protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/18mar15h/protomo_alignments/tiltseries0002_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2977.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2515 --r1_region_y=2237 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2977.0 --r4_lowpass_apod_y=13.0 --r4_lowpass_apod_x=13.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=27.0 --r3_lowpass_apod_y=27.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0002_thick50 --r2_region_y=2237 --r2_region_x=2515 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1489.0 --defocus_ang_positive=90 --r5_mask_width_x=2490 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2977.0 --r3_highpass_apod_x=1489.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=603 --r2_mask_width_y=534 --r5_region_x=2515 --r5_region_y=2237 --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=5.32 --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=2977.0 --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=2212 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1489.0 --r3_iters=5 --r1_highpass_diameter_x=2977.0 --r2_lowpass_diameter_y=21.28 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=2.66 --r5_lowpass_diameter_x=2.66 --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=2490 --r4_mask_width_y=2212 --r5_highpass_apod_y=1489.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar15h --exclude_images=999999 --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=1489.0 --r1_highpass_apod_x=1489.0 --r2_highpass_apod_x=1489.0 --sampling=8 --starting_tlt_file=Coarse_Iter_1 --r5_lowpass_apod_x=7.0 --r5_lowpass_apod_y=7.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=42.56 --r1_lowpass_diameter_x=42.56 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=2 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1093 --r3_mask_width_x=1232 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=2977.0 --r4_highpass_diameter_x=2977.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=106.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=2977.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1489.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2977.0 --defocus_max=0 --r4_region_y=2237 --r4_region_x=2515 --r5_kernel_y=5 --r3_region_x=2515 --r3_region_y=2237 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=6300 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=506 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=10.64 --r3_lowpass_diameter_x=10.64 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.331 --link=False --r2_highpass_diameter_x=2977.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=53.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=53.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --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=21.28 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=106.0 --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=1489.0 --r4_highpass_apod_y=1489.0 --azimuth=true --r1_mask_width_y=254 --r1_mask_width_x=289 --jobtype=protomo --from_multirefine=True

node46
Start time: 2018yr03m15d-11hr35m02s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
lowpass = 42.56 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 10.648 Angstroms, Nyquist is 21.296 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 47.125e0
map.sampling = 8
window.highpass.diameter = { 0.00715351024521 0.00715351024521 }
window.highpass.apodization = { 0.0143022162525 0.0143022162525 }
window.mask.apodization = { 10 10 }
align.mask.width = { 289 254 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 6.64097919949
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 314 279 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 289 254 }
reference.body = 6.64097919949
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.09393 for Iteration #1 of Tilt-Series #2.
CCMS(rotations) = 1.482 for Iteration #1 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0766 for iteration 1 of Tilt-Series #2.
Alignment quality for Iteration #1 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04677 for Iteration #2 of Tilt-Series #2.
CCMS(rotations) = 0.09585 for Iteration #2 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0253 for iteration 2 of Tilt-Series #2.
Alignment quality for Iteration #2 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #3 of Tilt-Series #2.
CCMS(rotations) = 0.25023 for Iteration #3 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00731 for iteration 3 of Tilt-Series #2.
Alignment quality for Iteration #3 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00453 for Iteration #4 of Tilt-Series #2.
CCMS(rotations) = 0.2608 for Iteration #4 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00748 for iteration 4 of Tilt-Series #2.
Alignment quality for Iteration #4 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00482 for Iteration #5 of Tilt-Series #2.
CCMS(rotations) = 0.26316 for Iteration #5 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00767 for iteration 5 of Tilt-Series #2.
Alignment quality for Iteration #5 of Tilt-Series #2 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (18mar15h): Very StableCreating 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00437 for Iteration #6 of Tilt-Series #2.
CCMS(rotations) = 0.24518 for Iteration #6 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00709 for iteration 6 of Tilt-Series #2.
Alignment quality for Iteration #6 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (18mar15h): Very StableCreating 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00479 for Iteration #7 of Tilt-Series #2.
CCMS(rotations) = 0.25899 for Iteration #7 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00757 for iteration 7 of Tilt-Series #2.
Alignment quality for Iteration #7 of Tilt-Series #2 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00449 for Iteration #8 of Tilt-Series #2.
CCMS(rotations) = 0.24751 for Iteration #8 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0072 for iteration 8 of Tilt-Series #2.
Alignment quality for Iteration #8 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (18mar15h): Very 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00475 for Iteration #9 of Tilt-Series #2.
CCMS(rotations) = 0.2656 for Iteration #9 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00769 for iteration 9 of Tilt-Series #2.
Alignment quality for Iteration #9 of Tilt-Series #2 (18mar15h): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00443 for Iteration #10 of Tilt-Series #2.
CCMS(rotations) = 0.2502 for Iteration #10 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00722 for iteration 10 of Tilt-Series #2.
Alignment quality for Iteration #10 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)
lowpass = 21.28 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 5.324 Angstroms, Nyquist is 10.648 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 94.25e0
map.sampling = 4
window.highpass.diameter = { 0.00357675512261 0.00357675512261 }
window.highpass.apodization = { 0.00715110812626 0.00715110812626 }
window.mask.apodization = { 10 10 }
align.mask.width = { 603 534 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 13.281958399
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 628 559 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 603 534 }
reference.body = 13.281958399
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00486 for Iteration #11 of Tilt-Series #2.
CCMS(rotations) = 0.25111 for Iteration #11 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00745 for iteration 11 of Tilt-Series #2.
Alignment quality for Iteration #11 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00504 for Iteration #12 of Tilt-Series #2.
CCMS(rotations) = 0.22014 for Iteration #12 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00692 for iteration 12 of Tilt-Series #2.
Alignment quality for Iteration #12 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00472 for Iteration #13 of Tilt-Series #2.
CCMS(rotations) = 0.23703 for Iteration #13 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0071 for iteration 13 of Tilt-Series #2.
Alignment quality for Iteration #13 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00501 for Iteration #14 of Tilt-Series #2.
CCMS(rotations) = 0.22137 for Iteration #14 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00693 for iteration 14 of Tilt-Series #2.
Alignment quality for Iteration #14 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00483 for Iteration #15 of Tilt-Series #2.
CCMS(rotations) = 0.23874 for Iteration #15 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00719 for iteration 15 of Tilt-Series #2.
Alignment quality for Iteration #15 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.005 for Iteration #16 of Tilt-Series #2.
CCMS(rotations) = 0.22136 for Iteration #16 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00693 for iteration 16 of Tilt-Series #2.
Alignment quality for Iteration #16 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00474 for Iteration #17 of Tilt-Series #2.
CCMS(rotations) = 0.24038 for Iteration #17 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00718 for iteration 17 of Tilt-Series #2.
Alignment quality for Iteration #17 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00491 for Iteration #18 of Tilt-Series #2.
CCMS(rotations) = 0.22187 for Iteration #18 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00689 for iteration 18 of Tilt-Series #2.
Alignment quality for Iteration #18 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00489 for Iteration #19 of Tilt-Series #2.
CCMS(rotations) = 0.24545 for Iteration #19 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00735 for iteration 19 of Tilt-Series #2.
Alignment quality for Iteration #19 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00495 for Iteration #20 of Tilt-Series #2.
CCMS(rotations) = 0.22103 for Iteration #20 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0069 for iteration 20 of Tilt-Series #2.
Alignment quality for Iteration #20 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)
lowpass = 10.64 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 2.662 Angstroms, Nyquist is 5.324 Angstroms)
window.lowpass.apodization = { 0.197185185185 0.197185185185 }
align.translimit = 188.5e0
map.sampling = 2
window.highpass.diameter = { 0.0017883775613 0.0017883775613 }
window.highpass.apodization = { 0.00357555406313 0.00357555406313 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1232 1093 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 26.563916798
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1257 1118 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1232 1093 }
reference.body = 26.563916798
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #21 of Tilt-Series #2.
CCMS(rotations) = 0.21682 for Iteration #21 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00716 for iteration 21 of Tilt-Series #2.
Alignment quality for Iteration #21 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (18mar15h): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00556 for Iteration #22 of Tilt-Series #2.
CCMS(rotations) = 0.20734 for Iteration #22 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00693 for iteration 22 of Tilt-Series #2.
Alignment quality for Iteration #22 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00583 for Iteration #23 of Tilt-Series #2.
CCMS(rotations) = 0.19372 for Iteration #23 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00679 for iteration 23 of Tilt-Series #2.
Alignment quality for Iteration #23 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00562 for Iteration #24 of Tilt-Series #2.
CCMS(rotations) = 0.19945 for Iteration #24 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0068 for iteration 24 of Tilt-Series #2.
Alignment quality for Iteration #24 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #25 of Tilt-Series #2.
CCMS(rotations) = 0.2151 for Iteration #25 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00714 for iteration 25 of Tilt-Series #2.
Alignment quality for Iteration #25 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)
lowpass = 5.32 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.331 Angstroms, Nyquist is 2.662 Angstroms)
window.lowpass.apodization = { 0.204769230769 0.204769230769 }
align.translimit = 377.0e0
map.sampling = 1
window.highpass.diameter = { 0.000894188780652 0.000894188780652 }
window.highpass.apodization = { 0.00178777703156 0.00178777703156 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2490 2212 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 53.1278335959
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2515 2237 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2490 2212 }
reference.body = 53.1278335959
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00678 for Iteration #26 of Tilt-Series #2.
CCMS(rotations) = 0.19993 for Iteration #26 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00739 for iteration 26 of Tilt-Series #2.
Alignment quality for Iteration #26 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #27 of Tilt-Series #2.
CCMS(rotations) = 0.20064 for Iteration #27 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00721 for iteration 27 of Tilt-Series #2.
Alignment quality for Iteration #27 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0067 for Iteration #28 of Tilt-Series #2.
CCMS(rotations) = 0.16091 for Iteration #28 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00657 for iteration 28 of Tilt-Series #2.
Alignment quality for Iteration #28 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00555 for Iteration #29 of Tilt-Series #2.
CCMS(rotations) = 0.1571 for Iteration #29 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00592 for iteration 29 of Tilt-Series #2.
Alignment quality for Iteration #29 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00506 for Iteration #30 of Tilt-Series #2.
CCMS(rotations) = 0.17831 for Iteration #30 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0061 for iteration 30 of Tilt-Series #2.
Alignment quality for Iteration #30 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00555 for Iteration #31 of Tilt-Series #2.
CCMS(rotations) = 0.1861 for Iteration #31 of Tilt-Series #2.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2.
The scaled sum of CCMS values is #0.0065 for iteration 31 of Tilt-Series #2.
Alignment quality for Iteration #31 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00366 for Iteration #32 of Tilt-Series #2.
CCMS(rotations) = 0.19714 for Iteration #32 of Tilt-Series #2.
CCMS(scale) = 0.00245 for Iteration #32 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00466 for iteration 32 of Tilt-Series #2.
Alignment quality for Iteration #32 of Tilt-Series #2 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #33 of Tilt-Series #2.
CCMS(rotations) = 0.22001 for Iteration #33 of Tilt-Series #2.
CCMS(scale) = 0.00246 for Iteration #33 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00514 for iteration 33 of Tilt-Series #2.
Alignment quality for Iteration #33 of Tilt-Series #2 (18mar15h): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (18mar15h): StableCreating 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #34 of Tilt-Series #2.
CCMS(rotations) = 0.18317 for Iteration #34 of Tilt-Series #2.
CCMS(scale) = 0.00259 for Iteration #34 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00451 for iteration 34 of Tilt-Series #2.
Alignment quality for Iteration #34 of Tilt-Series #2 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00353 for Iteration #35 of Tilt-Series #2.
CCMS(rotations) = 0.1921 for Iteration #35 of Tilt-Series #2.
CCMS(scale) = 0.00261 for Iteration #35 of Tilt-Series #2.
The scaled sum of CCMS values is #0.00461 for iteration 35 of Tilt-Series #2.
Alignment quality for Iteration #35 of Tilt-Series #2 (18mar15h): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (18mar15h): 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 #2 (tiltseries0002_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2018yr03m15d-22hr20m18s