protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/18mar15h/protomo_alignments/tiltseries0007_thick425 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3189.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2830 --r1_region_y=2396 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3189.0 --r4_lowpass_apod_y=13.0 --r4_lowpass_apod_x=13.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=27.0 --r3_lowpass_apod_y=27.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0007_thick425 --r2_region_y=2396 --r2_region_x=2830 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1595.0 --defocus_ang_positive=90 --r5_mask_width_x=2805 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3189.0 --r3_highpass_apod_x=1595.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=682 --r2_mask_width_y=574 --r5_region_x=2830 --r5_region_y=2396 --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=5.32 --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=3189.0 --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=2371 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1595.0 --r3_iters=5 --r1_highpass_diameter_x=3189.0 --r2_lowpass_diameter_y=21.28 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=2.66 --r5_lowpass_diameter_x=2.66 --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=2805 --r4_mask_width_y=2371 --r5_highpass_apod_y=1595.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar15h --exclude_images=999999 --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=1595.0 --r1_highpass_apod_x=1595.0 --r2_highpass_apod_x=1595.0 --sampling=8 --starting_tlt_file=Coarse_Iter_1 --r5_lowpass_apod_x=7.0 --r5_lowpass_apod_y=7.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=42.56 --r1_lowpass_diameter_x=42.56 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=7 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1173 --r3_mask_width_x=1390 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3189.0 --r4_highpass_diameter_x=3189.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=106.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3189.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1595.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3189.0 --defocus_max=0 --r4_region_y=2396 --r4_region_x=2830 --r5_kernel_y=5 --r3_region_x=2830 --r3_region_y=2396 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=425 --expid=6300 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=506 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=10.64 --r3_lowpass_diameter_x=10.64 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.331 --link=False --r2_highpass_diameter_x=3189.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=53.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=53.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --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=21.28 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=106.0 --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=1595.0 --r4_highpass_apod_y=1595.0 --azimuth=true --r1_mask_width_y=274 --r1_mask_width_x=328 --jobtype=protomo --from_multirefine=True

node08
Start time: 2018yr03m15d-13hr07m36s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
lowpass = 42.56 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 10.648 Angstroms, Nyquist is 21.296 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 47.125e0
map.sampling = 8
window.highpass.diameter = { 0.00667795547193 0.00667795547193 }
window.highpass.apodization = { 0.0133517241379 0.0133517241379 }
window.mask.apodization = { 10 10 }
align.mask.width = { 328 274 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 56.4473379436
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 353 299 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 328 274 }
reference.body = 56.4473379436
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0416 for Iteration #1 of Tilt-Series #7.
CCMS(rotations) = 1.39873 for Iteration #1 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7.
The scaled sum of CCMS values is #0.04877 for iteration 1 of Tilt-Series #7.
Alignment quality for Iteration #1 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00504 for Iteration #2 of Tilt-Series #7.
CCMS(rotations) = 0.10155 for Iteration #2 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00455 for iteration 2 of Tilt-Series #7.
Alignment quality for Iteration #2 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00348 for Iteration #3 of Tilt-Series #7.
CCMS(rotations) = 0.17824 for Iteration #3 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0053 for iteration 3 of Tilt-Series #7.
Alignment quality for Iteration #3 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00406 for Iteration #4 of Tilt-Series #7.
CCMS(rotations) = 0.11109 for Iteration #4 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00425 for iteration 4 of Tilt-Series #7.
Alignment quality for Iteration #4 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00314 for Iteration #5 of Tilt-Series #7.
CCMS(rotations) = 0.18468 for Iteration #5 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00526 for iteration 5 of Tilt-Series #7.
Alignment quality for Iteration #5 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00428 for Iteration #6 of Tilt-Series #7.
CCMS(rotations) = 0.11625 for Iteration #6 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00446 for iteration 6 of Tilt-Series #7.
Alignment quality for Iteration #6 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00325 for Iteration #7 of Tilt-Series #7.
CCMS(rotations) = 0.18933 for Iteration #7 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00541 for iteration 7 of Tilt-Series #7.
Alignment quality for Iteration #7 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00396 for Iteration #8 of Tilt-Series #7.
CCMS(rotations) = 0.11554 for Iteration #8 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00429 for iteration 8 of Tilt-Series #7.
Alignment quality for Iteration #8 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00307 for Iteration #9 of Tilt-Series #7.
CCMS(rotations) = 0.18124 for Iteration #9 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00516 for iteration 9 of Tilt-Series #7.
Alignment quality for Iteration #9 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00304 for Iteration #10 of Tilt-Series #7.
CCMS(rotations) = 0.11914 for Iteration #10 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0039 for iteration 10 of Tilt-Series #7.
Alignment quality for Iteration #10 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)
lowpass = 21.28 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 5.324 Angstroms, Nyquist is 10.648 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 94.25e0
map.sampling = 4
window.highpass.diameter = { 0.00333897773597 0.00333897773597 }
window.highpass.apodization = { 0.00667586206897 0.00667586206897 }
window.mask.apodization = { 10 10 }
align.mask.width = { 682 574 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 112.894675887
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 707 599 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 682 574 }
reference.body = 112.894675887
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00752 for Iteration #11 of Tilt-Series #7.
CCMS(rotations) = 0.11437 for Iteration #11 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00605 for iteration 11 of Tilt-Series #7.
Alignment quality for Iteration #11 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00225 for Iteration #12 of Tilt-Series #7.
CCMS(rotations) = 0.11305 for Iteration #12 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00339 for iteration 12 of Tilt-Series #7.
Alignment quality for Iteration #12 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00238 for Iteration #13 of Tilt-Series #7.
CCMS(rotations) = 0.13053 for Iteration #13 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0038 for iteration 13 of Tilt-Series #7.
Alignment quality for Iteration #13 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00282 for Iteration #14 of Tilt-Series #7.
CCMS(rotations) = 0.1253 for Iteration #14 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00391 for iteration 14 of Tilt-Series #7.
Alignment quality for Iteration #14 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00251 for Iteration #15 of Tilt-Series #7.
CCMS(rotations) = 0.13127 for Iteration #15 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00388 for iteration 15 of Tilt-Series #7.
Alignment quality for Iteration #15 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00278 for Iteration #16 of Tilt-Series #7.
CCMS(rotations) = 0.12856 for Iteration #16 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00396 for iteration 16 of Tilt-Series #7.
Alignment quality for Iteration #16 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #7 (18mar15h): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00247 for Iteration #17 of Tilt-Series #7.
CCMS(rotations) = 0.13749 for Iteration #17 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00399 for iteration 17 of Tilt-Series #7.
Alignment quality for Iteration #17 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00271 for Iteration #18 of Tilt-Series #7.
CCMS(rotations) = 0.1297 for Iteration #18 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00395 for iteration 18 of Tilt-Series #7.
Alignment quality for Iteration #18 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00265 for Iteration #19 of Tilt-Series #7.
CCMS(rotations) = 0.1291 for Iteration #19 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00391 for iteration 19 of Tilt-Series #7.
Alignment quality for Iteration #19 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00289 for Iteration #20 of Tilt-Series #7.
CCMS(rotations) = 0.13757 for Iteration #20 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0042 for iteration 20 of Tilt-Series #7.
Alignment quality for Iteration #20 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)
lowpass = 10.64 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 2.662 Angstroms, Nyquist is 5.324 Angstroms)
window.lowpass.apodization = { 0.197185185185 0.197185185185 }
align.translimit = 188.5e0
map.sampling = 2
window.highpass.diameter = { 0.00166948886798 0.00166948886798 }
window.highpass.apodization = { 0.00333793103448 0.00333793103448 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1390 1173 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 225.789351774
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1415 1198 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1390 1173 }
reference.body = 225.789351774
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00309 for Iteration #21 of Tilt-Series #7.
CCMS(rotations) = 0.0945 for Iteration #21 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00344 for iteration 21 of Tilt-Series #7.
Alignment quality for Iteration #21 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00253 for Iteration #22 of Tilt-Series #7.
CCMS(rotations) = 0.1254 for Iteration #22 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00377 for iteration 22 of Tilt-Series #7.
Alignment quality for Iteration #22 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00264 for Iteration #23 of Tilt-Series #7.
CCMS(rotations) = 0.12116 for Iteration #23 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00375 for iteration 23 of Tilt-Series #7.
Alignment quality for Iteration #23 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00279 for Iteration #24 of Tilt-Series #7.
CCMS(rotations) = 0.1251 for Iteration #24 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0039 for iteration 24 of Tilt-Series #7.
Alignment quality for Iteration #24 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00249 for Iteration #25 of Tilt-Series #7.
CCMS(rotations) = 0.11411 for Iteration #25 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00353 for iteration 25 of Tilt-Series #7.
Alignment quality for Iteration #25 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)
lowpass = 5.32 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.331 Angstroms, Nyquist is 2.662 Angstroms)
window.lowpass.apodization = { 0.204769230769 0.204769230769 }
align.translimit = 377.0e0
map.sampling = 1
window.highpass.diameter = { 0.000834744433992 0.000834744433992 }
window.highpass.apodization = { 0.00166896551724 0.00166896551724 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2805 2371 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 451.578703549
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2830 2396 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2805 2371 }
reference.body = 451.578703549
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00491 for Iteration #26 of Tilt-Series #7.
CCMS(rotations) = 0.14317 for Iteration #26 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00532 for iteration 26 of Tilt-Series #7.
Alignment quality for Iteration #26 of Tilt-Series #7 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00286 for Iteration #27 of Tilt-Series #7.
CCMS(rotations) = 0.13444 for Iteration #27 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00412 for iteration 27 of Tilt-Series #7.
Alignment quality for Iteration #27 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00301 for Iteration #28 of Tilt-Series #7.
CCMS(rotations) = 0.12614 for Iteration #28 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00403 for iteration 28 of Tilt-Series #7.
Alignment quality for Iteration #28 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #29 of Tilt-Series #7.
CCMS(rotations) = 0.11102 for Iteration #29 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00444 for iteration 29 of Tilt-Series #7.
Alignment quality for Iteration #29 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00339 for Iteration #30 of Tilt-Series #7.
CCMS(rotations) = 0.13318 for Iteration #30 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00436 for iteration 30 of Tilt-Series #7.
Alignment quality for Iteration #30 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00376 for Iteration #31 of Tilt-Series #7.
CCMS(rotations) = 0.13746 for Iteration #31 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00463 for iteration 31 of Tilt-Series #7.
Alignment quality for Iteration #31 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00262 for Iteration #32 of Tilt-Series #7.
CCMS(rotations) = 0.11078 for Iteration #32 of Tilt-Series #7.
CCMS(scale) = 0.00145 for Iteration #32 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00283 for iteration 32 of Tilt-Series #7.
Alignment quality for Iteration #32 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00285 for Iteration #33 of Tilt-Series #7.
CCMS(rotations) = 0.13752 for Iteration #33 of Tilt-Series #7.
CCMS(scale) = 0.00131 for Iteration #33 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00322 for iteration 33 of Tilt-Series #7.
Alignment quality for Iteration #33 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00284 for Iteration #34 of Tilt-Series #7.
CCMS(rotations) = 0.11039 for Iteration #34 of Tilt-Series #7.
CCMS(scale) = 0.00147 for Iteration #34 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00291 for iteration 34 of Tilt-Series #7.
Alignment quality for Iteration #34 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #7 (tiltseries0007_thick425)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00276 for Iteration #35 of Tilt-Series #7.
CCMS(rotations) = 0.14683 for Iteration #35 of Tilt-Series #7.
CCMS(scale) = 0.00134 for Iteration #35 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00333 for iteration 35 of Tilt-Series #7.
Alignment quality for Iteration #35 of Tilt-Series #7 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #7 (18mar15h): 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 #7 (tiltseries0007_thick425)!
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: 2018yr03m16d-02hr43m51s