protomo2aligner.py --parallel=True --starting_tlt_file=Coarse_Iter_2 --r1_region_x=1855 --r2_region_x=1855 --r3_region_x=1855 --r4_region_x=1855 --r5_region_x=1855 --r1_region_y=1919 --r2_region_y=1919 --r3_region_y=1919 --r4_region_y=1919 --r5_region_y=1919 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=206 --r2_mask_width_x=438 --r3_mask_width_x=902 --r4_mask_width_x=1830 --r5_mask_width_x=1830 --r1_mask_width_y=214 --r2_mask_width_y=454 --r3_mask_width_y=934 --r4_mask_width_y=1894 --r5_mask_width_y=1894 --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=3270 --r2_highpass_diameter_x=3270 --r3_highpass_diameter_x=3270 --r4_highpass_diameter_x=3270 --r5_highpass_diameter_x=3270 --r1_highpass_diameter_y=3270 --r2_highpass_diameter_y=3270 --r3_highpass_diameter_y=3270 --r4_highpass_diameter_y=3270 --r5_highpass_diameter_y=3270 --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=1635 --r2_highpass_apod_x=1635 --r3_highpass_apod_x=1635 --r4_highpass_apod_x=1635 --r5_highpass_apod_x=1635 --r1_highpass_apod_y=1635 --r2_highpass_apod_y=1635 --r3_highpass_apod_y=1635 --r4_highpass_apod_y=1635 --r5_highpass_apod_y=1635 --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=tiltseries0003 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0003 --tiltseries=3 --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-16hr26m18s Description: coarse_series0003_iter2.tlt not found, using coarse_series0003.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0003.tlt to series0003.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 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 = { 0.00862639755352 0.00862639755352 } window.highpass.apodization = { 0.017252795107 0.017252795107 } window.mask.apodization = { 10 10 } align.mask.width = { 206 214 } 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 = { 231 239 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 206 214 } 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) = 0.02918 for Iteration #1 of Tilt-Series #3. CCMS(rotations) = 0.48803 for Iteration #1 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3. The scaled sum of CCMS values is #0.02435 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.0112 for Iteration #2 of Tilt-Series #3. CCMS(rotations) = 0.37342 for Iteration #2 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3. The scaled sum of CCMS values is #0.01307 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01348 for Iteration #3 of Tilt-Series #3. CCMS(rotations) = 0.41112 for Iteration #3 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3. The scaled sum of CCMS values is #0.01496 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01059 for Iteration #4 of Tilt-Series #3. CCMS(rotations) = 0.32322 for Iteration #4 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3. The scaled sum of CCMS values is #0.01176 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00923 for Iteration #5 of Tilt-Series #3. CCMS(rotations) = 0.25159 for Iteration #5 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3. The scaled sum of CCMS values is #0.00965 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01072 for Iteration #6 of Tilt-Series #3. CCMS(rotations) = 0.25991 for Iteration #6 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3. The scaled sum of CCMS values is #0.01056 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00868 for Iteration #7 of Tilt-Series #3. CCMS(rotations) = 0.23432 for Iteration #7 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3. The scaled sum of CCMS values is #0.00903 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01012 for Iteration #8 of Tilt-Series #3. CCMS(rotations) = 0.24439 for Iteration #8 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3. The scaled sum of CCMS values is #0.00995 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00816 for Iteration #9 of Tilt-Series #3. CCMS(rotations) = 0.23239 for Iteration #9 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3. The scaled sum of CCMS values is #0.00873 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00976 for Iteration #10 of Tilt-Series #3. CCMS(rotations) = 0.24996 for Iteration #10 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3. The scaled sum of CCMS values is #0.00988 for Tilt-Series #3. 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 #3 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 = { 0.00431319877676 0.00431319877676 } window.highpass.apodization = { 0.00862639755352 0.00862639755352 } window.mask.apodization = { 10 10 } align.mask.width = { 438 454 } 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 = { 463 479 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 438 454 } 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) = 0.0133 for Iteration #11 of Tilt-Series #3. CCMS(rotations) = 0.56028 for Iteration #11 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3. The scaled sum of CCMS values is #0.01786 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.01343 for Iteration #12 of Tilt-Series #3. CCMS(rotations) = 0.50274 for Iteration #12 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3. The scaled sum of CCMS values is #0.01677 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01165 for Iteration #13 of Tilt-Series #3. CCMS(rotations) = 0.39231 for Iteration #13 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3. The scaled sum of CCMS values is #0.01367 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00964 for Iteration #14 of Tilt-Series #3. CCMS(rotations) = 0.16405 for Iteration #14 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3. The scaled sum of CCMS values is #0.0081 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00802 for Iteration #15 of Tilt-Series #3. CCMS(rotations) = 0.19094 for Iteration #15 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3. The scaled sum of CCMS values is #0.00783 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00848 for Iteration #16 of Tilt-Series #3. CCMS(rotations) = 0.17963 for Iteration #16 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3. The scaled sum of CCMS values is #0.00783 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00789 for Iteration #17 of Tilt-Series #3. CCMS(rotations) = 0.18857 for Iteration #17 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3. The scaled sum of CCMS values is #0.00772 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.01087 for Iteration #18 of Tilt-Series #3. CCMS(rotations) = 0.18728 for Iteration #18 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3. The scaled sum of CCMS values is #0.00918 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00678 for Iteration #19 of Tilt-Series #3. CCMS(rotations) = 0.1846 for Iteration #19 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3. The scaled sum of CCMS values is #0.00708 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #3 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00652 for Iteration #20 of Tilt-Series #3. CCMS(rotations) = 0.22161 for Iteration #20 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3. The scaled sum of CCMS values is #0.00769 for Tilt-Series #3. 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 #3 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 = { 0.00215659938838 0.00215659938838 } window.highpass.apodization = { 0.00431319877676 0.00431319877676 } window.mask.apodization = { 10 10 } align.mask.width = { 902 934 } 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 = { 927 959 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 902 934 } 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) = 0.01564 for Iteration #21 of Tilt-Series #3. CCMS(rotations) = 0.10855 for Iteration #21 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3. The scaled sum of CCMS values is #0.00999 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #3 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00615 for Iteration #22 of Tilt-Series #3. CCMS(rotations) = 0.07589 for Iteration #22 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3. The scaled sum of CCMS values is #0.00459 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #3 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00891 for Iteration #23 of Tilt-Series #3. CCMS(rotations) = 0.18649 for Iteration #23 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3. The scaled sum of CCMS values is #0.00819 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #3 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00562 for Iteration #24 of Tilt-Series #3. CCMS(rotations) = 0.1166 for Iteration #24 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3. The scaled sum of CCMS values is #0.00514 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #3 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00651 for Iteration #25 of Tilt-Series #3. CCMS(rotations) = 0.08866 for Iteration #25 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3. The scaled sum of CCMS values is #0.00503 for Tilt-Series #3. 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 #3 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 = { 0.00107829969419 0.00107829969419 } window.highpass.apodization = { 0.00215659938838 0.00215659938838 } window.mask.apodization = { 10 10 } align.mask.width = { 1830 1894 } 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 = { 1855 1919 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1830 1894 } 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) = 0.01957 for Iteration #26 of Tilt-Series #3. CCMS(rotations) = 0.66741 for Iteration #26 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3. The scaled sum of CCMS values is #0.02313 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00869 for Iteration #27 of Tilt-Series #3. CCMS(rotations) = 0.22482 for Iteration #27 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3. The scaled sum of CCMS values is #0.00884 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00767 for Iteration #28 of Tilt-Series #3. CCMS(rotations) = 0.18566 for Iteration #28 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3. The scaled sum of CCMS values is #0.00755 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01018 for Iteration #29 of Tilt-Series #3. CCMS(rotations) = 0.19047 for Iteration #29 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3. The scaled sum of CCMS values is #0.0089 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00989 for Iteration #30 of Tilt-Series #3. CCMS(rotations) = 0.26126 for Iteration #30 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3. The scaled sum of CCMS values is #0.01017 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #3 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.01036 for Iteration #31 of Tilt-Series #3. CCMS(rotations) = 0.16868 for Iteration #31 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3. The scaled sum of CCMS values is #0.00855 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00989 for Iteration #32 of Tilt-Series #3. CCMS(rotations) = 0.2523 for Iteration #32 of Tilt-Series #3. CCMS(scale) = 0.00302 for Iteration #32 of Tilt-Series #3. The scaled sum of CCMS values is #0.00767 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00863 for Iteration #33 of Tilt-Series #3. CCMS(rotations) = 0.30517 for Iteration #33 of Tilt-Series #3. CCMS(scale) = 0.00447 for Iteration #33 of Tilt-Series #3. The scaled sum of CCMS values is #0.00843 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01039 for Iteration #34 of Tilt-Series #3. CCMS(rotations) = 0.36801 for Iteration #34 of Tilt-Series #3. CCMS(scale) = 0.00557 for Iteration #34 of Tilt-Series #3. The scaled sum of CCMS values is #0.01023 for Tilt-Series #3. 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 #3 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #3 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00965 for Iteration #35 of Tilt-Series #3. CCMS(rotations) = 0.19629 for Iteration #35 of Tilt-Series #3. CCMS(scale) = 0.0055 for Iteration #35 of Tilt-Series #3. The scaled sum of CCMS values is #0.00767 for Tilt-Series #3. 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 #3! 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-01hr32m47s