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/jbrasch/19mar29h/protomo_alignments/tiltseries0002_thick1000 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4834.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2633 --r1_region_y=3083 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4834.0 --r4_lowpass_apod_y=18.0 --r4_lowpass_apod_x=18.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=37.0 --r3_lowpass_apod_y=37.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0002_thick1000 --r2_region_y=3083 --r2_region_x=2633 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2417.0 --defocus_ang_positive=90 --r5_mask_width_x=2608 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4834.0 --r3_highpass_apod_x=2417.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=633 --r2_mask_width_y=745 --r5_region_x=2633 --r5_region_y=3083 --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=7.36 --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=4834.0 --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=3058 --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=2417.0 --r3_iters=5 --r1_highpass_diameter_x=4834.0 --r2_lowpass_diameter_y=29.44 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.68 --r5_lowpass_diameter_x=3.68 --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=2608 --r4_mask_width_y=3058 --r5_highpass_apod_y=2417.0 --logging=true --DefocusTol=200 --filter=median --sessionname=19mar29h --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=2417.0 --r1_highpass_apod_x=2417.0 --r2_highpass_apod_x=2417.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=9.0 --r5_lowpass_apod_y=9.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=58.88 --r1_lowpass_diameter_x=58.88 --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=2 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1516 --r3_mask_width_x=1291 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4834.0 --r4_highpass_diameter_x=4834.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=147.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4834.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2417.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4834.0 --defocus_max=0 --r4_region_y=3083 --r4_region_x=2633 --r5_kernel_y=5 --r3_region_x=2633 --r3_region_y=3083 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=1000 --expid=8799 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=14.72 --r3_lowpass_diameter_x=14.72 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=4834.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=74.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=74.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=301.0 --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=29.44 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=147.0 --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=2.5 --tilt_clip=true --r4_highpass_apod_x=2417.0 --r4_highpass_apod_y=2417.0 --azimuth=true --r1_mask_width_y=360 --r1_mask_width_x=304 --jobtype=protomo --from_multirefine=True

node18
Start time: 2019yr05m16d-12hr13m00s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
lowpass = 58.88 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.199821496599 0.199821496599 }
align.translimit = 37.625e0
map.sampling = 8
window.highpass.diameter = { 0.00607649151841 0.00607649151841 }
window.highpass.apodization = { 0.0121529830368 0.0121529830368 }
window.mask.apodization = { 10 10 }
align.mask.width = { 304 360 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 110.575922404
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 329 385 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 304 360 }
reference.body = 110.575922404
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.10651 for Iteration #1 of Tilt-Series #2.
CCMS(rotations) = 1.50416 for Iteration #1 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2.
The scaled sum of CCMS values is #0.08334 for iteration 1 of Tilt-Series #2.
Alignment quality for Iteration #1 of Tilt-Series #2 (19mar29h): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.09554 for Iteration #2 of Tilt-Series #2.
CCMS(rotations) = 1.89496 for Iteration #2 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2.
The scaled sum of CCMS values is #0.08567 for iteration 2 of Tilt-Series #2.
Alignment quality for Iteration #2 of Tilt-Series #2 (19mar29h): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.04256 for Iteration #3 of Tilt-Series #2.
CCMS(rotations) = 0.41364 for Iteration #3 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02955 for iteration 3 of Tilt-Series #2.
Alignment quality for Iteration #3 of Tilt-Series #2 (19mar29h): Okay (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01335 for Iteration #4 of Tilt-Series #2.
CCMS(rotations) = 0.1645 for Iteration #4 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00997 for iteration 4 of Tilt-Series #2.
Alignment quality for Iteration #4 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (19mar29h): StableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00912 for Iteration #5 of Tilt-Series #2.
CCMS(rotations) = 0.18896 for Iteration #5 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00834 for iteration 5 of Tilt-Series #2.
Alignment quality for Iteration #5 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (19mar29h): StableCreating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00862 for Iteration #6 of Tilt-Series #2.
CCMS(rotations) = 0.21983 for Iteration #6 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00871 for iteration 6 of Tilt-Series #2.
Alignment quality for Iteration #6 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (19mar29h): StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00755 for Iteration #7 of Tilt-Series #2.
CCMS(rotations) = 0.18696 for Iteration #7 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00751 for iteration 7 of Tilt-Series #2.
Alignment quality for Iteration #7 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00703 for Iteration #8 of Tilt-Series #2.
CCMS(rotations) = 0.20171 for Iteration #8 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00755 for iteration 8 of Tilt-Series #2.
Alignment quality for Iteration #8 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00754 for Iteration #9 of Tilt-Series #2.
CCMS(rotations) = 0.21288 for Iteration #9 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00803 for iteration 9 of Tilt-Series #2.
Alignment quality for Iteration #9 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00713 for Iteration #10 of Tilt-Series #2.
CCMS(rotations) = 0.18188 for Iteration #10 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0072 for iteration 10 of Tilt-Series #2.
Alignment quality for Iteration #10 of Tilt-Series #2 (19mar29h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
lowpass = 29.44 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.198471351351 0.198471351351 }
align.translimit = 75.25e0
map.sampling = 4
window.highpass.diameter = { 0.00303824575921 0.00303824575921 }
window.highpass.apodization = { 0.00607649151841 0.00607649151841 }
window.mask.apodization = { 10 10 }
align.mask.width = { 633 745 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 221.151844808
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 658 770 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 633 745 }
reference.body = 221.151844808
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01261 for Iteration #11 of Tilt-Series #2.
CCMS(rotations) = 0.3359 for Iteration #11 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01302 for iteration 11 of Tilt-Series #2.
Alignment quality for Iteration #11 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (19mar29h): UnstableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00957 for Iteration #12 of Tilt-Series #2.
CCMS(rotations) = 0.19617 for Iteration #12 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00871 for iteration 12 of Tilt-Series #2.
Alignment quality for Iteration #12 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00792 for Iteration #13 of Tilt-Series #2.
CCMS(rotations) = 0.13431 for Iteration #13 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00664 for iteration 13 of Tilt-Series #2.
Alignment quality for Iteration #13 of Tilt-Series #2 (19mar29h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00951 for Iteration #14 of Tilt-Series #2.
CCMS(rotations) = 0.18076 for Iteration #14 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00837 for iteration 14 of Tilt-Series #2.
Alignment quality for Iteration #14 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00916 for Iteration #15 of Tilt-Series #2.
CCMS(rotations) = 0.17025 for Iteration #15 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00799 for iteration 15 of Tilt-Series #2.
Alignment quality for Iteration #15 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00904 for Iteration #16 of Tilt-Series #2.
CCMS(rotations) = 0.21231 for Iteration #16 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00877 for iteration 16 of Tilt-Series #2.
Alignment quality for Iteration #16 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00952 for Iteration #17 of Tilt-Series #2.
CCMS(rotations) = 0.26174 for Iteration #17 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01 for iteration 17 of Tilt-Series #2.
Alignment quality for Iteration #17 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (19mar29h): Very StableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00958 for Iteration #18 of Tilt-Series #2.
CCMS(rotations) = 0.14493 for Iteration #18 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00769 for iteration 18 of Tilt-Series #2.
Alignment quality for Iteration #18 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00855 for Iteration #19 of Tilt-Series #2.
CCMS(rotations) = 0.23809 for Iteration #19 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00904 for iteration 19 of Tilt-Series #2.
Alignment quality for Iteration #19 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00945 for Iteration #20 of Tilt-Series #2.
CCMS(rotations) = 0.22104 for Iteration #20 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00914 for iteration 20 of Tilt-Series #2.
Alignment quality for Iteration #20 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (19mar29h): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...

Beginning Refinement Iteration #21, Round #3 of Tilt-Series #2 (tiltseries0002_thick1000)
lowpass = 14.72 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.198471351351 0.198471351351 }
align.translimit = 150.5e0
map.sampling = 2
window.highpass.diameter = { 0.0015191228796 0.0015191228796 }
window.highpass.apodization = { 0.00303824575921 0.00303824575921 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1291 1516 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 442.303689615
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1316 1541 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1291 1516 }
reference.body = 442.303689615
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00865 for Iteration #21 of Tilt-Series #2.
CCMS(rotations) = 0.2686 for Iteration #21 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0097 for iteration 21 of Tilt-Series #2.
Alignment quality for Iteration #21 of Tilt-Series #2 (19mar29h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01313 for Iteration #22 of Tilt-Series #2.
CCMS(rotations) = 0.40903 for Iteration #22 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01474 for iteration 22 of Tilt-Series #2.
Alignment quality for Iteration #22 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01091 for Iteration #23 of Tilt-Series #2.
CCMS(rotations) = 0.42529 for Iteration #23 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01396 for iteration 23 of Tilt-Series #2.
Alignment quality for Iteration #23 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01205 for Iteration #24 of Tilt-Series #2.
CCMS(rotations) = 0.50935 for Iteration #24 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01621 for iteration 24 of Tilt-Series #2.
Alignment quality for Iteration #24 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (19mar29h): Very StableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00984 for Iteration #25 of Tilt-Series #2.
CCMS(rotations) = 0.4775 for Iteration #25 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01447 for iteration 25 of Tilt-Series #2.
Alignment quality for Iteration #25 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)
lowpass = 7.36 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.203984444444 0.203984444444 }
align.translimit = 301.0e0
map.sampling = 1
window.highpass.diameter = { 0.000759561439801 0.000759561439801 }
window.highpass.apodization = { 0.0015191228796 0.0015191228796 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2608 3058 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 884.60737923
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2633 3083 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2608 3058 }
reference.body = 884.60737923
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01278 for Iteration #26 of Tilt-Series #2.
CCMS(rotations) = 0.45117 for Iteration #26 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01541 for iteration 26 of Tilt-Series #2.
Alignment quality for Iteration #26 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (19mar29h): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01095 for Iteration #27 of Tilt-Series #2.
CCMS(rotations) = 0.58427 for Iteration #27 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01716 for iteration 27 of Tilt-Series #2.
Alignment quality for Iteration #27 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (19mar29h): Very 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01217 for Iteration #28 of Tilt-Series #2.
CCMS(rotations) = 0.57809 for Iteration #28 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01765 for iteration 28 of Tilt-Series #2.
Alignment quality for Iteration #28 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0113 for Iteration #29 of Tilt-Series #2.
CCMS(rotations) = 0.59884 for Iteration #29 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01763 for iteration 29 of Tilt-Series #2.
Alignment quality for Iteration #29 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (19mar29h): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01226 for Iteration #30 of Tilt-Series #2.
CCMS(rotations) = 0.70056 for Iteration #30 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02014 for iteration 30 of Tilt-Series #2.
Alignment quality for Iteration #30 of Tilt-Series #2 (19mar29h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01435 for Iteration #31 of Tilt-Series #2.
CCMS(rotations) = 0.74999 for Iteration #31 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02218 for iteration 31 of Tilt-Series #2.
Alignment quality for Iteration #31 of Tilt-Series #2 (19mar29h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (19mar29h): Very 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0116 for Iteration #32 of Tilt-Series #2.
CCMS(rotations) = 0.86419 for Iteration #32 of Tilt-Series #2.
CCMS(scale) = 0.00506 for Iteration #32 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01708 for iteration 32 of Tilt-Series #2.
Alignment quality for Iteration #32 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (19mar29h): Very 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01176 for Iteration #33 of Tilt-Series #2.
CCMS(rotations) = 0.97809 for Iteration #33 of Tilt-Series #2.
CCMS(scale) = 0.00697 for Iteration #33 of Tilt-Series #2.
The scaled sum of CCMS values is #0.01928 for iteration 33 of Tilt-Series #2.
Alignment quality for Iteration #33 of Tilt-Series #2 (19mar29h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (19mar29h): Very StableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01363 for Iteration #34 of Tilt-Series #2.
CCMS(rotations) = 1.16277 for Iteration #34 of Tilt-Series #2.
CCMS(scale) = 0.00726 for Iteration #34 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02247 for iteration 34 of Tilt-Series #2.
Alignment quality for Iteration #34 of Tilt-Series #2 (19mar29h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (19mar29h): 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 #2 (tiltseries0002_thick1000)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick1000)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01378 for Iteration #35 of Tilt-Series #2.
CCMS(rotations) = 1.23887 for Iteration #35 of Tilt-Series #2.
CCMS(scale) = 0.00944 for Iteration #35 of Tilt-Series #2.
The scaled sum of CCMS values is #0.02426 for iteration 35 of Tilt-Series #2.
Alignment quality for Iteration #35 of Tilt-Series #2 (19mar29h): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (19mar29h): Very StableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #2 (tiltseries0002_thick1000)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly post your issue on the following Appion-Protomo Google group or email Alex at anoble@nysbc.org explaining the issue and include this log file.
https://groups.google.com/forum/#!topic/appion-protomo
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: 2019yr05m18d-08hr59m40s