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/tiltseries0001_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=tiltseries0001_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=1 --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

node35
Start time: 2017yr07m06d-12hr03m46s
Description: 
coarse_series0001_iter2.tlt not found, using coarse_series0001.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0001.tlt to series0001.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_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) = 0.08769 for Iteration #1 of Tilt-Series #1.
CCMS(rotations) = 0.79924 for Iteration #1 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #1.
The scaled sum of CCMS values is #0.05983 for iteration 1 of Tilt-Series #1.
Alignment quality for Iteration #1 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.08642 for Iteration #2 of Tilt-Series #1.
CCMS(rotations) = 0.49973 for Iteration #2 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0532 for iteration 2 of Tilt-Series #1.
Alignment quality for Iteration #2 of Tilt-Series #1 (17jul06c): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.06686 for Iteration #3 of Tilt-Series #1.
CCMS(rotations) = 0.24738 for Iteration #3 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #1.
The scaled sum of CCMS values is #0.03838 for iteration 3 of Tilt-Series #1.
Alignment quality for Iteration #3 of Tilt-Series #1 (17jul06c): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0127 for Iteration #4 of Tilt-Series #1.
CCMS(rotations) = 0.23265 for Iteration #4 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #1.
The scaled sum of CCMS values is #0.011 for iteration 4 of Tilt-Series #1.
Alignment quality for Iteration #4 of Tilt-Series #1 (17jul06c): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (17jul06c): UnstableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00554 for Iteration #5 of Tilt-Series #1.
CCMS(rotations) = 0.06778 for Iteration #5 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00413 for iteration 5 of Tilt-Series #1.
Alignment quality for Iteration #5 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00621 for Iteration #6 of Tilt-Series #1.
CCMS(rotations) = 0.06768 for Iteration #6 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00446 for iteration 6 of Tilt-Series #1.
Alignment quality for Iteration #6 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00554 for Iteration #7 of Tilt-Series #1.
CCMS(rotations) = 0.06476 for Iteration #7 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00407 for iteration 7 of Tilt-Series #1.
Alignment quality for Iteration #7 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00633 for Iteration #8 of Tilt-Series #1.
CCMS(rotations) = 0.07016 for Iteration #8 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00457 for iteration 8 of Tilt-Series #1.
Alignment quality for Iteration #8 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00547 for Iteration #9 of Tilt-Series #1.
CCMS(rotations) = 0.06304 for Iteration #9 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00399 for iteration 9 of Tilt-Series #1.
Alignment quality for Iteration #9 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00668 for Iteration #10 of Tilt-Series #1.
CCMS(rotations) = 0.07713 for Iteration #10 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00488 for iteration 10 of Tilt-Series #1.
Alignment quality for Iteration #10 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_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) = 0.00669 for Iteration #11 of Tilt-Series #1.
CCMS(rotations) = 0.1158 for Iteration #11 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00566 for iteration 11 of Tilt-Series #1.
Alignment quality for Iteration #11 of Tilt-Series #1 (17jul06c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #12 of Tilt-Series #1.
CCMS(rotations) = 0.05275 for Iteration #12 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00357 for iteration 12 of Tilt-Series #1.
Alignment quality for Iteration #12 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (17jul06c): Very 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00494 for Iteration #13 of Tilt-Series #1.
CCMS(rotations) = 0.04867 for Iteration #13 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00344 for iteration 13 of Tilt-Series #1.
Alignment quality for Iteration #13 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00488 for Iteration #14 of Tilt-Series #1.
CCMS(rotations) = 0.04626 for Iteration #14 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00337 for iteration 14 of Tilt-Series #1.
Alignment quality for Iteration #14 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00487 for Iteration #15 of Tilt-Series #1.
CCMS(rotations) = 0.04608 for Iteration #15 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00335 for iteration 15 of Tilt-Series #1.
Alignment quality for Iteration #15 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00487 for Iteration #16 of Tilt-Series #1.
CCMS(rotations) = 0.04454 for Iteration #16 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00333 for iteration 16 of Tilt-Series #1.
Alignment quality for Iteration #16 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00465 for Iteration #17 of Tilt-Series #1.
CCMS(rotations) = 0.04923 for Iteration #17 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00331 for iteration 17 of Tilt-Series #1.
Alignment quality for Iteration #17 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00491 for Iteration #18 of Tilt-Series #1.
CCMS(rotations) = 0.04353 for Iteration #18 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00332 for iteration 18 of Tilt-Series #1.
Alignment quality for Iteration #18 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #19 of Tilt-Series #1.
CCMS(rotations) = 0.04927 for Iteration #19 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0034 for iteration 19 of Tilt-Series #1.
Alignment quality for Iteration #19 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00486 for Iteration #20 of Tilt-Series #1.
CCMS(rotations) = 0.04697 for Iteration #20 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00337 for iteration 20 of Tilt-Series #1.
Alignment quality for Iteration #20 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (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 #1 (tiltseries0001_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) = 0.00439 for Iteration #21 of Tilt-Series #1.
CCMS(rotations) = 0.08845 for Iteration #21 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00397 for iteration 21 of Tilt-Series #1.
Alignment quality for Iteration #21 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00497 for Iteration #22 of Tilt-Series #1.
CCMS(rotations) = 0.04874 for Iteration #22 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00346 for iteration 22 of Tilt-Series #1.
Alignment quality for Iteration #22 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00467 for Iteration #23 of Tilt-Series #1.
CCMS(rotations) = 0.04371 for Iteration #23 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00321 for iteration 23 of Tilt-Series #1.
Alignment quality for Iteration #23 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00445 for Iteration #24 of Tilt-Series #1.
CCMS(rotations) = 0.05314 for Iteration #24 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00329 for iteration 24 of Tilt-Series #1.
Alignment quality for Iteration #24 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00487 for Iteration #25 of Tilt-Series #1.
CCMS(rotations) = 0.04571 for Iteration #25 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00335 for iteration 25 of Tilt-Series #1.
Alignment quality for Iteration #25 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (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 #1 (tiltseries0001_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) = 0.00785 for Iteration #26 of Tilt-Series #1.
CCMS(rotations) = 0.06468 for Iteration #26 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00522 for iteration 26 of Tilt-Series #1.
Alignment quality for Iteration #26 of Tilt-Series #1 (17jul06c): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (17jul06c): Rock Solid!Creating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00691 for Iteration #27 of Tilt-Series #1.
CCMS(rotations) = 0.06889 for Iteration #27 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00483 for iteration 27 of Tilt-Series #1.
Alignment quality for Iteration #27 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00675 for Iteration #28 of Tilt-Series #1.
CCMS(rotations) = 0.05815 for Iteration #28 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00454 for iteration 28 of Tilt-Series #1.
Alignment quality for Iteration #28 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00669 for Iteration #29 of Tilt-Series #1.
CCMS(rotations) = 0.05693 for Iteration #29 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00448 for iteration 29 of Tilt-Series #1.
Alignment quality for Iteration #29 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #30 of Tilt-Series #1.
CCMS(rotations) = 0.05999 for Iteration #30 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00439 for iteration 30 of Tilt-Series #1.
Alignment quality for Iteration #30 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #31 of Tilt-Series #1.
CCMS(rotations) = 0.06696 for Iteration #31 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00471 for iteration 31 of Tilt-Series #1.
Alignment quality for Iteration #31 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (17jul06c): 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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0056 for Iteration #32 of Tilt-Series #1.
CCMS(rotations) = 0.06823 for Iteration #32 of Tilt-Series #1.
CCMS(scale) = 0.00305 for Iteration #32 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00379 for iteration 32 of Tilt-Series #1.
Alignment quality for Iteration #32 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00541 for Iteration #33 of Tilt-Series #1.
CCMS(rotations) = 0.05513 for Iteration #33 of Tilt-Series #1.
CCMS(scale) = 0.00318 for Iteration #33 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0036 for iteration 33 of Tilt-Series #1.
Alignment quality for Iteration #33 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00609 for Iteration #34 of Tilt-Series #1.
CCMS(rotations) = 0.05996 for Iteration #34 of Tilt-Series #1.
CCMS(scale) = 0.00291 for Iteration #34 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0038 for iteration 34 of Tilt-Series #1.
Alignment quality for Iteration #34 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (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 #1 (tiltseries0001_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00585 for Iteration #35 of Tilt-Series #1.
CCMS(rotations) = 0.05935 for Iteration #35 of Tilt-Series #1.
CCMS(scale) = 0.0029 for Iteration #35 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00371 for iteration 35 of Tilt-Series #1.
Alignment quality for Iteration #35 of Tilt-Series #1 (17jul06c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (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 #1 (tiltseries0001_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-23hr15m01s