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/17dec26e/protomo_alignments/tiltseries0009_thick200 --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=tiltseries0009_thick200 --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=17dec26e --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=9 --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=200 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --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=90.0 --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

node04
Start time: 2017yr12m26d-19hr12m31s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0009.tlt to series0009.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
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 = 18.3522754867
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 = 18.3522754867
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.12461 for Iteration #1 of Tilt-Series #9.
CCMS(rotations) = 2.61554 for Iteration #1 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #9.
The scaled sum of CCMS values is #0.11462 for iteration 1 of Tilt-Series #9.
Alignment quality for Iteration #1 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.12181 for Iteration #2 of Tilt-Series #9.
CCMS(rotations) = 1.91882 for Iteration #2 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #9.
The scaled sum of CCMS values is #0.09928 for iteration 2 of Tilt-Series #9.
Alignment quality for Iteration #2 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02127 for Iteration #3 of Tilt-Series #9.
CCMS(rotations) = 0.78833 for Iteration #3 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0264 for iteration 3 of Tilt-Series #9.
Alignment quality for Iteration #3 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00606 for Iteration #4 of Tilt-Series #9.
CCMS(rotations) = 0.23025 for Iteration #4 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00763 for iteration 4 of Tilt-Series #9.
Alignment quality for Iteration #4 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00625 for Iteration #5 of Tilt-Series #9.
CCMS(rotations) = 0.24072 for Iteration #5 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00794 for iteration 5 of Tilt-Series #9.
Alignment quality for Iteration #5 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00562 for Iteration #6 of Tilt-Series #9.
CCMS(rotations) = 0.23497 for Iteration #6 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00751 for iteration 6 of Tilt-Series #9.
Alignment quality for Iteration #6 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00618 for Iteration #7 of Tilt-Series #9.
CCMS(rotations) = 0.25223 for Iteration #7 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00813 for iteration 7 of Tilt-Series #9.
Alignment quality for Iteration #7 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00589 for Iteration #8 of Tilt-Series #9.
CCMS(rotations) = 0.22668 for Iteration #8 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00748 for iteration 8 of Tilt-Series #9.
Alignment quality for Iteration #8 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00626 for Iteration #9 of Tilt-Series #9.
CCMS(rotations) = 0.25754 for Iteration #9 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00828 for iteration 9 of Tilt-Series #9.
Alignment quality for Iteration #9 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #10 of Tilt-Series #9.
CCMS(rotations) = 0.22325 for Iteration #10 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00729 for iteration 10 of Tilt-Series #9.
Alignment quality for Iteration #10 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)
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 = 36.7045509734
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 = 36.7045509734
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0059 for Iteration #11 of Tilt-Series #9.
CCMS(rotations) = 0.2021 for Iteration #11 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00699 for iteration 11 of Tilt-Series #9.
Alignment quality for Iteration #11 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #9 (17dec26e): Very StableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00515 for Iteration #12 of Tilt-Series #9.
CCMS(rotations) = 0.22837 for Iteration #12 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00714 for iteration 12 of Tilt-Series #9.
Alignment quality for Iteration #12 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00546 for Iteration #13 of Tilt-Series #9.
CCMS(rotations) = 0.25451 for Iteration #13 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00782 for iteration 13 of Tilt-Series #9.
Alignment quality for Iteration #13 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00508 for Iteration #14 of Tilt-Series #9.
CCMS(rotations) = 0.23535 for Iteration #14 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00724 for iteration 14 of Tilt-Series #9.
Alignment quality for Iteration #14 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00543 for Iteration #15 of Tilt-Series #9.
CCMS(rotations) = 0.24917 for Iteration #15 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0077 for iteration 15 of Tilt-Series #9.
Alignment quality for Iteration #15 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #9 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #16 of Tilt-Series #9.
CCMS(rotations) = 0.22963 for Iteration #16 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00711 for iteration 16 of Tilt-Series #9.
Alignment quality for Iteration #16 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00544 for Iteration #17 of Tilt-Series #9.
CCMS(rotations) = 0.24545 for Iteration #17 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00763 for iteration 17 of Tilt-Series #9.
Alignment quality for Iteration #17 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00495 for Iteration #18 of Tilt-Series #9.
CCMS(rotations) = 0.22575 for Iteration #18 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00699 for iteration 18 of Tilt-Series #9.
Alignment quality for Iteration #18 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00551 for Iteration #19 of Tilt-Series #9.
CCMS(rotations) = 0.23673 for Iteration #19 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00749 for iteration 19 of Tilt-Series #9.
Alignment quality for Iteration #19 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00499 for Iteration #20 of Tilt-Series #9.
CCMS(rotations) = 0.22756 for Iteration #20 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00705 for iteration 20 of Tilt-Series #9.
Alignment quality for Iteration #20 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)
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 = 73.4091019469
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 = 73.4091019469
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00499 for Iteration #21 of Tilt-Series #9.
CCMS(rotations) = 0.23019 for Iteration #21 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0071 for iteration 21 of Tilt-Series #9.
Alignment quality for Iteration #21 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #9 (17dec26e): Rock Solid!Creating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00482 for Iteration #22 of Tilt-Series #9.
CCMS(rotations) = 0.2222 for Iteration #22 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00685 for iteration 22 of Tilt-Series #9.
Alignment quality for Iteration #22 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00525 for Iteration #23 of Tilt-Series #9.
CCMS(rotations) = 0.24262 for Iteration #23 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00748 for iteration 23 of Tilt-Series #9.
Alignment quality for Iteration #23 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00506 for Iteration #24 of Tilt-Series #9.
CCMS(rotations) = 0.22572 for Iteration #24 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00704 for iteration 24 of Tilt-Series #9.
Alignment quality for Iteration #24 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #25 of Tilt-Series #9.
CCMS(rotations) = 0.22873 for Iteration #25 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00709 for iteration 25 of Tilt-Series #9.
Alignment quality for Iteration #25 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)
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 = 146.818203894
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 = 146.818203894
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00519 for Iteration #26 of Tilt-Series #9.
CCMS(rotations) = 0.25086 for Iteration #26 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00761 for iteration 26 of Tilt-Series #9.
Alignment quality for Iteration #26 of Tilt-Series #9 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #27 of Tilt-Series #9.
CCMS(rotations) = 0.20767 for Iteration #27 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00671 for iteration 27 of Tilt-Series #9.
Alignment quality for Iteration #27 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00462 for Iteration #28 of Tilt-Series #9.
CCMS(rotations) = 0.19114 for Iteration #28 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00613 for iteration 28 of Tilt-Series #9.
Alignment quality for Iteration #28 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00468 for Iteration #29 of Tilt-Series #9.
CCMS(rotations) = 0.21616 for Iteration #29 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00666 for iteration 29 of Tilt-Series #9.
Alignment quality for Iteration #29 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00482 for Iteration #30 of Tilt-Series #9.
CCMS(rotations) = 0.22462 for Iteration #30 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0069 for iteration 30 of Tilt-Series #9.
Alignment quality for Iteration #30 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #9 (17dec26e): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00477 for Iteration #31 of Tilt-Series #9.
CCMS(rotations) = 0.24104 for Iteration #31 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00721 for iteration 31 of Tilt-Series #9.
Alignment quality for Iteration #31 of Tilt-Series #9 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #9 (17dec26e): Rock Solid!Creating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00312 for Iteration #32 of Tilt-Series #9.
CCMS(rotations) = 0.21524 for Iteration #32 of Tilt-Series #9.
CCMS(scale) = 0.00212 for Iteration #32 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00462 for iteration 32 of Tilt-Series #9.
Alignment quality for Iteration #32 of Tilt-Series #9 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #9 (17dec26e): Rock Solid!Creating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00312 for Iteration #33 of Tilt-Series #9.
CCMS(rotations) = 0.22585 for Iteration #33 of Tilt-Series #9.
CCMS(scale) = 0.00223 for Iteration #33 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0048 for iteration 33 of Tilt-Series #9.
Alignment quality for Iteration #33 of Tilt-Series #9 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #9 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00302 for Iteration #34 of Tilt-Series #9.
CCMS(rotations) = 0.22441 for Iteration #34 of Tilt-Series #9.
CCMS(scale) = 0.00222 for Iteration #34 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00474 for iteration 34 of Tilt-Series #9.
Alignment quality for Iteration #34 of Tilt-Series #9 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #9 (17dec26e): Rock Solid!Creating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00278 for Iteration #35 of Tilt-Series #9.
CCMS(rotations) = 0.22389 for Iteration #35 of Tilt-Series #9.
CCMS(scale) = 0.0021 for Iteration #35 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00461 for iteration 35 of Tilt-Series #9.
Alignment quality for Iteration #35 of Tilt-Series #9 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #9 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #9 (tiltseries0009_thick200)!
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: 2017yr12m27d-04hr16m19s