protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-44.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0052_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=tiltseries0052_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=52 --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

node10
Start time: 2017yr09m06d-17hr39m02s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0052.tlt to series0052.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #52 (tiltseries0052_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) = 0.063 for Iteration #1 of Tilt-Series #52.
CCMS(rotations) = 1.59804 for Iteration #1 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #52.
The scaled sum of CCMS values is #0.06346 for iteration 1 of Tilt-Series #52.
Alignment quality for Iteration #1 of Tilt-Series #52 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.967742%)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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04628 for Iteration #2 of Tilt-Series #52.
CCMS(rotations) = 1.31073 for Iteration #2 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #52.
The scaled sum of CCMS values is #0.04935 for iteration 2 of Tilt-Series #52.
Alignment quality for Iteration #2 of Tilt-Series #52 (17aug18i): Bad (confidence: 0.967742%)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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.06389 for Iteration #3 of Tilt-Series #52.
CCMS(rotations) = 1.53595 for Iteration #3 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #52.
The scaled sum of CCMS values is #0.06266 for iteration 3 of Tilt-Series #52.
Alignment quality for Iteration #3 of Tilt-Series #52 (17aug18i): Bad (confidence: 0.967742%)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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.06259 for Iteration #4 of Tilt-Series #52.
CCMS(rotations) = 1.47398 for Iteration #4 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #52.
The scaled sum of CCMS values is #0.06077 for iteration 4 of Tilt-Series #52.
Alignment quality for Iteration #4 of Tilt-Series #52 (17aug18i): Bad (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #52 (17aug18i): UnstableCreating 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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00589 for Iteration #5 of Tilt-Series #52.
CCMS(rotations) = 0.15058 for Iteration #5 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00595 for iteration 5 of Tilt-Series #52.
Alignment quality for Iteration #5 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #52 (17aug18i): Very StableCreating 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 #52 (tiltseries0052_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) = 0.00472 for Iteration #6 of Tilt-Series #52.
CCMS(rotations) = 0.13203 for Iteration #6 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #52.
The scaled sum of CCMS values is #0.005 for iteration 6 of Tilt-Series #52.
Alignment quality for Iteration #6 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00441 for Iteration #7 of Tilt-Series #52.
CCMS(rotations) = 0.12 for Iteration #7 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00461 for iteration 7 of Tilt-Series #52.
Alignment quality for Iteration #7 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00433 for Iteration #8 of Tilt-Series #52.
CCMS(rotations) = 0.13057 for Iteration #8 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00478 for iteration 8 of Tilt-Series #52.
Alignment quality for Iteration #8 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00428 for Iteration #9 of Tilt-Series #52.
CCMS(rotations) = 0.12736 for Iteration #9 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00469 for iteration 9 of Tilt-Series #52.
Alignment quality for Iteration #9 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00415 for Iteration #10 of Tilt-Series #52.
CCMS(rotations) = 0.11917 for Iteration #10 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00446 for iteration 10 of Tilt-Series #52.
Alignment quality for Iteration #10 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00408 for Iteration #11 of Tilt-Series #52.
CCMS(rotations) = 0.12418 for Iteration #11 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00453 for iteration 11 of Tilt-Series #52.
Alignment quality for Iteration #11 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #12 of Tilt-Series #52.
CCMS(rotations) = 0.11955 for Iteration #12 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00447 for iteration 12 of Tilt-Series #52.
Alignment quality for Iteration #12 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00415 for Iteration #13 of Tilt-Series #52.
CCMS(rotations) = 0.12845 for Iteration #13 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00464 for iteration 13 of Tilt-Series #52.
Alignment quality for Iteration #13 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00412 for Iteration #14 of Tilt-Series #52.
CCMS(rotations) = 0.12395 for Iteration #14 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00454 for iteration 14 of Tilt-Series #52.
Alignment quality for Iteration #14 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #15 of Tilt-Series #52.
CCMS(rotations) = 0.12079 for Iteration #15 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00449 for iteration 15 of Tilt-Series #52.
Alignment quality for Iteration #15 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #52 (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 #52 (tiltseries0052_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) = 0.0055 for Iteration #16 of Tilt-Series #52.
CCMS(rotations) = 0.10778 for Iteration #16 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00491 for iteration 16 of Tilt-Series #52.
Alignment quality for Iteration #16 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #17 of Tilt-Series #52.
CCMS(rotations) = 0.14542 for Iteration #17 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00575 for iteration 17 of Tilt-Series #52.
Alignment quality for Iteration #17 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #18 of Tilt-Series #52.
CCMS(rotations) = 0.17406 for Iteration #18 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00632 for iteration 18 of Tilt-Series #52.
Alignment quality for Iteration #18 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0054 for Iteration #19 of Tilt-Series #52.
CCMS(rotations) = 0.16997 for Iteration #19 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #52.
The scaled sum of CCMS values is #0.0061 for iteration 19 of Tilt-Series #52.
Alignment quality for Iteration #19 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #20 of Tilt-Series #52.
CCMS(rotations) = 0.14735 for Iteration #20 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00571 for iteration 20 of Tilt-Series #52.
Alignment quality for Iteration #20 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #52 (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 #52 (tiltseries0052_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) = 0.00856 for Iteration #21 of Tilt-Series #52.
CCMS(rotations) = 0.15929 for Iteration #21 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00747 for iteration 21 of Tilt-Series #52.
Alignment quality for Iteration #21 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #22 of Tilt-Series #52.
CCMS(rotations) = 0.1254 for Iteration #22 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00664 for iteration 22 of Tilt-Series #52.
Alignment quality for Iteration #22 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #52 (17aug18i): UnstableCreating 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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00833 for Iteration #23 of Tilt-Series #52.
CCMS(rotations) = 0.23649 for Iteration #23 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00889 for iteration 23 of Tilt-Series #52.
Alignment quality for Iteration #23 of Tilt-Series #52 (17aug18i): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #52 (17aug18i): StableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #24 of Tilt-Series #52.
CCMS(rotations) = 0.1641 for Iteration #24 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00717 for iteration 24 of Tilt-Series #52.
Alignment quality for Iteration #24 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00819 for Iteration #25 of Tilt-Series #52.
CCMS(rotations) = 0.17797 for Iteration #25 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00766 for iteration 25 of Tilt-Series #52.
Alignment quality for Iteration #25 of Tilt-Series #52 (17aug18i): Very Good (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0077 for Iteration #26 of Tilt-Series #52.
CCMS(rotations) = 0.1692 for Iteration #26 of Tilt-Series #52.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00723 for iteration 26 of Tilt-Series #52.
Alignment quality for Iteration #26 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00638 for Iteration #27 of Tilt-Series #52.
CCMS(rotations) = 0.15943 for Iteration #27 of Tilt-Series #52.
CCMS(scale) = 0.00288 for Iteration #27 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00521 for iteration 27 of Tilt-Series #52.
Alignment quality for Iteration #27 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00593 for Iteration #28 of Tilt-Series #52.
CCMS(rotations) = 0.14273 for Iteration #28 of Tilt-Series #52.
CCMS(scale) = 0.00269 for Iteration #28 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00477 for iteration 28 of Tilt-Series #52.
Alignment quality for Iteration #28 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #29 of Tilt-Series #52.
CCMS(rotations) = 0.15364 for Iteration #29 of Tilt-Series #52.
CCMS(scale) = 0.00289 for Iteration #29 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00502 for iteration 29 of Tilt-Series #52.
Alignment quality for Iteration #29 of Tilt-Series #52 (17aug18i): Excellent (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #52 (tiltseries0052_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00661 for Iteration #30 of Tilt-Series #52.
CCMS(rotations) = 0.13629 for Iteration #30 of Tilt-Series #52.
CCMS(scale) = 0.00257 for Iteration #30 of Tilt-Series #52.
The scaled sum of CCMS values is #0.00488 for iteration 30 of Tilt-Series #52.
Alignment quality for Iteration #30 of Tilt-Series #52 (17aug18i): Perfection! (confidence: 0.967742%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #52 (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 #52 (tiltseries0052_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m08d-01hr46m24s