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/tiltseries0011_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=tiltseries0011_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=11 --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

node06
Start time: 2017yr09m04d-14hr46m52s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0011.tlt to series0011.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #11 (tiltseries0011_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 = 15.7966358577
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 = 15.7966358577
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.12878 for Iteration #1 of Tilt-Series #11.
CCMS(rotations) = 0.4179 for Iteration #1 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #11.
The scaled sum of CCMS values is #0.07275 for iteration 1 of Tilt-Series #11.
Alignment quality for Iteration #1 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.1069 for Iteration #2 of Tilt-Series #11.
CCMS(rotations) = 0.53161 for Iteration #2 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #11.
The scaled sum of CCMS values is #0.06408 for iteration 2 of Tilt-Series #11.
Alignment quality for Iteration #2 of Tilt-Series #11 (17aug18i): Bad (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.14911 for Iteration #3 of Tilt-Series #11.
CCMS(rotations) = 0.95253 for Iteration #3 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0936 for iteration 3 of Tilt-Series #11.
Alignment quality for Iteration #3 of Tilt-Series #11 (17aug18i): Bad (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02151 for Iteration #4 of Tilt-Series #11.
CCMS(rotations) = 0.62708 for Iteration #4 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0233 for iteration 4 of Tilt-Series #11.
Alignment quality for Iteration #4 of Tilt-Series #11 (17aug18i): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #5 of Tilt-Series #11.
CCMS(rotations) = 0.20137 for Iteration #5 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00688 for iteration 5 of Tilt-Series #11.
Alignment quality for Iteration #5 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #11 (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 #11 (tiltseries0011_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 = 31.5932717154
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 = 31.5932717154
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00742 for Iteration #6 of Tilt-Series #11.
CCMS(rotations) = 0.20462 for Iteration #6 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0078 for iteration 6 of Tilt-Series #11.
Alignment quality for Iteration #6 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00713 for Iteration #7 of Tilt-Series #11.
CCMS(rotations) = 0.19955 for Iteration #7 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00756 for iteration 7 of Tilt-Series #11.
Alignment quality for Iteration #7 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.0071 for Iteration #8 of Tilt-Series #11.
CCMS(rotations) = 0.19089 for Iteration #8 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00737 for iteration 8 of Tilt-Series #11.
Alignment quality for Iteration #8 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00716 for Iteration #9 of Tilt-Series #11.
CCMS(rotations) = 0.20088 for Iteration #9 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0076 for iteration 9 of Tilt-Series #11.
Alignment quality for Iteration #9 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00747 for Iteration #10 of Tilt-Series #11.
CCMS(rotations) = 0.19456 for Iteration #10 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00763 for iteration 10 of Tilt-Series #11.
Alignment quality for Iteration #10 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00728 for Iteration #11 of Tilt-Series #11.
CCMS(rotations) = 0.20135 for Iteration #11 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00766 for iteration 11 of Tilt-Series #11.
Alignment quality for Iteration #11 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00736 for Iteration #12 of Tilt-Series #11.
CCMS(rotations) = 0.19766 for Iteration #12 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00763 for iteration 12 of Tilt-Series #11.
Alignment quality for Iteration #12 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #13 of Tilt-Series #11.
CCMS(rotations) = 0.2032 for Iteration #13 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00769 for iteration 13 of Tilt-Series #11.
Alignment quality for Iteration #13 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00715 for Iteration #14 of Tilt-Series #11.
CCMS(rotations) = 0.20224 for Iteration #14 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00762 for iteration 14 of Tilt-Series #11.
Alignment quality for Iteration #14 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00723 for Iteration #15 of Tilt-Series #11.
CCMS(rotations) = 0.1965 for Iteration #15 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00754 for iteration 15 of Tilt-Series #11.
Alignment quality for Iteration #15 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #11 (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 #11 (tiltseries0011_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 = 63.1865434307
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 = 63.1865434307
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0076 for Iteration #16 of Tilt-Series #11.
CCMS(rotations) = 0.16537 for Iteration #16 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00711 for iteration 16 of Tilt-Series #11.
Alignment quality for Iteration #16 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00703 for Iteration #17 of Tilt-Series #11.
CCMS(rotations) = 0.21337 for Iteration #17 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00778 for iteration 17 of Tilt-Series #11.
Alignment quality for Iteration #17 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #18 of Tilt-Series #11.
CCMS(rotations) = 0.19213 for Iteration #18 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00739 for iteration 18 of Tilt-Series #11.
Alignment quality for Iteration #18 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00682 for Iteration #19 of Tilt-Series #11.
CCMS(rotations) = 0.23515 for Iteration #19 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00811 for iteration 19 of Tilt-Series #11.
Alignment quality for Iteration #19 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00714 for Iteration #20 of Tilt-Series #11.
CCMS(rotations) = 0.19697 for Iteration #20 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00751 for iteration 20 of Tilt-Series #11.
Alignment quality for Iteration #20 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #11 (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 #11 (tiltseries0011_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 = 126.373086861
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 = 126.373086861
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00963 for Iteration #21 of Tilt-Series #11.
CCMS(rotations) = 0.20664 for Iteration #21 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00895 for iteration 21 of Tilt-Series #11.
Alignment quality for Iteration #21 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00758 for Iteration #22 of Tilt-Series #11.
CCMS(rotations) = 0.26084 for Iteration #22 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00901 for iteration 22 of Tilt-Series #11.
Alignment quality for Iteration #22 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00801 for Iteration #23 of Tilt-Series #11.
CCMS(rotations) = 0.26237 for Iteration #23 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00925 for iteration 23 of Tilt-Series #11.
Alignment quality for Iteration #23 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #11 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00807 for Iteration #24 of Tilt-Series #11.
CCMS(rotations) = 0.21653 for Iteration #24 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00837 for iteration 24 of Tilt-Series #11.
Alignment quality for Iteration #24 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00784 for Iteration #25 of Tilt-Series #11.
CCMS(rotations) = 0.2484 for Iteration #25 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00889 for iteration 25 of Tilt-Series #11.
Alignment quality for Iteration #25 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00748 for Iteration #26 of Tilt-Series #11.
CCMS(rotations) = 0.27259 for Iteration #26 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00919 for iteration 26 of Tilt-Series #11.
Alignment quality for Iteration #26 of Tilt-Series #11 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00752 for Iteration #27 of Tilt-Series #11.
CCMS(rotations) = 0.20431 for Iteration #27 of Tilt-Series #11.
CCMS(scale) = 0.00253 for Iteration #27 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00607 for iteration 27 of Tilt-Series #11.
Alignment quality for Iteration #27 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #11 (17aug18i): Very StableCreating 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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #28 of Tilt-Series #11.
CCMS(rotations) = 0.26634 for Iteration #28 of Tilt-Series #11.
CCMS(scale) = 0.00259 for Iteration #28 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00663 for iteration 28 of Tilt-Series #11.
Alignment quality for Iteration #28 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00617 for Iteration #29 of Tilt-Series #11.
CCMS(rotations) = 0.2645 for Iteration #29 of Tilt-Series #11.
CCMS(scale) = 0.00256 for Iteration #29 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00644 for iteration 29 of Tilt-Series #11.
Alignment quality for Iteration #29 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #11 (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 #11 (tiltseries0011_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #11 (tiltseries0011_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00872 for Iteration #30 of Tilt-Series #11.
CCMS(rotations) = 0.26862 for Iteration #30 of Tilt-Series #11.
CCMS(scale) = 0.00256 for Iteration #30 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00734 for iteration 30 of Tilt-Series #11.
Alignment quality for Iteration #30 of Tilt-Series #11 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #11 (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 #11 (tiltseries0011_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: 2017yr09m05d-21hr23m21s