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/tiltseries0038_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=tiltseries0038_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=38 --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

node27
Start time: 2017yr09m04d-16hr24m36s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0038.tlt to series0038.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #38 (tiltseries0038_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 = 15.7960845569
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 = 15.7960845569
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03458 for Iteration #1 of Tilt-Series #38.
CCMS(rotations) = 1.22872 for Iteration #1 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #38.
The scaled sum of CCMS values is #0.04186 for iteration 1 of Tilt-Series #38.
Alignment quality for Iteration #1 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #2 of Tilt-Series #38.
CCMS(rotations) = 0.15303 for Iteration #2 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00672 for iteration 2 of Tilt-Series #38.
Alignment quality for Iteration #2 of Tilt-Series #38 (17aug18i): Excellent (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00724 for Iteration #3 of Tilt-Series #38.
CCMS(rotations) = 0.15975 for Iteration #3 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00681 for iteration 3 of Tilt-Series #38.
Alignment quality for Iteration #3 of Tilt-Series #38 (17aug18i): Excellent (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00702 for Iteration #4 of Tilt-Series #38.
CCMS(rotations) = 0.17713 for Iteration #4 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00705 for iteration 4 of Tilt-Series #38.
Alignment quality for Iteration #4 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #38 (17aug18i): Very StableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00804 for Iteration #5 of Tilt-Series #38.
CCMS(rotations) = 0.1574 for Iteration #5 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00717 for iteration 5 of Tilt-Series #38.
Alignment quality for Iteration #5 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_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 = 31.5921691138
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 = 31.5921691138
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00654 for Iteration #6 of Tilt-Series #38.
CCMS(rotations) = 0.16136 for Iteration #6 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #38.
The scaled sum of CCMS values is #0.0065 for iteration 6 of Tilt-Series #38.
Alignment quality for Iteration #6 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #7 of Tilt-Series #38.
CCMS(rotations) = 0.17166 for Iteration #7 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00627 for iteration 7 of Tilt-Series #38.
Alignment quality for Iteration #7 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00537 for Iteration #8 of Tilt-Series #38.
CCMS(rotations) = 0.13665 for Iteration #8 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00542 for iteration 8 of Tilt-Series #38.
Alignment quality for Iteration #8 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #9 of Tilt-Series #38.
CCMS(rotations) = 0.14227 for Iteration #9 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00566 for iteration 9 of Tilt-Series #38.
Alignment quality for Iteration #9 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00579 for Iteration #10 of Tilt-Series #38.
CCMS(rotations) = 0.15004 for Iteration #10 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #38.
The scaled sum of CCMS values is #0.0059 for iteration 10 of Tilt-Series #38.
Alignment quality for Iteration #10 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00579 for Iteration #11 of Tilt-Series #38.
CCMS(rotations) = 0.14602 for Iteration #11 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00582 for iteration 11 of Tilt-Series #38.
Alignment quality for Iteration #11 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00605 for Iteration #12 of Tilt-Series #38.
CCMS(rotations) = 0.14206 for Iteration #12 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00587 for iteration 12 of Tilt-Series #38.
Alignment quality for Iteration #12 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00577 for Iteration #13 of Tilt-Series #38.
CCMS(rotations) = 0.14537 for Iteration #13 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00579 for iteration 13 of Tilt-Series #38.
Alignment quality for Iteration #13 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #14 of Tilt-Series #38.
CCMS(rotations) = 0.14721 for Iteration #14 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00594 for iteration 14 of Tilt-Series #38.
Alignment quality for Iteration #14 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00572 for Iteration #15 of Tilt-Series #38.
CCMS(rotations) = 0.14593 for Iteration #15 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00578 for iteration 15 of Tilt-Series #38.
Alignment quality for Iteration #15 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #38 (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 #38 (tiltseries0038_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 = 63.1843382277
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 = 63.1843382277
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00595 for Iteration #16 of Tilt-Series #38.
CCMS(rotations) = 0.13675 for Iteration #16 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00571 for iteration 16 of Tilt-Series #38.
Alignment quality for Iteration #16 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #38 (17aug18i): Rock Solid!Creating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #17 of Tilt-Series #38.
CCMS(rotations) = 0.1594 for Iteration #17 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #38.
The scaled sum of CCMS values is #0.006 for iteration 17 of Tilt-Series #38.
Alignment quality for Iteration #17 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00573 for Iteration #18 of Tilt-Series #38.
CCMS(rotations) = 0.15028 for Iteration #18 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00587 for iteration 18 of Tilt-Series #38.
Alignment quality for Iteration #18 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #19 of Tilt-Series #38.
CCMS(rotations) = 0.15323 for Iteration #19 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00599 for iteration 19 of Tilt-Series #38.
Alignment quality for Iteration #19 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00549 for Iteration #20 of Tilt-Series #38.
CCMS(rotations) = 0.15287 for Iteration #20 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #38.
The scaled sum of CCMS values is #0.0058 for iteration 20 of Tilt-Series #38.
Alignment quality for Iteration #20 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #38 (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 #38 (tiltseries0038_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 = 126.368676455
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 = 126.368676455
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00783 for Iteration #21 of Tilt-Series #38.
CCMS(rotations) = 0.18028 for Iteration #21 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00752 for iteration 21 of Tilt-Series #38.
Alignment quality for Iteration #21 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00813 for Iteration #22 of Tilt-Series #38.
CCMS(rotations) = 0.24214 for Iteration #22 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00891 for iteration 22 of Tilt-Series #38.
Alignment quality for Iteration #22 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00821 for Iteration #23 of Tilt-Series #38.
CCMS(rotations) = 0.20996 for Iteration #23 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #38.
The scaled sum of CCMS values is #0.0083 for iteration 23 of Tilt-Series #38.
Alignment quality for Iteration #23 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00852 for Iteration #24 of Tilt-Series #38.
CCMS(rotations) = 0.32346 for Iteration #24 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #38.
The scaled sum of CCMS values is #0.01073 for iteration 24 of Tilt-Series #38.
Alignment quality for Iteration #24 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0089 for Iteration #25 of Tilt-Series #38.
CCMS(rotations) = 0.22926 for Iteration #25 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00903 for iteration 25 of Tilt-Series #38.
Alignment quality for Iteration #25 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.008 for Iteration #26 of Tilt-Series #38.
CCMS(rotations) = 0.26849 for Iteration #26 of Tilt-Series #38.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00937 for iteration 26 of Tilt-Series #38.
Alignment quality for Iteration #26 of Tilt-Series #38 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00766 for Iteration #27 of Tilt-Series #38.
CCMS(rotations) = 0.23923 for Iteration #27 of Tilt-Series #38.
CCMS(scale) = 0.00361 for Iteration #27 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00694 for iteration 27 of Tilt-Series #38.
Alignment quality for Iteration #27 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #38 (17aug18i): UnstableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00605 for Iteration #28 of Tilt-Series #38.
CCMS(rotations) = 0.19685 for Iteration #28 of Tilt-Series #38.
CCMS(scale) = 0.00405 for Iteration #28 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00599 for iteration 28 of Tilt-Series #38.
Alignment quality for Iteration #28 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #38 (17aug18i): Very StableCreating 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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00541 for Iteration #29 of Tilt-Series #38.
CCMS(rotations) = 0.24577 for Iteration #29 of Tilt-Series #38.
CCMS(scale) = 0.00325 for Iteration #29 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00616 for iteration 29 of Tilt-Series #38.
Alignment quality for Iteration #29 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #38 (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 #38 (tiltseries0038_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #38 (tiltseries0038_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0053 for Iteration #30 of Tilt-Series #38.
CCMS(rotations) = 0.22643 for Iteration #30 of Tilt-Series #38.
CCMS(scale) = 0.00359 for Iteration #30 of Tilt-Series #38.
The scaled sum of CCMS values is #0.00598 for iteration 30 of Tilt-Series #38.
Alignment quality for Iteration #30 of Tilt-Series #38 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #38 (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 #38 (tiltseries0038_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: 2017yr09m06d-04hr23m47s