protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17sep08r/protomo_alignments/tiltseries0015_thick100 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=5211.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2227 --r1_region_y=2990 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=5211.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=2990 --r2_region_x=2227 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2606.0 --defocus_ang_positive=90 --r5_mask_width_x=2202 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=5211.0 --r3_highpass_apod_x=2606.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=531 --r2_mask_width_y=722 --r5_region_x=2227 --r5_region_y=2990 --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=6.25 --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=5211.0 --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=2965 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2606.0 --runname=tiltseries0015_thick100 --r1_highpass_diameter_x=5211.0 --r2_lowpass_diameter_y=25.0 --map_size_y=623 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --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=2202 --r4_mask_width_y=2965 --r5_highpass_apod_y=2606.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17sep08r --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=2606.0 --r1_highpass_apod_x=2606.0 --r2_highpass_apod_x=2606.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=15 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1470 --r3_mask_width_x=1088 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=5211.0 --r4_highpass_diameter_x=5211.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=5211.0 --tilt_azimuth=-96.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2606.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=5211.0 --defocus_max=0 --r4_region_y=2990 --r4_region_x=2227 --r5_kernel_y=5 --r3_region_x=2227 --r3_region_y=2990 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=100 --expid=4896 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=464 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.34 --link=False --r2_highpass_diameter_x=5211.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1246.0 --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=25.0 --dimx=3712 --dimy=4984 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2606.0 --r4_highpass_apod_y=2606.0 --azimuth=true --r1_mask_width_y=348 --r1_mask_width_x=253 --jobtype=protomo

node30
Start time: 2017yr09m14d-19hr11m29s
Description: 
coarse_series0015_iter2.tlt not found, using coarse_series0015.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0015.tlt to series0015.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 18.72 Angstroms, Nyquist is 37.44 Angstroms)
window.lowpass.apodization = { 0.29952 0.29952 }
map.sampling = 8
window.highpass.diameter = { 0.00718480138169 0.00718480138169 }
window.highpass.apodization = { 0.0143668457406 0.0143668457406 }
window.mask.apodization = { 10 10 }
align.mask.width = { 253 348 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 7.39104790774
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 278 373 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 253 348 }
reference.body = 7.39104790774
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03802 for Iteration #1 of Tilt-Series #15.
CCMS(rotations) = 0.93027 for Iteration #1 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #15.
The scaled sum of CCMS values is #0.03762 for iteration 1 of Tilt-Series #15.
Alignment quality for Iteration #1 of Tilt-Series #15 (17sep08r): 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 0.524000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02237 for Iteration #2 of Tilt-Series #15.
CCMS(rotations) = 0.68286 for Iteration #2 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #15.
The scaled sum of CCMS values is #0.02484 for iteration 2 of Tilt-Series #15.
Alignment quality for Iteration #2 of Tilt-Series #15 (17sep08r): Okay (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 0.197000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02197 for Iteration #3 of Tilt-Series #15.
CCMS(rotations) = 0.51951 for Iteration #3 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #15.
The scaled sum of CCMS values is #0.02138 for iteration 3 of Tilt-Series #15.
Alignment quality for Iteration #3 of Tilt-Series #15 (17sep08r): Okay (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 0.159000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01815 for Iteration #4 of Tilt-Series #15.
CCMS(rotations) = 0.39119 for Iteration #4 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0169 for iteration 4 of Tilt-Series #15.
Alignment quality for Iteration #4 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #15 (17sep08r): 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 0.406000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01834 for Iteration #5 of Tilt-Series #15.
CCMS(rotations) = 0.36171 for Iteration #5 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01641 for iteration 5 of Tilt-Series #15.
Alignment quality for Iteration #5 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #15 (17sep08r): 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 0.466000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01553 for Iteration #6 of Tilt-Series #15.
CCMS(rotations) = 0.31505 for Iteration #6 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01407 for iteration 6 of Tilt-Series #15.
Alignment quality for Iteration #6 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #15 (17sep08r): StableCreating 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 0.526000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01579 for Iteration #7 of Tilt-Series #15.
CCMS(rotations) = 0.30036 for Iteration #7 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0139 for iteration 7 of Tilt-Series #15.
Alignment quality for Iteration #7 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #15 (17sep08r): 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 0.645000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01576 for Iteration #8 of Tilt-Series #15.
CCMS(rotations) = 0.245 for Iteration #8 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01278 for iteration 8 of Tilt-Series #15.
Alignment quality for Iteration #8 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #15 (17sep08r): 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 0.728000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01591 for Iteration #9 of Tilt-Series #15.
CCMS(rotations) = 0.26557 for Iteration #9 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01326 for iteration 9 of Tilt-Series #15.
Alignment quality for Iteration #9 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #15 (17sep08r): 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 0.947000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.02034 for Iteration #10 of Tilt-Series #15.
CCMS(rotations) = 0.24502 for Iteration #10 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01507 for iteration 10 of Tilt-Series #15.
Alignment quality for Iteration #10 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #15 (17sep08r): 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 0.920000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 9.36 Angstroms, Nyquist is 18.72 Angstroms)
window.lowpass.apodization = { 0.297142857143 0.297142857143 }
map.sampling = 4
window.highpass.diameter = { 0.00359240069085 0.00359240069085 }
window.highpass.apodization = { 0.0071834228703 0.0071834228703 }
window.mask.apodization = { 10 10 }
align.mask.width = { 531 722 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 14.7820958155
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 556 747 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 531 722 }
reference.body = 14.7820958155
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01972 for Iteration #11 of Tilt-Series #15.
CCMS(rotations) = 0.24183 for Iteration #11 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0147 for iteration 11 of Tilt-Series #15.
Alignment quality for Iteration #11 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #15 (17sep08r): 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 0.942000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01942 for Iteration #12 of Tilt-Series #15.
CCMS(rotations) = 0.23263 for Iteration #12 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01436 for iteration 12 of Tilt-Series #15.
Alignment quality for Iteration #12 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...
The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 1.143000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01712 for Iteration #13 of Tilt-Series #15.
CCMS(rotations) = 0.27083 for Iteration #13 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01398 for iteration 13 of Tilt-Series #15.
Alignment quality for Iteration #13 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #15 (17sep08r): 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 1.163000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01676 for Iteration #14 of Tilt-Series #15.
CCMS(rotations) = 0.24583 for Iteration #14 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0133 for iteration 14 of Tilt-Series #15.
Alignment quality for Iteration #14 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #15 (17sep08r): 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 1.088000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01643 for Iteration #15 of Tilt-Series #15.
CCMS(rotations) = 0.27162 for Iteration #15 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01365 for iteration 15 of Tilt-Series #15.
Alignment quality for Iteration #15 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #15 (17sep08r): 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 1.637000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01346 for Iteration #16 of Tilt-Series #15.
CCMS(rotations) = 0.22075 for Iteration #16 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01115 for iteration 16 of Tilt-Series #15.
Alignment quality for Iteration #16 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #15 (17sep08r): 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 1.737000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01313 for Iteration #17 of Tilt-Series #15.
CCMS(rotations) = 0.18701 for Iteration #17 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01031 for iteration 17 of Tilt-Series #15.
Alignment quality for Iteration #17 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...
The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 1.931000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01353 for Iteration #18 of Tilt-Series #15.
CCMS(rotations) = 0.21262 for Iteration #18 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01102 for iteration 18 of Tilt-Series #15.
Alignment quality for Iteration #18 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...
The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 2.000000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01037 for Iteration #19 of Tilt-Series #15.
CCMS(rotations) = 0.22306 for Iteration #19 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00964 for iteration 19 of Tilt-Series #15.
Alignment quality for Iteration #19 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #15 (17sep08r): StableCreating 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 2.104000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.0109 for Iteration #20 of Tilt-Series #15.
CCMS(rotations) = 0.19205 for Iteration #20 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00929 for iteration 20 of Tilt-Series #15.
Alignment quality for Iteration #20 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #15 (17sep08r): 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 2.041000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.68 Angstroms, Nyquist is 9.36 Angstroms)
window.lowpass.apodization = { 0.301935483871 0.301935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00179620034542 0.00179620034542 }
window.highpass.apodization = { 0.00359171143515 0.00359171143515 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1088 1470 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 29.564191631
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1113 1495 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1088 1470 }
reference.body = 29.564191631
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01147 for Iteration #21 of Tilt-Series #15.
CCMS(rotations) = 0.19398 for Iteration #21 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00962 for iteration 21 of Tilt-Series #15.
Alignment quality for Iteration #21 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #15 (17sep08r): 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 1.635000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01294 for Iteration #22 of Tilt-Series #15.
CCMS(rotations) = 0.27185 for Iteration #22 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01191 for iteration 22 of Tilt-Series #15.
Alignment quality for Iteration #22 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...
The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 1.185000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01325 for Iteration #23 of Tilt-Series #15.
CCMS(rotations) = 0.23048 for Iteration #23 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01123 for iteration 23 of Tilt-Series #15.
Alignment quality for Iteration #23 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...
The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 1.441000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01135 for Iteration #24 of Tilt-Series #15.
CCMS(rotations) = 0.21286 for Iteration #24 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00993 for iteration 24 of Tilt-Series #15.
Alignment quality for Iteration #24 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #15 (17sep08r): 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 1.382000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01243 for Iteration #25 of Tilt-Series #15.
CCMS(rotations) = 0.22786 for Iteration #25 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01077 for iteration 25 of Tilt-Series #15.
Alignment quality for Iteration #25 of Tilt-Series #15 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...
The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 1.400000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.34 Angstroms, Nyquist is 4.68 Angstroms)
window.lowpass.apodization = { 0.2925 0.2925 }
map.sampling = 1
window.highpass.diameter = { 0.000898100172712 0.000898100172712 }
window.highpass.apodization = { 0.00179585571757 0.00179585571757 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2202 2965 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 59.1283832619
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2227 2990 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2202 2965 }
reference.body = 59.1283832619
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01362 for Iteration #26 of Tilt-Series #15.
CCMS(rotations) = 0.32929 for Iteration #26 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01339 for iteration 26 of Tilt-Series #15.
Alignment quality for Iteration #26 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #15 (17sep08r): 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 0.899000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01233 for Iteration #27 of Tilt-Series #15.
CCMS(rotations) = 0.35307 for Iteration #27 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01323 for iteration 27 of Tilt-Series #15.
Alignment quality for Iteration #27 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #15 (17sep08r): 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 0.860000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01558 for Iteration #28 of Tilt-Series #15.
CCMS(rotations) = 0.43276 for Iteration #28 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01645 for iteration 28 of Tilt-Series #15.
Alignment quality for Iteration #28 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #15 (17sep08r): 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 0.744000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01392 for Iteration #29 of Tilt-Series #15.
CCMS(rotations) = 0.31069 for Iteration #29 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01317 for iteration 29 of Tilt-Series #15.
Alignment quality for Iteration #29 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #15 (17sep08r): 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 0.653000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01162 for Iteration #30 of Tilt-Series #15.
CCMS(rotations) = 0.37897 for Iteration #30 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01339 for iteration 30 of Tilt-Series #15.
Alignment quality for Iteration #30 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #15 (17sep08r): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 0.273000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01451 for Iteration #31 of Tilt-Series #15.
CCMS(rotations) = 0.39618 for Iteration #31 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01518 for iteration 31 of Tilt-Series #15.
Alignment quality for Iteration #31 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #15 (17sep08r): StableCreating 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 0.460000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01525 for Iteration #32 of Tilt-Series #15.
CCMS(rotations) = 0.51077 for Iteration #32 of Tilt-Series #15.
CCMS(scale) = 0.00576 for Iteration #32 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01382 for iteration 32 of Tilt-Series #15.
Alignment quality for Iteration #32 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #15 (17sep08r): 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 0.176000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01693 for Iteration #33 of Tilt-Series #15.
CCMS(rotations) = 0.61584 for Iteration #33 of Tilt-Series #15.
CCMS(scale) = 0.00623 for Iteration #33 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01593 for iteration 33 of Tilt-Series #15.
Alignment quality for Iteration #33 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #15 (17sep08r): Very StableCreating 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 0.100000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01755 for Iteration #34 of Tilt-Series #15.
CCMS(rotations) = 0.55158 for Iteration #34 of Tilt-Series #15.
CCMS(scale) = 0.00707 for Iteration #34 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01556 for iteration 34 of Tilt-Series #15.
Alignment quality for Iteration #34 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #15 (17sep08r): 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 0.017000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0172 for Iteration #35 of Tilt-Series #15.
CCMS(rotations) = 0.50039 for Iteration #35 of Tilt-Series #15.
CCMS(scale) = 0.00896 for Iteration #35 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01539 for iteration 35 of Tilt-Series #15.
Alignment quality for Iteration #35 of Tilt-Series #15 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #15 (17sep08r): 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 0.418000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #15 (tiltseries0015_thick100)!
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: 2017yr09m15d-18hr41m01s