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/tiltseries0007_thick300 --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=tiltseries0007_thick300 --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=7 --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=300 --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

node23
Start time: 2017yr07m06d-14hr01m55s
Description: 
coarse_series0007_iter2.tlt not found, using coarse_series0007.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0007.tlt to series0007.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
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 = 27.485560687
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 = 27.485560687
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07921 for Iteration #1 of Tilt-Series #7.
CCMS(rotations) = 2.96675 for Iteration #1 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7.
The scaled sum of CCMS values is #0.09894 for iteration 1 of Tilt-Series #7.
Alignment quality for Iteration #1 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01455 for Iteration #2 of Tilt-Series #7.
CCMS(rotations) = 0.57382 for Iteration #2 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01875 for iteration 2 of Tilt-Series #7.
Alignment quality for Iteration #2 of Tilt-Series #7 (17jul05d): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #3 of Tilt-Series #7.
CCMS(rotations) = 0.09463 for Iteration #3 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00375 for iteration 3 of Tilt-Series #7.
Alignment quality for Iteration #3 of Tilt-Series #7 (17jul05d): 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00418 for Iteration #4 of Tilt-Series #7.
CCMS(rotations) = 0.06195 for Iteration #4 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00333 for iteration 4 of Tilt-Series #7.
Alignment quality for Iteration #4 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #7 (17jul05d): StableCreating 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #5 of Tilt-Series #7.
CCMS(rotations) = 0.10663 for Iteration #5 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00388 for iteration 5 of Tilt-Series #7.
Alignment quality for Iteration #5 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.0038 for Iteration #6 of Tilt-Series #7.
CCMS(rotations) = 0.06284 for Iteration #6 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00316 for iteration 6 of Tilt-Series #7.
Alignment quality for Iteration #6 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00403 for Iteration #7 of Tilt-Series #7.
CCMS(rotations) = 0.11209 for Iteration #7 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00426 for iteration 7 of Tilt-Series #7.
Alignment quality for Iteration #7 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00455 for Iteration #8 of Tilt-Series #7.
CCMS(rotations) = 0.06354 for Iteration #8 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00354 for iteration 8 of Tilt-Series #7.
Alignment quality for Iteration #8 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #7 (17jul05d): StableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00397 for Iteration #9 of Tilt-Series #7.
CCMS(rotations) = 0.133 for Iteration #9 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00464 for iteration 9 of Tilt-Series #7.
Alignment quality for Iteration #9 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00408 for Iteration #10 of Tilt-Series #7.
CCMS(rotations) = 0.06313 for Iteration #10 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00331 for iteration 10 of Tilt-Series #7.
Alignment quality for Iteration #10 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
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 = 54.9711213741
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 = 54.9711213741
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00449 for Iteration #11 of Tilt-Series #7.
CCMS(rotations) = 0.11378 for Iteration #11 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00452 for iteration 11 of Tilt-Series #7.
Alignment quality for Iteration #11 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #7 (17jul05d): 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #12 of Tilt-Series #7.
CCMS(rotations) = 0.09657 for Iteration #12 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00415 for iteration 12 of Tilt-Series #7.
Alignment quality for Iteration #12 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #7 (17jul05d): UnstableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00339 for Iteration #13 of Tilt-Series #7.
CCMS(rotations) = 0.07972 for Iteration #13 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00329 for iteration 13 of Tilt-Series #7.
Alignment quality for Iteration #13 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00335 for Iteration #14 of Tilt-Series #7.
CCMS(rotations) = 0.1309 for Iteration #14 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00429 for iteration 14 of Tilt-Series #7.
Alignment quality for Iteration #14 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00336 for Iteration #15 of Tilt-Series #7.
CCMS(rotations) = 0.08653 for Iteration #15 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00341 for iteration 15 of Tilt-Series #7.
Alignment quality for Iteration #15 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00403 for Iteration #16 of Tilt-Series #7.
CCMS(rotations) = 0.15408 for Iteration #16 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0051 for iteration 16 of Tilt-Series #7.
Alignment quality for Iteration #16 of Tilt-Series #7 (17jul05d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00384 for Iteration #17 of Tilt-Series #7.
CCMS(rotations) = 0.1173 for Iteration #17 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00427 for iteration 17 of Tilt-Series #7.
Alignment quality for Iteration #17 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #18 of Tilt-Series #7.
CCMS(rotations) = 0.1347 for Iteration #18 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0045 for iteration 18 of Tilt-Series #7.
Alignment quality for Iteration #18 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...

No Round parameters changed for Iteration #19 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00354 for Iteration #19 of Tilt-Series #7.
CCMS(rotations) = 0.09019 for Iteration #19 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00357 for iteration 19 of Tilt-Series #7.
Alignment quality for Iteration #19 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00341 for Iteration #20 of Tilt-Series #7.
CCMS(rotations) = 0.10972 for Iteration #20 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0039 for iteration 20 of Tilt-Series #7.
Alignment quality for Iteration #20 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #7 (17jul05d): Very StableCreating 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 #7 (tiltseries0007_thick300)
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 = 109.942242748
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 = 109.942242748
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00413 for Iteration #21 of Tilt-Series #7.
CCMS(rotations) = 0.08455 for Iteration #21 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00376 for iteration 21 of Tilt-Series #7.
Alignment quality for Iteration #21 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #7 (17jul05d): 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00412 for Iteration #22 of Tilt-Series #7.
CCMS(rotations) = 0.11287 for Iteration #22 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00432 for iteration 22 of Tilt-Series #7.
Alignment quality for Iteration #22 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00345 for Iteration #23 of Tilt-Series #7.
CCMS(rotations) = 0.09817 for Iteration #23 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00369 for iteration 23 of Tilt-Series #7.
Alignment quality for Iteration #23 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #24 of Tilt-Series #7.
CCMS(rotations) = 0.10868 for Iteration #24 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00386 for iteration 24 of Tilt-Series #7.
Alignment quality for Iteration #24 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00332 for Iteration #25 of Tilt-Series #7.
CCMS(rotations) = 0.09666 for Iteration #25 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00359 for iteration 25 of Tilt-Series #7.
Alignment quality for Iteration #25 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)
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 = 219.884485496
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 = 219.884485496
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00531 for Iteration #26 of Tilt-Series #7.
CCMS(rotations) = 0.08031 for Iteration #26 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00426 for iteration 26 of Tilt-Series #7.
Alignment quality for Iteration #26 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #7 (17jul05d): 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00407 for Iteration #27 of Tilt-Series #7.
CCMS(rotations) = 0.07669 for Iteration #27 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00357 for iteration 27 of Tilt-Series #7.
Alignment quality for Iteration #27 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #7 (17jul05d): 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00359 for Iteration #28 of Tilt-Series #7.
CCMS(rotations) = 0.06938 for Iteration #28 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00318 for iteration 28 of Tilt-Series #7.
Alignment quality for Iteration #28 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #7 (17jul05d): Very StableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00276 for Iteration #29 of Tilt-Series #7.
CCMS(rotations) = 0.05514 for Iteration #29 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00248 for iteration 29 of Tilt-Series #7.
Alignment quality for Iteration #29 of Tilt-Series #7 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00256 for Iteration #30 of Tilt-Series #7.
CCMS(rotations) = 0.0585 for Iteration #30 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00245 for iteration 30 of Tilt-Series #7.
Alignment quality for Iteration #30 of Tilt-Series #7 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00272 for Iteration #31 of Tilt-Series #7.
CCMS(rotations) = 0.06542 for Iteration #31 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00267 for iteration 31 of Tilt-Series #7.
Alignment quality for Iteration #31 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00404 for Iteration #32 of Tilt-Series #7.
CCMS(rotations) = 0.06564 for Iteration #32 of Tilt-Series #7.
CCMS(scale) = 0.00099 for Iteration #32 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00255 for iteration 32 of Tilt-Series #7.
Alignment quality for Iteration #32 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #7 (17jul05d): UnstableCreating 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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00298 for Iteration #33 of Tilt-Series #7.
CCMS(rotations) = 0.07455 for Iteration #33 of Tilt-Series #7.
CCMS(scale) = 0.00138 for Iteration #33 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00245 for iteration 33 of Tilt-Series #7.
Alignment quality for Iteration #33 of Tilt-Series #7 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00349 for Iteration #34 of Tilt-Series #7.
CCMS(rotations) = 0.08149 for Iteration #34 of Tilt-Series #7.
CCMS(scale) = 0.0015 for Iteration #34 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00275 for iteration 34 of Tilt-Series #7.
Alignment quality for Iteration #34 of Tilt-Series #7 (17jul05d): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #7 (17jul05d): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #7 (tiltseries0007_thick300)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #7 (tiltseries0007_thick300)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00208 for Iteration #35 of Tilt-Series #7.
CCMS(rotations) = 0.06262 for Iteration #35 of Tilt-Series #7.
CCMS(scale) = 0.00105 for Iteration #35 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00188 for iteration 35 of Tilt-Series #7.
Alignment quality for Iteration #35 of Tilt-Series #7 (17jul05d): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #7 (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 #7 (tiltseries0007_thick300)!
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-00hr51m38s