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/tiltseries0051_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=tiltseries0051_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=51 --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

node09
Start time: 2017yr09m06d-17hr35m18s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0051.tlt to series0051.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #51 (tiltseries0051_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 = 15.798565865
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 = 15.798565865
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0885 for Iteration #1 of Tilt-Series #51.
CCMS(rotations) = 1.311 for Iteration #1 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #51.
The scaled sum of CCMS values is #0.07047 for iteration 1 of Tilt-Series #51.
Alignment quality for Iteration #1 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00611 for Iteration #2 of Tilt-Series #51.
CCMS(rotations) = 0.12645 for Iteration #2 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00558 for iteration 2 of Tilt-Series #51.
Alignment quality for Iteration #2 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00606 for Iteration #3 of Tilt-Series #51.
CCMS(rotations) = 0.11999 for Iteration #3 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00543 for iteration 3 of Tilt-Series #51.
Alignment quality for Iteration #3 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00641 for Iteration #4 of Tilt-Series #51.
CCMS(rotations) = 0.13253 for Iteration #4 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00585 for iteration 4 of Tilt-Series #51.
Alignment quality for Iteration #4 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00567 for Iteration #5 of Tilt-Series #51.
CCMS(rotations) = 0.12628 for Iteration #5 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00536 for iteration 5 of Tilt-Series #51.
Alignment quality for Iteration #5 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #51 (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 #51 (tiltseries0051_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 = 31.5971317301
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 = 31.5971317301
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00748 for Iteration #6 of Tilt-Series #51.
CCMS(rotations) = 0.12409 for Iteration #6 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00622 for iteration 6 of Tilt-Series #51.
Alignment quality for Iteration #6 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #51 (17aug18i): Rock Solid!Creating 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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.0072 for Iteration #7 of Tilt-Series #51.
CCMS(rotations) = 0.12923 for Iteration #7 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00619 for iteration 7 of Tilt-Series #51.
Alignment quality for Iteration #7 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #8 of Tilt-Series #51.
CCMS(rotations) = 0.12791 for Iteration #8 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0061 for iteration 8 of Tilt-Series #51.
Alignment quality for Iteration #8 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0069 for Iteration #9 of Tilt-Series #51.
CCMS(rotations) = 0.13024 for Iteration #9 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00605 for iteration 9 of Tilt-Series #51.
Alignment quality for Iteration #9 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00662 for Iteration #10 of Tilt-Series #51.
CCMS(rotations) = 0.12389 for Iteration #10 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00579 for iteration 10 of Tilt-Series #51.
Alignment quality for Iteration #10 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00708 for Iteration #11 of Tilt-Series #51.
CCMS(rotations) = 0.12971 for Iteration #11 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00613 for iteration 11 of Tilt-Series #51.
Alignment quality for Iteration #11 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00713 for Iteration #12 of Tilt-Series #51.
CCMS(rotations) = 0.1312 for Iteration #12 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00619 for iteration 12 of Tilt-Series #51.
Alignment quality for Iteration #12 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0068 for Iteration #13 of Tilt-Series #51.
CCMS(rotations) = 0.13087 for Iteration #13 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00602 for iteration 13 of Tilt-Series #51.
Alignment quality for Iteration #13 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.0065 for Iteration #14 of Tilt-Series #51.
CCMS(rotations) = 0.12781 for Iteration #14 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00581 for iteration 14 of Tilt-Series #51.
Alignment quality for Iteration #14 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00679 for Iteration #15 of Tilt-Series #51.
CCMS(rotations) = 0.12946 for Iteration #15 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00598 for iteration 15 of Tilt-Series #51.
Alignment quality for Iteration #15 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #51 (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 #51 (tiltseries0051_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 = 63.1942634601
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 = 63.1942634601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #16 of Tilt-Series #51.
CCMS(rotations) = 0.17666 for Iteration #16 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0067 for iteration 16 of Tilt-Series #51.
Alignment quality for Iteration #16 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #51 (17aug18i): Rock Solid!Creating 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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00653 for Iteration #17 of Tilt-Series #51.
CCMS(rotations) = 0.1817 for Iteration #17 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0069 for iteration 17 of Tilt-Series #51.
Alignment quality for Iteration #17 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00662 for Iteration #18 of Tilt-Series #51.
CCMS(rotations) = 0.19587 for Iteration #18 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00723 for iteration 18 of Tilt-Series #51.
Alignment quality for Iteration #18 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00646 for Iteration #19 of Tilt-Series #51.
CCMS(rotations) = 0.19681 for Iteration #19 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00717 for iteration 19 of Tilt-Series #51.
Alignment quality for Iteration #19 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00651 for Iteration #20 of Tilt-Series #51.
CCMS(rotations) = 0.19103 for Iteration #20 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00708 for iteration 20 of Tilt-Series #51.
Alignment quality for Iteration #20 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #51 (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 #51 (tiltseries0051_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 = 126.38852692
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 = 126.38852692
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00859 for Iteration #21 of Tilt-Series #51.
CCMS(rotations) = 0.2141 for Iteration #21 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00858 for iteration 21 of Tilt-Series #51.
Alignment quality for Iteration #21 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00818 for Iteration #22 of Tilt-Series #51.
CCMS(rotations) = 0.25359 for Iteration #22 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00916 for iteration 22 of Tilt-Series #51.
Alignment quality for Iteration #22 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #51 (17aug18i): Rock Solid!Creating 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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00908 for Iteration #23 of Tilt-Series #51.
CCMS(rotations) = 0.21161 for Iteration #23 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00877 for iteration 23 of Tilt-Series #51.
Alignment quality for Iteration #23 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #51 (17aug18i): Rock Solid!Creating 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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #24 of Tilt-Series #51.
CCMS(rotations) = 0.2287 for Iteration #24 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0087 for iteration 24 of Tilt-Series #51.
Alignment quality for Iteration #24 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0082 for Iteration #25 of Tilt-Series #51.
CCMS(rotations) = 0.22613 for Iteration #25 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00862 for iteration 25 of Tilt-Series #51.
Alignment quality for Iteration #25 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #51 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

No Round parameters changed for Iteration #26 of Tilt-Series #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0081 for Iteration #26 of Tilt-Series #51.
CCMS(rotations) = 0.23741 for Iteration #26 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0088 for iteration 26 of Tilt-Series #51.
Alignment quality for Iteration #26 of Tilt-Series #51 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #51 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00673 for Iteration #27 of Tilt-Series #51.
CCMS(rotations) = 0.23029 for Iteration #27 of Tilt-Series #51.
CCMS(scale) = 0.00345 for Iteration #27 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00646 for iteration 27 of Tilt-Series #51.
Alignment quality for Iteration #27 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00703 for Iteration #28 of Tilt-Series #51.
CCMS(rotations) = 0.20076 for Iteration #28 of Tilt-Series #51.
CCMS(scale) = 0.00366 for Iteration #28 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00624 for iteration 28 of Tilt-Series #51.
Alignment quality for Iteration #28 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #51 (17aug18i): Very 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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00621 for Iteration #29 of Tilt-Series #51.
CCMS(rotations) = 0.22337 for Iteration #29 of Tilt-Series #51.
CCMS(scale) = 0.00434 for Iteration #29 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0065 for iteration 29 of Tilt-Series #51.
Alignment quality for Iteration #29 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #51 (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 #51 (tiltseries0051_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #51 (tiltseries0051_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00566 for Iteration #30 of Tilt-Series #51.
CCMS(rotations) = 0.22629 for Iteration #30 of Tilt-Series #51.
CCMS(scale) = 0.00378 for Iteration #30 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00616 for iteration 30 of Tilt-Series #51.
Alignment quality for Iteration #30 of Tilt-Series #51 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #51 (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 #51 (tiltseries0051_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-02hr21m06s