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/tiltseries0037_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=24 --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0037_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=37 --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=0.1 --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

node26
Start time: 2017yr09m04d-16hr19m37s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0037.tlt to series0037.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #37 (tiltseries0037_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 = 15.7971872162
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 = 15.7971872162
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.02452 for Iteration #1 of Tilt-Series #37.
CCMS(rotations) = 0.28598 for Iteration #1 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #37.
The scaled sum of CCMS values is #0.01798 for iteration 1 of Tilt-Series #37.
Alignment quality for Iteration #1 of Tilt-Series #37 (17aug18i): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00828 for Iteration #2 of Tilt-Series #37.
CCMS(rotations) = 0.11185 for Iteration #2 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00638 for iteration 2 of Tilt-Series #37.
Alignment quality for Iteration #2 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00878 for Iteration #3 of Tilt-Series #37.
CCMS(rotations) = 0.12778 for Iteration #3 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00695 for iteration 3 of Tilt-Series #37.
Alignment quality for Iteration #3 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00899 for Iteration #4 of Tilt-Series #37.
CCMS(rotations) = 0.11875 for Iteration #4 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00687 for iteration 4 of Tilt-Series #37.
Alignment quality for Iteration #4 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00861 for Iteration #5 of Tilt-Series #37.
CCMS(rotations) = 0.13752 for Iteration #5 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00705 for iteration 5 of Tilt-Series #37.
Alignment quality for Iteration #5 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #37 (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 #37 (tiltseries0037_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 = 31.5943744323
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 = 31.5943744323
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00803 for Iteration #6 of Tilt-Series #37.
CCMS(rotations) = 0.13079 for Iteration #6 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00663 for iteration 6 of Tilt-Series #37.
Alignment quality for Iteration #6 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00704 for Iteration #7 of Tilt-Series #37.
CCMS(rotations) = 0.10339 for Iteration #7 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00559 for iteration 7 of Tilt-Series #37.
Alignment quality for Iteration #7 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #8 of Tilt-Series #37.
CCMS(rotations) = 0.13835 for Iteration #8 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00642 for iteration 8 of Tilt-Series #37.
Alignment quality for Iteration #8 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0068 for Iteration #9 of Tilt-Series #37.
CCMS(rotations) = 0.13953 for Iteration #9 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00619 for iteration 9 of Tilt-Series #37.
Alignment quality for Iteration #9 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00703 for Iteration #10 of Tilt-Series #37.
CCMS(rotations) = 0.13313 for Iteration #10 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00618 for iteration 10 of Tilt-Series #37.
Alignment quality for Iteration #10 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #37 (17aug18i): StableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00713 for Iteration #11 of Tilt-Series #37.
CCMS(rotations) = 0.12275 for Iteration #11 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00602 for iteration 11 of Tilt-Series #37.
Alignment quality for Iteration #11 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #37 (17aug18i): Very StableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00692 for Iteration #12 of Tilt-Series #37.
CCMS(rotations) = 0.13771 for Iteration #12 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00621 for iteration 12 of Tilt-Series #37.
Alignment quality for Iteration #12 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00694 for Iteration #13 of Tilt-Series #37.
CCMS(rotations) = 0.12646 for Iteration #13 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #37.
The scaled sum of CCMS values is #0.006 for iteration 13 of Tilt-Series #37.
Alignment quality for Iteration #13 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #37 (17aug18i): Very StableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00715 for Iteration #14 of Tilt-Series #37.
CCMS(rotations) = 0.12991 for Iteration #14 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00618 for iteration 14 of Tilt-Series #37.
Alignment quality for Iteration #14 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #37 (17aug18i): Very StableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00695 for Iteration #15 of Tilt-Series #37.
CCMS(rotations) = 0.14963 for Iteration #15 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00647 for iteration 15 of Tilt-Series #37.
Alignment quality for Iteration #15 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_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 = 63.1887488647
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 = 63.1887488647
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #16 of Tilt-Series #37.
CCMS(rotations) = 0.14339 for Iteration #16 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00627 for iteration 16 of Tilt-Series #37.
Alignment quality for Iteration #16 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00659 for Iteration #17 of Tilt-Series #37.
CCMS(rotations) = 0.11127 for Iteration #17 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00552 for iteration 17 of Tilt-Series #37.
Alignment quality for Iteration #17 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #18 of Tilt-Series #37.
CCMS(rotations) = 0.10437 for Iteration #18 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00552 for iteration 18 of Tilt-Series #37.
Alignment quality for Iteration #18 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #37 (17aug18i): StableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00675 for Iteration #19 of Tilt-Series #37.
CCMS(rotations) = 0.11894 for Iteration #19 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00576 for iteration 19 of Tilt-Series #37.
Alignment quality for Iteration #19 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00668 for Iteration #20 of Tilt-Series #37.
CCMS(rotations) = 0.09626 for Iteration #20 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00526 for iteration 20 of Tilt-Series #37.
Alignment quality for Iteration #20 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_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 = 126.377497729
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 = 126.377497729
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00859 for Iteration #21 of Tilt-Series #37.
CCMS(rotations) = 0.18777 for Iteration #21 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00805 for iteration 21 of Tilt-Series #37.
Alignment quality for Iteration #21 of Tilt-Series #37 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00787 for Iteration #22 of Tilt-Series #37.
CCMS(rotations) = 0.15062 for Iteration #22 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00695 for iteration 22 of Tilt-Series #37.
Alignment quality for Iteration #22 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #23 of Tilt-Series #37.
CCMS(rotations) = 0.17939 for Iteration #23 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00772 for iteration 23 of Tilt-Series #37.
Alignment quality for Iteration #23 of Tilt-Series #37 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00781 for Iteration #24 of Tilt-Series #37.
CCMS(rotations) = 0.16148 for Iteration #24 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00713 for iteration 24 of Tilt-Series #37.
Alignment quality for Iteration #24 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00856 for Iteration #25 of Tilt-Series #37.
CCMS(rotations) = 0.15511 for Iteration #25 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00738 for iteration 25 of Tilt-Series #37.
Alignment quality for Iteration #25 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00784 for Iteration #26 of Tilt-Series #37.
CCMS(rotations) = 0.15028 for Iteration #26 of Tilt-Series #37.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00693 for iteration 26 of Tilt-Series #37.
Alignment quality for Iteration #26 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0066 for Iteration #27 of Tilt-Series #37.
CCMS(rotations) = 0.17481 for Iteration #27 of Tilt-Series #37.
CCMS(scale) = 0.00292 for Iteration #27 of Tilt-Series #37.
The scaled sum of CCMS values is #0.0055 for iteration 27 of Tilt-Series #37.
Alignment quality for Iteration #27 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #37 (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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0063 for Iteration #28 of Tilt-Series #37.
CCMS(rotations) = 0.16477 for Iteration #28 of Tilt-Series #37.
CCMS(scale) = 0.00355 for Iteration #28 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00548 for iteration 28 of Tilt-Series #37.
Alignment quality for Iteration #28 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00647 for Iteration #29 of Tilt-Series #37.
CCMS(rotations) = 0.1611 for Iteration #29 of Tilt-Series #37.
CCMS(scale) = 0.00322 for Iteration #29 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00538 for iteration 29 of Tilt-Series #37.
Alignment quality for Iteration #29 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #37 (tiltseries0037_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00631 for Iteration #30 of Tilt-Series #37.
CCMS(rotations) = 0.15967 for Iteration #30 of Tilt-Series #37.
CCMS(scale) = 0.00365 for Iteration #30 of Tilt-Series #37.
The scaled sum of CCMS values is #0.00545 for iteration 30 of Tilt-Series #37.
Alignment quality for Iteration #30 of Tilt-Series #37 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #37 (17aug18i): UnstableCreating 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 #37 (tiltseries0037_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-01hr17m30s