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/18mar12b/protomo_alignments/tiltseries0005_thick550 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2591.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1947 --r1_region_y=2431 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2591.0 --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=tiltseries0005_thick550 --r2_region_y=2431 --r2_region_x=1947 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1296.0 --defocus_ang_positive=90 --r5_mask_width_x=1922 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2591.0 --r3_highpass_apod_x=1296.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=461 --r2_mask_width_y=582 --r5_region_x=1947 --r5_region_y=2431 --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=2591.0 --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=2406 --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=1296.0 --r3_iters=5 --r1_highpass_diameter_x=2591.0 --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=1922 --r4_mask_width_y=2406 --r5_highpass_apod_y=1296.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar12b --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=1296.0 --r1_highpass_apod_x=1296.0 --r2_highpass_apod_x=1296.0 --sampling=8 --starting_tlt_file=Manual --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=44.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-44.0 --parallel=True --tiltseries=5 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1190 --r3_mask_width_x=948 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2591.0 --r4_highpass_diameter_x=2591.0 --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=2591.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1296.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2591.0 --defocus_max=0 --r4_region_y=2431 --r4_region_x=1947 --r5_kernel_y=5 --r3_region_x=1947 --r3_region_y=2431 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=550 --expid=6268 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=340 --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=2591.0 --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=1296.0 --r4_highpass_apod_y=1296.0 --azimuth=true --r1_mask_width_y=278 --r1_mask_width_x=219 --jobtype=protomo --from_multirefine=True

node39
Start time: 2018yr03m12d-13hr15m45s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
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 = { 0.00821922037823 0.00821922037823 }
window.highpass.apodization = { 0.0164320987654 0.0164320987654 }
window.mask.apodization = { 10 10 }
align.mask.width = { 219 278 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 73.0494961623
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 243 303 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 219 278 }
reference.body = 73.0494961623
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04763 for Iteration #1 of Tilt-Series #5.
CCMS(rotations) = 0.63081 for Iteration #1 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03643 for iteration 1 of Tilt-Series #5.
Alignment quality for Iteration #1 of Tilt-Series #5 (18mar12b): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 93.548387%)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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03468 for Iteration #2 of Tilt-Series #5.
CCMS(rotations) = 0.55082 for Iteration #2 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02836 for iteration 2 of Tilt-Series #5.
Alignment quality for Iteration #2 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02435 for Iteration #3 of Tilt-Series #5.
CCMS(rotations) = 0.33494 for Iteration #3 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01888 for iteration 3 of Tilt-Series #5.
Alignment quality for Iteration #3 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02755 for Iteration #4 of Tilt-Series #5.
CCMS(rotations) = 0.25861 for Iteration #4 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01895 for iteration 4 of Tilt-Series #5.
Alignment quality for Iteration #4 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.02425 for Iteration #5 of Tilt-Series #5.
CCMS(rotations) = 0.65339 for Iteration #5 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02519 for iteration 5 of Tilt-Series #5.
Alignment quality for Iteration #5 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.03049 for Iteration #6 of Tilt-Series #5.
CCMS(rotations) = 0.81328 for Iteration #6 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03151 for iteration 6 of Tilt-Series #5.
Alignment quality for Iteration #6 of Tilt-Series #5 (18mar12b): Bad (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01515 for Iteration #7 of Tilt-Series #5.
CCMS(rotations) = 0.59029 for Iteration #7 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01938 for iteration 7 of Tilt-Series #5.
Alignment quality for Iteration #7 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.02092 for Iteration #8 of Tilt-Series #5.
CCMS(rotations) = 0.66925 for Iteration #8 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02384 for iteration 8 of Tilt-Series #5.
Alignment quality for Iteration #8 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.02204 for Iteration #9 of Tilt-Series #5.
CCMS(rotations) = 0.59024 for Iteration #9 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02282 for iteration 9 of Tilt-Series #5.
Alignment quality for Iteration #9 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.02071 for Iteration #10 of Tilt-Series #5.
CCMS(rotations) = 0.5765 for Iteration #10 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02188 for iteration 10 of Tilt-Series #5.
Alignment quality for Iteration #10 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)
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 = { 0.00410961018912 0.00410961018912 }
window.highpass.apodization = { 0.00821604938272 0.00821604938272 }
window.mask.apodization = { 10 10 }
align.mask.width = { 461 582 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 146.098992325
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 486 607 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 461 582 }
reference.body = 146.098992325
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01927 for Iteration #11 of Tilt-Series #5.
CCMS(rotations) = 0.6419 for Iteration #11 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02247 for iteration 11 of Tilt-Series #5.
Alignment quality for Iteration #11 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #5 (18mar12b): Very StableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.02215 for Iteration #12 of Tilt-Series #5.
CCMS(rotations) = 0.68392 for Iteration #12 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02475 for iteration 12 of Tilt-Series #5.
Alignment quality for Iteration #12 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01867 for Iteration #13 of Tilt-Series #5.
CCMS(rotations) = 0.58147 for Iteration #13 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02096 for iteration 13 of Tilt-Series #5.
Alignment quality for Iteration #13 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01255 for Iteration #14 of Tilt-Series #5.
CCMS(rotations) = 0.64934 for Iteration #14 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01926 for iteration 14 of Tilt-Series #5.
Alignment quality for Iteration #14 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01426 for Iteration #15 of Tilt-Series #5.
CCMS(rotations) = 0.46187 for Iteration #15 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01637 for iteration 15 of Tilt-Series #5.
Alignment quality for Iteration #15 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01327 for Iteration #16 of Tilt-Series #5.
CCMS(rotations) = 0.4024 for Iteration #16 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01468 for iteration 16 of Tilt-Series #5.
Alignment quality for Iteration #16 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01132 for Iteration #17 of Tilt-Series #5.
CCMS(rotations) = 0.41146 for Iteration #17 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01389 for iteration 17 of Tilt-Series #5.
Alignment quality for Iteration #17 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01251 for Iteration #18 of Tilt-Series #5.
CCMS(rotations) = 0.43273 for Iteration #18 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01491 for iteration 18 of Tilt-Series #5.
Alignment quality for Iteration #18 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01083 for Iteration #19 of Tilt-Series #5.
CCMS(rotations) = 0.34525 for Iteration #19 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01232 for iteration 19 of Tilt-Series #5.
Alignment quality for Iteration #19 of Tilt-Series #5 (18mar12b): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01086 for Iteration #20 of Tilt-Series #5.
CCMS(rotations) = 0.41412 for Iteration #20 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01371 for iteration 20 of Tilt-Series #5.
Alignment quality for Iteration #20 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)
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 = { 0.00205480509456 0.00205480509456 }
window.highpass.apodization = { 0.00410802469136 0.00410802469136 }
window.mask.apodization = { 10 10 }
align.mask.width = { 948 1190 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 292.197984649
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 973 1215 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 948 1190 }
reference.body = 292.197984649
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01263 for Iteration #21 of Tilt-Series #5.
CCMS(rotations) = 0.51494 for Iteration #21 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01662 for iteration 21 of Tilt-Series #5.
Alignment quality for Iteration #21 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #5 (18mar12b): UnstableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01434 for Iteration #22 of Tilt-Series #5.
CCMS(rotations) = 0.29778 for Iteration #22 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01312 for iteration 22 of Tilt-Series #5.
Alignment quality for Iteration #22 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01385 for Iteration #23 of Tilt-Series #5.
CCMS(rotations) = 0.37473 for Iteration #23 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01442 for iteration 23 of Tilt-Series #5.
Alignment quality for Iteration #23 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01494 for Iteration #24 of Tilt-Series #5.
CCMS(rotations) = 0.20135 for Iteration #24 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0115 for iteration 24 of Tilt-Series #5.
Alignment quality for Iteration #24 of Tilt-Series #5 (18mar12b): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01601 for Iteration #25 of Tilt-Series #5.
CCMS(rotations) = 0.33503 for Iteration #25 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0147 for iteration 25 of Tilt-Series #5.
Alignment quality for Iteration #25 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)
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 = { 0.00102740254728 0.00102740254728 }
window.highpass.apodization = { 0.00205401234568 0.00205401234568 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1922 2406 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 584.395969298
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1947 2431 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1922 2406 }
reference.body = 584.395969298
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01895 for Iteration #26 of Tilt-Series #5.
CCMS(rotations) = 0.4472 for Iteration #26 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01842 for iteration 26 of Tilt-Series #5.
Alignment quality for Iteration #26 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01768 for Iteration #27 of Tilt-Series #5.
CCMS(rotations) = 0.55108 for Iteration #27 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01986 for iteration 27 of Tilt-Series #5.
Alignment quality for Iteration #27 of Tilt-Series #5 (18mar12b): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01629 for Iteration #28 of Tilt-Series #5.
CCMS(rotations) = 0.67278 for Iteration #28 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0216 for iteration 28 of Tilt-Series #5.
Alignment quality for Iteration #28 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01764 for Iteration #29 of Tilt-Series #5.
CCMS(rotations) = 0.80232 for Iteration #29 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02486 for iteration 29 of Tilt-Series #5.
Alignment quality for Iteration #29 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01264 for Iteration #30 of Tilt-Series #5.
CCMS(rotations) = 0.90566 for Iteration #30 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02443 for iteration 30 of Tilt-Series #5.
Alignment quality for Iteration #30 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01869 for Iteration #31 of Tilt-Series #5.
CCMS(rotations) = 0.96103 for Iteration #31 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02856 for iteration 31 of Tilt-Series #5.
Alignment quality for Iteration #31 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #5 (18mar12b): UnstableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01758 for Iteration #32 of Tilt-Series #5.
CCMS(rotations) = 1.08636 for Iteration #32 of Tilt-Series #5.
CCMS(scale) = 0.00517 for Iteration #32 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02207 for iteration 32 of Tilt-Series #5.
Alignment quality for Iteration #32 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #5 (18mar12b): UnstableCreating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01586 for Iteration #33 of Tilt-Series #5.
CCMS(rotations) = 1.11976 for Iteration #33 of Tilt-Series #5.
CCMS(scale) = 0.00717 for Iteration #33 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02261 for iteration 33 of Tilt-Series #5.
Alignment quality for Iteration #33 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #5 (18mar12b): 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01715 for Iteration #34 of Tilt-Series #5.
CCMS(rotations) = 1.16423 for Iteration #34 of Tilt-Series #5.
CCMS(scale) = 0.00983 for Iteration #34 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02452 for iteration 34 of Tilt-Series #5.
Alignment quality for Iteration #34 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #5 (tiltseries0005_thick550)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01974 for Iteration #35 of Tilt-Series #5.
CCMS(rotations) = 1.15623 for Iteration #35 of Tilt-Series #5.
CCMS(scale) = 0.00996 for Iteration #35 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02531 for iteration 35 of Tilt-Series #5.
Alignment quality for Iteration #35 of Tilt-Series #5 (18mar12b): Okay (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #5 (18mar12b): UnstableCreating 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 #5 (tiltseries0005_thick550)!
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: 2018yr03m13d-10hr43m06s