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/tiltseries0004_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=tiltseries0004_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=4 --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=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node22
Start time: 2017yr08m18d-18hr50m59s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0004.tlt to series0004.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_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) = 0.08039 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 0.2281 for Iteration #1 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4.
The scaled sum of CCMS values is #0.04476 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (17aug18i): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00693 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.22503 for Iteration #2 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00796 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17aug18i): Very Good (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.19013 for Iteration #3 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00746 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (17aug18i): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0073 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.2116 for Iteration #4 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00788 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00765 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.17017 for Iteration #5 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00723 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (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 #4 (tiltseries0004_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) = 0.00643 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.22033 for Iteration #6 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00762 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (17aug18i): Very StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00658 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.19089 for Iteration #7 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00711 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00635 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.19563 for Iteration #8 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00709 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00623 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.19812 for Iteration #9 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00708 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.20241 for Iteration #10 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00742 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00642 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.20542 for Iteration #11 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00732 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00611 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.20712 for Iteration #12 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0072 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00642 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.19139 for Iteration #13 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00704 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00626 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.2014 for Iteration #14 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00716 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00616 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.20421 for Iteration #15 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00716 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (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 #4 (tiltseries0004_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) = 0.00737 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.18804 for Iteration #16 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00745 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00717 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.22053 for Iteration #17 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4.
The scaled sum of CCMS values is #0.008 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00698 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.21127 for Iteration #18 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00772 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00676 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.19665 for Iteration #19 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00731 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00678 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.20375 for Iteration #20 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00746 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (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 #4 (tiltseries0004_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) = 0.00738 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.24075 for Iteration #21 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00851 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00708 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.25502 for Iteration #22 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00864 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00694 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.22583 for Iteration #23 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00799 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00706 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.229 for Iteration #24 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00811 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00721 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.25479 for Iteration #25 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0087 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00687 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.27429 for Iteration #26 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00892 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (17aug18i): StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00647 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.22633 for Iteration #27 of Tilt-Series #4.
CCMS(scale) = 0.0027 for Iteration #27 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00608 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.21612 for Iteration #28 of Tilt-Series #4.
CCMS(scale) = 0.00372 for Iteration #28 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00579 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.25739 for Iteration #29 of Tilt-Series #4.
CCMS(scale) = 0.00367 for Iteration #29 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00625 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (17aug18i): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00421 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.23829 for Iteration #30 of Tilt-Series #4.
CCMS(scale) = 0.00377 for Iteration #30 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00584 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (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 #4 (tiltseries0004_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: 2017yr08m20d-09hr07m47s