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/tiltseries0012_thick150 --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=tiltseries0012_thick150 --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=12 --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=150 --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

node33
Start time: 2017yr09m14d-19hr10m53s
Description: 
coarse_series0012_iter2.tlt not found, using coarse_series0012.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0012.tlt to series0012.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
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 = 11.0033645869
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 = 11.0033645869
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04602 for Iteration #1 of Tilt-Series #12.
CCMS(rotations) = 0.84715 for Iteration #1 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #12.
The scaled sum of CCMS values is #0.03995 for iteration 1 of Tilt-Series #12.
Alignment quality for Iteration #1 of Tilt-Series #12 (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 0.683000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.05387 for Iteration #2 of Tilt-Series #12.
CCMS(rotations) = 1.15671 for Iteration #2 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #12.
The scaled sum of CCMS values is #0.05007 for iteration 2 of Tilt-Series #12.
Alignment quality for Iteration #2 of Tilt-Series #12 (17sep08r): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...
The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.934000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02782 for Iteration #3 of Tilt-Series #12.
CCMS(rotations) = 0.79659 for Iteration #3 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02984 for iteration 3 of Tilt-Series #12.
Alignment quality for Iteration #3 of Tilt-Series #12 (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 0.868000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01549 for Iteration #4 of Tilt-Series #12.
CCMS(rotations) = 0.67075 for Iteration #4 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02116 for iteration 4 of Tilt-Series #12.
Alignment quality for Iteration #4 of Tilt-Series #12 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #12 (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 1.024000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01461 for Iteration #5 of Tilt-Series #12.
CCMS(rotations) = 0.64667 for Iteration #5 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02024 for iteration 5 of Tilt-Series #12.
Alignment quality for Iteration #5 of Tilt-Series #12 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 0.965000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01393 for Iteration #6 of Tilt-Series #12.
CCMS(rotations) = 0.68001 for Iteration #6 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02057 for iteration 6 of Tilt-Series #12.
Alignment quality for Iteration #6 of Tilt-Series #12 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #12 (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 1.013000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01335 for Iteration #7 of Tilt-Series #12.
CCMS(rotations) = 0.61481 for Iteration #7 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01897 for iteration 7 of Tilt-Series #12.
Alignment quality for Iteration #7 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 0.794000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01317 for Iteration #8 of Tilt-Series #12.
CCMS(rotations) = 0.62755 for Iteration #8 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01914 for iteration 8 of Tilt-Series #12.
Alignment quality for Iteration #8 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 0.878000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01301 for Iteration #9 of Tilt-Series #12.
CCMS(rotations) = 0.62327 for Iteration #9 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01897 for iteration 9 of Tilt-Series #12.
Alignment quality for Iteration #9 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #12 (17sep08r): StableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...
The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.778000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01364 for Iteration #10 of Tilt-Series #12.
CCMS(rotations) = 0.64006 for Iteration #10 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01962 for iteration 10 of Tilt-Series #12.
Alignment quality for Iteration #10 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #12 (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 0.900000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
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 = 22.0067291739
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 = 22.0067291739
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0207 for Iteration #11 of Tilt-Series #12.
CCMS(rotations) = 0.63824 for Iteration #11 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02311 for iteration 11 of Tilt-Series #12.
Alignment quality for Iteration #11 of Tilt-Series #12 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #12 (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 0.449000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.02125 for Iteration #12 of Tilt-Series #12.
CCMS(rotations) = 0.42701 for Iteration #12 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01917 for iteration 12 of Tilt-Series #12.
Alignment quality for Iteration #12 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #12 (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 0.383000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01717 for Iteration #13 of Tilt-Series #12.
CCMS(rotations) = 0.28414 for Iteration #13 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01427 for iteration 13 of Tilt-Series #12.
Alignment quality for Iteration #13 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #12 (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 0.744000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01678 for Iteration #14 of Tilt-Series #12.
CCMS(rotations) = 0.17756 for Iteration #14 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01194 for iteration 14 of Tilt-Series #12.
Alignment quality for Iteration #14 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #12 (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 1.089000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01113 for Iteration #15 of Tilt-Series #12.
CCMS(rotations) = 0.14281 for Iteration #15 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00842 for iteration 15 of Tilt-Series #12.
Alignment quality for Iteration #15 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #12 (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 1.498000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0094 for Iteration #16 of Tilt-Series #12.
CCMS(rotations) = 0.17436 for Iteration #16 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00819 for iteration 16 of Tilt-Series #12.
Alignment quality for Iteration #16 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 1.539000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01018 for Iteration #17 of Tilt-Series #12.
CCMS(rotations) = 0.22348 for Iteration #17 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00956 for iteration 17 of Tilt-Series #12.
Alignment quality for Iteration #17 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #12 (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 1.359000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01101 for Iteration #18 of Tilt-Series #12.
CCMS(rotations) = 0.16506 for Iteration #18 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00881 for iteration 18 of Tilt-Series #12.
Alignment quality for Iteration #18 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #12 (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 1.616000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00934 for Iteration #19 of Tilt-Series #12.
CCMS(rotations) = 0.18425 for Iteration #19 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00835 for iteration 19 of Tilt-Series #12.
Alignment quality for Iteration #19 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #12 (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 1.601000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00945 for Iteration #20 of Tilt-Series #12.
CCMS(rotations) = 0.18686 for Iteration #20 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00846 for iteration 20 of Tilt-Series #12.
Alignment quality for Iteration #20 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 1.631000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #12 (tiltseries0012_thick150)
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 = 44.0134583477
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 = 44.0134583477
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01068 for Iteration #21 of Tilt-Series #12.
CCMS(rotations) = 0.16713 for Iteration #21 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00868 for iteration 21 of Tilt-Series #12.
Alignment quality for Iteration #21 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 1.556000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01018 for Iteration #22 of Tilt-Series #12.
CCMS(rotations) = 0.19576 for Iteration #22 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00901 for iteration 22 of Tilt-Series #12.
Alignment quality for Iteration #22 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #12 (17sep08r): Very StableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...
The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 1.770000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01351 for Iteration #23 of Tilt-Series #12.
CCMS(rotations) = 0.29488 for Iteration #23 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01265 for iteration 23 of Tilt-Series #12.
Alignment quality for Iteration #23 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #12 (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 1.619000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01047 for Iteration #24 of Tilt-Series #12.
CCMS(rotations) = 0.14932 for Iteration #24 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00822 for iteration 24 of Tilt-Series #12.
Alignment quality for Iteration #24 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #12 (17sep08r): 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 1.580000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01107 for Iteration #25 of Tilt-Series #12.
CCMS(rotations) = 0.19304 for Iteration #25 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #12.
The scaled sum of CCMS values is #0.0094 for iteration 25 of Tilt-Series #12.
Alignment quality for Iteration #25 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #12 (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 1.677000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
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 = 88.0269166954
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 = 88.0269166954
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01354 for Iteration #26 of Tilt-Series #12.
CCMS(rotations) = 0.26059 for Iteration #26 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01198 for iteration 26 of Tilt-Series #12.
Alignment quality for Iteration #26 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #12 (17sep08r): Very StableCreating 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 1.751000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01318 for Iteration #27 of Tilt-Series #12.
CCMS(rotations) = 0.17944 for Iteration #27 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01018 for iteration 27 of Tilt-Series #12.
Alignment quality for Iteration #27 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #12 (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 1.387000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01416 for Iteration #28 of Tilt-Series #12.
CCMS(rotations) = 0.21944 for Iteration #28 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01147 for iteration 28 of Tilt-Series #12.
Alignment quality for Iteration #28 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 1.770000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01483 for Iteration #29 of Tilt-Series #12.
CCMS(rotations) = 0.19285 for Iteration #29 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01127 for iteration 29 of Tilt-Series #12.
Alignment quality for Iteration #29 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #12 (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 1.757000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01603 for Iteration #30 of Tilt-Series #12.
CCMS(rotations) = 0.25997 for Iteration #30 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01322 for iteration 30 of Tilt-Series #12.
Alignment quality for Iteration #30 of Tilt-Series #12 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #12 (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 1.482000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01164 for Iteration #31 of Tilt-Series #12.
CCMS(rotations) = 0.20956 for Iteration #31 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01001 for iteration 31 of Tilt-Series #12.
Alignment quality for Iteration #31 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #12 (17sep08r): Rock Solid!Creating 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 1.110000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01066 for Iteration #32 of Tilt-Series #12.
CCMS(rotations) = 0.23078 for Iteration #32 of Tilt-Series #12.
CCMS(scale) = 0.00459 for Iteration #32 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00816 for iteration 32 of Tilt-Series #12.
Alignment quality for Iteration #32 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #12 (17sep08r): Very 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 1.166000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01044 for Iteration #33 of Tilt-Series #12.
CCMS(rotations) = 0.16378 for Iteration #33 of Tilt-Series #12.
CCMS(scale) = 0.00472 for Iteration #33 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00724 for iteration 33 of Tilt-Series #12.
Alignment quality for Iteration #33 of Tilt-Series #12 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #12 (17sep08r): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...
The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 1.333000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01021 for Iteration #34 of Tilt-Series #12.
CCMS(rotations) = 0.17184 for Iteration #34 of Tilt-Series #12.
CCMS(scale) = 0.00486 for Iteration #34 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00731 for iteration 34 of Tilt-Series #12.
Alignment quality for Iteration #34 of Tilt-Series #12 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #12 (17sep08r): 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 1.035000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #12 (tiltseries0012_thick150)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #12 (tiltseries0012_thick150)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01115 for Iteration #35 of Tilt-Series #12.
CCMS(rotations) = 0.29851 for Iteration #35 of Tilt-Series #12.
CCMS(scale) = 0.00511 for Iteration #35 of Tilt-Series #12.
The scaled sum of CCMS values is #0.0094 for iteration 35 of Tilt-Series #12.
Alignment quality for Iteration #35 of Tilt-Series #12 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #12 (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 0.286000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #12 (tiltseries0012_thick150)!
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-11hr17m59s