protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=2878 --r2_region_x=2878 --r3_region_x=2878 --r4_region_x=2878 --r5_region_x=2878 --r1_region_y=2782 --r2_region_y=2782 --r3_region_y=2782 --r4_region_y=2782 --r5_region_y=2782 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=334 --r2_mask_width_x=694 --r3_mask_width_x=1414 --r4_mask_width_x=2853 --r5_mask_width_x=2853 --r1_mask_width_y=322 --r2_mask_width_y=670 --r3_mask_width_y=1366 --r4_mask_width_y=2757 --r5_mask_width_y=2757 --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=5107 --r2_highpass_diameter_x=5107 --r3_highpass_diameter_x=5107 --r4_highpass_diameter_x=5107 --r5_highpass_diameter_x=5107 --r1_highpass_diameter_y=5107 --r2_highpass_diameter_y=5107 --r3_highpass_diameter_y=5107 --r4_highpass_diameter_y=5107 --r5_highpass_diameter_y=5107 --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=2554 --r2_highpass_apod_x=2554 --r3_highpass_apod_x=2554 --r4_highpass_apod_x=2554 --r5_highpass_apod_x=2554 --r1_highpass_apod_y=2554 --r2_highpass_apod_y=2554 --r3_highpass_apod_y=2554 --r4_highpass_apod_y=2554 --r5_highpass_apod_y=2554 --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 --tilt_azimuth=-79.4 --azimuth_stability_check=True --azimuth_max_deviation=1 --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=479 --map_size_y=463 --tilt_clip=true --video_type=html5vid --runname=tiltseries0008 --rundir=/gpfs/appion/jbrasch/17mar28c/protomo_alignments/tiltseries0008 --tiltseries=8 --sessionname=17mar28c --pixelsize=1.83586 --dimx=3838 --dimy=3710 --image_file_type=mrc --coarse=False --projectid=282 --expid=3714 --jobtype=protomo node05 Start time: 2017yr03m28d-20hr24m23s Description: Using Manual alignment for Refinement by copying manual_series0008.tlt to series0008.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 (tiltseries0008) lowpass = 50.0 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 = { 0.23499008 0.23499008 } map.sampling = 8 window.highpass.diameter = { 0.00575166634032 0.00575166634032 } window.highpass.apodization = { 0.0115010806578 0.0115010806578 } window.mask.apodization = { 10 10 } align.mask.width = { 334 322 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 173.740592882 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 359 347 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 334 322 } reference.body = 173.740592882 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.03409 for Iteration #1 of Tilt-Series #8. CCMS(rotations) = 0.5947 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 #0.02894 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... The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.775000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #2 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.02739 for Iteration #2 of Tilt-Series #8. CCMS(rotations) = 0.66874 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 #0.02707 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... The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 1.231000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -79.400000 for the next iteration. No Round parameters changed for Iteration #3 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.04161 for Iteration #3 of Tilt-Series #8. CCMS(rotations) = 0.90373 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 #0.03888 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... The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.665000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #4 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.02803 for Iteration #4 of Tilt-Series #8. CCMS(rotations) = 0.68402 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 #0.0277 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... The tilt azimuth after iteration #4 deviated from the initial tilt azimuth by 0.584000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #5 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.02317 for Iteration #5 of Tilt-Series #8. CCMS(rotations) = 0.6051 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 #0.02369 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... The tilt azimuth after iteration #5 deviated from the initial tilt azimuth by 0.345000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #6 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.022 for Iteration #6 of Tilt-Series #8. CCMS(rotations) = 0.51985 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 #0.02139 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... The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.368000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #7 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.02413 for Iteration #7 of Tilt-Series #8. CCMS(rotations) = 0.5167 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 #0.0224 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... The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 0.370000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #8 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01997 for Iteration #8 of Tilt-Series #8. CCMS(rotations) = 0.50105 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 #0.02001 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... The tilt azimuth after iteration #8 deviated from the initial tilt azimuth by 0.189000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #9 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01933 for Iteration #9 of Tilt-Series #8. CCMS(rotations) = 0.54826 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 #0.02063 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... The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.166000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #10 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01457 for Iteration #10 of Tilt-Series #8. CCMS(rotations) = 0.35301 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 #0.01434 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... The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 0.443000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #11, Round #2 of Tilt-Series #8 (tiltseries0008) lowpass = 25.0 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 = { 0.233125079365 0.233125079365 } map.sampling = 4 window.highpass.diameter = { 0.00287583317016 0.00287583317016 } window.highpass.apodization = { 0.0057505403289 0.0057505403289 } window.mask.apodization = { 10 10 } align.mask.width = { 694 670 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 347.481185764 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 719 695 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 694 670 } reference.body = 347.481185764 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.02423 for Iteration #11 of Tilt-Series #8. CCMS(rotations) = 0.34551 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 #0.01902 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... The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 0.213000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #12 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.0153 for Iteration #12 of Tilt-Series #8. CCMS(rotations) = 0.31925 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 #0.01403 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... The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 0.120000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #13 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01142 for Iteration #13 of Tilt-Series #8. CCMS(rotations) = 0.29884 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 #0.01169 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... The tilt azimuth after iteration #13 deviated from the initial tilt azimuth by 0.187000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #14 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.01022 for Iteration #14 of Tilt-Series #8. CCMS(rotations) = 0.1881 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 #0.00887 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... The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 0.299000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #15 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.006 for Iteration #15 of Tilt-Series #8. CCMS(rotations) = 0.23162 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 #0.00763 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... The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 0.463000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #16 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00533 for Iteration #16 of Tilt-Series #8. CCMS(rotations) = 0.2353 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 #0.00737 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... The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.326000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #17 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00557 for Iteration #17 of Tilt-Series #8. CCMS(rotations) = 0.16392 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 #0.00606 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... The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 0.344000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #18 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00624 for Iteration #18 of Tilt-Series #8. CCMS(rotations) = 0.24075 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 #0.00793 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... The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 0.422000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #19 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00816 for Iteration #19 of Tilt-Series #8. CCMS(rotations) = 0.22782 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 #0.00864 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... The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.509000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #20 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00562 for Iteration #20 of Tilt-Series #8. CCMS(rotations) = 0.27099 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 #0.00823 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... The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 0.582000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #21, Round #3 of Tilt-Series #8 (tiltseries0008) lowpass = 12.5 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 = { 0.23688516129 0.23688516129 } map.sampling = 2 window.highpass.diameter = { 0.00143791658508 0.00143791658508 } window.highpass.apodization = { 0.00287527016445 0.00287527016445 } window.mask.apodization = { 10 10 } align.mask.width = { 1414 1366 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 694.962371527 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1439 1391 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1414 1366 } reference.body = 694.962371527 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00625 for Iteration #21 of Tilt-Series #8. CCMS(rotations) = 0.21895 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 #0.0075 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... The tilt azimuth after iteration #21 deviated from the initial tilt azimuth by 0.269000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #22 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00633 for Iteration #22 of Tilt-Series #8. CCMS(rotations) = 0.17842 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 #0.00673 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... The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 0.337000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #23 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00768 for Iteration #23 of Tilt-Series #8. CCMS(rotations) = 0.16779 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 #0.00719 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... The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 0.287000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #24 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.0089 for Iteration #24 of Tilt-Series #8. CCMS(rotations) = 0.24032 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 #0.00926 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... The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.379000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #25 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00757 for Iteration #25 of Tilt-Series #8. CCMS(rotations) = 0.29508 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 #0.00969 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... The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 0.431000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #26, Round #4 of Tilt-Series #8 (tiltseries0008) lowpass = 6.25 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 = { 0.2294825 0.2294825 } map.sampling = 1 window.highpass.diameter = { 0.00071895829254 0.00071895829254 } window.highpass.apodization = { 0.00143763508222 0.00143763508222 } window.mask.apodization = { 10 10 } align.mask.width = { 2853 2757 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 1389.92474305 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2878 2782 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2853 2757 } reference.body = 1389.92474305 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.01212 for Iteration #26 of Tilt-Series #8. CCMS(rotations) = 0.28956 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 #0.01185 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... The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 0.643000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #27 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00938 for Iteration #27 of Tilt-Series #8. CCMS(rotations) = 0.30391 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 #0.01077 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... The tilt azimuth after iteration #27 deviated from the initial tilt azimuth by 0.560000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #28 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01201 for Iteration #28 of Tilt-Series #8. CCMS(rotations) = 0.30801 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 #0.01216 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... The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 0.813000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #29 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00964 for Iteration #29 of Tilt-Series #8. CCMS(rotations) = 0.34083 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 #0.01164 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... The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 0.343000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #30 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01033 for Iteration #30 of Tilt-Series #8. CCMS(rotations) = 0.26651 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 #0.0105 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... The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 0.308000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #31 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #8 (tiltseries0008) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00907 for Iteration #31 of Tilt-Series #8. CCMS(rotations) = 0.26667 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 #0.00987 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... The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 0.173000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #32 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.01498 for Iteration #32 of Tilt-Series #8. CCMS(rotations) = 0.26945 for Iteration #32 of Tilt-Series #8. CCMS(scale) = 0.00332 for Iteration #32 of Tilt-Series #8. The scaled sum of CCMS values is #0.00969 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... The tilt azimuth after iteration #32 deviated from the initial tilt azimuth by 0.144000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #33 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.0166 for Iteration #33 of Tilt-Series #8. CCMS(rotations) = 0.28202 for Iteration #33 of Tilt-Series #8. CCMS(scale) = 0.00738 for Iteration #33 of Tilt-Series #8. The scaled sum of CCMS values is #0.01176 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... The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 0.221000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #34 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01431 for Iteration #34 of Tilt-Series #8. CCMS(rotations) = 0.27639 for Iteration #34 of Tilt-Series #8. CCMS(scale) = 0.00899 for Iteration #34 of Tilt-Series #8. The scaled sum of CCMS values is #0.01145 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... The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 0.656000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #35 of Tilt-Series #8 (tiltseries0008) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #8 (tiltseries0008) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.01628 for Iteration #35 of Tilt-Series #8. CCMS(rotations) = 0.28019 for Iteration #35 of Tilt-Series #8. CCMS(scale) = 0.00768 for Iteration #35 of Tilt-Series #8. The scaled sum of CCMS values is #0.01172 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... The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.789000, which is less than the maximum allowed deviation of 1.000000.Finished Refinement for Tilt-Series #8 (tiltseries0008)! 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: 2017yr03m30d-17hr34m06s