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/17nov27o/protomo_alignments/tiltseries0003_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --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=8.64 --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=4015.0 --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=1894 --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=2008.0 --runname=tiltseries0003_thick50 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17nov27o --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=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --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=3 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=934 --r3_mask_width_x=902 --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=4015.0 --r4_highpass_diameter_x=4015.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=5456 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=207 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=31.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --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=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --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=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo

node39
Start time: 2017yr12m01d-11hr23m46s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0003.tlt to series0003.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 69.12 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms)
window.lowpass.apodization = { 0.20016 0.20016 }
map.sampling = 8
window.highpass.diameter = { 0.00862457783313 0.00862457783313 }
window.highpass.apodization = { 0.0172448605578 0.0172448605578 }
window.mask.apodization = { 10 10 }
align.mask.width = { 206 214 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 4.08312886301
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 4.08312886301
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06666 for Iteration #1 of Tilt-Series #3.
CCMS(rotations) = 0.1891 for Iteration #1 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3.
The scaled sum of CCMS values is #0.03711 for iteration 1 of Tilt-Series #3.
Alignment quality for Iteration #1 of Tilt-Series #3 (17nov27o): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 80.000000%)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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00901 for Iteration #2 of Tilt-Series #3.
CCMS(rotations) = 0.10859 for Iteration #2 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00667 for iteration 2 of Tilt-Series #3.
Alignment quality for Iteration #2 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00886 for Iteration #3 of Tilt-Series #3.
CCMS(rotations) = 0.1081 for Iteration #3 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00659 for iteration 3 of Tilt-Series #3.
Alignment quality for Iteration #3 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00882 for Iteration #4 of Tilt-Series #3.
CCMS(rotations) = 0.09468 for Iteration #4 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0063 for iteration 4 of Tilt-Series #3.
Alignment quality for Iteration #4 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00866 for Iteration #5 of Tilt-Series #3.
CCMS(rotations) = 0.09879 for Iteration #5 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00631 for iteration 5 of Tilt-Series #3.
Alignment quality for Iteration #5 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #3 (17nov27o): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00817 for Iteration #6 of Tilt-Series #3.
CCMS(rotations) = 0.10557 for Iteration #6 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0062 for iteration 6 of Tilt-Series #3.
Alignment quality for Iteration #6 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00883 for Iteration #7 of Tilt-Series #3.
CCMS(rotations) = 0.1009 for Iteration #7 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00643 for iteration 7 of Tilt-Series #3.
Alignment quality for Iteration #7 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00876 for Iteration #8 of Tilt-Series #3.
CCMS(rotations) = 0.10029 for Iteration #8 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00639 for iteration 8 of Tilt-Series #3.
Alignment quality for Iteration #8 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00912 for Iteration #9 of Tilt-Series #3.
CCMS(rotations) = 0.09384 for Iteration #9 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00644 for iteration 9 of Tilt-Series #3.
Alignment quality for Iteration #9 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00877 for Iteration #10 of Tilt-Series #3.
CCMS(rotations) = 0.09739 for Iteration #10 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00634 for iteration 10 of Tilt-Series #3.
Alignment quality for Iteration #10 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)
lowpass = 34.56 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 4
window.highpass.diameter = { 0.00431228891656 0.00431228891656 }
window.highpass.apodization = { 0.00862243027888 0.00862243027888 }
window.mask.apodization = { 10 10 }
align.mask.width = { 438 454 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 8.16625772602
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 8.16625772602
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00654 for Iteration #11 of Tilt-Series #3.
CCMS(rotations) = 0.11376 for Iteration #11 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00555 for iteration 11 of Tilt-Series #3.
Alignment quality for Iteration #11 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0059 for Iteration #12 of Tilt-Series #3.
CCMS(rotations) = 0.06989 for Iteration #12 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00435 for iteration 12 of Tilt-Series #3.
Alignment quality for Iteration #12 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #3 (17nov27o): Very StableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00578 for Iteration #13 of Tilt-Series #3.
CCMS(rotations) = 0.07621 for Iteration #13 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00441 for iteration 13 of Tilt-Series #3.
Alignment quality for Iteration #13 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00607 for Iteration #14 of Tilt-Series #3.
CCMS(rotations) = 0.05969 for Iteration #14 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00423 for iteration 14 of Tilt-Series #3.
Alignment quality for Iteration #14 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00499 for Iteration #15 of Tilt-Series #3.
CCMS(rotations) = 0.09285 for Iteration #15 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00435 for iteration 15 of Tilt-Series #3.
Alignment quality for Iteration #15 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00627 for Iteration #16 of Tilt-Series #3.
CCMS(rotations) = 0.0759 for Iteration #16 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00466 for iteration 16 of Tilt-Series #3.
Alignment quality for Iteration #16 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #17 of Tilt-Series #3.
CCMS(rotations) = 0.07966 for Iteration #17 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00441 for iteration 17 of Tilt-Series #3.
Alignment quality for Iteration #17 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00608 for Iteration #18 of Tilt-Series #3.
CCMS(rotations) = 0.06991 for Iteration #18 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00444 for iteration 18 of Tilt-Series #3.
Alignment quality for Iteration #18 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #19 of Tilt-Series #3.
CCMS(rotations) = 0.08239 for Iteration #19 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00446 for iteration 19 of Tilt-Series #3.
Alignment quality for Iteration #19 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00602 for Iteration #20 of Tilt-Series #3.
CCMS(rotations) = 0.0696 for Iteration #20 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0044 for iteration 20 of Tilt-Series #3.
Alignment quality for Iteration #20 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)
lowpass = 17.28 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 2
window.highpass.diameter = { 0.00215614445828 0.00215614445828 }
window.highpass.apodization = { 0.00431121513944 0.00431121513944 }
window.mask.apodization = { 10 10 }
align.mask.width = { 902 934 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 16.332515452
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 16.332515452
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #21 of Tilt-Series #3.
CCMS(rotations) = 0.08083 for Iteration #21 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00417 for iteration 21 of Tilt-Series #3.
Alignment quality for Iteration #21 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00669 for Iteration #22 of Tilt-Series #3.
CCMS(rotations) = 0.05389 for Iteration #22 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00442 for iteration 22 of Tilt-Series #3.
Alignment quality for Iteration #22 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00524 for Iteration #23 of Tilt-Series #3.
CCMS(rotations) = 0.07875 for Iteration #23 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00419 for iteration 23 of Tilt-Series #3.
Alignment quality for Iteration #23 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00547 for Iteration #24 of Tilt-Series #3.
CCMS(rotations) = 0.07894 for Iteration #24 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00431 for iteration 24 of Tilt-Series #3.
Alignment quality for Iteration #24 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #25 of Tilt-Series #3.
CCMS(rotations) = 0.07804 for Iteration #25 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00426 for iteration 25 of Tilt-Series #3.
Alignment quality for Iteration #25 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #3 (17nov27o): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 8.64 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms)
window.lowpass.apodization = { 0.196748181818 0.196748181818 }
map.sampling = 1
window.highpass.diameter = { 0.00107807222914 0.00107807222914 }
window.highpass.apodization = { 0.00215560756972 0.00215560756972 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1830 1894 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 32.6650309041
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 32.6650309041
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00677 for Iteration #26 of Tilt-Series #3.
CCMS(rotations) = 0.09652 for Iteration #26 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00531 for iteration 26 of Tilt-Series #3.
Alignment quality for Iteration #26 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00508 for Iteration #27 of Tilt-Series #3.
CCMS(rotations) = 0.11851 for Iteration #27 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00491 for iteration 27 of Tilt-Series #3.
Alignment quality for Iteration #27 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00508 for Iteration #28 of Tilt-Series #3.
CCMS(rotations) = 0.12427 for Iteration #28 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00502 for iteration 28 of Tilt-Series #3.
Alignment quality for Iteration #28 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #3 (17nov27o): StableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00533 for Iteration #29 of Tilt-Series #3.
CCMS(rotations) = 0.10542 for Iteration #29 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00477 for iteration 29 of Tilt-Series #3.
Alignment quality for Iteration #29 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #3 (17nov27o): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.0055 for Iteration #30 of Tilt-Series #3.
CCMS(rotations) = 0.11929 for Iteration #30 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00514 for iteration 30 of Tilt-Series #3.
Alignment quality for Iteration #30 of Tilt-Series #3 (17nov27o): Excellent (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #3 (17nov27o): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00536 for Iteration #31 of Tilt-Series #3.
CCMS(rotations) = 0.09052 for Iteration #31 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00449 for iteration 31 of Tilt-Series #3.
Alignment quality for Iteration #31 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #32 of Tilt-Series #3.
CCMS(rotations) = 0.08836 for Iteration #32 of Tilt-Series #3.
CCMS(scale) = 0.0028 for Iteration #32 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0034 for iteration 32 of Tilt-Series #3.
Alignment quality for Iteration #32 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.0046 for Iteration #33 of Tilt-Series #3.
CCMS(rotations) = 0.08911 for Iteration #33 of Tilt-Series #3.
CCMS(scale) = 0.00294 for Iteration #33 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0037 for iteration 33 of Tilt-Series #3.
Alignment quality for Iteration #33 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #3 (17nov27o): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00358 for Iteration #34 of Tilt-Series #3.
CCMS(rotations) = 0.10639 for Iteration #34 of Tilt-Series #3.
CCMS(scale) = 0.00239 for Iteration #34 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00341 for iteration 34 of Tilt-Series #3.
Alignment quality for Iteration #34 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #3 (17nov27o): Very StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00415 for Iteration #35 of Tilt-Series #3.
CCMS(rotations) = 0.09947 for Iteration #35 of Tilt-Series #3.
CCMS(scale) = 0.00232 for Iteration #35 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00348 for iteration 35 of Tilt-Series #3.
Alignment quality for Iteration #35 of Tilt-Series #3 (17nov27o): Perfection! (confidence: 80.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #3 (17nov27o): 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 #3 (tiltseries0003_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: 2017yr12m01d-17hr23m25s