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/tiltseries0048_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=tiltseries0048_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=48 --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

node07
Start time: 2017yr09m06d-17hr29m01s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0048.tlt to series0048.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #48 (tiltseries0048_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) = 0.05114 for Iteration #1 of Tilt-Series #48.
CCMS(rotations) = 1.70228 for Iteration #1 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #48.
The scaled sum of CCMS values is #0.05961 for iteration 1 of Tilt-Series #48.
Alignment quality for Iteration #1 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #2 of Tilt-Series #48.
CCMS(rotations) = 0.1568 for Iteration #2 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00597 for iteration 2 of Tilt-Series #48.
Alignment quality for Iteration #2 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #3 of Tilt-Series #48.
CCMS(rotations) = 0.14426 for Iteration #3 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00573 for iteration 3 of Tilt-Series #48.
Alignment quality for Iteration #3 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #4 of Tilt-Series #48.
CCMS(rotations) = 0.15082 for Iteration #4 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00552 for iteration 4 of Tilt-Series #48.
Alignment quality for Iteration #4 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00533 for Iteration #5 of Tilt-Series #48.
CCMS(rotations) = 0.13875 for Iteration #5 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00544 for iteration 5 of Tilt-Series #48.
Alignment quality for Iteration #5 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #48 (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 #48 (tiltseries0048_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) = 0.00509 for Iteration #6 of Tilt-Series #48.
CCMS(rotations) = 0.18344 for Iteration #6 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00621 for iteration 6 of Tilt-Series #48.
Alignment quality for Iteration #6 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #48 (17aug18i): StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00469 for Iteration #7 of Tilt-Series #48.
CCMS(rotations) = 0.16284 for Iteration #7 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #48.
The scaled sum of CCMS values is #0.0056 for iteration 7 of Tilt-Series #48.
Alignment quality for Iteration #7 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00468 for Iteration #8 of Tilt-Series #48.
CCMS(rotations) = 0.16356 for Iteration #8 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00561 for iteration 8 of Tilt-Series #48.
Alignment quality for Iteration #8 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00466 for Iteration #9 of Tilt-Series #48.
CCMS(rotations) = 0.16331 for Iteration #9 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #48.
The scaled sum of CCMS values is #0.0056 for iteration 9 of Tilt-Series #48.
Alignment quality for Iteration #9 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0047 for Iteration #10 of Tilt-Series #48.
CCMS(rotations) = 0.16422 for Iteration #10 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00564 for iteration 10 of Tilt-Series #48.
Alignment quality for Iteration #10 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #11 of Tilt-Series #48.
CCMS(rotations) = 0.16362 for Iteration #11 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00558 for iteration 11 of Tilt-Series #48.
Alignment quality for Iteration #11 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00473 for Iteration #12 of Tilt-Series #48.
CCMS(rotations) = 0.16451 for Iteration #12 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00566 for iteration 12 of Tilt-Series #48.
Alignment quality for Iteration #12 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00469 for Iteration #13 of Tilt-Series #48.
CCMS(rotations) = 0.16398 for Iteration #13 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00563 for iteration 13 of Tilt-Series #48.
Alignment quality for Iteration #13 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #14 of Tilt-Series #48.
CCMS(rotations) = 0.16474 for Iteration #14 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00563 for iteration 14 of Tilt-Series #48.
Alignment quality for Iteration #14 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #15 of Tilt-Series #48.
CCMS(rotations) = 0.16111 for Iteration #15 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00562 for iteration 15 of Tilt-Series #48.
Alignment quality for Iteration #15 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #48 (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 #48 (tiltseries0048_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) = 0.00541 for Iteration #16 of Tilt-Series #48.
CCMS(rotations) = 0.16866 for Iteration #16 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00608 for iteration 16 of Tilt-Series #48.
Alignment quality for Iteration #16 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00533 for Iteration #17 of Tilt-Series #48.
CCMS(rotations) = 0.17581 for Iteration #17 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00618 for iteration 17 of Tilt-Series #48.
Alignment quality for Iteration #17 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00533 for Iteration #18 of Tilt-Series #48.
CCMS(rotations) = 0.17636 for Iteration #18 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00619 for iteration 18 of Tilt-Series #48.
Alignment quality for Iteration #18 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0053 for Iteration #19 of Tilt-Series #48.
CCMS(rotations) = 0.17715 for Iteration #19 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00619 for iteration 19 of Tilt-Series #48.
Alignment quality for Iteration #19 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00549 for Iteration #20 of Tilt-Series #48.
CCMS(rotations) = 0.17853 for Iteration #20 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00632 for iteration 20 of Tilt-Series #48.
Alignment quality for Iteration #20 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #48 (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 #48 (tiltseries0048_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) = 0.00607 for Iteration #21 of Tilt-Series #48.
CCMS(rotations) = 0.14652 for Iteration #21 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00596 for iteration 21 of Tilt-Series #48.
Alignment quality for Iteration #21 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00625 for Iteration #22 of Tilt-Series #48.
CCMS(rotations) = 0.17044 for Iteration #22 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00653 for iteration 22 of Tilt-Series #48.
Alignment quality for Iteration #22 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #23 of Tilt-Series #48.
CCMS(rotations) = 0.16106 for Iteration #23 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00655 for iteration 23 of Tilt-Series #48.
Alignment quality for Iteration #23 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #48 (17aug18i): 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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00593 for Iteration #24 of Tilt-Series #48.
CCMS(rotations) = 0.20095 for Iteration #24 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00699 for iteration 24 of Tilt-Series #48.
Alignment quality for Iteration #24 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00627 for Iteration #25 of Tilt-Series #48.
CCMS(rotations) = 0.13424 for Iteration #25 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00582 for iteration 25 of Tilt-Series #48.
Alignment quality for Iteration #25 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0063 for Iteration #26 of Tilt-Series #48.
CCMS(rotations) = 0.17875 for Iteration #26 of Tilt-Series #48.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00672 for iteration 26 of Tilt-Series #48.
Alignment quality for Iteration #26 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #48 (17aug18i): Very StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #27 of Tilt-Series #48.
CCMS(rotations) = 0.18303 for Iteration #27 of Tilt-Series #48.
CCMS(scale) = 0.00232 for Iteration #27 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00484 for iteration 27 of Tilt-Series #48.
Alignment quality for Iteration #27 of Tilt-Series #48 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #48 (17aug18i): 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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00512 for Iteration #28 of Tilt-Series #48.
CCMS(rotations) = 0.17693 for Iteration #28 of Tilt-Series #48.
CCMS(scale) = 0.00261 for Iteration #28 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00493 for iteration 28 of Tilt-Series #48.
Alignment quality for Iteration #28 of Tilt-Series #48 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #48 (17aug18i): StableCreating 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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #29 of Tilt-Series #48.
CCMS(rotations) = 0.17352 for Iteration #29 of Tilt-Series #48.
CCMS(scale) = 0.00241 for Iteration #29 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00474 for iteration 29 of Tilt-Series #48.
Alignment quality for Iteration #29 of Tilt-Series #48 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #48 (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 #48 (tiltseries0048_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #48 (tiltseries0048_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00495 for Iteration #30 of Tilt-Series #48.
CCMS(rotations) = 0.19726 for Iteration #30 of Tilt-Series #48.
CCMS(scale) = 0.00266 for Iteration #30 of Tilt-Series #48.
The scaled sum of CCMS values is #0.00517 for iteration 30 of Tilt-Series #48.
Alignment quality for Iteration #30 of Tilt-Series #48 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #48 (17aug18i): 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 #48 (tiltseries0048_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: 2017yr09m08d-00hr11m51s