protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-44.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17nov27o/protomo_alignments/tiltseries0005_thick50 --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=tiltseries0005_thick50 --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=17nov27o --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=5 --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=50 --expid=5456 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=207 --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=44.0 --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

node22
Start time: 2017yr12m01d-11hr54m35s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0005.tlt to series0005.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
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 = 4.08355632041
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 = 4.08355632041
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0591 for Iteration #1 of Tilt-Series #5.
CCMS(rotations) = 0.50486 for Iteration #1 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03965 for iteration 1 of Tilt-Series #5.
Alignment quality for Iteration #1 of Tilt-Series #5 (17nov27o): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 93.548387%)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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.06122 for Iteration #2 of Tilt-Series #5.
CCMS(rotations) = 0.51324 for Iteration #2 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5.
The scaled sum of CCMS values is #0.04088 for iteration 2 of Tilt-Series #5.
Alignment quality for Iteration #2 of Tilt-Series #5 (17nov27o): Bad (confidence: 93.548387%)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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.05835 for Iteration #3 of Tilt-Series #5.
CCMS(rotations) = 0.3522 for Iteration #3 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03622 for iteration 3 of Tilt-Series #5.
Alignment quality for Iteration #3 of Tilt-Series #5 (17nov27o): Bad (confidence: 93.548387%)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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.05273 for Iteration #4 of Tilt-Series #5.
CCMS(rotations) = 0.24244 for Iteration #4 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03122 for iteration 4 of Tilt-Series #5.
Alignment quality for Iteration #4 of Tilt-Series #5 (17nov27o): Bad (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01378 for Iteration #5 of Tilt-Series #5.
CCMS(rotations) = 0.194 for Iteration #5 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01077 for iteration 5 of Tilt-Series #5.
Alignment quality for Iteration #5 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01033 for Iteration #6 of Tilt-Series #5.
CCMS(rotations) = 0.25364 for Iteration #6 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01024 for iteration 6 of Tilt-Series #5.
Alignment quality for Iteration #6 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01118 for Iteration #7 of Tilt-Series #5.
CCMS(rotations) = 0.1549 for Iteration #7 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00869 for iteration 7 of Tilt-Series #5.
Alignment quality for Iteration #7 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01136 for Iteration #8 of Tilt-Series #5.
CCMS(rotations) = 0.24221 for Iteration #8 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01053 for iteration 8 of Tilt-Series #5.
Alignment quality for Iteration #8 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01409 for Iteration #9 of Tilt-Series #5.
CCMS(rotations) = 0.17655 for Iteration #9 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01058 for iteration 9 of Tilt-Series #5.
Alignment quality for Iteration #9 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00948 for Iteration #10 of Tilt-Series #5.
CCMS(rotations) = 0.24416 for Iteration #10 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00962 for iteration 10 of Tilt-Series #5.
Alignment quality for Iteration #10 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
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 = 8.16711264082
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 = 8.16711264082
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.0264 for Iteration #11 of Tilt-Series #5.
CCMS(rotations) = 0.95854 for Iteration #11 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03237 for iteration 11 of Tilt-Series #5.
Alignment quality for Iteration #11 of Tilt-Series #5 (17nov27o): Bad (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00771 for Iteration #12 of Tilt-Series #5.
CCMS(rotations) = 0.22987 for Iteration #12 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00845 for iteration 12 of Tilt-Series #5.
Alignment quality for Iteration #12 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0068 for Iteration #13 of Tilt-Series #5.
CCMS(rotations) = 0.18936 for Iteration #13 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00719 for iteration 13 of Tilt-Series #5.
Alignment quality for Iteration #13 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00676 for Iteration #14 of Tilt-Series #5.
CCMS(rotations) = 0.18595 for Iteration #14 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0071 for iteration 14 of Tilt-Series #5.
Alignment quality for Iteration #14 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00692 for Iteration #15 of Tilt-Series #5.
CCMS(rotations) = 0.19491 for Iteration #15 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00736 for iteration 15 of Tilt-Series #5.
Alignment quality for Iteration #15 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00685 for Iteration #16 of Tilt-Series #5.
CCMS(rotations) = 0.17796 for Iteration #16 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00698 for iteration 16 of Tilt-Series #5.
Alignment quality for Iteration #16 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #17 of Tilt-Series #5.
CCMS(rotations) = 0.19457 for Iteration #17 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00732 for iteration 17 of Tilt-Series #5.
Alignment quality for Iteration #17 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00687 for Iteration #18 of Tilt-Series #5.
CCMS(rotations) = 0.1762 for Iteration #18 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00696 for iteration 18 of Tilt-Series #5.
Alignment quality for Iteration #18 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00685 for Iteration #19 of Tilt-Series #5.
CCMS(rotations) = 0.19514 for Iteration #19 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00733 for iteration 19 of Tilt-Series #5.
Alignment quality for Iteration #19 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00687 for Iteration #20 of Tilt-Series #5.
CCMS(rotations) = 0.17771 for Iteration #20 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00699 for iteration 20 of Tilt-Series #5.
Alignment quality for Iteration #20 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)
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 = 16.3342252816
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 = 16.3342252816
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00626 for Iteration #21 of Tilt-Series #5.
CCMS(rotations) = 0.15566 for Iteration #21 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00625 for iteration 21 of Tilt-Series #5.
Alignment quality for Iteration #21 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #5 (17nov27o): Rock Solid!Creating 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00612 for Iteration #22 of Tilt-Series #5.
CCMS(rotations) = 0.14156 for Iteration #22 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00589 for iteration 22 of Tilt-Series #5.
Alignment quality for Iteration #22 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00659 for Iteration #23 of Tilt-Series #5.
CCMS(rotations) = 0.13722 for Iteration #23 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00604 for iteration 23 of Tilt-Series #5.
Alignment quality for Iteration #23 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00656 for Iteration #24 of Tilt-Series #5.
CCMS(rotations) = 0.15549 for Iteration #24 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00639 for iteration 24 of Tilt-Series #5.
Alignment quality for Iteration #24 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #25 of Tilt-Series #5.
CCMS(rotations) = 0.15046 for Iteration #25 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00606 for iteration 25 of Tilt-Series #5.
Alignment quality for Iteration #25 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)
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 = 32.6684505633
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 = 32.6684505633
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00865 for Iteration #26 of Tilt-Series #5.
CCMS(rotations) = 0.16849 for Iteration #26 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0077 for iteration 26 of Tilt-Series #5.
Alignment quality for Iteration #26 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #5 (17nov27o): Very StableCreating 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #27 of Tilt-Series #5.
CCMS(rotations) = 0.21401 for Iteration #27 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00765 for iteration 27 of Tilt-Series #5.
Alignment quality for Iteration #27 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #28 of Tilt-Series #5.
CCMS(rotations) = 0.20087 for Iteration #28 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00756 for iteration 28 of Tilt-Series #5.
Alignment quality for Iteration #28 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #29 of Tilt-Series #5.
CCMS(rotations) = 0.22993 for Iteration #29 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00769 for iteration 29 of Tilt-Series #5.
Alignment quality for Iteration #29 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #30 of Tilt-Series #5.
CCMS(rotations) = 0.1975 for Iteration #30 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00712 for iteration 30 of Tilt-Series #5.
Alignment quality for Iteration #30 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #5 (17nov27o): StableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00638 for Iteration #31 of Tilt-Series #5.
CCMS(rotations) = 0.1708 for Iteration #31 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5.
The scaled sum of CCMS values is #0.00661 for iteration 31 of Tilt-Series #5.
Alignment quality for Iteration #31 of Tilt-Series #5 (17nov27o): Excellent (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #5 (17nov27o): 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01372 for Iteration #32 of Tilt-Series #5.
CCMS(rotations) = 0.33429 for Iteration #32 of Tilt-Series #5.
CCMS(scale) = 0.00365 for Iteration #32 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01025 for iteration 32 of Tilt-Series #5.
Alignment quality for Iteration #32 of Tilt-Series #5 (17nov27o): Very Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #5 (17nov27o): UnstableCreating 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 #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.02194 for Iteration #33 of Tilt-Series #5.
CCMS(rotations) = 0.62924 for Iteration #33 of Tilt-Series #5.
CCMS(scale) = 0.0045 for Iteration #33 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0172 for iteration 33 of Tilt-Series #5.
Alignment quality for Iteration #33 of Tilt-Series #5 (17nov27o): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.02086 for Iteration #34 of Tilt-Series #5.
CCMS(rotations) = 0.41791 for Iteration #34 of Tilt-Series #5.
CCMS(scale) = 0.00567 for Iteration #34 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01441 for iteration 34 of Tilt-Series #5.
Alignment quality for Iteration #34 of Tilt-Series #5 (17nov27o): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #5 (tiltseries0005_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #5 (tiltseries0005_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01274 for Iteration #35 of Tilt-Series #5.
CCMS(rotations) = 0.45835 for Iteration #35 of Tilt-Series #5.
CCMS(scale) = 0.00947 for Iteration #35 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01351 for iteration 35 of Tilt-Series #5.
Alignment quality for Iteration #35 of Tilt-Series #5 (17nov27o): Good (confidence: 93.548387%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #5 (17nov27o): UnstableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #5 (tiltseries0005_thick50)!
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: 2017yr12m01d-21hr40m57s