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/tiltseries0009_thick150 --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=tiltseries0009_thick150 --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=9 --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=150 --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

node04
Start time: 2017yr09m04d-14hr14m58s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0009.tlt to series0009.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #9 (tiltseries0009_thick150)
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 = 47.389907573
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 = 47.389907573
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.11756 for Iteration #1 of Tilt-Series #9.
CCMS(rotations) = 1.27037 for Iteration #1 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #9.
The scaled sum of CCMS values is #0.08419 for iteration 1 of Tilt-Series #9.
Alignment quality for Iteration #1 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03924 for Iteration #2 of Tilt-Series #9.
CCMS(rotations) = 0.28444 for Iteration #2 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #9.
The scaled sum of CCMS values is #0.02531 for iteration 2 of Tilt-Series #9.
Alignment quality for Iteration #2 of Tilt-Series #9 (17aug18i): Okay (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #3 of Tilt-Series #9.
CCMS(rotations) = 0.21666 for Iteration #3 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00715 for iteration 3 of Tilt-Series #9.
Alignment quality for Iteration #3 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00529 for Iteration #4 of Tilt-Series #9.
CCMS(rotations) = 0.21324 for Iteration #4 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00691 for iteration 4 of Tilt-Series #9.
Alignment quality for Iteration #4 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00463 for Iteration #5 of Tilt-Series #9.
CCMS(rotations) = 0.19853 for Iteration #5 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00628 for iteration 5 of Tilt-Series #9.
Alignment quality for Iteration #5 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)
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 = 94.7798151461
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 = 94.7798151461
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.0067 for Iteration #6 of Tilt-Series #9.
CCMS(rotations) = 0.27344 for Iteration #6 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00882 for iteration 6 of Tilt-Series #9.
Alignment quality for Iteration #6 of Tilt-Series #9 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #7 of Tilt-Series #9.
CCMS(rotations) = 0.14681 for Iteration #7 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00557 for iteration 7 of Tilt-Series #9.
Alignment quality for Iteration #7 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00509 for Iteration #8 of Tilt-Series #9.
CCMS(rotations) = 0.17318 for Iteration #8 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00601 for iteration 8 of Tilt-Series #9.
Alignment quality for Iteration #8 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0049 for Iteration #9 of Tilt-Series #9.
CCMS(rotations) = 0.17178 for Iteration #9 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00589 for iteration 9 of Tilt-Series #9.
Alignment quality for Iteration #9 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00506 for Iteration #10 of Tilt-Series #9.
CCMS(rotations) = 0.1769 for Iteration #10 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00607 for iteration 10 of Tilt-Series #9.
Alignment quality for Iteration #10 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00528 for Iteration #11 of Tilt-Series #9.
CCMS(rotations) = 0.13392 for Iteration #11 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00532 for iteration 11 of Tilt-Series #9.
Alignment quality for Iteration #11 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #9 (17aug18i): UnstableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00579 for Iteration #12 of Tilt-Series #9.
CCMS(rotations) = 0.21568 for Iteration #12 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00721 for iteration 12 of Tilt-Series #9.
Alignment quality for Iteration #12 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #9 (17aug18i): UnstableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #13 of Tilt-Series #9.
CCMS(rotations) = 0.15512 for Iteration #13 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00566 for iteration 13 of Tilt-Series #9.
Alignment quality for Iteration #13 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00512 for Iteration #14 of Tilt-Series #9.
CCMS(rotations) = 0.15121 for Iteration #14 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00558 for iteration 14 of Tilt-Series #9.
Alignment quality for Iteration #14 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.005 for Iteration #15 of Tilt-Series #9.
CCMS(rotations) = 0.16304 for Iteration #15 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00576 for iteration 15 of Tilt-Series #9.
Alignment quality for Iteration #15 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)
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 = 189.559630292
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 = 189.559630292
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00749 for Iteration #16 of Tilt-Series #9.
CCMS(rotations) = 0.25591 for Iteration #16 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00886 for iteration 16 of Tilt-Series #9.
Alignment quality for Iteration #16 of Tilt-Series #9 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #9 (17aug18i): UnstableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00856 for Iteration #17 of Tilt-Series #9.
CCMS(rotations) = 0.14544 for Iteration #17 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00719 for iteration 17 of Tilt-Series #9.
Alignment quality for Iteration #17 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #9 (17aug18i): UnstableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00913 for Iteration #18 of Tilt-Series #9.
CCMS(rotations) = 0.26911 for Iteration #18 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00995 for iteration 18 of Tilt-Series #9.
Alignment quality for Iteration #18 of Tilt-Series #9 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #9 (17aug18i): UnstableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00851 for Iteration #19 of Tilt-Series #9.
CCMS(rotations) = 0.16595 for Iteration #19 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00757 for iteration 19 of Tilt-Series #9.
Alignment quality for Iteration #19 of Tilt-Series #9 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #9 (17aug18i): Very StableCreating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00575 for Iteration #20 of Tilt-Series #9.
CCMS(rotations) = 0.19258 for Iteration #20 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00673 for iteration 20 of Tilt-Series #9.
Alignment quality for Iteration #20 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)
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 = 379.119260584
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 = 379.119260584
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00735 for Iteration #21 of Tilt-Series #9.
CCMS(rotations) = 0.14207 for Iteration #21 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00652 for iteration 21 of Tilt-Series #9.
Alignment quality for Iteration #21 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00807 for Iteration #22 of Tilt-Series #9.
CCMS(rotations) = 0.14896 for Iteration #22 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00702 for iteration 22 of Tilt-Series #9.
Alignment quality for Iteration #22 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00964 for Iteration #23 of Tilt-Series #9.
CCMS(rotations) = 0.20928 for Iteration #23 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #9.
The scaled sum of CCMS values is #0.009 for iteration 23 of Tilt-Series #9.
Alignment quality for Iteration #23 of Tilt-Series #9 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00873 for Iteration #24 of Tilt-Series #9.
CCMS(rotations) = 0.15268 for Iteration #24 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00742 for iteration 24 of Tilt-Series #9.
Alignment quality for Iteration #24 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00886 for Iteration #25 of Tilt-Series #9.
CCMS(rotations) = 0.12012 for Iteration #25 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00683 for iteration 25 of Tilt-Series #9.
Alignment quality for Iteration #25 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00679 for Iteration #26 of Tilt-Series #9.
CCMS(rotations) = 0.18146 for Iteration #26 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00702 for iteration 26 of Tilt-Series #9.
Alignment quality for Iteration #26 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #27 of Tilt-Series #9.
CCMS(rotations) = 0.18087 for Iteration #27 of Tilt-Series #9.
CCMS(scale) = 0.00225 for Iteration #27 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00483 for iteration 27 of Tilt-Series #9.
Alignment quality for Iteration #27 of Tilt-Series #9 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #9 (17aug18i): Rock Solid!Creating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.006 for Iteration #28 of Tilt-Series #9.
CCMS(rotations) = 0.14673 for Iteration #28 of Tilt-Series #9.
CCMS(scale) = 0.00254 for Iteration #28 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0048 for iteration 28 of Tilt-Series #9.
Alignment quality for Iteration #28 of Tilt-Series #9 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #9 (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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #29 of Tilt-Series #9.
CCMS(rotations) = 0.21225 for Iteration #29 of Tilt-Series #9.
CCMS(scale) = 0.00317 for Iteration #29 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00572 for iteration 29 of Tilt-Series #9.
Alignment quality for Iteration #29 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #9 (17aug18i): Very StableCreating 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 #9 (tiltseries0009_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #9 (tiltseries0009_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #30 of Tilt-Series #9.
CCMS(rotations) = 0.23311 for Iteration #30 of Tilt-Series #9.
CCMS(scale) = 0.0028 for Iteration #30 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00605 for iteration 30 of Tilt-Series #9.
Alignment quality for Iteration #30 of Tilt-Series #9 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #9 (17aug18i): Very StableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #9 (tiltseries0009_thick150)!
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: 2017yr09m05d-19hr43m18s