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/tiltseries0010_thick150 --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=tiltseries0010_thick150 --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=10 --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=150 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node05
Start time: 2017yr09m04d-14hr19m41s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0010.tlt to series0010.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #10 (tiltseries0010_thick150)
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 = 47.389907573
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 = 47.389907573
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0365 for Iteration #1 of Tilt-Series #10.
CCMS(rotations) = 0.48089 for Iteration #1 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #10.
The scaled sum of CCMS values is #0.02787 for iteration 1 of Tilt-Series #10.
Alignment quality for Iteration #1 of Tilt-Series #10 (17aug18i): Okay (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.0062 for Iteration #2 of Tilt-Series #10.
CCMS(rotations) = 0.15075 for Iteration #2 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00611 for iteration 2 of Tilt-Series #10.
Alignment quality for Iteration #2 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #3 of Tilt-Series #10.
CCMS(rotations) = 0.22478 for Iteration #3 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00757 for iteration 3 of Tilt-Series #10.
Alignment quality for Iteration #3 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00659 for Iteration #4 of Tilt-Series #10.
CCMS(rotations) = 0.18151 for Iteration #4 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00692 for iteration 4 of Tilt-Series #10.
Alignment quality for Iteration #4 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #5 of Tilt-Series #10.
CCMS(rotations) = 0.19496 for Iteration #5 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00723 for iteration 5 of Tilt-Series #10.
Alignment quality for Iteration #5 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)
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 = 94.7798151461
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 = 94.7798151461
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00972 for Iteration #6 of Tilt-Series #10.
CCMS(rotations) = 0.37969 for Iteration #6 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01245 for iteration 6 of Tilt-Series #10.
Alignment quality for Iteration #6 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00653 for Iteration #7 of Tilt-Series #10.
CCMS(rotations) = 0.17209 for Iteration #7 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00671 for iteration 7 of Tilt-Series #10.
Alignment quality for Iteration #7 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #10 (17aug18i): Very StableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00662 for Iteration #8 of Tilt-Series #10.
CCMS(rotations) = 0.19887 for Iteration #8 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00729 for iteration 8 of Tilt-Series #10.
Alignment quality for Iteration #8 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #9 of Tilt-Series #10.
CCMS(rotations) = 0.17989 for Iteration #9 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00697 for iteration 9 of Tilt-Series #10.
Alignment quality for Iteration #9 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #10 of Tilt-Series #10.
CCMS(rotations) = 0.18314 for Iteration #10 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00699 for iteration 10 of Tilt-Series #10.
Alignment quality for Iteration #10 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0066 for Iteration #11 of Tilt-Series #10.
CCMS(rotations) = 0.20362 for Iteration #11 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00737 for iteration 11 of Tilt-Series #10.
Alignment quality for Iteration #11 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #10 (17aug18i): StableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #12 of Tilt-Series #10.
CCMS(rotations) = 0.19114 for Iteration #12 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00699 for iteration 12 of Tilt-Series #10.
Alignment quality for Iteration #12 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00692 for Iteration #13 of Tilt-Series #10.
CCMS(rotations) = 0.17729 for Iteration #13 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00701 for iteration 13 of Tilt-Series #10.
Alignment quality for Iteration #13 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00613 for Iteration #14 of Tilt-Series #10.
CCMS(rotations) = 0.17975 for Iteration #14 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00666 for iteration 14 of Tilt-Series #10.
Alignment quality for Iteration #14 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00669 for Iteration #15 of Tilt-Series #10.
CCMS(rotations) = 0.1771 for Iteration #15 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00689 for iteration 15 of Tilt-Series #10.
Alignment quality for Iteration #15 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)
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 = 189.559630292
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 = 189.559630292
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00849 for Iteration #16 of Tilt-Series #10.
CCMS(rotations) = 0.27152 for Iteration #16 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00967 for iteration 16 of Tilt-Series #10.
Alignment quality for Iteration #16 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00744 for Iteration #17 of Tilt-Series #10.
CCMS(rotations) = 0.17095 for Iteration #17 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00714 for iteration 17 of Tilt-Series #10.
Alignment quality for Iteration #17 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00744 for Iteration #18 of Tilt-Series #10.
CCMS(rotations) = 0.18468 for Iteration #18 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00742 for iteration 18 of Tilt-Series #10.
Alignment quality for Iteration #18 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #10 (17aug18i): StableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00733 for Iteration #19 of Tilt-Series #10.
CCMS(rotations) = 0.16606 for Iteration #19 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00699 for iteration 19 of Tilt-Series #10.
Alignment quality for Iteration #19 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00756 for Iteration #20 of Tilt-Series #10.
CCMS(rotations) = 0.18396 for Iteration #20 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00746 for iteration 20 of Tilt-Series #10.
Alignment quality for Iteration #20 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)
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 = 379.119260584
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 = 379.119260584
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.0104 for Iteration #21 of Tilt-Series #10.
CCMS(rotations) = 0.21469 for Iteration #21 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00949 for iteration 21 of Tilt-Series #10.
Alignment quality for Iteration #21 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01011 for Iteration #22 of Tilt-Series #10.
CCMS(rotations) = 0.22334 for Iteration #22 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00952 for iteration 22 of Tilt-Series #10.
Alignment quality for Iteration #22 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01014 for Iteration #23 of Tilt-Series #10.
CCMS(rotations) = 0.35761 for Iteration #23 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01222 for iteration 23 of Tilt-Series #10.
Alignment quality for Iteration #23 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01265 for Iteration #24 of Tilt-Series #10.
CCMS(rotations) = 0.1641 for Iteration #24 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00961 for iteration 24 of Tilt-Series #10.
Alignment quality for Iteration #24 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01362 for Iteration #25 of Tilt-Series #10.
CCMS(rotations) = 0.36926 for Iteration #25 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01419 for iteration 25 of Tilt-Series #10.
Alignment quality for Iteration #25 of Tilt-Series #10 (17aug18i): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.00922 for Iteration #26 of Tilt-Series #10.
CCMS(rotations) = 0.23397 for Iteration #26 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00929 for iteration 26 of Tilt-Series #10.
Alignment quality for Iteration #26 of Tilt-Series #10 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00728 for Iteration #27 of Tilt-Series #10.
CCMS(rotations) = 0.26244 for Iteration #27 of Tilt-Series #10.
CCMS(scale) = 0.00257 for Iteration #27 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00678 for iteration 27 of Tilt-Series #10.
Alignment quality for Iteration #27 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #28 of Tilt-Series #10.
CCMS(rotations) = 0.2015 for Iteration #28 of Tilt-Series #10.
CCMS(scale) = 0.00318 for Iteration #28 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00596 for iteration 28 of Tilt-Series #10.
Alignment quality for Iteration #28 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0064 for Iteration #29 of Tilt-Series #10.
CCMS(rotations) = 0.24144 for Iteration #29 of Tilt-Series #10.
CCMS(scale) = 0.00387 for Iteration #29 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00664 for iteration 29 of Tilt-Series #10.
Alignment quality for Iteration #29 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #10 (17aug18i): UnstableCreating 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 #10 (tiltseries0010_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #10 (tiltseries0010_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00812 for Iteration #30 of Tilt-Series #10.
CCMS(rotations) = 0.13906 for Iteration #30 of Tilt-Series #10.
CCMS(scale) = 0.00352 for Iteration #30 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00573 for iteration 30 of Tilt-Series #10.
Alignment quality for Iteration #30 of Tilt-Series #10 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #10 (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 #10 (tiltseries0010_thick150)!
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-21hr31m23s