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/tiltseries0017_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=tiltseries0017_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=MoreManual --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=17 --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=42.0 --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

node28
Start time: 2017yr09m14d-19hr17m21s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0017.tlt to series0017.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #17 (tiltseries0017_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 = 7.39154136205
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 = 7.39154136205
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.01586 for Iteration #1 of Tilt-Series #17.
CCMS(rotations) = 0.67733 for Iteration #1 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #17.
The scaled sum of CCMS values is #0.02148 for iteration 1 of Tilt-Series #17.
Alignment quality for Iteration #1 of Tilt-Series #17 (17sep08r): Okay (confidence: 96.875000%)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 0.298000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01382 for Iteration #2 of Tilt-Series #17.
CCMS(rotations) = 0.63691 for Iteration #2 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01965 for iteration 2 of Tilt-Series #17.
Alignment quality for Iteration #2 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)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 0.064000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01071 for Iteration #3 of Tilt-Series #17.
CCMS(rotations) = 0.59658 for Iteration #3 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01728 for iteration 3 of Tilt-Series #17.
Alignment quality for Iteration #3 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)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 0.008000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01108 for Iteration #4 of Tilt-Series #17.
CCMS(rotations) = 0.57715 for Iteration #4 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01708 for iteration 4 of Tilt-Series #17.
Alignment quality for Iteration #4 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #17 (17sep08r): Rock Solid!Creating 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 0.017000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01169 for Iteration #5 of Tilt-Series #17.
CCMS(rotations) = 0.39039 for Iteration #5 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01365 for iteration 5 of Tilt-Series #17.
Alignment quality for Iteration #5 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #17 (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 0.493000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01107 for Iteration #6 of Tilt-Series #17.
CCMS(rotations) = 0.37444 for Iteration #6 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01302 for iteration 6 of Tilt-Series #17.
Alignment quality for Iteration #6 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #17 (17sep08r): UnstableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...
The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.783000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00946 for Iteration #7 of Tilt-Series #17.
CCMS(rotations) = 0.30141 for Iteration #7 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01076 for iteration 7 of Tilt-Series #17.
Alignment quality for Iteration #7 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #17 (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 0.967000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00903 for Iteration #8 of Tilt-Series #17.
CCMS(rotations) = 0.30657 for Iteration #8 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01065 for iteration 8 of Tilt-Series #17.
Alignment quality for Iteration #8 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #17 (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 1.111000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00925 for Iteration #9 of Tilt-Series #17.
CCMS(rotations) = 0.26303 for Iteration #9 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00989 for iteration 9 of Tilt-Series #17.
Alignment quality for Iteration #9 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #17 (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 1.106000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00863 for Iteration #10 of Tilt-Series #17.
CCMS(rotations) = 0.26549 for Iteration #10 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00963 for iteration 10 of Tilt-Series #17.
Alignment quality for Iteration #10 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #17 (17sep08r): StableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...
The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 1.146000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #17 (tiltseries0017_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 = 14.7830827241
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 = 14.7830827241
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00844 for Iteration #11 of Tilt-Series #17.
CCMS(rotations) = 0.23389 for Iteration #11 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #17.
The scaled sum of CCMS values is #0.0089 for iteration 11 of Tilt-Series #17.
Alignment quality for Iteration #11 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #17 (17sep08r): Rock Solid!Creating 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 1.101000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #12 of Tilt-Series #17.
CCMS(rotations) = 0.27178 for Iteration #12 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00932 for iteration 12 of Tilt-Series #17.
Alignment quality for Iteration #12 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #17 (17sep08r): Rock Solid!Creating 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 0.956000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00733 for Iteration #13 of Tilt-Series #17.
CCMS(rotations) = 0.21794 for Iteration #13 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00802 for iteration 13 of Tilt-Series #17.
Alignment quality for Iteration #13 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #17 (17sep08r): Rock Solid!Creating 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 1.091000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00913 for Iteration #14 of Tilt-Series #17.
CCMS(rotations) = 0.21791 for Iteration #14 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00892 for iteration 14 of Tilt-Series #17.
Alignment quality for Iteration #14 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #17 (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 1.177000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00898 for Iteration #15 of Tilt-Series #17.
CCMS(rotations) = 0.18667 for Iteration #15 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00822 for iteration 15 of Tilt-Series #17.
Alignment quality for Iteration #15 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #17 (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 1.214000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00796 for Iteration #16 of Tilt-Series #17.
CCMS(rotations) = 0.19429 for Iteration #16 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00787 for iteration 16 of Tilt-Series #17.
Alignment quality for Iteration #16 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #17 (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 1.256000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00839 for Iteration #17 of Tilt-Series #17.
CCMS(rotations) = 0.21238 for Iteration #17 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00844 for iteration 17 of Tilt-Series #17.
Alignment quality for Iteration #17 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #17 (17sep08r): Very StableCreating 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 1.436000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00757 for Iteration #18 of Tilt-Series #17.
CCMS(rotations) = 0.2126 for Iteration #18 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00804 for iteration 18 of Tilt-Series #17.
Alignment quality for Iteration #18 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #17 (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 1.457000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00794 for Iteration #19 of Tilt-Series #17.
CCMS(rotations) = 0.21301 for Iteration #19 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00823 for iteration 19 of Tilt-Series #17.
Alignment quality for Iteration #19 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #17 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...
The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 1.468000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00699 for Iteration #20 of Tilt-Series #17.
CCMS(rotations) = 0.20887 for Iteration #20 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00767 for iteration 20 of Tilt-Series #17.
Alignment quality for Iteration #20 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #17 (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 1.468000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #17 (tiltseries0017_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 = 29.5661654482
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 = 29.5661654482
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00723 for Iteration #21 of Tilt-Series #17.
CCMS(rotations) = 0.19041 for Iteration #21 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00742 for iteration 21 of Tilt-Series #17.
Alignment quality for Iteration #21 of Tilt-Series #17 (17sep08r): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #17 (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 1.114000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00694 for Iteration #22 of Tilt-Series #17.
CCMS(rotations) = 0.22022 for Iteration #22 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00788 for iteration 22 of Tilt-Series #17.
Alignment quality for Iteration #22 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #17 (17sep08r): Rock Solid!Creating 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 1.039000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #23 of Tilt-Series #17.
CCMS(rotations) = 0.27123 for Iteration #23 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00862 for iteration 23 of Tilt-Series #17.
Alignment quality for Iteration #23 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #17 (17sep08r): 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 0.935000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00696 for Iteration #24 of Tilt-Series #17.
CCMS(rotations) = 0.20595 for Iteration #24 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #17.
The scaled sum of CCMS values is #0.0076 for iteration 24 of Tilt-Series #17.
Alignment quality for Iteration #24 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #17 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...
The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.792000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00635 for Iteration #25 of Tilt-Series #17.
CCMS(rotations) = 0.22769 for Iteration #25 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00773 for iteration 25 of Tilt-Series #17.
Alignment quality for Iteration #25 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #17 (17sep08r): StableCreating 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 0.981000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #17 (tiltseries0017_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 = 59.1323308964
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 = 59.1323308964
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00996 for Iteration #26 of Tilt-Series #17.
CCMS(rotations) = 0.30956 for Iteration #26 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01117 for iteration 26 of Tilt-Series #17.
Alignment quality for Iteration #26 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #17 (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 1.150000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00776 for Iteration #27 of Tilt-Series #17.
CCMS(rotations) = 0.26951 for Iteration #27 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00927 for iteration 27 of Tilt-Series #17.
Alignment quality for Iteration #27 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #17 (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 1.011000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00962 for Iteration #28 of Tilt-Series #17.
CCMS(rotations) = 0.27171 for Iteration #28 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01024 for iteration 28 of Tilt-Series #17.
Alignment quality for Iteration #28 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #17 (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 1.077000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01034 for Iteration #29 of Tilt-Series #17.
CCMS(rotations) = 0.36517 for Iteration #29 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01247 for iteration 29 of Tilt-Series #17.
Alignment quality for Iteration #29 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #17 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...
The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 1.151000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01469 for Iteration #30 of Tilt-Series #17.
CCMS(rotations) = 0.30467 for Iteration #30 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #17.
The scaled sum of CCMS values is #0.01344 for iteration 30 of Tilt-Series #17.
Alignment quality for Iteration #30 of Tilt-Series #17 (17sep08r): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #17 (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 0.712000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01214 for Iteration #31 of Tilt-Series #17.
CCMS(rotations) = 0.22117 for Iteration #31 of Tilt-Series #17.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #17.
The scaled sum of CCMS values is #0.0105 for iteration 31 of Tilt-Series #17.
Alignment quality for Iteration #31 of Tilt-Series #17 (17sep08r): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #17 (17sep08r): 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 0.891000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00726 for Iteration #32 of Tilt-Series #17.
CCMS(rotations) = 0.22364 for Iteration #32 of Tilt-Series #17.
CCMS(scale) = 0.00386 for Iteration #32 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00669 for iteration 32 of Tilt-Series #17.
Alignment quality for Iteration #32 of Tilt-Series #17 (17sep08r): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #17 (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 0.717000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00658 for Iteration #33 of Tilt-Series #17.
CCMS(rotations) = 0.2274 for Iteration #33 of Tilt-Series #17.
CCMS(scale) = 0.00336 for Iteration #33 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00634 for iteration 33 of Tilt-Series #17.
Alignment quality for Iteration #33 of Tilt-Series #17 (17sep08r): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #17 (17sep08r): 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, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #34 of Tilt-Series #17.
CCMS(rotations) = 0.24706 for Iteration #34 of Tilt-Series #17.
CCMS(scale) = 0.00399 for Iteration #34 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00722 for iteration 34 of Tilt-Series #17.
Alignment quality for Iteration #34 of Tilt-Series #17 (17sep08r): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #17 (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 0.397000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #17 (tiltseries0017_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #17 (tiltseries0017_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00626 for Iteration #35 of Tilt-Series #17.
CCMS(rotations) = 0.2305 for Iteration #35 of Tilt-Series #17.
CCMS(scale) = 0.00478 for Iteration #35 of Tilt-Series #17.
The scaled sum of CCMS values is #0.00675 for iteration 35 of Tilt-Series #17.
Alignment quality for Iteration #35 of Tilt-Series #17 (17sep08r): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #17 (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 0.228000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #17 (tiltseries0017_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-14hr24m21s