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/tiltseries0005_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=tiltseries0005_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=5 --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

node39
Start time: 2017yr08m18d-18hr55m45s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0005.tlt to series0005.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #5 (tiltseries0005_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) = 0.04672 for Iteration #1 of Tilt-Series #5.
CCMS(rotations) = 0.85647 for Iteration #1 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5.
The scaled sum of CCMS values is #0.04049 for iteration 1 of Tilt-Series #5.
Alignment quality for Iteration #1 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00545 for Iteration #2 of Tilt-Series #5.
CCMS(rotations) = 0.14437 for Iteration #2 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00561 for iteration 2 of Tilt-Series #5.
Alignment quality for Iteration #2 of Tilt-Series #5 (17aug18i): Excellent (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00491 for Iteration #3 of Tilt-Series #5.
CCMS(rotations) = 0.15244 for Iteration #3 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0055 for iteration 3 of Tilt-Series #5.
Alignment quality for Iteration #3 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00505 for Iteration #4 of Tilt-Series #5.
CCMS(rotations) = 0.13751 for Iteration #4 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00527 for iteration 4 of Tilt-Series #5.
Alignment quality for Iteration #4 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #5 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00469 for Iteration #5 of Tilt-Series #5.
CCMS(rotations) = 0.13332 for Iteration #5 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00501 for iteration 5 of Tilt-Series #5.
Alignment quality for Iteration #5 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #5 (17aug18i): UnstableCreating 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 #5 (tiltseries0005_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) = 0.00519 for Iteration #6 of Tilt-Series #5.
CCMS(rotations) = 0.16182 for Iteration #6 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00583 for iteration 6 of Tilt-Series #5.
Alignment quality for Iteration #6 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00446 for Iteration #7 of Tilt-Series #5.
CCMS(rotations) = 0.14354 for Iteration #7 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0051 for iteration 7 of Tilt-Series #5.
Alignment quality for Iteration #7 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00438 for Iteration #8 of Tilt-Series #5.
CCMS(rotations) = 0.13365 for Iteration #8 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00486 for iteration 8 of Tilt-Series #5.
Alignment quality for Iteration #8 of Tilt-Series #5 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #5 (17aug18i): Very StableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00433 for Iteration #9 of Tilt-Series #5.
CCMS(rotations) = 0.16679 for Iteration #9 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0055 for iteration 9 of Tilt-Series #5.
Alignment quality for Iteration #9 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #5 (17aug18i): UnstableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00433 for Iteration #10 of Tilt-Series #5.
CCMS(rotations) = 0.16197 for Iteration #10 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00541 for iteration 10 of Tilt-Series #5.
Alignment quality for Iteration #10 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0042 for Iteration #11 of Tilt-Series #5.
CCMS(rotations) = 0.15295 for Iteration #11 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00516 for iteration 11 of Tilt-Series #5.
Alignment quality for Iteration #11 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00422 for Iteration #12 of Tilt-Series #5.
CCMS(rotations) = 0.15306 for Iteration #12 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00517 for iteration 12 of Tilt-Series #5.
Alignment quality for Iteration #12 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #5 (17aug18i): StableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00426 for Iteration #13 of Tilt-Series #5.
CCMS(rotations) = 0.15426 for Iteration #13 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00522 for iteration 13 of Tilt-Series #5.
Alignment quality for Iteration #13 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00412 for Iteration #14 of Tilt-Series #5.
CCMS(rotations) = 0.16431 for Iteration #14 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00535 for iteration 14 of Tilt-Series #5.
Alignment quality for Iteration #14 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00425 for Iteration #15 of Tilt-Series #5.
CCMS(rotations) = 0.16407 for Iteration #15 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0054 for iteration 15 of Tilt-Series #5.
Alignment quality for Iteration #15 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #5 (17aug18i): Very StableCreating 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 #5 (tiltseries0005_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) = 0.00618 for Iteration #16 of Tilt-Series #5.
CCMS(rotations) = 0.11207 for Iteration #16 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00533 for iteration 16 of Tilt-Series #5.
Alignment quality for Iteration #16 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #5 (17aug18i): Very 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00559 for Iteration #17 of Tilt-Series #5.
CCMS(rotations) = 0.14375 for Iteration #17 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00567 for iteration 17 of Tilt-Series #5.
Alignment quality for Iteration #17 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00542 for Iteration #18 of Tilt-Series #5.
CCMS(rotations) = 0.15553 for Iteration #18 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00582 for iteration 18 of Tilt-Series #5.
Alignment quality for Iteration #18 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #19 of Tilt-Series #5.
CCMS(rotations) = 0.13626 for Iteration #19 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00557 for iteration 19 of Tilt-Series #5.
Alignment quality for Iteration #19 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #5 (17aug18i): StableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00542 for Iteration #20 of Tilt-Series #5.
CCMS(rotations) = 0.16631 for Iteration #20 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00604 for iteration 20 of Tilt-Series #5.
Alignment quality for Iteration #20 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #5 (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 #5 (tiltseries0005_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) = 0.00692 for Iteration #21 of Tilt-Series #5.
CCMS(rotations) = 0.16129 for Iteration #21 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00669 for iteration 21 of Tilt-Series #5.
Alignment quality for Iteration #21 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00648 for Iteration #22 of Tilt-Series #5.
CCMS(rotations) = 0.1565 for Iteration #22 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00637 for iteration 22 of Tilt-Series #5.
Alignment quality for Iteration #22 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #5 (17aug18i): UnstableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #23 of Tilt-Series #5.
CCMS(rotations) = 0.13003 for Iteration #23 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00567 for iteration 23 of Tilt-Series #5.
Alignment quality for Iteration #23 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00589 for Iteration #24 of Tilt-Series #5.
CCMS(rotations) = 0.18453 for Iteration #24 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00664 for iteration 24 of Tilt-Series #5.
Alignment quality for Iteration #24 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00644 for Iteration #25 of Tilt-Series #5.
CCMS(rotations) = 0.12479 for Iteration #25 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00572 for iteration 25 of Tilt-Series #5.
Alignment quality for Iteration #25 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #5 (17aug18i): Very StableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00624 for Iteration #26 of Tilt-Series #5.
CCMS(rotations) = 0.16088 for Iteration #26 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00634 for iteration 26 of Tilt-Series #5.
Alignment quality for Iteration #26 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #5 (17aug18i): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00548 for Iteration #27 of Tilt-Series #5.
CCMS(rotations) = 0.14364 for Iteration #27 of Tilt-Series #5.
CCMS(scale) = 0.00326 for Iteration #27 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00483 for iteration 27 of Tilt-Series #5.
Alignment quality for Iteration #27 of Tilt-Series #5 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #5 (17aug18i): UnstableCreating 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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00507 for Iteration #28 of Tilt-Series #5.
CCMS(rotations) = 0.15718 for Iteration #28 of Tilt-Series #5.
CCMS(scale) = 0.00317 for Iteration #28 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00484 for iteration 28 of Tilt-Series #5.
Alignment quality for Iteration #28 of Tilt-Series #5 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #29 of Tilt-Series #5.
CCMS(rotations) = 0.14272 for Iteration #29 of Tilt-Series #5.
CCMS(scale) = 0.00334 for Iteration #29 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00493 for iteration 29 of Tilt-Series #5.
Alignment quality for Iteration #29 of Tilt-Series #5 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #5 (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 #5 (tiltseries0005_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #5 (tiltseries0005_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00599 for Iteration #30 of Tilt-Series #5.
CCMS(rotations) = 0.16111 for Iteration #30 of Tilt-Series #5.
CCMS(scale) = 0.00345 for Iteration #30 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00529 for iteration 30 of Tilt-Series #5.
Alignment quality for Iteration #30 of Tilt-Series #5 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #5 (17aug18i): UnstableCreating 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 #5 (tiltseries0005_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: 2017yr08m20d-03hr50m26s