protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/18mar15h/protomo_alignments/tiltseries0001_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2938.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2207 --r1_region_y=2514 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2938.0 --r4_lowpass_apod_y=13.0 --r4_lowpass_apod_x=13.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=27.0 --r3_lowpass_apod_y=27.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0001_thick50 --r2_region_y=2514 --r2_region_x=2207 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1469.0 --defocus_ang_positive=90 --r5_mask_width_x=2182 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2938.0 --r3_highpass_apod_x=1469.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=526 --r2_mask_width_y=603 --r5_region_x=2207 --r5_region_y=2514 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=5.32 --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=2938.0 --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=2489 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1469.0 --r3_iters=5 --r1_highpass_diameter_x=2938.0 --r2_lowpass_diameter_y=21.28 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=2.66 --r5_lowpass_diameter_x=2.66 --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=2182 --r4_mask_width_y=2489 --r5_highpass_apod_y=1469.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar15h --exclude_images=999999 --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=1469.0 --r1_highpass_apod_x=1469.0 --r2_highpass_apod_x=1469.0 --sampling=8 --starting_tlt_file=Coarse_Iter_1 --r5_lowpass_apod_x=7.0 --r5_lowpass_apod_y=7.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=42.56 --r1_lowpass_diameter_x=42.56 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=1 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1232 --r3_mask_width_x=1078 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2938.0 --r4_highpass_diameter_x=2938.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=106.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2938.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1469.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2938.0 --defocus_max=0 --r4_region_y=2514 --r4_region_x=2207 --r5_kernel_y=5 --r3_region_x=2207 --r3_region_y=2514 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=6300 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=506 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=10.64 --r3_lowpass_diameter_x=10.64 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.331 --link=False --r2_highpass_diameter_x=2938.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=53.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=53.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --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=21.28 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=106.0 --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=1469.0 --r4_highpass_apod_y=1469.0 --azimuth=true --r1_mask_width_y=289 --r1_mask_width_x=250 --jobtype=protomo --from_multirefine=True node47 Start time: 2018yr03m15d-11hr24m22s Description: Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) lowpass = 42.56 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 10.648 Angstroms, Nyquist is 21.296 Angstroms) window.lowpass.apodization = { 0.200905660377 0.200905660377 } align.translimit = 47.125e0 map.sampling = 8 window.highpass.diameter = { 0.00724846834581 0.00724846834581 } window.highpass.apodization = { 0.0144969366916 0.0144969366916 } window.mask.apodization = { 10 10 } align.mask.width = { 250 289 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 6.64097919949 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 275 314 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 250 289 } reference.body = 6.64097919949 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.07832 for Iteration #1 of Tilt-Series #1. CCMS(rotations) = 0.86997 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 #0.05656 for iteration 1 of Tilt-Series #1. Alignment quality for Iteration #1 of Tilt-Series #1 (18mar15h): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)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_thick50) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.0855 for Iteration #2 of Tilt-Series #1. CCMS(rotations) = 0.18905 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 #0.04653 for iteration 2 of Tilt-Series #1. Alignment quality for Iteration #2 of Tilt-Series #1 (18mar15h): Bad (confidence: 100.000000%)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_thick50) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.03505 for Iteration #3 of Tilt-Series #1. CCMS(rotations) = 0.25672 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 #0.02266 for iteration 3 of Tilt-Series #1. Alignment quality for Iteration #3 of Tilt-Series #1 (18mar15h): Okay (confidence: 100.000000%)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_thick50) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00681 for Iteration #4 of Tilt-Series #1. CCMS(rotations) = 0.25531 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 #0.00851 for iteration 4 of Tilt-Series #1. Alignment quality for Iteration #4 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00735 for Iteration #5 of Tilt-Series #1. CCMS(rotations) = 0.23692 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 #0.00841 for iteration 5 of Tilt-Series #1. Alignment quality for Iteration #5 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00717 for Iteration #6 of Tilt-Series #1. CCMS(rotations) = 0.23719 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 #0.00833 for iteration 6 of Tilt-Series #1. Alignment quality for Iteration #6 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00731 for Iteration #7 of Tilt-Series #1. CCMS(rotations) = 0.24175 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 #0.00849 for iteration 7 of Tilt-Series #1. Alignment quality for Iteration #7 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00705 for Iteration #8 of Tilt-Series #1. CCMS(rotations) = 0.24181 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 #0.00836 for iteration 8 of Tilt-Series #1. Alignment quality for Iteration #8 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.0073 for Iteration #9 of Tilt-Series #1. CCMS(rotations) = 0.2398 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 #0.00844 for iteration 9 of Tilt-Series #1. Alignment quality for Iteration #9 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.0072 for Iteration #10 of Tilt-Series #1. CCMS(rotations) = 0.23946 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 #0.00839 for iteration 10 of Tilt-Series #1. Alignment quality for Iteration #10 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) lowpass = 21.28 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 5.324 Angstroms, Nyquist is 10.648 Angstroms) window.lowpass.apodization = { 0.200905660377 0.200905660377 } align.translimit = 94.25e0 map.sampling = 4 window.highpass.diameter = { 0.00362423417291 0.00362423417291 } window.highpass.apodization = { 0.00724846834581 0.00724846834581 } window.mask.apodization = { 10 10 } align.mask.width = { 526 603 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 13.281958399 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 551 628 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 526 603 } reference.body = 13.281958399 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00603 for Iteration #11 of Tilt-Series #1. CCMS(rotations) = 0.18119 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 #0.00664 for iteration 11 of Tilt-Series #1. Alignment quality for Iteration #11 of Tilt-Series #1 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (18mar15h): StableCreating 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_thick50) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00648 for Iteration #12 of Tilt-Series #1. CCMS(rotations) = 0.2359 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 #0.00796 for iteration 12 of Tilt-Series #1. Alignment quality for Iteration #12 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00669 for Iteration #13 of Tilt-Series #1. CCMS(rotations) = 0.24227 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 #0.00819 for iteration 13 of Tilt-Series #1. Alignment quality for Iteration #13 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00654 for Iteration #14 of Tilt-Series #1. CCMS(rotations) = 0.24006 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 #0.00807 for iteration 14 of Tilt-Series #1. Alignment quality for Iteration #14 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00658 for Iteration #15 of Tilt-Series #1. CCMS(rotations) = 0.23717 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 #0.00804 for iteration 15 of Tilt-Series #1. Alignment quality for Iteration #15 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00663 for Iteration #16 of Tilt-Series #1. CCMS(rotations) = 0.23545 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 #0.00802 for iteration 16 of Tilt-Series #1. Alignment quality for Iteration #16 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00666 for Iteration #17 of Tilt-Series #1. CCMS(rotations) = 0.24016 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 #0.00813 for iteration 17 of Tilt-Series #1. Alignment quality for Iteration #17 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00657 for Iteration #18 of Tilt-Series #1. CCMS(rotations) = 0.2314 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 #0.00791 for iteration 18 of Tilt-Series #1. Alignment quality for Iteration #18 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00676 for Iteration #19 of Tilt-Series #1. CCMS(rotations) = 0.23667 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 #0.00811 for iteration 19 of Tilt-Series #1. Alignment quality for Iteration #19 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00659 for Iteration #20 of Tilt-Series #1. CCMS(rotations) = 0.23443 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 #0.00798 for iteration 20 of Tilt-Series #1. Alignment quality for Iteration #20 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) lowpass = 10.64 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 2.662 Angstroms, Nyquist is 5.324 Angstroms) window.lowpass.apodization = { 0.197185185185 0.197185185185 } align.translimit = 188.5e0 map.sampling = 2 window.highpass.diameter = { 0.00181211708645 0.00181211708645 } window.highpass.apodization = { 0.00362423417291 0.00362423417291 } window.mask.apodization = { 10 10 } align.mask.width = { 1078 1232 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 26.563916798 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1103 1257 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1078 1232 } reference.body = 26.563916798 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.0066 for Iteration #21 of Tilt-Series #1. CCMS(rotations) = 0.21306 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 #0.00756 for iteration 21 of Tilt-Series #1. Alignment quality for Iteration #21 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00629 for Iteration #22 of Tilt-Series #1. CCMS(rotations) = 0.22847 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 #0.00772 for iteration 22 of Tilt-Series #1. Alignment quality for Iteration #22 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.0061 for Iteration #23 of Tilt-Series #1. CCMS(rotations) = 0.23112 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 #0.00767 for iteration 23 of Tilt-Series #1. Alignment quality for Iteration #23 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00616 for Iteration #24 of Tilt-Series #1. CCMS(rotations) = 0.2347 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 #0.00778 for iteration 24 of Tilt-Series #1. Alignment quality for Iteration #24 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00608 for Iteration #25 of Tilt-Series #1. CCMS(rotations) = 0.22763 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 #0.00759 for iteration 25 of Tilt-Series #1. Alignment quality for Iteration #25 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) lowpass = 5.32 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.331 Angstroms, Nyquist is 2.662 Angstroms) window.lowpass.apodization = { 0.204769230769 0.204769230769 } align.translimit = 377.0e0 map.sampling = 1 window.highpass.diameter = { 0.000906058543227 0.000906058543227 } window.highpass.apodization = { 0.00181211708645 0.00181211708645 } window.mask.apodization = { 10 10 } align.mask.width = { 2182 2489 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 53.1278335959 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2207 2514 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2182 2489 } reference.body = 53.1278335959 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00823 for Iteration #26 of Tilt-Series #1. CCMS(rotations) = 0.26741 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 #0.00946 for iteration 26 of Tilt-Series #1. Alignment quality for Iteration #26 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00809 for Iteration #27 of Tilt-Series #1. CCMS(rotations) = 0.28717 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 #0.00979 for iteration 27 of Tilt-Series #1. Alignment quality for Iteration #27 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00816 for Iteration #28 of Tilt-Series #1. CCMS(rotations) = 0.30792 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 #0.01024 for iteration 28 of Tilt-Series #1. Alignment quality for Iteration #28 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00813 for Iteration #29 of Tilt-Series #1. CCMS(rotations) = 0.28316 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 #0.00973 for iteration 29 of Tilt-Series #1. Alignment quality for Iteration #29 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00793 for Iteration #30 of Tilt-Series #1. CCMS(rotations) = 0.28025 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 #0.00957 for iteration 30 of Tilt-Series #1. Alignment quality for Iteration #30 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00794 for Iteration #31 of Tilt-Series #1. CCMS(rotations) = 0.3145 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 #0.01026 for iteration 31 of Tilt-Series #1. Alignment quality for Iteration #31 of Tilt-Series #1 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00446 for Iteration #32 of Tilt-Series #1. CCMS(rotations) = 0.28337 for Iteration #32 of Tilt-Series #1. CCMS(scale) = 0.00386 for Iteration #32 of Tilt-Series #1. The scaled sum of CCMS values is #0.00655 for iteration 32 of Tilt-Series #1. Alignment quality for Iteration #32 of Tilt-Series #1 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00466 for Iteration #33 of Tilt-Series #1. CCMS(rotations) = 0.31747 for Iteration #33 of Tilt-Series #1. CCMS(scale) = 0.00381 for Iteration #33 of Tilt-Series #1. The scaled sum of CCMS values is #0.00706 for iteration 33 of Tilt-Series #1. Alignment quality for Iteration #33 of Tilt-Series #1 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (18mar15h): Rock Solid!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_thick50) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00537 for Iteration #34 of Tilt-Series #1. CCMS(rotations) = 0.30175 for Iteration #34 of Tilt-Series #1. CCMS(scale) = 0.0044 for Iteration #34 of Tilt-Series #1. The scaled sum of CCMS values is #0.00728 for iteration 34 of Tilt-Series #1. Alignment quality for Iteration #34 of Tilt-Series #1 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (18mar15h): Very StableCreating 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_thick50) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick50) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00495 for Iteration #35 of Tilt-Series #1. CCMS(rotations) = 0.29335 for Iteration #35 of Tilt-Series #1. CCMS(scale) = 0.00461 for Iteration #35 of Tilt-Series #1. The scaled sum of CCMS values is #0.0071 for iteration 35 of Tilt-Series #1. Alignment quality for Iteration #35 of Tilt-Series #1 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (18mar15h): Very StableCreating 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_thick50)! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file. If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2018yr03m16d-17hr12m24s