protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0006_thick300 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2911.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1592 --r1_region_y=1345 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2911.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1345 --r2_region_x=1592 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1456.0 --defocus_ang_positive=90 --r5_mask_width_x=1567 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2911.0 --r3_highpass_apod_x=1456.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=373 --r2_mask_width_y=311 --r5_region_x=1592 --r5_region_y=1345 --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=8.64 --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=2911.0 --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=1320 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1456.0 --runname=tiltseries0006_thick300 --r1_highpass_diameter_x=2911.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --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=1567 --r4_mask_width_y=1320 --r5_highpass_apod_y=1456.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --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=1456.0 --r1_highpass_apod_x=1456.0 --r2_highpass_apod_x=1456.0 --sampling=8 --starting_tlt_file=Imod_Coarse --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=6 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=647 --r3_mask_width_x=771 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2911.0 --r4_highpass_diameter_x=2911.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2911.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1456.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2911.0 --defocus_max=0 --r4_region_y=1345 --r4_region_x=1592 --r5_kernel_y=5 --r3_region_x=1592 --r3_region_y=1345 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=300 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=2911.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --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=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --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=1456.0 --r4_highpass_apod_y=1456.0 --azimuth=true --r1_mask_width_y=151 --r1_mask_width_x=179 --jobtype=protomo node39 Start time: 2018yr01m23d-17hr34m40s Description: Using Imod Coarse alignment for Refinement by copying imod_coarse_series0006.tlt to series0006.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) lowpass = 69.12 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms) window.lowpass.apodization = { 0.20016 0.20016 } align.translimit = 47.125e0 map.sampling = 8 window.highpass.diameter = { 0.0118954586053 0.0118954586053 } window.highpass.apodization = { 0.0237827472527 0.0237827472527 } window.mask.apodization = { 10 10 } align.mask.width = { 179 151 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 27.5278200959 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 199 168 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 179 151 } reference.body = 27.5278200959 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.11175 for Iteration #1 of Tilt-Series #6. CCMS(rotations) = 0.47263 for Iteration #1 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6. The scaled sum of CCMS values is #0.06533 for iteration 1 of Tilt-Series #6. Alignment quality for Iteration #1 of Tilt-Series #6 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 16.666667%)Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... Refinement Iteration #1 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1280 No Round parameters changed for Iteration #2 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #2 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.05856 for Iteration #2 of Tilt-Series #6. CCMS(rotations) = 0.55229 for Iteration #2 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6. The scaled sum of CCMS values is #0.04032 for iteration 2 of Tilt-Series #6. Alignment quality for Iteration #2 of Tilt-Series #6 (17dec26e): Bad (confidence: 23.333333%)Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... Refinement Iteration #2 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #3 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #3 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.02144 for Iteration #3 of Tilt-Series #6. CCMS(rotations) = 0.61566 for Iteration #3 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6. The scaled sum of CCMS values is #0.02304 for iteration 3 of Tilt-Series #6. Alignment quality for Iteration #3 of Tilt-Series #6 (17dec26e): Okay (confidence: 23.333333%)Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... Refinement Iteration #3 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #4 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #4 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01374 for Iteration #4 of Tilt-Series #6. CCMS(rotations) = 0.61349 for Iteration #4 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6. The scaled sum of CCMS values is #0.01914 for iteration 4 of Tilt-Series #6. Alignment quality for Iteration #4 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... Refinement Iteration #4 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #5 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #5 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00677 for Iteration #5 of Tilt-Series #6. CCMS(rotations) = 0.63107 for Iteration #5 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6. The scaled sum of CCMS values is #0.01601 for iteration 5 of Tilt-Series #6. Alignment quality for Iteration #5 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... Refinement Iteration #5 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #6 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #6 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0125 for Iteration #6 of Tilt-Series #6. CCMS(rotations) = 0.60525 for Iteration #6 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6. The scaled sum of CCMS values is #0.01835 for iteration 6 of Tilt-Series #6. Alignment quality for Iteration #6 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... Refinement Iteration #6 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #7 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #7 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00702 for Iteration #7 of Tilt-Series #6. CCMS(rotations) = 0.60991 for Iteration #7 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6. The scaled sum of CCMS values is #0.01571 for iteration 7 of Tilt-Series #6. Alignment quality for Iteration #7 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... Refinement Iteration #7 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #8 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #8 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01206 for Iteration #8 of Tilt-Series #6. CCMS(rotations) = 0.60197 for Iteration #8 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6. The scaled sum of CCMS values is #0.01807 for iteration 8 of Tilt-Series #6. Alignment quality for Iteration #8 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... Refinement Iteration #8 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #9 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #9 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00775 for Iteration #9 of Tilt-Series #6. CCMS(rotations) = 0.62372 for Iteration #9 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6. The scaled sum of CCMS values is #0.01635 for iteration 9 of Tilt-Series #6. Alignment quality for Iteration #9 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... Refinement Iteration #9 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #10 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #10 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1440, 1280) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1344, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01182 for Iteration #10 of Tilt-Series #6. CCMS(rotations) = 0.60069 for Iteration #10 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6. The scaled sum of CCMS values is #0.01792 for iteration 10 of Tilt-Series #6. Alignment quality for Iteration #10 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... Refinement Iteration #10 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1344 Window Size (y) was windowed down to 1200 Beginning Refinement Iteration #11, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) lowpass = 34.56 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms) window.lowpass.apodization = { 0.20132372093 0.20132372093 } align.translimit = 94.25e0 map.sampling = 4 window.highpass.diameter = { 0.00594772930265 0.00594772930265 } window.highpass.apodization = { 0.0118913736264 0.0118913736264 } window.mask.apodization = { 10 10 } align.mask.width = { 373 311 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 55.0556401919 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 398 336 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 373 311 } reference.body = 55.0556401919 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.01154 for Iteration #11 of Tilt-Series #6. CCMS(rotations) = 0.66722 for Iteration #11 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6. The scaled sum of CCMS values is #0.01911 for iteration 11 of Tilt-Series #6. Alignment quality for Iteration #11 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #6 (17dec26e): UnstableCreating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... Refinement Iteration #11 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #12 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #12 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00706 for Iteration #12 of Tilt-Series #6. CCMS(rotations) = 0.46041 for Iteration #12 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6. The scaled sum of CCMS values is #0.01274 for iteration 12 of Tilt-Series #6. Alignment quality for Iteration #12 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... Refinement Iteration #12 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #13 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #13 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00569 for Iteration #13 of Tilt-Series #6. CCMS(rotations) = 0.44258 for Iteration #13 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6. The scaled sum of CCMS values is #0.0117 for iteration 13 of Tilt-Series #6. Alignment quality for Iteration #13 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... Refinement Iteration #13 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #14 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #14 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.0055 for Iteration #14 of Tilt-Series #6. CCMS(rotations) = 0.44774 for Iteration #14 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6. The scaled sum of CCMS values is #0.0117 for iteration 14 of Tilt-Series #6. Alignment quality for Iteration #14 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... Refinement Iteration #14 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #15 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #15 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00617 for Iteration #15 of Tilt-Series #6. CCMS(rotations) = 0.43833 for Iteration #15 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6. The scaled sum of CCMS values is #0.01185 for iteration 15 of Tilt-Series #6. Alignment quality for Iteration #15 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... Refinement Iteration #15 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #16 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #16 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00579 for Iteration #16 of Tilt-Series #6. CCMS(rotations) = 0.44483 for Iteration #16 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6. The scaled sum of CCMS values is #0.01179 for iteration 16 of Tilt-Series #6. Alignment quality for Iteration #16 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... Refinement Iteration #16 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #17 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #17 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00611 for Iteration #17 of Tilt-Series #6. CCMS(rotations) = 0.43163 for Iteration #17 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6. The scaled sum of CCMS values is #0.01169 for iteration 17 of Tilt-Series #6. Alignment quality for Iteration #17 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #6 (17dec26e): Very StableCreating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... Refinement Iteration #17 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #18 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #18 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00671 for Iteration #18 of Tilt-Series #6. CCMS(rotations) = 0.44734 for Iteration #18 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6. The scaled sum of CCMS values is #0.0123 for iteration 18 of Tilt-Series #6. Alignment quality for Iteration #18 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... Refinement Iteration #18 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #19 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #19 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00666 for Iteration #19 of Tilt-Series #6. CCMS(rotations) = 0.45017 for Iteration #19 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6. The scaled sum of CCMS values is #0.01233 for iteration 19 of Tilt-Series #6. Alignment quality for Iteration #19 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... Refinement Iteration #19 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #20 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #20 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1440, 1200) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00668 for Iteration #20 of Tilt-Series #6. CCMS(rotations) = 0.45141 for Iteration #20 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6. The scaled sum of CCMS values is #0.01237 for iteration 20 of Tilt-Series #6. Alignment quality for Iteration #20 of Tilt-Series #6 (17dec26e): Very Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Refinement Iteration #20 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1200 Beginning Refinement Iteration #21, Round #3 of Tilt-Series #6 (tiltseries0006_thick300) lowpass = 17.28 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms) window.lowpass.apodization = { 0.20132372093 0.20132372093 } align.translimit = 188.5e0 map.sampling = 2 window.highpass.diameter = { 0.00297386465132 0.00297386465132 } window.highpass.apodization = { 0.00594568681319 0.00594568681319 } window.mask.apodization = { 10 10 } align.mask.width = { 771 647 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 110.111280384 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 796 672 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 771 647 } reference.body = 110.111280384 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00875 for Iteration #21 of Tilt-Series #6. CCMS(rotations) = 0.51382 for Iteration #21 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6. The scaled sum of CCMS values is #0.01465 for iteration 21 of Tilt-Series #6. Alignment quality for Iteration #21 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #6 (17dec26e): StableCreating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... Refinement Iteration #21 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #22 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #22 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00758 for Iteration #22 of Tilt-Series #6. CCMS(rotations) = 0.47543 for Iteration #22 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6. The scaled sum of CCMS values is #0.0133 for iteration 22 of Tilt-Series #6. Alignment quality for Iteration #22 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... Refinement Iteration #22 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #23 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #23 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00909 for Iteration #23 of Tilt-Series #6. CCMS(rotations) = 0.45367 for Iteration #23 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6. The scaled sum of CCMS values is #0.01362 for iteration 23 of Tilt-Series #6. Alignment quality for Iteration #23 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... Refinement Iteration #23 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #24 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #24 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00694 for Iteration #24 of Tilt-Series #6. CCMS(rotations) = 0.45482 for Iteration #24 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6. The scaled sum of CCMS values is #0.01257 for iteration 24 of Tilt-Series #6. Alignment quality for Iteration #24 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... Refinement Iteration #24 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #25 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #25 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.0081 for Iteration #25 of Tilt-Series #6. CCMS(rotations) = 0.44134 for Iteration #25 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6. The scaled sum of CCMS values is #0.01288 for iteration 25 of Tilt-Series #6. Alignment quality for Iteration #25 of Tilt-Series #6 (17dec26e): Good (confidence: 23.333333%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Refinement Iteration #25 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 Beginning Refinement Iteration #26, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) lowpass = 8.64 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms) window.lowpass.apodization = { 0.196748181818 0.196748181818 } align.translimit = 377.0e0 map.sampling = 1 window.highpass.diameter = { 0.00148693232566 0.00148693232566 } window.highpass.apodization = { 0.00297284340659 0.00297284340659 } window.mask.apodization = { 10 10 } align.mask.width = { 1567 1320 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 220.222560768 map.lowpass.diameter = { 0.500979166667 0.500979166667 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1592 1345 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1567 1320 } reference.body = 220.222560768 window.lowpass.diameter = { 0.500979166667 0.500979166667 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01263 for Iteration #26 of Tilt-Series #6. CCMS(rotations) = 0.5646 for Iteration #26 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6. The scaled sum of CCMS values is #0.01761 for iteration 26 of Tilt-Series #6. Alignment quality for Iteration #26 of Tilt-Series #6 (17dec26e): Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #6 (17dec26e): UnstableCreating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... Refinement Iteration #26 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #27 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #27 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00853 for Iteration #27 of Tilt-Series #6. CCMS(rotations) = 0.34253 for Iteration #27 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6. The scaled sum of CCMS values is #0.01112 for iteration 27 of Tilt-Series #6. Alignment quality for Iteration #27 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... Refinement Iteration #27 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #28 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #28 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0082 for Iteration #28 of Tilt-Series #6. CCMS(rotations) = 0.31242 for Iteration #28 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6. The scaled sum of CCMS values is #0.01035 for iteration 28 of Tilt-Series #6. Alignment quality for Iteration #28 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... Refinement Iteration #28 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #29 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #29 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00825 for Iteration #29 of Tilt-Series #6. CCMS(rotations) = 0.41605 for Iteration #29 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6. The scaled sum of CCMS values is #0.01245 for iteration 29 of Tilt-Series #6. Alignment quality for Iteration #29 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #6 (17dec26e): Very StableCreating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... Refinement Iteration #29 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #30 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #30 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00731 for Iteration #30 of Tilt-Series #6. CCMS(rotations) = 0.4289 for Iteration #30 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6. The scaled sum of CCMS values is #0.01223 for iteration 30 of Tilt-Series #6. Alignment quality for Iteration #30 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... Refinement Iteration #30 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #31 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) fit.scale switched from false to true on Iteration #31Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00667 for Iteration #31 of Tilt-Series #6. CCMS(rotations) = 0.40868 for Iteration #31 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6. The scaled sum of CCMS values is #0.01151 for iteration 31 of Tilt-Series #6. Alignment quality for Iteration #31 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... Refinement Iteration #31 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #32 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #32 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00661 for Iteration #32 of Tilt-Series #6. CCMS(rotations) = 0.3127 for Iteration #32 of Tilt-Series #6. CCMS(scale) = 0.00232 for Iteration #32 of Tilt-Series #6. The scaled sum of CCMS values is #0.00715 for iteration 32 of Tilt-Series #6. Alignment quality for Iteration #32 of Tilt-Series #6 (17dec26e): Excellent (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... Refinement Iteration #32 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #33 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #33 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00541 for Iteration #33 of Tilt-Series #6. CCMS(rotations) = 0.40048 for Iteration #33 of Tilt-Series #6. CCMS(scale) = 0.00317 for Iteration #33 of Tilt-Series #6. The scaled sum of CCMS values is #0.0082 for iteration 33 of Tilt-Series #6. Alignment quality for Iteration #33 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... Refinement Iteration #33 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #34 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #34 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0059 for Iteration #34 of Tilt-Series #6. CCMS(rotations) = 0.41958 for Iteration #34 of Tilt-Series #6. CCMS(scale) = 0.00261 for Iteration #34 of Tilt-Series #6. The scaled sum of CCMS values is #0.00843 for iteration 34 of Tilt-Series #6. Alignment quality for Iteration #34 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... Refinement Iteration #34 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 No Round parameters changed for Iteration #35 of Tilt-Series #6 (tiltseries0006_thick300) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006_thick300) No parameters were switched for Iteration #35 Refinement failed. Retry #1 with Window Size: (1536, 1296) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (1512, 1280) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (1500, 1260) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00497 for Iteration #35 of Tilt-Series #6. CCMS(rotations) = 0.41279 for Iteration #35 of Tilt-Series #6. CCMS(scale) = 0.00262 for Iteration #35 of Tilt-Series #6. The scaled sum of CCMS values is #0.00803 for iteration 35 of Tilt-Series #6. Alignment quality for Iteration #35 of Tilt-Series #6 (17dec26e): Very Good (confidence: 26.666667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #6 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... Refinement Iteration #35 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1500 Window Size (y) was windowed down to 1260 Finished Refinement for Tilt-Series #6 (tiltseries0006_thick300)! 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: 2018yr01m23d-23hr42m23s