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/tiltseries0046_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=2076.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=3685 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0046_thick50 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=46 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node05
Start time: 2017yr09m06d-17hr21m50s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0046.tlt to series0046.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #46 (tiltseries0046_thick50)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 15.7963602001
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 15.7963602001
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.08357 for Iteration #1 of Tilt-Series #46.
CCMS(rotations) = 2.7364 for Iteration #1 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #46.
The scaled sum of CCMS values is #0.09652 for iteration 1 of Tilt-Series #46.
Alignment quality for Iteration #1 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.0079 for Iteration #2 of Tilt-Series #46.
CCMS(rotations) = 0.21499 for Iteration #2 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00825 for iteration 2 of Tilt-Series #46.
Alignment quality for Iteration #2 of Tilt-Series #46 (17aug18i): Very Good (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00756 for Iteration #3 of Tilt-Series #46.
CCMS(rotations) = 0.2028 for Iteration #3 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00784 for iteration 3 of Tilt-Series #46.
Alignment quality for Iteration #3 of Tilt-Series #46 (17aug18i): Very Good (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00796 for Iteration #4 of Tilt-Series #46.
CCMS(rotations) = 0.19456 for Iteration #4 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00787 for iteration 4 of Tilt-Series #46.
Alignment quality for Iteration #4 of Tilt-Series #46 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00734 for Iteration #5 of Tilt-Series #46.
CCMS(rotations) = 0.19692 for Iteration #5 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00761 for iteration 5 of Tilt-Series #46.
Alignment quality for Iteration #5 of Tilt-Series #46 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 31.5927204002
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 31.5927204002
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00677 for Iteration #6 of Tilt-Series #46.
CCMS(rotations) = 0.22623 for Iteration #6 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00791 for iteration 6 of Tilt-Series #46.
Alignment quality for Iteration #6 of Tilt-Series #46 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #46 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00705 for Iteration #7 of Tilt-Series #46.
CCMS(rotations) = 0.13971 for Iteration #7 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00632 for iteration 7 of Tilt-Series #46.
Alignment quality for Iteration #7 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00696 for Iteration #8 of Tilt-Series #46.
CCMS(rotations) = 0.14411 for Iteration #8 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00636 for iteration 8 of Tilt-Series #46.
Alignment quality for Iteration #8 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00705 for Iteration #9 of Tilt-Series #46.
CCMS(rotations) = 0.14333 for Iteration #9 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00639 for iteration 9 of Tilt-Series #46.
Alignment quality for Iteration #9 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #10 of Tilt-Series #46.
CCMS(rotations) = 0.1475 for Iteration #10 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00632 for iteration 10 of Tilt-Series #46.
Alignment quality for Iteration #10 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00696 for Iteration #11 of Tilt-Series #46.
CCMS(rotations) = 0.1421 for Iteration #11 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00632 for iteration 11 of Tilt-Series #46.
Alignment quality for Iteration #11 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00693 for Iteration #12 of Tilt-Series #46.
CCMS(rotations) = 0.14411 for Iteration #12 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00635 for iteration 12 of Tilt-Series #46.
Alignment quality for Iteration #12 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00676 for Iteration #13 of Tilt-Series #46.
CCMS(rotations) = 0.14259 for Iteration #13 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00623 for iteration 13 of Tilt-Series #46.
Alignment quality for Iteration #13 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00696 for Iteration #14 of Tilt-Series #46.
CCMS(rotations) = 0.13922 for Iteration #14 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00626 for iteration 14 of Tilt-Series #46.
Alignment quality for Iteration #14 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00696 for Iteration #15 of Tilt-Series #46.
CCMS(rotations) = 0.14427 for Iteration #15 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00636 for iteration 15 of Tilt-Series #46.
Alignment quality for Iteration #15 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 63.1854408003
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 63.1854408003
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #16 of Tilt-Series #46.
CCMS(rotations) = 0.17027 for Iteration #16 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00633 for iteration 16 of Tilt-Series #46.
Alignment quality for Iteration #16 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00572 for Iteration #17 of Tilt-Series #46.
CCMS(rotations) = 0.14171 for Iteration #17 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #46.
The scaled sum of CCMS values is #0.0057 for iteration 17 of Tilt-Series #46.
Alignment quality for Iteration #17 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #18 of Tilt-Series #46.
CCMS(rotations) = 0.13269 for Iteration #18 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #46.
The scaled sum of CCMS values is #0.0057 for iteration 18 of Tilt-Series #46.
Alignment quality for Iteration #18 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00617 for Iteration #19 of Tilt-Series #46.
CCMS(rotations) = 0.13987 for Iteration #19 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00588 for iteration 19 of Tilt-Series #46.
Alignment quality for Iteration #19 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00606 for Iteration #20 of Tilt-Series #46.
CCMS(rotations) = 0.13476 for Iteration #20 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00573 for iteration 20 of Tilt-Series #46.
Alignment quality for Iteration #20 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 126.370881601
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 126.370881601
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00719 for Iteration #21 of Tilt-Series #46.
CCMS(rotations) = 0.14422 for Iteration #21 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00648 for iteration 21 of Tilt-Series #46.
Alignment quality for Iteration #21 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00711 for Iteration #22 of Tilt-Series #46.
CCMS(rotations) = 0.15721 for Iteration #22 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #46.
The scaled sum of CCMS values is #0.0067 for iteration 22 of Tilt-Series #46.
Alignment quality for Iteration #22 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #23 of Tilt-Series #46.
CCMS(rotations) = 0.15666 for Iteration #23 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00679 for iteration 23 of Tilt-Series #46.
Alignment quality for Iteration #23 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #24 of Tilt-Series #46.
CCMS(rotations) = 0.14731 for Iteration #24 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00637 for iteration 24 of Tilt-Series #46.
Alignment quality for Iteration #24 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #25 of Tilt-Series #46.
CCMS(rotations) = 0.14882 for Iteration #25 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #46.
The scaled sum of CCMS values is #0.0066 for iteration 25 of Tilt-Series #46.
Alignment quality for Iteration #25 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00706 for Iteration #26 of Tilt-Series #46.
CCMS(rotations) = 0.13714 for Iteration #26 of Tilt-Series #46.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00627 for iteration 26 of Tilt-Series #46.
Alignment quality for Iteration #26 of Tilt-Series #46 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00506 for Iteration #27 of Tilt-Series #46.
CCMS(rotations) = 0.15591 for Iteration #27 of Tilt-Series #46.
CCMS(scale) = 0.00272 for Iteration #27 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00467 for iteration 27 of Tilt-Series #46.
Alignment quality for Iteration #27 of Tilt-Series #46 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00513 for Iteration #28 of Tilt-Series #46.
CCMS(rotations) = 0.13552 for Iteration #28 of Tilt-Series #46.
CCMS(scale) = 0.00278 for Iteration #28 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00444 for iteration 28 of Tilt-Series #46.
Alignment quality for Iteration #28 of Tilt-Series #46 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #29 of Tilt-Series #46.
CCMS(rotations) = 0.14269 for Iteration #29 of Tilt-Series #46.
CCMS(scale) = 0.00304 for Iteration #29 of Tilt-Series #46.
The scaled sum of CCMS values is #0.00454 for iteration 29 of Tilt-Series #46.
Alignment quality for Iteration #29 of Tilt-Series #46 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #46 (tiltseries0046_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #30 of Tilt-Series #46.
CCMS(rotations) = 0.14686 for Iteration #30 of Tilt-Series #46.
CCMS(scale) = 0.00311 for Iteration #30 of Tilt-Series #46.
The scaled sum of CCMS values is #0.0046 for iteration 30 of Tilt-Series #46.
Alignment quality for Iteration #30 of Tilt-Series #46 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #46 (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 #46 (tiltseries0046_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m07d-22hr58m15s