-17hr28m16s Description: coarse_series0008_iter2.tlt not found, using coarse_series0008.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0008.tlt to series0008.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 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) = 0.03803 for Iteration #1 of Tilt-Series #8. CCMS(rotations) = 1.09835 for Iteration #1 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8. The scaled sum of CCMS values is #0.04098 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.02136 for Iteration #2 of Tilt-Series #8. CCMS(rotations) = 0.1384 for Iteration #2 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8. The scaled sum of CCMS values is #0.01345 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00576 for Iteration #3 of Tilt-Series #8. CCMS(rotations) = 0.22738 for Iteration #3 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8. The scaled sum of CCMS values is #0.00743 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00506 for Iteration #4 of Tilt-Series #8. CCMS(rotations) = 0.1913 for Iteration #4 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8. The scaled sum of CCMS values is #0.00636 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00581 for Iteration #5 of Tilt-Series #8. CCMS(rotations) = 0.21462 for Iteration #5 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8. The scaled sum of CCMS values is #0.0072 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00602 for Iteration #6 of Tilt-Series #8. CCMS(rotations) = 0.16093 for Iteration #6 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8. The scaled sum of CCMS values is #0.00623 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00696 for Iteration #7 of Tilt-Series #8. CCMS(rotations) = 0.22092 for Iteration #7 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8. The scaled sum of CCMS values is #0.0079 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00548 for Iteration #8 of Tilt-Series #8. CCMS(rotations) = 0.16031 for Iteration #8 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8. The scaled sum of CCMS values is #0.00594 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00713 for Iteration #9 of Tilt-Series #8. CCMS(rotations) = 0.21836 for Iteration #9 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8. The scaled sum of CCMS values is #0.00793 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #8 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00585 for Iteration #10 of Tilt-Series #8. CCMS(rotations) = 0.1808 for Iteration #10 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8. The scaled sum of CCMS values is #0.00654 for Tilt-Series #8. 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 #8 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) = 0.00673 for Iteration #11 of Tilt-Series #8. CCMS(rotations) = 0.18186 for Iteration #11 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8. The scaled sum of CCMS values is #0.007 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00494 for Iteration #12 of Tilt-Series #8. CCMS(rotations) = 0.1743 for Iteration #12 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8. The scaled sum of CCMS values is #0.00596 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00446 for Iteration #13 of Tilt-Series #8. CCMS(rotations) = 0.20126 for Iteration #13 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8. The scaled sum of CCMS values is #0.00625 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00635 for Iteration #14 of Tilt-Series #8. CCMS(rotations) = 0.1825 for Iteration #14 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8. The scaled sum of CCMS values is #0.00683 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.0046 for Iteration #15 of Tilt-Series #8. CCMS(rotations) = 0.14986 for Iteration #15 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8. The scaled sum of CCMS values is #0.0053 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00617 for Iteration #16 of Tilt-Series #8. CCMS(rotations) = 0.15579 for Iteration #16 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8. The scaled sum of CCMS values is #0.0062 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00478 for Iteration #17 of Tilt-Series #8. CCMS(rotations) = 0.17103 for Iteration #17 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8. The scaled sum of CCMS values is #0.00581 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00599 for Iteration #18 of Tilt-Series #8. CCMS(rotations) = 0.12052 for Iteration #18 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8. The scaled sum of CCMS values is #0.0054 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00421 for Iteration #19 of Tilt-Series #8. CCMS(rotations) = 0.12213 for Iteration #19 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8. The scaled sum of CCMS values is #0.00455 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #8 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00636 for Iteration #20 of Tilt-Series #8. CCMS(rotations) = 0.16706 for Iteration #20 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8. The scaled sum of CCMS values is #0.00652 for Tilt-Series #8. 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 #8 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) = 0.00835 for Iteration #21 of Tilt-Series #8. CCMS(rotations) = 0.25656 for Iteration #21 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8. The scaled sum of CCMS values is #0.00931 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #8 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00614 for Iteration #22 of Tilt-Series #8. CCMS(rotations) = 0.12183 for Iteration #22 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8. The scaled sum of CCMS values is #0.00551 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #8 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00814 for Iteration #23 of Tilt-Series #8. CCMS(rotations) = 0.16326 for Iteration #23 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8. The scaled sum of CCMS values is #0.00733 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #8 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00671 for Iteration #24 of Tilt-Series #8. CCMS(rotations) = 0.1228 for Iteration #24 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8. The scaled sum of CCMS values is #0.00581 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #8 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00787 for Iteration #25 of Tilt-Series #8. CCMS(rotations) = 0.24317 for Iteration #25 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8. The scaled sum of CCMS values is #0.0088 for Tilt-Series #8. 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 #8 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) = 0.0073 for Iteration #26 of Tilt-Series #8. CCMS(rotations) = 0.09188 for Iteration #26 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8. The scaled sum of CCMS values is #0.00549 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00591 for Iteration #27 of Tilt-Series #8. CCMS(rotations) = 0.18717 for Iteration #27 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #8. The scaled sum of CCMS values is #0.0067 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00541 for Iteration #28 of Tilt-Series #8. CCMS(rotations) = 0.17909 for Iteration #28 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #8. The scaled sum of CCMS values is #0.00629 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00509 for Iteration #29 of Tilt-Series #8. CCMS(rotations) = 0.22981 for Iteration #29 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #8. The scaled sum of CCMS values is #0.00714 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00861 for Iteration #30 of Tilt-Series #8. CCMS(rotations) = 0.17446 for Iteration #30 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #8. The scaled sum of CCMS values is #0.0078 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #8 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.0062 for Iteration #31 of Tilt-Series #8. CCMS(rotations) = 0.23775 for Iteration #31 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #8. The scaled sum of CCMS values is #0.00785 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00647 for Iteration #32 of Tilt-Series #8. CCMS(rotations) = 0.15997 for Iteration #32 of Tilt-Series #8. CCMS(scale) = 0.00206 for Iteration #32 of Tilt-Series #8. The scaled sum of CCMS values is #0.00498 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00466 for Iteration #33 of Tilt-Series #8. CCMS(rotations) = 0.25943 for Iteration #33 of Tilt-Series #8. CCMS(scale) = 0.0024 for Iteration #33 of Tilt-Series #8. The scaled sum of CCMS values is #0.00581 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00423 for Iteration #34 of Tilt-Series #8. CCMS(rotations) = 0.22582 for Iteration #34 of Tilt-Series #8. CCMS(scale) = 0.00197 for Iteration #34 of Tilt-Series #8. The scaled sum of CCMS values is #0.00508 for Tilt-Series #8. 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 #8 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #8 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00565 for Iteration #35 of Tilt-Series #8. CCMS(rotations) = 0.17145 for Iteration #35 of Tilt-Series #8. CCMS(scale) = 0.00191 for Iteration #35 of Tilt-Series #8. The scaled sum of CCMS values is #0.0048 for Tilt-Series #8. 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 #8! 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-05hr14m27s