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/17may19b/protomo_alignments/tiltseries0002_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=tiltseries0002_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=17may19b --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=2 --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=4066 --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=90.0 --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-12hr25m30s
Description: 
coarse_series0002_iter2.tlt not found, using coarse_series0002.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0002.tlt to series0002.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_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 = 19.2565087358
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 = 19.2565087358
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.08246 for Iteration #1 of Tilt-Series #2.
CCMS(rotations) = 1.48733 for Iteration #1 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2.
The scaled sum of CCMS values is #0.07098 for iteration 1 of Tilt-Series #2.
Alignment quality for Iteration #1 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03218 for Iteration #2 of Tilt-Series #2.
CCMS(rotations) = 0.90728 for Iteration #2 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2.
The scaled sum of CCMS values is #0.03424 for iteration 2 of Tilt-Series #2.
Alignment quality for Iteration #2 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00675 for Iteration #3 of Tilt-Series #2.
CCMS(rotations) = 0.16461 for Iteration #3 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00667 for iteration 3 of Tilt-Series #2.
Alignment quality for Iteration #3 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00645 for Iteration #4 of Tilt-Series #2.
CCMS(rotations) = 0.25311 for Iteration #4 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00829 for iteration 4 of Tilt-Series #2.
Alignment quality for Iteration #4 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00655 for Iteration #5 of Tilt-Series #2.
CCMS(rotations) = 0.12218 for Iteration #5 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00572 for iteration 5 of Tilt-Series #2.
Alignment quality for Iteration #5 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (17may19b): UnstableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #6 of Tilt-Series #2.
CCMS(rotations) = 0.27913 for Iteration #6 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00899 for iteration 6 of Tilt-Series #2.
Alignment quality for Iteration #6 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (17may19b): UnstableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00557 for Iteration #7 of Tilt-Series #2.
CCMS(rotations) = 0.16666 for Iteration #7 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00612 for iteration 7 of Tilt-Series #2.
Alignment quality for Iteration #7 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00645 for Iteration #8 of Tilt-Series #2.
CCMS(rotations) = 0.20767 for Iteration #8 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00738 for iteration 8 of Tilt-Series #2.
Alignment quality for Iteration #8 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00549 for Iteration #9 of Tilt-Series #2.
CCMS(rotations) = 0.18618 for Iteration #9 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00647 for iteration 9 of Tilt-Series #2.
Alignment quality for Iteration #9 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00643 for Iteration #10 of Tilt-Series #2.
CCMS(rotations) = 0.22067 for Iteration #10 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00763 for iteration 10 of Tilt-Series #2.
Alignment quality for Iteration #10 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_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 = 38.5130174717
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 = 38.5130174717
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00413 for Iteration #11 of Tilt-Series #2.
CCMS(rotations) = 0.20234 for Iteration #11 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00611 for iteration 11 of Tilt-Series #2.
Alignment quality for Iteration #11 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0039 for Iteration #12 of Tilt-Series #2.
CCMS(rotations) = 0.22783 for Iteration #12 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00651 for iteration 12 of Tilt-Series #2.
Alignment quality for Iteration #12 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #13 of Tilt-Series #2.
CCMS(rotations) = 0.23804 for Iteration #13 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00657 for iteration 13 of Tilt-Series #2.
Alignment quality for Iteration #13 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #14 of Tilt-Series #2.
CCMS(rotations) = 0.24439 for Iteration #14 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00694 for iteration 14 of Tilt-Series #2.
Alignment quality for Iteration #14 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #15 of Tilt-Series #2.
CCMS(rotations) = 0.25447 for Iteration #15 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00689 for iteration 15 of Tilt-Series #2.
Alignment quality for Iteration #15 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00406 for Iteration #16 of Tilt-Series #2.
CCMS(rotations) = 0.23095 for Iteration #16 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00665 for iteration 16 of Tilt-Series #2.
Alignment quality for Iteration #16 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (17may19b): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00357 for Iteration #17 of Tilt-Series #2.
CCMS(rotations) = 0.25321 for Iteration #17 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00685 for iteration 17 of Tilt-Series #2.
Alignment quality for Iteration #17 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (17may19b): Very StableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00427 for Iteration #18 of Tilt-Series #2.
CCMS(rotations) = 0.22736 for Iteration #18 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00668 for iteration 18 of Tilt-Series #2.
Alignment quality for Iteration #18 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (17may19b): Very StableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #19 of Tilt-Series #2.
CCMS(rotations) = 0.23863 for Iteration #19 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00669 for iteration 19 of Tilt-Series #2.
Alignment quality for Iteration #19 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00424 for Iteration #20 of Tilt-Series #2.
CCMS(rotations) = 0.23508 for Iteration #20 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00682 for iteration 20 of Tilt-Series #2.
Alignment quality for Iteration #20 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (17may19b): 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 #3 of Tilt-Series #2 (tiltseries0002_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 = 77.0260349434
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 = 77.0260349434
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00576 for Iteration #21 of Tilt-Series #2.
CCMS(rotations) = 0.24895 for Iteration #21 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00786 for iteration 21 of Tilt-Series #2.
Alignment quality for Iteration #21 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (17may19b): UnstableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #22 of Tilt-Series #2.
CCMS(rotations) = 0.2545 for Iteration #22 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00793 for iteration 22 of Tilt-Series #2.
Alignment quality for Iteration #22 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #23 of Tilt-Series #2.
CCMS(rotations) = 0.24803 for Iteration #23 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00781 for iteration 23 of Tilt-Series #2.
Alignment quality for Iteration #23 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (17may19b): StableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00583 for Iteration #24 of Tilt-Series #2.
CCMS(rotations) = 0.29551 for Iteration #24 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00882 for iteration 24 of Tilt-Series #2.
Alignment quality for Iteration #24 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (17may19b): UnstableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00484 for Iteration #25 of Tilt-Series #2.
CCMS(rotations) = 0.29511 for Iteration #25 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00832 for iteration 25 of Tilt-Series #2.
Alignment quality for Iteration #25 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (17may19b): Rock Solid!Creating 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 #2 (tiltseries0002_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 = 154.052069887
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 = 154.052069887
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00801 for Iteration #26 of Tilt-Series #2.
CCMS(rotations) = 0.23162 for Iteration #26 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00864 for iteration 26 of Tilt-Series #2.
Alignment quality for Iteration #26 of Tilt-Series #2 (17may19b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00492 for Iteration #27 of Tilt-Series #2.
CCMS(rotations) = 0.17672 for Iteration #27 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00599 for iteration 27 of Tilt-Series #2.
Alignment quality for Iteration #27 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (17may19b): Very StableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00471 for Iteration #28 of Tilt-Series #2.
CCMS(rotations) = 0.23474 for Iteration #28 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00705 for iteration 28 of Tilt-Series #2.
Alignment quality for Iteration #28 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00481 for Iteration #29 of Tilt-Series #2.
CCMS(rotations) = 0.20872 for Iteration #29 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00658 for iteration 29 of Tilt-Series #2.
Alignment quality for Iteration #29 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00509 for Iteration #30 of Tilt-Series #2.
CCMS(rotations) = 0.24143 for Iteration #30 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00737 for iteration 30 of Tilt-Series #2.
Alignment quality for Iteration #30 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (17may19b): Rock Solid!Creating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00514 for Iteration #31 of Tilt-Series #2.
CCMS(rotations) = 0.22868 for Iteration #31 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00714 for iteration 31 of Tilt-Series #2.
Alignment quality for Iteration #31 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (17may19b): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00391 for Iteration #32 of Tilt-Series #2.
CCMS(rotations) = 0.23742 for Iteration #32 of Tilt-Series #2.
CCMS(scale) = 0.00201 for Iteration #32 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00514 for iteration 32 of Tilt-Series #2.
Alignment quality for Iteration #32 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (17may19b): Rock Solid!Creating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #33 of Tilt-Series #2.
CCMS(rotations) = 0.22806 for Iteration #33 of Tilt-Series #2.
CCMS(scale) = 0.00174 for Iteration #33 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00494 for iteration 33 of Tilt-Series #2.
Alignment quality for Iteration #33 of Tilt-Series #2 (17may19b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (17may19b): Very StableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00457 for Iteration #34 of Tilt-Series #2.
CCMS(rotations) = 0.30773 for Iteration #34 of Tilt-Series #2.
CCMS(scale) = 0.00189 for Iteration #34 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00626 for iteration 34 of Tilt-Series #2.
Alignment quality for Iteration #34 of Tilt-Series #2 (17may19b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (17may19b): UnstableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00375 for Iteration #35 of Tilt-Series #2.
CCMS(rotations) = 0.20787 for Iteration #35 of Tilt-Series #2.
CCMS(scale) = 0.00202 for Iteration #35 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0047 for iteration 35 of Tilt-Series #2.
Alignment quality for Iteration #35 of Tilt-Series #2 (17may19b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (17may19b): UnstableCreating 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 #2 (tiltseries0002_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-21hr46m00s