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/17jul05d/protomo_alignments/tiltseries0009_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=tiltseries0009_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=17jul05d --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=9 --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=4317 --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

node20
Start time: 2017yr07m06d-14hr03m35s
Description: 
coarse_series0009_iter2.tlt not found, using coarse_series0009.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0009.tlt to series0009.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #9 (tiltseries0009_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 = 18.3242830282
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 = 18.3242830282
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.08834 for Iteration #1 of Tilt-Series #9.
CCMS(rotations) = 2.73061 for Iteration #1 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #9.
The scaled sum of CCMS values is #0.09878 for iteration 1 of Tilt-Series #9.
Alignment quality for Iteration #1 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02069 for Iteration #2 of Tilt-Series #9.
CCMS(rotations) = 0.60833 for Iteration #2 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #9.
The scaled sum of CCMS values is #0.02251 for iteration 2 of Tilt-Series #9.
Alignment quality for Iteration #2 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00781 for Iteration #3 of Tilt-Series #9.
CCMS(rotations) = 0.11205 for Iteration #3 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00615 for iteration 3 of Tilt-Series #9.
Alignment quality for Iteration #3 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0075 for Iteration #4 of Tilt-Series #9.
CCMS(rotations) = 0.1207 for Iteration #4 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00616 for iteration 4 of Tilt-Series #9.
Alignment quality for Iteration #4 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00861 for Iteration #5 of Tilt-Series #9.
CCMS(rotations) = 0.09687 for Iteration #5 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00624 for iteration 5 of Tilt-Series #9.
Alignment quality for Iteration #5 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00744 for Iteration #6 of Tilt-Series #9.
CCMS(rotations) = 0.13824 for Iteration #6 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00648 for iteration 6 of Tilt-Series #9.
Alignment quality for Iteration #6 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00883 for Iteration #7 of Tilt-Series #9.
CCMS(rotations) = 0.08681 for Iteration #7 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00615 for iteration 7 of Tilt-Series #9.
Alignment quality for Iteration #7 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00751 for Iteration #8 of Tilt-Series #9.
CCMS(rotations) = 0.1348 for Iteration #8 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00645 for iteration 8 of Tilt-Series #9.
Alignment quality for Iteration #8 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00888 for Iteration #9 of Tilt-Series #9.
CCMS(rotations) = 0.09027 for Iteration #9 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00624 for iteration 9 of Tilt-Series #9.
Alignment quality for Iteration #9 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0074 for Iteration #10 of Tilt-Series #9.
CCMS(rotations) = 0.14086 for Iteration #10 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00652 for iteration 10 of Tilt-Series #9.
Alignment quality for Iteration #10 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_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 = 36.6485660564
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 = 36.6485660564
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01009 for Iteration #11 of Tilt-Series #9.
CCMS(rotations) = 0.07255 for Iteration #11 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00649 for iteration 11 of Tilt-Series #9.
Alignment quality for Iteration #11 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #9 (17jul05d): Very StableCreating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00837 for Iteration #12 of Tilt-Series #9.
CCMS(rotations) = 0.10058 for Iteration #12 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0062 for iteration 12 of Tilt-Series #9.
Alignment quality for Iteration #12 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00863 for Iteration #13 of Tilt-Series #9.
CCMS(rotations) = 0.10695 for Iteration #13 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00646 for iteration 13 of Tilt-Series #9.
Alignment quality for Iteration #13 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00845 for Iteration #14 of Tilt-Series #9.
CCMS(rotations) = 0.10907 for Iteration #14 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00641 for iteration 14 of Tilt-Series #9.
Alignment quality for Iteration #14 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00842 for Iteration #15 of Tilt-Series #9.
CCMS(rotations) = 0.1346 for Iteration #15 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0069 for iteration 15 of Tilt-Series #9.
Alignment quality for Iteration #15 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0086 for Iteration #16 of Tilt-Series #9.
CCMS(rotations) = 0.08918 for Iteration #16 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00608 for iteration 16 of Tilt-Series #9.
Alignment quality for Iteration #16 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.0085 for Iteration #17 of Tilt-Series #9.
CCMS(rotations) = 0.12341 for Iteration #17 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00672 for iteration 17 of Tilt-Series #9.
Alignment quality for Iteration #17 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0089 for Iteration #18 of Tilt-Series #9.
CCMS(rotations) = 0.10334 for Iteration #18 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00652 for iteration 18 of Tilt-Series #9.
Alignment quality for Iteration #18 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00841 for Iteration #19 of Tilt-Series #9.
CCMS(rotations) = 0.13478 for Iteration #19 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #9.
The scaled sum of CCMS values is #0.0069 for iteration 19 of Tilt-Series #9.
Alignment quality for Iteration #19 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00867 for Iteration #20 of Tilt-Series #9.
CCMS(rotations) = 0.10504 for Iteration #20 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00644 for iteration 20 of Tilt-Series #9.
Alignment quality for Iteration #20 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_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 = 73.2971321128
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 = 73.2971321128
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00721 for Iteration #21 of Tilt-Series #9.
CCMS(rotations) = 0.17591 for Iteration #21 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00713 for iteration 21 of Tilt-Series #9.
Alignment quality for Iteration #21 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #9 (17jul05d): Very StableCreating 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00704 for Iteration #22 of Tilt-Series #9.
CCMS(rotations) = 0.09688 for Iteration #22 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00546 for iteration 22 of Tilt-Series #9.
Alignment quality for Iteration #22 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00697 for Iteration #23 of Tilt-Series #9.
CCMS(rotations) = 0.10894 for Iteration #23 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00566 for iteration 23 of Tilt-Series #9.
Alignment quality for Iteration #23 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00695 for Iteration #24 of Tilt-Series #9.
CCMS(rotations) = 0.11037 for Iteration #24 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00568 for iteration 24 of Tilt-Series #9.
Alignment quality for Iteration #24 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00694 for Iteration #25 of Tilt-Series #9.
CCMS(rotations) = 0.10937 for Iteration #25 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00566 for iteration 25 of Tilt-Series #9.
Alignment quality for Iteration #25 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_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 = 146.594264226
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 = 146.594264226
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00739 for Iteration #26 of Tilt-Series #9.
CCMS(rotations) = 0.13641 for Iteration #26 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00642 for iteration 26 of Tilt-Series #9.
Alignment quality for Iteration #26 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #9 (17jul05d): Very StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00685 for Iteration #27 of Tilt-Series #9.
CCMS(rotations) = 0.0931 for Iteration #27 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00529 for iteration 27 of Tilt-Series #9.
Alignment quality for Iteration #27 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00561 for Iteration #28 of Tilt-Series #9.
CCMS(rotations) = 0.13054 for Iteration #28 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00542 for iteration 28 of Tilt-Series #9.
Alignment quality for Iteration #28 of Tilt-Series #9 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00542 for Iteration #29 of Tilt-Series #9.
CCMS(rotations) = 0.09676 for Iteration #29 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00465 for iteration 29 of Tilt-Series #9.
Alignment quality for Iteration #29 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00573 for Iteration #30 of Tilt-Series #9.
CCMS(rotations) = 0.07586 for Iteration #30 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00438 for iteration 30 of Tilt-Series #9.
Alignment quality for Iteration #30 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #31 of Tilt-Series #9.
CCMS(rotations) = 0.08599 for Iteration #31 of Tilt-Series #9.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00459 for iteration 31 of Tilt-Series #9.
Alignment quality for Iteration #31 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #9 (17jul05d): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00214 for Iteration #32 of Tilt-Series #9.
CCMS(rotations) = 0.09297 for Iteration #32 of Tilt-Series #9.
CCMS(scale) = 0.00272 for Iteration #32 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00286 for iteration 32 of Tilt-Series #9.
Alignment quality for Iteration #32 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00239 for Iteration #33 of Tilt-Series #9.
CCMS(rotations) = 0.11336 for Iteration #33 of Tilt-Series #9.
CCMS(scale) = 0.00287 for Iteration #33 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00327 for iteration 33 of Tilt-Series #9.
Alignment quality for Iteration #33 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #34 of Tilt-Series #9.
CCMS(rotations) = 0.07208 for Iteration #34 of Tilt-Series #9.
CCMS(scale) = 0.00253 for Iteration #34 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00297 for iteration 34 of Tilt-Series #9.
Alignment quality for Iteration #34 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #9 (tiltseries0009_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00264 for Iteration #35 of Tilt-Series #9.
CCMS(rotations) = 0.11205 for Iteration #35 of Tilt-Series #9.
CCMS(scale) = 0.00332 for Iteration #35 of Tilt-Series #9.
The scaled sum of CCMS values is #0.00348 for iteration 35 of Tilt-Series #9.
Alignment quality for Iteration #35 of Tilt-Series #9 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #9 (17jul05d): 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 #9 (tiltseries0009_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: 2017yr07m07d-00hr49m40s