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/tiltseries0049_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= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0049_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=49 --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

node08
Start time: 2017yr09m06d-17hr31m11s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0049.tlt to series0049.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #49 (tiltseries0049_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 = 31.5927204002
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 = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06474 for Iteration #1 of Tilt-Series #49.
CCMS(rotations) = 2.6382 for Iteration #1 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #49.
The scaled sum of CCMS values is #0.08513 for iteration 1 of Tilt-Series #49.
Alignment quality for Iteration #1 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00519 for Iteration #2 of Tilt-Series #49.
CCMS(rotations) = 0.17652 for Iteration #2 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00612 for iteration 2 of Tilt-Series #49.
Alignment quality for Iteration #2 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #3 of Tilt-Series #49.
CCMS(rotations) = 0.13967 for Iteration #3 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00513 for iteration 3 of Tilt-Series #49.
Alignment quality for Iteration #3 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00449 for Iteration #4 of Tilt-Series #49.
CCMS(rotations) = 0.13942 for Iteration #4 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00503 for iteration 4 of Tilt-Series #49.
Alignment quality for Iteration #4 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #5 of Tilt-Series #49.
CCMS(rotations) = 0.13712 for Iteration #5 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00526 for iteration 5 of Tilt-Series #49.
Alignment quality for Iteration #5 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #49 (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 #49 (tiltseries0049_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 = 63.1854408003
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 = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00497 for Iteration #6 of Tilt-Series #49.
CCMS(rotations) = 0.16376 for Iteration #6 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00576 for iteration 6 of Tilt-Series #49.
Alignment quality for Iteration #6 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #49 (17aug18i): Very StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00487 for Iteration #7 of Tilt-Series #49.
CCMS(rotations) = 0.12577 for Iteration #7 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00495 for iteration 7 of Tilt-Series #49.
Alignment quality for Iteration #7 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00476 for Iteration #8 of Tilt-Series #49.
CCMS(rotations) = 0.13174 for Iteration #8 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00502 for iteration 8 of Tilt-Series #49.
Alignment quality for Iteration #8 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0048 for Iteration #9 of Tilt-Series #49.
CCMS(rotations) = 0.12972 for Iteration #9 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00499 for iteration 9 of Tilt-Series #49.
Alignment quality for Iteration #9 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #10 of Tilt-Series #49.
CCMS(rotations) = 0.12578 for Iteration #10 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00485 for iteration 10 of Tilt-Series #49.
Alignment quality for Iteration #10 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #11 of Tilt-Series #49.
CCMS(rotations) = 0.12168 for Iteration #11 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00483 for iteration 11 of Tilt-Series #49.
Alignment quality for Iteration #11 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #12 of Tilt-Series #49.
CCMS(rotations) = 0.13005 for Iteration #12 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00499 for iteration 12 of Tilt-Series #49.
Alignment quality for Iteration #12 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00469 for Iteration #13 of Tilt-Series #49.
CCMS(rotations) = 0.12097 for Iteration #13 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00476 for iteration 13 of Tilt-Series #49.
Alignment quality for Iteration #13 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00478 for Iteration #14 of Tilt-Series #49.
CCMS(rotations) = 0.12845 for Iteration #14 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00496 for iteration 14 of Tilt-Series #49.
Alignment quality for Iteration #14 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00463 for Iteration #15 of Tilt-Series #49.
CCMS(rotations) = 0.12663 for Iteration #15 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00485 for iteration 15 of Tilt-Series #49.
Alignment quality for Iteration #15 of Tilt-Series #49 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #49 (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 #49 (tiltseries0049_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 = 126.370881601
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 = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00664 for Iteration #16 of Tilt-Series #49.
CCMS(rotations) = 0.15898 for Iteration #16 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #49.
The scaled sum of CCMS values is #0.0065 for iteration 16 of Tilt-Series #49.
Alignment quality for Iteration #16 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00629 for Iteration #17 of Tilt-Series #49.
CCMS(rotations) = 0.17624 for Iteration #17 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00667 for iteration 17 of Tilt-Series #49.
Alignment quality for Iteration #17 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00663 for Iteration #18 of Tilt-Series #49.
CCMS(rotations) = 0.1561 for Iteration #18 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00643 for iteration 18 of Tilt-Series #49.
Alignment quality for Iteration #18 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00687 for Iteration #19 of Tilt-Series #49.
CCMS(rotations) = 0.15436 for Iteration #19 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00652 for iteration 19 of Tilt-Series #49.
Alignment quality for Iteration #19 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #20 of Tilt-Series #49.
CCMS(rotations) = 0.1623 for Iteration #20 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00626 for iteration 20 of Tilt-Series #49.
Alignment quality for Iteration #20 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #49 (17aug18i): Very StableCreating 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 #49 (tiltseries0049_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 = 252.741763201
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 = 252.741763201
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00883 for Iteration #21 of Tilt-Series #49.
CCMS(rotations) = 0.19936 for Iteration #21 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #49.
The scaled sum of CCMS values is #0.0084 for iteration 21 of Tilt-Series #49.
Alignment quality for Iteration #21 of Tilt-Series #49 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00864 for Iteration #22 of Tilt-Series #49.
CCMS(rotations) = 0.22713 for Iteration #22 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00886 for iteration 22 of Tilt-Series #49.
Alignment quality for Iteration #22 of Tilt-Series #49 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00802 for Iteration #23 of Tilt-Series #49.
CCMS(rotations) = 0.13599 for Iteration #23 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00673 for iteration 23 of Tilt-Series #49.
Alignment quality for Iteration #23 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.0094 for Iteration #24 of Tilt-Series #49.
CCMS(rotations) = 0.29123 for Iteration #24 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #49.
The scaled sum of CCMS values is #0.01053 for iteration 24 of Tilt-Series #49.
Alignment quality for Iteration #24 of Tilt-Series #49 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #49 (17aug18i): StableCreating 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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00832 for Iteration #25 of Tilt-Series #49.
CCMS(rotations) = 0.1297 for Iteration #25 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00675 for iteration 25 of Tilt-Series #49.
Alignment quality for Iteration #25 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #49 (17aug18i): UnstableCreating 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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00893 for Iteration #26 of Tilt-Series #49.
CCMS(rotations) = 0.18655 for Iteration #26 of Tilt-Series #49.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00819 for iteration 26 of Tilt-Series #49.
Alignment quality for Iteration #26 of Tilt-Series #49 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00959 for Iteration #27 of Tilt-Series #49.
CCMS(rotations) = 0.13163 for Iteration #27 of Tilt-Series #49.
CCMS(scale) = 0.00345 for Iteration #27 of Tilt-Series #49.
The scaled sum of CCMS values is #0.0061 for iteration 27 of Tilt-Series #49.
Alignment quality for Iteration #27 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #28 of Tilt-Series #49.
CCMS(rotations) = 0.28087 for Iteration #28 of Tilt-Series #49.
CCMS(scale) = 0.00333 for Iteration #28 of Tilt-Series #49.
The scaled sum of CCMS values is #0.0073 for iteration 28 of Tilt-Series #49.
Alignment quality for Iteration #28 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #49 (17aug18i): StableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00516 for Iteration #29 of Tilt-Series #49.
CCMS(rotations) = 0.18985 for Iteration #29 of Tilt-Series #49.
CCMS(scale) = 0.00396 for Iteration #29 of Tilt-Series #49.
The scaled sum of CCMS values is #0.00557 for iteration 29 of Tilt-Series #49.
Alignment quality for Iteration #29 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #49 (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 #49 (tiltseries0049_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #49 (tiltseries0049_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.007 for Iteration #30 of Tilt-Series #49.
CCMS(rotations) = 0.24532 for Iteration #30 of Tilt-Series #49.
CCMS(scale) = 0.00359 for Iteration #30 of Tilt-Series #49.
The scaled sum of CCMS values is #0.0068 for iteration 30 of Tilt-Series #49.
Alignment quality for Iteration #30 of Tilt-Series #49 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #49 (17aug18i): StableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #49 (tiltseries0049_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: 2017yr09m08d-00hr02m38s