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/18mar12b/protomo_alignments/tiltseries0001_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2647.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1989 --r1_region_y=2079 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2647.0 --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=2079 --r2_region_x=1989 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1324.0 --defocus_ang_positive=90 --r5_mask_width_x=1964 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2647.0 --r3_highpass_apod_x=1324.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=472 --r2_mask_width_y=494 --r5_region_x=1989 --r5_region_y=2079 --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=2647.0 --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=2054 --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=1324.0 --r3_iters=5 --r1_highpass_diameter_x=2647.0 --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=1964 --r4_mask_width_y=2054 --r5_highpass_apod_y=1324.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar12b --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=1324.0 --r1_highpass_apod_x=1324.0 --r2_highpass_apod_x=1324.0 --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=1014 --r3_mask_width_x=969 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2647.0 --r4_highpass_diameter_x=2647.0 --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=2647.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1324.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2647.0 --defocus_max=0 --r4_region_y=2079 --r4_region_x=1989 --r5_kernel_y=5 --r3_region_x=1989 --r3_region_y=2079 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=6268 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=340 --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=2647.0 --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=1324.0 --r4_highpass_apod_y=1324.0 --azimuth=true --r1_mask_width_y=234 --r1_mask_width_x=223 --jobtype=protomo --from_multirefine=True node03 Start time: 2018yr03m12d-11hr14m35s 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 = { 0.00804533434076 0.00804533434076 } window.highpass.apodization = { 0.016084592145 0.016084592145 } window.mask.apodization = { 10 10 } align.mask.width = { 223 234 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 6.64086328748 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 248 259 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 223 234 } reference.body = 6.64086328748 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.08361 for Iteration #1 of Tilt-Series #1. CCMS(rotations) = 0.18176 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 #0.04544 for iteration 1 of Tilt-Series #1. Alignment quality for Iteration #1 of Tilt-Series #1 (18mar12b): 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) = 0.00536 for Iteration #2 of Tilt-Series #1. CCMS(rotations) = 0.17523 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 #0.00619 for iteration 2 of Tilt-Series #1. Alignment quality for Iteration #2 of Tilt-Series #1 (18mar12b): Excellent (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) = 0.00527 for Iteration #3 of Tilt-Series #1. CCMS(rotations) = 0.16853 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 #0.00601 for iteration 3 of Tilt-Series #1. Alignment quality for Iteration #3 of Tilt-Series #1 (18mar12b): Excellent (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) = 0.00591 for Iteration #4 of Tilt-Series #1. CCMS(rotations) = 0.15013 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 #0.00596 for iteration 4 of Tilt-Series #1. Alignment quality for Iteration #4 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (18mar12b): 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) = 0.00508 for Iteration #5 of Tilt-Series #1. CCMS(rotations) = 0.15247 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 #0.00559 for iteration 5 of Tilt-Series #1. Alignment quality for Iteration #5 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (18mar12b): 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) = 0.00548 for Iteration #6 of Tilt-Series #1. CCMS(rotations) = 0.15095 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 #0.00576 for iteration 6 of Tilt-Series #1. Alignment quality for Iteration #6 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (18mar12b): 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) = 0.0054 for Iteration #7 of Tilt-Series #1. CCMS(rotations) = 0.15375 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 #0.00577 for iteration 7 of Tilt-Series #1. Alignment quality for Iteration #7 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (18mar12b): 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) = 0.00533 for Iteration #8 of Tilt-Series #1. CCMS(rotations) = 0.15643 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 #0.00579 for iteration 8 of Tilt-Series #1. Alignment quality for Iteration #8 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (18mar12b): 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) = 0.00533 for Iteration #9 of Tilt-Series #1. CCMS(rotations) = 0.15601 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 #0.00578 for iteration 9 of Tilt-Series #1. Alignment quality for Iteration #9 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (18mar12b): 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) = 0.00529 for Iteration #10 of Tilt-Series #1. CCMS(rotations) = 0.15563 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 #0.00576 for iteration 10 of Tilt-Series #1. Alignment quality for Iteration #10 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (18mar12b): 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 = { 0.00402266717038 0.00402266717038 } window.highpass.apodization = { 0.00804229607251 0.00804229607251 } window.mask.apodization = { 10 10 } align.mask.width = { 472 494 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 13.281726575 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 497 519 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 472 494 } reference.body = 13.281726575 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00462 for Iteration #11 of Tilt-Series #1. CCMS(rotations) = 0.1442 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 #0.00519 for iteration 11 of Tilt-Series #1. Alignment quality for Iteration #11 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (18mar12b): 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) = 0.00415 for Iteration #12 of Tilt-Series #1. CCMS(rotations) = 0.1311 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 #0.0047 for iteration 12 of Tilt-Series #1. Alignment quality for Iteration #12 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (18mar12b): Very StableCreating 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) = 0.00415 for Iteration #13 of Tilt-Series #1. CCMS(rotations) = 0.11931 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 #0.00446 for iteration 13 of Tilt-Series #1. Alignment quality for Iteration #13 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (18mar12b): 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) = 0.00403 for Iteration #14 of Tilt-Series #1. CCMS(rotations) = 0.12666 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 #0.00455 for iteration 14 of Tilt-Series #1. Alignment quality for Iteration #14 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (18mar12b): 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) = 0.00408 for Iteration #15 of Tilt-Series #1. CCMS(rotations) = 0.12426 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 #0.00453 for iteration 15 of Tilt-Series #1. Alignment quality for Iteration #15 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (18mar12b): 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) = 0.00397 for Iteration #16 of Tilt-Series #1. CCMS(rotations) = 0.12767 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 #0.00454 for iteration 16 of Tilt-Series #1. Alignment quality for Iteration #16 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (18mar12b): 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) = 0.00408 for Iteration #17 of Tilt-Series #1. CCMS(rotations) = 0.12222 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 #0.00448 for iteration 17 of Tilt-Series #1. Alignment quality for Iteration #17 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (18mar12b): 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) = 0.004 for Iteration #18 of Tilt-Series #1. CCMS(rotations) = 0.1299 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 #0.0046 for iteration 18 of Tilt-Series #1. Alignment quality for Iteration #18 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (18mar12b): 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) = 0.00416 for Iteration #19 of Tilt-Series #1. CCMS(rotations) = 0.12355 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 #0.00455 for iteration 19 of Tilt-Series #1. Alignment quality for Iteration #19 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (18mar12b): 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) = 0.00407 for Iteration #20 of Tilt-Series #1. CCMS(rotations) = 0.13114 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 #0.00466 for iteration 20 of Tilt-Series #1. Alignment quality for Iteration #20 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (18mar12b): 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 = { 0.00201133358519 0.00201133358519 } window.highpass.apodization = { 0.00402114803625 0.00402114803625 } window.mask.apodization = { 10 10 } align.mask.width = { 969 1014 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 26.5634531499 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 994 1039 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 969 1014 } reference.body = 26.5634531499 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #21 of Tilt-Series #1. CCMS(rotations) = 0.16423 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 #0.00537 for iteration 21 of Tilt-Series #1. Alignment quality for Iteration #21 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (18mar12b): UnstableCreating 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) = 0.0035 for Iteration #22 of Tilt-Series #1. CCMS(rotations) = 0.14895 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 #0.00473 for iteration 22 of Tilt-Series #1. Alignment quality for Iteration #22 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (18mar12b): 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) = 0.00366 for Iteration #23 of Tilt-Series #1. CCMS(rotations) = 0.14976 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 #0.00482 for iteration 23 of Tilt-Series #1. Alignment quality for Iteration #23 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (18mar12b): 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) = 0.0035 for Iteration #24 of Tilt-Series #1. CCMS(rotations) = 0.14894 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 #0.00473 for iteration 24 of Tilt-Series #1. Alignment quality for Iteration #24 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (18mar12b): 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) = 0.00347 for Iteration #25 of Tilt-Series #1. CCMS(rotations) = 0.1544 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 #0.00482 for iteration 25 of Tilt-Series #1. Alignment quality for Iteration #25 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (18mar12b): 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 = { 0.0010056667926 0.0010056667926 } window.highpass.apodization = { 0.00201057401813 0.00201057401813 } window.mask.apodization = { 10 10 } align.mask.width = { 1964 2054 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 53.1269062999 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1989 2079 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1964 2054 } reference.body = 53.1269062999 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00767 for Iteration #26 of Tilt-Series #1. CCMS(rotations) = 0.2278 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 #0.00839 for iteration 26 of Tilt-Series #1. Alignment quality for Iteration #26 of Tilt-Series #1 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (18mar12b): UnstableCreating 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) = 0.00667 for Iteration #27 of Tilt-Series #1. CCMS(rotations) = 0.21499 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 #0.00763 for iteration 27 of Tilt-Series #1. Alignment quality for Iteration #27 of Tilt-Series #1 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (18mar12b): UnstableCreating 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) = 0.00557 for Iteration #28 of Tilt-Series #1. CCMS(rotations) = 0.17962 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 #0.00638 for iteration 28 of Tilt-Series #1. Alignment quality for Iteration #28 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (18mar12b): UnstableCreating 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) = 0.00596 for Iteration #29 of Tilt-Series #1. CCMS(rotations) = 0.16972 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 #0.00638 for iteration 29 of Tilt-Series #1. Alignment quality for Iteration #29 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (18mar12b): Very StableCreating 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) = 0.00611 for Iteration #30 of Tilt-Series #1. CCMS(rotations) = 0.19252 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 #0.00691 for iteration 30 of Tilt-Series #1. Alignment quality for Iteration #30 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (18mar12b): 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) = 0.00595 for Iteration #31 of Tilt-Series #1. CCMS(rotations) = 0.1787 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 #0.00655 for iteration 31 of Tilt-Series #1. Alignment quality for Iteration #31 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (18mar12b): 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) = 0.00519 for Iteration #32 of Tilt-Series #1. CCMS(rotations) = 0.22494 for Iteration #32 of Tilt-Series #1. CCMS(scale) = 0.00204 for Iteration #32 of Tilt-Series #1. The scaled sum of CCMS values is #0.00541 for iteration 32 of Tilt-Series #1. Alignment quality for Iteration #32 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (18mar12b): 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) = 0.00534 for Iteration #33 of Tilt-Series #1. CCMS(rotations) = 0.15962 for Iteration #33 of Tilt-Series #1. CCMS(scale) = 0.00237 for Iteration #33 of Tilt-Series #1. The scaled sum of CCMS values is #0.0047 for iteration 33 of Tilt-Series #1. Alignment quality for Iteration #33 of Tilt-Series #1 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (18mar12b): 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) = 0.00528 for Iteration #34 of Tilt-Series #1. CCMS(rotations) = 0.22641 for Iteration #34 of Tilt-Series #1. CCMS(scale) = 0.00231 for Iteration #34 of Tilt-Series #1. The scaled sum of CCMS values is #0.00555 for iteration 34 of Tilt-Series #1. Alignment quality for Iteration #34 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (18mar12b): Rock Solid!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_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) = 0.0047 for Iteration #35 of Tilt-Series #1. CCMS(rotations) = 0.24806 for Iteration #35 of Tilt-Series #1. CCMS(scale) = 0.00176 for Iteration #35 of Tilt-Series #1. The scaled sum of CCMS values is #0.00546 for iteration 35 of Tilt-Series #1. Alignment quality for Iteration #35 of Tilt-Series #1 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (18mar12b): Rock Solid!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_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: 2018yr03m12d-22hr24m22s