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/tiltseries0006_thick425 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3154.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2676 --r1_region_y=2370 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3154.0 --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=tiltseries0006_thick425 --r2_region_y=2370 --r2_region_x=2676 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1577.0 --defocus_ang_positive=90 --r5_mask_width_x=2651 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3154.0 --r3_highpass_apod_x=1577.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=644 --r2_mask_width_y=567 --r5_region_x=2676 --r5_region_y=2370 --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=3154.0 --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=2345 --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=1577.0 --r3_iters=5 --r1_highpass_diameter_x=3154.0 --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=2651 --r4_mask_width_y=2345 --r5_highpass_apod_y=1577.0 --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=1577.0 --r1_highpass_apod_x=1577.0 --r2_highpass_apod_x=1577.0 --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=6 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1160 --r3_mask_width_x=1313 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3154.0 --r4_highpass_diameter_x=3154.0 --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=3154.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1577.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3154.0 --defocus_max=0 --r4_region_y=2370 --r4_region_x=2676 --r5_kernel_y=5 --r3_region_x=2676 --r3_region_y=2370 --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=3154.0 --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=1577.0 --r4_highpass_apod_y=1577.0 --azimuth=true --r1_mask_width_y=271 --r1_mask_width_x=309 --jobtype=protomo --from_multirefine=True

node06
Start time: 2018yr03m15d-13hr00m32s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006_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 = { 0.00675206087508 0.00675206087508 }
window.highpass.apodization = { 0.0135041217502 0.0135041217502 }
window.mask.apodization = { 10 10 }
align.mask.width = { 309 271 }
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 = { 334 296 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 309 271 }
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) = 0.06563 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 1.38587 for Iteration #1 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6.
The scaled sum of CCMS values is #0.06053 for iteration 1 of Tilt-Series #6.
Alignment quality for Iteration #1 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 0.11079 for Iteration #2 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00477 for iteration 2 of Tilt-Series #6.
Alignment quality for Iteration #2 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00602 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 0.12644 for Iteration #3 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00554 for iteration 3 of Tilt-Series #6.
Alignment quality for Iteration #3 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00557 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 0.16004 for Iteration #4 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00599 for iteration 4 of Tilt-Series #6.
Alignment quality for Iteration #4 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #6 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00556 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 0.14069 for Iteration #5 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00559 for iteration 5 of Tilt-Series #6.
Alignment quality for Iteration #5 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00587 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 0.1351 for Iteration #6 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00564 for iteration 6 of Tilt-Series #6.
Alignment quality for Iteration #6 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00587 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 0.15112 for Iteration #7 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00596 for iteration 7 of Tilt-Series #6.
Alignment quality for Iteration #7 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #6 (18mar15h): 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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00583 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 0.11833 for Iteration #8 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00528 for iteration 8 of Tilt-Series #6.
Alignment quality for Iteration #8 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00524 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 0.15665 for Iteration #9 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00575 for iteration 9 of Tilt-Series #6.
Alignment quality for Iteration #9 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00587 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 0.11897 for Iteration #10 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00532 for iteration 10 of Tilt-Series #6.
Alignment quality for Iteration #10 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #6 (tiltseries0006_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 = { 0.00337603043754 0.00337603043754 }
window.highpass.apodization = { 0.00675206087508 0.00675206087508 }
window.mask.apodization = { 10 10 }
align.mask.width = { 644 567 }
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 = { 669 592 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 644 567 }
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) = 0.00558 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 0.08583 for Iteration #11 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00451 for iteration 11 of Tilt-Series #6.
Alignment quality for Iteration #11 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00411 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 0.13294 for Iteration #12 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00471 for iteration 12 of Tilt-Series #6.
Alignment quality for Iteration #12 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00458 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 0.12547 for Iteration #13 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0048 for iteration 13 of Tilt-Series #6.
Alignment quality for Iteration #13 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00414 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 0.15167 for Iteration #14 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0051 for iteration 14 of Tilt-Series #6.
Alignment quality for Iteration #14 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00376 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 0.14268 for Iteration #15 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00473 for iteration 15 of Tilt-Series #6.
Alignment quality for Iteration #15 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 0.14136 for Iteration #16 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00527 for iteration 16 of Tilt-Series #6.
Alignment quality for Iteration #16 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #17 of Tilt-Series #6.
CCMS(rotations) = 0.13376 for Iteration #17 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00457 for iteration 17 of Tilt-Series #6.
Alignment quality for Iteration #17 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00474 for Iteration #18 of Tilt-Series #6.
CCMS(rotations) = 0.15094 for Iteration #18 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00539 for iteration 18 of Tilt-Series #6.
Alignment quality for Iteration #18 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00385 for Iteration #19 of Tilt-Series #6.
CCMS(rotations) = 0.12955 for Iteration #19 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00452 for iteration 19 of Tilt-Series #6.
Alignment quality for Iteration #19 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00474 for Iteration #20 of Tilt-Series #6.
CCMS(rotations) = 0.1383 for Iteration #20 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00513 for iteration 20 of Tilt-Series #6.
Alignment quality for Iteration #20 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #6 (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 #6 (tiltseries0006_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 = { 0.00168801521877 0.00168801521877 }
window.highpass.apodization = { 0.00337603043754 0.00337603043754 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1313 1160 }
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 = { 1338 1185 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1313 1160 }
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) = 0.00465 for Iteration #21 of Tilt-Series #6.
CCMS(rotations) = 0.13945 for Iteration #21 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00511 for iteration 21 of Tilt-Series #6.
Alignment quality for Iteration #21 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00499 for Iteration #22 of Tilt-Series #6.
CCMS(rotations) = 0.1382 for Iteration #22 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00526 for iteration 22 of Tilt-Series #6.
Alignment quality for Iteration #22 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00464 for Iteration #23 of Tilt-Series #6.
CCMS(rotations) = 0.14145 for Iteration #23 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00515 for iteration 23 of Tilt-Series #6.
Alignment quality for Iteration #23 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #6 (18mar15h): Very StableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00457 for Iteration #24 of Tilt-Series #6.
CCMS(rotations) = 0.13349 for Iteration #24 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00496 for iteration 24 of Tilt-Series #6.
Alignment quality for Iteration #24 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #25 of Tilt-Series #6.
CCMS(rotations) = 0.14104 for Iteration #25 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00524 for iteration 25 of Tilt-Series #6.
Alignment quality for Iteration #25 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #6 (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 #6 (tiltseries0006_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 = { 0.000844007609385 0.000844007609385 }
window.highpass.apodization = { 0.00168801521877 0.00168801521877 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2651 2345 }
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 = { 2676 2370 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2651 2345 }
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) = 0.00562 for Iteration #26 of Tilt-Series #6.
CCMS(rotations) = 0.17143 for Iteration #26 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00624 for iteration 26 of Tilt-Series #6.
Alignment quality for Iteration #26 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00614 for Iteration #27 of Tilt-Series #6.
CCMS(rotations) = 0.10297 for Iteration #27 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00513 for iteration 27 of Tilt-Series #6.
Alignment quality for Iteration #27 of Tilt-Series #6 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #6 (18mar15h): StableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00457 for Iteration #28 of Tilt-Series #6.
CCMS(rotations) = 0.11165 for Iteration #28 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00452 for iteration 28 of Tilt-Series #6.
Alignment quality for Iteration #28 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #6 (18mar15h): 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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #29 of Tilt-Series #6.
CCMS(rotations) = 0.10872 for Iteration #29 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00498 for iteration 29 of Tilt-Series #6.
Alignment quality for Iteration #29 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0054 for Iteration #30 of Tilt-Series #6.
CCMS(rotations) = 0.08603 for Iteration #30 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00442 for iteration 30 of Tilt-Series #6.
Alignment quality for Iteration #30 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #6 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00543 for Iteration #31 of Tilt-Series #6.
CCMS(rotations) = 0.08501 for Iteration #31 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00442 for iteration 31 of Tilt-Series #6.
Alignment quality for Iteration #31 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #32 of Tilt-Series #6.
CCMS(rotations) = 0.09818 for Iteration #32 of Tilt-Series #6.
CCMS(scale) = 0.00229 for Iteration #32 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0032 for iteration 32 of Tilt-Series #6.
Alignment quality for Iteration #32 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #6 (18mar15h): StableCreating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00285 for Iteration #33 of Tilt-Series #6.
CCMS(rotations) = 0.11774 for Iteration #33 of Tilt-Series #6.
CCMS(scale) = 0.00167 for Iteration #33 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00308 for iteration 33 of Tilt-Series #6.
Alignment quality for Iteration #33 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #6 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00243 for Iteration #34 of Tilt-Series #6.
CCMS(rotations) = 0.11858 for Iteration #34 of Tilt-Series #6.
CCMS(scale) = 0.00164 for Iteration #34 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00294 for iteration 34 of Tilt-Series #6.
Alignment quality for Iteration #34 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #6 (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 #6 (tiltseries0006_thick425)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006_thick425)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00274 for Iteration #35 of Tilt-Series #6.
CCMS(rotations) = 0.11765 for Iteration #35 of Tilt-Series #6.
CCMS(scale) = 0.00183 for Iteration #35 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00309 for iteration 35 of Tilt-Series #6.
Alignment quality for Iteration #35 of Tilt-Series #6 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #6 (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 #6 (tiltseries0006_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-04hr36m18s