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/jbrasch/18nov10g/protomo_alignments/tiltseries0047_thick600 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3962.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2158 --r1_region_y=2952 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3962.0 --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=tiltseries0047_thick600 --r2_region_y=2952 --r2_region_x=2158 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1981.0 --defocus_ang_positive=90 --r5_mask_width_x=2133 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3962.0 --r3_highpass_apod_x=1981.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=514 --r2_mask_width_y=713 --r5_region_x=2158 --r5_region_y=2952 --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=True --r1_highpass_diameter_y=3962.0 --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=2927 --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=1981.0 --r3_iters=5 --r1_highpass_diameter_x=3962.0 --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=2133 --r4_mask_width_y=2927 --r5_highpass_apod_y=1981.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18nov10g --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=1981.0 --r1_highpass_apod_x=1981.0 --r2_highpass_apod_x=1981.0 --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=47 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1451 --r3_mask_width_x=1054 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3962.0 --r4_highpass_diameter_x=3962.0 --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=3962.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1981.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3962.0 --defocus_max=0 --r4_region_y=2952 --r4_region_x=2158 --r5_kernel_y=5 --r3_region_x=2158 --r3_region_y=2952 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=600 --expid=7953 --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=3962.0 --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=301.0 --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=2.5 --tilt_clip=true --r4_highpass_apod_x=1981.0 --r4_highpass_apod_y=1981.0 --azimuth=true --r1_mask_width_y=344 --r1_mask_width_x=244 --jobtype=protomo --from_multirefine=True

node39
Start time: 2018yr12m11d-16hr03m11s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
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 = 37.625e0
map.sampling = 8
window.highpass.diameter = { 0.00741387178193 0.00741387178193 }
window.highpass.apodization = { 0.0148277435639 0.0148277435639 }
window.mask.apodization = { 10 10 }
align.mask.width = { 244 344 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 67.5607227262
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 269 369 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 244 344 }
reference.body = 67.5607227262
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05574 for Iteration #1 of Tilt-Series #47.
CCMS(rotations) = 0.77351 for Iteration #1 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04334 for iteration 1 of Tilt-Series #47.
Alignment quality for Iteration #1 of Tilt-Series #47 (18nov10g): 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...
The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.230000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #2 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04951 for Iteration #2 of Tilt-Series #47.
CCMS(rotations) = 1.05715 for Iteration #2 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #47.
The scaled sum of CCMS values is #0.0459 for iteration 2 of Tilt-Series #47.
Alignment quality for Iteration #2 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...
The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.870000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #3 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.04403 for Iteration #3 of Tilt-Series #47.
CCMS(rotations) = 1.35649 for Iteration #3 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04914 for iteration 3 of Tilt-Series #47.
Alignment quality for Iteration #3 of Tilt-Series #47 (18nov10g): Bad (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...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.649000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #4 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.05008 for Iteration #4 of Tilt-Series #47.
CCMS(rotations) = 1.08813 for Iteration #4 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #47.
The scaled sum of CCMS values is #0.0468 for iteration 4 of Tilt-Series #47.
Alignment quality for Iteration #4 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...
The tilt azimuth after iteration #4 deviated from the initial tilt azimuth by 0.738000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #5 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.04335 for Iteration #5 of Tilt-Series #47.
CCMS(rotations) = 0.93394 for Iteration #5 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04036 for iteration 5 of Tilt-Series #47.
Alignment quality for Iteration #5 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...
The tilt azimuth after iteration #5 deviated from the initial tilt azimuth by 1.674000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #6 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.03422 for Iteration #6 of Tilt-Series #47.
CCMS(rotations) = 1.54375 for Iteration #6 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04798 for iteration 6 of Tilt-Series #47.
Alignment quality for Iteration #6 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...
The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 1.994000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #7 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.0321 for Iteration #7 of Tilt-Series #47.
CCMS(rotations) = 1.7367 for Iteration #7 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #47.
The scaled sum of CCMS values is #0.05079 for iteration 7 of Tilt-Series #47.
Alignment quality for Iteration #7 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...
The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 2.247000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #8 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.0273 for Iteration #8 of Tilt-Series #47.
CCMS(rotations) = 1.57735 for Iteration #8 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #47.
The scaled sum of CCMS values is #0.0452 for iteration 8 of Tilt-Series #47.
Alignment quality for Iteration #8 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...
The tilt azimuth after iteration #8 deviated from the initial tilt azimuth by 2.231000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #9 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.03962 for Iteration #9 of Tilt-Series #47.
CCMS(rotations) = 1.49679 for Iteration #9 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04975 for iteration 9 of Tilt-Series #47.
Alignment quality for Iteration #9 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #47 (18nov10g): Very StableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...
The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 1.785000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #10 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.04745 for Iteration #10 of Tilt-Series #47.
CCMS(rotations) = 1.59912 for Iteration #10 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #47.
The scaled sum of CCMS values is #0.05571 for iteration 10 of Tilt-Series #47.
Alignment quality for Iteration #10 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...
The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 1.526000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
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 = 75.25e0
map.sampling = 4
window.highpass.diameter = { 0.00370693589096 0.00370693589096 }
window.highpass.apodization = { 0.00741387178193 0.00741387178193 }
window.mask.apodization = { 10 10 }
align.mask.width = { 514 713 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 135.121445452
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 539 738 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 514 713 }
reference.body = 135.121445452
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.03007 for Iteration #11 of Tilt-Series #47.
CCMS(rotations) = 1.13371 for Iteration #11 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #47.
The scaled sum of CCMS values is #0.03771 for iteration 11 of Tilt-Series #47.
Alignment quality for Iteration #11 of Tilt-Series #47 (18nov10g): Bad (confidence: 97.916667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...
The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 0.937000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #12 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.03368 for Iteration #12 of Tilt-Series #47.
CCMS(rotations) = 1.22729 for Iteration #12 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04139 for iteration 12 of Tilt-Series #47.
Alignment quality for Iteration #12 of Tilt-Series #47 (18nov10g): Bad (confidence: 97.916667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...
The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 1.010000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #13 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.04189 for Iteration #13 of Tilt-Series #47.
CCMS(rotations) = 1.04842 for Iteration #13 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04191 for iteration 13 of Tilt-Series #47.
Alignment quality for Iteration #13 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...
The tilt azimuth after iteration #13 deviated from the initial tilt azimuth by 0.801000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #14 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.04333 for Iteration #14 of Tilt-Series #47.
CCMS(rotations) = 1.19715 for Iteration #14 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04561 for iteration 14 of Tilt-Series #47.
Alignment quality for Iteration #14 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...
The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 0.049000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #15 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.04504 for Iteration #15 of Tilt-Series #47.
CCMS(rotations) = 1.45679 for Iteration #15 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #47.
The scaled sum of CCMS values is #0.05166 for iteration 15 of Tilt-Series #47.
Alignment quality for Iteration #15 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...
The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 0.996000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #16 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.04463 for Iteration #16 of Tilt-Series #47.
CCMS(rotations) = 1.26268 for Iteration #16 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04757 for iteration 16 of Tilt-Series #47.
Alignment quality for Iteration #16 of Tilt-Series #47 (18nov10g): Bad (confidence: 97.916667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...
The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.644000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #17 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.0475 for Iteration #17 of Tilt-Series #47.
CCMS(rotations) = 1.61209 for Iteration #17 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #47.
The scaled sum of CCMS values is #0.05599 for iteration 17 of Tilt-Series #47.
Alignment quality for Iteration #17 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...
The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 1.457000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #18 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.04597 for Iteration #18 of Tilt-Series #47.
CCMS(rotations) = 2.05141 for Iteration #18 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06401 for iteration 18 of Tilt-Series #47.
Alignment quality for Iteration #18 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...
The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 2.071000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #19 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0548 for Iteration #19 of Tilt-Series #47.
CCMS(rotations) = 2.15449 for Iteration #19 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #47.
The scaled sum of CCMS values is #0.07049 for iteration 19 of Tilt-Series #47.
Alignment quality for Iteration #19 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #47 (18nov10g): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...
The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 1.983000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #20 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.04379 for Iteration #20 of Tilt-Series #47.
CCMS(rotations) = 2.21322 for Iteration #20 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06616 for iteration 20 of Tilt-Series #47.
Alignment quality for Iteration #20 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...
The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 1.245000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #47 (tiltseries0047_thick600)
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 = 150.5e0
map.sampling = 2
window.highpass.diameter = { 0.00185346794548 0.00185346794548 }
window.highpass.apodization = { 0.00370693589096 0.00370693589096 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1054 1451 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 270.242890905
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1079 1476 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1054 1451 }
reference.body = 270.242890905
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.04165 for Iteration #21 of Tilt-Series #47.
CCMS(rotations) = 2.18568 for Iteration #21 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06454 for iteration 21 of Tilt-Series #47.
Alignment quality for Iteration #21 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #47 (18nov10g): Very StableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...
The tilt azimuth after iteration #21 deviated from the initial tilt azimuth by 1.176000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #22 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.03901 for Iteration #22 of Tilt-Series #47.
CCMS(rotations) = 2.09945 for Iteration #22 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #47.
The scaled sum of CCMS values is #0.0615 for iteration 22 of Tilt-Series #47.
Alignment quality for Iteration #22 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...
The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 1.219000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #23 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0489 for Iteration #23 of Tilt-Series #47.
CCMS(rotations) = 2.41206 for Iteration #23 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #47.
The scaled sum of CCMS values is #0.07269 for iteration 23 of Tilt-Series #47.
Alignment quality for Iteration #23 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...
The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 1.390000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #24 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.04393 for Iteration #24 of Tilt-Series #47.
CCMS(rotations) = 2.28418 for Iteration #24 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06765 for iteration 24 of Tilt-Series #47.
Alignment quality for Iteration #24 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...
The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 2.161000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #25 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.03817 for Iteration #25 of Tilt-Series #47.
CCMS(rotations) = 2.17792 for Iteration #25 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06264 for iteration 25 of Tilt-Series #47.
Alignment quality for Iteration #25 of Tilt-Series #47 (18nov10g): Bad (confidence: 97.916667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...
The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 1.755000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
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 = 301.0e0
map.sampling = 1
window.highpass.diameter = { 0.000926733972741 0.000926733972741 }
window.highpass.apodization = { 0.00185346794548 0.00185346794548 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2133 2927 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 540.48578181
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2158 2952 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2133 2927 }
reference.body = 540.48578181
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.04207 for Iteration #26 of Tilt-Series #47.
CCMS(rotations) = 2.88996 for Iteration #26 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #47.
The scaled sum of CCMS values is #0.07883 for iteration 26 of Tilt-Series #47.
Alignment quality for Iteration #26 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...
The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 3.027000 degrees, which is greater than the maximum allowed deviation of 2.500000 degrees.Changing the tilt azimuth back to the initial tilt azimuth of -80.000000 degrees for the next iteration.
No Round parameters changed for Iteration #27 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0374 for Iteration #27 of Tilt-Series #47.
CCMS(rotations) = 2.57825 for Iteration #27 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #47.
The scaled sum of CCMS values is #0.07026 for iteration 27 of Tilt-Series #47.
Alignment quality for Iteration #27 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...
The tilt azimuth after iteration #27 deviated from the initial tilt azimuth by 1.551000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #28 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.03047 for Iteration #28 of Tilt-Series #47.
CCMS(rotations) = 2.44348 for Iteration #28 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #47.
The scaled sum of CCMS values is #0.0641 for iteration 28 of Tilt-Series #47.
Alignment quality for Iteration #28 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...
The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 2.105000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #29 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.03317 for Iteration #29 of Tilt-Series #47.
CCMS(rotations) = 2.27274 for Iteration #29 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06204 for iteration 29 of Tilt-Series #47.
Alignment quality for Iteration #29 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...
The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 1.898000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #30 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.03167 for Iteration #30 of Tilt-Series #47.
CCMS(rotations) = 2.57357 for Iteration #30 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #47.
The scaled sum of CCMS values is #0.06731 for iteration 30 of Tilt-Series #47.
Alignment quality for Iteration #30 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 2.688000 degrees, which is greater than the maximum allowed deviation of 2.500000 degrees.Changing the tilt azimuth back to the initial tilt azimuth of -80.000000 degrees for the next iteration.
No Round parameters changed for Iteration #31 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
fit.scale switched from false to true on Iteration #31Refinement failed. Retry #1 with Window Size: (2058, 2916) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.04522 for Iteration #31 of Tilt-Series #47.
CCMS(rotations) = 4.32256 for Iteration #31 of Tilt-Series #47.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #47.
The scaled sum of CCMS values is #0.10906 for iteration 31 of Tilt-Series #47.
Alignment quality for Iteration #31 of Tilt-Series #47 (18nov10g): Bad (confidence: 29.166667%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...
The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 0.262000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Refinement Iteration #31 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2058
Window Size (y) was windowed down to 2916

No Round parameters changed for Iteration #32 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.03428 for Iteration #32 of Tilt-Series #47.
CCMS(rotations) = 2.21645 for Iteration #32 of Tilt-Series #47.
CCMS(scale) = 0.01218 for Iteration #32 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04504 for iteration 32 of Tilt-Series #47.
Alignment quality for Iteration #32 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...
The tilt azimuth after iteration #32 deviated from the initial tilt azimuth by 0.860000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #33 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.02415 for Iteration #33 of Tilt-Series #47.
CCMS(rotations) = 1.694 for Iteration #33 of Tilt-Series #47.
CCMS(scale) = 0.01928 for Iteration #33 of Tilt-Series #47.
The scaled sum of CCMS values is #0.03706 for iteration 33 of Tilt-Series #47.
Alignment quality for Iteration #33 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...
The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 0.498000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #34 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.02996 for Iteration #34 of Tilt-Series #47.
CCMS(rotations) = 2.19805 for Iteration #34 of Tilt-Series #47.
CCMS(scale) = 0.02206 for Iteration #34 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04665 for iteration 34 of Tilt-Series #47.
Alignment quality for Iteration #34 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...
The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 1.419000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #35 of Tilt-Series #47 (tiltseries0047_thick600)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #47 (tiltseries0047_thick600)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.02749 for Iteration #35 of Tilt-Series #47.
CCMS(rotations) = 1.7556 for Iteration #35 of Tilt-Series #47.
CCMS(scale) = 0.02812 for Iteration #35 of Tilt-Series #47.
The scaled sum of CCMS values is #0.04194 for iteration 35 of Tilt-Series #47.
Alignment quality for Iteration #35 of Tilt-Series #47 (18nov10g): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #47 (18nov10g): UnstableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.796000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Finished Refinement for Tilt-Series #47 (tiltseries0047_thick600)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly post your issue on the following Appion-Protomo Google group or email Alex at anoble@nysbc.org explaining the issue and include this log file.
https://groups.google.com/forum/#!topic/appion-protomo
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: 2018yr12m12d-20hr57m24s