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/tiltseries0014_thick100 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=2076.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=3685 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle=24,-33 --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0014_thick100 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=14 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=100 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node09
Start time: 2017yr09m04d-15hr04m59s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0014.tlt to series0014.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #14 (tiltseries0014_thick100)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 30.0604528399
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 = 30.0604528399
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06138 for Iteration #1 of Tilt-Series #14.
CCMS(rotations) = 1.46515 for Iteration #1 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #14.
The scaled sum of CCMS values is #0.05999 for iteration 1 of Tilt-Series #14.
Alignment quality for Iteration #1 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00595 for Iteration #2 of Tilt-Series #14.
CCMS(rotations) = 0.12935 for Iteration #2 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00556 for iteration 2 of Tilt-Series #14.
Alignment quality for Iteration #2 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00591 for Iteration #3 of Tilt-Series #14.
CCMS(rotations) = 0.17506 for Iteration #3 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00646 for iteration 3 of Tilt-Series #14.
Alignment quality for Iteration #3 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00625 for Iteration #4 of Tilt-Series #14.
CCMS(rotations) = 0.17919 for Iteration #4 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00671 for iteration 4 of Tilt-Series #14.
Alignment quality for Iteration #4 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00576 for Iteration #5 of Tilt-Series #14.
CCMS(rotations) = 0.17499 for Iteration #5 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00638 for iteration 5 of Tilt-Series #14.
Alignment quality for Iteration #5 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 60.1209056798
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 = 60.1209056798
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #6 of Tilt-Series #14.
CCMS(rotations) = 0.12781 for Iteration #6 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00596 for iteration 6 of Tilt-Series #14.
Alignment quality for Iteration #6 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00688 for Iteration #7 of Tilt-Series #14.
CCMS(rotations) = 0.17423 for Iteration #7 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00692 for iteration 7 of Tilt-Series #14.
Alignment quality for Iteration #7 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00692 for Iteration #8 of Tilt-Series #14.
CCMS(rotations) = 0.17689 for Iteration #8 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #14.
The scaled sum of CCMS values is #0.007 for iteration 8 of Tilt-Series #14.
Alignment quality for Iteration #8 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00693 for Iteration #9 of Tilt-Series #14.
CCMS(rotations) = 0.17369 for Iteration #9 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00694 for iteration 9 of Tilt-Series #14.
Alignment quality for Iteration #9 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #10 of Tilt-Series #14.
CCMS(rotations) = 0.16678 for Iteration #10 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00677 for iteration 10 of Tilt-Series #14.
Alignment quality for Iteration #10 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00683 for Iteration #11 of Tilt-Series #14.
CCMS(rotations) = 0.16912 for Iteration #11 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #14.
The scaled sum of CCMS values is #0.0068 for iteration 11 of Tilt-Series #14.
Alignment quality for Iteration #11 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00684 for Iteration #12 of Tilt-Series #14.
CCMS(rotations) = 0.18355 for Iteration #12 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00709 for iteration 12 of Tilt-Series #14.
Alignment quality for Iteration #12 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00684 for Iteration #13 of Tilt-Series #14.
CCMS(rotations) = 0.16411 for Iteration #13 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #14.
The scaled sum of CCMS values is #0.0067 for iteration 13 of Tilt-Series #14.
Alignment quality for Iteration #13 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00671 for Iteration #14 of Tilt-Series #14.
CCMS(rotations) = 0.17067 for Iteration #14 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00677 for iteration 14 of Tilt-Series #14.
Alignment quality for Iteration #14 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00684 for Iteration #15 of Tilt-Series #14.
CCMS(rotations) = 0.17801 for Iteration #15 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00698 for iteration 15 of Tilt-Series #14.
Alignment quality for Iteration #15 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 120.24181136
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 = 120.24181136
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00565 for Iteration #16 of Tilt-Series #14.
CCMS(rotations) = 0.21563 for Iteration #16 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00714 for iteration 16 of Tilt-Series #14.
Alignment quality for Iteration #16 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #17 of Tilt-Series #14.
CCMS(rotations) = 0.24749 for Iteration #17 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00777 for iteration 17 of Tilt-Series #14.
Alignment quality for Iteration #17 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00562 for Iteration #18 of Tilt-Series #14.
CCMS(rotations) = 0.20628 for Iteration #18 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00693 for iteration 18 of Tilt-Series #14.
Alignment quality for Iteration #18 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00528 for Iteration #19 of Tilt-Series #14.
CCMS(rotations) = 0.23964 for Iteration #19 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00743 for iteration 19 of Tilt-Series #14.
Alignment quality for Iteration #19 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #20 of Tilt-Series #14.
CCMS(rotations) = 0.20431 for Iteration #20 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00685 for iteration 20 of Tilt-Series #14.
Alignment quality for Iteration #20 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 240.483622719
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 = 240.483622719
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00591 for Iteration #21 of Tilt-Series #14.
CCMS(rotations) = 0.21946 for Iteration #21 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00734 for iteration 21 of Tilt-Series #14.
Alignment quality for Iteration #21 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #14 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #22 of Tilt-Series #14.
CCMS(rotations) = 0.2437 for Iteration #22 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00774 for iteration 22 of Tilt-Series #14.
Alignment quality for Iteration #22 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #23 of Tilt-Series #14.
CCMS(rotations) = 0.28099 for Iteration #23 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00867 for iteration 23 of Tilt-Series #14.
Alignment quality for Iteration #23 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #14 (17aug18i): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00641 for Iteration #24 of Tilt-Series #14.
CCMS(rotations) = 0.21706 for Iteration #24 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00755 for iteration 24 of Tilt-Series #14.
Alignment quality for Iteration #24 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00723 for Iteration #25 of Tilt-Series #14.
CCMS(rotations) = 0.21396 for Iteration #25 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00789 for iteration 25 of Tilt-Series #14.
Alignment quality for Iteration #25 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00676 for Iteration #26 of Tilt-Series #14.
CCMS(rotations) = 0.24778 for Iteration #26 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00834 for iteration 26 of Tilt-Series #14.
Alignment quality for Iteration #26 of Tilt-Series #14 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #14 (17aug18i): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00447 for Iteration #27 of Tilt-Series #14.
CCMS(rotations) = 0.2358 for Iteration #27 of Tilt-Series #14.
CCMS(scale) = 0.00307 for Iteration #27 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00566 for iteration 27 of Tilt-Series #14.
Alignment quality for Iteration #27 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00403 for Iteration #28 of Tilt-Series #14.
CCMS(rotations) = 0.24265 for Iteration #28 of Tilt-Series #14.
CCMS(scale) = 0.00298 for Iteration #28 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00557 for iteration 28 of Tilt-Series #14.
Alignment quality for Iteration #28 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #14 (17aug18i): Rock Solid!Creating 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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00342 for Iteration #29 of Tilt-Series #14.
CCMS(rotations) = 0.23561 for Iteration #29 of Tilt-Series #14.
CCMS(scale) = 0.00325 for Iteration #29 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00537 for iteration 29 of Tilt-Series #14.
Alignment quality for Iteration #29 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #14 (tiltseries0014_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00343 for Iteration #30 of Tilt-Series #14.
CCMS(rotations) = 0.24491 for Iteration #30 of Tilt-Series #14.
CCMS(scale) = 0.0028 for Iteration #30 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00534 for iteration 30 of Tilt-Series #14.
Alignment quality for Iteration #30 of Tilt-Series #14 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #14 (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 #14 (tiltseries0014_thick100)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m05d-14hr37m33s