protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-35.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0015_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=tiltseries0015_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=15 --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

node10
Start time: 2017yr09m04d-15hr09m34s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0015.tlt to series0015.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #15 (tiltseries0015_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) = 0.07281 for Iteration #1 of Tilt-Series #15.
CCMS(rotations) = 0.78548 for Iteration #1 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #15.
The scaled sum of CCMS values is #0.05211 for iteration 1 of Tilt-Series #15.
Alignment quality for Iteration #1 of Tilt-Series #15 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.964286%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00622 for Iteration #2 of Tilt-Series #15.
CCMS(rotations) = 0.09434 for Iteration #2 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #15.
The scaled sum of CCMS values is #0.005 for iteration 2 of Tilt-Series #15.
Alignment quality for Iteration #2 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00565 for Iteration #3 of Tilt-Series #15.
CCMS(rotations) = 0.13002 for Iteration #3 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00543 for iteration 3 of Tilt-Series #15.
Alignment quality for Iteration #3 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00508 for Iteration #4 of Tilt-Series #15.
CCMS(rotations) = 0.1277 for Iteration #4 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00509 for iteration 4 of Tilt-Series #15.
Alignment quality for Iteration #4 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #15 (17aug18i): Rock Solid!Creating 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00433 for Iteration #5 of Tilt-Series #15.
CCMS(rotations) = 0.13935 for Iteration #5 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00495 for iteration 5 of Tilt-Series #15.
Alignment quality for Iteration #5 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #15 (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 #15 (tiltseries0015_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) = 0.00489 for Iteration #6 of Tilt-Series #15.
CCMS(rotations) = 0.12637 for Iteration #6 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00497 for iteration 6 of Tilt-Series #15.
Alignment quality for Iteration #6 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #15 (17aug18i): StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00436 for Iteration #7 of Tilt-Series #15.
CCMS(rotations) = 0.13197 for Iteration #7 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00482 for iteration 7 of Tilt-Series #15.
Alignment quality for Iteration #7 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #15 (17aug18i): StableCreating 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00455 for Iteration #8 of Tilt-Series #15.
CCMS(rotations) = 0.13465 for Iteration #8 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00497 for iteration 8 of Tilt-Series #15.
Alignment quality for Iteration #8 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #9 of Tilt-Series #15.
CCMS(rotations) = 0.13349 for Iteration #9 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00489 for iteration 9 of Tilt-Series #15.
Alignment quality for Iteration #9 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0042 for Iteration #10 of Tilt-Series #15.
CCMS(rotations) = 0.13223 for Iteration #10 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00475 for iteration 10 of Tilt-Series #15.
Alignment quality for Iteration #10 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00424 for Iteration #11 of Tilt-Series #15.
CCMS(rotations) = 0.1268 for Iteration #11 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00466 for iteration 11 of Tilt-Series #15.
Alignment quality for Iteration #11 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00439 for Iteration #12 of Tilt-Series #15.
CCMS(rotations) = 0.13724 for Iteration #12 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00494 for iteration 12 of Tilt-Series #15.
Alignment quality for Iteration #12 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #15 (17aug18i): Very StableCreating 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #13 of Tilt-Series #15.
CCMS(rotations) = 0.14734 for Iteration #13 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00517 for iteration 13 of Tilt-Series #15.
Alignment quality for Iteration #13 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #14 of Tilt-Series #15.
CCMS(rotations) = 0.13313 for Iteration #14 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00497 for iteration 14 of Tilt-Series #15.
Alignment quality for Iteration #14 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #15 of Tilt-Series #15.
CCMS(rotations) = 0.13643 for Iteration #15 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00499 for iteration 15 of Tilt-Series #15.
Alignment quality for Iteration #15 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #15 (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 #15 (tiltseries0015_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) = 0.00711 for Iteration #16 of Tilt-Series #15.
CCMS(rotations) = 0.1351 for Iteration #16 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00626 for iteration 16 of Tilt-Series #15.
Alignment quality for Iteration #16 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #17 of Tilt-Series #15.
CCMS(rotations) = 0.13092 for Iteration #17 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00595 for iteration 17 of Tilt-Series #15.
Alignment quality for Iteration #17 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00663 for Iteration #18 of Tilt-Series #15.
CCMS(rotations) = 0.12788 for Iteration #18 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00587 for iteration 18 of Tilt-Series #15.
Alignment quality for Iteration #18 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00671 for Iteration #19 of Tilt-Series #15.
CCMS(rotations) = 0.13832 for Iteration #19 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00612 for iteration 19 of Tilt-Series #15.
Alignment quality for Iteration #19 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #15 (17aug18i): Very StableCreating 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00678 for Iteration #20 of Tilt-Series #15.
CCMS(rotations) = 0.12451 for Iteration #20 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00588 for iteration 20 of Tilt-Series #15.
Alignment quality for Iteration #20 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #15 (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 #15 (tiltseries0015_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) = 0.00846 for Iteration #21 of Tilt-Series #15.
CCMS(rotations) = 0.1231 for Iteration #21 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00669 for iteration 21 of Tilt-Series #15.
Alignment quality for Iteration #21 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00851 for Iteration #22 of Tilt-Series #15.
CCMS(rotations) = 0.10087 for Iteration #22 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00627 for iteration 22 of Tilt-Series #15.
Alignment quality for Iteration #22 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00802 for Iteration #23 of Tilt-Series #15.
CCMS(rotations) = 0.11038 for Iteration #23 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00622 for iteration 23 of Tilt-Series #15.
Alignment quality for Iteration #23 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00867 for Iteration #24 of Tilt-Series #15.
CCMS(rotations) = 0.09389 for Iteration #24 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00621 for iteration 24 of Tilt-Series #15.
Alignment quality for Iteration #24 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #15 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00855 for Iteration #25 of Tilt-Series #15.
CCMS(rotations) = 0.09698 for Iteration #25 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00622 for iteration 25 of Tilt-Series #15.
Alignment quality for Iteration #25 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #15 (17aug18i): Rock Solid!Creating 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00874 for Iteration #26 of Tilt-Series #15.
CCMS(rotations) = 0.104 for Iteration #26 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00645 for iteration 26 of Tilt-Series #15.
Alignment quality for Iteration #26 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00831 for Iteration #27 of Tilt-Series #15.
CCMS(rotations) = 0.10163 for Iteration #27 of Tilt-Series #15.
CCMS(scale) = 0.00256 for Iteration #27 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00498 for iteration 27 of Tilt-Series #15.
Alignment quality for Iteration #27 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00814 for Iteration #28 of Tilt-Series #15.
CCMS(rotations) = 0.09928 for Iteration #28 of Tilt-Series #15.
CCMS(scale) = 0.00242 for Iteration #28 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00484 for iteration 28 of Tilt-Series #15.
Alignment quality for Iteration #28 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00839 for Iteration #29 of Tilt-Series #15.
CCMS(rotations) = 0.10829 for Iteration #29 of Tilt-Series #15.
CCMS(scale) = 0.00232 for Iteration #29 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00501 for iteration 29 of Tilt-Series #15.
Alignment quality for Iteration #29 of Tilt-Series #15 (17aug18i): Excellent (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00793 for Iteration #30 of Tilt-Series #15.
CCMS(rotations) = 0.10484 for Iteration #30 of Tilt-Series #15.
CCMS(scale) = 0.00225 for Iteration #30 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00479 for iteration 30 of Tilt-Series #15.
Alignment quality for Iteration #30 of Tilt-Series #15 (17aug18i): Perfection! (confidence: 0.964286%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m05d-17hr35m27s