protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-43.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0010_thick350 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --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=8.64 --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=4015.0 --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=1894 --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=2008.0 --runname=tiltseries0010_thick350 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --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=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --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=False --r3_mask_width_y=934 --r3_mask_width_x=902 --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=4015.0 --r4_highpass_diameter_x=4015.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=350 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=28.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --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=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo

node08
Start time: 2017yr12m26d-20hr00m18s
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_thick350)
lowpass = 69.12 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms)
window.lowpass.apodization = { 0.20016 0.20016 }
map.sampling = 8
window.highpass.diameter = { 0.00862457783313 0.00862457783313 }
window.highpass.apodization = { 0.0172448605578 0.0172448605578 }
window.mask.apodization = { 10 10 }
align.mask.width = { 206 214 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 32.1157901119
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 32.1157901119
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.09421 for Iteration #1 of Tilt-Series #10.
CCMS(rotations) = 2.85005 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 #0.1041 for iteration 1 of Tilt-Series #10.
Alignment quality for Iteration #1 of Tilt-Series #10 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 68.571429%)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_thick350)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.05613 for Iteration #2 of Tilt-Series #10.
CCMS(rotations) = 0.21578 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 #0.03238 for iteration 2 of Tilt-Series #10.
Alignment quality for Iteration #2 of Tilt-Series #10 (17dec26e): Bad (confidence: 68.571429%)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_thick350)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00665 for Iteration #3 of Tilt-Series #10.
CCMS(rotations) = 0.17758 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 #0.00688 for iteration 3 of Tilt-Series #10.
Alignment quality for Iteration #3 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)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_thick350)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00528 for Iteration #4 of Tilt-Series #10.
CCMS(rotations) = 0.27163 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 #0.00807 for iteration 4 of Tilt-Series #10.
Alignment quality for Iteration #4 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #10 (17dec26e): Very StableCreating 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_thick350)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00836 for Iteration #5 of Tilt-Series #10.
CCMS(rotations) = 0.29938 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 #0.01017 for iteration 5 of Tilt-Series #10.
Alignment quality for Iteration #5 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #10 (17dec26e): UnstableCreating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #6 of Tilt-Series #10.
CCMS(rotations) = 0.23355 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 #0.00784 for iteration 6 of Tilt-Series #10.
Alignment quality for Iteration #6 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00835 for Iteration #7 of Tilt-Series #10.
CCMS(rotations) = 0.29093 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 #0.01 for iteration 7 of Tilt-Series #10.
Alignment quality for Iteration #7 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #10 (17dec26e): UnstableCreating 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_thick350)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00653 for Iteration #8 of Tilt-Series #10.
CCMS(rotations) = 0.26375 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 #0.00854 for iteration 8 of Tilt-Series #10.
Alignment quality for Iteration #8 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00813 for Iteration #9 of Tilt-Series #10.
CCMS(rotations) = 0.27032 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 #0.00947 for iteration 9 of Tilt-Series #10.
Alignment quality for Iteration #9 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00582 for Iteration #10 of Tilt-Series #10.
CCMS(rotations) = 0.2754 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 #0.00842 for iteration 10 of Tilt-Series #10.
Alignment quality for Iteration #10 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #10 (17dec26e): UnstableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
lowpass = 34.56 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 4
window.highpass.diameter = { 0.00431228891656 0.00431228891656 }
window.highpass.apodization = { 0.00862243027888 0.00862243027888 }
window.mask.apodization = { 10 10 }
align.mask.width = { 438 454 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 64.2315802239
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 64.2315802239
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00641 for Iteration #11 of Tilt-Series #10.
CCMS(rotations) = 0.20904 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 #0.00738 for iteration 11 of Tilt-Series #10.
Alignment quality for Iteration #11 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #10 (17dec26e): Very 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_thick350)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00548 for Iteration #12 of Tilt-Series #10.
CCMS(rotations) = 0.16657 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 #0.00607 for iteration 12 of Tilt-Series #10.
Alignment quality for Iteration #12 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00517 for Iteration #13 of Tilt-Series #10.
CCMS(rotations) = 0.23232 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 #0.00723 for iteration 13 of Tilt-Series #10.
Alignment quality for Iteration #13 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00524 for Iteration #14 of Tilt-Series #10.
CCMS(rotations) = 0.19491 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 #0.00652 for iteration 14 of Tilt-Series #10.
Alignment quality for Iteration #14 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00525 for Iteration #15 of Tilt-Series #10.
CCMS(rotations) = 0.22762 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 #0.00718 for iteration 15 of Tilt-Series #10.
Alignment quality for Iteration #15 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00507 for Iteration #16 of Tilt-Series #10.
CCMS(rotations) = 0.20445 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 #0.00663 for iteration 16 of Tilt-Series #10.
Alignment quality for Iteration #16 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00526 for Iteration #17 of Tilt-Series #10.
CCMS(rotations) = 0.22143 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 #0.00706 for iteration 17 of Tilt-Series #10.
Alignment quality for Iteration #17 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00509 for Iteration #18 of Tilt-Series #10.
CCMS(rotations) = 0.18823 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 #0.00631 for iteration 18 of Tilt-Series #10.
Alignment quality for Iteration #18 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00517 for Iteration #19 of Tilt-Series #10.
CCMS(rotations) = 0.23737 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 #0.00733 for iteration 19 of Tilt-Series #10.
Alignment quality for Iteration #19 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.0051 for Iteration #20 of Tilt-Series #10.
CCMS(rotations) = 0.18865 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 #0.00632 for iteration 20 of Tilt-Series #10.
Alignment quality for Iteration #20 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #10 (17dec26e): 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 #3 of Tilt-Series #10 (tiltseries0010_thick350)
lowpass = 17.28 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 2
window.highpass.diameter = { 0.00215614445828 0.00215614445828 }
window.highpass.apodization = { 0.00431121513944 0.00431121513944 }
window.mask.apodization = { 10 10 }
align.mask.width = { 902 934 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 128.463160448
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 128.463160448
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00555 for Iteration #21 of Tilt-Series #10.
CCMS(rotations) = 0.21236 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 #0.00702 for iteration 21 of Tilt-Series #10.
Alignment quality for Iteration #21 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #22 of Tilt-Series #10.
CCMS(rotations) = 0.1917 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 #0.0069 for iteration 22 of Tilt-Series #10.
Alignment quality for Iteration #22 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00548 for Iteration #23 of Tilt-Series #10.
CCMS(rotations) = 0.22472 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 #0.00723 for iteration 23 of Tilt-Series #10.
Alignment quality for Iteration #23 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00609 for Iteration #24 of Tilt-Series #10.
CCMS(rotations) = 0.19417 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 #0.00693 for iteration 24 of Tilt-Series #10.
Alignment quality for Iteration #24 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #25 of Tilt-Series #10.
CCMS(rotations) = 0.23294 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 #0.00741 for iteration 25 of Tilt-Series #10.
Alignment quality for Iteration #25 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #10 (17dec26e): Very StableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
lowpass = 8.64 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms)
window.lowpass.apodization = { 0.196748181818 0.196748181818 }
map.sampling = 1
window.highpass.diameter = { 0.00107807222914 0.00107807222914 }
window.highpass.apodization = { 0.00215560756972 0.00215560756972 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1830 1894 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 256.926320895
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 256.926320895
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00787 for Iteration #26 of Tilt-Series #10.
CCMS(rotations) = 0.23707 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 #0.00868 for iteration 26 of Tilt-Series #10.
Alignment quality for Iteration #26 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #10 (17dec26e): 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_thick350)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0062 for Iteration #27 of Tilt-Series #10.
CCMS(rotations) = 0.26224 for Iteration #27 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00835 for iteration 27 of Tilt-Series #10.
Alignment quality for Iteration #27 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #28 of Tilt-Series #10.
CCMS(rotations) = 0.32006 for Iteration #28 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00922 for iteration 28 of Tilt-Series #10.
Alignment quality for Iteration #28 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00552 for Iteration #29 of Tilt-Series #10.
CCMS(rotations) = 0.28427 for Iteration #29 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00845 for iteration 29 of Tilt-Series #10.
Alignment quality for Iteration #29 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #10 (17dec26e): 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 #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00631 for Iteration #30 of Tilt-Series #10.
CCMS(rotations) = 0.32963 for Iteration #30 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00975 for iteration 30 of Tilt-Series #10.
Alignment quality for Iteration #30 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #31 of Tilt-Series #10.
CCMS(rotations) = 0.308 for Iteration #31 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00915 for iteration 31 of Tilt-Series #10.
Alignment quality for Iteration #31 of Tilt-Series #10 (17dec26e): Very Good (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #32 of Tilt-Series #10.
CCMS(rotations) = 0.32709 for Iteration #32 of Tilt-Series #10.
CCMS(scale) = 0.00288 for Iteration #32 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00661 for iteration 32 of Tilt-Series #10.
Alignment quality for Iteration #32 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #33 of Tilt-Series #10.
CCMS(rotations) = 0.33847 for Iteration #33 of Tilt-Series #10.
CCMS(scale) = 0.00278 for Iteration #33 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00667 for iteration 33 of Tilt-Series #10.
Alignment quality for Iteration #33 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00417 for Iteration #34 of Tilt-Series #10.
CCMS(rotations) = 0.32784 for Iteration #34 of Tilt-Series #10.
CCMS(scale) = 0.00276 for Iteration #34 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00668 for iteration 34 of Tilt-Series #10.
Alignment quality for Iteration #34 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #10 (tiltseries0010_thick350)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #10 (tiltseries0010_thick350)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00452 for Iteration #35 of Tilt-Series #10.
CCMS(rotations) = 0.36731 for Iteration #35 of Tilt-Series #10.
CCMS(scale) = 0.00292 for Iteration #35 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00738 for iteration 35 of Tilt-Series #10.
Alignment quality for Iteration #35 of Tilt-Series #10 (17dec26e): Excellent (confidence: 68.571429%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #10 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #10 (tiltseries0010_thick350)!
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: 2017yr12m27d-02hr50m50s