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/tiltseries0002_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=tiltseries0002_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=2 --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

node22
Start time: 2017yr07m05d-13hr46m45s
Description: 
coarse_series0002_iter2.tlt not found, using coarse_series0002.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0002.tlt to series0002.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_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 = 19.2548288016
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 = 19.2548288016
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06312 for Iteration #1 of Tilt-Series #2.
CCMS(rotations) = 1.13987 for Iteration #1 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05436 for iteration 1 of Tilt-Series #2.
Alignment quality for Iteration #1 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.05683 for Iteration #2 of Tilt-Series #2.
CCMS(rotations) = 0.74333 for Iteration #2 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04328 for iteration 2 of Tilt-Series #2.
Alignment quality for Iteration #2 of Tilt-Series #2 (17jul05d): Bad (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.0487 for Iteration #3 of Tilt-Series #2.
CCMS(rotations) = 1.22859 for Iteration #3 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04892 for iteration 3 of Tilt-Series #2.
Alignment quality for Iteration #3 of Tilt-Series #2 (17jul05d): Bad (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.04699 for Iteration #4 of Tilt-Series #2.
CCMS(rotations) = 1.45366 for Iteration #4 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05257 for iteration 4 of Tilt-Series #2.
Alignment quality for Iteration #4 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (17jul05d): Very StableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.04867 for Iteration #5 of Tilt-Series #2.
CCMS(rotations) = 1.24907 for Iteration #5 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04932 for iteration 5 of Tilt-Series #2.
Alignment quality for Iteration #5 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.04722 for Iteration #6 of Tilt-Series #2.
CCMS(rotations) = 1.40527 for Iteration #6 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05172 for iteration 6 of Tilt-Series #2.
Alignment quality for Iteration #6 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.0477 for Iteration #7 of Tilt-Series #2.
CCMS(rotations) = 1.27754 for Iteration #7 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0494 for iteration 7 of Tilt-Series #2.
Alignment quality for Iteration #7 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.04826 for Iteration #8 of Tilt-Series #2.
CCMS(rotations) = 1.40334 for Iteration #8 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0522 for iteration 8 of Tilt-Series #2.
Alignment quality for Iteration #8 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.04675 for Iteration #9 of Tilt-Series #2.
CCMS(rotations) = 1.33972 for Iteration #9 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05017 for iteration 9 of Tilt-Series #2.
Alignment quality for Iteration #9 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.04864 for Iteration #10 of Tilt-Series #2.
CCMS(rotations) = 1.35366 for Iteration #10 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05139 for iteration 10 of Tilt-Series #2.
Alignment quality for Iteration #10 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (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 #2 (tiltseries0002_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 = 38.5096576032
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 = 38.5096576032
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0471 for Iteration #11 of Tilt-Series #2.
CCMS(rotations) = 1.42485 for Iteration #11 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05204 for iteration 11 of Tilt-Series #2.
Alignment quality for Iteration #11 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.04745 for Iteration #12 of Tilt-Series #2.
CCMS(rotations) = 1.41282 for Iteration #12 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05198 for iteration 12 of Tilt-Series #2.
Alignment quality for Iteration #12 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.04723 for Iteration #13 of Tilt-Series #2.
CCMS(rotations) = 1.40552 for Iteration #13 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05173 for iteration 13 of Tilt-Series #2.
Alignment quality for Iteration #13 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.04715 for Iteration #14 of Tilt-Series #2.
CCMS(rotations) = 1.43077 for Iteration #14 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05219 for iteration 14 of Tilt-Series #2.
Alignment quality for Iteration #14 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.04685 for Iteration #15 of Tilt-Series #2.
CCMS(rotations) = 1.42214 for Iteration #15 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05187 for iteration 15 of Tilt-Series #2.
Alignment quality for Iteration #15 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0475 for Iteration #16 of Tilt-Series #2.
CCMS(rotations) = 1.4267 for Iteration #16 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05228 for iteration 16 of Tilt-Series #2.
Alignment quality for Iteration #16 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.0466 for Iteration #17 of Tilt-Series #2.
CCMS(rotations) = 1.43722 for Iteration #17 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05204 for iteration 17 of Tilt-Series #2.
Alignment quality for Iteration #17 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.04747 for Iteration #18 of Tilt-Series #2.
CCMS(rotations) = 1.4305 for Iteration #18 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05235 for iteration 18 of Tilt-Series #2.
Alignment quality for Iteration #18 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0471 for Iteration #19 of Tilt-Series #2.
CCMS(rotations) = 1.43002 for Iteration #19 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05215 for iteration 19 of Tilt-Series #2.
Alignment quality for Iteration #19 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.04693 for Iteration #20 of Tilt-Series #2.
CCMS(rotations) = 1.44696 for Iteration #20 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0524 for iteration 20 of Tilt-Series #2.
Alignment quality for Iteration #20 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (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 #2 (tiltseries0002_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 = 77.0193152064
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 = 77.0193152064
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.04489 for Iteration #21 of Tilt-Series #2.
CCMS(rotations) = 1.38716 for Iteration #21 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05019 for iteration 21 of Tilt-Series #2.
Alignment quality for Iteration #21 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.04643 for Iteration #22 of Tilt-Series #2.
CCMS(rotations) = 1.3966 for Iteration #22 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05115 for iteration 22 of Tilt-Series #2.
Alignment quality for Iteration #22 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.04667 for Iteration #23 of Tilt-Series #2.
CCMS(rotations) = 1.41009 for Iteration #23 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05154 for iteration 23 of Tilt-Series #2.
Alignment quality for Iteration #23 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.04702 for Iteration #24 of Tilt-Series #2.
CCMS(rotations) = 1.40935 for Iteration #24 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0517 for iteration 24 of Tilt-Series #2.
Alignment quality for Iteration #24 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.04662 for Iteration #25 of Tilt-Series #2.
CCMS(rotations) = 1.41532 for Iteration #25 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2.
The scaled sum of CCMS values is #0.05162 for iteration 25 of Tilt-Series #2.
Alignment quality for Iteration #25 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (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 #2 (tiltseries0002_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 = 154.038630413
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 = 154.038630413
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.04661 for Iteration #26 of Tilt-Series #2.
CCMS(rotations) = 1.27545 for Iteration #26 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04882 for iteration 26 of Tilt-Series #2.
Alignment quality for Iteration #26 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.04564 for Iteration #27 of Tilt-Series #2.
CCMS(rotations) = 1.2905 for Iteration #27 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04863 for iteration 27 of Tilt-Series #2.
Alignment quality for Iteration #27 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.04619 for Iteration #28 of Tilt-Series #2.
CCMS(rotations) = 1.24163 for Iteration #28 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04793 for iteration 28 of Tilt-Series #2.
Alignment quality for Iteration #28 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.04591 for Iteration #29 of Tilt-Series #2.
CCMS(rotations) = 1.13298 for Iteration #29 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04561 for iteration 29 of Tilt-Series #2.
Alignment quality for Iteration #29 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.04566 for Iteration #30 of Tilt-Series #2.
CCMS(rotations) = 1.01489 for Iteration #30 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04313 for iteration 30 of Tilt-Series #2.
Alignment quality for Iteration #30 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (17jul05d): Very StableCreating 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.04505 for Iteration #31 of Tilt-Series #2.
CCMS(rotations) = 1.32943 for Iteration #31 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2.
The scaled sum of CCMS values is #0.04912 for iteration 31 of Tilt-Series #2.
Alignment quality for Iteration #31 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.02538 for Iteration #32 of Tilt-Series #2.
CCMS(rotations) = 1.03625 for Iteration #32 of Tilt-Series #2.
CCMS(scale) = 0.02206 for Iteration #32 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02963 for iteration 32 of Tilt-Series #2.
Alignment quality for Iteration #32 of Tilt-Series #2 (17jul05d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.02171 for Iteration #33 of Tilt-Series #2.
CCMS(rotations) = 1.22035 for Iteration #33 of Tilt-Series #2.
CCMS(scale) = 0.02542 for Iteration #33 of Tilt-Series #2.
The scaled sum of CCMS values is #0.03198 for iteration 33 of Tilt-Series #2.
Alignment quality for Iteration #33 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (17jul05d): 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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.02164 for Iteration #34 of Tilt-Series #2.
CCMS(rotations) = 1.25656 for Iteration #34 of Tilt-Series #2.
CCMS(scale) = 0.02633 for Iteration #34 of Tilt-Series #2.
The scaled sum of CCMS values is #0.03274 for iteration 34 of Tilt-Series #2.
Alignment quality for Iteration #34 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (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 #2 (tiltseries0002_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.02236 for Iteration #35 of Tilt-Series #2.
CCMS(rotations) = 1.31827 for Iteration #35 of Tilt-Series #2.
CCMS(scale) = 0.0266 for Iteration #35 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0339 for iteration 35 of Tilt-Series #2.
Alignment quality for Iteration #35 of Tilt-Series #2 (17jul05d): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (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 #2 (tiltseries0002_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-06hr13m22s