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/tiltseries0001_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=24,27 --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2008.0 --runname=tiltseries0001_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=1 --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

node39
Start time: 2017yr10m05d-11hr44m10s
Description: 
coarse_series0001_iter2.tlt not found, using coarse_series0001.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0001.tlt to series0001.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_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 = 7.43050095576
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 = 7.43050095576
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06061 for Iteration #1 of Tilt-Series #1.
CCMS(rotations) = 0.96206 for Iteration #1 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #1.
The scaled sum of CCMS values is #0.04955 for iteration 1 of Tilt-Series #1.
Alignment quality for Iteration #1 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02099 for Iteration #2 of Tilt-Series #1.
CCMS(rotations) = 0.21714 for Iteration #2 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #1.
The scaled sum of CCMS values is #0.01484 for iteration 2 of Tilt-Series #1.
Alignment quality for Iteration #2 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00525 for Iteration #3 of Tilt-Series #1.
CCMS(rotations) = 0.16811 for Iteration #3 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00599 for iteration 3 of Tilt-Series #1.
Alignment quality for Iteration #3 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #4 of Tilt-Series #1.
CCMS(rotations) = 0.13659 for Iteration #4 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00495 for iteration 4 of Tilt-Series #1.
Alignment quality for Iteration #4 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00505 for Iteration #5 of Tilt-Series #1.
CCMS(rotations) = 0.16125 for Iteration #5 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00575 for iteration 5 of Tilt-Series #1.
Alignment quality for Iteration #5 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #6 of Tilt-Series #1.
CCMS(rotations) = 0.12943 for Iteration #6 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0045 for iteration 6 of Tilt-Series #1.
Alignment quality for Iteration #6 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00485 for Iteration #7 of Tilt-Series #1.
CCMS(rotations) = 0.16419 for Iteration #7 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00571 for iteration 7 of Tilt-Series #1.
Alignment quality for Iteration #7 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #8 of Tilt-Series #1.
CCMS(rotations) = 0.12868 for Iteration #8 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00447 for iteration 8 of Tilt-Series #1.
Alignment quality for Iteration #8 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00496 for Iteration #9 of Tilt-Series #1.
CCMS(rotations) = 0.16467 for Iteration #9 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00577 for iteration 9 of Tilt-Series #1.
Alignment quality for Iteration #9 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00425 for Iteration #10 of Tilt-Series #1.
CCMS(rotations) = 0.12476 for Iteration #10 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00462 for iteration 10 of Tilt-Series #1.
Alignment quality for Iteration #10 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_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 = 14.8610019115
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 = 14.8610019115
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #11 of Tilt-Series #1.
CCMS(rotations) = 0.14965 for Iteration #11 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0058 for iteration 11 of Tilt-Series #1.
Alignment quality for Iteration #11 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00459 for Iteration #12 of Tilt-Series #1.
CCMS(rotations) = 0.08954 for Iteration #12 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00409 for iteration 12 of Tilt-Series #1.
Alignment quality for Iteration #12 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #13 of Tilt-Series #1.
CCMS(rotations) = 0.11272 for Iteration #13 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00422 for iteration 13 of Tilt-Series #1.
Alignment quality for Iteration #13 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #14 of Tilt-Series #1.
CCMS(rotations) = 0.14268 for Iteration #14 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00516 for iteration 14 of Tilt-Series #1.
Alignment quality for Iteration #14 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.0038 for Iteration #15 of Tilt-Series #1.
CCMS(rotations) = 0.1091 for Iteration #15 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00408 for iteration 15 of Tilt-Series #1.
Alignment quality for Iteration #15 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (17oct05c): Very StableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00478 for Iteration #16 of Tilt-Series #1.
CCMS(rotations) = 0.15316 for Iteration #16 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00545 for iteration 16 of Tilt-Series #1.
Alignment quality for Iteration #16 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (17oct05c): Very StableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #17 of Tilt-Series #1.
CCMS(rotations) = 0.10769 for Iteration #17 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00407 for iteration 17 of Tilt-Series #1.
Alignment quality for Iteration #17 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #18 of Tilt-Series #1.
CCMS(rotations) = 0.12873 for Iteration #18 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0048 for iteration 18 of Tilt-Series #1.
Alignment quality for Iteration #18 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (17oct05c): Very StableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #19 of Tilt-Series #1.
CCMS(rotations) = 0.10458 for Iteration #19 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00407 for iteration 19 of Tilt-Series #1.
Alignment quality for Iteration #19 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00465 for Iteration #20 of Tilt-Series #1.
CCMS(rotations) = 0.15325 for Iteration #20 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00539 for iteration 20 of Tilt-Series #1.
Alignment quality for Iteration #20 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (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 #1 (tiltseries0001_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 = 29.722003823
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 = 29.722003823
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00388 for Iteration #21 of Tilt-Series #1.
CCMS(rotations) = 0.09035 for Iteration #21 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00375 for iteration 21 of Tilt-Series #1.
Alignment quality for Iteration #21 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00378 for Iteration #22 of Tilt-Series #1.
CCMS(rotations) = 0.14068 for Iteration #22 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00471 for iteration 22 of Tilt-Series #1.
Alignment quality for Iteration #22 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (17oct05c): Very StableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00391 for Iteration #23 of Tilt-Series #1.
CCMS(rotations) = 0.1416 for Iteration #23 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00479 for iteration 23 of Tilt-Series #1.
Alignment quality for Iteration #23 of Tilt-Series #1 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (17oct05c): UnstableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00523 for Iteration #24 of Tilt-Series #1.
CCMS(rotations) = 0.12611 for Iteration #24 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00514 for iteration 24 of Tilt-Series #1.
Alignment quality for Iteration #24 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (17oct05c): UnstableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00472 for Iteration #25 of Tilt-Series #1.
CCMS(rotations) = 0.13655 for Iteration #25 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00509 for iteration 25 of Tilt-Series #1.
Alignment quality for Iteration #25 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (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 #1 (tiltseries0001_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 = 59.4440076461
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 = 59.4440076461
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00833 for Iteration #26 of Tilt-Series #1.
CCMS(rotations) = 0.12596 for Iteration #26 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00668 for iteration 26 of Tilt-Series #1.
Alignment quality for Iteration #26 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00885 for Iteration #27 of Tilt-Series #1.
CCMS(rotations) = 0.14676 for Iteration #27 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00736 for iteration 27 of Tilt-Series #1.
Alignment quality for Iteration #27 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (17oct05c): UnstableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0084 for Iteration #28 of Tilt-Series #1.
CCMS(rotations) = 0.19792 for Iteration #28 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00816 for iteration 28 of Tilt-Series #1.
Alignment quality for Iteration #28 of Tilt-Series #1 (17oct05c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #29 of Tilt-Series #1.
CCMS(rotations) = 0.11323 for Iteration #29 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00512 for iteration 29 of Tilt-Series #1.
Alignment quality for Iteration #29 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (17oct05c): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00843 for Iteration #30 of Tilt-Series #1.
CCMS(rotations) = 0.25101 for Iteration #30 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00924 for iteration 30 of Tilt-Series #1.
Alignment quality for Iteration #30 of Tilt-Series #1 (17oct05c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (17oct05c): UnstableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00629 for Iteration #31 of Tilt-Series #1.
CCMS(rotations) = 0.25779 for Iteration #31 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0083 for iteration 31 of Tilt-Series #1.
Alignment quality for Iteration #31 of Tilt-Series #1 (17oct05c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (17oct05c): UnstableCreating 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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0046 for Iteration #32 of Tilt-Series #1.
CCMS(rotations) = 0.25001 for Iteration #32 of Tilt-Series #1.
CCMS(scale) = 0.00232 for Iteration #32 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00564 for iteration 32 of Tilt-Series #1.
Alignment quality for Iteration #32 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (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 #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.0047 for Iteration #33 of Tilt-Series #1.
CCMS(rotations) = 0.24278 for Iteration #33 of Tilt-Series #1.
CCMS(scale) = 0.00192 for Iteration #33 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00544 for iteration 33 of Tilt-Series #1.
Alignment quality for Iteration #33 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (17oct05c): StableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.0042 for Iteration #34 of Tilt-Series #1.
CCMS(rotations) = 0.23155 for Iteration #34 of Tilt-Series #1.
CCMS(scale) = 0.0025 for Iteration #34 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00532 for iteration 34 of Tilt-Series #1.
Alignment quality for Iteration #34 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (17oct05c): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #1 (tiltseries0001_thick100)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick100)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00448 for Iteration #35 of Tilt-Series #1.
CCMS(rotations) = 0.23938 for Iteration #35 of Tilt-Series #1.
CCMS(scale) = 0.00173 for Iteration #35 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00526 for iteration 35 of Tilt-Series #1.
Alignment quality for Iteration #35 of Tilt-Series #1 (17oct05c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (17oct05c): 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 #1 (tiltseries0001_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-20hr55m59s