protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17mar28c/protomo_alignments/tiltseries0050_thick900 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3622.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1973 --r1_region_y=2323 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3622.0 --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=tiltseries0050_thick900 --r2_region_y=2323 --r2_region_x=1973 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1811.0 --defocus_ang_positive=90 --r5_mask_width_x=1948 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3622.0 --r3_highpass_apod_x=1811.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=468 --r2_mask_width_y=555 --r5_region_x=1973 --r5_region_y=2323 --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=3622.0 --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=2298 --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=1811.0 --r3_iters=5 --r1_highpass_diameter_x=3622.0 --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=1948 --r4_mask_width_y=2298 --r5_highpass_apod_y=1811.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17mar28c --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=1811.0 --r1_highpass_apod_x=1811.0 --r2_highpass_apod_x=1811.0 --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=50 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1136 --r3_mask_width_x=961 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3622.0 --r4_highpass_diameter_x=3622.0 --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=3622.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1811.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3622.0 --defocus_max=0 --r4_region_y=2323 --r4_region_x=1973 --r5_kernel_y=5 --r3_region_x=1973 --r3_region_y=2323 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=900 --expid=3714 --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=3622.0 --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=2.0 --tilt_clip=true --r4_highpass_apod_x=1811.0 --r4_highpass_apod_y=1811.0 --azimuth=true --r1_mask_width_y=265 --r1_mask_width_x=221 --jobtype=protomo --from_multirefine=True

node47
Start time: 2018yr07m02d-13hr09m09s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
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 = { 0.00810981778023 0.00810981778023 }
window.highpass.apodization = { 0.0162196355605 0.0162196355605 }
window.mask.apodization = { 10 10 }
align.mask.width = { 221 265 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 104.236844918
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 246 290 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 221 265 }
reference.body = 104.236844918
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05908 for Iteration #1 of Tilt-Series #50.
CCMS(rotations) = 1.53792 for Iteration #1 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0603 for iteration 1 of Tilt-Series #50.
Alignment quality for Iteration #1 of Tilt-Series #50 (17mar28c): 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 0.798000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #2 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04562 for Iteration #2 of Tilt-Series #50.
CCMS(rotations) = 0.70879 for Iteration #2 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #50.
The scaled sum of CCMS values is #0.03698 for iteration 2 of Tilt-Series #50.
Alignment quality for Iteration #2 of Tilt-Series #50 (17mar28c): 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 0.069000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #3 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.03377 for Iteration #3 of Tilt-Series #50.
CCMS(rotations) = 0.12093 for Iteration #3 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0193 for iteration 3 of Tilt-Series #50.
Alignment quality for Iteration #3 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.680000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #4 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.05197 for Iteration #4 of Tilt-Series #50.
CCMS(rotations) = 0.92046 for Iteration #4 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #50.
The scaled sum of CCMS values is #0.04439 for iteration 4 of Tilt-Series #50.
Alignment quality for Iteration #4 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #50 (17mar28c): 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 0.135000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #5 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.03678 for Iteration #5 of Tilt-Series #50.
CCMS(rotations) = 0.18526 for Iteration #5 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0221 for iteration 5 of Tilt-Series #50.
Alignment quality for Iteration #5 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #50 (17mar28c): 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 0.829000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #6 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.0576 for Iteration #6 of Tilt-Series #50.
CCMS(rotations) = 1.07458 for Iteration #6 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #50.
The scaled sum of CCMS values is #0.05029 for iteration 6 of Tilt-Series #50.
Alignment quality for Iteration #6 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #50 (17mar28c): 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 0.014000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #7 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.03565 for Iteration #7 of Tilt-Series #50.
CCMS(rotations) = 0.213 for Iteration #7 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02208 for iteration 7 of Tilt-Series #50.
Alignment quality for Iteration #7 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #50 (17mar28c): 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 0.755000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #8 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.05904 for Iteration #8 of Tilt-Series #50.
CCMS(rotations) = 1.02821 for Iteration #8 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #50.
The scaled sum of CCMS values is #0.05009 for iteration 8 of Tilt-Series #50.
Alignment quality for Iteration #8 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #50 (17mar28c): 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 0.097000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #9 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.03662 for Iteration #9 of Tilt-Series #50.
CCMS(rotations) = 0.29225 for Iteration #9 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02416 for iteration 9 of Tilt-Series #50.
Alignment quality for Iteration #9 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #50 (17mar28c): UnstableCreating 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 0.751000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #10 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.05431 for Iteration #10 of Tilt-Series #50.
CCMS(rotations) = 0.86212 for Iteration #10 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0444 for iteration 10 of Tilt-Series #50.
Alignment quality for Iteration #10 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #50 (17mar28c): 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 0.345000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
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 = { 0.00405490889012 0.00405490889012 }
window.highpass.apodization = { 0.00810981778023 0.00810981778023 }
window.mask.apodization = { 10 10 }
align.mask.width = { 468 555 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 208.473689837
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 493 580 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 468 555 }
reference.body = 208.473689837
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.03163 for Iteration #11 of Tilt-Series #50.
CCMS(rotations) = 0.43304 for Iteration #11 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02448 for iteration 11 of Tilt-Series #50.
Alignment quality for Iteration #11 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #50 (17mar28c): 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 0.300000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #12 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0335 for Iteration #12 of Tilt-Series #50.
CCMS(rotations) = 0.51017 for Iteration #12 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02695 for iteration 12 of Tilt-Series #50.
Alignment quality for Iteration #12 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #50 (17mar28c): 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 0.162000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #13 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.03097 for Iteration #13 of Tilt-Series #50.
CCMS(rotations) = 0.1799 for Iteration #13 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01908 for iteration 13 of Tilt-Series #50.
Alignment quality for Iteration #13 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #50 (17mar28c): 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 0.258000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #14 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.03694 for Iteration #14 of Tilt-Series #50.
CCMS(rotations) = 0.42295 for Iteration #14 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02693 for iteration 14 of Tilt-Series #50.
Alignment quality for Iteration #14 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #50 (17mar28c): 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 0.547000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #15 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.02983 for Iteration #15 of Tilt-Series #50.
CCMS(rotations) = 0.3579 for Iteration #15 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02208 for iteration 15 of Tilt-Series #50.
Alignment quality for Iteration #15 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #50 (17mar28c): 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 0.072000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #16 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.03413 for Iteration #16 of Tilt-Series #50.
CCMS(rotations) = 0.51738 for Iteration #16 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02741 for iteration 16 of Tilt-Series #50.
Alignment quality for Iteration #16 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #50 (17mar28c): Very StableCreating 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 0.049000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #17 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.02941 for Iteration #17 of Tilt-Series #50.
CCMS(rotations) = 0.23725 for Iteration #17 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01945 for iteration 17 of Tilt-Series #50.
Alignment quality for Iteration #17 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #50 (17mar28c): 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 0.290000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #18 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.04101 for Iteration #18 of Tilt-Series #50.
CCMS(rotations) = 0.52781 for Iteration #18 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #50.
The scaled sum of CCMS values is #0.03106 for iteration 18 of Tilt-Series #50.
Alignment quality for Iteration #18 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #50 (17mar28c): 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 0.142000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #19 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0306 for Iteration #19 of Tilt-Series #50.
CCMS(rotations) = 0.36897 for Iteration #19 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02268 for iteration 19 of Tilt-Series #50.
Alignment quality for Iteration #19 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #50 (17mar28c): UnstableCreating 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 0.386000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #20 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.03708 for Iteration #20 of Tilt-Series #50.
CCMS(rotations) = 0.59808 for Iteration #20 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0305 for iteration 20 of Tilt-Series #50.
Alignment quality for Iteration #20 of Tilt-Series #50 (17mar28c): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #50 (17mar28c): 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 0.097000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #50 (tiltseries0050_thick900)
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 = { 0.00202745444506 0.00202745444506 }
window.highpass.apodization = { 0.00405490889012 0.00405490889012 }
window.mask.apodization = { 10 10 }
align.mask.width = { 961 1136 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 416.947379673
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 986 1161 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 961 1136 }
reference.body = 416.947379673
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.02109 for Iteration #21 of Tilt-Series #50.
CCMS(rotations) = 0.34807 for Iteration #21 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01751 for iteration 21 of Tilt-Series #50.
Alignment quality for Iteration #21 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #50 (17mar28c): UnstableCreating 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 0.145000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #22 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01264 for Iteration #22 of Tilt-Series #50.
CCMS(rotations) = 0.2646 for Iteration #22 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01161 for iteration 22 of Tilt-Series #50.
Alignment quality for Iteration #22 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #50 (17mar28c): Very StableCreating 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 0.183000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #23 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01156 for Iteration #23 of Tilt-Series #50.
CCMS(rotations) = 0.27324 for Iteration #23 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01125 for iteration 23 of Tilt-Series #50.
Alignment quality for Iteration #23 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #50 (17mar28c): 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 0.102000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #24 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01241 for Iteration #24 of Tilt-Series #50.
CCMS(rotations) = 0.29217 for Iteration #24 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01205 for iteration 24 of Tilt-Series #50.
Alignment quality for Iteration #24 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #50 (17mar28c): Rock Solid!Creating 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 0.320000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #25 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.02466 for Iteration #25 of Tilt-Series #50.
CCMS(rotations) = 0.47998 for Iteration #25 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #50.
The scaled sum of CCMS values is #0.02193 for iteration 25 of Tilt-Series #50.
Alignment quality for Iteration #25 of Tilt-Series #50 (17mar28c): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #50 (17mar28c): 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 0.209000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
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 = { 0.00101372722253 0.00101372722253 }
window.highpass.apodization = { 0.00202745444506 0.00202745444506 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1948 2298 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 833.894759347
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1973 2323 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1948 2298 }
reference.body = 833.894759347
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01405 for Iteration #26 of Tilt-Series #50.
CCMS(rotations) = 0.31733 for Iteration #26 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01337 for iteration 26 of Tilt-Series #50.
Alignment quality for Iteration #26 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #50 (17mar28c): 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 0.516000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #27 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01032 for Iteration #27 of Tilt-Series #50.
CCMS(rotations) = 0.335 for Iteration #27 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01186 for iteration 27 of Tilt-Series #50.
Alignment quality for Iteration #27 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #50 (17mar28c): 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 0.500000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #28 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01023 for Iteration #28 of Tilt-Series #50.
CCMS(rotations) = 0.34417 for Iteration #28 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #50.
The scaled sum of CCMS values is #0.012 for iteration 28 of Tilt-Series #50.
Alignment quality for Iteration #28 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #50 (17mar28c): 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 0.717000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #29 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01117 for Iteration #29 of Tilt-Series #50.
CCMS(rotations) = 0.42821 for Iteration #29 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01415 for iteration 29 of Tilt-Series #50.
Alignment quality for Iteration #29 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #50 (17mar28c): 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 0.405000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #30 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00869 for Iteration #30 of Tilt-Series #50.
CCMS(rotations) = 0.38395 for Iteration #30 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01202 for iteration 30 of Tilt-Series #50.
Alignment quality for Iteration #30 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #50 (17mar28c): Rock Solid!Creating 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 0.262000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #31 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01138 for Iteration #31 of Tilt-Series #50.
CCMS(rotations) = 0.33269 for Iteration #31 of Tilt-Series #50.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01234 for iteration 31 of Tilt-Series #50.
Alignment quality for Iteration #31 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #50 (17mar28c): 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 0.442000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #32 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01641 for Iteration #32 of Tilt-Series #50.
CCMS(rotations) = 0.3783 for Iteration #32 of Tilt-Series #50.
CCMS(scale) = 0.005 for Iteration #32 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01218 for iteration 32 of Tilt-Series #50.
Alignment quality for Iteration #32 of Tilt-Series #50 (17mar28c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #50 (17mar28c): 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 0.403000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #33 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01461 for Iteration #33 of Tilt-Series #50.
CCMS(rotations) = 0.42319 for Iteration #33 of Tilt-Series #50.
CCMS(scale) = 0.00773 for Iteration #33 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01309 for iteration 33 of Tilt-Series #50.
Alignment quality for Iteration #33 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #50 (17mar28c): 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 0.457000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #34 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01262 for Iteration #34 of Tilt-Series #50.
CCMS(rotations) = 0.48379 for Iteration #34 of Tilt-Series #50.
CCMS(scale) = 0.00629 for Iteration #34 of Tilt-Series #50.
The scaled sum of CCMS values is #0.01276 for iteration 34 of Tilt-Series #50.
Alignment quality for Iteration #34 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #50 (17mar28c): 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 0.905000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.
No Round parameters changed for Iteration #35 of Tilt-Series #50 (tiltseries0050_thick900)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #50 (tiltseries0050_thick900)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01144 for Iteration #35 of Tilt-Series #50.
CCMS(rotations) = 0.56157 for Iteration #35 of Tilt-Series #50.
CCMS(scale) = 0.00629 for Iteration #35 of Tilt-Series #50.
The scaled sum of CCMS values is #0.0134 for iteration 35 of Tilt-Series #50.
Alignment quality for Iteration #35 of Tilt-Series #50 (17mar28c): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #50 (17mar28c): 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 0.938000 degrees, which is less than the maximum allowed deviation of 2.000000 degrees.Finished Refinement for Tilt-Series #50 (tiltseries0050_thick900)!
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: 2018yr07m05d-00hr16m30s