protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17aug18i/protomo_alignments/tiltseries0008_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --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=6.25 --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=2076.0 --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=3685 --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 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1038.0 --runname=tiltseries0008_thick50 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --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=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --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=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=26 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=8 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2076.0 --r4_highpass_diameter_x=2076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=37.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --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=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node03
Start time: 2017yr09m04d-14hr05m20s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0008.tlt to series0008.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 (tiltseries0008_thick50)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 15.7966358577
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 15.7966358577
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.13115 for Iteration #1 of Tilt-Series #8.
CCMS(rotations) = 0.82934 for Iteration #1 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8.
The scaled sum of CCMS values is #0.08216 for iteration 1 of Tilt-Series #8.
Alignment quality for Iteration #1 of Tilt-Series #8 (17aug18i): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 0.903226%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01654 for Iteration #2 of Tilt-Series #8.
CCMS(rotations) = 0.15836 for Iteration #2 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01144 for iteration 2 of Tilt-Series #8.
Alignment quality for Iteration #2 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00831 for Iteration #3 of Tilt-Series #8.
CCMS(rotations) = 0.13845 for Iteration #3 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00693 for iteration 3 of Tilt-Series #8.
Alignment quality for Iteration #3 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0077 for Iteration #4 of Tilt-Series #8.
CCMS(rotations) = 0.13674 for Iteration #4 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00659 for iteration 4 of Tilt-Series #8.
Alignment quality for Iteration #4 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #5 of Tilt-Series #8.
CCMS(rotations) = 0.12273 for Iteration #5 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00659 for iteration 5 of Tilt-Series #8.
Alignment quality for Iteration #5 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

Beginning Refinement Iteration #6, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 31.5932717154
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 31.5932717154
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #6 of Tilt-Series #8.
CCMS(rotations) = 0.15218 for Iteration #6 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00624 for iteration 6 of Tilt-Series #8.
Alignment quality for Iteration #6 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00635 for Iteration #7 of Tilt-Series #8.
CCMS(rotations) = 0.10533 for Iteration #7 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00528 for iteration 7 of Tilt-Series #8.
Alignment quality for Iteration #7 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.0068 for Iteration #8 of Tilt-Series #8.
CCMS(rotations) = 0.10205 for Iteration #8 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00544 for iteration 8 of Tilt-Series #8.
Alignment quality for Iteration #8 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00672 for Iteration #9 of Tilt-Series #8.
CCMS(rotations) = 0.11275 for Iteration #9 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00562 for iteration 9 of Tilt-Series #8.
Alignment quality for Iteration #9 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00683 for Iteration #10 of Tilt-Series #8.
CCMS(rotations) = 0.1078 for Iteration #10 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00557 for iteration 10 of Tilt-Series #8.
Alignment quality for Iteration #10 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

No Round parameters changed for Iteration #11 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00684 for Iteration #11 of Tilt-Series #8.
CCMS(rotations) = 0.10046 for Iteration #11 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00543 for iteration 11 of Tilt-Series #8.
Alignment quality for Iteration #11 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00675 for Iteration #12 of Tilt-Series #8.
CCMS(rotations) = 0.11508 for Iteration #12 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00568 for iteration 12 of Tilt-Series #8.
Alignment quality for Iteration #12 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00654 for Iteration #13 of Tilt-Series #8.
CCMS(rotations) = 0.11102 for Iteration #13 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00549 for iteration 13 of Tilt-Series #8.
Alignment quality for Iteration #13 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00678 for Iteration #14 of Tilt-Series #8.
CCMS(rotations) = 0.10964 for Iteration #14 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00558 for iteration 14 of Tilt-Series #8.
Alignment quality for Iteration #14 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #15 of Tilt-Series #8.
CCMS(rotations) = 0.10407 for Iteration #15 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00541 for iteration 15 of Tilt-Series #8.
Alignment quality for Iteration #15 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

Beginning Refinement Iteration #16, Round #3 of Tilt-Series #8 (tiltseries0008_thick50)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 63.1865434307
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 63.1865434307
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00646 for Iteration #16 of Tilt-Series #8.
CCMS(rotations) = 0.12588 for Iteration #16 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00575 for iteration 16 of Tilt-Series #8.
Alignment quality for Iteration #16 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #8 (17aug18i): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00579 for Iteration #17 of Tilt-Series #8.
CCMS(rotations) = 0.12327 for Iteration #17 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00536 for iteration 17 of Tilt-Series #8.
Alignment quality for Iteration #17 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0058 for Iteration #18 of Tilt-Series #8.
CCMS(rotations) = 0.12034 for Iteration #18 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0053 for iteration 18 of Tilt-Series #8.
Alignment quality for Iteration #18 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0056 for Iteration #19 of Tilt-Series #8.
CCMS(rotations) = 0.1115 for Iteration #19 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00503 for iteration 19 of Tilt-Series #8.
Alignment quality for Iteration #19 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00567 for Iteration #20 of Tilt-Series #8.
CCMS(rotations) = 0.11363 for Iteration #20 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00511 for iteration 20 of Tilt-Series #8.
Alignment quality for Iteration #20 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #8 (17aug18i): 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 #4 of Tilt-Series #8 (tiltseries0008_thick50)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 126.373086861
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 126.373086861
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00842 for Iteration #21 of Tilt-Series #8.
CCMS(rotations) = 0.16338 for Iteration #21 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00748 for iteration 21 of Tilt-Series #8.
Alignment quality for Iteration #21 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #8 (17aug18i): 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 #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00898 for Iteration #22 of Tilt-Series #8.
CCMS(rotations) = 0.20849 for Iteration #22 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00866 for iteration 22 of Tilt-Series #8.
Alignment quality for Iteration #22 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00986 for Iteration #23 of Tilt-Series #8.
CCMS(rotations) = 0.21153 for Iteration #23 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00916 for iteration 23 of Tilt-Series #8.
Alignment quality for Iteration #23 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01039 for Iteration #24 of Tilt-Series #8.
CCMS(rotations) = 0.16993 for Iteration #24 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00859 for iteration 24 of Tilt-Series #8.
Alignment quality for Iteration #24 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00995 for Iteration #25 of Tilt-Series #8.
CCMS(rotations) = 0.17325 for Iteration #25 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00844 for iteration 25 of Tilt-Series #8.
Alignment quality for Iteration #25 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

No Round parameters changed for Iteration #26 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.01078 for Iteration #26 of Tilt-Series #8.
CCMS(rotations) = 0.204 for Iteration #26 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00947 for iteration 26 of Tilt-Series #8.
Alignment quality for Iteration #26 of Tilt-Series #8 (17aug18i): Very Good (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00671 for Iteration #27 of Tilt-Series #8.
CCMS(rotations) = 0.17787 for Iteration #27 of Tilt-Series #8.
CCMS(scale) = 0.0049 for Iteration #27 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00624 for iteration 27 of Tilt-Series #8.
Alignment quality for Iteration #27 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0058 for Iteration #28 of Tilt-Series #8.
CCMS(rotations) = 0.16251 for Iteration #28 of Tilt-Series #8.
CCMS(scale) = 0.00501 for Iteration #28 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00577 for iteration 28 of Tilt-Series #8.
Alignment quality for Iteration #28 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00613 for Iteration #29 of Tilt-Series #8.
CCMS(rotations) = 0.16513 for Iteration #29 of Tilt-Series #8.
CCMS(scale) = 0.00496 for Iteration #29 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0059 for iteration 29 of Tilt-Series #8.
Alignment quality for Iteration #29 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #8 (17aug18i): Very StableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #8 (tiltseries0008_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 (tiltseries0008_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00622 for Iteration #30 of Tilt-Series #8.
CCMS(rotations) = 0.19677 for Iteration #30 of Tilt-Series #8.
CCMS(scale) = 0.00542 for Iteration #30 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0065 for iteration 30 of Tilt-Series #8.
Alignment quality for Iteration #30 of Tilt-Series #8 (17aug18i): Excellent (confidence: 0.903226%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #8 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #8 (tiltseries0008_thick50)!
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: 2017yr09m05d-18hr34m42s