protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-31.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0031_thick100 --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=tiltseries0031_thick100 --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=31 --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=100 --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

node21
Start time: 2017yr09m04d-15hr58m57s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0031.tlt to series0031.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #31 (tiltseries0031_thick100)
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 = 31.5921691138
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 = 31.5921691138
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.1238 for Iteration #1 of Tilt-Series #31.
CCMS(rotations) = 2.14328 for Iteration #1 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #31.
The scaled sum of CCMS values is #0.10477 for iteration 1 of Tilt-Series #31.
Alignment quality for Iteration #1 of Tilt-Series #31 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.962963%)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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.06542 for Iteration #2 of Tilt-Series #31.
CCMS(rotations) = 0.23252 for Iteration #2 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #31.
The scaled sum of CCMS values is #0.03736 for iteration 2 of Tilt-Series #31.
Alignment quality for Iteration #2 of Tilt-Series #31 (17aug18i): Bad (confidence: 0.962963%)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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00724 for Iteration #3 of Tilt-Series #31.
CCMS(rotations) = 0.22755 for Iteration #3 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00817 for iteration 3 of Tilt-Series #31.
Alignment quality for Iteration #3 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00707 for Iteration #4 of Tilt-Series #31.
CCMS(rotations) = 0.25692 for Iteration #4 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00867 for iteration 4 of Tilt-Series #31.
Alignment quality for Iteration #4 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #31 (17aug18i): 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00729 for Iteration #5 of Tilt-Series #31.
CCMS(rotations) = 0.22134 for Iteration #5 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00807 for iteration 5 of Tilt-Series #31.
Alignment quality for Iteration #5 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)
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 = 63.1843382277
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 = 63.1843382277
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00788 for Iteration #6 of Tilt-Series #31.
CCMS(rotations) = 0.21465 for Iteration #6 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00823 for iteration 6 of Tilt-Series #31.
Alignment quality for Iteration #6 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00702 for Iteration #7 of Tilt-Series #31.
CCMS(rotations) = 0.28633 for Iteration #7 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00924 for iteration 7 of Tilt-Series #31.
Alignment quality for Iteration #7 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00683 for Iteration #8 of Tilt-Series #31.
CCMS(rotations) = 0.24516 for Iteration #8 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00832 for iteration 8 of Tilt-Series #31.
Alignment quality for Iteration #8 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00751 for Iteration #9 of Tilt-Series #31.
CCMS(rotations) = 0.22573 for Iteration #9 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00827 for iteration 9 of Tilt-Series #31.
Alignment quality for Iteration #9 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #31 (17aug18i): Very StableCreating 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00715 for Iteration #10 of Tilt-Series #31.
CCMS(rotations) = 0.19695 for Iteration #10 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00751 for iteration 10 of Tilt-Series #31.
Alignment quality for Iteration #10 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00679 for Iteration #11 of Tilt-Series #31.
CCMS(rotations) = 0.21107 for Iteration #11 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00762 for iteration 11 of Tilt-Series #31.
Alignment quality for Iteration #11 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00679 for Iteration #12 of Tilt-Series #31.
CCMS(rotations) = 0.20038 for Iteration #12 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #31.
The scaled sum of CCMS values is #0.0074 for iteration 12 of Tilt-Series #31.
Alignment quality for Iteration #12 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0066 for Iteration #13 of Tilt-Series #31.
CCMS(rotations) = 0.20706 for Iteration #13 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00744 for iteration 13 of Tilt-Series #31.
Alignment quality for Iteration #13 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00721 for Iteration #14 of Tilt-Series #31.
CCMS(rotations) = 0.19207 for Iteration #14 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00744 for iteration 14 of Tilt-Series #31.
Alignment quality for Iteration #14 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00658 for Iteration #15 of Tilt-Series #31.
CCMS(rotations) = 0.21412 for Iteration #15 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00757 for iteration 15 of Tilt-Series #31.
Alignment quality for Iteration #15 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)
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 = 126.368676455
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 = 126.368676455
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01211 for Iteration #16 of Tilt-Series #31.
CCMS(rotations) = 0.37729 for Iteration #16 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #31.
The scaled sum of CCMS values is #0.0136 for iteration 16 of Tilt-Series #31.
Alignment quality for Iteration #16 of Tilt-Series #31 (17aug18i): Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00873 for Iteration #17 of Tilt-Series #31.
CCMS(rotations) = 0.2538 for Iteration #17 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00944 for iteration 17 of Tilt-Series #31.
Alignment quality for Iteration #17 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #31 (17aug18i): Very StableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00923 for Iteration #18 of Tilt-Series #31.
CCMS(rotations) = 0.24072 for Iteration #18 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00943 for iteration 18 of Tilt-Series #31.
Alignment quality for Iteration #18 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #31 (17aug18i): Very StableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00928 for Iteration #19 of Tilt-Series #31.
CCMS(rotations) = 0.26009 for Iteration #19 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00984 for iteration 19 of Tilt-Series #31.
Alignment quality for Iteration #19 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00875 for Iteration #20 of Tilt-Series #31.
CCMS(rotations) = 0.24584 for Iteration #20 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00929 for iteration 20 of Tilt-Series #31.
Alignment quality for Iteration #20 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)
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 = 252.737352911
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 = 252.737352911
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01145 for Iteration #21 of Tilt-Series #31.
CCMS(rotations) = 0.34728 for Iteration #21 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #31.
The scaled sum of CCMS values is #0.01267 for iteration 21 of Tilt-Series #31.
Alignment quality for Iteration #21 of Tilt-Series #31 (17aug18i): Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00969 for Iteration #22 of Tilt-Series #31.
CCMS(rotations) = 0.17145 for Iteration #22 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00827 for iteration 22 of Tilt-Series #31.
Alignment quality for Iteration #22 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #31 (17aug18i): 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00793 for Iteration #23 of Tilt-Series #31.
CCMS(rotations) = 0.11841 for Iteration #23 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00633 for iteration 23 of Tilt-Series #31.
Alignment quality for Iteration #23 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #31 (17aug18i): UnstableCreating 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00833 for Iteration #24 of Tilt-Series #31.
CCMS(rotations) = 0.20492 for Iteration #24 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00827 for iteration 24 of Tilt-Series #31.
Alignment quality for Iteration #24 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00789 for Iteration #25 of Tilt-Series #31.
CCMS(rotations) = 0.18949 for Iteration #25 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00774 for iteration 25 of Tilt-Series #31.
Alignment quality for Iteration #25 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00916 for Iteration #26 of Tilt-Series #31.
CCMS(rotations) = 0.19171 for Iteration #26 of Tilt-Series #31.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00842 for iteration 26 of Tilt-Series #31.
Alignment quality for Iteration #26 of Tilt-Series #31 (17aug18i): Very Good (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #31 (17aug18i): 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00719 for Iteration #27 of Tilt-Series #31.
CCMS(rotations) = 0.13641 for Iteration #27 of Tilt-Series #31.
CCMS(scale) = 0.00248 for Iteration #27 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00504 for iteration 27 of Tilt-Series #31.
Alignment quality for Iteration #27 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00744 for Iteration #28 of Tilt-Series #31.
CCMS(rotations) = 0.19881 for Iteration #28 of Tilt-Series #31.
CCMS(scale) = 0.00224 for Iteration #28 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00588 for iteration 28 of Tilt-Series #31.
Alignment quality for Iteration #28 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #31 (17aug18i): UnstableCreating 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 #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00751 for Iteration #29 of Tilt-Series #31.
CCMS(rotations) = 0.22201 for Iteration #29 of Tilt-Series #31.
CCMS(scale) = 0.00215 for Iteration #29 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00618 for iteration 29 of Tilt-Series #31.
Alignment quality for Iteration #29 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #31 (17aug18i): Very StableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #31 (tiltseries0031_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #31 (tiltseries0031_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00672 for Iteration #30 of Tilt-Series #31.
CCMS(rotations) = 0.15206 for Iteration #30 of Tilt-Series #31.
CCMS(scale) = 0.00234 for Iteration #30 of Tilt-Series #31.
The scaled sum of CCMS values is #0.00505 for iteration 30 of Tilt-Series #31.
Alignment quality for Iteration #30 of Tilt-Series #31 (17aug18i): Excellent (confidence: 0.962963%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #31 (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 #31 (tiltseries0031_thick100)!
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: 2017yr09m05d-19hr49m38s