protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-28.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0013_thick150 --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=tiltseries0013_thick150 --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=13 --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=150 --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=90.0 --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

node38
Start time: 2017yr12m26d-20hr19m51s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0013.tlt to series0013.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
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 = 12.945272933
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 = 12.945272933
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.08924 for Iteration #1 of Tilt-Series #13.
CCMS(rotations) = 1.4218 for Iteration #1 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #13.
The scaled sum of CCMS values is #0.07305 for iteration 1 of Tilt-Series #13.
Alignment quality for Iteration #1 of Tilt-Series #13 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 92.857143%)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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #2 of Tilt-Series #13.
CCMS(rotations) = 0.35693 for Iteration #2 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00989 for iteration 2 of Tilt-Series #13.
Alignment quality for Iteration #2 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00617 for Iteration #3 of Tilt-Series #13.
CCMS(rotations) = 0.30267 for Iteration #3 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00914 for iteration 3 of Tilt-Series #13.
Alignment quality for Iteration #3 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.006 for Iteration #4 of Tilt-Series #13.
CCMS(rotations) = 0.34178 for Iteration #4 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00984 for iteration 4 of Tilt-Series #13.
Alignment quality for Iteration #4 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #5 of Tilt-Series #13.
CCMS(rotations) = 0.30319 for Iteration #5 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00913 for iteration 5 of Tilt-Series #13.
Alignment quality for Iteration #5 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #13 (17dec26e): Very StableCreating 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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00594 for Iteration #6 of Tilt-Series #13.
CCMS(rotations) = 0.33795 for Iteration #6 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00973 for iteration 6 of Tilt-Series #13.
Alignment quality for Iteration #6 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #13 (17dec26e): Very StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00612 for Iteration #7 of Tilt-Series #13.
CCMS(rotations) = 0.30382 for Iteration #7 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00914 for iteration 7 of Tilt-Series #13.
Alignment quality for Iteration #7 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #13 (17dec26e): 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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00606 for Iteration #8 of Tilt-Series #13.
CCMS(rotations) = 0.3357 for Iteration #8 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00975 for iteration 8 of Tilt-Series #13.
Alignment quality for Iteration #8 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #13 (17dec26e): Very StableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00602 for Iteration #9 of Tilt-Series #13.
CCMS(rotations) = 0.3006 for Iteration #9 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00902 for iteration 9 of Tilt-Series #13.
Alignment quality for Iteration #9 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #13 (17dec26e): Very StableCreating 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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #10 of Tilt-Series #13.
CCMS(rotations) = 0.3388 for Iteration #10 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00976 for iteration 10 of Tilt-Series #13.
Alignment quality for Iteration #10 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #13 (17dec26e): Very StableCreating 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 #13 (tiltseries0013_thick150)
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 = 25.890545866
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 = 25.890545866
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00508 for Iteration #11 of Tilt-Series #13.
CCMS(rotations) = 0.27437 for Iteration #11 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00803 for iteration 11 of Tilt-Series #13.
Alignment quality for Iteration #11 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #13 (17dec26e): UnstableCreating 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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00588 for Iteration #12 of Tilt-Series #13.
CCMS(rotations) = 0.3169 for Iteration #12 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00928 for iteration 12 of Tilt-Series #13.
Alignment quality for Iteration #12 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00547 for Iteration #13 of Tilt-Series #13.
CCMS(rotations) = 0.31001 for Iteration #13 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00893 for iteration 13 of Tilt-Series #13.
Alignment quality for Iteration #13 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00594 for Iteration #14 of Tilt-Series #13.
CCMS(rotations) = 0.31271 for Iteration #14 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00922 for iteration 14 of Tilt-Series #13.
Alignment quality for Iteration #14 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00547 for Iteration #15 of Tilt-Series #13.
CCMS(rotations) = 0.30466 for Iteration #15 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00883 for iteration 15 of Tilt-Series #13.
Alignment quality for Iteration #15 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00586 for Iteration #16 of Tilt-Series #13.
CCMS(rotations) = 0.3142 for Iteration #16 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00921 for iteration 16 of Tilt-Series #13.
Alignment quality for Iteration #16 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00549 for Iteration #17 of Tilt-Series #13.
CCMS(rotations) = 0.30244 for Iteration #17 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00879 for iteration 17 of Tilt-Series #13.
Alignment quality for Iteration #17 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #18 of Tilt-Series #13.
CCMS(rotations) = 0.30827 for Iteration #18 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00909 for iteration 18 of Tilt-Series #13.
Alignment quality for Iteration #18 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #19 of Tilt-Series #13.
CCMS(rotations) = 0.30746 for Iteration #19 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00891 for iteration 19 of Tilt-Series #13.
Alignment quality for Iteration #19 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00588 for Iteration #20 of Tilt-Series #13.
CCMS(rotations) = 0.31316 for Iteration #20 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0092 for iteration 20 of Tilt-Series #13.
Alignment quality for Iteration #20 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)
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 = 51.781091732
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 = 51.781091732
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.0055 for Iteration #21 of Tilt-Series #13.
CCMS(rotations) = 0.31523 for Iteration #21 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00905 for iteration 21 of Tilt-Series #13.
Alignment quality for Iteration #21 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00547 for Iteration #22 of Tilt-Series #13.
CCMS(rotations) = 0.30927 for Iteration #22 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00892 for iteration 22 of Tilt-Series #13.
Alignment quality for Iteration #22 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00522 for Iteration #23 of Tilt-Series #13.
CCMS(rotations) = 0.29965 for Iteration #23 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0086 for iteration 23 of Tilt-Series #13.
Alignment quality for Iteration #23 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #24 of Tilt-Series #13.
CCMS(rotations) = 0.30458 for Iteration #24 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00884 for iteration 24 of Tilt-Series #13.
Alignment quality for Iteration #24 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00523 for Iteration #25 of Tilt-Series #13.
CCMS(rotations) = 0.30262 for Iteration #25 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00867 for iteration 25 of Tilt-Series #13.
Alignment quality for Iteration #25 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #13 (17dec26e): Rock Solid!Creating 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 #13 (tiltseries0013_thick150)
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 = 103.562183464
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 = 103.562183464
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #26 of Tilt-Series #13.
CCMS(rotations) = 0.32998 for Iteration #26 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01001 for iteration 26 of Tilt-Series #13.
Alignment quality for Iteration #26 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00545 for Iteration #27 of Tilt-Series #13.
CCMS(rotations) = 0.30214 for Iteration #27 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00877 for iteration 27 of Tilt-Series #13.
Alignment quality for Iteration #27 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #13 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #28 of Tilt-Series #13.
CCMS(rotations) = 0.29944 for Iteration #28 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00881 for iteration 28 of Tilt-Series #13.
Alignment quality for Iteration #28 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #29 of Tilt-Series #13.
CCMS(rotations) = 0.30305 for Iteration #29 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00876 for iteration 29 of Tilt-Series #13.
Alignment quality for Iteration #29 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0056 for Iteration #30 of Tilt-Series #13.
CCMS(rotations) = 0.30177 for Iteration #30 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00884 for iteration 30 of Tilt-Series #13.
Alignment quality for Iteration #30 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #31 of Tilt-Series #13.
CCMS(rotations) = 0.30159 for Iteration #31 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00873 for iteration 31 of Tilt-Series #13.
Alignment quality for Iteration #31 of Tilt-Series #13 (17dec26e): Very Good (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0047 for Iteration #32 of Tilt-Series #13.
CCMS(rotations) = 0.30909 for Iteration #32 of Tilt-Series #13.
CCMS(scale) = 0.00251 for Iteration #32 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00652 for iteration 32 of Tilt-Series #13.
Alignment quality for Iteration #32 of Tilt-Series #13 (17dec26e): Excellent (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #33 of Tilt-Series #13.
CCMS(rotations) = 0.31503 for Iteration #33 of Tilt-Series #13.
CCMS(scale) = 0.00268 for Iteration #33 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00665 for iteration 33 of Tilt-Series #13.
Alignment quality for Iteration #33 of Tilt-Series #13 (17dec26e): Excellent (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00481 for Iteration #34 of Tilt-Series #13.
CCMS(rotations) = 0.30759 for Iteration #34 of Tilt-Series #13.
CCMS(scale) = 0.00252 for Iteration #34 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00655 for iteration 34 of Tilt-Series #13.
Alignment quality for Iteration #34 of Tilt-Series #13 (17dec26e): Excellent (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #13 (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 #13 (tiltseries0013_thick150)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #13 (tiltseries0013_thick150)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00474 for Iteration #35 of Tilt-Series #13.
CCMS(rotations) = 0.3038 for Iteration #35 of Tilt-Series #13.
CCMS(scale) = 0.00268 for Iteration #35 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00652 for iteration 35 of Tilt-Series #13.
Alignment quality for Iteration #35 of Tilt-Series #13 (17dec26e): Excellent (confidence: 92.857143%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #13 (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 #13 (tiltseries0013_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: 2017yr12m27d-03hr31m48s