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/17aug18i/protomo_alignments/tiltseries0032_thick150 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2076.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3838 --r1_region_y=3710 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2076.0 --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=3710 --r2_region_x=3838 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1038.0 --defocus_ang_positive=90 --r5_mask_width_x=3813 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2076.0 --r3_highpass_apod_x=1038.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=934 --r2_mask_width_y=902 --r5_region_x=3838 --r5_region_y=3710 --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=2076.0 --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=3685 --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=1038.0 --runname=tiltseries0032_thick150 --r1_highpass_diameter_x=2076.0 --r2_lowpass_diameter_y=25.0 --map_size_y=927 --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=3813 --r4_mask_width_y=3685 --r5_highpass_apod_y=1038.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17aug18i --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=1038.0 --r1_highpass_apod_x=1038.0 --r2_highpass_apod_x=1038.0 --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=26 --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=32 --r5_corr_mode=pcf --change_refimg=True --r3_mask_width_y=1830 --r3_mask_width_x=1894 --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=2076.0 --r4_highpass_diameter_x=2076.0 --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=2076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1038.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2076.0 --defocus_max=0 --r4_region_y=3710 --r4_region_x=3838 --r5_kernel_y=5 --r3_region_x=3838 --r3_region_y=3710 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=150 --expid=4732 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=959 --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=0.5595 --link=False --r2_highpass_diameter_x=2076.0 --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=1919.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=5 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=7676 --dimy=7420 --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=1038.0 --r4_highpass_apod_y=1038.0 --azimuth=true --r1_mask_width_y=438 --r1_mask_width_x=454 --jobtype=protomo

node23
Start time: 2017yr09m04d-16hr01m13s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0032.tlt to series0032.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #32 (tiltseries0032_thick150)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 4.476 Angstroms, Nyquist is 8.952 Angstroms)
window.lowpass.apodization = { 0.071616 0.071616 }
map.sampling = 8
window.highpass.diameter = { 0.00431213872832 0.00431213872832 }
window.highpass.apodization = { 0.00862427745665 0.00862427745665 }
window.mask.apodization = { 10 10 }
align.mask.width = { 454 438 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 47.389907573
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 479 463 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 454 438 }
reference.body = 47.389907573
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.124 for Iteration #1 of Tilt-Series #32.
CCMS(rotations) = 1.203 for Iteration #1 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #32.
The scaled sum of CCMS values is #0.08606 for iteration 1 of Tilt-Series #32.
Alignment quality for Iteration #1 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.09329 for Iteration #2 of Tilt-Series #32.
CCMS(rotations) = 1.99833 for Iteration #2 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #32.
The scaled sum of CCMS values is #0.08661 for iteration 2 of Tilt-Series #32.
Alignment quality for Iteration #2 of Tilt-Series #32 (17aug18i): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.07481 for Iteration #3 of Tilt-Series #32.
CCMS(rotations) = 0.43506 for Iteration #3 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #32.
The scaled sum of CCMS values is #0.04611 for iteration 3 of Tilt-Series #32.
Alignment quality for Iteration #3 of Tilt-Series #32 (17aug18i): Bad (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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00549 for Iteration #4 of Tilt-Series #32.
CCMS(rotations) = 0.21557 for Iteration #4 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00706 for iteration 4 of Tilt-Series #32.
Alignment quality for Iteration #4 of Tilt-Series #32 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00558 for Iteration #5 of Tilt-Series #32.
CCMS(rotations) = 0.26002 for Iteration #5 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00799 for iteration 5 of Tilt-Series #32.
Alignment quality for Iteration #5 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #32 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

Beginning Refinement Iteration #6, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 2.238 Angstroms, Nyquist is 4.476 Angstroms)
window.lowpass.apodization = { 0.0710476190476 0.0710476190476 }
map.sampling = 4
window.highpass.diameter = { 0.00215606936416 0.00215606936416 }
window.highpass.apodization = { 0.00431213872832 0.00431213872832 }
window.mask.apodization = { 10 10 }
align.mask.width = { 934 902 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 94.7798151461
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 959 927 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 934 902 }
reference.body = 94.7798151461
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00638 for Iteration #6 of Tilt-Series #32.
CCMS(rotations) = 0.22607 for Iteration #6 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00771 for iteration 6 of Tilt-Series #32.
Alignment quality for Iteration #6 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #32 (17aug18i): StableCreating 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #7, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #7 of Tilt-Series #32.
CCMS(rotations) = 0.32089 for Iteration #7 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00947 for iteration 7 of Tilt-Series #32.
Alignment quality for Iteration #7 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #8, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #8 of Tilt-Series #32.
CCMS(rotations) = 0.36989 for Iteration #8 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01039 for iteration 8 of Tilt-Series #32.
Alignment quality for Iteration #8 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #9, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00618 for Iteration #9 of Tilt-Series #32.
CCMS(rotations) = 0.34347 for Iteration #9 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00996 for iteration 9 of Tilt-Series #32.
Alignment quality for Iteration #9 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #10, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #10 of Tilt-Series #32.
CCMS(rotations) = 0.33015 for Iteration #10 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00953 for iteration 10 of Tilt-Series #32.
Alignment quality for Iteration #10 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #32 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

No Round parameters changed for Iteration #11 of Tilt-Series #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00595 for Iteration #11 of Tilt-Series #32.
CCMS(rotations) = 0.38554 for Iteration #11 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01069 for iteration 11 of Tilt-Series #32.
Alignment quality for Iteration #11 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #32 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...

No Round parameters changed for Iteration #12 of Tilt-Series #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #12 of Tilt-Series #32.
CCMS(rotations) = 0.38875 for Iteration #12 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #32.
The scaled sum of CCMS values is #0.0107 for iteration 12 of Tilt-Series #32.
Alignment quality for Iteration #12 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00582 for Iteration #13 of Tilt-Series #32.
CCMS(rotations) = 0.36925 for Iteration #13 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01029 for iteration 13 of Tilt-Series #32.
Alignment quality for Iteration #13 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00613 for Iteration #14 of Tilt-Series #32.
CCMS(rotations) = 0.40737 for Iteration #14 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01121 for iteration 14 of Tilt-Series #32.
Alignment quality for Iteration #14 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #15 of Tilt-Series #32.
CCMS(rotations) = 0.37728 for Iteration #15 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01064 for iteration 15 of Tilt-Series #32.
Alignment quality for Iteration #15 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #32 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

Beginning Refinement Iteration #16, Round #3 of Tilt-Series #32 (tiltseries0032_thick150)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 1.119 Angstroms, Nyquist is 2.238 Angstroms)
window.lowpass.apodization = { 0.0721935483871 0.0721935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00107803468208 0.00107803468208 }
window.highpass.apodization = { 0.00215606936416 0.00215606936416 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1894 1830 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 189.559630292
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1919 1855 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1894 1830 }
reference.body = 189.559630292
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00744 for Iteration #16 of Tilt-Series #32.
CCMS(rotations) = 0.41366 for Iteration #16 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #32.
The scaled sum of CCMS values is #0.012 for iteration 16 of Tilt-Series #32.
Alignment quality for Iteration #16 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #17, Round #3 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00643 for Iteration #17 of Tilt-Series #32.
CCMS(rotations) = 0.25053 for Iteration #17 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00823 for iteration 17 of Tilt-Series #32.
Alignment quality for Iteration #17 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #18, Round #3 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #18 of Tilt-Series #32.
CCMS(rotations) = 0.27694 for Iteration #18 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00864 for iteration 18 of Tilt-Series #32.
Alignment quality for Iteration #18 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #19, Round #3 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00625 for Iteration #19 of Tilt-Series #32.
CCMS(rotations) = 0.2561 for Iteration #19 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00825 for iteration 19 of Tilt-Series #32.
Alignment quality for Iteration #19 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #20, Round #3 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00628 for Iteration #20 of Tilt-Series #32.
CCMS(rotations) = 0.26283 for Iteration #20 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00839 for iteration 20 of Tilt-Series #32.
Alignment quality for Iteration #20 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #32 (17aug18i): 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 #4 of Tilt-Series #32 (tiltseries0032_thick150)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 0.5595 Angstroms, Nyquist is 1.119 Angstroms)
window.lowpass.apodization = { 0.0699375 0.0699375 }
map.sampling = 1
window.highpass.diameter = { 0.00053901734104 0.00053901734104 }
window.highpass.apodization = { 0.00107803468208 0.00107803468208 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3813 3685 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 379.119260584
map.lowpass.diameter = { 0.17904 0.17904 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3838 3710 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3813 3685 }
reference.body = 379.119260584
window.lowpass.diameter = { 0.17904 0.17904 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00816 for Iteration #21 of Tilt-Series #32.
CCMS(rotations) = 0.14419 for Iteration #21 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00696 for iteration 21 of Tilt-Series #32.
Alignment quality for Iteration #21 of Tilt-Series #32 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #22, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00943 for Iteration #22 of Tilt-Series #32.
CCMS(rotations) = 0.40406 for Iteration #22 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01279 for iteration 22 of Tilt-Series #32.
Alignment quality for Iteration #22 of Tilt-Series #32 (17aug18i): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #23, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00978 for Iteration #23 of Tilt-Series #32.
CCMS(rotations) = 0.19113 for Iteration #23 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00871 for iteration 23 of Tilt-Series #32.
Alignment quality for Iteration #23 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #24, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00795 for Iteration #24 of Tilt-Series #32.
CCMS(rotations) = 0.37934 for Iteration #24 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01156 for iteration 24 of Tilt-Series #32.
Alignment quality for Iteration #24 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #25, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00728 for Iteration #25 of Tilt-Series #32.
CCMS(rotations) = 0.26362 for Iteration #25 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00891 for iteration 25 of Tilt-Series #32.
Alignment quality for Iteration #25 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #32 (17aug18i): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

No Round parameters changed for Iteration #26 of Tilt-Series #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
fit.scale switched from false to true on Iteration #26Creating quality assessment statistics...
CCMS(shift) = 0.0075 for Iteration #26 of Tilt-Series #32.
CCMS(rotations) = 0.35783 for Iteration #26 of Tilt-Series #32.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #32.
The scaled sum of CCMS values is #0.01091 for iteration 26 of Tilt-Series #32.
Alignment quality for Iteration #26 of Tilt-Series #32 (17aug18i): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00466 for Iteration #27 of Tilt-Series #32.
CCMS(rotations) = 0.13649 for Iteration #27 of Tilt-Series #32.
CCMS(scale) = 0.00418 for Iteration #27 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00477 for iteration 27 of Tilt-Series #32.
Alignment quality for Iteration #27 of Tilt-Series #32 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #32 (17aug18i): Very StableCreating 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00632 for Iteration #28 of Tilt-Series #32.
CCMS(rotations) = 0.12722 for Iteration #28 of Tilt-Series #32.
CCMS(scale) = 0.0042 for Iteration #28 of Tilt-Series #32.
The scaled sum of CCMS values is #0.0052 for iteration 28 of Tilt-Series #32.
Alignment quality for Iteration #28 of Tilt-Series #32 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #32 (17aug18i): 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00559 for Iteration #29 of Tilt-Series #32.
CCMS(rotations) = 0.15462 for Iteration #29 of Tilt-Series #32.
CCMS(scale) = 0.00521 for Iteration #29 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00566 for iteration 29 of Tilt-Series #32.
Alignment quality for Iteration #29 of Tilt-Series #32 (17aug18i): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #32 (17aug18i): StableCreating 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 #32 (tiltseries0032_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #32 (tiltseries0032_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #30 of Tilt-Series #32.
CCMS(rotations) = 0.10365 for Iteration #30 of Tilt-Series #32.
CCMS(scale) = 0.00404 for Iteration #30 of Tilt-Series #32.
The scaled sum of CCMS values is #0.00434 for iteration 30 of Tilt-Series #32.
Alignment quality for Iteration #30 of Tilt-Series #32 (17aug18i): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #32 (17aug18i): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
Finished Refinement for Tilt-Series #32 (tiltseries0032_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: 2017yr09m05d-14hr56m09s