protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0040_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=2076.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=3685 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0040_thick50 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=40 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=35.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node03
Start time: 2017yr09m06d-17hr04m40s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0040.tlt to series0040.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #40 (tiltseries0040_thick50)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 15.7963602001
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 15.7963602001
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05183 for Iteration #1 of Tilt-Series #40.
CCMS(rotations) = 1.33738 for Iteration #1 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #40.
The scaled sum of CCMS values is #0.05266 for iteration 1 of Tilt-Series #40.
Alignment quality for Iteration #1 of Tilt-Series #40 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.870968%)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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00604 for Iteration #2 of Tilt-Series #40.
CCMS(rotations) = 0.13793 for Iteration #2 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00578 for iteration 2 of Tilt-Series #40.
Alignment quality for Iteration #2 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00607 for Iteration #3 of Tilt-Series #40.
CCMS(rotations) = 0.1267 for Iteration #3 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00557 for iteration 3 of Tilt-Series #40.
Alignment quality for Iteration #3 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00613 for Iteration #4 of Tilt-Series #40.
CCMS(rotations) = 0.12911 for Iteration #4 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00565 for iteration 4 of Tilt-Series #40.
Alignment quality for Iteration #4 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #40 (17aug18i): Very StableCreating 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00594 for Iteration #5 of Tilt-Series #40.
CCMS(rotations) = 0.1273 for Iteration #5 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00551 for iteration 5 of Tilt-Series #40.
Alignment quality for Iteration #5 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

Beginning Refinement Iteration #6, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 31.5927204002
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #6 of Tilt-Series #40.
CCMS(rotations) = 0.09377 for Iteration #6 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00525 for iteration 6 of Tilt-Series #40.
Alignment quality for Iteration #6 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #7 of Tilt-Series #40.
CCMS(rotations) = 0.09948 for Iteration #7 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00508 for iteration 7 of Tilt-Series #40.
Alignment quality for Iteration #7 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #8 of Tilt-Series #40.
CCMS(rotations) = 0.11104 for Iteration #8 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00539 for iteration 8 of Tilt-Series #40.
Alignment quality for Iteration #8 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #9 of Tilt-Series #40.
CCMS(rotations) = 0.10203 for Iteration #9 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00509 for iteration 9 of Tilt-Series #40.
Alignment quality for Iteration #9 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00635 for Iteration #10 of Tilt-Series #40.
CCMS(rotations) = 0.11516 for Iteration #10 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00548 for iteration 10 of Tilt-Series #40.
Alignment quality for Iteration #10 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

No Round parameters changed for Iteration #11 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #11 of Tilt-Series #40.
CCMS(rotations) = 0.10564 for Iteration #11 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00528 for iteration 11 of Tilt-Series #40.
Alignment quality for Iteration #11 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00633 for Iteration #12 of Tilt-Series #40.
CCMS(rotations) = 0.11022 for Iteration #12 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00537 for iteration 12 of Tilt-Series #40.
Alignment quality for Iteration #12 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00651 for Iteration #13 of Tilt-Series #40.
CCMS(rotations) = 0.11151 for Iteration #13 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00548 for iteration 13 of Tilt-Series #40.
Alignment quality for Iteration #13 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00615 for Iteration #14 of Tilt-Series #40.
CCMS(rotations) = 0.10928 for Iteration #14 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00526 for iteration 14 of Tilt-Series #40.
Alignment quality for Iteration #14 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00637 for Iteration #15 of Tilt-Series #40.
CCMS(rotations) = 0.10674 for Iteration #15 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00532 for iteration 15 of Tilt-Series #40.
Alignment quality for Iteration #15 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

Beginning Refinement Iteration #16, Round #3 of Tilt-Series #40 (tiltseries0040_thick50)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 63.1854408003
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00729 for Iteration #16 of Tilt-Series #40.
CCMS(rotations) = 0.11126 for Iteration #16 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00587 for iteration 16 of Tilt-Series #40.
Alignment quality for Iteration #16 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #40 (17aug18i): UnstableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00692 for Iteration #17 of Tilt-Series #40.
CCMS(rotations) = 0.11647 for Iteration #17 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00579 for iteration 17 of Tilt-Series #40.
Alignment quality for Iteration #17 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00701 for Iteration #18 of Tilt-Series #40.
CCMS(rotations) = 0.11846 for Iteration #18 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00588 for iteration 18 of Tilt-Series #40.
Alignment quality for Iteration #18 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00699 for Iteration #19 of Tilt-Series #40.
CCMS(rotations) = 0.11904 for Iteration #19 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00587 for iteration 19 of Tilt-Series #40.
Alignment quality for Iteration #19 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.0073 for Iteration #20 of Tilt-Series #40.
CCMS(rotations) = 0.11732 for Iteration #20 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #40.
The scaled sum of CCMS values is #0.006 for iteration 20 of Tilt-Series #40.
Alignment quality for Iteration #20 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 126.370881601
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00748 for Iteration #21 of Tilt-Series #40.
CCMS(rotations) = 0.18798 for Iteration #21 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #40.
The scaled sum of CCMS values is #0.0075 for iteration 21 of Tilt-Series #40.
Alignment quality for Iteration #21 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00904 for Iteration #22 of Tilt-Series #40.
CCMS(rotations) = 0.14025 for Iteration #22 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00733 for iteration 22 of Tilt-Series #40.
Alignment quality for Iteration #22 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #40 (17aug18i): Very 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00894 for Iteration #23 of Tilt-Series #40.
CCMS(rotations) = 0.12018 for Iteration #23 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00687 for iteration 23 of Tilt-Series #40.
Alignment quality for Iteration #23 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #40 (17aug18i): Very 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00814 for Iteration #24 of Tilt-Series #40.
CCMS(rotations) = 0.15273 for Iteration #24 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00712 for iteration 24 of Tilt-Series #40.
Alignment quality for Iteration #24 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00863 for Iteration #25 of Tilt-Series #40.
CCMS(rotations) = 0.1306 for Iteration #25 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00693 for iteration 25 of Tilt-Series #40.
Alignment quality for Iteration #25 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

No Round parameters changed for Iteration #26 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0078 for Iteration #26 of Tilt-Series #40.
CCMS(rotations) = 0.16034 for Iteration #26 of Tilt-Series #40.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00711 for iteration 26 of Tilt-Series #40.
Alignment quality for Iteration #26 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00654 for Iteration #27 of Tilt-Series #40.
CCMS(rotations) = 0.12914 for Iteration #27 of Tilt-Series #40.
CCMS(scale) = 0.00316 for Iteration #27 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00495 for iteration 27 of Tilt-Series #40.
Alignment quality for Iteration #27 of Tilt-Series #40 (17aug18i): Perfection! (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00663 for Iteration #28 of Tilt-Series #40.
CCMS(rotations) = 0.15548 for Iteration #28 of Tilt-Series #40.
CCMS(scale) = 0.00351 for Iteration #28 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00545 for iteration 28 of Tilt-Series #40.
Alignment quality for Iteration #28 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00673 for Iteration #29 of Tilt-Series #40.
CCMS(rotations) = 0.14299 for Iteration #29 of Tilt-Series #40.
CCMS(scale) = 0.00347 for Iteration #29 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00531 for iteration 29 of Tilt-Series #40.
Alignment quality for Iteration #29 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #40 (17aug18i): 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 #40 (tiltseries0040_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #40 (tiltseries0040_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00691 for Iteration #30 of Tilt-Series #40.
CCMS(rotations) = 0.15239 for Iteration #30 of Tilt-Series #40.
CCMS(scale) = 0.00365 for Iteration #30 of Tilt-Series #40.
The scaled sum of CCMS values is #0.00555 for iteration 30 of Tilt-Series #40.
Alignment quality for Iteration #30 of Tilt-Series #40 (17aug18i): Excellent (confidence: 0.870968%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #40 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #40 (tiltseries0040_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: 2017yr09m07d-22hr22m25s