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/17may19d/protomo_alignments/tiltseries0001_thick300 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3406.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1919 --r1_region_y=1855 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3406.0 --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=1855 --r2_region_x=1919 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1703.0 --defocus_ang_positive=90 --r5_mask_width_x=1894 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3406.0 --r3_highpass_apod_x=1703.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=454 --r2_mask_width_y=438 --r5_region_x=1919 --r5_region_y=1855 --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=3406.0 --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=1830 --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=1703.0 --runname=tiltseries0001_thick300 --r1_highpass_diameter_x=3406.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --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=1894 --r4_mask_width_y=1830 --logging=true --DefocusTol=200 --filter=median --sessionname=17may19d --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=1703.0 --r1_highpass_apod_x=1703.0 --r2_highpass_apod_x=1703.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --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=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=1 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=902 --r3_mask_width_x=934 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3406.0 --r4_highpass_diameter_x=3406.0 --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=3406.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=1703.0 --r5_highpass_apod_x=1703.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3406.0 --defocus_max=0 --r4_region_y=1855 --r4_region_x=1919 --r5_kernel_y=5 --r3_region_x=1919 --r3_region_y=1855 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=300 --expid=4069 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --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=1.83586 --link=False --r2_highpass_diameter_x=3406.0 --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=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=25.0 --dimx=3838 --dimy=3710 --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=1703.0 --r4_highpass_apod_y=1703.0 --azimuth=true --r1_mask_width_y=206 --r1_mask_width_x=214 --jobtype=protomo

node39
Start time: 2017yr06m21d-12hr22m04s
Description: 
coarse_series0001_iter2.tlt not found, using coarse_series0001.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0001.tlt to series0001.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.23499008 0.23499008 }
map.sampling = 8
window.highpass.diameter = { 0.0086241221374 0.0086241221374 }
window.highpass.apodization = { 0.0172482442748 0.0172482442748 }
window.mask.apodization = { 10 10 }
align.mask.width = { 214 206 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 28.8862753612
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 239 231 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 214 206 }
reference.body = 28.8862753612
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03881 for Iteration #1 of Tilt-Series #1.
CCMS(rotations) = 0.6962 for Iteration #1 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #1.
The scaled sum of CCMS values is #0.03333 for iteration 1 of Tilt-Series #1.
Alignment quality for Iteration #1 of Tilt-Series #1 (17may19d): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00597 for Iteration #2 of Tilt-Series #1.
CCMS(rotations) = 0.19187 for Iteration #2 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00682 for iteration 2 of Tilt-Series #1.
Alignment quality for Iteration #2 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00651 for Iteration #3 of Tilt-Series #1.
CCMS(rotations) = 0.18923 for Iteration #3 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00704 for iteration 3 of Tilt-Series #1.
Alignment quality for Iteration #3 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #4 of Tilt-Series #1.
CCMS(rotations) = 0.18643 for Iteration #4 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00762 for iteration 4 of Tilt-Series #1.
Alignment quality for Iteration #4 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00724 for Iteration #5 of Tilt-Series #1.
CCMS(rotations) = 0.18727 for Iteration #5 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00736 for iteration 5 of Tilt-Series #1.
Alignment quality for Iteration #5 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00837 for Iteration #6 of Tilt-Series #1.
CCMS(rotations) = 0.18219 for Iteration #6 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00783 for iteration 6 of Tilt-Series #1.
Alignment quality for Iteration #6 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00751 for Iteration #7 of Tilt-Series #1.
CCMS(rotations) = 0.17722 for Iteration #7 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0073 for iteration 7 of Tilt-Series #1.
Alignment quality for Iteration #7 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00885 for Iteration #8 of Tilt-Series #1.
CCMS(rotations) = 0.17308 for Iteration #8 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00789 for iteration 8 of Tilt-Series #1.
Alignment quality for Iteration #8 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (17may19d): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00718 for Iteration #9 of Tilt-Series #1.
CCMS(rotations) = 0.17929 for Iteration #9 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00718 for iteration 9 of Tilt-Series #1.
Alignment quality for Iteration #9 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00834 for Iteration #10 of Tilt-Series #1.
CCMS(rotations) = 0.17862 for Iteration #10 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00774 for iteration 10 of Tilt-Series #1.
Alignment quality for Iteration #10 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (17may19d): Rock Solid!Creating 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 #1 (tiltseries0001_thick300)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.233125079365 0.233125079365 }
map.sampling = 4
window.highpass.diameter = { 0.0043120610687 0.0043120610687 }
window.highpass.apodization = { 0.0086241221374 0.0086241221374 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 57.7725507225
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 57.7725507225
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00418 for Iteration #11 of Tilt-Series #1.
CCMS(rotations) = 0.12301 for Iteration #11 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00455 for iteration 11 of Tilt-Series #1.
Alignment quality for Iteration #11 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00515 for Iteration #12 of Tilt-Series #1.
CCMS(rotations) = 0.09278 for Iteration #12 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00443 for iteration 12 of Tilt-Series #1.
Alignment quality for Iteration #12 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00406 for Iteration #13 of Tilt-Series #1.
CCMS(rotations) = 0.10041 for Iteration #13 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00404 for iteration 13 of Tilt-Series #1.
Alignment quality for Iteration #13 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00476 for Iteration #14 of Tilt-Series #1.
CCMS(rotations) = 0.14093 for Iteration #14 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0052 for iteration 14 of Tilt-Series #1.
Alignment quality for Iteration #14 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00455 for Iteration #15 of Tilt-Series #1.
CCMS(rotations) = 0.07685 for Iteration #15 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00381 for iteration 15 of Tilt-Series #1.
Alignment quality for Iteration #15 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00458 for Iteration #16 of Tilt-Series #1.
CCMS(rotations) = 0.08329 for Iteration #16 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00396 for iteration 16 of Tilt-Series #1.
Alignment quality for Iteration #16 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (17may19d): Very StableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00471 for Iteration #17 of Tilt-Series #1.
CCMS(rotations) = 0.0715 for Iteration #17 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00379 for iteration 17 of Tilt-Series #1.
Alignment quality for Iteration #17 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00455 for Iteration #18 of Tilt-Series #1.
CCMS(rotations) = 0.09438 for Iteration #18 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00416 for iteration 18 of Tilt-Series #1.
Alignment quality for Iteration #18 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00466 for Iteration #19 of Tilt-Series #1.
CCMS(rotations) = 0.08795 for Iteration #19 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00409 for iteration 19 of Tilt-Series #1.
Alignment quality for Iteration #19 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (17may19d): Very StableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00536 for Iteration #20 of Tilt-Series #1.
CCMS(rotations) = 0.08723 for Iteration #20 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00442 for iteration 20 of Tilt-Series #1.
Alignment quality for Iteration #20 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.23688516129 0.23688516129 }
map.sampling = 2
window.highpass.diameter = { 0.00215603053435 0.00215603053435 }
window.highpass.apodization = { 0.0043120610687 0.0043120610687 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 115.545101445
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 115.545101445
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00699 for Iteration #21 of Tilt-Series #1.
CCMS(rotations) = 0.21341 for Iteration #21 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00776 for iteration 21 of Tilt-Series #1.
Alignment quality for Iteration #21 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00431 for Iteration #22 of Tilt-Series #1.
CCMS(rotations) = 0.09908 for Iteration #22 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00414 for iteration 22 of Tilt-Series #1.
Alignment quality for Iteration #22 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00524 for Iteration #23 of Tilt-Series #1.
CCMS(rotations) = 0.08379 for Iteration #23 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0043 for iteration 23 of Tilt-Series #1.
Alignment quality for Iteration #23 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00438 for Iteration #24 of Tilt-Series #1.
CCMS(rotations) = 0.10555 for Iteration #24 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0043 for iteration 24 of Tilt-Series #1.
Alignment quality for Iteration #24 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00462 for Iteration #25 of Tilt-Series #1.
CCMS(rotations) = 0.07868 for Iteration #25 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00388 for iteration 25 of Tilt-Series #1.
Alignment quality for Iteration #25 of Tilt-Series #1 (17may19d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.2294825 0.2294825 }
map.sampling = 1
window.highpass.diameter = { 0.00107801526718 0.00107801526718 }
window.highpass.apodization = { 0.00215603053435 0.00215603053435 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 231.09020289
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 231.09020289
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01217 for Iteration #26 of Tilt-Series #1.
CCMS(rotations) = 0.17025 for Iteration #26 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00949 for iteration 26 of Tilt-Series #1.
Alignment quality for Iteration #26 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00961 for Iteration #27 of Tilt-Series #1.
CCMS(rotations) = 0.20122 for Iteration #27 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00883 for iteration 27 of Tilt-Series #1.
Alignment quality for Iteration #27 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00809 for Iteration #28 of Tilt-Series #1.
CCMS(rotations) = 0.21317 for Iteration #28 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00831 for iteration 28 of Tilt-Series #1.
Alignment quality for Iteration #28 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00945 for Iteration #29 of Tilt-Series #1.
CCMS(rotations) = 0.18039 for Iteration #29 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00833 for iteration 29 of Tilt-Series #1.
Alignment quality for Iteration #29 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00844 for Iteration #30 of Tilt-Series #1.
CCMS(rotations) = 0.26761 for Iteration #30 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00957 for iteration 30 of Tilt-Series #1.
Alignment quality for Iteration #30 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (17may19d): 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00866 for Iteration #31 of Tilt-Series #1.
CCMS(rotations) = 0.27743 for Iteration #31 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00988 for iteration 31 of Tilt-Series #1.
Alignment quality for Iteration #31 of Tilt-Series #1 (17may19d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00727 for Iteration #32 of Tilt-Series #1.
CCMS(rotations) = 0.26638 for Iteration #32 of Tilt-Series #1.
CCMS(scale) = 0.00224 for Iteration #32 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00672 for iteration 32 of Tilt-Series #1.
Alignment quality for Iteration #32 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01004 for Iteration #33 of Tilt-Series #1.
CCMS(rotations) = 0.24699 for Iteration #33 of Tilt-Series #1.
CCMS(scale) = 0.0019 for Iteration #33 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00728 for iteration 33 of Tilt-Series #1.
Alignment quality for Iteration #33 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00852 for Iteration #34 of Tilt-Series #1.
CCMS(rotations) = 0.29626 for Iteration #34 of Tilt-Series #1.
CCMS(scale) = 0.00208 for Iteration #34 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00748 for iteration 34 of Tilt-Series #1.
Alignment quality for Iteration #34 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick300)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0077 for Iteration #35 of Tilt-Series #1.
CCMS(rotations) = 0.19421 for Iteration #35 of Tilt-Series #1.
CCMS(scale) = 0.00348 for Iteration #35 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00632 for iteration 35 of Tilt-Series #1.
Alignment quality for Iteration #35 of Tilt-Series #1 (17may19d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (17may19d): UnstableCreating 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 #1 (tiltseries0001_thick300)!
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: 2017yr06m21d-21hr13m29s