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/tiltseries0006_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=tiltseries0006_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=6 --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 --tilt_azimuth=-79.5 --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

node34
Start time: 2017yr07m06d-14hr00m52s
Description: 
coarse_series0006_iter2.tlt not found, using coarse_series0006.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0006.tlt to series0006.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006_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 = 18.322267622
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 = 18.322267622
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04451 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 1.45212 for Iteration #1 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0513 for iteration 1 of Tilt-Series #6.
Alignment quality for Iteration #1 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00492 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 0.07463 for Iteration #2 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00395 for iteration 2 of Tilt-Series #6.
Alignment quality for Iteration #2 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 0.0644 for Iteration #3 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00368 for iteration 3 of Tilt-Series #6.
Alignment quality for Iteration #3 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 0.0909 for Iteration #4 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00408 for iteration 4 of Tilt-Series #6.
Alignment quality for Iteration #4 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00472 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 0.07437 for Iteration #5 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00385 for iteration 5 of Tilt-Series #6.
Alignment quality for Iteration #5 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00457 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 0.09422 for Iteration #6 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00417 for iteration 6 of Tilt-Series #6.
Alignment quality for Iteration #6 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00529 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 0.05688 for Iteration #7 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00378 for iteration 7 of Tilt-Series #6.
Alignment quality for Iteration #7 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 0.11602 for Iteration #8 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00459 for iteration 8 of Tilt-Series #6.
Alignment quality for Iteration #8 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00466 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 0.07678 for Iteration #9 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00387 for iteration 9 of Tilt-Series #6.
Alignment quality for Iteration #9 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 0.09429 for Iteration #10 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00415 for iteration 10 of Tilt-Series #6.
Alignment quality for Iteration #10 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #6 (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 #6 (tiltseries0006_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 = 36.6445352439
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 = 36.6445352439
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00408 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 0.10527 for Iteration #11 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00415 for iteration 11 of Tilt-Series #6.
Alignment quality for Iteration #11 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00377 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 0.08463 for Iteration #12 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00358 for iteration 12 of Tilt-Series #6.
Alignment quality for Iteration #12 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #6 (17jul05d): StableCreating 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00348 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 0.07705 for Iteration #13 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00328 for iteration 13 of Tilt-Series #6.
Alignment quality for Iteration #13 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 0.08512 for Iteration #14 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00362 for iteration 14 of Tilt-Series #6.
Alignment quality for Iteration #14 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00306 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 0.08251 for Iteration #15 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00318 for iteration 15 of Tilt-Series #6.
Alignment quality for Iteration #15 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #6 (17jul05d): Very StableCreating 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00373 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 0.06641 for Iteration #16 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0032 for iteration 16 of Tilt-Series #6.
Alignment quality for Iteration #16 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #17 of Tilt-Series #6.
CCMS(rotations) = 0.07788 for Iteration #17 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00325 for iteration 17 of Tilt-Series #6.
Alignment quality for Iteration #17 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #18 of Tilt-Series #6.
CCMS(rotations) = 0.06875 for Iteration #18 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0033 for iteration 18 of Tilt-Series #6.
Alignment quality for Iteration #18 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00333 for Iteration #19 of Tilt-Series #6.
CCMS(rotations) = 0.07811 for Iteration #19 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00323 for iteration 19 of Tilt-Series #6.
Alignment quality for Iteration #19 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00382 for Iteration #20 of Tilt-Series #6.
CCMS(rotations) = 0.0682 for Iteration #20 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00328 for iteration 20 of Tilt-Series #6.
Alignment quality for Iteration #20 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_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 = 73.2890704878
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 = 73.2890704878
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00437 for Iteration #21 of Tilt-Series #6.
CCMS(rotations) = 0.09526 for Iteration #21 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00409 for iteration 21 of Tilt-Series #6.
Alignment quality for Iteration #21 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00295 for Iteration #22 of Tilt-Series #6.
CCMS(rotations) = 0.0954 for Iteration #22 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00338 for iteration 22 of Tilt-Series #6.
Alignment quality for Iteration #22 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #6 (17jul05d): Very StableCreating 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00305 for Iteration #23 of Tilt-Series #6.
CCMS(rotations) = 0.09808 for Iteration #23 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00349 for iteration 23 of Tilt-Series #6.
Alignment quality for Iteration #23 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00295 for Iteration #24 of Tilt-Series #6.
CCMS(rotations) = 0.09546 for Iteration #24 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00338 for iteration 24 of Tilt-Series #6.
Alignment quality for Iteration #24 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.003 for Iteration #25 of Tilt-Series #6.
CCMS(rotations) = 0.09118 for Iteration #25 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00332 for iteration 25 of Tilt-Series #6.
Alignment quality for Iteration #25 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_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 = 146.578140976
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 = 146.578140976
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00401 for Iteration #26 of Tilt-Series #6.
CCMS(rotations) = 0.07008 for Iteration #26 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00341 for iteration 26 of Tilt-Series #6.
Alignment quality for Iteration #26 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #6 (17jul05d): StableCreating 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #27 of Tilt-Series #6.
CCMS(rotations) = 0.07953 for Iteration #27 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00351 for iteration 27 of Tilt-Series #6.
Alignment quality for Iteration #27 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #6 (17jul05d): StableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00334 for Iteration #28 of Tilt-Series #6.
CCMS(rotations) = 0.0637 for Iteration #28 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00294 for iteration 28 of Tilt-Series #6.
Alignment quality for Iteration #28 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00375 for Iteration #29 of Tilt-Series #6.
CCMS(rotations) = 0.06417 for Iteration #29 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00316 for iteration 29 of Tilt-Series #6.
Alignment quality for Iteration #29 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #6 (17jul05d): Very StableCreating 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #30 of Tilt-Series #6.
CCMS(rotations) = 0.07999 for Iteration #30 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00342 for iteration 30 of Tilt-Series #6.
Alignment quality for Iteration #30 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #31 of Tilt-Series #6.
CCMS(rotations) = 0.06172 for Iteration #31 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00308 for iteration 31 of Tilt-Series #6.
Alignment quality for Iteration #31 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00283 for Iteration #32 of Tilt-Series #6.
CCMS(rotations) = 0.09005 for Iteration #32 of Tilt-Series #6.
CCMS(scale) = 0.00138 for Iteration #32 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0026 for iteration 32 of Tilt-Series #6.
Alignment quality for Iteration #32 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00237 for Iteration #33 of Tilt-Series #6.
CCMS(rotations) = 0.07424 for Iteration #33 of Tilt-Series #6.
CCMS(scale) = 0.00136 for Iteration #33 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00224 for iteration 33 of Tilt-Series #6.
Alignment quality for Iteration #33 of Tilt-Series #6 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #6 (17jul05d): 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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00287 for Iteration #34 of Tilt-Series #6.
CCMS(rotations) = 0.06453 for Iteration #34 of Tilt-Series #6.
CCMS(scale) = 0.00128 for Iteration #34 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00224 for iteration 34 of Tilt-Series #6.
Alignment quality for Iteration #34 of Tilt-Series #6 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #6 (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 #6 (tiltseries0006_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00315 for Iteration #35 of Tilt-Series #6.
CCMS(rotations) = 0.10338 for Iteration #35 of Tilt-Series #6.
CCMS(scale) = 0.00143 for Iteration #35 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00291 for iteration 35 of Tilt-Series #6.
Alignment quality for Iteration #35 of Tilt-Series #6 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #6 (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 #6 (tiltseries0006_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: 2017yr07m07d-00hr12m19s