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/tiltseries0033_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=tiltseries0033_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=33 --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

node24
Start time: 2017yr09m04d-16hr05m09s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0033.tlt to series0033.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #33 (tiltseries0033_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) = 0.1302 for Iteration #1 of Tilt-Series #33.
CCMS(rotations) = 2.49689 for Iteration #1 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #33.
The scaled sum of CCMS values is #0.11504 for iteration 1 of Tilt-Series #33.
Alignment quality for Iteration #1 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.07696 for Iteration #2 of Tilt-Series #33.
CCMS(rotations) = 1.33849 for Iteration #2 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #33.
The scaled sum of CCMS values is #0.06525 for iteration 2 of Tilt-Series #33.
Alignment quality for Iteration #2 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.04699 for Iteration #3 of Tilt-Series #33.
CCMS(rotations) = 0.77736 for Iteration #3 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #33.
The scaled sum of CCMS values is #0.03904 for iteration 3 of Tilt-Series #33.
Alignment quality for Iteration #3 of Tilt-Series #33 (17aug18i): Bad (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02533 for Iteration #4 of Tilt-Series #33.
CCMS(rotations) = 0.31134 for Iteration #4 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #33.
The scaled sum of CCMS values is #0.01889 for iteration 4 of Tilt-Series #33.
Alignment quality for Iteration #4 of Tilt-Series #33 (17aug18i): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00392 for Iteration #5 of Tilt-Series #33.
CCMS(rotations) = 0.11907 for Iteration #5 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00434 for iteration 5 of Tilt-Series #33.
Alignment quality for Iteration #5 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #33 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

Beginning Refinement Iteration #6, Round #2 of Tilt-Series #33 (tiltseries0033_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) = 0.00478 for Iteration #6 of Tilt-Series #33.
CCMS(rotations) = 0.11717 for Iteration #6 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00473 for iteration 6 of Tilt-Series #33.
Alignment quality for Iteration #6 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #33 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00465 for Iteration #7 of Tilt-Series #33.
CCMS(rotations) = 0.13342 for Iteration #7 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00499 for iteration 7 of Tilt-Series #33.
Alignment quality for Iteration #7 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #8 of Tilt-Series #33.
CCMS(rotations) = 0.13373 for Iteration #8 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #33.
The scaled sum of CCMS values is #0.0049 for iteration 8 of Tilt-Series #33.
Alignment quality for Iteration #8 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00465 for Iteration #9 of Tilt-Series #33.
CCMS(rotations) = 0.14381 for Iteration #9 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #33.
The scaled sum of CCMS values is #0.0052 for iteration 9 of Tilt-Series #33.
Alignment quality for Iteration #9 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00448 for Iteration #10 of Tilt-Series #33.
CCMS(rotations) = 0.13476 for Iteration #10 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00493 for iteration 10 of Tilt-Series #33.
Alignment quality for Iteration #10 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00448 for Iteration #11 of Tilt-Series #33.
CCMS(rotations) = 0.1308 for Iteration #11 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00486 for iteration 11 of Tilt-Series #33.
Alignment quality for Iteration #11 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #12 of Tilt-Series #33.
CCMS(rotations) = 0.1424 for Iteration #12 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00518 for iteration 12 of Tilt-Series #33.
Alignment quality for Iteration #12 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00451 for Iteration #13 of Tilt-Series #33.
CCMS(rotations) = 0.13649 for Iteration #13 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00498 for iteration 13 of Tilt-Series #33.
Alignment quality for Iteration #13 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #14 of Tilt-Series #33.
CCMS(rotations) = 0.13636 for Iteration #14 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00503 for iteration 14 of Tilt-Series #33.
Alignment quality for Iteration #14 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00448 for Iteration #15 of Tilt-Series #33.
CCMS(rotations) = 0.13357 for Iteration #15 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00491 for iteration 15 of Tilt-Series #33.
Alignment quality for Iteration #15 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #33 (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 #33 (tiltseries0033_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) = 0.00678 for Iteration #16 of Tilt-Series #33.
CCMS(rotations) = 0.14623 for Iteration #16 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00632 for iteration 16 of Tilt-Series #33.
Alignment quality for Iteration #16 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00668 for Iteration #17 of Tilt-Series #33.
CCMS(rotations) = 0.13066 for Iteration #17 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00596 for iteration 17 of Tilt-Series #33.
Alignment quality for Iteration #17 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0066 for Iteration #18 of Tilt-Series #33.
CCMS(rotations) = 0.13138 for Iteration #18 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00593 for iteration 18 of Tilt-Series #33.
Alignment quality for Iteration #18 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00664 for Iteration #19 of Tilt-Series #33.
CCMS(rotations) = 0.13046 for Iteration #19 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00593 for iteration 19 of Tilt-Series #33.
Alignment quality for Iteration #19 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00687 for Iteration #20 of Tilt-Series #33.
CCMS(rotations) = 0.11455 for Iteration #20 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00573 for iteration 20 of Tilt-Series #33.
Alignment quality for Iteration #20 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #33 (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 #33 (tiltseries0033_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) = 0.00855 for Iteration #21 of Tilt-Series #33.
CCMS(rotations) = 0.13067 for Iteration #21 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00689 for iteration 21 of Tilt-Series #33.
Alignment quality for Iteration #21 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #33 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00823 for Iteration #22 of Tilt-Series #33.
CCMS(rotations) = 0.09797 for Iteration #22 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00607 for iteration 22 of Tilt-Series #33.
Alignment quality for Iteration #22 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #33 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00798 for Iteration #23 of Tilt-Series #33.
CCMS(rotations) = 0.12541 for Iteration #23 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #33.
The scaled sum of CCMS values is #0.0065 for iteration 23 of Tilt-Series #33.
Alignment quality for Iteration #23 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #33 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00733 for Iteration #24 of Tilt-Series #33.
CCMS(rotations) = 0.13946 for Iteration #24 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00645 for iteration 24 of Tilt-Series #33.
Alignment quality for Iteration #24 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #33 (17aug18i): Very StableCreating 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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00846 for Iteration #25 of Tilt-Series #33.
CCMS(rotations) = 0.10652 for Iteration #25 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00636 for iteration 25 of Tilt-Series #33.
Alignment quality for Iteration #25 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #33 (17aug18i): Very StableCreating 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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00656 for Iteration #26 of Tilt-Series #33.
CCMS(rotations) = 0.13477 for Iteration #26 of Tilt-Series #33.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00598 for iteration 26 of Tilt-Series #33.
Alignment quality for Iteration #26 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #33 (17aug18i): Very StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00784 for Iteration #27 of Tilt-Series #33.
CCMS(rotations) = 0.1124 for Iteration #27 of Tilt-Series #33.
CCMS(scale) = 0.0026 for Iteration #27 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00498 for iteration 27 of Tilt-Series #33.
Alignment quality for Iteration #27 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00818 for Iteration #28 of Tilt-Series #33.
CCMS(rotations) = 0.12083 for Iteration #28 of Tilt-Series #33.
CCMS(scale) = 0.0028 for Iteration #28 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00527 for iteration 28 of Tilt-Series #33.
Alignment quality for Iteration #28 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00705 for Iteration #29 of Tilt-Series #33.
CCMS(rotations) = 0.14126 for Iteration #29 of Tilt-Series #33.
CCMS(scale) = 0.00329 for Iteration #29 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00533 for iteration 29 of Tilt-Series #33.
Alignment quality for Iteration #29 of Tilt-Series #33 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #33 (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 #33 (tiltseries0033_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #33 (tiltseries0033_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00682 for Iteration #30 of Tilt-Series #33.
CCMS(rotations) = 0.10709 for Iteration #30 of Tilt-Series #33.
CCMS(scale) = 0.00273 for Iteration #30 of Tilt-Series #33.
The scaled sum of CCMS values is #0.00461 for iteration 30 of Tilt-Series #33.
Alignment quality for Iteration #30 of Tilt-Series #33 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #33 (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 #33 (tiltseries0033_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: 2017yr09m05d-17hr34m28s