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/tiltseries0015_thick100 --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=tiltseries0015_thick100 --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=Coarse_Iter_2 --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=15 --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=100 --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=43.0 --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

node46
Start time: 2017yr12m26d-20hr57m11s
Description: 
coarse_series0015_iter2.tlt not found, using coarse_series0015.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0015.tlt to series0015.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
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 = 8.16625772602
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 = 8.16625772602
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.15652 for Iteration #1 of Tilt-Series #15.
CCMS(rotations) = 2.52429 for Iteration #1 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #15.
The scaled sum of CCMS values is #0.12875 for iteration 1 of Tilt-Series #15.
Alignment quality for Iteration #1 of Tilt-Series #15 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 96.774194%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.05028 for Iteration #2 of Tilt-Series #15.
CCMS(rotations) = 0.34356 for Iteration #2 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #15.
The scaled sum of CCMS values is #0.03201 for iteration 2 of Tilt-Series #15.
Alignment quality for Iteration #2 of Tilt-Series #15 (17dec26e): Bad (confidence: 96.774194%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00815 for Iteration #3 of Tilt-Series #15.
CCMS(rotations) = 0.27093 for Iteration #3 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00949 for iteration 3 of Tilt-Series #15.
Alignment quality for Iteration #3 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00844 for Iteration #4 of Tilt-Series #15.
CCMS(rotations) = 0.26516 for Iteration #4 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00952 for iteration 4 of Tilt-Series #15.
Alignment quality for Iteration #4 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00876 for Iteration #5 of Tilt-Series #15.
CCMS(rotations) = 0.26829 for Iteration #5 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00975 for iteration 5 of Tilt-Series #15.
Alignment quality for Iteration #5 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00839 for Iteration #6 of Tilt-Series #15.
CCMS(rotations) = 0.25358 for Iteration #6 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00927 for iteration 6 of Tilt-Series #15.
Alignment quality for Iteration #6 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00868 for Iteration #7 of Tilt-Series #15.
CCMS(rotations) = 0.26641 for Iteration #7 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00967 for iteration 7 of Tilt-Series #15.
Alignment quality for Iteration #7 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00843 for Iteration #8 of Tilt-Series #15.
CCMS(rotations) = 0.25024 for Iteration #8 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00922 for iteration 8 of Tilt-Series #15.
Alignment quality for Iteration #8 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00879 for Iteration #9 of Tilt-Series #15.
CCMS(rotations) = 0.26735 for Iteration #9 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00974 for iteration 9 of Tilt-Series #15.
Alignment quality for Iteration #9 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00841 for Iteration #10 of Tilt-Series #15.
CCMS(rotations) = 0.25101 for Iteration #10 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00923 for iteration 10 of Tilt-Series #15.
Alignment quality for Iteration #10 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)
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 = 16.332515452
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 = 16.332515452
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00871 for Iteration #11 of Tilt-Series #15.
CCMS(rotations) = 0.26115 for Iteration #11 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00958 for iteration 11 of Tilt-Series #15.
Alignment quality for Iteration #11 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #15 (17dec26e): 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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00768 for Iteration #12 of Tilt-Series #15.
CCMS(rotations) = 0.24866 for Iteration #12 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00881 for iteration 12 of Tilt-Series #15.
Alignment quality for Iteration #12 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00859 for Iteration #13 of Tilt-Series #15.
CCMS(rotations) = 0.27809 for Iteration #13 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00986 for iteration 13 of Tilt-Series #15.
Alignment quality for Iteration #13 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00762 for Iteration #14 of Tilt-Series #15.
CCMS(rotations) = 0.24911 for Iteration #14 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00879 for iteration 14 of Tilt-Series #15.
Alignment quality for Iteration #14 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00861 for Iteration #15 of Tilt-Series #15.
CCMS(rotations) = 0.28082 for Iteration #15 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00992 for iteration 15 of Tilt-Series #15.
Alignment quality for Iteration #15 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00832 for Iteration #16 of Tilt-Series #15.
CCMS(rotations) = 0.25295 for Iteration #16 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00922 for iteration 16 of Tilt-Series #15.
Alignment quality for Iteration #16 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00802 for Iteration #17 of Tilt-Series #15.
CCMS(rotations) = 0.25684 for Iteration #17 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00915 for iteration 17 of Tilt-Series #15.
Alignment quality for Iteration #17 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0082 for Iteration #18 of Tilt-Series #15.
CCMS(rotations) = 0.26931 for Iteration #18 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00948 for iteration 18 of Tilt-Series #15.
Alignment quality for Iteration #18 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00803 for Iteration #19 of Tilt-Series #15.
CCMS(rotations) = 0.25987 for Iteration #19 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00921 for iteration 19 of Tilt-Series #15.
Alignment quality for Iteration #19 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00825 for Iteration #20 of Tilt-Series #15.
CCMS(rotations) = 0.27136 for Iteration #20 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00955 for iteration 20 of Tilt-Series #15.
Alignment quality for Iteration #20 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)
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 = 32.6650309041
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 = 32.6650309041
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00846 for Iteration #21 of Tilt-Series #15.
CCMS(rotations) = 0.25294 for Iteration #21 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00929 for iteration 21 of Tilt-Series #15.
Alignment quality for Iteration #21 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00805 for Iteration #22 of Tilt-Series #15.
CCMS(rotations) = 0.26843 for Iteration #22 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0094 for iteration 22 of Tilt-Series #15.
Alignment quality for Iteration #22 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00811 for Iteration #23 of Tilt-Series #15.
CCMS(rotations) = 0.27765 for Iteration #23 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00961 for iteration 23 of Tilt-Series #15.
Alignment quality for Iteration #23 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00818 for Iteration #24 of Tilt-Series #15.
CCMS(rotations) = 0.2654 for Iteration #24 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #15.
The scaled sum of CCMS values is #0.0094 for iteration 24 of Tilt-Series #15.
Alignment quality for Iteration #24 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00813 for Iteration #25 of Tilt-Series #15.
CCMS(rotations) = 0.27597 for Iteration #25 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00958 for iteration 25 of Tilt-Series #15.
Alignment quality for Iteration #25 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)
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 = 65.3300618081
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 = 65.3300618081
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00836 for Iteration #26 of Tilt-Series #15.
CCMS(rotations) = 0.29115 for Iteration #26 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #15.
The scaled sum of CCMS values is #0.01001 for iteration 26 of Tilt-Series #15.
Alignment quality for Iteration #26 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00853 for Iteration #27 of Tilt-Series #15.
CCMS(rotations) = 0.26466 for Iteration #27 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00956 for iteration 27 of Tilt-Series #15.
Alignment quality for Iteration #27 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00818 for Iteration #28 of Tilt-Series #15.
CCMS(rotations) = 0.26444 for Iteration #28 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00938 for iteration 28 of Tilt-Series #15.
Alignment quality for Iteration #28 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00821 for Iteration #29 of Tilt-Series #15.
CCMS(rotations) = 0.26742 for Iteration #29 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00945 for iteration 29 of Tilt-Series #15.
Alignment quality for Iteration #29 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00811 for Iteration #30 of Tilt-Series #15.
CCMS(rotations) = 0.27325 for Iteration #30 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00952 for iteration 30 of Tilt-Series #15.
Alignment quality for Iteration #30 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00834 for Iteration #31 of Tilt-Series #15.
CCMS(rotations) = 0.26885 for Iteration #31 of Tilt-Series #15.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00954 for iteration 31 of Tilt-Series #15.
Alignment quality for Iteration #31 of Tilt-Series #15 (17dec26e): Very Good (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #15 (17dec26e): Very StableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00214 for Iteration #32 of Tilt-Series #15.
CCMS(rotations) = 0.29042 for Iteration #32 of Tilt-Series #15.
CCMS(scale) = 0.00469 for Iteration #32 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00615 for iteration 32 of Tilt-Series #15.
Alignment quality for Iteration #32 of Tilt-Series #15 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00216 for Iteration #33 of Tilt-Series #15.
CCMS(rotations) = 0.28363 for Iteration #33 of Tilt-Series #15.
CCMS(scale) = 0.00464 for Iteration #33 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00605 for iteration 33 of Tilt-Series #15.
Alignment quality for Iteration #33 of Tilt-Series #15 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00214 for Iteration #34 of Tilt-Series #15.
CCMS(rotations) = 0.28956 for Iteration #34 of Tilt-Series #15.
CCMS(scale) = 0.00462 for Iteration #34 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00611 for iteration 34 of Tilt-Series #15.
Alignment quality for Iteration #34 of Tilt-Series #15 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #15 (tiltseries0015_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00204 for Iteration #35 of Tilt-Series #15.
CCMS(rotations) = 0.28952 for Iteration #35 of Tilt-Series #15.
CCMS(scale) = 0.00464 for Iteration #35 of Tilt-Series #15.
The scaled sum of CCMS values is #0.00609 for iteration 35 of Tilt-Series #15.
Alignment quality for Iteration #35 of Tilt-Series #15 (17dec26e): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #15 (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 #15 (tiltseries0015_thick100)!
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-03hr06m26s