protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-12.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0016_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=tiltseries0016_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=16 --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

node11
Start time: 2017yr09m04d-15hr14m15s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0016.tlt to series0016.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #16 (tiltseries0016_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 = 31.5932717154
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 = 31.5932717154
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04246 for Iteration #1 of Tilt-Series #16.
CCMS(rotations) = 0.96775 for Iteration #1 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #16.
The scaled sum of CCMS values is #0.04058 for iteration 1 of Tilt-Series #16.
Alignment quality for Iteration #1 of Tilt-Series #16 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.655172%)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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00405 for Iteration #2 of Tilt-Series #16.
CCMS(rotations) = 0.13523 for Iteration #2 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00473 for iteration 2 of Tilt-Series #16.
Alignment quality for Iteration #2 of Tilt-Series #16 (17aug18i): Perfection! (confidence: 0.655172%)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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #3 of Tilt-Series #16.
CCMS(rotations) = 0.12668 for Iteration #3 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00446 for iteration 3 of Tilt-Series #16.
Alignment quality for Iteration #3 of Tilt-Series #16 (17aug18i): Perfection! (confidence: 0.655172%)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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #4 of Tilt-Series #16.
CCMS(rotations) = 0.21436 for Iteration #4 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00626 for iteration 4 of Tilt-Series #16.
Alignment quality for Iteration #4 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00433 for Iteration #5 of Tilt-Series #16.
CCMS(rotations) = 0.11652 for Iteration #5 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0045 for iteration 5 of Tilt-Series #16.
Alignment quality for Iteration #5 of Tilt-Series #16 (17aug18i): Perfection! (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #16 (17aug18i): UnstableCreating 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 #16 (tiltseries0016_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 = 63.1865434307
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 = 63.1865434307
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00464 for Iteration #6 of Tilt-Series #16.
CCMS(rotations) = 0.13558 for Iteration #6 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00503 for iteration 6 of Tilt-Series #16.
Alignment quality for Iteration #6 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00347 for Iteration #7 of Tilt-Series #16.
CCMS(rotations) = 0.17382 for Iteration #7 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00521 for iteration 7 of Tilt-Series #16.
Alignment quality for Iteration #7 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00348 for Iteration #8 of Tilt-Series #16.
CCMS(rotations) = 0.16376 for Iteration #8 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00501 for iteration 8 of Tilt-Series #16.
Alignment quality for Iteration #8 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #16 (17aug18i): Very StableCreating 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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00354 for Iteration #9 of Tilt-Series #16.
CCMS(rotations) = 0.16325 for Iteration #9 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00504 for iteration 9 of Tilt-Series #16.
Alignment quality for Iteration #9 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00348 for Iteration #10 of Tilt-Series #16.
CCMS(rotations) = 0.17005 for Iteration #10 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00514 for iteration 10 of Tilt-Series #16.
Alignment quality for Iteration #10 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00342 for Iteration #11 of Tilt-Series #16.
CCMS(rotations) = 0.18254 for Iteration #11 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00536 for iteration 11 of Tilt-Series #16.
Alignment quality for Iteration #11 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #12 of Tilt-Series #16.
CCMS(rotations) = 0.16464 for Iteration #12 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00504 for iteration 12 of Tilt-Series #16.
Alignment quality for Iteration #12 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00351 for Iteration #13 of Tilt-Series #16.
CCMS(rotations) = 0.17197 for Iteration #13 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0052 for iteration 13 of Tilt-Series #16.
Alignment quality for Iteration #13 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00344 for Iteration #14 of Tilt-Series #16.
CCMS(rotations) = 0.16655 for Iteration #14 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00505 for iteration 14 of Tilt-Series #16.
Alignment quality for Iteration #14 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00342 for Iteration #15 of Tilt-Series #16.
CCMS(rotations) = 0.17411 for Iteration #15 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00519 for iteration 15 of Tilt-Series #16.
Alignment quality for Iteration #15 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #16 (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 #16 (tiltseries0016_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 = 126.373086861
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 = 126.373086861
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00405 for Iteration #16 of Tilt-Series #16.
CCMS(rotations) = 0.22192 for Iteration #16 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00646 for iteration 16 of Tilt-Series #16.
Alignment quality for Iteration #16 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #16 (17aug18i): UnstableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00373 for Iteration #17 of Tilt-Series #16.
CCMS(rotations) = 0.28124 for Iteration #17 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00749 for iteration 17 of Tilt-Series #16.
Alignment quality for Iteration #17 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #18 of Tilt-Series #16.
CCMS(rotations) = 0.29267 for Iteration #18 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00775 for iteration 18 of Tilt-Series #16.
Alignment quality for Iteration #18 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #19 of Tilt-Series #16.
CCMS(rotations) = 0.29525 for Iteration #19 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00776 for iteration 19 of Tilt-Series #16.
Alignment quality for Iteration #19 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #20 of Tilt-Series #16.
CCMS(rotations) = 0.29152 for Iteration #20 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00768 for iteration 20 of Tilt-Series #16.
Alignment quality for Iteration #20 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #16 (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 #16 (tiltseries0016_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 = 252.746173723
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 = 252.746173723
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #21 of Tilt-Series #16.
CCMS(rotations) = 0.33563 for Iteration #21 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00976 for iteration 21 of Tilt-Series #16.
Alignment quality for Iteration #21 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #16 (17aug18i): UnstableCreating 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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #22 of Tilt-Series #16.
CCMS(rotations) = 0.41929 for Iteration #22 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01119 for iteration 22 of Tilt-Series #16.
Alignment quality for Iteration #22 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #23 of Tilt-Series #16.
CCMS(rotations) = 0.45709 for Iteration #23 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01184 for iteration 23 of Tilt-Series #16.
Alignment quality for Iteration #23 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #16 (17aug18i): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00555 for Iteration #24 of Tilt-Series #16.
CCMS(rotations) = 0.43608 for Iteration #24 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01149 for iteration 24 of Tilt-Series #16.
Alignment quality for Iteration #24 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #16 (17aug18i): UnstableCreating 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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #25 of Tilt-Series #16.
CCMS(rotations) = 0.45908 for Iteration #25 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01182 for iteration 25 of Tilt-Series #16.
Alignment quality for Iteration #25 of Tilt-Series #16 (17aug18i): Very Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00543 for Iteration #26 of Tilt-Series #16.
CCMS(rotations) = 0.50084 for Iteration #26 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01273 for iteration 26 of Tilt-Series #16.
Alignment quality for Iteration #26 of Tilt-Series #16 (17aug18i): Good (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #16 (17aug18i): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00481 for Iteration #27 of Tilt-Series #16.
CCMS(rotations) = 0.30932 for Iteration #27 of Tilt-Series #16.
CCMS(scale) = 0.00193 for Iteration #27 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00637 for iteration 27 of Tilt-Series #16.
Alignment quality for Iteration #27 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #28 of Tilt-Series #16.
CCMS(rotations) = 0.37146 for Iteration #28 of Tilt-Series #16.
CCMS(scale) = 0.00182 for Iteration #28 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00723 for iteration 28 of Tilt-Series #16.
Alignment quality for Iteration #28 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #16 (17aug18i): UnstableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00504 for Iteration #29 of Tilt-Series #16.
CCMS(rotations) = 0.28011 for Iteration #29 of Tilt-Series #16.
CCMS(scale) = 0.00185 for Iteration #29 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00603 for iteration 29 of Tilt-Series #16.
Alignment quality for Iteration #29 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #16 (tiltseries0016_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00413 for Iteration #30 of Tilt-Series #16.
CCMS(rotations) = 0.3376 for Iteration #30 of Tilt-Series #16.
CCMS(scale) = 0.00215 for Iteration #30 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00659 for iteration 30 of Tilt-Series #16.
Alignment quality for Iteration #30 of Tilt-Series #16 (17aug18i): Excellent (confidence: 0.655172%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #16 (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 #16 (tiltseries0016_thick100)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr09m05d-10hr37m24s