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/17feb10h/protomo_alignments/tiltseries0052_thick1400 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3740.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2037 --r1_region_y=2813 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3740.0 --r4_lowpass_apod_y=18.0 --r4_lowpass_apod_x=18.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=37.0 --r3_lowpass_apod_y=37.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0052_thick1400 --r2_region_y=2813 --r2_region_x=2037 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1870.0 --defocus_ang_positive=90 --r5_mask_width_x=2012 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3740.0 --r3_highpass_apod_x=1870.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=484 --r2_mask_width_y=678 --r5_region_x=2037 --r5_region_y=2813 --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=7.36 --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=3740.0 --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=2788 --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=1870.0 --r3_iters=5 --r1_highpass_diameter_x=3740.0 --r2_lowpass_diameter_y=29.44 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.68 --r5_lowpass_diameter_x=3.68 --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=2012 --r4_mask_width_y=2788 --r5_highpass_apod_y=1870.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17feb10h --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=1870.0 --r1_highpass_apod_x=1870.0 --r2_highpass_apod_x=1870.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=9.0 --r5_lowpass_apod_y=9.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=58.88 --r1_lowpass_diameter_x=58.88 --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=52 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1381 --r3_mask_width_x=993 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3740.0 --r4_highpass_diameter_x=3740.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=147.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3740.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1870.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3740.0 --defocus_max=0 --r4_region_y=2813 --r4_region_x=2037 --r5_kernel_y=5 --r3_region_x=2037 --r3_region_y=2813 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=1400 --expid=3450 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=14.72 --r3_lowpass_diameter_x=14.72 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=3740.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=74.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=74.0 --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=29.44 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=147.0 --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=1870.0 --r4_highpass_apod_y=1870.0 --azimuth=true --r1_mask_width_y=326 --r1_mask_width_x=229 --jobtype=protomo --from_multirefine=True node46 Start time: 2018yr02m21d-17hr57m38s Description: Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) lowpass = 58.88 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms) window.lowpass.apodization = { 0.199821496599 0.199821496599 } align.translimit = 47.125e0 map.sampling = 8 window.highpass.diameter = { 0.00785394652406 0.00785394652406 } window.highpass.apodization = { 0.0157078930481 0.0157078930481 } window.mask.apodization = { 10 10 } align.mask.width = { 229 326 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 162.153991959 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 254 351 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 229 326 } reference.body = 162.153991959 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.04678 for Iteration #1 of Tilt-Series #52. CCMS(rotations) = 1.27909 for Iteration #1 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #52. The scaled sum of CCMS values is #0.04897 for iteration 1 of Tilt-Series #52. Alignment quality for Iteration #1 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.02833 for Iteration #2 of Tilt-Series #52. CCMS(rotations) = 0.22197 for Iteration #2 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #52. The scaled sum of CCMS values is #0.0186 for iteration 2 of Tilt-Series #52. Alignment quality for Iteration #2 of Tilt-Series #52 (17feb10h): Good (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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.02053 for Iteration #3 of Tilt-Series #52. CCMS(rotations) = 0.21086 for Iteration #3 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #52. The scaled sum of CCMS values is #0.01448 for iteration 3 of Tilt-Series #52. Alignment quality for Iteration #3 of Tilt-Series #52 (17feb10h): Good (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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.0199 for Iteration #4 of Tilt-Series #52. CCMS(rotations) = 0.26831 for Iteration #4 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #52. The scaled sum of CCMS values is #0.01532 for iteration 4 of Tilt-Series #52. Alignment quality for Iteration #4 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.02282 for Iteration #5 of Tilt-Series #52. CCMS(rotations) = 0.43696 for Iteration #5 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #52. The scaled sum of CCMS values is #0.02015 for iteration 5 of Tilt-Series #52. Alignment quality for Iteration #5 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01901 for Iteration #6 of Tilt-Series #52. CCMS(rotations) = 0.25136 for Iteration #6 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #52. The scaled sum of CCMS values is #0.01453 for iteration 6 of Tilt-Series #52. Alignment quality for Iteration #6 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.02061 for Iteration #7 of Tilt-Series #52. CCMS(rotations) = 0.29191 for Iteration #7 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #52. The scaled sum of CCMS values is #0.01614 for iteration 7 of Tilt-Series #52. Alignment quality for Iteration #7 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.02096 for Iteration #8 of Tilt-Series #52. CCMS(rotations) = 0.33736 for Iteration #8 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #52. The scaled sum of CCMS values is #0.01723 for iteration 8 of Tilt-Series #52. Alignment quality for Iteration #8 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01919 for Iteration #9 of Tilt-Series #52. CCMS(rotations) = 0.26837 for Iteration #9 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #52. The scaled sum of CCMS values is #0.01496 for iteration 9 of Tilt-Series #52. Alignment quality for Iteration #9 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01461 for Iteration #10 of Tilt-Series #52. CCMS(rotations) = 0.22427 for Iteration #10 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #52. The scaled sum of CCMS values is #0.01179 for iteration 10 of Tilt-Series #52. Alignment quality for Iteration #10 of Tilt-Series #52 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) lowpass = 29.44 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms) window.lowpass.apodization = { 0.198471351351 0.198471351351 } align.translimit = 94.25e0 map.sampling = 4 window.highpass.diameter = { 0.00392697326203 0.00392697326203 } window.highpass.apodization = { 0.00785394652406 0.00785394652406 } window.mask.apodization = { 10 10 } align.mask.width = { 484 678 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 324.307983918 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 509 703 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 484 678 } reference.body = 324.307983918 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.02613 for Iteration #11 of Tilt-Series #52. CCMS(rotations) = 0.35028 for Iteration #11 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #52. The scaled sum of CCMS values is #0.02007 for iteration 11 of Tilt-Series #52. Alignment quality for Iteration #11 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.02084 for Iteration #12 of Tilt-Series #52. CCMS(rotations) = 0.33416 for Iteration #12 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #52. The scaled sum of CCMS values is #0.0171 for iteration 12 of Tilt-Series #52. Alignment quality for Iteration #12 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01588 for Iteration #13 of Tilt-Series #52. CCMS(rotations) = 0.32946 for Iteration #13 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #52. The scaled sum of CCMS values is #0.01453 for iteration 13 of Tilt-Series #52. Alignment quality for Iteration #13 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #52 (17feb10h): Very StableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.01802 for Iteration #14 of Tilt-Series #52. CCMS(rotations) = 0.50849 for Iteration #14 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #52. The scaled sum of CCMS values is #0.01918 for iteration 14 of Tilt-Series #52. Alignment quality for Iteration #14 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.01398 for Iteration #15 of Tilt-Series #52. CCMS(rotations) = 0.50587 for Iteration #15 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #52. The scaled sum of CCMS values is #0.01711 for iteration 15 of Tilt-Series #52. Alignment quality for Iteration #15 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.01645 for Iteration #16 of Tilt-Series #52. CCMS(rotations) = 0.41648 for Iteration #16 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #52. The scaled sum of CCMS values is #0.01655 for iteration 16 of Tilt-Series #52. Alignment quality for Iteration #16 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.01544 for Iteration #17 of Tilt-Series #52. CCMS(rotations) = 0.55388 for Iteration #17 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #52. The scaled sum of CCMS values is #0.0188 for iteration 17 of Tilt-Series #52. Alignment quality for Iteration #17 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.01581 for Iteration #18 of Tilt-Series #52. CCMS(rotations) = 0.3716 for Iteration #18 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #52. The scaled sum of CCMS values is #0.01534 for iteration 18 of Tilt-Series #52. Alignment quality for Iteration #18 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.01658 for Iteration #19 of Tilt-Series #52. CCMS(rotations) = 0.52405 for Iteration #19 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #52. The scaled sum of CCMS values is #0.01877 for iteration 19 of Tilt-Series #52. Alignment quality for Iteration #19 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.01218 for Iteration #20 of Tilt-Series #52. CCMS(rotations) = 0.33708 for Iteration #20 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #52. The scaled sum of CCMS values is #0.01283 for iteration 20 of Tilt-Series #52. Alignment quality for Iteration #20 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) lowpass = 14.72 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms) window.lowpass.apodization = { 0.198471351351 0.198471351351 } align.translimit = 188.5e0 map.sampling = 2 window.highpass.diameter = { 0.00196348663102 0.00196348663102 } window.highpass.apodization = { 0.00392697326203 0.00392697326203 } window.mask.apodization = { 10 10 } align.mask.width = { 993 1381 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 648.615967835 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1018 1406 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 993 1381 } reference.body = 648.615967835 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.01473 for Iteration #21 of Tilt-Series #52. CCMS(rotations) = 0.60985 for Iteration #21 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #52. The scaled sum of CCMS values is #0.01956 for iteration 21 of Tilt-Series #52. Alignment quality for Iteration #21 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.01162 for Iteration #22 of Tilt-Series #52. CCMS(rotations) = 0.53391 for Iteration #22 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #52. The scaled sum of CCMS values is #0.01649 for iteration 22 of Tilt-Series #52. Alignment quality for Iteration #22 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.01137 for Iteration #23 of Tilt-Series #52. CCMS(rotations) = 0.51478 for Iteration #23 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #52. The scaled sum of CCMS values is #0.01598 for iteration 23 of Tilt-Series #52. Alignment quality for Iteration #23 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #52 (17feb10h): StableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.01106 for Iteration #24 of Tilt-Series #52. CCMS(rotations) = 0.45531 for Iteration #24 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #52. The scaled sum of CCMS values is #0.01464 for iteration 24 of Tilt-Series #52. Alignment quality for Iteration #24 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #52 (17feb10h): StableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.01308 for Iteration #25 of Tilt-Series #52. CCMS(rotations) = 0.65251 for Iteration #25 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #52. The scaled sum of CCMS values is #0.01959 for iteration 25 of Tilt-Series #52. Alignment quality for Iteration #25 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) lowpass = 7.36 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms) window.lowpass.apodization = { 0.203984444444 0.203984444444 } align.translimit = 377.0e0 map.sampling = 1 window.highpass.diameter = { 0.000981743315508 0.000981743315508 } window.highpass.apodization = { 0.00196348663102 0.00196348663102 } window.mask.apodization = { 10 10 } align.mask.width = { 2012 2788 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 1297.23193567 map.lowpass.diameter = { 0.498875 0.498875 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2037 2813 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2012 2788 } reference.body = 1297.23193567 window.lowpass.diameter = { 0.498875 0.498875 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.01513 for Iteration #26 of Tilt-Series #52. CCMS(rotations) = 0.5411 for Iteration #26 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #52. The scaled sum of CCMS values is #0.01838 for iteration 26 of Tilt-Series #52. Alignment quality for Iteration #26 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.01465 for Iteration #27 of Tilt-Series #52. CCMS(rotations) = 0.86926 for Iteration #27 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #52. The scaled sum of CCMS values is #0.02471 for iteration 27 of Tilt-Series #52. Alignment quality for Iteration #27 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01607 for Iteration #28 of Tilt-Series #52. CCMS(rotations) = 0.71428 for Iteration #28 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #52. The scaled sum of CCMS values is #0.02232 for iteration 28 of Tilt-Series #52. Alignment quality for Iteration #28 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #52 (17feb10h): StableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01604 for Iteration #29 of Tilt-Series #52. CCMS(rotations) = 0.70863 for Iteration #29 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #52. The scaled sum of CCMS values is #0.02219 for iteration 29 of Tilt-Series #52. Alignment quality for Iteration #29 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01698 for Iteration #30 of Tilt-Series #52. CCMS(rotations) = 0.65649 for Iteration #30 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #52. The scaled sum of CCMS values is #0.02162 for iteration 30 of Tilt-Series #52. Alignment quality for Iteration #30 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.01534 for Iteration #31 of Tilt-Series #52. CCMS(rotations) = 0.69076 for Iteration #31 of Tilt-Series #52. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #52. The scaled sum of CCMS values is #0.02148 for iteration 31 of Tilt-Series #52. Alignment quality for Iteration #31 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.01908 for Iteration #32 of Tilt-Series #52. CCMS(rotations) = 0.77865 for Iteration #32 of Tilt-Series #52. CCMS(scale) = 0.00536 for Iteration #32 of Tilt-Series #52. The scaled sum of CCMS values is #0.01853 for iteration 32 of Tilt-Series #52. Alignment quality for Iteration #32 of Tilt-Series #52 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.02031 for Iteration #33 of Tilt-Series #52. CCMS(rotations) = 0.95506 for Iteration #33 of Tilt-Series #52. CCMS(scale) = 0.00802 for Iteration #33 of Tilt-Series #52. The scaled sum of CCMS values is #0.02218 for iteration 33 of Tilt-Series #52. Alignment quality for Iteration #33 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01992 for Iteration #34 of Tilt-Series #52. CCMS(rotations) = 0.89785 for Iteration #34 of Tilt-Series #52. CCMS(scale) = 0.01058 for Iteration #34 of Tilt-Series #52. The scaled sum of CCMS values is #0.02214 for iteration 34 of Tilt-Series #52. Alignment quality for Iteration #34 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #52 (17feb10h): UnstableCreating 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 #52 (tiltseries0052_thick1400) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #52 (tiltseries0052_thick1400) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.0196 for Iteration #35 of Tilt-Series #52. CCMS(rotations) = 1.03388 for Iteration #35 of Tilt-Series #52. CCMS(scale) = 0.0089 for Iteration #35 of Tilt-Series #52. The scaled sum of CCMS values is #0.02329 for iteration 35 of Tilt-Series #52. Alignment quality for Iteration #35 of Tilt-Series #52 (17feb10h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #52 (17feb10h): 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 #52 (tiltseries0052_thick1400)! 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: 2018yr02m23d-07hr50m23s