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/tiltseries0039_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=tiltseries0039_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=39 --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

node22
Start time: 2017yr09m06d-16hr48m32s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0039.tlt to series0039.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #39 (tiltseries0039_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 = 15.7980143622
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 = 15.7980143622
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03121 for Iteration #1 of Tilt-Series #39.
CCMS(rotations) = 1.15867 for Iteration #1 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #39.
The scaled sum of CCMS values is #0.03878 for iteration 1 of Tilt-Series #39.
Alignment quality for Iteration #1 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00703 for Iteration #2 of Tilt-Series #39.
CCMS(rotations) = 0.12123 for Iteration #2 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00594 for iteration 2 of Tilt-Series #39.
Alignment quality for Iteration #2 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00691 for Iteration #3 of Tilt-Series #39.
CCMS(rotations) = 0.1463 for Iteration #3 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00638 for iteration 3 of Tilt-Series #39.
Alignment quality for Iteration #3 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #4 of Tilt-Series #39.
CCMS(rotations) = 0.14203 for Iteration #4 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00617 for iteration 4 of Tilt-Series #39.
Alignment quality for Iteration #4 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00706 for Iteration #5 of Tilt-Series #39.
CCMS(rotations) = 0.13856 for Iteration #5 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #39.
The scaled sum of CCMS values is #0.0063 for iteration 5 of Tilt-Series #39.
Alignment quality for Iteration #5 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #39 (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 #39 (tiltseries0039_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 = 31.5960287244
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 = 31.5960287244
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #6 of Tilt-Series #39.
CCMS(rotations) = 0.10096 for Iteration #6 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00482 for iteration 6 of Tilt-Series #39.
Alignment quality for Iteration #6 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #39 (17aug18i): Very StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00546 for Iteration #7 of Tilt-Series #39.
CCMS(rotations) = 0.10421 for Iteration #7 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00481 for iteration 7 of Tilt-Series #39.
Alignment quality for Iteration #7 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00522 for Iteration #8 of Tilt-Series #39.
CCMS(rotations) = 0.09347 for Iteration #8 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00448 for iteration 8 of Tilt-Series #39.
Alignment quality for Iteration #8 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #9 of Tilt-Series #39.
CCMS(rotations) = 0.09069 for Iteration #9 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00458 for iteration 9 of Tilt-Series #39.
Alignment quality for Iteration #9 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00531 for Iteration #10 of Tilt-Series #39.
CCMS(rotations) = 0.09554 for Iteration #10 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00457 for iteration 10 of Tilt-Series #39.
Alignment quality for Iteration #10 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00532 for Iteration #11 of Tilt-Series #39.
CCMS(rotations) = 0.09571 for Iteration #11 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00458 for iteration 11 of Tilt-Series #39.
Alignment quality for Iteration #11 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00562 for Iteration #12 of Tilt-Series #39.
CCMS(rotations) = 0.09584 for Iteration #12 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00473 for iteration 12 of Tilt-Series #39.
Alignment quality for Iteration #12 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00538 for Iteration #13 of Tilt-Series #39.
CCMS(rotations) = 0.09042 for Iteration #13 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #39.
The scaled sum of CCMS values is #0.0045 for iteration 13 of Tilt-Series #39.
Alignment quality for Iteration #13 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00538 for Iteration #14 of Tilt-Series #39.
CCMS(rotations) = 0.09037 for Iteration #14 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #39.
The scaled sum of CCMS values is #0.0045 for iteration 14 of Tilt-Series #39.
Alignment quality for Iteration #14 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #15 of Tilt-Series #39.
CCMS(rotations) = 0.0951 for Iteration #15 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #39.
The scaled sum of CCMS values is #0.0046 for iteration 15 of Tilt-Series #39.
Alignment quality for Iteration #15 of Tilt-Series #39 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #39 (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 #39 (tiltseries0039_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 = 63.1920574487
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 = 63.1920574487
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0086 for Iteration #16 of Tilt-Series #39.
CCMS(rotations) = 0.10101 for Iteration #16 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00632 for iteration 16 of Tilt-Series #39.
Alignment quality for Iteration #16 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00813 for Iteration #17 of Tilt-Series #39.
CCMS(rotations) = 0.10632 for Iteration #17 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00619 for iteration 17 of Tilt-Series #39.
Alignment quality for Iteration #17 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0081 for Iteration #18 of Tilt-Series #39.
CCMS(rotations) = 0.10436 for Iteration #18 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00614 for iteration 18 of Tilt-Series #39.
Alignment quality for Iteration #18 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00803 for Iteration #19 of Tilt-Series #39.
CCMS(rotations) = 0.10346 for Iteration #19 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00608 for iteration 19 of Tilt-Series #39.
Alignment quality for Iteration #19 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00782 for Iteration #20 of Tilt-Series #39.
CCMS(rotations) = 0.10211 for Iteration #20 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00595 for iteration 20 of Tilt-Series #39.
Alignment quality for Iteration #20 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #39 (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 #39 (tiltseries0039_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 = 126.384114897
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 = 126.384114897
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00904 for Iteration #21 of Tilt-Series #39.
CCMS(rotations) = 0.16546 for Iteration #21 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00783 for iteration 21 of Tilt-Series #39.
Alignment quality for Iteration #21 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00905 for Iteration #22 of Tilt-Series #39.
CCMS(rotations) = 0.17368 for Iteration #22 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #39.
The scaled sum of CCMS values is #0.008 for iteration 22 of Tilt-Series #39.
Alignment quality for Iteration #22 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00985 for Iteration #23 of Tilt-Series #39.
CCMS(rotations) = 0.14155 for Iteration #23 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00776 for iteration 23 of Tilt-Series #39.
Alignment quality for Iteration #23 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.0092 for Iteration #24 of Tilt-Series #39.
CCMS(rotations) = 0.14651 for Iteration #24 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00753 for iteration 24 of Tilt-Series #39.
Alignment quality for Iteration #24 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #39 (17aug18i): Very StableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00955 for Iteration #25 of Tilt-Series #39.
CCMS(rotations) = 0.16757 for Iteration #25 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00813 for iteration 25 of Tilt-Series #39.
Alignment quality for Iteration #25 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.01025 for Iteration #26 of Tilt-Series #39.
CCMS(rotations) = 0.20022 for Iteration #26 of Tilt-Series #39.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00913 for iteration 26 of Tilt-Series #39.
Alignment quality for Iteration #26 of Tilt-Series #39 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00803 for Iteration #27 of Tilt-Series #39.
CCMS(rotations) = 0.19361 for Iteration #27 of Tilt-Series #39.
CCMS(scale) = 0.00331 for Iteration #27 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00636 for iteration 27 of Tilt-Series #39.
Alignment quality for Iteration #27 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00815 for Iteration #28 of Tilt-Series #39.
CCMS(rotations) = 0.17031 for Iteration #28 of Tilt-Series #39.
CCMS(scale) = 0.00372 for Iteration #28 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00623 for iteration 28 of Tilt-Series #39.
Alignment quality for Iteration #28 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #39 (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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00712 for Iteration #29 of Tilt-Series #39.
CCMS(rotations) = 0.15473 for Iteration #29 of Tilt-Series #39.
CCMS(scale) = 0.00347 for Iteration #29 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00559 for iteration 29 of Tilt-Series #39.
Alignment quality for Iteration #29 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #39 (17aug18i): StableCreating 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 #39 (tiltseries0039_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #39 (tiltseries0039_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00771 for Iteration #30 of Tilt-Series #39.
CCMS(rotations) = 0.19021 for Iteration #30 of Tilt-Series #39.
CCMS(scale) = 0.00315 for Iteration #30 of Tilt-Series #39.
The scaled sum of CCMS values is #0.00616 for iteration 30 of Tilt-Series #39.
Alignment quality for Iteration #30 of Tilt-Series #39 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #39 (17aug18i): UnstableCreating 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 #39 (tiltseries0039_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-03hr56m10s