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/tiltseries0008_thick350 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3571.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2835 --r1_region_y=2683 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3571.0 --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=tiltseries0008_thick350 --r2_region_y=2683 --r2_region_x=2835 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1786.0 --defocus_ang_positive=90 --r5_mask_width_x=2810 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3571.0 --r3_highpass_apod_x=1786.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=683 --r2_mask_width_y=645 --r5_region_x=2835 --r5_region_y=2683 --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=3571.0 --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=2658 --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=1786.0 --r3_iters=5 --r1_highpass_diameter_x=3571.0 --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=2810 --r4_mask_width_y=2658 --r5_highpass_apod_y=1786.0 --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=1786.0 --r1_highpass_apod_x=1786.0 --r2_highpass_apod_x=1786.0 --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=8 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1316 --r3_mask_width_x=1392 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3571.0 --r4_highpass_diameter_x=3571.0 --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=3571.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1786.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3571.0 --defocus_max=0 --r4_region_y=2683 --r4_region_x=2835 --r5_kernel_y=5 --r3_region_x=2835 --r3_region_y=2683 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=350 --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=3571.0 --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=1786.0 --r4_highpass_apod_y=1786.0 --azimuth=true --r1_mask_width_y=310 --r1_mask_width_x=329 --jobtype=protomo --from_multirefine=True

node38
Start time: 2018yr03m15d-13hr28m33s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
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 = { 0.00596359563148 0.00596359563148 }
window.highpass.apodization = { 0.0119238521837 0.0119238521837 }
window.mask.apodization = { 10 10 }
align.mask.width = { 329 310 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 46.4860430124
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 354 335 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 329 310 }
reference.body = 46.4860430124
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07847 for Iteration #1 of Tilt-Series #8.
CCMS(rotations) = 1.26504 for Iteration #1 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8.
The scaled sum of CCMS values is #0.06453 for iteration 1 of Tilt-Series #8.
Alignment quality for Iteration #1 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #2 of Tilt-Series #8.
CCMS(rotations) = 0.22038 for Iteration #2 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00758 for iteration 2 of Tilt-Series #8.
Alignment quality for Iteration #2 of Tilt-Series #8 (18mar15h): Very Good (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00653 for Iteration #3 of Tilt-Series #8.
CCMS(rotations) = 0.1488 for Iteration #3 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00624 for iteration 3 of Tilt-Series #8.
Alignment quality for Iteration #3 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00617 for Iteration #4 of Tilt-Series #8.
CCMS(rotations) = 0.19321 for Iteration #4 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00695 for iteration 4 of Tilt-Series #8.
Alignment quality for Iteration #4 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #8 (18mar15h): 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00785 for Iteration #5 of Tilt-Series #8.
CCMS(rotations) = 0.16521 for Iteration #5 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00723 for iteration 5 of Tilt-Series #8.
Alignment quality for Iteration #5 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #6 of Tilt-Series #8.
CCMS(rotations) = 0.17503 for Iteration #6 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00657 for iteration 6 of Tilt-Series #8.
Alignment quality for Iteration #6 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #8 (18mar15h): 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00811 for Iteration #7 of Tilt-Series #8.
CCMS(rotations) = 0.18087 for Iteration #7 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00767 for iteration 7 of Tilt-Series #8.
Alignment quality for Iteration #7 of Tilt-Series #8 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #8 (18mar15h): Very StableCreating 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00607 for Iteration #8 of Tilt-Series #8.
CCMS(rotations) = 0.17997 for Iteration #8 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00664 for iteration 8 of Tilt-Series #8.
Alignment quality for Iteration #8 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #8 (18mar15h): Very StableCreating 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00618 for Iteration #9 of Tilt-Series #8.
CCMS(rotations) = 0.16501 for Iteration #9 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00639 for iteration 9 of Tilt-Series #8.
Alignment quality for Iteration #9 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00524 for Iteration #10 of Tilt-Series #8.
CCMS(rotations) = 0.19584 for Iteration #10 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00654 for iteration 10 of Tilt-Series #8.
Alignment quality for Iteration #10 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)
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 = { 0.00298179781574 0.00298179781574 }
window.highpass.apodization = { 0.00596192609183 0.00596192609183 }
window.mask.apodization = { 10 10 }
align.mask.width = { 683 645 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 92.9720860248
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 708 670 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 683 645 }
reference.body = 92.9720860248
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0039 for Iteration #11 of Tilt-Series #8.
CCMS(rotations) = 0.21745 for Iteration #11 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0063 for iteration 11 of Tilt-Series #8.
Alignment quality for Iteration #11 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #8 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00315 for Iteration #12 of Tilt-Series #8.
CCMS(rotations) = 0.18914 for Iteration #12 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00536 for iteration 12 of Tilt-Series #8.
Alignment quality for Iteration #12 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00324 for Iteration #13 of Tilt-Series #8.
CCMS(rotations) = 0.193 for Iteration #13 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00548 for iteration 13 of Tilt-Series #8.
Alignment quality for Iteration #13 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00303 for Iteration #14 of Tilt-Series #8.
CCMS(rotations) = 0.19058 for Iteration #14 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00533 for iteration 14 of Tilt-Series #8.
Alignment quality for Iteration #14 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00304 for Iteration #15 of Tilt-Series #8.
CCMS(rotations) = 0.19009 for Iteration #15 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00532 for iteration 15 of Tilt-Series #8.
Alignment quality for Iteration #15 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #8 (18mar15h): 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00317 for Iteration #16 of Tilt-Series #8.
CCMS(rotations) = 0.18323 for Iteration #16 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00525 for iteration 16 of Tilt-Series #8.
Alignment quality for Iteration #16 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #8 (18mar15h): 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00312 for Iteration #17 of Tilt-Series #8.
CCMS(rotations) = 0.19712 for Iteration #17 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0055 for iteration 17 of Tilt-Series #8.
Alignment quality for Iteration #17 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00328 for Iteration #18 of Tilt-Series #8.
CCMS(rotations) = 0.18069 for Iteration #18 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00525 for iteration 18 of Tilt-Series #8.
Alignment quality for Iteration #18 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #8 (18mar15h): Very StableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #19 of Tilt-Series #8.
CCMS(rotations) = 0.20454 for Iteration #19 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00606 for iteration 19 of Tilt-Series #8.
Alignment quality for Iteration #19 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #8 (18mar15h): UnstableCreating 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00317 for Iteration #20 of Tilt-Series #8.
CCMS(rotations) = 0.19141 for Iteration #20 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00541 for iteration 20 of Tilt-Series #8.
Alignment quality for Iteration #20 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #8 (18mar15h): Very StableCreating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #3 of Tilt-Series #8 (tiltseries0008_thick350)
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 = { 0.00149089890787 0.00149089890787 }
window.highpass.apodization = { 0.00298096304591 0.00298096304591 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1392 1316 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 185.94417205
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1417 1341 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1392 1316 }
reference.body = 185.94417205
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00406 for Iteration #21 of Tilt-Series #8.
CCMS(rotations) = 0.21532 for Iteration #21 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00634 for iteration 21 of Tilt-Series #8.
Alignment quality for Iteration #21 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00381 for Iteration #22 of Tilt-Series #8.
CCMS(rotations) = 0.2043 for Iteration #22 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00599 for iteration 22 of Tilt-Series #8.
Alignment quality for Iteration #22 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #23 of Tilt-Series #8.
CCMS(rotations) = 0.2153 for Iteration #23 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00623 for iteration 23 of Tilt-Series #8.
Alignment quality for Iteration #23 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00392 for Iteration #24 of Tilt-Series #8.
CCMS(rotations) = 0.20353 for Iteration #24 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00603 for iteration 24 of Tilt-Series #8.
Alignment quality for Iteration #24 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00401 for Iteration #25 of Tilt-Series #8.
CCMS(rotations) = 0.21962 for Iteration #25 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0064 for iteration 25 of Tilt-Series #8.
Alignment quality for Iteration #25 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #8 (18mar15h): Very StableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
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 = { 0.000745449453934 0.000745449453934 }
window.highpass.apodization = { 0.00149048152296 0.00149048152296 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2810 2658 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 371.888344099
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2835 2683 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2810 2658 }
reference.body = 371.888344099
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #26 of Tilt-Series #8.
CCMS(rotations) = 0.19276 for Iteration #26 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00668 for iteration 26 of Tilt-Series #8.
Alignment quality for Iteration #26 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00381 for Iteration #27 of Tilt-Series #8.
CCMS(rotations) = 0.2672 for Iteration #27 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00725 for iteration 27 of Tilt-Series #8.
Alignment quality for Iteration #27 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00419 for Iteration #28 of Tilt-Series #8.
CCMS(rotations) = 0.27124 for Iteration #28 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00752 for iteration 28 of Tilt-Series #8.
Alignment quality for Iteration #28 of Tilt-Series #8 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00397 for Iteration #29 of Tilt-Series #8.
CCMS(rotations) = 0.30259 for Iteration #29 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00803 for iteration 29 of Tilt-Series #8.
Alignment quality for Iteration #29 of Tilt-Series #8 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #8 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00378 for Iteration #30 of Tilt-Series #8.
CCMS(rotations) = 0.27318 for Iteration #30 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00735 for iteration 30 of Tilt-Series #8.
Alignment quality for Iteration #30 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00331 for Iteration #31 of Tilt-Series #8.
CCMS(rotations) = 0.2927 for Iteration #31 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00751 for iteration 31 of Tilt-Series #8.
Alignment quality for Iteration #31 of Tilt-Series #8 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #8 (18mar15h): StableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00293 for Iteration #32 of Tilt-Series #8.
CCMS(rotations) = 0.30204 for Iteration #32 of Tilt-Series #8.
CCMS(scale) = 0.0016 for Iteration #32 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00554 for iteration 32 of Tilt-Series #8.
Alignment quality for Iteration #32 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #8 (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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00404 for Iteration #33 of Tilt-Series #8.
CCMS(rotations) = 0.27214 for Iteration #33 of Tilt-Series #8.
CCMS(scale) = 0.002 for Iteration #33 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00564 for iteration 33 of Tilt-Series #8.
Alignment quality for Iteration #33 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #8 (18mar15h): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00286 for Iteration #34 of Tilt-Series #8.
CCMS(rotations) = 0.24871 for Iteration #34 of Tilt-Series #8.
CCMS(scale) = 0.00149 for Iteration #34 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00477 for iteration 34 of Tilt-Series #8.
Alignment quality for Iteration #34 of Tilt-Series #8 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #8 (18mar15h): Very StableCreating 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 #8 (tiltseries0008_thick350)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #8 (tiltseries0008_thick350)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #35 of Tilt-Series #8.
CCMS(rotations) = 0.27425 for Iteration #35 of Tilt-Series #8.
CCMS(scale) = 0.00137 for Iteration #35 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00535 for iteration 35 of Tilt-Series #8.
Alignment quality for Iteration #35 of Tilt-Series #8 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #8 (18mar15h): Rock Solid!Creating 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 #8 (tiltseries0008_thick350)!
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-07hr39m53s