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/17may19d/protomo_alignments/tiltseries0004_thick200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3406.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1919 --r1_region_y=1855 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3406.0 --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=1855 --r2_region_x=1919 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1703.0 --defocus_ang_positive=90 --r5_mask_width_x=1894 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3406.0 --r3_highpass_apod_x=1703.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=454 --r2_mask_width_y=438 --r5_region_x=1919 --r5_region_y=1855 --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=3406.0 --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=1830 --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=1703.0 --runname=tiltseries0004_thick200 --r1_highpass_diameter_x=3406.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --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=1894 --r4_mask_width_y=1830 --logging=true --DefocusTol=200 --filter=median --sessionname=17may19d --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=1703.0 --r1_highpass_apod_x=1703.0 --r2_highpass_apod_x=1703.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --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=31 --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=4 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=902 --r3_mask_width_x=934 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3406.0 --r4_highpass_diameter_x=3406.0 --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=3406.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=1703.0 --r5_highpass_apod_x=1703.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3406.0 --defocus_max=0 --r4_region_y=1855 --r4_region_x=1919 --r5_kernel_y=5 --r3_region_x=1919 --r3_region_y=1855 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=200 --expid=4069 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=44.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=3406.0 --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=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=3838 --dimy=3710 --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=1703.0 --r4_highpass_apod_y=1703.0 --azimuth=true --r1_mask_width_y=206 --r1_mask_width_x=214 --jobtype=protomo

node37
Start time: 2017yr06m21d-12hr22m23s
Description: 
coarse_series0004_iter2.tlt not found, using coarse_series0004.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0004.tlt to series0004.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.23499008 0.23499008 }
map.sampling = 8
window.highpass.diameter = { 0.0086241221374 0.0086241221374 }
window.highpass.apodization = { 0.0172482442748 0.0172482442748 }
window.mask.apodization = { 10 10 }
align.mask.width = { 214 206 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 19.2561727138
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 239 231 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 214 206 }
reference.body = 19.2561727138
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07536 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 0.77507 for Iteration #1 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4.
The scaled sum of CCMS values is #0.05318 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (17may19d): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.967742%)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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04437 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.61945 for Iteration #2 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4.
The scaled sum of CCMS values is #0.03458 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17may19d): Bad (confidence: 0.967742%)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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00545 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.20482 for Iteration #3 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00682 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00493 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.20579 for Iteration #4 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00658 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00486 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.14342 for Iteration #5 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0053 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (17may19d): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00451 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.23541 for Iteration #6 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00696 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00477 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.18509 for Iteration #7 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00609 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.21114 for Iteration #8 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00666 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.18548 for Iteration #9 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00593 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00515 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.18403 for Iteration #10 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00626 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (17may19d): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.233125079365 0.233125079365 }
map.sampling = 4
window.highpass.diameter = { 0.0043120610687 0.0043120610687 }
window.highpass.apodization = { 0.0086241221374 0.0086241221374 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 38.5123454276
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 38.5123454276
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00359 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.17655 for Iteration #11 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00533 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (17may19d): UnstableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00399 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.12343 for Iteration #12 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00446 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (17may19d): UnstableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00407 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.17676 for Iteration #13 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00557 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (17may19d): UnstableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00435 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.12458 for Iteration #14 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00466 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (17may19d): UnstableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00427 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.16688 for Iteration #15 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00547 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (17may19d): Very StableCreating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00431 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.13905 for Iteration #16 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00494 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00421 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.17618 for Iteration #17 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00563 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (17may19d): UnstableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.1477 for Iteration #18 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0048 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00352 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.15024 for Iteration #19 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00477 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.15665 for Iteration #20 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00505 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.23688516129 0.23688516129 }
map.sampling = 2
window.highpass.diameter = { 0.00215603053435 0.00215603053435 }
window.highpass.apodization = { 0.0043120610687 0.0043120610687 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 77.0246908552
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 77.0246908552
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00322 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.11518 for Iteration #21 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00391 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (17may19d): Very StableCreating 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00307 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.11716 for Iteration #22 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00388 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (17may19d): StableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.10863 for Iteration #23 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00392 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.0036 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.1361 for Iteration #24 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00452 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00343 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.10726 for Iteration #25 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00386 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.2294825 0.2294825 }
map.sampling = 1
window.highpass.diameter = { 0.00107801526718 0.00107801526718 }
window.highpass.apodization = { 0.00215603053435 0.00215603053435 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 154.04938171
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 154.04938171
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.2867 for Iteration #26 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00849 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17may19d): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00432 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.17992 for Iteration #27 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00576 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00505 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.19232 for Iteration #28 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00637 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00423 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.20746 for Iteration #29 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00626 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (17may19d): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00452 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.19688 for Iteration #30 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0062 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #31 of Tilt-Series #4.
CCMS(rotations) = 0.20779 for Iteration #31 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00607 for iteration 31 of Tilt-Series #4.
Alignment quality for Iteration #31 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (17may19d): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00454 for Iteration #32 of Tilt-Series #4.
CCMS(rotations) = 0.21559 for Iteration #32 of Tilt-Series #4.
CCMS(scale) = 0.00135 for Iteration #32 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00484 for iteration 32 of Tilt-Series #4.
Alignment quality for Iteration #32 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (17may19d): StableCreating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00462 for Iteration #33 of Tilt-Series #4.
CCMS(rotations) = 0.2312 for Iteration #33 of Tilt-Series #4.
CCMS(scale) = 0.00133 for Iteration #33 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00507 for iteration 33 of Tilt-Series #4.
Alignment quality for Iteration #33 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (17may19d): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00535 for Iteration #34 of Tilt-Series #4.
CCMS(rotations) = 0.22892 for Iteration #34 of Tilt-Series #4.
CCMS(scale) = 0.00128 for Iteration #34 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00526 for iteration 34 of Tilt-Series #4.
Alignment quality for Iteration #34 of Tilt-Series #4 (17may19d): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (17may19d): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00355 for Iteration #35 of Tilt-Series #4.
CCMS(rotations) = 0.21864 for Iteration #35 of Tilt-Series #4.
CCMS(scale) = 0.00153 for Iteration #35 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00461 for iteration 35 of Tilt-Series #4.
Alignment quality for Iteration #35 of Tilt-Series #4 (17may19d): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (17may19d): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #4 (tiltseries0004_thick200)!
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: 2017yr06m21d-21hr23m32s