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/tiltseries0029_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=tiltseries0029_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=29 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=100 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node20
Start time: 2017yr09m04d-15hr55m11s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0029.tlt to series0029.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #29 (tiltseries0029_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) = 0.0594 for Iteration #1 of Tilt-Series #29.
CCMS(rotations) = 1.67553 for Iteration #1 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #29.
The scaled sum of CCMS values is #0.06321 for iteration 1 of Tilt-Series #29.
Alignment quality for Iteration #1 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03682 for Iteration #2 of Tilt-Series #29.
CCMS(rotations) = 1.3595 for Iteration #2 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #29.
The scaled sum of CCMS values is #0.0456 for iteration 2 of Tilt-Series #29.
Alignment quality for Iteration #2 of Tilt-Series #29 (17aug18i): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01476 for Iteration #3 of Tilt-Series #29.
CCMS(rotations) = 0.81356 for Iteration #3 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #29.
The scaled sum of CCMS values is #0.02365 for iteration 3 of Tilt-Series #29.
Alignment quality for Iteration #3 of Tilt-Series #29 (17aug18i): Okay (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01875 for Iteration #4 of Tilt-Series #29.
CCMS(rotations) = 0.33465 for Iteration #4 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #29.
The scaled sum of CCMS values is #0.01607 for iteration 4 of Tilt-Series #29.
Alignment quality for Iteration #4 of Tilt-Series #29 (17aug18i): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01091 for Iteration #5 of Tilt-Series #29.
CCMS(rotations) = 0.17436 for Iteration #5 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00894 for iteration 5 of Tilt-Series #29.
Alignment quality for Iteration #5 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #29 (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 #29 (tiltseries0029_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) = 0.00621 for Iteration #6 of Tilt-Series #29.
CCMS(rotations) = 0.11136 for Iteration #6 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00533 for iteration 6 of Tilt-Series #29.
Alignment quality for Iteration #6 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #29 (17aug18i): Very 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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #7 of Tilt-Series #29.
CCMS(rotations) = 0.17227 for Iteration #7 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #29.
The scaled sum of CCMS values is #0.0065 for iteration 7 of Tilt-Series #29.
Alignment quality for Iteration #7 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #8 of Tilt-Series #29.
CCMS(rotations) = 0.15475 for Iteration #8 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00608 for iteration 8 of Tilt-Series #29.
Alignment quality for Iteration #8 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00636 for Iteration #9 of Tilt-Series #29.
CCMS(rotations) = 0.16418 for Iteration #9 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00646 for iteration 9 of Tilt-Series #29.
Alignment quality for Iteration #9 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00604 for Iteration #10 of Tilt-Series #29.
CCMS(rotations) = 0.18085 for Iteration #10 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00664 for iteration 10 of Tilt-Series #29.
Alignment quality for Iteration #10 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00593 for Iteration #11 of Tilt-Series #29.
CCMS(rotations) = 0.18072 for Iteration #11 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00658 for iteration 11 of Tilt-Series #29.
Alignment quality for Iteration #11 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #12 of Tilt-Series #29.
CCMS(rotations) = 0.16831 for Iteration #12 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00638 for iteration 12 of Tilt-Series #29.
Alignment quality for Iteration #12 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00601 for Iteration #13 of Tilt-Series #29.
CCMS(rotations) = 0.16875 for Iteration #13 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00638 for iteration 13 of Tilt-Series #29.
Alignment quality for Iteration #13 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00605 for Iteration #14 of Tilt-Series #29.
CCMS(rotations) = 0.16013 for Iteration #14 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00623 for iteration 14 of Tilt-Series #29.
Alignment quality for Iteration #14 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00622 for Iteration #15 of Tilt-Series #29.
CCMS(rotations) = 0.16515 for Iteration #15 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00641 for iteration 15 of Tilt-Series #29.
Alignment quality for Iteration #15 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #29 (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 #29 (tiltseries0029_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) = 0.00696 for Iteration #16 of Tilt-Series #29.
CCMS(rotations) = 0.15905 for Iteration #16 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00666 for iteration 16 of Tilt-Series #29.
Alignment quality for Iteration #16 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00683 for Iteration #17 of Tilt-Series #29.
CCMS(rotations) = 0.17271 for Iteration #17 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00687 for iteration 17 of Tilt-Series #29.
Alignment quality for Iteration #17 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00662 for Iteration #18 of Tilt-Series #29.
CCMS(rotations) = 0.17576 for Iteration #18 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00683 for iteration 18 of Tilt-Series #29.
Alignment quality for Iteration #18 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00682 for Iteration #19 of Tilt-Series #29.
CCMS(rotations) = 0.18585 for Iteration #19 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00713 for iteration 19 of Tilt-Series #29.
Alignment quality for Iteration #19 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.0065 for Iteration #20 of Tilt-Series #29.
CCMS(rotations) = 0.17959 for Iteration #20 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00684 for iteration 20 of Tilt-Series #29.
Alignment quality for Iteration #20 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #29 (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 #29 (tiltseries0029_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) = 0.01058 for Iteration #21 of Tilt-Series #29.
CCMS(rotations) = 0.21653 for Iteration #21 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00962 for iteration 21 of Tilt-Series #29.
Alignment quality for Iteration #21 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00877 for Iteration #22 of Tilt-Series #29.
CCMS(rotations) = 0.19848 for Iteration #22 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00836 for iteration 22 of Tilt-Series #29.
Alignment quality for Iteration #22 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00893 for Iteration #23 of Tilt-Series #29.
CCMS(rotations) = 0.21623 for Iteration #23 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00879 for iteration 23 of Tilt-Series #29.
Alignment quality for Iteration #23 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.0103 for Iteration #24 of Tilt-Series #29.
CCMS(rotations) = 0.21033 for Iteration #24 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00936 for iteration 24 of Tilt-Series #29.
Alignment quality for Iteration #24 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00984 for Iteration #25 of Tilt-Series #29.
CCMS(rotations) = 0.24048 for Iteration #25 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00973 for iteration 25 of Tilt-Series #29.
Alignment quality for Iteration #25 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00864 for Iteration #26 of Tilt-Series #29.
CCMS(rotations) = 0.205 for Iteration #26 of Tilt-Series #29.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00842 for iteration 26 of Tilt-Series #29.
Alignment quality for Iteration #26 of Tilt-Series #29 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0086 for Iteration #27 of Tilt-Series #29.
CCMS(rotations) = 0.21769 for Iteration #27 of Tilt-Series #29.
CCMS(scale) = 0.00309 for Iteration #27 of Tilt-Series #29.
The scaled sum of CCMS values is #0.0068 for iteration 27 of Tilt-Series #29.
Alignment quality for Iteration #27 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00764 for Iteration #28 of Tilt-Series #29.
CCMS(rotations) = 0.21134 for Iteration #28 of Tilt-Series #29.
CCMS(scale) = 0.004 for Iteration #28 of Tilt-Series #29.
The scaled sum of CCMS values is #0.0067 for iteration 28 of Tilt-Series #29.
Alignment quality for Iteration #28 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #29 (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 #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00922 for Iteration #29 of Tilt-Series #29.
CCMS(rotations) = 0.21448 for Iteration #29 of Tilt-Series #29.
CCMS(scale) = 0.00342 for Iteration #29 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00707 for iteration 29 of Tilt-Series #29.
Alignment quality for Iteration #29 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #29 (17aug18i): Very StableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #29 (tiltseries0029_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #29 (tiltseries0029_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00811 for Iteration #30 of Tilt-Series #29.
CCMS(rotations) = 0.1925 for Iteration #30 of Tilt-Series #29.
CCMS(scale) = 0.00417 for Iteration #30 of Tilt-Series #29.
The scaled sum of CCMS values is #0.00666 for iteration 30 of Tilt-Series #29.
Alignment quality for Iteration #30 of Tilt-Series #29 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #29 (17aug18i): StableCreating 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 #29 (tiltseries0029_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: 2017yr09m06d-02hr23m07s