protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17apr16c/protomo_alignments/tiltseries0001_thick500 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1919 --r1_region_y=1855 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1855 --r2_region_x=1919 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1894 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=454 --r2_mask_width_y=438 --r5_region_x=1919 --r5_region_y=1855 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --restart_from_run= --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=4015.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=1830 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2008.0 --runname=tiltseries0001_thick500 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=1894 --r4_mask_width_y=1830 --logging=true --DefocusTol=200 --filter=median --sessionname=17apr16c --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=1 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=902 --r3_mask_width_x=934 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4015.0 --r4_highpass_diameter_x=4015.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2008.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1855 --r4_region_x=1919 --r5_kernel_y=5 --r3_region_x=1919 --r3_region_y=1855 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=500 --restart_from_iteration=0 --expid=3854 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=206 --r1_mask_width_x=214 --jobtype=protomo node48 Start time: 2017yr04m19d-12hr48m30s Description: coarse_series0001_iter2.tlt not found, using coarse_series0001.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0001.tlt to series0001.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms) window.lowpass.apodization = { 0.27702144 0.27702144 } map.sampling = 8 window.highpass.diameter = { 0.00862457783313 0.00862457783313 } window.highpass.apodization = { 0.0172448605578 0.0172448605578 } window.mask.apodization = { 10 10 } align.mask.width = { 214 206 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 40.8341381969 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 239 231 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 214 206 } reference.body = 40.8341381969 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.07322 for Iteration #1 of Tilt-Series #1. CCMS(rotations) = 3.98541 for Iteration #1 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #1. The scaled sum of CCMS values is #0.11632 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01157 for Iteration #2 of Tilt-Series #1. CCMS(rotations) = 1.29819 for Iteration #2 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #1. The scaled sum of CCMS values is #0.03175 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01216 for Iteration #3 of Tilt-Series #1. CCMS(rotations) = 1.16153 for Iteration #3 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #1. The scaled sum of CCMS values is #0.02931 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01287 for Iteration #4 of Tilt-Series #1. CCMS(rotations) = 1.11362 for Iteration #4 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #1. The scaled sum of CCMS values is #0.02871 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.0132 for Iteration #5 of Tilt-Series #1. CCMS(rotations) = 1.0044 for Iteration #5 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #1. The scaled sum of CCMS values is #0.02669 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01285 for Iteration #6 of Tilt-Series #1. CCMS(rotations) = 0.8823 for Iteration #6 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #1. The scaled sum of CCMS values is #0.02407 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01324 for Iteration #7 of Tilt-Series #1. CCMS(rotations) = 0.81157 for Iteration #7 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #1. The scaled sum of CCMS values is #0.02285 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01146 for Iteration #8 of Tilt-Series #1. CCMS(rotations) = 0.84459 for Iteration #8 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #1. The scaled sum of CCMS values is #0.02262 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.0132 for Iteration #9 of Tilt-Series #1. CCMS(rotations) = 0.75641 for Iteration #9 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #1. The scaled sum of CCMS values is #0.02173 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01223 for Iteration #10 of Tilt-Series #1. CCMS(rotations) = 0.77046 for Iteration #10 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #1. The scaled sum of CCMS values is #0.02152 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms) window.lowpass.apodization = { 0.274822857143 0.274822857143 } map.sampling = 4 window.highpass.diameter = { 0.00431228891656 0.00431228891656 } window.highpass.apodization = { 0.00862243027888 0.00862243027888 } window.mask.apodization = { 10 10 } align.mask.width = { 454 438 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 81.6682763938 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 479 463 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 454 438 } reference.body = 81.6682763938 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.03203 for Iteration #11 of Tilt-Series #1. CCMS(rotations) = 0.59319 for Iteration #11 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #1. The scaled sum of CCMS values is #0.02788 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00783 for Iteration #12 of Tilt-Series #1. CCMS(rotations) = 0.23757 for Iteration #12 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #1. The scaled sum of CCMS values is #0.00867 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00689 for Iteration #13 of Tilt-Series #1. CCMS(rotations) = 0.2626 for Iteration #13 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #1. The scaled sum of CCMS values is #0.0087 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00854 for Iteration #14 of Tilt-Series #1. CCMS(rotations) = 0.2794 for Iteration #14 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #1. The scaled sum of CCMS values is #0.00986 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00771 for Iteration #15 of Tilt-Series #1. CCMS(rotations) = 0.22348 for Iteration #15 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #1. The scaled sum of CCMS values is #0.00832 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00836 for Iteration #16 of Tilt-Series #1. CCMS(rotations) = 0.30192 for Iteration #16 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #1. The scaled sum of CCMS values is #0.01022 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00713 for Iteration #17 of Tilt-Series #1. CCMS(rotations) = 0.2193 for Iteration #17 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #1. The scaled sum of CCMS values is #0.00795 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00846 for Iteration #18 of Tilt-Series #1. CCMS(rotations) = 0.28961 for Iteration #18 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #1. The scaled sum of CCMS values is #0.01002 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00832 for Iteration #19 of Tilt-Series #1. CCMS(rotations) = 0.23493 for Iteration #19 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #1. The scaled sum of CCMS values is #0.00886 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.01043 for Iteration #20 of Tilt-Series #1. CCMS(rotations) = 0.22889 for Iteration #20 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #1. The scaled sum of CCMS values is #0.00979 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms) window.lowpass.apodization = { 0.279255483871 0.279255483871 } map.sampling = 2 window.highpass.diameter = { 0.00215614445828 0.00215614445828 } window.highpass.apodization = { 0.00431121513944 0.00431121513944 } window.mask.apodization = { 10 10 } align.mask.width = { 934 902 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 163.336552788 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 959 927 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 934 902 } reference.body = 163.336552788 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00824 for Iteration #21 of Tilt-Series #1. CCMS(rotations) = 0.1544 for Iteration #21 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #1. The scaled sum of CCMS values is #0.00721 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00682 for Iteration #22 of Tilt-Series #1. CCMS(rotations) = 0.26756 for Iteration #22 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #1. The scaled sum of CCMS values is #0.00876 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00677 for Iteration #23 of Tilt-Series #1. CCMS(rotations) = 0.15872 for Iteration #23 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #1. The scaled sum of CCMS values is #0.00656 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00605 for Iteration #24 of Tilt-Series #1. CCMS(rotations) = 0.24792 for Iteration #24 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #1. The scaled sum of CCMS values is #0.00798 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00731 for Iteration #25 of Tilt-Series #1. CCMS(rotations) = 0.15658 for Iteration #25 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #1. The scaled sum of CCMS values is #0.00679 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms) window.lowpass.apodization = { 0.27052875 0.27052875 } map.sampling = 1 window.highpass.diameter = { 0.00107807222914 0.00107807222914 } window.highpass.apodization = { 0.00215560756972 0.00215560756972 } window.mask.apodization = { 10 10 } align.mask.width = { 1894 1830 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 326.673105575 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1919 1855 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1894 1830 } reference.body = 326.673105575 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.02226 for Iteration #26 of Tilt-Series #1. CCMS(rotations) = 0.51754 for Iteration #26 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #1. The scaled sum of CCMS values is #0.02148 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.01418 for Iteration #27 of Tilt-Series #1. CCMS(rotations) = 0.30008 for Iteration #27 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #1. The scaled sum of CCMS values is #0.01309 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.0128 for Iteration #28 of Tilt-Series #1. CCMS(rotations) = 0.22055 for Iteration #28 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #1. The scaled sum of CCMS values is #0.01081 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01585 for Iteration #29 of Tilt-Series #1. CCMS(rotations) = 0.31209 for Iteration #29 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #1. The scaled sum of CCMS values is #0.01417 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01367 for Iteration #30 of Tilt-Series #1. CCMS(rotations) = 0.35678 for Iteration #30 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #1. The scaled sum of CCMS values is #0.01397 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.01581 for Iteration #31 of Tilt-Series #1. CCMS(rotations) = 0.48152 for Iteration #31 of Tilt-Series #1. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #1. The scaled sum of CCMS values is #0.01754 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.01153 for Iteration #32 of Tilt-Series #1. CCMS(rotations) = 0.39622 for Iteration #32 of Tilt-Series #1. CCMS(scale) = 0.00519 for Iteration #32 of Tilt-Series #1. The scaled sum of CCMS values is #0.01086 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.01684 for Iteration #33 of Tilt-Series #1. CCMS(rotations) = 0.33281 for Iteration #33 of Tilt-Series #1. CCMS(scale) = 0.00585 for Iteration #33 of Tilt-Series #1. The scaled sum of CCMS values is #0.012 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01209 for Iteration #34 of Tilt-Series #1. CCMS(rotations) = 0.36527 for Iteration #34 of Tilt-Series #1. CCMS(scale) = 0.00587 for Iteration #34 of Tilt-Series #1. The scaled sum of CCMS values is #0.01086 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick500) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.0164 for Iteration #35 of Tilt-Series #1. CCMS(rotations) = 0.51309 for Iteration #35 of Tilt-Series #1. CCMS(scale) = 0.00549 for Iteration #35 of Tilt-Series #1. The scaled sum of CCMS values is #0.01414 for Tilt-Series #1. 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 #1 (tiltseries0001_thick500)! 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: 2017yr04m19d-20hr34m57s