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/18mar12b/protomo_alignments/tiltseries0006_thick550 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3146.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2644 --r1_region_y=2364 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3146.0 --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=tiltseries0006_thick550 --r2_region_y=2364 --r2_region_x=2644 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1573.0 --defocus_ang_positive=90 --r5_mask_width_x=2619 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3146.0 --r3_highpass_apod_x=1573.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=636 --r2_mask_width_y=566 --r5_region_x=2644 --r5_region_y=2364 --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=3146.0 --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=2339 --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=1573.0 --r3_iters=5 --r1_highpass_diameter_x=3146.0 --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=2619 --r4_mask_width_y=2339 --r5_highpass_apod_y=1573.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar12b --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=1573.0 --r1_highpass_apod_x=1573.0 --r2_highpass_apod_x=1573.0 --sampling=8 --starting_tlt_file=Manual --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=6 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1157 --r3_mask_width_x=1297 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3146.0 --r4_highpass_diameter_x=3146.0 --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=3146.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1573.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3146.0 --defocus_max=0 --r4_region_y=2364 --r4_region_x=2644 --r5_kernel_y=5 --r3_region_x=2644 --r3_region_y=2364 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=550 --expid=6268 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=340 --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=3146.0 --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=1573.0 --r4_highpass_apod_y=1573.0 --azimuth=true --r1_mask_width_y=270 --r1_mask_width_x=305 --jobtype=protomo --from_multirefine=True

node39
Start time: 2018yr03m12d-13hr48m36s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
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 = { 0.00676923076923 0.00676923076923 }
window.highpass.apodization = { 0.0135384615385 0.0135384615385 }
window.mask.apodization = { 10 10 }
align.mask.width = { 305 270 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 73.0494961623
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 330 295 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 305 270 }
reference.body = 73.0494961623
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06759 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 0.72226 for Iteration #1 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6.
The scaled sum of CCMS values is #0.04824 for iteration 1 of Tilt-Series #6.
Alignment quality for Iteration #1 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.06352 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 0.60321 for Iteration #2 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6.
The scaled sum of CCMS values is #0.04383 for iteration 2 of Tilt-Series #6.
Alignment quality for Iteration #2 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.04479 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 0.48193 for Iteration #3 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6.
The scaled sum of CCMS values is #0.03204 for iteration 3 of Tilt-Series #6.
Alignment quality for Iteration #3 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01209 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 0.25141 for Iteration #4 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01107 for iteration 4 of Tilt-Series #6.
Alignment quality for Iteration #4 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01106 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 0.25901 for Iteration #5 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01071 for iteration 5 of Tilt-Series #6.
Alignment quality for Iteration #5 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01135 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 0.30485 for Iteration #6 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01177 for iteration 6 of Tilt-Series #6.
Alignment quality for Iteration #6 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00996 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 0.25409 for Iteration #7 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01006 for iteration 7 of Tilt-Series #6.
Alignment quality for Iteration #7 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00958 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 0.26486 for Iteration #8 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01009 for iteration 8 of Tilt-Series #6.
Alignment quality for Iteration #8 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01211 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 0.26077 for Iteration #9 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01127 for iteration 9 of Tilt-Series #6.
Alignment quality for Iteration #9 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01083 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 0.30021 for Iteration #10 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01142 for iteration 10 of Tilt-Series #6.
Alignment quality for Iteration #10 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #6 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
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 = { 0.00338461538462 0.00338461538462 }
window.highpass.apodization = { 0.00676923076923 0.00676923076923 }
window.mask.apodization = { 10 10 }
align.mask.width = { 636 566 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 146.098992325
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 661 591 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 636 566 }
reference.body = 146.098992325
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.015 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 0.37472 for Iteration #11 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01499 for iteration 11 of Tilt-Series #6.
Alignment quality for Iteration #11 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00624 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 0.11474 for Iteration #12 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00541 for iteration 12 of Tilt-Series #6.
Alignment quality for Iteration #12 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 0.10544 for Iteration #13 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00548 for iteration 13 of Tilt-Series #6.
Alignment quality for Iteration #13 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 0.09406 for Iteration #14 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00543 for iteration 14 of Tilt-Series #6.
Alignment quality for Iteration #14 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #6 (18mar12b): Very StableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00684 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 0.09159 for Iteration #15 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00525 for iteration 15 of Tilt-Series #6.
Alignment quality for Iteration #15 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #6 (18mar12b): Very StableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00819 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 0.11337 for Iteration #16 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00636 for iteration 16 of Tilt-Series #6.
Alignment quality for Iteration #16 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01155 for Iteration #17 of Tilt-Series #6.
CCMS(rotations) = 0.14758 for Iteration #17 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00873 for iteration 17 of Tilt-Series #6.
Alignment quality for Iteration #17 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00979 for Iteration #18 of Tilt-Series #6.
CCMS(rotations) = 0.10512 for Iteration #18 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6.
The scaled sum of CCMS values is #0.007 for iteration 18 of Tilt-Series #6.
Alignment quality for Iteration #18 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01202 for Iteration #19 of Tilt-Series #6.
CCMS(rotations) = 0.14724 for Iteration #19 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00895 for iteration 19 of Tilt-Series #6.
Alignment quality for Iteration #19 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #20 of Tilt-Series #6.
CCMS(rotations) = 0.11774 for Iteration #20 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00578 for iteration 20 of Tilt-Series #6.
Alignment quality for Iteration #20 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)
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 = { 0.00169230769231 0.00169230769231 }
window.highpass.apodization = { 0.00338461538462 0.00338461538462 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1297 1157 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 292.197984649
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1322 1182 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1297 1157 }
reference.body = 292.197984649
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00935 for Iteration #21 of Tilt-Series #6.
CCMS(rotations) = 0.21529 for Iteration #21 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00898 for iteration 21 of Tilt-Series #6.
Alignment quality for Iteration #21 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00974 for Iteration #22 of Tilt-Series #6.
CCMS(rotations) = 0.13692 for Iteration #22 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00761 for iteration 22 of Tilt-Series #6.
Alignment quality for Iteration #22 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00907 for Iteration #23 of Tilt-Series #6.
CCMS(rotations) = 0.14019 for Iteration #23 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00734 for iteration 23 of Tilt-Series #6.
Alignment quality for Iteration #23 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00772 for Iteration #24 of Tilt-Series #6.
CCMS(rotations) = 0.17624 for Iteration #24 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00739 for iteration 24 of Tilt-Series #6.
Alignment quality for Iteration #24 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #6 (18mar12b): StableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00858 for Iteration #25 of Tilt-Series #6.
CCMS(rotations) = 0.15696 for Iteration #25 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6.
The scaled sum of CCMS values is #0.00743 for iteration 25 of Tilt-Series #6.
Alignment quality for Iteration #25 of Tilt-Series #6 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)
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 = { 0.000846153846154 0.000846153846154 }
window.highpass.apodization = { 0.00169230769231 0.00169230769231 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2619 2339 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 584.395969298
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2644 2364 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2619 2339 }
reference.body = 584.395969298
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01627 for Iteration #26 of Tilt-Series #6.
CCMS(rotations) = 0.35922 for Iteration #26 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01532 for iteration 26 of Tilt-Series #6.
Alignment quality for Iteration #26 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #6 (18mar12b): Very StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0194 for Iteration #27 of Tilt-Series #6.
CCMS(rotations) = 0.48239 for Iteration #27 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01935 for iteration 27 of Tilt-Series #6.
Alignment quality for Iteration #27 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01512 for Iteration #28 of Tilt-Series #6.
CCMS(rotations) = 0.22759 for Iteration #28 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01211 for iteration 28 of Tilt-Series #6.
Alignment quality for Iteration #28 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01737 for Iteration #29 of Tilt-Series #6.
CCMS(rotations) = 0.29486 for Iteration #29 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01458 for iteration 29 of Tilt-Series #6.
Alignment quality for Iteration #29 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01638 for Iteration #30 of Tilt-Series #6.
CCMS(rotations) = 0.35514 for Iteration #30 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01529 for iteration 30 of Tilt-Series #6.
Alignment quality for Iteration #30 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01274 for Iteration #31 of Tilt-Series #6.
CCMS(rotations) = 0.37483 for Iteration #31 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01387 for iteration 31 of Tilt-Series #6.
Alignment quality for Iteration #31 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01446 for Iteration #32 of Tilt-Series #6.
CCMS(rotations) = 0.43206 for Iteration #32 of Tilt-Series #6.
CCMS(scale) = 0.00529 for Iteration #32 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01235 for iteration 32 of Tilt-Series #6.
Alignment quality for Iteration #32 of Tilt-Series #6 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #6 (18mar12b): 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01609 for Iteration #33 of Tilt-Series #6.
CCMS(rotations) = 0.44153 for Iteration #33 of Tilt-Series #6.
CCMS(scale) = 0.00562 for Iteration #33 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01312 for iteration 33 of Tilt-Series #6.
Alignment quality for Iteration #33 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01775 for Iteration #34 of Tilt-Series #6.
CCMS(rotations) = 0.60562 for Iteration #34 of Tilt-Series #6.
CCMS(scale) = 0.00592 for Iteration #34 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01596 for iteration 34 of Tilt-Series #6.
Alignment quality for Iteration #34 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #6 (18mar12b): UnstableCreating 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 #6 (tiltseries0006_thick550)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006_thick550)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01435 for Iteration #35 of Tilt-Series #6.
CCMS(rotations) = 0.48266 for Iteration #35 of Tilt-Series #6.
CCMS(scale) = 0.00617 for Iteration #35 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01328 for iteration 35 of Tilt-Series #6.
Alignment quality for Iteration #35 of Tilt-Series #6 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #6 (18mar12b): StableCreating 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 #6 (tiltseries0006_thick550)!
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: 2018yr03m13d-10hr15m27s