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/17oct05c/protomo_alignments/tiltseries0003_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=6.25 --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=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=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=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=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=tiltseries0003_thick100 --r1_highpass_diameter_x=4015.0 --r2_lowpass_diameter_y=25.0 --map_size_y=479 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17oct05c --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=Coarse_Iter_2 --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=3 --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=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=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=5089 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --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=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --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=25.0 --dimx=3710 --dimy=3838 --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=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: 2017yr10m05d-11hr19m58s
Description: 
coarse_series0003_iter2.tlt not found, using coarse_series0003.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0003.tlt to series0003.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
lowpass = 50.0 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 = { 0.27702144 0.27702144 }
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 = 7.43092086066
map.lowpass.diameter = { 0.6925536 0.6925536 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 7.43092086066
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04553 for Iteration #1 of Tilt-Series #3.
CCMS(rotations) = 1.53507 for Iteration #1 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3.
The scaled sum of CCMS values is #0.05347 for iteration 1 of Tilt-Series #3.
Alignment quality for Iteration #1 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01523 for Iteration #2 of Tilt-Series #3.
CCMS(rotations) = 0.45688 for Iteration #2 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3.
The scaled sum of CCMS values is #0.01675 for iteration 2 of Tilt-Series #3.
Alignment quality for Iteration #2 of Tilt-Series #3 (17oct05c): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01056 for Iteration #3 of Tilt-Series #3.
CCMS(rotations) = 0.20014 for Iteration #3 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00928 for iteration 3 of Tilt-Series #3.
Alignment quality for Iteration #3 of Tilt-Series #3 (17oct05c): Very Good (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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00779 for Iteration #4 of Tilt-Series #3.
CCMS(rotations) = 0.20404 for Iteration #4 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00798 for iteration 4 of Tilt-Series #3.
Alignment quality for Iteration #4 of Tilt-Series #3 (17oct05c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00643 for Iteration #5 of Tilt-Series #3.
CCMS(rotations) = 0.20757 for Iteration #5 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00736 for iteration 5 of Tilt-Series #3.
Alignment quality for Iteration #5 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00645 for Iteration #6 of Tilt-Series #3.
CCMS(rotations) = 0.20429 for Iteration #6 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00731 for iteration 6 of Tilt-Series #3.
Alignment quality for Iteration #6 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00604 for Iteration #7 of Tilt-Series #3.
CCMS(rotations) = 0.19679 for Iteration #7 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00696 for iteration 7 of Tilt-Series #3.
Alignment quality for Iteration #7 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #3 (17oct05c): StableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00602 for Iteration #8 of Tilt-Series #3.
CCMS(rotations) = 0.19611 for Iteration #8 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00693 for iteration 8 of Tilt-Series #3.
Alignment quality for Iteration #8 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #3 (17oct05c): Very StableCreating 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00587 for Iteration #9 of Tilt-Series #3.
CCMS(rotations) = 0.19155 for Iteration #9 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00677 for iteration 9 of Tilt-Series #3.
Alignment quality for Iteration #9 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #3 (17oct05c): Very StableCreating 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00596 for Iteration #10 of Tilt-Series #3.
CCMS(rotations) = 0.1833 for Iteration #10 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00665 for iteration 10 of Tilt-Series #3.
Alignment quality for Iteration #10 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #3 (17oct05c): Very StableCreating 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 #3 (tiltseries0003_thick100)
lowpass = 25.0 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 = { 0.274822857143 0.274822857143 }
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 = 14.8618417213
map.lowpass.diameter = { 0.6925536 0.6925536 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 14.8618417213
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00536 for Iteration #11 of Tilt-Series #3.
CCMS(rotations) = 0.1125 for Iteration #11 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00493 for iteration 11 of Tilt-Series #3.
Alignment quality for Iteration #11 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00535 for Iteration #12 of Tilt-Series #3.
CCMS(rotations) = 0.13079 for Iteration #12 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00529 for iteration 12 of Tilt-Series #3.
Alignment quality for Iteration #12 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00567 for Iteration #13 of Tilt-Series #3.
CCMS(rotations) = 0.14024 for Iteration #13 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00564 for iteration 13 of Tilt-Series #3.
Alignment quality for Iteration #13 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00566 for Iteration #14 of Tilt-Series #3.
CCMS(rotations) = 0.13753 for Iteration #14 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00558 for iteration 14 of Tilt-Series #3.
Alignment quality for Iteration #14 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00581 for Iteration #15 of Tilt-Series #3.
CCMS(rotations) = 0.13406 for Iteration #15 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00559 for iteration 15 of Tilt-Series #3.
Alignment quality for Iteration #15 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #16 of Tilt-Series #3.
CCMS(rotations) = 0.14549 for Iteration #16 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00573 for iteration 16 of Tilt-Series #3.
Alignment quality for Iteration #16 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00594 for Iteration #17 of Tilt-Series #3.
CCMS(rotations) = 0.12084 for Iteration #17 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00539 for iteration 17 of Tilt-Series #3.
Alignment quality for Iteration #17 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00584 for Iteration #18 of Tilt-Series #3.
CCMS(rotations) = 0.15099 for Iteration #18 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00594 for iteration 18 of Tilt-Series #3.
Alignment quality for Iteration #18 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00601 for Iteration #19 of Tilt-Series #3.
CCMS(rotations) = 0.12355 for Iteration #19 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00548 for iteration 19 of Tilt-Series #3.
Alignment quality for Iteration #19 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00584 for Iteration #20 of Tilt-Series #3.
CCMS(rotations) = 0.14974 for Iteration #20 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00592 for iteration 20 of Tilt-Series #3.
Alignment quality for Iteration #20 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)
lowpass = 12.5 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 = { 0.279255483871 0.279255483871 }
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 = 29.7236834426
map.lowpass.diameter = { 0.6925536 0.6925536 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 29.7236834426
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00534 for Iteration #21 of Tilt-Series #3.
CCMS(rotations) = 0.10272 for Iteration #21 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00472 for iteration 21 of Tilt-Series #3.
Alignment quality for Iteration #21 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00533 for Iteration #22 of Tilt-Series #3.
CCMS(rotations) = 0.11373 for Iteration #22 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00494 for iteration 22 of Tilt-Series #3.
Alignment quality for Iteration #22 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #23 of Tilt-Series #3.
CCMS(rotations) = 0.11706 for Iteration #23 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00497 for iteration 23 of Tilt-Series #3.
Alignment quality for Iteration #23 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00527 for Iteration #24 of Tilt-Series #3.
CCMS(rotations) = 0.12222 for Iteration #24 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00508 for iteration 24 of Tilt-Series #3.
Alignment quality for Iteration #24 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #25 of Tilt-Series #3.
CCMS(rotations) = 0.11826 for Iteration #25 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0052 for iteration 25 of Tilt-Series #3.
Alignment quality for Iteration #25 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)
lowpass = 6.25 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 = { 0.27052875 0.27052875 }
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 = 59.4473668853
map.lowpass.diameter = { 0.6925536 0.6925536 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 59.4473668853
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00732 for Iteration #26 of Tilt-Series #3.
CCMS(rotations) = 0.1562 for Iteration #26 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00678 for iteration 26 of Tilt-Series #3.
Alignment quality for Iteration #26 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.006 for Iteration #27 of Tilt-Series #3.
CCMS(rotations) = 0.12173 for Iteration #27 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00544 for iteration 27 of Tilt-Series #3.
Alignment quality for Iteration #27 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00621 for Iteration #28 of Tilt-Series #3.
CCMS(rotations) = 0.10658 for Iteration #28 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00524 for iteration 28 of Tilt-Series #3.
Alignment quality for Iteration #28 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #3 (17oct05c): Very StableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00596 for Iteration #29 of Tilt-Series #3.
CCMS(rotations) = 0.11113 for Iteration #29 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0052 for iteration 29 of Tilt-Series #3.
Alignment quality for Iteration #29 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00595 for Iteration #30 of Tilt-Series #3.
CCMS(rotations) = 0.11723 for Iteration #30 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00532 for iteration 30 of Tilt-Series #3.
Alignment quality for Iteration #30 of Tilt-Series #3 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #31 of Tilt-Series #3.
CCMS(rotations) = 0.10497 for Iteration #31 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00491 for iteration 31 of Tilt-Series #3.
Alignment quality for Iteration #31 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #32 of Tilt-Series #3.
CCMS(rotations) = 0.10044 for Iteration #32 of Tilt-Series #3.
CCMS(scale) = 0.0025 for Iteration #32 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00354 for iteration 32 of Tilt-Series #3.
Alignment quality for Iteration #32 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #33 of Tilt-Series #3.
CCMS(rotations) = 0.1126 for Iteration #33 of Tilt-Series #3.
CCMS(scale) = 0.0028 for Iteration #33 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00371 for iteration 33 of Tilt-Series #3.
Alignment quality for Iteration #33 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00408 for Iteration #34 of Tilt-Series #3.
CCMS(rotations) = 0.11082 for Iteration #34 of Tilt-Series #3.
CCMS(scale) = 0.00277 for Iteration #34 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00376 for iteration 34 of Tilt-Series #3.
Alignment quality for Iteration #34 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #3 (tiltseries0003_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00366 for Iteration #35 of Tilt-Series #3.
CCMS(rotations) = 0.10787 for Iteration #35 of Tilt-Series #3.
CCMS(scale) = 0.00286 for Iteration #35 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00361 for iteration 35 of Tilt-Series #3.
Alignment quality for Iteration #35 of Tilt-Series #3 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #3 (17oct05c): 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 #3 (tiltseries0003_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: 2017yr10m05d-17hr38m18s