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/tiltseries0007_thick500 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3281.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2747 --r1_region_y=2465 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3281.0 --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=tiltseries0007_thick500 --r2_region_y=2465 --r2_region_x=2747 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1641.0 --defocus_ang_positive=90 --r5_mask_width_x=2722 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3281.0 --r3_highpass_apod_x=1641.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=661 --r2_mask_width_y=591 --r5_region_x=2747 --r5_region_y=2465 --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=3281.0 --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=2440 --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=1641.0 --r3_iters=5 --r1_highpass_diameter_x=3281.0 --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=2722 --r4_mask_width_y=2440 --r5_highpass_apod_y=1641.0 --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=1641.0 --r1_highpass_apod_x=1641.0 --r2_highpass_apod_x=1641.0 --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=7 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1207 --r3_mask_width_x=1348 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3281.0 --r4_highpass_diameter_x=3281.0 --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=3281.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1641.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3281.0 --defocus_max=0 --r4_region_y=2465 --r4_region_x=2747 --r5_kernel_y=5 --r3_region_x=2747 --r3_region_y=2465 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=500 --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=3281.0 --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=1641.0 --r4_highpass_apod_y=1641.0 --azimuth=true --r1_mask_width_y=283 --r1_mask_width_x=318 --jobtype=protomo --from_multirefine=True

node06
Start time: 2018yr03m12d-13hr03m22s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
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 = { 0.00649070405364 0.00649070405364 }
window.highpass.apodization = { 0.0129774527727 0.0129774527727 }
window.mask.apodization = { 10 10 }
align.mask.width = { 318 283 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 66.4086328748
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 343 308 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 318 283 }
reference.body = 66.4086328748
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04539 for Iteration #1 of Tilt-Series #7.
CCMS(rotations) = 0.77362 for Iteration #1 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7.
The scaled sum of CCMS values is #0.03817 for iteration 1 of Tilt-Series #7.
Alignment quality for Iteration #1 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04065 for Iteration #2 of Tilt-Series #7.
CCMS(rotations) = 0.82269 for Iteration #2 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7.
The scaled sum of CCMS values is #0.03678 for iteration 2 of Tilt-Series #7.
Alignment quality for Iteration #2 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.02487 for Iteration #3 of Tilt-Series #7.
CCMS(rotations) = 0.84731 for Iteration #3 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7.
The scaled sum of CCMS values is #0.02938 for iteration 3 of Tilt-Series #7.
Alignment quality for Iteration #3 of Tilt-Series #7 (18mar12b): Okay (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.02644 for Iteration #4 of Tilt-Series #7.
CCMS(rotations) = 0.2004 for Iteration #4 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01723 for iteration 4 of Tilt-Series #7.
Alignment quality for Iteration #4 of Tilt-Series #7 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #7 (18mar12b): 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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00913 for Iteration #5 of Tilt-Series #7.
CCMS(rotations) = 0.26279 for Iteration #5 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00982 for iteration 5 of Tilt-Series #7.
Alignment quality for Iteration #5 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00728 for Iteration #6 of Tilt-Series #7.
CCMS(rotations) = 0.17037 for Iteration #6 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00705 for iteration 6 of Tilt-Series #7.
Alignment quality for Iteration #6 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.011 for Iteration #7 of Tilt-Series #7.
CCMS(rotations) = 0.24112 for Iteration #7 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01032 for iteration 7 of Tilt-Series #7.
Alignment quality for Iteration #7 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00871 for Iteration #8 of Tilt-Series #7.
CCMS(rotations) = 0.16995 for Iteration #8 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00775 for iteration 8 of Tilt-Series #7.
Alignment quality for Iteration #8 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #9 of Tilt-Series #7.
CCMS(rotations) = 0.17865 for Iteration #9 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00712 for iteration 9 of Tilt-Series #7.
Alignment quality for Iteration #9 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #7 (18mar12b): StableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00945 for Iteration #10 of Tilt-Series #7.
CCMS(rotations) = 0.21351 for Iteration #10 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7.
The scaled sum of CCMS values is #0.009 for iteration 10 of Tilt-Series #7.
Alignment quality for Iteration #10 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
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 = { 0.00324535202682 0.00324535202682 }
window.highpass.apodization = { 0.00648872638635 0.00648872638635 }
window.mask.apodization = { 10 10 }
align.mask.width = { 661 591 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 132.81726575
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 686 616 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 661 591 }
reference.body = 132.81726575
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.02209 for Iteration #11 of Tilt-Series #7.
CCMS(rotations) = 0.1753 for Iteration #11 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01455 for iteration 11 of Tilt-Series #7.
Alignment quality for Iteration #11 of Tilt-Series #7 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0067 for Iteration #12 of Tilt-Series #7.
CCMS(rotations) = 0.1995 for Iteration #12 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00734 for iteration 12 of Tilt-Series #7.
Alignment quality for Iteration #12 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #7 (18mar12b): 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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00596 for Iteration #13 of Tilt-Series #7.
CCMS(rotations) = 0.20248 for Iteration #13 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00703 for iteration 13 of Tilt-Series #7.
Alignment quality for Iteration #13 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #7 (18mar12b): Very StableCreating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00598 for Iteration #14 of Tilt-Series #7.
CCMS(rotations) = 0.21586 for Iteration #14 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00731 for iteration 14 of Tilt-Series #7.
Alignment quality for Iteration #14 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.0062 for Iteration #15 of Tilt-Series #7.
CCMS(rotations) = 0.19121 for Iteration #15 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00693 for iteration 15 of Tilt-Series #7.
Alignment quality for Iteration #15 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0061 for Iteration #16 of Tilt-Series #7.
CCMS(rotations) = 0.20149 for Iteration #16 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00708 for iteration 16 of Tilt-Series #7.
Alignment quality for Iteration #16 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #7 (18mar12b): StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00584 for Iteration #17 of Tilt-Series #7.
CCMS(rotations) = 0.19977 for Iteration #17 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00692 for iteration 17 of Tilt-Series #7.
Alignment quality for Iteration #17 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #7 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...

No Round parameters changed for Iteration #18 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00539 for Iteration #18 of Tilt-Series #7.
CCMS(rotations) = 0.19657 for Iteration #18 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00663 for iteration 18 of Tilt-Series #7.
Alignment quality for Iteration #18 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #7 (18mar12b): 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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00559 for Iteration #19 of Tilt-Series #7.
CCMS(rotations) = 0.18875 for Iteration #19 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00657 for iteration 19 of Tilt-Series #7.
Alignment quality for Iteration #19 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #7 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...

No Round parameters changed for Iteration #20 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #20 of Tilt-Series #7.
CCMS(rotations) = 0.20033 for Iteration #20 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00685 for iteration 20 of Tilt-Series #7.
Alignment quality for Iteration #20 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #7 (18mar12b): 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 #7 (tiltseries0007_thick500)
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 = { 0.00162267601341 0.00162267601341 }
window.highpass.apodization = { 0.00324436319317 0.00324436319317 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1348 1207 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 265.634531499
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1373 1232 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1348 1207 }
reference.body = 265.634531499
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00639 for Iteration #21 of Tilt-Series #7.
CCMS(rotations) = 0.17758 for Iteration #21 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00675 for iteration 21 of Tilt-Series #7.
Alignment quality for Iteration #21 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...

No Round parameters changed for Iteration #22 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00612 for Iteration #22 of Tilt-Series #7.
CCMS(rotations) = 0.24732 for Iteration #22 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7.
The scaled sum of CCMS values is #0.008 for iteration 22 of Tilt-Series #7.
Alignment quality for Iteration #22 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #7 (18mar12b): 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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00556 for Iteration #23 of Tilt-Series #7.
CCMS(rotations) = 0.23444 for Iteration #23 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00747 for iteration 23 of Tilt-Series #7.
Alignment quality for Iteration #23 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00495 for Iteration #24 of Tilt-Series #7.
CCMS(rotations) = 0.26107 for Iteration #24 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00769 for iteration 24 of Tilt-Series #7.
Alignment quality for Iteration #24 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00562 for Iteration #25 of Tilt-Series #7.
CCMS(rotations) = 0.29114 for Iteration #25 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00863 for iteration 25 of Tilt-Series #7.
Alignment quality for Iteration #25 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
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 = { 0.000811338006705 0.000811338006705 }
window.highpass.apodization = { 0.00162218159659 0.00162218159659 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2722 2440 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 531.269062999
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2747 2465 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2722 2440 }
reference.body = 531.269062999
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01002 for Iteration #26 of Tilt-Series #7.
CCMS(rotations) = 0.1591 for Iteration #26 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00819 for iteration 26 of Tilt-Series #7.
Alignment quality for Iteration #26 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...

No Round parameters changed for Iteration #27 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0104 for Iteration #27 of Tilt-Series #7.
CCMS(rotations) = 0.2057 for Iteration #27 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00931 for iteration 27 of Tilt-Series #7.
Alignment quality for Iteration #27 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #7 (18mar12b): StableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0091 for Iteration #28 of Tilt-Series #7.
CCMS(rotations) = 0.21135 for Iteration #28 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00878 for iteration 28 of Tilt-Series #7.
Alignment quality for Iteration #28 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00933 for Iteration #29 of Tilt-Series #7.
CCMS(rotations) = 0.23961 for Iteration #29 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00946 for iteration 29 of Tilt-Series #7.
Alignment quality for Iteration #29 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #7 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01156 for Iteration #30 of Tilt-Series #7.
CCMS(rotations) = 0.23032 for Iteration #30 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01039 for iteration 30 of Tilt-Series #7.
Alignment quality for Iteration #30 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01383 for Iteration #31 of Tilt-Series #7.
CCMS(rotations) = 0.28614 for Iteration #31 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01264 for iteration 31 of Tilt-Series #7.
Alignment quality for Iteration #31 of Tilt-Series #7 (18mar12b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0129 for Iteration #32 of Tilt-Series #7.
CCMS(rotations) = 0.12183 for Iteration #32 of Tilt-Series #7.
CCMS(scale) = 0.00313 for Iteration #32 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00697 for iteration 32 of Tilt-Series #7.
Alignment quality for Iteration #32 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01268 for Iteration #33 of Tilt-Series #7.
CCMS(rotations) = 0.18005 for Iteration #33 of Tilt-Series #7.
CCMS(scale) = 0.00365 for Iteration #33 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00784 for iteration 33 of Tilt-Series #7.
Alignment quality for Iteration #33 of Tilt-Series #7 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #7 (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 #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00973 for Iteration #34 of Tilt-Series #7.
CCMS(rotations) = 0.19216 for Iteration #34 of Tilt-Series #7.
CCMS(scale) = 0.00284 for Iteration #34 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00675 for iteration 34 of Tilt-Series #7.
Alignment quality for Iteration #34 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #7 (18mar12b): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #7 (tiltseries0007_thick500)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #7 (tiltseries0007_thick500)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01018 for Iteration #35 of Tilt-Series #7.
CCMS(rotations) = 0.20143 for Iteration #35 of Tilt-Series #7.
CCMS(scale) = 0.00336 for Iteration #35 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0072 for iteration 35 of Tilt-Series #7.
Alignment quality for Iteration #35 of Tilt-Series #7 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #7 (18mar12b): UnstableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #7 (tiltseries0007_thick500)!
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-03hr03m58s