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/tiltseries0013_thick100 --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=tiltseries0013_thick100 --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=13 --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=100 --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

node08
Start time: 2017yr09m04d-14hr54m07s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0013.tlt to series0013.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #13 (tiltseries0013_thick100)
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 = 31.5932717154
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 = 31.5932717154
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.18232 for Iteration #1 of Tilt-Series #13.
CCMS(rotations) = 0.95019 for Iteration #1 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #13.
The scaled sum of CCMS values is #0.11016 for iteration 1 of Tilt-Series #13.
Alignment quality for Iteration #1 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.15754 for Iteration #2 of Tilt-Series #13.
CCMS(rotations) = 1.37161 for Iteration #2 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #13.
The scaled sum of CCMS values is #0.1062 for iteration 2 of Tilt-Series #13.
Alignment quality for Iteration #2 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00689 for Iteration #3 of Tilt-Series #13.
CCMS(rotations) = 0.22361 for Iteration #3 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00792 for iteration 3 of Tilt-Series #13.
Alignment quality for Iteration #3 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0058 for Iteration #4 of Tilt-Series #13.
CCMS(rotations) = 0.30583 for Iteration #4 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00902 for iteration 4 of Tilt-Series #13.
Alignment quality for Iteration #4 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00705 for Iteration #5 of Tilt-Series #13.
CCMS(rotations) = 0.2006 for Iteration #5 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00754 for iteration 5 of Tilt-Series #13.
Alignment quality for Iteration #5 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #13 (17aug18i): Very StableCreating 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 #13 (tiltseries0013_thick100)
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 = 63.1865434307
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 = 63.1865434307
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00721 for Iteration #6 of Tilt-Series #13.
CCMS(rotations) = 0.32731 for Iteration #6 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01015 for iteration 6 of Tilt-Series #13.
Alignment quality for Iteration #6 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00742 for Iteration #7 of Tilt-Series #13.
CCMS(rotations) = 0.28739 for Iteration #7 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00946 for iteration 7 of Tilt-Series #13.
Alignment quality for Iteration #7 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00766 for Iteration #8 of Tilt-Series #13.
CCMS(rotations) = 0.27059 for Iteration #8 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00924 for iteration 8 of Tilt-Series #13.
Alignment quality for Iteration #8 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00757 for Iteration #9 of Tilt-Series #13.
CCMS(rotations) = 0.29243 for Iteration #9 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00963 for iteration 9 of Tilt-Series #13.
Alignment quality for Iteration #9 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00712 for Iteration #10 of Tilt-Series #13.
CCMS(rotations) = 0.26675 for Iteration #10 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00889 for iteration 10 of Tilt-Series #13.
Alignment quality for Iteration #10 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00711 for Iteration #11 of Tilt-Series #13.
CCMS(rotations) = 0.27778 for Iteration #11 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00911 for iteration 11 of Tilt-Series #13.
Alignment quality for Iteration #11 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00736 for Iteration #12 of Tilt-Series #13.
CCMS(rotations) = 0.30717 for Iteration #12 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00982 for iteration 12 of Tilt-Series #13.
Alignment quality for Iteration #12 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0072 for Iteration #13 of Tilt-Series #13.
CCMS(rotations) = 0.27946 for Iteration #13 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00919 for iteration 13 of Tilt-Series #13.
Alignment quality for Iteration #13 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00729 for Iteration #14 of Tilt-Series #13.
CCMS(rotations) = 0.28683 for Iteration #14 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00938 for iteration 14 of Tilt-Series #13.
Alignment quality for Iteration #14 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.0072 for Iteration #15 of Tilt-Series #13.
CCMS(rotations) = 0.27719 for Iteration #15 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00914 for iteration 15 of Tilt-Series #13.
Alignment quality for Iteration #15 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)
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 = 126.373086861
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 = 126.373086861
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00839 for Iteration #16 of Tilt-Series #13.
CCMS(rotations) = 0.31942 for Iteration #16 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01058 for iteration 16 of Tilt-Series #13.
Alignment quality for Iteration #16 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #13 (17aug18i): 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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00762 for Iteration #17 of Tilt-Series #13.
CCMS(rotations) = 0.21808 for Iteration #17 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00817 for iteration 17 of Tilt-Series #13.
Alignment quality for Iteration #17 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00791 for Iteration #18 of Tilt-Series #13.
CCMS(rotations) = 0.22811 for Iteration #18 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00851 for iteration 18 of Tilt-Series #13.
Alignment quality for Iteration #18 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00771 for Iteration #19 of Tilt-Series #13.
CCMS(rotations) = 0.23466 for Iteration #19 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00855 for iteration 19 of Tilt-Series #13.
Alignment quality for Iteration #19 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00821 for Iteration #20 of Tilt-Series #13.
CCMS(rotations) = 0.2181 for Iteration #20 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00847 for iteration 20 of Tilt-Series #13.
Alignment quality for Iteration #20 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)
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 = 252.746173723
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 = 252.746173723
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01079 for Iteration #21 of Tilt-Series #13.
CCMS(rotations) = 0.25226 for Iteration #21 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01044 for iteration 21 of Tilt-Series #13.
Alignment quality for Iteration #21 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #13 (17aug18i): StableCreating 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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.0121 for Iteration #22 of Tilt-Series #13.
CCMS(rotations) = 0.13318 for Iteration #22 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00871 for iteration 22 of Tilt-Series #13.
Alignment quality for Iteration #22 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #13 (17aug18i): StableCreating 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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01226 for Iteration #23 of Tilt-Series #13.
CCMS(rotations) = 0.18652 for Iteration #23 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00986 for iteration 23 of Tilt-Series #13.
Alignment quality for Iteration #23 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #13 (17aug18i): Rock Solid!Creating 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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01115 for Iteration #24 of Tilt-Series #13.
CCMS(rotations) = 0.24595 for Iteration #24 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0105 for iteration 24 of Tilt-Series #13.
Alignment quality for Iteration #24 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01111 for Iteration #25 of Tilt-Series #13.
CCMS(rotations) = 0.23868 for Iteration #25 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01033 for iteration 25 of Tilt-Series #13.
Alignment quality for Iteration #25 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.01092 for Iteration #26 of Tilt-Series #13.
CCMS(rotations) = 0.20768 for Iteration #26 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00961 for iteration 26 of Tilt-Series #13.
Alignment quality for Iteration #26 of Tilt-Series #13 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0079 for Iteration #27 of Tilt-Series #13.
CCMS(rotations) = 0.16348 for Iteration #27 of Tilt-Series #13.
CCMS(scale) = 0.005 for Iteration #27 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00648 for iteration 27 of Tilt-Series #13.
Alignment quality for Iteration #27 of Tilt-Series #13 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0067 for Iteration #28 of Tilt-Series #13.
CCMS(rotations) = 0.22466 for Iteration #28 of Tilt-Series #13.
CCMS(scale) = 0.005 for Iteration #28 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0069 for iteration 28 of Tilt-Series #13.
Alignment quality for Iteration #28 of Tilt-Series #13 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00607 for Iteration #29 of Tilt-Series #13.
CCMS(rotations) = 0.21565 for Iteration #29 of Tilt-Series #13.
CCMS(scale) = 0.00502 for Iteration #29 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00657 for iteration 29 of Tilt-Series #13.
Alignment quality for Iteration #29 of Tilt-Series #13 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #13 (17aug18i): Rock Solid!Creating 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 #13 (tiltseries0013_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #13 (tiltseries0013_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #30 of Tilt-Series #13.
CCMS(rotations) = 0.19395 for Iteration #30 of Tilt-Series #13.
CCMS(scale) = 0.00538 for Iteration #30 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0068 for iteration 30 of Tilt-Series #13.
Alignment quality for Iteration #30 of Tilt-Series #13 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #13 (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 #13 (tiltseries0013_thick100)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m05d-22hr38m10s