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/tiltseries0004_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=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=tiltseries0004_thick50 --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=4 --r5_corr_mode=pcf --change_refimg=True --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=50 --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

node38
Start time: 2017yr10m05d-13hr57m53s
Description: 
coarse_series0004_iter2.tlt not found, using coarse_series0004.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0004.tlt to series0004.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
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 = 3.71546043033
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 = 3.71546043033
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07997 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 1.85047 for Iteration #1 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4.
The scaled sum of CCMS values is #0.07699 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.13151 for Iteration #2 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00449 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17oct05c): Perfection! (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00332 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.07614 for Iteration #3 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00318 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (17oct05c): Perfection! (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.10683 for Iteration #4 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00395 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00347 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.07168 for Iteration #5 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00317 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00373 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.10163 for Iteration #6 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0039 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00346 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.07516 for Iteration #7 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00324 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00357 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.09855 for Iteration #8 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00376 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00347 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.07489 for Iteration #9 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00323 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00363 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.10269 for Iteration #10 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00387 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
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 = 7.43092086066
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 = 7.43092086066
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00313 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.09575 for Iteration #11 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00348 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00295 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.08473 for Iteration #12 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00317 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00303 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.08462 for Iteration #13 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00321 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00294 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.08009 for Iteration #14 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00307 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00304 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.08149 for Iteration #15 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00315 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0029 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.08353 for Iteration #16 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00312 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00305 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.08111 for Iteration #17 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00315 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00294 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.08338 for Iteration #18 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00314 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.003 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.08347 for Iteration #19 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00317 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00295 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.08535 for Iteration #20 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00318 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)
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 = 14.8618417213
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 = 14.8618417213
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00366 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.08159 for Iteration #21 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00346 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (17oct05c): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00329 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.08097 for Iteration #22 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00326 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0035 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.08363 for Iteration #23 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00342 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00333 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.08304 for Iteration #24 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00333 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00329 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.08657 for Iteration #25 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00337 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)
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 = 29.7236834426
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 = 29.7236834426
window.lowpass.diameter = { 0.6925536 0.6925536 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00378 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.06932 for Iteration #26 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00328 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.09177 for Iteration #27 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00376 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.08775 for Iteration #28 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00365 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (17oct05c): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00398 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.08168 for Iteration #29 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00362 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.08457 for Iteration #30 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00361 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00376 for Iteration #31 of Tilt-Series #4.
CCMS(rotations) = 0.09805 for Iteration #31 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00384 for iteration 31 of Tilt-Series #4.
Alignment quality for Iteration #31 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (17oct05c): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00241 for Iteration #32 of Tilt-Series #4.
CCMS(rotations) = 0.09103 for Iteration #32 of Tilt-Series #4.
CCMS(scale) = 0.00159 for Iteration #32 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00255 for iteration 32 of Tilt-Series #4.
Alignment quality for Iteration #32 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00253 for Iteration #33 of Tilt-Series #4.
CCMS(rotations) = 0.09323 for Iteration #33 of Tilt-Series #4.
CCMS(scale) = 0.00175 for Iteration #33 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00267 for iteration 33 of Tilt-Series #4.
Alignment quality for Iteration #33 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00242 for Iteration #34 of Tilt-Series #4.
CCMS(rotations) = 0.09641 for Iteration #34 of Tilt-Series #4.
CCMS(scale) = 0.00169 for Iteration #34 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00265 for iteration 34 of Tilt-Series #4.
Alignment quality for Iteration #34 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00256 for Iteration #35 of Tilt-Series #4.
CCMS(rotations) = 0.09297 for Iteration #35 of Tilt-Series #4.
CCMS(scale) = 0.00179 for Iteration #35 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00269 for iteration 35 of Tilt-Series #4.
Alignment quality for Iteration #35 of Tilt-Series #4 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (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 #4 (tiltseries0004_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: 2017yr10m05d-20hr18m31s