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/17aug18i/protomo_alignments/tiltseries0012_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --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=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --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=False --r1_highpass_diameter_y=2076.0 --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=3685 --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=1038.0 --runname=tiltseries0012_thick50 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --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=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --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=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --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=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --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=2076.0 --r4_highpass_diameter_x=2076.0 --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=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --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=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --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=1919.0 --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=25.0 --dimx=7676 --dimy=7420 --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=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node07
Start time: 2017yr09m04d-14hr51m49s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0012.tlt to series0012.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #12 (tiltseries0012_thick50)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 15.7977386324
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 15.7977386324
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.18228 for Iteration #1 of Tilt-Series #12.
CCMS(rotations) = 1.15721 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 #0.11429 for iteration 1 of Tilt-Series #12.
Alignment quality for Iteration #1 of Tilt-Series #12 (17aug18i): 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...

No Round parameters changed for Iteration #2 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.16024 for Iteration #2 of Tilt-Series #12.
CCMS(rotations) = 0.16367 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 #0.08339 for iteration 2 of Tilt-Series #12.
Alignment quality for Iteration #2 of Tilt-Series #12 (17aug18i): 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...

No Round parameters changed for Iteration #3 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01482 for Iteration #3 of Tilt-Series #12.
CCMS(rotations) = 0.12406 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 #0.00989 for iteration 3 of Tilt-Series #12.
Alignment quality for Iteration #3 of Tilt-Series #12 (17aug18i): Very 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...

No Round parameters changed for Iteration #4 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01304 for Iteration #4 of Tilt-Series #12.
CCMS(rotations) = 0.14506 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 #0.00942 for iteration 4 of Tilt-Series #12.
Alignment quality for Iteration #4 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01423 for Iteration #5 of Tilt-Series #12.
CCMS(rotations) = 0.11386 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 #0.00939 for iteration 5 of Tilt-Series #12.
Alignment quality for Iteration #5 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

Beginning Refinement Iteration #6, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 31.5954772648
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 31.5954772648
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01682 for Iteration #6 of Tilt-Series #12.
CCMS(rotations) = 0.16716 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 #0.01175 for iteration 6 of Tilt-Series #12.
Alignment quality for Iteration #6 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01343 for Iteration #7 of Tilt-Series #12.
CCMS(rotations) = 0.18685 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 #0.01045 for iteration 7 of Tilt-Series #12.
Alignment quality for Iteration #7 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01286 for Iteration #8 of Tilt-Series #12.
CCMS(rotations) = 0.17549 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 #0.00994 for iteration 8 of Tilt-Series #12.
Alignment quality for Iteration #8 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01269 for Iteration #9 of Tilt-Series #12.
CCMS(rotations) = 0.1771 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 #0.00989 for iteration 9 of Tilt-Series #12.
Alignment quality for Iteration #9 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01247 for Iteration #10 of Tilt-Series #12.
CCMS(rotations) = 0.17467 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 #0.00973 for iteration 10 of Tilt-Series #12.
Alignment quality for Iteration #10 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

No Round parameters changed for Iteration #11 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01258 for Iteration #11 of Tilt-Series #12.
CCMS(rotations) = 0.17504 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 #0.00979 for iteration 11 of Tilt-Series #12.
Alignment quality for Iteration #11 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01285 for Iteration #12 of Tilt-Series #12.
CCMS(rotations) = 0.17234 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 #0.00987 for iteration 12 of Tilt-Series #12.
Alignment quality for Iteration #12 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01277 for Iteration #13 of Tilt-Series #12.
CCMS(rotations) = 0.17609 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 #0.00991 for iteration 13 of Tilt-Series #12.
Alignment quality for Iteration #13 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01252 for Iteration #14 of Tilt-Series #12.
CCMS(rotations) = 0.1743 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 #0.00974 for iteration 14 of Tilt-Series #12.
Alignment quality for Iteration #14 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01257 for Iteration #15 of Tilt-Series #12.
CCMS(rotations) = 0.16975 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 #0.00968 for iteration 15 of Tilt-Series #12.
Alignment quality for Iteration #15 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

Beginning Refinement Iteration #16, Round #3 of Tilt-Series #12 (tiltseries0012_thick50)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 63.1909545296
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 63.1909545296
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01274 for Iteration #16 of Tilt-Series #12.
CCMS(rotations) = 0.19023 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 #0.01018 for iteration 16 of Tilt-Series #12.
Alignment quality for Iteration #16 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #12 (17aug18i): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01189 for Iteration #17 of Tilt-Series #12.
CCMS(rotations) = 0.13641 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 #0.00867 for iteration 17 of Tilt-Series #12.
Alignment quality for Iteration #17 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01146 for Iteration #18 of Tilt-Series #12.
CCMS(rotations) = 0.12416 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 #0.00821 for iteration 18 of Tilt-Series #12.
Alignment quality for Iteration #18 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01169 for Iteration #19 of Tilt-Series #12.
CCMS(rotations) = 0.13839 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 #0.00861 for iteration 19 of Tilt-Series #12.
Alignment quality for Iteration #19 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01111 for Iteration #20 of Tilt-Series #12.
CCMS(rotations) = 0.13345 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 #0.00823 for iteration 20 of Tilt-Series #12.
Alignment quality for Iteration #20 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 126.381909059
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 126.381909059
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01132 for Iteration #21 of Tilt-Series #12.
CCMS(rotations) = 0.20146 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 #0.00969 for iteration 21 of Tilt-Series #12.
Alignment quality for Iteration #21 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #12 (17aug18i): UnstableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01071 for Iteration #22 of Tilt-Series #12.
CCMS(rotations) = 0.13181 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 #0.00799 for iteration 22 of Tilt-Series #12.
Alignment quality for Iteration #22 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01153 for Iteration #23 of Tilt-Series #12.
CCMS(rotations) = 0.14483 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 #0.00866 for iteration 23 of Tilt-Series #12.
Alignment quality for Iteration #23 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #12 (17aug18i): Very StableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01119 for Iteration #24 of Tilt-Series #12.
CCMS(rotations) = 0.13126 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 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01053 for Iteration #25 of Tilt-Series #12.
CCMS(rotations) = 0.12508 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 #0.00777 for iteration 25 of Tilt-Series #12.
Alignment quality for Iteration #25 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

No Round parameters changed for Iteration #26 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.01126 for Iteration #26 of Tilt-Series #12.
CCMS(rotations) = 0.1323 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 #0.00828 for iteration 26 of Tilt-Series #12.
Alignment quality for Iteration #26 of Tilt-Series #12 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00989 for Iteration #27 of Tilt-Series #12.
CCMS(rotations) = 0.17338 for Iteration #27 of Tilt-Series #12.
CCMS(scale) = 0.00356 for Iteration #27 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00679 for iteration 27 of Tilt-Series #12.
Alignment quality for Iteration #27 of Tilt-Series #12 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00836 for Iteration #28 of Tilt-Series #12.
CCMS(rotations) = 0.12248 for Iteration #28 of Tilt-Series #12.
CCMS(scale) = 0.00333 for Iteration #28 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00553 for iteration 28 of Tilt-Series #12.
Alignment quality for Iteration #28 of Tilt-Series #12 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00819 for Iteration #29 of Tilt-Series #12.
CCMS(rotations) = 0.14185 for Iteration #29 of Tilt-Series #12.
CCMS(scale) = 0.00378 for Iteration #29 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00588 for iteration 29 of Tilt-Series #12.
Alignment quality for Iteration #29 of Tilt-Series #12 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #12 (17aug18i): Very StableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #12 (tiltseries0012_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #12 (tiltseries0012_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00943 for Iteration #30 of Tilt-Series #12.
CCMS(rotations) = 0.12337 for Iteration #30 of Tilt-Series #12.
CCMS(scale) = 0.00314 for Iteration #30 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00583 for iteration 30 of Tilt-Series #12.
Alignment quality for Iteration #30 of Tilt-Series #12 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #12 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #12 (tiltseries0012_thick50)!
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: 2017yr09m05d-21hr23m41s