protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17feb10h/protomo_alignments/tiltseries0051_thick800 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4518.0 --r4_lowpass_diameter_x=7.36 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2461 --r1_region_y=2696 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4518.0 --r4_lowpass_apod_y=18.0 --r4_lowpass_apod_x=18.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=37.0 --r3_lowpass_apod_y=37.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0051_thick800 --r2_region_y=2696 --r2_region_x=2461 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2259.0 --defocus_ang_positive=90 --r5_mask_width_x=2436 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4518.0 --r3_highpass_apod_x=2259.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=590 --r2_mask_width_y=649 --r5_region_x=2461 --r5_region_y=2696 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=7.36 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=4518.0 --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=2671 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=2259.0 --r3_iters=5 --r1_highpass_diameter_x=4518.0 --r2_lowpass_diameter_y=29.44 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.68 --r5_lowpass_diameter_x=3.68 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=2436 --r4_mask_width_y=2671 --r5_highpass_apod_y=2259.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17feb10h --exclude_images=999999 --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=2259.0 --r1_highpass_apod_x=2259.0 --r2_highpass_apod_x=2259.0 --sampling=8 --starting_tlt_file=Manual --r5_lowpass_apod_x=9.0 --r5_lowpass_apod_y=9.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=58.88 --r1_lowpass_diameter_x=58.88 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=51 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1323 --r3_mask_width_x=1205 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4518.0 --r4_highpass_diameter_x=4518.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=147.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4518.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2259.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4518.0 --defocus_max=0 --r4_region_y=2696 --r4_region_x=2461 --r5_kernel_y=5 --r3_region_x=2461 --r3_region_y=2696 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=800 --expid=3450 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=14.72 --r3_lowpass_diameter_x=14.72 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=4518.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=74.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=74.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=29.44 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=147.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2259.0 --r4_highpass_apod_y=2259.0 --azimuth=true --r1_mask_width_y=312 --r1_mask_width_x=282 --jobtype=protomo --from_multirefine=True

node39
Start time: 2018yr02m21d-12hr14m14s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
lowpass = 58.88 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.199821496599 0.199821496599 }
align.translimit = 47.125e0
map.sampling = 8
window.highpass.diameter = { 0.00650149623727 0.00650149623727 }
window.highpass.apodization = { 0.0130029924745 0.0130029924745 }
window.mask.apodization = { 10 10 }
align.mask.width = { 282 312 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 92.6594239765
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 307 337 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 282 312 }
reference.body = 92.6594239765
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04649 for Iteration #1 of Tilt-Series #51.
CCMS(rotations) = 0.16274 for Iteration #1 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0265 for iteration 1 of Tilt-Series #51.
Alignment quality for Iteration #1 of Tilt-Series #51 (17feb10h): Okay (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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01026 for Iteration #2 of Tilt-Series #51.
CCMS(rotations) = 0.19755 for Iteration #2 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00908 for iteration 2 of Tilt-Series #51.
Alignment quality for Iteration #2 of Tilt-Series #51 (17feb10h): Very Good (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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00738 for Iteration #3 of Tilt-Series #51.
CCMS(rotations) = 0.13681 for Iteration #3 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00642 for iteration 3 of Tilt-Series #51.
Alignment quality for Iteration #3 of Tilt-Series #51 (17feb10h): Excellent (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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #4 of Tilt-Series #51.
CCMS(rotations) = 0.18259 for Iteration #4 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00754 for iteration 4 of Tilt-Series #51.
Alignment quality for Iteration #4 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00655 for Iteration #5 of Tilt-Series #51.
CCMS(rotations) = 0.19121 for Iteration #5 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0071 for iteration 5 of Tilt-Series #51.
Alignment quality for Iteration #5 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01408 for Iteration #6 of Tilt-Series #51.
CCMS(rotations) = 0.19448 for Iteration #6 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01093 for iteration 6 of Tilt-Series #51.
Alignment quality for Iteration #6 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01122 for Iteration #7 of Tilt-Series #51.
CCMS(rotations) = 0.17964 for Iteration #7 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00921 for iteration 7 of Tilt-Series #51.
Alignment quality for Iteration #7 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00864 for Iteration #8 of Tilt-Series #51.
CCMS(rotations) = 0.18318 for Iteration #8 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00798 for iteration 8 of Tilt-Series #51.
Alignment quality for Iteration #8 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00774 for Iteration #9 of Tilt-Series #51.
CCMS(rotations) = 0.17629 for Iteration #9 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00739 for iteration 9 of Tilt-Series #51.
Alignment quality for Iteration #9 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00922 for Iteration #10 of Tilt-Series #51.
CCMS(rotations) = 0.177 for Iteration #10 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00815 for iteration 10 of Tilt-Series #51.
Alignment quality for Iteration #10 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)
lowpass = 29.44 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.198471351351 0.198471351351 }
align.translimit = 94.25e0
map.sampling = 4
window.highpass.diameter = { 0.00325074811864 0.00325074811864 }
window.highpass.apodization = { 0.00650149623727 0.00650149623727 }
window.mask.apodization = { 10 10 }
align.mask.width = { 590 649 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 185.318847953
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 615 674 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 590 649 }
reference.body = 185.318847953
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01127 for Iteration #11 of Tilt-Series #51.
CCMS(rotations) = 0.29926 for Iteration #11 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01162 for iteration 11 of Tilt-Series #51.
Alignment quality for Iteration #11 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00843 for Iteration #12 of Tilt-Series #51.
CCMS(rotations) = 0.14762 for Iteration #12 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00717 for iteration 12 of Tilt-Series #51.
Alignment quality for Iteration #12 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #13 of Tilt-Series #51.
CCMS(rotations) = 0.20537 for Iteration #13 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00754 for iteration 13 of Tilt-Series #51.
Alignment quality for Iteration #13 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00859 for Iteration #14 of Tilt-Series #51.
CCMS(rotations) = 0.1604 for Iteration #14 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0075 for iteration 14 of Tilt-Series #51.
Alignment quality for Iteration #14 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #15 of Tilt-Series #51.
CCMS(rotations) = 0.14863 for Iteration #15 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0066 for iteration 15 of Tilt-Series #51.
Alignment quality for Iteration #15 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00739 for Iteration #16 of Tilt-Series #51.
CCMS(rotations) = 0.14377 for Iteration #16 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00657 for iteration 16 of Tilt-Series #51.
Alignment quality for Iteration #16 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.0082 for Iteration #17 of Tilt-Series #51.
CCMS(rotations) = 0.11603 for Iteration #17 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00642 for iteration 17 of Tilt-Series #51.
Alignment quality for Iteration #17 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #51 (17feb10h): StableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00848 for Iteration #18 of Tilt-Series #51.
CCMS(rotations) = 0.15127 for Iteration #18 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00726 for iteration 18 of Tilt-Series #51.
Alignment quality for Iteration #18 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00875 for Iteration #19 of Tilt-Series #51.
CCMS(rotations) = 0.11938 for Iteration #19 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00676 for iteration 19 of Tilt-Series #51.
Alignment quality for Iteration #19 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #51 (17feb10h): Very StableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00761 for Iteration #20 of Tilt-Series #51.
CCMS(rotations) = 0.13958 for Iteration #20 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0066 for iteration 20 of Tilt-Series #51.
Alignment quality for Iteration #20 of Tilt-Series #51 (17feb10h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)
lowpass = 14.72 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.198471351351 0.198471351351 }
align.translimit = 188.5e0
map.sampling = 2
window.highpass.diameter = { 0.00162537405932 0.00162537405932 }
window.highpass.apodization = { 0.00325074811864 0.00325074811864 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1205 1323 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 370.637695906
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1230 1348 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1205 1323 }
reference.body = 370.637695906
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00717 for Iteration #21 of Tilt-Series #51.
CCMS(rotations) = 0.21165 for Iteration #21 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00782 for iteration 21 of Tilt-Series #51.
Alignment quality for Iteration #21 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00676 for Iteration #22 of Tilt-Series #51.
CCMS(rotations) = 0.25028 for Iteration #22 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00839 for iteration 22 of Tilt-Series #51.
Alignment quality for Iteration #22 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #51 (17feb10h): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00741 for Iteration #23 of Tilt-Series #51.
CCMS(rotations) = 0.20624 for Iteration #23 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00783 for iteration 23 of Tilt-Series #51.
Alignment quality for Iteration #23 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00649 for Iteration #24 of Tilt-Series #51.
CCMS(rotations) = 0.27808 for Iteration #24 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0088 for iteration 24 of Tilt-Series #51.
Alignment quality for Iteration #24 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0071 for Iteration #25 of Tilt-Series #51.
CCMS(rotations) = 0.21162 for Iteration #25 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #51.
The scaled sum of CCMS values is #0.00778 for iteration 25 of Tilt-Series #51.
Alignment quality for Iteration #25 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #51 (17feb10h): UnstableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
lowpass = 7.36 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.203984444444 0.203984444444 }
align.translimit = 377.0e0
map.sampling = 1
window.highpass.diameter = { 0.000812687029659 0.000812687029659 }
window.highpass.apodization = { 0.00162537405932 0.00162537405932 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2436 2671 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 741.275391812
map.lowpass.diameter = { 0.498875 0.498875 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2461 2696 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2436 2671 }
reference.body = 741.275391812
window.lowpass.diameter = { 0.498875 0.498875 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01413 for Iteration #26 of Tilt-Series #51.
CCMS(rotations) = 0.20591 for Iteration #26 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01118 for iteration 26 of Tilt-Series #51.
Alignment quality for Iteration #26 of Tilt-Series #51 (17feb10h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01952 for Iteration #27 of Tilt-Series #51.
CCMS(rotations) = 0.34086 for Iteration #27 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01658 for iteration 27 of Tilt-Series #51.
Alignment quality for Iteration #27 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.02191 for Iteration #28 of Tilt-Series #51.
CCMS(rotations) = 0.44674 for Iteration #28 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01989 for iteration 28 of Tilt-Series #51.
Alignment quality for Iteration #28 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.02525 for Iteration #29 of Tilt-Series #51.
CCMS(rotations) = 0.3087 for Iteration #29 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #51.
The scaled sum of CCMS values is #0.0188 for iteration 29 of Tilt-Series #51.
Alignment quality for Iteration #29 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #51 (17feb10h): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01838 for Iteration #30 of Tilt-Series #51.
CCMS(rotations) = 0.35326 for Iteration #30 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01626 for iteration 30 of Tilt-Series #51.
Alignment quality for Iteration #30 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #51 (17feb10h): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0198 for Iteration #31 of Tilt-Series #51.
CCMS(rotations) = 0.34425 for Iteration #31 of Tilt-Series #51.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01679 for iteration 31 of Tilt-Series #51.
Alignment quality for Iteration #31 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01857 for Iteration #32 of Tilt-Series #51.
CCMS(rotations) = 0.33749 for Iteration #32 of Tilt-Series #51.
CCMS(scale) = 0.00884 for Iteration #32 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01363 for iteration 32 of Tilt-Series #51.
Alignment quality for Iteration #32 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.02156 for Iteration #33 of Tilt-Series #51.
CCMS(rotations) = 0.32016 for Iteration #33 of Tilt-Series #51.
CCMS(scale) = 0.0112 for Iteration #33 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01519 for iteration 33 of Tilt-Series #51.
Alignment quality for Iteration #33 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #51 (17feb10h): 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 #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.02599 for Iteration #34 of Tilt-Series #51.
CCMS(rotations) = 0.27148 for Iteration #34 of Tilt-Series #51.
CCMS(scale) = 0.01193 for Iteration #34 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01626 for iteration 34 of Tilt-Series #51.
Alignment quality for Iteration #34 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #51 (17feb10h): UnstableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #51 (tiltseries0051_thick800)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #51 (tiltseries0051_thick800)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.02578 for Iteration #35 of Tilt-Series #51.
CCMS(rotations) = 0.3145 for Iteration #35 of Tilt-Series #51.
CCMS(scale) = 0.01421 for Iteration #35 of Tilt-Series #51.
The scaled sum of CCMS values is #0.01752 for iteration 35 of Tilt-Series #51.
Alignment quality for Iteration #35 of Tilt-Series #51 (17feb10h): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #51 (17feb10h): UnstableCreating 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 #51 (tiltseries0051_thick800)!
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: 2018yr02m23d-08hr45m55s