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/tiltseries0019_thick250 --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=tiltseries0019_thick250 --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_1 --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=19 --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=250 --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=33.0 --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

node07
Start time: 2017yr09m14d-19hr23m36s
Description: 
Using Coarse alignment iteration 1 for Refinement by copying coarse_series0019.tlt to series0019.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
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 = 18.475153262
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 = 18.475153262
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04196 for Iteration #1 of Tilt-Series #19.
CCMS(rotations) = 0.16059 for Iteration #1 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #19.
The scaled sum of CCMS values is #0.02419 for iteration 1 of Tilt-Series #19.
Alignment quality for Iteration #1 of Tilt-Series #19 (17sep08r): Okay (confidence: 84.375000%)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 0.965000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00749 for Iteration #2 of Tilt-Series #19.
CCMS(rotations) = 0.21285 for Iteration #2 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #19.
The scaled sum of CCMS values is #0.008 for iteration 2 of Tilt-Series #19.
Alignment quality for Iteration #2 of Tilt-Series #19 (17sep08r): Very Good (confidence: 84.375000%)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 0.525000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00644 for Iteration #3 of Tilt-Series #19.
CCMS(rotations) = 0.17222 for Iteration #3 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00666 for iteration 3 of Tilt-Series #19.
Alignment quality for Iteration #3 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 1.100000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00571 for Iteration #4 of Tilt-Series #19.
CCMS(rotations) = 0.1221 for Iteration #4 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0053 for iteration 4 of Tilt-Series #19.
Alignment quality for Iteration #4 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #19 (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 0.713000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00541 for Iteration #5 of Tilt-Series #19.
CCMS(rotations) = 0.13343 for Iteration #5 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00537 for iteration 5 of Tilt-Series #19.
Alignment quality for Iteration #5 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #19 (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 1.220000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #6 of Tilt-Series #19.
CCMS(rotations) = 0.09305 for Iteration #6 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00479 for iteration 6 of Tilt-Series #19.
Alignment quality for Iteration #6 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #19 (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 0.940000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #7 of Tilt-Series #19.
CCMS(rotations) = 0.11958 for Iteration #7 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00495 for iteration 7 of Tilt-Series #19.
Alignment quality for Iteration #7 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #19 (17sep08r): StableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...
The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 1.256000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00536 for Iteration #8 of Tilt-Series #19.
CCMS(rotations) = 0.08377 for Iteration #8 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00436 for iteration 8 of Tilt-Series #19.
Alignment quality for Iteration #8 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #19 (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 0.931000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #9 of Tilt-Series #19.
CCMS(rotations) = 0.11605 for Iteration #9 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00552 for iteration 9 of Tilt-Series #19.
Alignment quality for Iteration #9 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #19 (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 1.431000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #10 of Tilt-Series #19.
CCMS(rotations) = 0.08483 for Iteration #10 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00446 for iteration 10 of Tilt-Series #19.
Alignment quality for Iteration #10 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #19 (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 1.064000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
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 = 36.9503065239
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 = 36.9503065239
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00898 for Iteration #11 of Tilt-Series #19.
CCMS(rotations) = 0.29979 for Iteration #11 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #19.
The scaled sum of CCMS values is #0.01049 for iteration 11 of Tilt-Series #19.
Alignment quality for Iteration #11 of Tilt-Series #19 (17sep08r): Very Good (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #19 (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 1.457000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00474 for Iteration #12 of Tilt-Series #19.
CCMS(rotations) = 0.13236 for Iteration #12 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00502 for iteration 12 of Tilt-Series #19.
Alignment quality for Iteration #12 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #19 (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 1.402000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #13 of Tilt-Series #19.
CCMS(rotations) = 0.11218 for Iteration #13 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00464 for iteration 13 of Tilt-Series #19.
Alignment quality for Iteration #13 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #19 (17sep08r): Very StableCreating 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 1.496000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00454 for Iteration #14 of Tilt-Series #19.
CCMS(rotations) = 0.12521 for Iteration #14 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00477 for iteration 14 of Tilt-Series #19.
Alignment quality for Iteration #14 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #19 (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 1.431000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00507 for Iteration #15 of Tilt-Series #19.
CCMS(rotations) = 0.1158 for Iteration #15 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00485 for iteration 15 of Tilt-Series #19.
Alignment quality for Iteration #15 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #19 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...
The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 1.551000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00499 for Iteration #16 of Tilt-Series #19.
CCMS(rotations) = 0.12298 for Iteration #16 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00496 for iteration 16 of Tilt-Series #19.
Alignment quality for Iteration #16 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #19 (17sep08r): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...
The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 1.330000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #17 of Tilt-Series #19.
CCMS(rotations) = 0.10648 for Iteration #17 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00522 for iteration 17 of Tilt-Series #19.
Alignment quality for Iteration #17 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #19 (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 1.553000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00523 for Iteration #18 of Tilt-Series #19.
CCMS(rotations) = 0.12518 for Iteration #18 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00512 for iteration 18 of Tilt-Series #19.
Alignment quality for Iteration #18 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #19 (17sep08r): StableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...
The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 1.354000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00595 for Iteration #19 of Tilt-Series #19.
CCMS(rotations) = 0.12281 for Iteration #19 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00543 for iteration 19 of Tilt-Series #19.
Alignment quality for Iteration #19 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #19 (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 1.595000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00497 for Iteration #20 of Tilt-Series #19.
CCMS(rotations) = 0.13114 for Iteration #20 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00511 for iteration 20 of Tilt-Series #19.
Alignment quality for Iteration #20 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #19 (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 1.357000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #19 (tiltseries0019_thick250)
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 = 73.9006130478
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 = 73.9006130478
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #21 of Tilt-Series #19.
CCMS(rotations) = 0.13885 for Iteration #21 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0064 for iteration 21 of Tilt-Series #19.
Alignment quality for Iteration #21 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #19 (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 1.692000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00889 for Iteration #22 of Tilt-Series #19.
CCMS(rotations) = 0.19191 for Iteration #22 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00829 for iteration 22 of Tilt-Series #19.
Alignment quality for Iteration #22 of Tilt-Series #19 (17sep08r): Very Good (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #19 (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 1.704000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00731 for Iteration #23 of Tilt-Series #19.
CCMS(rotations) = 0.12647 for Iteration #23 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00618 for iteration 23 of Tilt-Series #19.
Alignment quality for Iteration #23 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #19 (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 1.407000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #24 of Tilt-Series #19.
CCMS(rotations) = 0.11653 for Iteration #24 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00484 for iteration 24 of Tilt-Series #19.
Alignment quality for Iteration #24 of Tilt-Series #19 (17sep08r): Perfection! (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #19 (17sep08r): UnstableCreating 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 1.416000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00577 for Iteration #25 of Tilt-Series #19.
CCMS(rotations) = 0.11161 for Iteration #25 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00512 for iteration 25 of Tilt-Series #19.
Alignment quality for Iteration #25 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #19 (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 1.344000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
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 = 147.801226096
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 = 147.801226096
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01349 for Iteration #26 of Tilt-Series #19.
CCMS(rotations) = 0.24321 for Iteration #26 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #19.
The scaled sum of CCMS values is #0.01161 for iteration 26 of Tilt-Series #19.
Alignment quality for Iteration #26 of Tilt-Series #19 (17sep08r): Very Good (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #19 (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 0.959000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00796 for Iteration #27 of Tilt-Series #19.
CCMS(rotations) = 0.13471 for Iteration #27 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00667 for iteration 27 of Tilt-Series #19.
Alignment quality for Iteration #27 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #19 (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 1.370000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00531 for Iteration #28 of Tilt-Series #19.
CCMS(rotations) = 0.13478 for Iteration #28 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00535 for iteration 28 of Tilt-Series #19.
Alignment quality for Iteration #28 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #19 (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 1.368000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00766 for Iteration #29 of Tilt-Series #19.
CCMS(rotations) = 0.1727 for Iteration #29 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00728 for iteration 29 of Tilt-Series #19.
Alignment quality for Iteration #29 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #19 (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 1.284000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0063 for Iteration #30 of Tilt-Series #19.
CCMS(rotations) = 0.15993 for Iteration #30 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00635 for iteration 30 of Tilt-Series #19.
Alignment quality for Iteration #30 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #19 (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 1.134000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00848 for Iteration #31 of Tilt-Series #19.
CCMS(rotations) = 0.13671 for Iteration #31 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00698 for iteration 31 of Tilt-Series #19.
Alignment quality for Iteration #31 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #19 (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 1.359000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00792 for Iteration #32 of Tilt-Series #19.
CCMS(rotations) = 0.16004 for Iteration #32 of Tilt-Series #19.
CCMS(scale) = 0.00308 for Iteration #32 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0058 for iteration 32 of Tilt-Series #19.
Alignment quality for Iteration #32 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #19 (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 1.010000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00743 for Iteration #33 of Tilt-Series #19.
CCMS(rotations) = 0.14966 for Iteration #33 of Tilt-Series #19.
CCMS(scale) = 0.00181 for Iteration #33 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00507 for iteration 33 of Tilt-Series #19.
Alignment quality for Iteration #33 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #19 (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 1.137000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00809 for Iteration #34 of Tilt-Series #19.
CCMS(rotations) = 0.12214 for Iteration #34 of Tilt-Series #19.
CCMS(scale) = 0.00236 for Iteration #34 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00511 for iteration 34 of Tilt-Series #19.
Alignment quality for Iteration #34 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #19 (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 0.927000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #19 (tiltseries0019_thick250)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #19 (tiltseries0019_thick250)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00926 for Iteration #35 of Tilt-Series #19.
CCMS(rotations) = 0.15964 for Iteration #35 of Tilt-Series #19.
CCMS(scale) = 0.0033 for Iteration #35 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00631 for iteration 35 of Tilt-Series #19.
Alignment quality for Iteration #35 of Tilt-Series #19 (17sep08r): Excellent (confidence: 84.375000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #19 (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 0.836000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #19 (tiltseries0019_thick250)!
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-11hr45m43s