protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-42.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17sep22z/protomo_alignments/tiltseries0006_thick150 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4343.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1856 --r1_region_y=2492 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4343.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=2492 --r2_region_x=1856 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2172.0 --defocus_ang_positive=90 --r5_mask_width_x=1831 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4343.0 --r3_highpass_apod_x=2172.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=439 --r2_mask_width_y=598 --r5_region_x=1856 --r5_region_y=2492 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=4343.0 --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=2467 --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=2172.0 --runname=tiltseries0006_thick150 --r1_highpass_diameter_x=4343.0 --r2_lowpass_diameter_y=25.0 --map_size_y=623 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=1831 --r4_mask_width_y=2467 --r5_highpass_apod_y=2172.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17sep22z --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=2172.0 --r1_highpass_apod_x=2172.0 --r2_highpass_apod_x=2172.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=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=6 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1221 --r3_mask_width_x=903 --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=4343.0 --r4_highpass_diameter_x=4343.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4343.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2172.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4343.0 --defocus_max=0 --r4_region_y=2492 --r4_region_x=1856 --r5_kernel_y=5 --r3_region_x=1856 --r3_region_y=2492 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=150 --expid=4984 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=422 --max_correction=999999 --map_size_x=464 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.34 --link=False --r2_highpass_diameter_x=4343.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=1246.0 --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=25.0 --dimx=3712 --dimy=4984 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2172.0 --r4_highpass_apod_y=2172.0 --azimuth=true --r1_mask_width_y=286 --r1_mask_width_x=207 --jobtype=protomo

node21
Start time: 2017yr09m22d-10hr59m29s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0006.tlt to series0006.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 18.72 Angstroms, Nyquist is 37.44 Angstroms)
window.lowpass.apodization = { 0.29952 0.29952 }
map.sampling = 8
window.highpass.diameter = { 0.00862076905365 0.00862076905365 }
window.highpass.apodization = { 0.0172375690608 0.0172375690608 }
window.mask.apodization = { 10 10 }
align.mask.width = { 207 286 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 11.0867568926
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 232 311 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 207 286 }
reference.body = 11.0867568926
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04561 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 1.2921 for Iteration #1 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6.
The scaled sum of CCMS values is #0.04865 for iteration 1 of Tilt-Series #6.
Alignment quality for Iteration #1 of Tilt-Series #6 (17sep22z): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 96.875000%)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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03174 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 1.14748 for Iteration #2 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6.
The scaled sum of CCMS values is #0.03882 for iteration 2 of Tilt-Series #6.
Alignment quality for Iteration #2 of Tilt-Series #6 (17sep22z): Bad (confidence: 96.875000%)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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02852 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 1.18294 for Iteration #3 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6.
The scaled sum of CCMS values is #0.03792 for iteration 3 of Tilt-Series #6.
Alignment quality for Iteration #3 of Tilt-Series #6 (17sep22z): Bad (confidence: 96.875000%)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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02965 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 1.00964 for Iteration #4 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6.
The scaled sum of CCMS values is #0.03502 for iteration 4 of Tilt-Series #6.
Alignment quality for Iteration #4 of Tilt-Series #6 (17sep22z): Bad (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.0242 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 0.78978 for Iteration #5 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0279 for iteration 5 of Tilt-Series #6.
Alignment quality for Iteration #5 of Tilt-Series #6 (17sep22z): Okay (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01985 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 0.60383 for Iteration #6 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6.
The scaled sum of CCMS values is #0.022 for iteration 6 of Tilt-Series #6.
Alignment quality for Iteration #6 of Tilt-Series #6 (17sep22z): Okay (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01619 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 0.45227 for Iteration #7 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01714 for iteration 7 of Tilt-Series #6.
Alignment quality for Iteration #7 of Tilt-Series #6 (17sep22z): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #6 (17sep22z): Very StableCreating 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01089 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 0.28112 for Iteration #8 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01107 for iteration 8 of Tilt-Series #6.
Alignment quality for Iteration #8 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01117 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 0.29647 for Iteration #9 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01151 for iteration 9 of Tilt-Series #6.
Alignment quality for Iteration #9 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01113 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 0.33154 for Iteration #10 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0122 for iteration 10 of Tilt-Series #6.
Alignment quality for Iteration #10 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 9.36 Angstroms, Nyquist is 18.72 Angstroms)
window.lowpass.apodization = { 0.297142857143 0.297142857143 }
map.sampling = 4
window.highpass.diameter = { 0.00431038452682 0.00431038452682 }
window.highpass.apodization = { 0.00861878453039 0.00861878453039 }
window.mask.apodization = { 10 10 }
align.mask.width = { 439 598 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 22.1735137853
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 464 623 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 439 598 }
reference.body = 22.1735137853
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0108 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 0.48677 for Iteration #11 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01513 for iteration 11 of Tilt-Series #6.
Alignment quality for Iteration #11 of Tilt-Series #6 (17sep22z): Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00868 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 0.31698 for Iteration #12 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01068 for iteration 12 of Tilt-Series #6.
Alignment quality for Iteration #12 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00794 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 0.34591 for Iteration #13 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01089 for iteration 13 of Tilt-Series #6.
Alignment quality for Iteration #13 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00778 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 0.32753 for Iteration #14 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01044 for iteration 14 of Tilt-Series #6.
Alignment quality for Iteration #14 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00776 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 0.35319 for Iteration #15 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01094 for iteration 15 of Tilt-Series #6.
Alignment quality for Iteration #15 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #6 (17sep22z): StableCreating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0075 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 0.29494 for Iteration #16 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00965 for iteration 16 of Tilt-Series #6.
Alignment quality for Iteration #16 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00824 for Iteration #17 of Tilt-Series #6.
CCMS(rotations) = 0.32227 for Iteration #17 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01056 for iteration 17 of Tilt-Series #6.
Alignment quality for Iteration #17 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #6 (17sep22z): Very 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00853 for Iteration #18 of Tilt-Series #6.
CCMS(rotations) = 0.29458 for Iteration #18 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01016 for iteration 18 of Tilt-Series #6.
Alignment quality for Iteration #18 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00821 for Iteration #19 of Tilt-Series #6.
CCMS(rotations) = 0.35759 for Iteration #19 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01126 for iteration 19 of Tilt-Series #6.
Alignment quality for Iteration #19 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00931 for Iteration #20 of Tilt-Series #6.
CCMS(rotations) = 0.37529 for Iteration #20 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01216 for iteration 20 of Tilt-Series #6.
Alignment quality for Iteration #20 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #6 (17sep22z): UnstableCreating 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 #6 (tiltseries0006_thick150)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.68 Angstroms, Nyquist is 9.36 Angstroms)
window.lowpass.apodization = { 0.301935483871 0.301935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00215519226341 0.00215519226341 }
window.highpass.apodization = { 0.00430939226519 0.00430939226519 }
window.mask.apodization = { 10 10 }
align.mask.width = { 903 1221 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 44.3470275706
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 928 1246 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 903 1221 }
reference.body = 44.3470275706
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01055 for Iteration #21 of Tilt-Series #6.
CCMS(rotations) = 0.29383 for Iteration #21 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01115 for iteration 21 of Tilt-Series #6.
Alignment quality for Iteration #21 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00839 for Iteration #22 of Tilt-Series #6.
CCMS(rotations) = 0.26575 for Iteration #22 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00951 for iteration 22 of Tilt-Series #6.
Alignment quality for Iteration #22 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #6 (17sep22z): Very StableCreating 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00964 for Iteration #23 of Tilt-Series #6.
CCMS(rotations) = 0.33207 for Iteration #23 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01146 for iteration 23 of Tilt-Series #6.
Alignment quality for Iteration #23 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #6 (17sep22z): Very StableCreating 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00918 for Iteration #24 of Tilt-Series #6.
CCMS(rotations) = 0.3475 for Iteration #24 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01154 for iteration 24 of Tilt-Series #6.
Alignment quality for Iteration #24 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #6 (17sep22z): Very StableCreating 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00905 for Iteration #25 of Tilt-Series #6.
CCMS(rotations) = 0.31426 for Iteration #25 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01081 for iteration 25 of Tilt-Series #6.
Alignment quality for Iteration #25 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #6 (17sep22z): StableCreating 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 #6 (tiltseries0006_thick150)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.34 Angstroms, Nyquist is 4.68 Angstroms)
window.lowpass.apodization = { 0.2925 0.2925 }
map.sampling = 1
window.highpass.diameter = { 0.00107759613171 0.00107759613171 }
window.highpass.apodization = { 0.0021546961326 0.0021546961326 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1831 2467 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 88.6940551411
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1856 2492 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1831 2467 }
reference.body = 88.6940551411
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01305 for Iteration #26 of Tilt-Series #6.
CCMS(rotations) = 0.27707 for Iteration #26 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01207 for iteration 26 of Tilt-Series #6.
Alignment quality for Iteration #26 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01095 for Iteration #27 of Tilt-Series #6.
CCMS(rotations) = 0.21501 for Iteration #27 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00978 for iteration 27 of Tilt-Series #6.
Alignment quality for Iteration #27 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0122 for Iteration #28 of Tilt-Series #6.
CCMS(rotations) = 0.26836 for Iteration #28 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01147 for iteration 28 of Tilt-Series #6.
Alignment quality for Iteration #28 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #6 (17sep22z): Very StableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0113 for Iteration #29 of Tilt-Series #6.
CCMS(rotations) = 0.25861 for Iteration #29 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01082 for iteration 29 of Tilt-Series #6.
Alignment quality for Iteration #29 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01132 for Iteration #30 of Tilt-Series #6.
CCMS(rotations) = 0.30261 for Iteration #30 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01171 for iteration 30 of Tilt-Series #6.
Alignment quality for Iteration #30 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #6 (17sep22z): StableCreating 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0123 for Iteration #31 of Tilt-Series #6.
CCMS(rotations) = 0.25716 for Iteration #31 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01129 for iteration 31 of Tilt-Series #6.
Alignment quality for Iteration #31 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00898 for Iteration #32 of Tilt-Series #6.
CCMS(rotations) = 0.21025 for Iteration #32 of Tilt-Series #6.
CCMS(scale) = 0.004 for Iteration #32 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00713 for iteration 32 of Tilt-Series #6.
Alignment quality for Iteration #32 of Tilt-Series #6 (17sep22z): Excellent (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01039 for Iteration #33 of Tilt-Series #6.
CCMS(rotations) = 0.3061 for Iteration #33 of Tilt-Series #6.
CCMS(scale) = 0.0044 for Iteration #33 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00901 for iteration 33 of Tilt-Series #6.
Alignment quality for Iteration #33 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #6 (17sep22z): 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 #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01017 for Iteration #34 of Tilt-Series #6.
CCMS(rotations) = 0.24509 for Iteration #34 of Tilt-Series #6.
CCMS(scale) = 0.00533 for Iteration #34 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00843 for iteration 34 of Tilt-Series #6.
Alignment quality for Iteration #34 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #6 (17sep22z): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #6 (tiltseries0006_thick150)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006_thick150)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00992 for Iteration #35 of Tilt-Series #6.
CCMS(rotations) = 0.2731 for Iteration #35 of Tilt-Series #6.
CCMS(scale) = 0.00444 for Iteration #35 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00843 for iteration 35 of Tilt-Series #6.
Alignment quality for Iteration #35 of Tilt-Series #6 (17sep22z): Very Good (confidence: 96.875000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #6 (17sep22z): Very StableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #6 (tiltseries0006_thick150)!
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: 2017yr09m23d-02hr17m49s