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/tiltseries0003_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=2076.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=3685 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0003_thick50 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=3 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node22
Start time: 2017yr08m18d-18hr50m09s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0003.tlt to series0003.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 15.7963602001
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 15.7963602001
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0605 for Iteration #1 of Tilt-Series #3.
CCMS(rotations) = 0.85356 for Iteration #1 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3.
The scaled sum of CCMS values is #0.04732 for iteration 1 of Tilt-Series #3.
Alignment quality for Iteration #1 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00505 for Iteration #2 of Tilt-Series #3.
CCMS(rotations) = 0.14101 for Iteration #2 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00534 for iteration 2 of Tilt-Series #3.
Alignment quality for Iteration #2 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00532 for Iteration #3 of Tilt-Series #3.
CCMS(rotations) = 0.15833 for Iteration #3 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00583 for iteration 3 of Tilt-Series #3.
Alignment quality for Iteration #3 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.005 for Iteration #4 of Tilt-Series #3.
CCMS(rotations) = 0.15721 for Iteration #4 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00565 for iteration 4 of Tilt-Series #3.
Alignment quality for Iteration #4 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00545 for Iteration #5 of Tilt-Series #3.
CCMS(rotations) = 0.16139 for Iteration #5 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00595 for iteration 5 of Tilt-Series #3.
Alignment quality for Iteration #5 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 31.5927204002
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #6 of Tilt-Series #3.
CCMS(rotations) = 0.14715 for Iteration #6 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00517 for iteration 6 of Tilt-Series #3.
Alignment quality for Iteration #6 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00411 for Iteration #7 of Tilt-Series #3.
CCMS(rotations) = 0.16536 for Iteration #7 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00536 for iteration 7 of Tilt-Series #3.
Alignment quality for Iteration #7 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00402 for Iteration #8 of Tilt-Series #3.
CCMS(rotations) = 0.16762 for Iteration #8 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00536 for iteration 8 of Tilt-Series #3.
Alignment quality for Iteration #8 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.004 for Iteration #9 of Tilt-Series #3.
CCMS(rotations) = 0.16645 for Iteration #9 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00533 for iteration 9 of Tilt-Series #3.
Alignment quality for Iteration #9 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00399 for Iteration #10 of Tilt-Series #3.
CCMS(rotations) = 0.16869 for Iteration #10 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00537 for iteration 10 of Tilt-Series #3.
Alignment quality for Iteration #10 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00436 for Iteration #11 of Tilt-Series #3.
CCMS(rotations) = 0.178 for Iteration #11 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00574 for iteration 11 of Tilt-Series #3.
Alignment quality for Iteration #11 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #12 of Tilt-Series #3.
CCMS(rotations) = 0.16634 for Iteration #12 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00526 for iteration 12 of Tilt-Series #3.
Alignment quality for Iteration #12 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00399 for Iteration #13 of Tilt-Series #3.
CCMS(rotations) = 0.16794 for Iteration #13 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00536 for iteration 13 of Tilt-Series #3.
Alignment quality for Iteration #13 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.004 for Iteration #14 of Tilt-Series #3.
CCMS(rotations) = 0.16468 for Iteration #14 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00529 for iteration 14 of Tilt-Series #3.
Alignment quality for Iteration #14 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00399 for Iteration #15 of Tilt-Series #3.
CCMS(rotations) = 0.17164 for Iteration #15 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00543 for iteration 15 of Tilt-Series #3.
Alignment quality for Iteration #15 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 63.1854408003
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #16 of Tilt-Series #3.
CCMS(rotations) = 0.19879 for Iteration #16 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00674 for iteration 16 of Tilt-Series #3.
Alignment quality for Iteration #16 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00525 for Iteration #17 of Tilt-Series #3.
CCMS(rotations) = 0.19246 for Iteration #17 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00648 for iteration 17 of Tilt-Series #3.
Alignment quality for Iteration #17 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00522 for Iteration #18 of Tilt-Series #3.
CCMS(rotations) = 0.19844 for Iteration #18 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00658 for iteration 18 of Tilt-Series #3.
Alignment quality for Iteration #18 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00513 for Iteration #19 of Tilt-Series #3.
CCMS(rotations) = 0.20297 for Iteration #19 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00662 for iteration 19 of Tilt-Series #3.
Alignment quality for Iteration #19 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00514 for Iteration #20 of Tilt-Series #3.
CCMS(rotations) = 0.19764 for Iteration #20 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00652 for iteration 20 of Tilt-Series #3.
Alignment quality for Iteration #20 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 126.370881601
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00669 for Iteration #21 of Tilt-Series #3.
CCMS(rotations) = 0.23814 for Iteration #21 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00811 for iteration 21 of Tilt-Series #3.
Alignment quality for Iteration #21 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #3 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00629 for Iteration #22 of Tilt-Series #3.
CCMS(rotations) = 0.30568 for Iteration #22 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00926 for iteration 22 of Tilt-Series #3.
Alignment quality for Iteration #22 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00609 for Iteration #23 of Tilt-Series #3.
CCMS(rotations) = 0.23822 for Iteration #23 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00781 for iteration 23 of Tilt-Series #3.
Alignment quality for Iteration #23 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #24 of Tilt-Series #3.
CCMS(rotations) = 0.27019 for Iteration #24 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00846 for iteration 24 of Tilt-Series #3.
Alignment quality for Iteration #24 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00548 for Iteration #25 of Tilt-Series #3.
CCMS(rotations) = 0.22458 for Iteration #25 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00723 for iteration 25 of Tilt-Series #3.
Alignment quality for Iteration #25 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0068 for Iteration #26 of Tilt-Series #3.
CCMS(rotations) = 0.27194 for Iteration #26 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00884 for iteration 26 of Tilt-Series #3.
Alignment quality for Iteration #26 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00959 for Iteration #27 of Tilt-Series #3.
CCMS(rotations) = 0.22773 for Iteration #27 of Tilt-Series #3.
CCMS(scale) = 0.00209 for Iteration #27 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00693 for iteration 27 of Tilt-Series #3.
Alignment quality for Iteration #27 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00786 for Iteration #28 of Tilt-Series #3.
CCMS(rotations) = 0.41064 for Iteration #28 of Tilt-Series #3.
CCMS(scale) = 0.00288 for Iteration #28 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00905 for iteration 28 of Tilt-Series #3.
Alignment quality for Iteration #28 of Tilt-Series #3 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00667 for Iteration #29 of Tilt-Series #3.
CCMS(rotations) = 0.32137 for Iteration #29 of Tilt-Series #3.
CCMS(scale) = 0.00211 for Iteration #29 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00721 for iteration 29 of Tilt-Series #3.
Alignment quality for Iteration #29 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00559 for Iteration #30 of Tilt-Series #3.
CCMS(rotations) = 0.27014 for Iteration #30 of Tilt-Series #3.
CCMS(scale) = 0.00204 for Iteration #30 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00615 for iteration 30 of Tilt-Series #3.
Alignment quality for Iteration #30 of Tilt-Series #3 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #3 (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 #3 (tiltseries0003_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr08m20d-10hr10m54s