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/17sep22z/protomo_alignments/tiltseries0004_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=tiltseries0004_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=4 --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

node32
Start time: 2017yr09m22d-10hr47m18s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0004.tlt to series0004.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_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 = 11.085831833
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 = 11.085831833
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06695 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 1.50376 for Iteration #1 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4.
The scaled sum of CCMS values is #0.06355 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (17sep22z): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01806 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.21048 for Iteration #2 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4.
The scaled sum of CCMS values is #0.01324 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00577 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.22968 for Iteration #3 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00748 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.22013 for Iteration #4 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00696 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00509 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.21016 for Iteration #5 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00675 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00529 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.19601 for Iteration #6 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00657 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00534 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.19052 for Iteration #7 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00648 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.17467 for Iteration #8 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00613 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.17509 for Iteration #9 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00614 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00513 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.17259 for Iteration #10 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00602 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (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 #4 (tiltseries0004_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 = 22.171663666
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 = 22.171663666
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00833 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.11034 for Iteration #11 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00637 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17sep22z): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00358 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.09491 for Iteration #12 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00369 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00376 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.09864 for Iteration #13 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00385 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (17sep22z): Very StableCreating 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00336 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.10506 for Iteration #14 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00378 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.11161 for Iteration #15 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00404 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00351 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.11433 for Iteration #16 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00404 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.11651 for Iteration #17 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00415 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00353 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.10852 for Iteration #18 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00393 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0037 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.11232 for Iteration #19 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00409 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00353 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.11235 for Iteration #20 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00401 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_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 = 44.3433273319
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 = 44.3433273319
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.0998 for Iteration #21 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00397 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (17sep22z): StableCreating 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.08987 for Iteration #22 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00362 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00354 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.0905 for Iteration #23 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00358 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00373 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.0912 for Iteration #24 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00369 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.09732 for Iteration #25 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00381 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_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 = 88.6866546639
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 = 88.6866546639
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00792 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.25151 for Iteration #26 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00899 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17sep22z): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00523 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.11529 for Iteration #27 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00492 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00472 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.11722 for Iteration #28 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0047 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00514 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.11082 for Iteration #29 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00478 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.11177 for Iteration #30 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00446 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00435 for Iteration #31 of Tilt-Series #4.
CCMS(rotations) = 0.09905 for Iteration #31 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00416 for iteration 31 of Tilt-Series #4.
Alignment quality for Iteration #31 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00355 for Iteration #32 of Tilt-Series #4.
CCMS(rotations) = 0.11714 for Iteration #32 of Tilt-Series #4.
CCMS(scale) = 0.00125 for Iteration #32 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00316 for iteration 32 of Tilt-Series #4.
Alignment quality for Iteration #32 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #33 of Tilt-Series #4.
CCMS(rotations) = 0.09935 for Iteration #33 of Tilt-Series #4.
CCMS(scale) = 0.00144 for Iteration #33 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00331 for iteration 33 of Tilt-Series #4.
Alignment quality for Iteration #33 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (17sep22z): StableCreating 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 #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00459 for Iteration #34 of Tilt-Series #4.
CCMS(rotations) = 0.1006 for Iteration #34 of Tilt-Series #4.
CCMS(scale) = 0.00174 for Iteration #34 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00345 for iteration 34 of Tilt-Series #4.
Alignment quality for Iteration #34 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (17sep22z): Very StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #4 (tiltseries0004_thick150)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick150)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #35 of Tilt-Series #4.
CCMS(rotations) = 0.10561 for Iteration #35 of Tilt-Series #4.
CCMS(scale) = 0.00145 for Iteration #35 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00337 for iteration 35 of Tilt-Series #4.
Alignment quality for Iteration #35 of Tilt-Series #4 (17sep22z): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (17sep22z): 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 #4 (tiltseries0004_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: 2017yr09m22d-22hr07m45s