protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-16.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0008_thick100 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=8.64 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=False --r1_highpass_diameter_y=4015.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=1894 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2008.0 --runname=tiltseries0008_thick100 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=8 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=934 --r3_mask_width_x=902 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4015.0 --r4_highpass_diameter_x=4015.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=100 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=43.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=3.0 --tilt_clip=true --r4_highpass_apod_x=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo

node06
Start time: 2017yr12m26d-18hr37m45s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0008.tlt to series0008.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
lowpass = 69.12 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms)
window.lowpass.apodization = { 0.20016 0.20016 }
map.sampling = 8
window.highpass.diameter = { 0.00862457783313 0.00862457783313 }
window.highpass.apodization = { 0.0172448605578 0.0172448605578 }
window.mask.apodization = { 10 10 }
align.mask.width = { 206 214 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 9.17594003198
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 9.17594003198
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0888 for Iteration #1 of Tilt-Series #8.
CCMS(rotations) = 0.80026 for Iteration #1 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0604 for iteration 1 of Tilt-Series #8.
Alignment quality for Iteration #1 of Tilt-Series #8 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 62.500000%)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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01204 for Iteration #2 of Tilt-Series #8.
CCMS(rotations) = 0.39936 for Iteration #2 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01401 for iteration 2 of Tilt-Series #8.
Alignment quality for Iteration #2 of Tilt-Series #8 (17dec26e): Good (confidence: 62.500000%)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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00578 for Iteration #3 of Tilt-Series #8.
CCMS(rotations) = 0.42357 for Iteration #3 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01136 for iteration 3 of Tilt-Series #8.
Alignment quality for Iteration #3 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00569 for Iteration #4 of Tilt-Series #8.
CCMS(rotations) = 0.45252 for Iteration #4 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0119 for iteration 4 of Tilt-Series #8.
Alignment quality for Iteration #4 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #5 of Tilt-Series #8.
CCMS(rotations) = 0.4274 for Iteration #5 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01137 for iteration 5 of Tilt-Series #8.
Alignment quality for Iteration #5 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #6 of Tilt-Series #8.
CCMS(rotations) = 0.44854 for Iteration #6 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01184 for iteration 6 of Tilt-Series #8.
Alignment quality for Iteration #6 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #7 of Tilt-Series #8.
CCMS(rotations) = 0.43012 for Iteration #7 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01147 for iteration 7 of Tilt-Series #8.
Alignment quality for Iteration #7 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00565 for Iteration #8 of Tilt-Series #8.
CCMS(rotations) = 0.44665 for Iteration #8 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01176 for iteration 8 of Tilt-Series #8.
Alignment quality for Iteration #8 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #9 of Tilt-Series #8.
CCMS(rotations) = 0.43007 for Iteration #9 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01145 for iteration 9 of Tilt-Series #8.
Alignment quality for Iteration #9 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #10 of Tilt-Series #8.
CCMS(rotations) = 0.45024 for Iteration #10 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8.
The scaled sum of CCMS values is #0.01185 for iteration 10 of Tilt-Series #8.
Alignment quality for Iteration #10 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
lowpass = 34.56 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 4
window.highpass.diameter = { 0.00431228891656 0.00431228891656 }
window.highpass.apodization = { 0.00862243027888 0.00862243027888 }
window.mask.apodization = { 10 10 }
align.mask.width = { 438 454 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 18.351880064
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 18.351880064
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01261 for Iteration #11 of Tilt-Series #8.
CCMS(rotations) = 0.21969 for Iteration #11 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0107 for iteration 11 of Tilt-Series #8.
Alignment quality for Iteration #11 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #8 (17dec26e): 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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0084 for Iteration #12 of Tilt-Series #8.
CCMS(rotations) = 0.25057 for Iteration #12 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00921 for iteration 12 of Tilt-Series #8.
Alignment quality for Iteration #12 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #8 (17dec26e): StableCreating 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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00376 for Iteration #13 of Tilt-Series #8.
CCMS(rotations) = 0.20196 for Iteration #13 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00592 for iteration 13 of Tilt-Series #8.
Alignment quality for Iteration #13 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #14 of Tilt-Series #8.
CCMS(rotations) = 0.24755 for Iteration #14 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00678 for iteration 14 of Tilt-Series #8.
Alignment quality for Iteration #14 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #15 of Tilt-Series #8.
CCMS(rotations) = 0.19625 for Iteration #15 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00586 for iteration 15 of Tilt-Series #8.
Alignment quality for Iteration #15 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0038 for Iteration #16 of Tilt-Series #8.
CCMS(rotations) = 0.24413 for Iteration #16 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00678 for iteration 16 of Tilt-Series #8.
Alignment quality for Iteration #16 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #17 of Tilt-Series #8.
CCMS(rotations) = 0.19755 for Iteration #17 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00587 for iteration 17 of Tilt-Series #8.
Alignment quality for Iteration #17 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00359 for Iteration #18 of Tilt-Series #8.
CCMS(rotations) = 0.24715 for Iteration #18 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00674 for iteration 18 of Tilt-Series #8.
Alignment quality for Iteration #18 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.004 for Iteration #19 of Tilt-Series #8.
CCMS(rotations) = 0.16644 for Iteration #19 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00533 for iteration 19 of Tilt-Series #8.
Alignment quality for Iteration #19 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #8 (17dec26e): StableCreating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00405 for Iteration #20 of Tilt-Series #8.
CCMS(rotations) = 0.24137 for Iteration #20 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00685 for iteration 20 of Tilt-Series #8.
Alignment quality for Iteration #20 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #8 (17dec26e): 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 #8 (tiltseries0008_thick100)
lowpass = 17.28 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
map.sampling = 2
window.highpass.diameter = { 0.00215614445828 0.00215614445828 }
window.highpass.apodization = { 0.00431121513944 0.00431121513944 }
window.mask.apodization = { 10 10 }
align.mask.width = { 902 934 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 36.7037601279
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 36.7037601279
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.009 for Iteration #21 of Tilt-Series #8.
CCMS(rotations) = 0.20988 for Iteration #21 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0087 for iteration 21 of Tilt-Series #8.
Alignment quality for Iteration #21 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #8 (17dec26e): 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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01056 for Iteration #22 of Tilt-Series #8.
CCMS(rotations) = 0.19086 for Iteration #22 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0091 for iteration 22 of Tilt-Series #8.
Alignment quality for Iteration #22 of Tilt-Series #8 (17dec26e): Very Good (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #8 (17dec26e): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00654 for Iteration #23 of Tilt-Series #8.
CCMS(rotations) = 0.19696 for Iteration #23 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00721 for iteration 23 of Tilt-Series #8.
Alignment quality for Iteration #23 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #24 of Tilt-Series #8.
CCMS(rotations) = 0.20836 for Iteration #24 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00586 for iteration 24 of Tilt-Series #8.
Alignment quality for Iteration #24 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00339 for Iteration #25 of Tilt-Series #8.
CCMS(rotations) = 0.19968 for Iteration #25 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00569 for iteration 25 of Tilt-Series #8.
Alignment quality for Iteration #25 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
lowpass = 8.64 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms)
window.lowpass.apodization = { 0.196748181818 0.196748181818 }
map.sampling = 1
window.highpass.diameter = { 0.00107807222914 0.00107807222914 }
window.highpass.apodization = { 0.00215560756972 0.00215560756972 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1830 1894 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 73.4075202558
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 73.4075202558
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #26 of Tilt-Series #8.
CCMS(rotations) = 0.20444 for Iteration #26 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00578 for iteration 26 of Tilt-Series #8.
Alignment quality for Iteration #26 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #27 of Tilt-Series #8.
CCMS(rotations) = 0.20865 for Iteration #27 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00586 for iteration 27 of Tilt-Series #8.
Alignment quality for Iteration #27 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00351 for Iteration #28 of Tilt-Series #8.
CCMS(rotations) = 0.20025 for Iteration #28 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00576 for iteration 28 of Tilt-Series #8.
Alignment quality for Iteration #28 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00346 for Iteration #29 of Tilt-Series #8.
CCMS(rotations) = 0.20174 for Iteration #29 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00576 for iteration 29 of Tilt-Series #8.
Alignment quality for Iteration #29 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00347 for Iteration #30 of Tilt-Series #8.
CCMS(rotations) = 0.19113 for Iteration #30 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00556 for iteration 30 of Tilt-Series #8.
Alignment quality for Iteration #30 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0035 for Iteration #31 of Tilt-Series #8.
CCMS(rotations) = 0.21669 for Iteration #31 of Tilt-Series #8.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00608 for iteration 31 of Tilt-Series #8.
Alignment quality for Iteration #31 of Tilt-Series #8 (17dec26e): Excellent (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #8 (17dec26e): 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 #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00221 for Iteration #32 of Tilt-Series #8.
CCMS(rotations) = 0.20021 for Iteration #32 of Tilt-Series #8.
CCMS(scale) = 0.00161 for Iteration #32 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00394 for iteration 32 of Tilt-Series #8.
Alignment quality for Iteration #32 of Tilt-Series #8 (17dec26e): Perfection! (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...

No Round parameters changed for Iteration #33 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00197 for Iteration #33 of Tilt-Series #8.
CCMS(rotations) = 0.21142 for Iteration #33 of Tilt-Series #8.
CCMS(scale) = 0.00176 for Iteration #33 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00406 for iteration 33 of Tilt-Series #8.
Alignment quality for Iteration #33 of Tilt-Series #8 (17dec26e): Perfection! (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00201 for Iteration #34 of Tilt-Series #8.
CCMS(rotations) = 0.20343 for Iteration #34 of Tilt-Series #8.
CCMS(scale) = 0.00177 for Iteration #34 of Tilt-Series #8.
The scaled sum of CCMS values is #0.00397 for iteration 34 of Tilt-Series #8.
Alignment quality for Iteration #34 of Tilt-Series #8 (17dec26e): Perfection! (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #8 (tiltseries0008_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #8 (tiltseries0008_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.002 for Iteration #35 of Tilt-Series #8.
CCMS(rotations) = 0.22138 for Iteration #35 of Tilt-Series #8.
CCMS(scale) = 0.00175 for Iteration #35 of Tilt-Series #8.
The scaled sum of CCMS values is #0.0042 for iteration 35 of Tilt-Series #8.
Alignment quality for Iteration #35 of Tilt-Series #8 (17dec26e): Perfection! (confidence: 62.500000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #8 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #8 (tiltseries0008_thick100)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr12m26d-23hr47m24s