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/17jul05d/protomo_alignments/tiltseries0005_thick200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4087.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2302 --r1_region_y=2226 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4087.0 --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=2226 --r2_region_x=2302 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2044.0 --defocus_ang_positive=90 --r5_mask_width_x=2277 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4087.0 --r3_highpass_apod_x=2044.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=550 --r2_mask_width_y=531 --r5_region_x=2302 --r5_region_y=2226 --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=4087.0 --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=2201 --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=2044.0 --runname=tiltseries0005_thick200 --r1_highpass_diameter_x=4087.0 --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=2277 --r4_mask_width_y=2201 --logging=true --DefocusTol=200 --filter=median --sessionname=17jul05d --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=2044.0 --r1_highpass_apod_x=2044.0 --r2_highpass_apod_x=2044.0 --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=5 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=1088 --r3_mask_width_x=1126 --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=4087.0 --r4_highpass_diameter_x=4087.0 --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=4087.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2044.0 --r5_highpass_apod_x=2044.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4087.0 --defocus_max=0 --r4_region_y=2226 --r4_region_x=2302 --r5_kernel_y=5 --r3_region_x=2302 --r3_region_y=2226 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=200 --expid=4317 --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=4087.0 --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=2044.0 --r4_highpass_apod_y=2044.0 --azimuth=true --r1_mask_width_y=253 --r1_mask_width_x=262 --jobtype=protomo

node39
Start time: 2017yr07m05d-15hr01m44s
Description: 
coarse_series0005_iter2.tlt not found, using coarse_series0005.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0005.tlt to series0005.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
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 = { 0.00718712013702 0.00718712013702 }
window.highpass.apodization = { 0.0143707240705 0.0143707240705 }
window.mask.apodization = { 10 10 }
align.mask.width = { 262 253 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 18.3225554932
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 287 278 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 262 253 }
reference.body = 18.3225554932
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05175 for Iteration #1 of Tilt-Series #5.
CCMS(rotations) = 0.81831 for Iteration #1 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5.
The scaled sum of CCMS values is #0.04224 for iteration 1 of Tilt-Series #5.
Alignment quality for Iteration #1 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00327 for Iteration #2 of Tilt-Series #5.
CCMS(rotations) = 0.07114 for Iteration #2 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00306 for iteration 2 of Tilt-Series #5.
Alignment quality for Iteration #2 of Tilt-Series #5 (17jul05d): Perfection! (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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00316 for Iteration #3 of Tilt-Series #5.
CCMS(rotations) = 0.07802 for Iteration #3 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00314 for iteration 3 of Tilt-Series #5.
Alignment quality for Iteration #3 of Tilt-Series #5 (17jul05d): Perfection! (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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00274 for Iteration #4 of Tilt-Series #5.
CCMS(rotations) = 0.08995 for Iteration #4 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00317 for iteration 4 of Tilt-Series #5.
Alignment quality for Iteration #4 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #5 (17jul05d): Rock Solid!Creating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00321 for Iteration #5 of Tilt-Series #5.
CCMS(rotations) = 0.08446 for Iteration #5 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00329 for iteration 5 of Tilt-Series #5.
Alignment quality for Iteration #5 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #5 (17jul05d): Rock Solid!Creating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00285 for Iteration #6 of Tilt-Series #5.
CCMS(rotations) = 0.09881 for Iteration #6 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0034 for iteration 6 of Tilt-Series #5.
Alignment quality for Iteration #6 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #5 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00339 for Iteration #7 of Tilt-Series #5.
CCMS(rotations) = 0.08586 for Iteration #7 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00341 for iteration 7 of Tilt-Series #5.
Alignment quality for Iteration #7 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #5 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00286 for Iteration #8 of Tilt-Series #5.
CCMS(rotations) = 0.10452 for Iteration #8 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00352 for iteration 8 of Tilt-Series #5.
Alignment quality for Iteration #8 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00343 for Iteration #9 of Tilt-Series #5.
CCMS(rotations) = 0.08383 for Iteration #9 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00339 for iteration 9 of Tilt-Series #5.
Alignment quality for Iteration #9 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #5 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00302 for Iteration #10 of Tilt-Series #5.
CCMS(rotations) = 0.09363 for Iteration #10 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00338 for iteration 10 of Tilt-Series #5.
Alignment quality for Iteration #10 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)
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 = { 0.00359356006851 0.00359356006851 }
window.highpass.apodization = { 0.00718536203523 0.00718536203523 }
window.mask.apodization = { 10 10 }
align.mask.width = { 550 531 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 36.6451109865
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 575 556 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 550 531 }
reference.body = 36.6451109865
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00314 for Iteration #11 of Tilt-Series #5.
CCMS(rotations) = 0.08736 for Iteration #11 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00332 for iteration 11 of Tilt-Series #5.
Alignment quality for Iteration #11 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #5 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00317 for Iteration #12 of Tilt-Series #5.
CCMS(rotations) = 0.0806 for Iteration #12 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0032 for iteration 12 of Tilt-Series #5.
Alignment quality for Iteration #12 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00378 for Iteration #13 of Tilt-Series #5.
CCMS(rotations) = 0.07502 for Iteration #13 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00339 for iteration 13 of Tilt-Series #5.
Alignment quality for Iteration #13 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #5 (17jul05d): StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00391 for Iteration #14 of Tilt-Series #5.
CCMS(rotations) = 0.09292 for Iteration #14 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00381 for iteration 14 of Tilt-Series #5.
Alignment quality for Iteration #14 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #5 (17jul05d): StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #15 of Tilt-Series #5.
CCMS(rotations) = 0.07471 for Iteration #15 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00339 for iteration 15 of Tilt-Series #5.
Alignment quality for Iteration #15 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #16 of Tilt-Series #5.
CCMS(rotations) = 0.08052 for Iteration #16 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00343 for iteration 16 of Tilt-Series #5.
Alignment quality for Iteration #16 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #17 of Tilt-Series #5.
CCMS(rotations) = 0.07839 for Iteration #17 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0035 for iteration 17 of Tilt-Series #5.
Alignment quality for Iteration #17 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #18 of Tilt-Series #5.
CCMS(rotations) = 0.0796 for Iteration #18 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0034 for iteration 18 of Tilt-Series #5.
Alignment quality for Iteration #18 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00381 for Iteration #19 of Tilt-Series #5.
CCMS(rotations) = 0.07252 for Iteration #19 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00335 for iteration 19 of Tilt-Series #5.
Alignment quality for Iteration #19 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00394 for Iteration #20 of Tilt-Series #5.
CCMS(rotations) = 0.08776 for Iteration #20 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00373 for iteration 20 of Tilt-Series #5.
Alignment quality for Iteration #20 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #5 (17jul05d): Very StableCreating 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 #5 (tiltseries0005_thick200)
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 = { 0.00179678003425 0.00179678003425 }
window.highpass.apodization = { 0.00359268101761 0.00359268101761 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1126 1088 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 73.290221973
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1151 1113 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1126 1088 }
reference.body = 73.290221973
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00279 for Iteration #21 of Tilt-Series #5.
CCMS(rotations) = 0.06958 for Iteration #21 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00279 for iteration 21 of Tilt-Series #5.
Alignment quality for Iteration #21 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #5 (17jul05d): StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00272 for Iteration #22 of Tilt-Series #5.
CCMS(rotations) = 0.08709 for Iteration #22 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0031 for iteration 22 of Tilt-Series #5.
Alignment quality for Iteration #22 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00248 for Iteration #23 of Tilt-Series #5.
CCMS(rotations) = 0.09139 for Iteration #23 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00307 for iteration 23 of Tilt-Series #5.
Alignment quality for Iteration #23 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00291 for Iteration #24 of Tilt-Series #5.
CCMS(rotations) = 0.09735 for Iteration #24 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0034 for iteration 24 of Tilt-Series #5.
Alignment quality for Iteration #24 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #5 (17jul05d): StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00255 for Iteration #25 of Tilt-Series #5.
CCMS(rotations) = 0.07475 for Iteration #25 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00277 for iteration 25 of Tilt-Series #5.
Alignment quality for Iteration #25 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)
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 = { 0.000898390017127 0.000898390017127 }
window.highpass.apodization = { 0.00179634050881 0.00179634050881 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2277 2201 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 146.580443946
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2302 2226 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2277 2201 }
reference.body = 146.580443946
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00517 for Iteration #26 of Tilt-Series #5.
CCMS(rotations) = 0.06621 for Iteration #26 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00391 for iteration 26 of Tilt-Series #5.
Alignment quality for Iteration #26 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #27 of Tilt-Series #5.
CCMS(rotations) = 0.14409 for Iteration #27 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00496 for iteration 27 of Tilt-Series #5.
Alignment quality for Iteration #27 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00381 for Iteration #28 of Tilt-Series #5.
CCMS(rotations) = 0.11057 for Iteration #28 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00412 for iteration 28 of Tilt-Series #5.
Alignment quality for Iteration #28 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00404 for Iteration #29 of Tilt-Series #5.
CCMS(rotations) = 0.1258 for Iteration #29 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00454 for iteration 29 of Tilt-Series #5.
Alignment quality for Iteration #29 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.004 for Iteration #30 of Tilt-Series #5.
CCMS(rotations) = 0.13602 for Iteration #30 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00472 for iteration 30 of Tilt-Series #5.
Alignment quality for Iteration #30 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00389 for Iteration #31 of Tilt-Series #5.
CCMS(rotations) = 0.12697 for Iteration #31 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00449 for iteration 31 of Tilt-Series #5.
Alignment quality for Iteration #31 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #5 (17jul05d): Very StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00286 for Iteration #32 of Tilt-Series #5.
CCMS(rotations) = 0.11767 for Iteration #32 of Tilt-Series #5.
CCMS(scale) = 0.0016 for Iteration #32 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00306 for iteration 32 of Tilt-Series #5.
Alignment quality for Iteration #32 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00307 for Iteration #33 of Tilt-Series #5.
CCMS(rotations) = 0.11483 for Iteration #33 of Tilt-Series #5.
CCMS(scale) = 0.00163 for Iteration #33 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0031 for iteration 33 of Tilt-Series #5.
Alignment quality for Iteration #33 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #5 (17jul05d): Very StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00294 for Iteration #34 of Tilt-Series #5.
CCMS(rotations) = 0.10293 for Iteration #34 of Tilt-Series #5.
CCMS(scale) = 0.00163 for Iteration #34 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00289 for iteration 34 of Tilt-Series #5.
Alignment quality for Iteration #34 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #5 (17jul05d): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00336 for Iteration #35 of Tilt-Series #5.
CCMS(rotations) = 0.12321 for Iteration #35 of Tilt-Series #5.
CCMS(scale) = 0.00162 for Iteration #35 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0033 for iteration 35 of Tilt-Series #5.
Alignment quality for Iteration #35 of Tilt-Series #5 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #5 (17jul05d): Very StableCreating 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 #5 (tiltseries0005_thick200)!
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: 2017yr07m06d-00hr58m03s