protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/jbrasch/18nov10g/protomo_alignments/tiltseries0010_thick1200_thick1200_thick1200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3820.0 --r4_lowpass_diameter_x=3.68 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2081 --r1_region_y=3146 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3820.0 --r4_lowpass_apod_y=9.0 --r4_lowpass_apod_x=9.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=9.0 --r3_lowpass_apod_y=9.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0010_thick1200_thick1200_thick1200 --r2_region_y=3146 --r2_region_x=2081 --r2_sampling=1 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1910.0 --defocus_ang_positive=90 --r5_mask_width_x=2056 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3820.0 --r3_highpass_apod_x=1910.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=2056 --r2_mask_width_y=3121 --r5_region_x=2081 --r5_region_y=3146 --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=3.68 --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=3820.0 --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=3121 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1910.0 --r3_iters=5 --r1_highpass_diameter_x=3820.0 --r2_lowpass_diameter_y=7.36 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.68 --r5_lowpass_diameter_x=3.68 --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=2056 --r4_mask_width_y=3121 --r5_highpass_apod_y=1910.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18nov10g --exclude_images=999999 --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=0 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1910.0 --r1_highpass_apod_x=1910.0 --r2_highpass_apod_x=1910.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=9.0 --r5_lowpass_apod_y=9.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=14.72 --r1_lowpass_diameter_x=14.72 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=16 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=10 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=3121 --r3_mask_width_x=2056 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3820.0 --r4_highpass_diameter_x=3820.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=37.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=2 --ctf_correct=False --r2_highpass_diameter_y=3820.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1910.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3820.0 --defocus_max=0 --r4_region_y=3146 --r4_region_x=2081 --r5_kernel_y=5 --r3_region_x=2081 --r3_region_y=3146 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=1200 --expid=7953 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=3.68 --r3_lowpass_diameter_x=3.68 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=3820.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=18.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=18.0 --defocus_ang_negative=-90 --r3_sampling=1 --description= --make_searchable=True --translimit=301.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=7.36 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=37.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=2.5 --tilt_clip=true --r4_highpass_apod_x=1910.0 --r4_highpass_apod_y=1910.0 --azimuth=true --r1_mask_width_y=1548 --r1_mask_width_x=1015 --jobtype=protomo --from_multirefine=True

node39
Start time: 2019yr06m18d-14hr42m22s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
lowpass = 14.72 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.198471351351 0.198471351351 }
align.translimit = 150.5e0
map.sampling = 2
window.highpass.diameter = { 0.00192236649215 0.00192236649215 }
window.highpass.apodization = { 0.00384473298429 0.00384473298429 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1015 1548 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 472.137319988
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1040 1573 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1015 1548 }
reference.body = 472.137319988
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.02718 for Iteration #1 of Tilt-Series #10.
CCMS(rotations) = 0.23755 for Iteration #1 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #1 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01637 for iteration 1 of Tilt-Series #10.
Alignment quality for Iteration #1 of Tilt-Series #10 (18nov10g): Good (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 0.816000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02287 for Iteration #2 of Tilt-Series #10.
CCMS(rotations) = 0.22372 for Iteration #2 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #2 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01475 for iteration 2 of Tilt-Series #10.
Alignment quality for Iteration #2 of Tilt-Series #10 (18nov10g): Good (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 0.843000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02311 for Iteration #3 of Tilt-Series #10.
CCMS(rotations) = 0.27452 for Iteration #3 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #3 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01551 for iteration 3 of Tilt-Series #10.
Alignment quality for Iteration #3 of Tilt-Series #10 (18nov10g): Good (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 0.852000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #4 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02866 for Iteration #4 of Tilt-Series #10.
CCMS(rotations) = 0.25728 for Iteration #4 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #4 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01713 for iteration 4 of Tilt-Series #10.
Alignment quality for Iteration #4 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #10 (18nov10g): StableCreating 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 0.877000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #5 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.02165 for Iteration #5 of Tilt-Series #10.
CCMS(rotations) = 0.22558 for Iteration #5 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #5 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01437 for iteration 5 of Tilt-Series #10.
Alignment quality for Iteration #5 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #10 (18nov10g): Very StableCreating 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 0.702000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #6, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
lowpass = 7.36 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.203984444444 0.203984444444 }
align.translimit = 301.0e0
map.sampling = 1
window.highpass.diameter = { 0.000961183246073 0.000961183246073 }
window.highpass.apodization = { 0.00192236649215 0.00192236649215 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2056 3121 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 944.274639976
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2081 3146 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2056 3121 }
reference.body = 944.274639976
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.02659 for Iteration #6 of Tilt-Series #10.
CCMS(rotations) = 0.37542 for Iteration #6 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #6 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01802 for iteration 6 of Tilt-Series #10.
Alignment quality for Iteration #6 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #10 (18nov10g): 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 0.276000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #7 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.02332 for Iteration #7 of Tilt-Series #10.
CCMS(rotations) = 0.43917 for Iteration #7 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #7 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01777 for iteration 7 of Tilt-Series #10.
Alignment quality for Iteration #7 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #10 (18nov10g): 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 0.085000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #8 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.02153 for Iteration #8 of Tilt-Series #10.
CCMS(rotations) = 0.42762 for Iteration #8 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #8 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01702 for iteration 8 of Tilt-Series #10.
Alignment quality for Iteration #8 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #10 (18nov10g): 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 0.082000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #9 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.02447 for Iteration #9 of Tilt-Series #10.
CCMS(rotations) = 0.26467 for Iteration #9 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #9 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01583 for iteration 9 of Tilt-Series #10.
Alignment quality for Iteration #9 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #10 (18nov10g): UnstableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...
The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.894000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #10 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.02587 for Iteration #10 of Tilt-Series #10.
CCMS(rotations) = 0.30134 for Iteration #10 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #10 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01679 for iteration 10 of Tilt-Series #10.
Alignment quality for Iteration #10 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #10 (18nov10g): 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 0.675000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #11 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0306 for Iteration #11 of Tilt-Series #10.
CCMS(rotations) = 0.25963 for Iteration #11 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #11 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01781 for iteration 11 of Tilt-Series #10.
Alignment quality for Iteration #11 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #10 (18nov10g): 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 0.507000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #12 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0265 for Iteration #12 of Tilt-Series #10.
CCMS(rotations) = 0.26199 for Iteration #12 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #12 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01647 for iteration 12 of Tilt-Series #10.
Alignment quality for Iteration #12 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #10 (18nov10g): 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 0.634000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #13 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.02987 for Iteration #13 of Tilt-Series #10.
CCMS(rotations) = 0.15017 for Iteration #13 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #13 of Tilt-Series #10.
The scaled sum of CCMS values is #0.0161 for iteration 13 of Tilt-Series #10.
Alignment quality for Iteration #13 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #10 (18nov10g): 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 0.698000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #14 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.0268 for Iteration #14 of Tilt-Series #10.
CCMS(rotations) = 0.24055 for Iteration #14 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #14 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01629 for iteration 14 of Tilt-Series #10.
Alignment quality for Iteration #14 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #10 (18nov10g): 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 0.535000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #15 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.02743 for Iteration #15 of Tilt-Series #10.
CCMS(rotations) = 0.18234 for Iteration #15 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #15 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01572 for iteration 15 of Tilt-Series #10.
Alignment quality for Iteration #15 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #10 (18nov10g): 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 0.728000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
Beginning Refinement Iteration #16, Round #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
lowpass = 3.68 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.407968888889 0.407968888889 }
align.translimit = 301.0e0
map.sampling = 1
window.highpass.diameter = { 0.000961183246073 0.000961183246073 }
window.highpass.apodization = { 0.00192236649215 0.00192236649215 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2056 3121 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 944.274639976
map.lowpass.diameter = { 0.99775 0.99775 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2081 3146 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2056 3121 }
reference.body = 944.274639976
window.lowpass.diameter = { 0.99775 0.99775 }
align.correlation.mode = mcf
fit.scale switched from false to true on Iteration #16Creating quality assessment statistics...
CCMS(shift) = 0.02741 for Iteration #16 of Tilt-Series #10.
CCMS(rotations) = 0.19263 for Iteration #16 of Tilt-Series #10.
CCMS(scale) = 0.01243 for Iteration #16 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01585 for iteration 16 of Tilt-Series #10.
Alignment quality for Iteration #16 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #10 (18nov10g): 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 0.758000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #17 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01896 for Iteration #17 of Tilt-Series #10.
CCMS(rotations) = 0.18356 for Iteration #17 of Tilt-Series #10.
CCMS(scale) = 0.00953 for Iteration #17 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01194 for iteration 17 of Tilt-Series #10.
Alignment quality for Iteration #17 of Tilt-Series #10 (18nov10g): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #10 (18nov10g): UnstableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...
The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 0.579000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #18 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01712 for Iteration #18 of Tilt-Series #10.
CCMS(rotations) = 0.29609 for Iteration #18 of Tilt-Series #10.
CCMS(scale) = 0.00926 for Iteration #18 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01274 for iteration 18 of Tilt-Series #10.
Alignment quality for Iteration #18 of Tilt-Series #10 (18nov10g): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #10 (18nov10g): 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 0.492000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #19 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01738 for Iteration #19 of Tilt-Series #10.
CCMS(rotations) = 0.21072 for Iteration #19 of Tilt-Series #10.
CCMS(scale) = 0.00917 for Iteration #19 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01166 for iteration 19 of Tilt-Series #10.
Alignment quality for Iteration #19 of Tilt-Series #10 (18nov10g): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #10 (18nov10g): UnstableCreating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...
The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.760000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.
No Round parameters changed for Iteration #20 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01734 for Iteration #20 of Tilt-Series #10.
CCMS(rotations) = 0.18427 for Iteration #20 of Tilt-Series #10.
CCMS(scale) = 0.00824 for Iteration #20 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01098 for iteration 20 of Tilt-Series #10.
Alignment quality for Iteration #20 of Tilt-Series #10 (18nov10g): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #10 (18nov10g): 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 0.508000 degrees, which is less than the maximum allowed deviation of 2.500000 degrees.Finished Refinement for Tilt-Series #10 (tiltseries0010_thick1200_thick1200_thick1200)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly post your issue on the following Appion-Protomo Google group or email Alex at anoble@nysbc.org explaining the issue and include this log file.
https://groups.google.com/forum/#!topic/appion-protomo
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2019yr06m19d-23hr27m28s