[Thu Dec 29 17:06:55 2016] finished run of protomo2aligner [ anoble@node05: Thu Dec 29 17:15:57 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --negative=-22 --positive=22 \ --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 --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 \ --orientation=true --azimuth=false --azimuth_switch=22 --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=tiltseries0005 \ --rundir=/gpfs/appion/anoble/16dec29d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16dec29d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=304 \ --expid=3178 --jobtype=protomo Start time: 2016yr12m29d-17hr15m57s Description: Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 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 = 50.1311259224 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 = 50.1311259224 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.01253 for Iteration #1 of Tilt-Series #5. CCMS(rotations) = 0.15965 for Iteration #1 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5. The scaled sum of CCMS values is #0.00946 for Tilt-Series #5. 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 Beginning Refinement Iteration #2, Round #1 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01035 for Iteration #2 of Tilt-Series #5. CCMS(rotations) = 0.11806 for Iteration #2 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5. The scaled sum of CCMS values is #0.00753 for Tilt-Series #5. 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 Beginning Refinement Iteration #3, Round #1 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01059 for Iteration #3 of Tilt-Series #5. CCMS(rotations) = 0.08997 for Iteration #3 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5. The scaled sum of CCMS values is #0.00709 for Tilt-Series #5. 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 Beginning Refinement Iteration #4, Round #1 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01212 for Iteration #4 of Tilt-Series #5. CCMS(rotations) = 0.09302 for Iteration #4 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5. The scaled sum of CCMS values is #0.00792 for Tilt-Series #5. 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 Beginning Refinement Iteration #5, Round #1 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01172 for Iteration #5 of Tilt-Series #5. CCMS(rotations) = 0.10059 for Iteration #5 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5. The scaled sum of CCMS values is #0.00787 for Tilt-Series #5. 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 Beginning Refinement Iteration #6, Round #1 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01067 for Iteration #6 of Tilt-Series #5. CCMS(rotations) = 0.1269 for Iteration #6 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5. The scaled sum of CCMS values is #0.00787 for Tilt-Series #5. 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 Beginning Refinement Iteration #7, Round #1 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01055 for Iteration #7 of Tilt-Series #5. CCMS(rotations) = 0.08626 for Iteration #7 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5. The scaled sum of CCMS values is #0.007 for Tilt-Series #5. 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 Beginning Refinement Iteration #8, Round #1 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01221 for Iteration #8 of Tilt-Series #5. CCMS(rotations) = 0.09582 for Iteration #8 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5. The scaled sum of CCMS values is #0.00802 for Tilt-Series #5. 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 Beginning Refinement Iteration #9, Round #1 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01166 for Iteration #9 of Tilt-Series #5. CCMS(rotations) = 0.1204 for Iteration #9 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5. The scaled sum of CCMS values is #0.00824 for Tilt-Series #5. 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 Beginning Refinement Iteration #10, Round #1 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01226 for Iteration #10 of Tilt-Series #5. CCMS(rotations) = 0.08766 for Iteration #10 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5. The scaled sum of CCMS values is #0.00788 for Tilt-Series #5. 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 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 = 100.262251845 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 = 100.262251845 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01103 for Iteration #11 of Tilt-Series #5. CCMS(rotations) = 0.10744 for Iteration #11 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5. The scaled sum of CCMS values is #0.00766 for Tilt-Series #5. 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 Beginning Refinement Iteration #12, Round #2 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.01142 for Iteration #12 of Tilt-Series #5. CCMS(rotations) = 0.10803 for Iteration #12 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5. The scaled sum of CCMS values is #0.00787 for Tilt-Series #5. 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 Beginning Refinement Iteration #13, Round #2 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01109 for Iteration #13 of Tilt-Series #5. CCMS(rotations) = 0.12957 for Iteration #13 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5. The scaled sum of CCMS values is #0.00814 for Tilt-Series #5. 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 Beginning Refinement Iteration #14, Round #2 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.01085 for Iteration #14 of Tilt-Series #5. CCMS(rotations) = 0.10216 for Iteration #14 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5. The scaled sum of CCMS values is #0.00747 for Tilt-Series #5. 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 Beginning Refinement Iteration #15, Round #2 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.01127 for Iteration #15 of Tilt-Series #5. CCMS(rotations) = 0.08208 for Iteration #15 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5. The scaled sum of CCMS values is #0.00727 for Tilt-Series #5. 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 Beginning Refinement Iteration #16, Round #2 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.01156 for Iteration #16 of Tilt-Series #5. CCMS(rotations) = 0.10608 for Iteration #16 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5. The scaled sum of CCMS values is #0.0079 for Tilt-Series #5. 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 Beginning Refinement Iteration #17, Round #2 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.01077 for Iteration #17 of Tilt-Series #5. CCMS(rotations) = 0.08574 for Iteration #17 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5. The scaled sum of CCMS values is #0.0071 for Tilt-Series #5. 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 Beginning Refinement Iteration #18, Round #2 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.01164 for Iteration #18 of Tilt-Series #5. CCMS(rotations) = 0.08351 for Iteration #18 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5. The scaled sum of CCMS values is #0.00749 for Tilt-Series #5. 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 Beginning Refinement Iteration #19, Round #2 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.01125 for Iteration #19 of Tilt-Series #5. CCMS(rotations) = 0.08397 for Iteration #19 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5. The scaled sum of CCMS values is #0.0073 for Tilt-Series #5. 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 Beginning Refinement Iteration #20, Round #2 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.01105 for Iteration #20 of Tilt-Series #5. CCMS(rotations) = 0.10722 for Iteration #20 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5. The scaled sum of CCMS values is #0.00767 for Tilt-Series #5. 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 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 = 200.52450369 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 = 200.52450369 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.01336 for Iteration #21 of Tilt-Series #5. CCMS(rotations) = 0.16157 for Iteration #21 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5. The scaled sum of CCMS values is #0.00991 for Tilt-Series #5. 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 Beginning Refinement Iteration #22, Round #3 fit.azimuth switched from false to true on Iteration #22Creating quality assessment statistics... CCMS(shift) = 0.01114 for Iteration #22 of Tilt-Series #5. CCMS(rotations) = 0.15748 for Iteration #22 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5. The scaled sum of CCMS values is #0.00872 for Tilt-Series #5. 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 Beginning Refinement Iteration #23, Round #3 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.01167 for Iteration #23 of Tilt-Series #5. CCMS(rotations) = 0.13395 for Iteration #23 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5. The scaled sum of CCMS values is #0.00852 for Tilt-Series #5. 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 Beginning Refinement Iteration #24, Round #3 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.01 for Iteration #24 of Tilt-Series #5. CCMS(rotations) = 0.26866 for Iteration #24 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5. The scaled sum of CCMS values is #0.01037 for Tilt-Series #5. 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 Beginning Refinement Iteration #25, Round #3 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.01001 for Iteration #25 of Tilt-Series #5. CCMS(rotations) = 0.19562 for Iteration #25 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5. The scaled sum of CCMS values is #0.00892 for Tilt-Series #5. 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 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 = 401.049007379 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 = 401.049007379 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.01303 for Iteration #26 of Tilt-Series #5. CCMS(rotations) = 0.20849 for Iteration #26 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5. The scaled sum of CCMS values is #0.01069 for Tilt-Series #5. 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 Beginning Refinement Iteration #27, Round #4 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.01142 for Iteration #27 of Tilt-Series #5. CCMS(rotations) = 0.23344 for Iteration #27 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5. The scaled sum of CCMS values is #0.01038 for Tilt-Series #5. 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 Beginning Refinement Iteration #28, Round #4 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01114 for Iteration #28 of Tilt-Series #5. CCMS(rotations) = 0.29232 for Iteration #28 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5. The scaled sum of CCMS values is #0.01141 for Tilt-Series #5. 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 Beginning Refinement Iteration #29, Round #4 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01167 for Iteration #29 of Tilt-Series #5. CCMS(rotations) = 0.17996 for Iteration #29 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5. The scaled sum of CCMS values is #0.00943 for Tilt-Series #5. 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 Beginning Refinement Iteration #30, Round #4 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01054 for Iteration #30 of Tilt-Series #5. CCMS(rotations) = 0.17573 for Iteration #30 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5. The scaled sum of CCMS values is #0.00879 for Tilt-Series #5. 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 Beginning Refinement Iteration #31, Round #4 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.01281 for Iteration #31 of Tilt-Series #5. CCMS(rotations) = 0.20398 for Iteration #31 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5. The scaled sum of CCMS values is #0.01048 for Tilt-Series #5. 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 Beginning Refinement Iteration #32, Round #4 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00872 for Iteration #32 of Tilt-Series #5. CCMS(rotations) = 0.18541 for Iteration #32 of Tilt-Series #5. CCMS(scale) = 0.00524 for Iteration #32 of Tilt-Series #5. The scaled sum of CCMS values is #0.00712 for Tilt-Series #5. 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 Beginning Refinement Iteration #33, Round #4 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.0074 for Iteration #33 of Tilt-Series #5. CCMS(rotations) = 0.17605 for Iteration #33 of Tilt-Series #5. CCMS(scale) = 0.0046 for Iteration #33 of Tilt-Series #5. The scaled sum of CCMS values is #0.00635 for Tilt-Series #5. 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 Beginning Refinement Iteration #34, Round #4 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.0074 for Iteration #34 of Tilt-Series #5. CCMS(rotations) = 0.17914 for Iteration #34 of Tilt-Series #5. CCMS(scale) = 0.0044 for Iteration #34 of Tilt-Series #5. The scaled sum of CCMS values is #0.00632 for Tilt-Series #5. 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 Beginning Refinement Iteration #35, Round #4 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.0085 for Iteration #35 of Tilt-Series #5. CCMS(rotations) = 0.19639 for Iteration #35 of Tilt-Series #5. CCMS(scale) = 0.00446 for Iteration #35 of Tilt-Series #5. The scaled sum of CCMS values is #0.00694 for Tilt-Series #5. 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 #5! 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! End time: 2016yr12m29d-21hr12m24s