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/tiltseries0019_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=tiltseries0019_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=19 --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=43.0 --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

node12
Start time: 2017yr09m04d-15hr21m12s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0019.tlt to series0019.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #19 (tiltseries0019_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 = 31.5927204002
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 = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.09399 for Iteration #1 of Tilt-Series #19.
CCMS(rotations) = 1.41131 for Iteration #1 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #19.
The scaled sum of CCMS values is #0.07522 for iteration 1 of Tilt-Series #19.
Alignment quality for Iteration #1 of Tilt-Series #19 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.967742%)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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.09165 for Iteration #2 of Tilt-Series #19.
CCMS(rotations) = 0.92825 for Iteration #2 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #19.
The scaled sum of CCMS values is #0.06439 for iteration 2 of Tilt-Series #19.
Alignment quality for Iteration #2 of Tilt-Series #19 (17aug18i): Bad (confidence: 0.967742%)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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.06941 for Iteration #3 of Tilt-Series #19.
CCMS(rotations) = 0.97675 for Iteration #3 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #19.
The scaled sum of CCMS values is #0.05424 for iteration 3 of Tilt-Series #19.
Alignment quality for Iteration #3 of Tilt-Series #19 (17aug18i): Bad (confidence: 0.967742%)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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0428 for Iteration #4 of Tilt-Series #19.
CCMS(rotations) = 0.19255 for Iteration #4 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #19.
The scaled sum of CCMS values is #0.02525 for iteration 4 of Tilt-Series #19.
Alignment quality for Iteration #4 of Tilt-Series #19 (17aug18i): Okay (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #19 (17aug18i): UnstableCreating 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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00793 for Iteration #5 of Tilt-Series #19.
CCMS(rotations) = 0.136 for Iteration #5 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00669 for iteration 5 of Tilt-Series #19.
Alignment quality for Iteration #5 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #19 (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 #19 (tiltseries0019_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 = 63.1854408003
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 = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01059 for Iteration #6 of Tilt-Series #19.
CCMS(rotations) = 0.12049 for Iteration #6 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0077 for iteration 6 of Tilt-Series #19.
Alignment quality for Iteration #6 of Tilt-Series #19 (17aug18i): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #19 (17aug18i): StableCreating 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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00679 for Iteration #7 of Tilt-Series #19.
CCMS(rotations) = 0.11974 for Iteration #7 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00579 for iteration 7 of Tilt-Series #19.
Alignment quality for Iteration #7 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00636 for Iteration #8 of Tilt-Series #19.
CCMS(rotations) = 0.13966 for Iteration #8 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00597 for iteration 8 of Tilt-Series #19.
Alignment quality for Iteration #8 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00582 for Iteration #9 of Tilt-Series #19.
CCMS(rotations) = 0.13022 for Iteration #9 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00551 for iteration 9 of Tilt-Series #19.
Alignment quality for Iteration #9 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0071 for Iteration #10 of Tilt-Series #19.
CCMS(rotations) = 0.11667 for Iteration #10 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00588 for iteration 10 of Tilt-Series #19.
Alignment quality for Iteration #10 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00618 for Iteration #11 of Tilt-Series #19.
CCMS(rotations) = 0.1569 for Iteration #11 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00623 for iteration 11 of Tilt-Series #19.
Alignment quality for Iteration #11 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00724 for Iteration #12 of Tilt-Series #19.
CCMS(rotations) = 0.13169 for Iteration #12 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00626 for iteration 12 of Tilt-Series #19.
Alignment quality for Iteration #12 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00572 for Iteration #13 of Tilt-Series #19.
CCMS(rotations) = 0.15186 for Iteration #13 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0059 for iteration 13 of Tilt-Series #19.
Alignment quality for Iteration #13 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00685 for Iteration #14 of Tilt-Series #19.
CCMS(rotations) = 0.13061 for Iteration #14 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00604 for iteration 14 of Tilt-Series #19.
Alignment quality for Iteration #14 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00611 for Iteration #15 of Tilt-Series #19.
CCMS(rotations) = 0.13706 for Iteration #15 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00579 for iteration 15 of Tilt-Series #19.
Alignment quality for Iteration #15 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #19 (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 #19 (tiltseries0019_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 = 126.370881601
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 = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0102 for Iteration #16 of Tilt-Series #19.
CCMS(rotations) = 0.08662 for Iteration #16 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00683 for iteration 16 of Tilt-Series #19.
Alignment quality for Iteration #16 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00604 for Iteration #17 of Tilt-Series #19.
CCMS(rotations) = 0.12363 for Iteration #17 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00549 for iteration 17 of Tilt-Series #19.
Alignment quality for Iteration #17 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00589 for Iteration #18 of Tilt-Series #19.
CCMS(rotations) = 0.07782 for Iteration #18 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0045 for iteration 18 of Tilt-Series #19.
Alignment quality for Iteration #18 of Tilt-Series #19 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00642 for Iteration #19 of Tilt-Series #19.
CCMS(rotations) = 0.13573 for Iteration #19 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00592 for iteration 19 of Tilt-Series #19.
Alignment quality for Iteration #19 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00572 for Iteration #20 of Tilt-Series #19.
CCMS(rotations) = 0.07735 for Iteration #20 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00441 for iteration 20 of Tilt-Series #19.
Alignment quality for Iteration #20 of Tilt-Series #19 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #19 (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 #19 (tiltseries0019_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 = 252.741763201
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 = 252.741763201
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00702 for Iteration #21 of Tilt-Series #19.
CCMS(rotations) = 0.12611 for Iteration #21 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00603 for iteration 21 of Tilt-Series #19.
Alignment quality for Iteration #21 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #19 (17aug18i): Rock Solid!Creating 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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #22 of Tilt-Series #19.
CCMS(rotations) = 0.10262 for Iteration #22 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00538 for iteration 22 of Tilt-Series #19.
Alignment quality for Iteration #22 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0089 for Iteration #23 of Tilt-Series #19.
CCMS(rotations) = 0.1316 for Iteration #23 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00708 for iteration 23 of Tilt-Series #19.
Alignment quality for Iteration #23 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00978 for Iteration #24 of Tilt-Series #19.
CCMS(rotations) = 0.12438 for Iteration #24 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00738 for iteration 24 of Tilt-Series #19.
Alignment quality for Iteration #24 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00997 for Iteration #25 of Tilt-Series #19.
CCMS(rotations) = 0.19914 for Iteration #25 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00897 for iteration 25 of Tilt-Series #19.
Alignment quality for Iteration #25 of Tilt-Series #19 (17aug18i): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #19 (17aug18i): UnstableCreating 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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00868 for Iteration #26 of Tilt-Series #19.
CCMS(rotations) = 0.18999 for Iteration #26 of Tilt-Series #19.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00814 for iteration 26 of Tilt-Series #19.
Alignment quality for Iteration #26 of Tilt-Series #19 (17aug18i): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #19 (17aug18i): Very StableCreating 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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00717 for Iteration #27 of Tilt-Series #19.
CCMS(rotations) = 0.10998 for Iteration #27 of Tilt-Series #19.
CCMS(scale) = 0.00254 for Iteration #27 of Tilt-Series #19.
The scaled sum of CCMS values is #0.0047 for iteration 27 of Tilt-Series #19.
Alignment quality for Iteration #27 of Tilt-Series #19 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00704 for Iteration #28 of Tilt-Series #19.
CCMS(rotations) = 0.11431 for Iteration #28 of Tilt-Series #19.
CCMS(scale) = 0.00262 for Iteration #28 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00475 for iteration 28 of Tilt-Series #19.
Alignment quality for Iteration #28 of Tilt-Series #19 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00697 for Iteration #29 of Tilt-Series #19.
CCMS(rotations) = 0.11283 for Iteration #29 of Tilt-Series #19.
CCMS(scale) = 0.00312 for Iteration #29 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00487 for iteration 29 of Tilt-Series #19.
Alignment quality for Iteration #29 of Tilt-Series #19 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #19 (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 #19 (tiltseries0019_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #19 (tiltseries0019_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0064 for Iteration #30 of Tilt-Series #19.
CCMS(rotations) = 0.16263 for Iteration #30 of Tilt-Series #19.
CCMS(scale) = 0.00281 for Iteration #30 of Tilt-Series #19.
The scaled sum of CCMS values is #0.00524 for iteration 30 of Tilt-Series #19.
Alignment quality for Iteration #30 of Tilt-Series #19 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #19 (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 #19 (tiltseries0019_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-23hr00m43s