protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-37.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0035_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=tiltseries0035_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=35 --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

node25
Start time: 2017yr09m04d-16hr10m25s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0035.tlt to series0035.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #35 (tiltseries0035_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 = 31.5927204002
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 = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07766 for Iteration #1 of Tilt-Series #35.
CCMS(rotations) = 1.5924 for Iteration #1 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #35.
The scaled sum of CCMS values is #0.07068 for iteration 1 of Tilt-Series #35.
Alignment quality for Iteration #1 of Tilt-Series #35 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.965517%)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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.06795 for Iteration #2 of Tilt-Series #35.
CCMS(rotations) = 1.53664 for Iteration #2 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #35.
The scaled sum of CCMS values is #0.06471 for iteration 2 of Tilt-Series #35.
Alignment quality for Iteration #2 of Tilt-Series #35 (17aug18i): Bad (confidence: 0.965517%)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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00797 for Iteration #3 of Tilt-Series #35.
CCMS(rotations) = 0.30633 for Iteration #3 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #35.
The scaled sum of CCMS values is #0.01011 for iteration 3 of Tilt-Series #35.
Alignment quality for Iteration #3 of Tilt-Series #35 (17aug18i): Very Good (confidence: 0.965517%)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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00877 for Iteration #4 of Tilt-Series #35.
CCMS(rotations) = 0.33067 for Iteration #4 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #35.
The scaled sum of CCMS values is #0.011 for iteration 4 of Tilt-Series #35.
Alignment quality for Iteration #4 of Tilt-Series #35 (17aug18i): Very Good (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00878 for Iteration #5 of Tilt-Series #35.
CCMS(rotations) = 0.31139 for Iteration #5 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #35.
The scaled sum of CCMS values is #0.01062 for iteration 5 of Tilt-Series #35.
Alignment quality for Iteration #5 of Tilt-Series #35 (17aug18i): Very Good (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #35 (17aug18i): Very StableCreating 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 #35 (tiltseries0035_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 = 63.1854408003
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 = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00739 for Iteration #6 of Tilt-Series #35.
CCMS(rotations) = 0.28746 for Iteration #6 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00945 for iteration 6 of Tilt-Series #35.
Alignment quality for Iteration #6 of Tilt-Series #35 (17aug18i): Very Good (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00529 for Iteration #7 of Tilt-Series #35.
CCMS(rotations) = 0.12533 for Iteration #7 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00515 for iteration 7 of Tilt-Series #35.
Alignment quality for Iteration #7 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #35 (17aug18i): StableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00492 for Iteration #8 of Tilt-Series #35.
CCMS(rotations) = 0.14773 for Iteration #8 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00541 for iteration 8 of Tilt-Series #35.
Alignment quality for Iteration #8 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00493 for Iteration #9 of Tilt-Series #35.
CCMS(rotations) = 0.14566 for Iteration #9 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00538 for iteration 9 of Tilt-Series #35.
Alignment quality for Iteration #9 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #10 of Tilt-Series #35.
CCMS(rotations) = 0.13043 for Iteration #10 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00511 for iteration 10 of Tilt-Series #35.
Alignment quality for Iteration #10 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00498 for Iteration #11 of Tilt-Series #35.
CCMS(rotations) = 0.14884 for Iteration #11 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00547 for iteration 11 of Tilt-Series #35.
Alignment quality for Iteration #11 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00492 for Iteration #12 of Tilt-Series #35.
CCMS(rotations) = 0.14543 for Iteration #12 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00537 for iteration 12 of Tilt-Series #35.
Alignment quality for Iteration #12 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00473 for Iteration #13 of Tilt-Series #35.
CCMS(rotations) = 0.13643 for Iteration #13 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #35.
The scaled sum of CCMS values is #0.0051 for iteration 13 of Tilt-Series #35.
Alignment quality for Iteration #13 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #14 of Tilt-Series #35.
CCMS(rotations) = 0.14108 for Iteration #14 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00523 for iteration 14 of Tilt-Series #35.
Alignment quality for Iteration #14 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.0048 for Iteration #15 of Tilt-Series #35.
CCMS(rotations) = 0.1375 for Iteration #15 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00515 for iteration 15 of Tilt-Series #35.
Alignment quality for Iteration #15 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #35 (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 #35 (tiltseries0035_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 = 126.370881601
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 = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00601 for Iteration #16 of Tilt-Series #35.
CCMS(rotations) = 0.14921 for Iteration #16 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00599 for iteration 16 of Tilt-Series #35.
Alignment quality for Iteration #16 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #35 (17aug18i): StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.005 for Iteration #17 of Tilt-Series #35.
CCMS(rotations) = 0.13519 for Iteration #17 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00521 for iteration 17 of Tilt-Series #35.
Alignment quality for Iteration #17 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00421 for Iteration #18 of Tilt-Series #35.
CCMS(rotations) = 0.11798 for Iteration #18 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00447 for iteration 18 of Tilt-Series #35.
Alignment quality for Iteration #18 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00426 for Iteration #19 of Tilt-Series #35.
CCMS(rotations) = 0.09969 for Iteration #19 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00412 for iteration 19 of Tilt-Series #35.
Alignment quality for Iteration #19 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00443 for Iteration #20 of Tilt-Series #35.
CCMS(rotations) = 0.12618 for Iteration #20 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00474 for iteration 20 of Tilt-Series #35.
Alignment quality for Iteration #20 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #35 (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 #35 (tiltseries0035_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 = 252.741763201
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 = 252.741763201
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #21 of Tilt-Series #35.
CCMS(rotations) = 0.12486 for Iteration #21 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00583 for iteration 21 of Tilt-Series #35.
Alignment quality for Iteration #21 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #35 (17aug18i): StableCreating 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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #22 of Tilt-Series #35.
CCMS(rotations) = 0.14853 for Iteration #22 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00602 for iteration 22 of Tilt-Series #35.
Alignment quality for Iteration #22 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00599 for Iteration #23 of Tilt-Series #35.
CCMS(rotations) = 0.11777 for Iteration #23 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00535 for iteration 23 of Tilt-Series #35.
Alignment quality for Iteration #23 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00586 for Iteration #24 of Tilt-Series #35.
CCMS(rotations) = 0.11712 for Iteration #24 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00527 for iteration 24 of Tilt-Series #35.
Alignment quality for Iteration #24 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00671 for Iteration #25 of Tilt-Series #35.
CCMS(rotations) = 0.11265 for Iteration #25 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00561 for iteration 25 of Tilt-Series #35.
Alignment quality for Iteration #25 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0064 for Iteration #26 of Tilt-Series #35.
CCMS(rotations) = 0.11291 for Iteration #26 of Tilt-Series #35.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00546 for iteration 26 of Tilt-Series #35.
Alignment quality for Iteration #26 of Tilt-Series #35 (17aug18i): Excellent (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00396 for Iteration #27 of Tilt-Series #35.
CCMS(rotations) = 0.10417 for Iteration #27 of Tilt-Series #35.
CCMS(scale) = 0.00263 for Iteration #27 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00359 for iteration 27 of Tilt-Series #35.
Alignment quality for Iteration #27 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #35 (17aug18i): Very StableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #28 of Tilt-Series #35.
CCMS(rotations) = 0.13017 for Iteration #28 of Tilt-Series #35.
CCMS(scale) = 0.00281 for Iteration #28 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00404 for iteration 28 of Tilt-Series #35.
Alignment quality for Iteration #28 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #29 of Tilt-Series #35.
CCMS(rotations) = 0.11086 for Iteration #29 of Tilt-Series #35.
CCMS(scale) = 0.00278 for Iteration #29 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00394 for iteration 29 of Tilt-Series #35.
Alignment quality for Iteration #29 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #35 (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 #35 (tiltseries0035_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #35 (tiltseries0035_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00456 for Iteration #30 of Tilt-Series #35.
CCMS(rotations) = 0.13312 for Iteration #30 of Tilt-Series #35.
CCMS(scale) = 0.00289 for Iteration #30 of Tilt-Series #35.
The scaled sum of CCMS values is #0.00426 for iteration 30 of Tilt-Series #35.
Alignment quality for Iteration #30 of Tilt-Series #35 (17aug18i): Perfection! (confidence: 0.965517%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #35 (17aug18i): Very StableCreating 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 #35 (tiltseries0035_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: 2017yr09m06d-01hr57m37s