protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-37.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0002_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --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=8.64 --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=4015.0 --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=1894 --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=2008.0 --runname=tiltseries0002_thick50 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --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=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --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 --change_refimg=False --r3_mask_width_y=934 --r3_mask_width_x=902 --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=4015.0 --r4_highpass_diameter_x=4015.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --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=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --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=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo

node09
Start time: 2017yr12m26d-17hr18m55s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0002.tlt to series0002.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
lowpass = 69.12 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms)
window.lowpass.apodization = { 0.20016 0.20016 }
map.sampling = 8
window.highpass.diameter = { 0.00862457783313 0.00862457783313 }
window.highpass.apodization = { 0.0172448605578 0.0172448605578 }
window.mask.apodization = { 10 10 }
align.mask.width = { 206 214 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 4.58797001599
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 4.58797001599
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05635 for Iteration #1 of Tilt-Series #2.
CCMS(rotations) = 1.23646 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 #0.05291 for iteration 1 of Tilt-Series #2.
Alignment quality for Iteration #1 of Tilt-Series #2 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 96.774194%)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_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00426 for Iteration #2 of Tilt-Series #2.
CCMS(rotations) = 0.20319 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 #0.00619 for iteration 2 of Tilt-Series #2.
Alignment quality for Iteration #2 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)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_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00421 for Iteration #3 of Tilt-Series #2.
CCMS(rotations) = 0.20805 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 #0.00626 for iteration 3 of Tilt-Series #2.
Alignment quality for Iteration #3 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)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_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #4 of Tilt-Series #2.
CCMS(rotations) = 0.1987 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 #0.00594 for iteration 4 of Tilt-Series #2.
Alignment quality for Iteration #4 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00407 for Iteration #5 of Tilt-Series #2.
CCMS(rotations) = 0.20456 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 #0.00613 for iteration 5 of Tilt-Series #2.
Alignment quality for Iteration #5 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #6 of Tilt-Series #2.
CCMS(rotations) = 0.2071 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 #0.00612 for iteration 6 of Tilt-Series #2.
Alignment quality for Iteration #6 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00407 for Iteration #7 of Tilt-Series #2.
CCMS(rotations) = 0.20737 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 #0.00618 for iteration 7 of Tilt-Series #2.
Alignment quality for Iteration #7 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #8 of Tilt-Series #2.
CCMS(rotations) = 0.20346 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 #0.006 for iteration 8 of Tilt-Series #2.
Alignment quality for Iteration #8 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #9 of Tilt-Series #2.
CCMS(rotations) = 0.20676 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 #0.0061 for iteration 9 of Tilt-Series #2.
Alignment quality for Iteration #9 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00389 for Iteration #10 of Tilt-Series #2.
CCMS(rotations) = 0.19903 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 #0.00593 for iteration 10 of Tilt-Series #2.
Alignment quality for Iteration #10 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (17dec26e): 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_thick50)
lowpass = 34.56 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 4
window.highpass.diameter = { 0.00431228891656 0.00431228891656 }
window.highpass.apodization = { 0.00862243027888 0.00862243027888 }
window.mask.apodization = { 10 10 }
align.mask.width = { 438 454 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 9.17594003198
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 9.17594003198
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #11 of Tilt-Series #2.
CCMS(rotations) = 0.21584 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 #0.00629 for iteration 11 of Tilt-Series #2.
Alignment quality for Iteration #11 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (17dec26e): StableCreating 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_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #12 of Tilt-Series #2.
CCMS(rotations) = 0.24754 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 #0.00675 for iteration 12 of Tilt-Series #2.
Alignment quality for Iteration #12 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00369 for Iteration #13 of Tilt-Series #2.
CCMS(rotations) = 0.24044 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 #0.00665 for iteration 13 of Tilt-Series #2.
Alignment quality for Iteration #13 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00359 for Iteration #14 of Tilt-Series #2.
CCMS(rotations) = 0.24328 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 #0.00666 for iteration 14 of Tilt-Series #2.
Alignment quality for Iteration #14 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #15 of Tilt-Series #2.
CCMS(rotations) = 0.24192 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 #0.00664 for iteration 15 of Tilt-Series #2.
Alignment quality for Iteration #15 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (17dec26e): Rock Solid!Creating 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_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00363 for Iteration #16 of Tilt-Series #2.
CCMS(rotations) = 0.24637 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 #0.00674 for iteration 16 of Tilt-Series #2.
Alignment quality for Iteration #16 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #17 of Tilt-Series #2.
CCMS(rotations) = 0.24075 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 #0.00664 for iteration 17 of Tilt-Series #2.
Alignment quality for Iteration #17 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00368 for Iteration #18 of Tilt-Series #2.
CCMS(rotations) = 0.24713 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 #0.00678 for iteration 18 of Tilt-Series #2.
Alignment quality for Iteration #18 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #19 of Tilt-Series #2.
CCMS(rotations) = 0.24097 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 #0.00664 for iteration 19 of Tilt-Series #2.
Alignment quality for Iteration #19 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00359 for Iteration #20 of Tilt-Series #2.
CCMS(rotations) = 0.244 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 #0.00668 for iteration 20 of Tilt-Series #2.
Alignment quality for Iteration #20 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (17dec26e): 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_thick50)
lowpass = 17.28 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 2
window.highpass.diameter = { 0.00215614445828 0.00215614445828 }
window.highpass.apodization = { 0.00431121513944 0.00431121513944 }
window.mask.apodization = { 10 10 }
align.mask.width = { 902 934 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 18.351880064
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 18.351880064
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #21 of Tilt-Series #2.
CCMS(rotations) = 0.22896 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 #0.00651 for iteration 21 of Tilt-Series #2.
Alignment quality for Iteration #21 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #22 of Tilt-Series #2.
CCMS(rotations) = 0.23867 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 #0.00663 for iteration 22 of Tilt-Series #2.
Alignment quality for Iteration #22 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00368 for Iteration #23 of Tilt-Series #2.
CCMS(rotations) = 0.23897 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 #0.00662 for iteration 23 of Tilt-Series #2.
Alignment quality for Iteration #23 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00373 for Iteration #24 of Tilt-Series #2.
CCMS(rotations) = 0.23977 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 #0.00666 for iteration 24 of Tilt-Series #2.
Alignment quality for Iteration #24 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00366 for Iteration #25 of Tilt-Series #2.
CCMS(rotations) = 0.23581 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 #0.00655 for iteration 25 of Tilt-Series #2.
Alignment quality for Iteration #25 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (17dec26e): 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_thick50)
lowpass = 8.64 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms)
window.lowpass.apodization = { 0.196748181818 0.196748181818 }
map.sampling = 1
window.highpass.diameter = { 0.00107807222914 0.00107807222914 }
window.highpass.apodization = { 0.00215560756972 0.00215560756972 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1830 1894 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 36.7037601279
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 36.7037601279
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00311 for Iteration #26 of Tilt-Series #2.
CCMS(rotations) = 0.19611 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 #0.00548 for iteration 26 of Tilt-Series #2.
Alignment quality for Iteration #26 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (17dec26e): Rock Solid!Creating 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_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00304 for Iteration #27 of Tilt-Series #2.
CCMS(rotations) = 0.18394 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 #0.0052 for iteration 27 of Tilt-Series #2.
Alignment quality for Iteration #27 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00279 for Iteration #28 of Tilt-Series #2.
CCMS(rotations) = 0.1927 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 #0.00525 for iteration 28 of Tilt-Series #2.
Alignment quality for Iteration #28 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0029 for Iteration #29 of Tilt-Series #2.
CCMS(rotations) = 0.18972 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 #0.00524 for iteration 29 of Tilt-Series #2.
Alignment quality for Iteration #29 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (17dec26e): Rock Solid!Creating 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_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00295 for Iteration #30 of Tilt-Series #2.
CCMS(rotations) = 0.18788 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 #0.00523 for iteration 30 of Tilt-Series #2.
Alignment quality for Iteration #30 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00293 for Iteration #31 of Tilt-Series #2.
CCMS(rotations) = 0.18371 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 #0.00514 for iteration 31 of Tilt-Series #2.
Alignment quality for Iteration #31 of Tilt-Series #2 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00186 for Iteration #32 of Tilt-Series #2.
CCMS(rotations) = 0.18695 for Iteration #32 of Tilt-Series #2.
CCMS(scale) = 0.00114 for Iteration #32 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00349 for iteration 32 of Tilt-Series #2.
Alignment quality for Iteration #32 of Tilt-Series #2 (17dec26e): Perfection! (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (17dec26e): 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_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00191 for Iteration #33 of Tilt-Series #2.
CCMS(rotations) = 0.19452 for Iteration #33 of Tilt-Series #2.
CCMS(scale) = 0.00118 for Iteration #33 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00363 for iteration 33 of Tilt-Series #2.
Alignment quality for Iteration #33 of Tilt-Series #2 (17dec26e): Perfection! (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (17dec26e): Rock Solid!Creating 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_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00181 for Iteration #34 of Tilt-Series #2.
CCMS(rotations) = 0.18548 for Iteration #34 of Tilt-Series #2.
CCMS(scale) = 0.00119 for Iteration #34 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00347 for iteration 34 of Tilt-Series #2.
Alignment quality for Iteration #34 of Tilt-Series #2 (17dec26e): Perfection! (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (17dec26e): Rock Solid!Creating 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_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00179 for Iteration #35 of Tilt-Series #2.
CCMS(rotations) = 0.19272 for Iteration #35 of Tilt-Series #2.
CCMS(scale) = 0.00115 for Iteration #35 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00355 for iteration 35 of Tilt-Series #2.
Alignment quality for Iteration #35 of Tilt-Series #2 (17dec26e): Perfection! (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (17dec26e): 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 #2 (tiltseries0002_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr12m27d-01hr24m34s