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/19feb06g/protomo_alignments/tiltseries0018_thick2000 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=5892.0 --r4_lowpass_diameter_x=11.2 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2106 --r1_region_y=3121 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=5892.0 --r4_lowpass_apod_y=28.0 --r4_lowpass_apod_x=28.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=56.0 --r3_lowpass_apod_y=56.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0018_thick2000 --r2_region_y=3121 --r2_region_x=2106 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2946.0 --defocus_ang_positive=90 --r5_mask_width_x=2081 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=5892.0 --r3_highpass_apod_x=2946.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=501 --r2_mask_width_y=755 --r5_region_x=2106 --r5_region_y=3121 --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=11.2 --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=5892.0 --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=3096 --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=-14.95 --r3_mask_apod_x=10 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=2946.0 --r3_iters=5 --r1_highpass_diameter_x=5892.0 --r2_lowpass_diameter_y=44.8 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=5.6 --r5_lowpass_diameter_x=5.6 --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=2081 --r4_mask_width_y=3096 --r5_highpass_apod_y=2946.0 --logging=true --DefocusTol=200 --filter=median --sessionname=19feb06g --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=2946.0 --r1_highpass_apod_x=2946.0 --r2_highpass_apod_x=2946.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=14.0 --r5_lowpass_apod_y=14.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=89.6 --r1_lowpass_diameter_x=89.6 --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=18 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1535 --r3_mask_width_x=1028 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=5892.0 --r4_highpass_diameter_x=5892.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=224.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=5892.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2946.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=5892.0 --defocus_max=0 --r4_region_y=3121 --r4_region_x=2106 --r5_kernel_y=5 --r3_region_x=2106 --r3_region_y=3121 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=2000 --expid=8521 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=22.4 --r3_lowpass_diameter_x=22.4 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.7975 --link=False --r2_highpass_diameter_x=5892.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=112.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=112.0 --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=44.8 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=224.0 --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=2946.0 --r4_highpass_apod_y=2946.0 --azimuth=true --r1_mask_width_y=365 --r1_mask_width_x=238 --jobtype=protomo --from_multirefine=True

node38
Start time: 2019yr02m12d-11hr04m12s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
lowpass = 89.6 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 22.38 Angstroms, Nyquist is 44.76 Angstroms)
window.lowpass.apodization = { 0.199821428571 0.199821428571 }
align.translimit = 37.625e0
map.sampling = 8
window.highpass.diameter = { 0.0075967413442 0.0075967413442 }
window.highpass.apodization = { 0.0151934826884 0.0151934826884 }
window.mask.apodization = { 10 10 }
align.mask.width = { 238 365 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 150.919613888
map.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 263 390 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 238 365 }
reference.body = 150.919613888
window.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04142 for Iteration #1 of Tilt-Series #18.
CCMS(rotations) = 0.46913 for Iteration #1 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03009 for iteration 1 of Tilt-Series #18.
Alignment quality for Iteration #1 of Tilt-Series #18 (19feb06g): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 97.674419%)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 0.102000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #2 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.0282 for Iteration #2 of Tilt-Series #18.
CCMS(rotations) = 0.49466 for Iteration #2 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02399 for iteration 2 of Tilt-Series #18.
Alignment quality for Iteration #2 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)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 0.755000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #3 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.03452 for Iteration #3 of Tilt-Series #18.
CCMS(rotations) = 0.63493 for Iteration #3 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02996 for iteration 3 of Tilt-Series #18.
Alignment quality for Iteration #3 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)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 1.415000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #4 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02602 for Iteration #4 of Tilt-Series #18.
CCMS(rotations) = 0.61696 for Iteration #4 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02535 for iteration 4 of Tilt-Series #18.
Alignment quality for Iteration #4 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #18 (19feb06g): 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 1.340000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #5 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.02039 for Iteration #5 of Tilt-Series #18.
CCMS(rotations) = 0.42596 for Iteration #5 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01872 for iteration 5 of Tilt-Series #18.
Alignment quality for Iteration #5 of Tilt-Series #18 (19feb06g): Good (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #18 (19feb06g): 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 0.847000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #6 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.02475 for Iteration #6 of Tilt-Series #18.
CCMS(rotations) = 0.53023 for Iteration #6 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02298 for iteration 6 of Tilt-Series #18.
Alignment quality for Iteration #6 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #18 (19feb06g): 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 1.117000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #7 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.02206 for Iteration #7 of Tilt-Series #18.
CCMS(rotations) = 0.69179 for Iteration #7 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02486 for iteration 7 of Tilt-Series #18.
Alignment quality for Iteration #7 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #18 (19feb06g): 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 1.470000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #8 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.016 for Iteration #8 of Tilt-Series #18.
CCMS(rotations) = 0.67049 for Iteration #8 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02141 for iteration 8 of Tilt-Series #18.
Alignment quality for Iteration #8 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #18 (19feb06g): 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 1.712000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #9 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01593 for Iteration #9 of Tilt-Series #18.
CCMS(rotations) = 0.76705 for Iteration #9 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02331 for iteration 9 of Tilt-Series #18.
Alignment quality for Iteration #9 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #18 (19feb06g): 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 2.117000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #10 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0166 for Iteration #10 of Tilt-Series #18.
CCMS(rotations) = 0.89984 for Iteration #10 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0263 for iteration 10 of Tilt-Series #18.
Alignment quality for Iteration #10 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #18 (19feb06g): Rock Solid!Creating 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 2.687000 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.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
lowpass = 44.8 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 11.19 Angstroms, Nyquist is 22.38 Angstroms)
window.lowpass.apodization = { 0.199821428571 0.199821428571 }
align.translimit = 75.25e0
map.sampling = 4
window.highpass.diameter = { 0.0037983706721 0.0037983706721 }
window.highpass.apodization = { 0.0075967413442 0.0075967413442 }
window.mask.apodization = { 10 10 }
align.mask.width = { 501 755 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 301.839227777
map.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 526 780 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 501 755 }
reference.body = 301.839227777
window.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.02708 for Iteration #11 of Tilt-Series #18.
CCMS(rotations) = 0.90944 for Iteration #11 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03173 for iteration 11 of Tilt-Series #18.
Alignment quality for Iteration #11 of Tilt-Series #18 (19feb06g): Bad (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #18 (19feb06g): 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 0.084000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #12 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01946 for Iteration #12 of Tilt-Series #18.
CCMS(rotations) = 0.44625 for Iteration #12 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01865 for iteration 12 of Tilt-Series #18.
Alignment quality for Iteration #12 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #18 (19feb06g): 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 0.176000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #13 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01636 for Iteration #13 of Tilt-Series #18.
CCMS(rotations) = 0.44266 for Iteration #13 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01704 for iteration 13 of Tilt-Series #18.
Alignment quality for Iteration #13 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #18 (19feb06g): 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 0.025000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #14 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01586 for Iteration #14 of Tilt-Series #18.
CCMS(rotations) = 0.38998 for Iteration #14 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01573 for iteration 14 of Tilt-Series #18.
Alignment quality for Iteration #14 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.120000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #15 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01654 for Iteration #15 of Tilt-Series #18.
CCMS(rotations) = 0.3942 for Iteration #15 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01615 for iteration 15 of Tilt-Series #18.
Alignment quality for Iteration #15 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #18 (19feb06g): Rock Solid!Creating 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 0.062000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #16 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01263 for Iteration #16 of Tilt-Series #18.
CCMS(rotations) = 0.37631 for Iteration #16 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01384 for iteration 16 of Tilt-Series #18.
Alignment quality for Iteration #16 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #18 (19feb06g): 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 0.056000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #17 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01537 for Iteration #17 of Tilt-Series #18.
CCMS(rotations) = 0.411 for Iteration #17 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01591 for iteration 17 of Tilt-Series #18.
Alignment quality for Iteration #17 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #18 (19feb06g): 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 0.113000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #18 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01286 for Iteration #18 of Tilt-Series #18.
CCMS(rotations) = 0.36389 for Iteration #18 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01371 for iteration 18 of Tilt-Series #18.
Alignment quality for Iteration #18 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #18 (19feb06g): StableCreating 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 0.089000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #19 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01425 for Iteration #19 of Tilt-Series #18.
CCMS(rotations) = 0.39002 for Iteration #19 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01493 for iteration 19 of Tilt-Series #18.
Alignment quality for Iteration #19 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #18 (19feb06g): 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 0.114000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #20 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01133 for Iteration #20 of Tilt-Series #18.
CCMS(rotations) = 0.36898 for Iteration #20 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01305 for iteration 20 of Tilt-Series #18.
Alignment quality for Iteration #20 of Tilt-Series #18 (19feb06g): Good (confidence: 95.348837%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.065000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #18 (tiltseries0018_thick2000)
lowpass = 22.4 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 5.595 Angstroms, Nyquist is 11.19 Angstroms)
window.lowpass.apodization = { 0.199821428571 0.199821428571 }
align.translimit = 150.5e0
map.sampling = 2
window.highpass.diameter = { 0.00189918533605 0.00189918533605 }
window.highpass.apodization = { 0.0037983706721 0.0037983706721 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1028 1535 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 603.678455554
map.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1053 1560 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1028 1535 }
reference.body = 603.678455554
window.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01994 for Iteration #21 of Tilt-Series #18.
CCMS(rotations) = 0.40114 for Iteration #21 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01799 for iteration 21 of Tilt-Series #18.
Alignment quality for Iteration #21 of Tilt-Series #18 (19feb06g): Good (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #18 (19feb06g): 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 0.072000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #22 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01432 for Iteration #22 of Tilt-Series #18.
CCMS(rotations) = 0.92878 for Iteration #22 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02573 for iteration 22 of Tilt-Series #18.
Alignment quality for Iteration #22 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #18 (19feb06g): 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 0.182000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #23 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01802 for Iteration #23 of Tilt-Series #18.
CCMS(rotations) = 0.9505 for Iteration #23 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02802 for iteration 23 of Tilt-Series #18.
Alignment quality for Iteration #23 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.396000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #24 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.02017 for Iteration #24 of Tilt-Series #18.
CCMS(rotations) = 0.52121 for Iteration #24 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02051 for iteration 24 of Tilt-Series #18.
Alignment quality for Iteration #24 of Tilt-Series #18 (19feb06g): Okay (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.583000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #25 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01369 for Iteration #25 of Tilt-Series #18.
CCMS(rotations) = 0.51359 for Iteration #25 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01712 for iteration 25 of Tilt-Series #18.
Alignment quality for Iteration #25 of Tilt-Series #18 (19feb06g): Good (confidence: 97.674419%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #18 (19feb06g): 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 0.667000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
lowpass = 11.2 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.7975 Angstroms, Nyquist is 5.595 Angstroms)
window.lowpass.apodization = { 0.199821428571 0.199821428571 }
align.translimit = 301.0e0
map.sampling = 1
window.highpass.diameter = { 0.000949592668024 0.000949592668024 }
window.highpass.apodization = { 0.00189918533605 0.00189918533605 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2081 3096 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 1207.35691111
map.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2106 3121 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2081 3096 }
reference.body = 1207.35691111
window.lowpass.diameter = { 0.499553571429 0.499553571429 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.0197 for Iteration #26 of Tilt-Series #18.
CCMS(rotations) = 0.99364 for Iteration #26 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02972 for iteration 26 of Tilt-Series #18.
Alignment quality for Iteration #26 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #18 (19feb06g): 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 0.778000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #27 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01508 for Iteration #27 of Tilt-Series #18.
CCMS(rotations) = 0.75245 for Iteration #27 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02259 for iteration 27 of Tilt-Series #18.
Alignment quality for Iteration #27 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #18 (19feb06g): Rock Solid!Creating 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 0.886000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #28 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.02775 for Iteration #28 of Tilt-Series #18.
CCMS(rotations) = 0.76049 for Iteration #28 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02908 for iteration 28 of Tilt-Series #18.
Alignment quality for Iteration #28 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #18 (19feb06g): 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 0.389000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #29 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01916 for Iteration #29 of Tilt-Series #18.
CCMS(rotations) = 0.57889 for Iteration #29 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02116 for iteration 29 of Tilt-Series #18.
Alignment quality for Iteration #29 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.289000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #30 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.017 for Iteration #30 of Tilt-Series #18.
CCMS(rotations) = 0.58749 for Iteration #30 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02025 for iteration 30 of Tilt-Series #18.
Alignment quality for Iteration #30 of Tilt-Series #18 (19feb06g): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #18 (19feb06g): StableCreating 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 0.188000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #31 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01932 for Iteration #31 of Tilt-Series #18.
CCMS(rotations) = 0.40184 for Iteration #31 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0177 for iteration 31 of Tilt-Series #18.
Alignment quality for Iteration #31 of Tilt-Series #18 (19feb06g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #18 (19feb06g): 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 0.206000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #32 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #32
Refinement failed. Retry #1 with Window Size: (2058, 3024) (at sampling 1)...
Refinement failed. Retry #2 with Window Size: (2048, 3000) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01836 for Iteration #32 of Tilt-Series #18.
CCMS(rotations) = 0.14546 for Iteration #32 of Tilt-Series #18.
CCMS(scale) = 0.01479 for Iteration #32 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01299 for iteration 32 of Tilt-Series #18.
Alignment quality for Iteration #32 of Tilt-Series #18 (19feb06g): Good (confidence: 11.627907%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #18 (19feb06g): StableCreating 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 0.481000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Refinement Iteration #32 finished after retrying 2 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2048
Window Size (y) was windowed down to 3000

No Round parameters changed for Iteration #33 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #33
Refinement failed. Retry #1 with Window Size: (2058, 3024) (at sampling 1)...
Refinement failed. Retry #2 with Window Size: (2048, 3000) (at sampling 1)...
Refinement failed. Retry #3 with Window Size: (2016, 2940) (at sampling 1)...
Refinement failed. Retry #4 with Window Size: (2000, 2916) (at sampling 1)...
Refinement failed. Retry #5 with Window Size: (1960, 2880) (at sampling 1)...
Refinement failed. Retry #6 with Window Size: (1944, 2800) (at sampling 1)...
Refinement failed. Retry #7 with Window Size: (1920, 2744) (at sampling 1)...
Refinement failed. Retry #8 with Window Size: (1890, 2700) (at sampling 1)...
Refinement failed. Retry #9 with Window Size: (1800, 2688) (at sampling 1)...
Refinement failed. Retry #10 with Window Size: (1792, 2646) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.00978 for Iteration #33 of Tilt-Series #18.
CCMS(rotations) = 0.24781 for Iteration #33 of Tilt-Series #18.
CCMS(scale) = 0.0074 for Iteration #33 of Tilt-Series #18.
The scaled sum of CCMS values is #0.00903 for iteration 33 of Tilt-Series #18.
Alignment quality for Iteration #33 of Tilt-Series #18 (19feb06g): Very Good (confidence: 11.627907%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #18 (19feb06g): Rock Solid!Creating 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 0.668000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Refinement Iteration #33 finished after retrying 10 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 1792
Window Size (y) was windowed down to 2646

No Round parameters changed for Iteration #34 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #34
Refinement failed. Retry #1 with Window Size: (2058, 3024) (at sampling 1)...
Refinement failed. Retry #2 with Window Size: (2048, 3000) (at sampling 1)...
Refinement failed. Retry #3 with Window Size: (2016, 2940) (at sampling 1)...
Refinement failed. Retry #4 with Window Size: (2000, 2916) (at sampling 1)...
Refinement failed. Retry #5 with Window Size: (1960, 2880) (at sampling 1)...
Refinement failed. Retry #6 with Window Size: (1944, 2800) (at sampling 1)...
Refinement failed. Retry #7 with Window Size: (1920, 2744) (at sampling 1)...
Refinement failed. Retry #8 with Window Size: (1890, 2700) (at sampling 1)...
Refinement failed. Retry #9 with Window Size: (1800, 2688) (at sampling 1)...
Refinement failed. Retry #10 with Window Size: (1792, 2646) (at sampling 1)...
Refinement failed. Retry #11 with Window Size: (1764, 2592) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01708 for Iteration #34 of Tilt-Series #18.
CCMS(rotations) = 0.28777 for Iteration #34 of Tilt-Series #18.
CCMS(scale) = 0.00853 for Iteration #34 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01237 for iteration 34 of Tilt-Series #18.
Alignment quality for Iteration #34 of Tilt-Series #18 (19feb06g): Very Good (confidence: 11.627907%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #18 (19feb06g): Very StableCreating 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 0.453000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Refinement Iteration #34 finished after retrying 11 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 1764
Window Size (y) was windowed down to 2592

No Round parameters changed for Iteration #35 of Tilt-Series #18 (tiltseries0018_thick2000)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #18 (tiltseries0018_thick2000)
No parameters were switched for Iteration #35
Refinement failed. Retry #1 with Window Size: (2058, 3024) (at sampling 1)...
Refinement failed. Retry #2 with Window Size: (2048, 3000) (at sampling 1)...
Refinement failed. Retry #3 with Window Size: (2016, 2940) (at sampling 1)...
Refinement failed. Retry #4 with Window Size: (2000, 2916) (at sampling 1)...
Refinement failed. Retry #5 with Window Size: (1960, 2880) (at sampling 1)...
Refinement failed. Retry #6 with Window Size: (1944, 2800) (at sampling 1)...
Refinement failed. Retry #7 with Window Size: (1920, 2744) (at sampling 1)...
Refinement failed. Retry #8 with Window Size: (1890, 2700) (at sampling 1)...
Refinement failed. Retry #9 with Window Size: (1800, 2688) (at sampling 1)...
Refinement failed. Retry #10 with Window Size: (1792, 2646) (at sampling 1)...
Refinement failed. Retry #11 with Window Size: (1764, 2592) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01338 for Iteration #35 of Tilt-Series #18.
CCMS(rotations) = 1.04565 for Iteration #35 of Tilt-Series #18.
CCMS(scale) = 0.01515 for Iteration #35 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02345 for iteration 35 of Tilt-Series #18.
Alignment quality for Iteration #35 of Tilt-Series #18 (19feb06g): Okay (confidence: 16.279070%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #18 (19feb06g): 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 0.317000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Refinement Iteration #35 finished after retrying 11 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 1764
Window Size (y) was windowed down to 2592
Finished Refinement for Tilt-Series #18 (tiltseries0018_thick2000)!
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: 2019yr02m13d-16hr15m51s