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/17jul06c/protomo_alignments/tiltseries0004_thick200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4087.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2302 --r1_region_y=2226 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4087.0 --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=2226 --r2_region_x=2302 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2044.0 --defocus_ang_positive=90 --r5_mask_width_x=2277 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4087.0 --r3_highpass_apod_x=2044.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=550 --r2_mask_width_y=531 --r5_region_x=2302 --r5_region_y=2226 --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=4087.0 --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=2201 --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=2044.0 --runname=tiltseries0004_thick200 --r1_highpass_diameter_x=4087.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --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=2277 --r4_mask_width_y=2201 --logging=true --DefocusTol=200 --filter=median --sessionname=17jul06c --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=2044.0 --r1_highpass_apod_x=2044.0 --r2_highpass_apod_x=2044.0 --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 --coarse=False --r3_mask_width_y=1088 --r3_mask_width_x=1126 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4087.0 --r4_highpass_diameter_x=4087.0 --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=4087.0 --tilt_azimuth=-79.5 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2044.0 --r5_highpass_apod_x=2044.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4087.0 --defocus_max=0 --r4_region_y=2226 --r4_region_x=2302 --r5_kernel_y=5 --r3_region_x=2302 --r3_region_y=2226 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=200 --expid=4328 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --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=1.83586 --link=False --r2_highpass_diameter_x=4087.0 --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=3838 --dimy=3710 --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=2044.0 --r4_highpass_apod_y=2044.0 --azimuth=true --r1_mask_width_y=253 --r1_mask_width_x=262 --jobtype=protomo

node23
Start time: 2017yr07m06d-12hr44m37s
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_thick200)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.23499008 0.23499008 }
map.sampling = 8
window.highpass.diameter = { 0.00718712013702 0.00718712013702 }
window.highpass.apodization = { 0.0143707240705 0.0143707240705 }
window.mask.apodization = { 10 10 }
align.mask.width = { 262 253 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 18.3225554932
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 287 278 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 262 253 }
reference.body = 18.3225554932
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07888 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 2.17779 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 #0.083 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03689 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.34162 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 #0.02528 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17jul06c): Okay (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_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00567 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.0724 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 #0.00428 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0047 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.10523 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 #0.00445 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00387 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.10257 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 #0.00399 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00471 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.0874 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 #0.0041 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00395 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.09621 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 #0.0039 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00464 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.09235 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 #0.00417 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00393 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.09841 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 #0.00393 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00463 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.09029 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 #0.00412 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (17jul06c): 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_thick200)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.233125079365 0.233125079365 }
map.sampling = 4
window.highpass.diameter = { 0.00359356006851 0.00359356006851 }
window.highpass.apodization = { 0.00718536203523 0.00718536203523 }
window.mask.apodization = { 10 10 }
align.mask.width = { 550 531 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 36.6451109865
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 575 556 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 550 531 }
reference.body = 36.6451109865
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00518 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.12472 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 #0.00508 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17jul06c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (17jul06c): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0034 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.09482 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 #0.0036 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (17jul06c): StableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00285 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.07615 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 #0.00295 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00281 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.07379 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 #0.00288 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.0028 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.06609 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 #0.00272 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0028 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.07515 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 #0.0029 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.0029 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.0712 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 #0.00288 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00286 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.07824 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 #0.00299 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0029 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.0731 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 #0.00291 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00289 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.07411 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 #0.00293 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (17jul06c): 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_thick200)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.23688516129 0.23688516129 }
map.sampling = 2
window.highpass.diameter = { 0.00179678003425 0.00179678003425 }
window.highpass.apodization = { 0.00359268101761 0.00359268101761 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1126 1088 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 73.290221973
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1151 1113 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1126 1088 }
reference.body = 73.290221973
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00331 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.06769 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 #0.00301 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00304 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.06463 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 #0.00281 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00308 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.05354 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 #0.00261 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00308 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.05823 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 #0.0027 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00297 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.05893 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 #0.00266 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (17jul06c): 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_thick200)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.2294825 0.2294825 }
map.sampling = 1
window.highpass.diameter = { 0.000898390017127 0.000898390017127 }
window.highpass.apodization = { 0.00179634050881 0.00179634050881 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2277 2201 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 146.580443946
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2302 2226 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2277 2201 }
reference.body = 146.580443946
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.007 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.05049 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 #0.00451 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (17jul06c): 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 #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00458 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.11593 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 #0.00461 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (17jul06c): Very StableCreating 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_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.15658 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 #0.00594 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17jul06c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0052 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.11607 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 #0.00492 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (17jul06c): StableCreating 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_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00521 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.12244 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 #0.00505 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17jul06c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (17jul06c): Very StableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...

No Round parameters changed for Iteration #31 of Tilt-Series #4 (tiltseries0004_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00466 for Iteration #31 of Tilt-Series #4.
CCMS(rotations) = 0.12543 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 #0.00484 for iteration 31 of Tilt-Series #4.
Alignment quality for Iteration #31 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00422 for Iteration #32 of Tilt-Series #4.
CCMS(rotations) = 0.13553 for Iteration #32 of Tilt-Series #4.
CCMS(scale) = 0.00139 for Iteration #32 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00368 for iteration 32 of Tilt-Series #4.
Alignment quality for Iteration #32 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00383 for Iteration #33 of Tilt-Series #4.
CCMS(rotations) = 0.10301 for Iteration #33 of Tilt-Series #4.
CCMS(scale) = 0.00188 for Iteration #33 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00327 for iteration 33 of Tilt-Series #4.
Alignment quality for Iteration #33 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #34 of Tilt-Series #4.
CCMS(rotations) = 0.12349 for Iteration #34 of Tilt-Series #4.
CCMS(scale) = 0.00137 for Iteration #34 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0033 for iteration 34 of Tilt-Series #4.
Alignment quality for Iteration #34 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (17jul06c): 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_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00355 for Iteration #35 of Tilt-Series #4.
CCMS(rotations) = 0.12447 for Iteration #35 of Tilt-Series #4.
CCMS(scale) = 0.00122 for Iteration #35 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00325 for iteration 35 of Tilt-Series #4.
Alignment quality for Iteration #35 of Tilt-Series #4 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (17jul06c): 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_thick200)!
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: 2017yr07m06d-23hr14m46s