protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0003_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3601.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2920 --r1_region_y=1664 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3601.0 --r4_lowpass_apod_y=22.0 --r4_lowpass_apod_x=22.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=43.0 --r3_lowpass_apod_y=43.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=1664 --r2_region_x=2920 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1801.0 --defocus_ang_positive=90 --r5_mask_width_x=2895 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3601.0 --r3_highpass_apod_x=1801.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=705 --r2_mask_width_y=391 --r5_region_x=2920 --r5_region_y=1664 --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=8.64 --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=3601.0 --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=1639 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=1801.0 --runname=tiltseries0003_thick50 --r1_highpass_diameter_x=3601.0 --r2_lowpass_diameter_y=34.56 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=4.32 --r5_lowpass_diameter_x=4.32 --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=2895 --r4_mask_width_y=1639 --r5_highpass_apod_y=1801.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17dec26e --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=1801.0 --r1_highpass_apod_x=1801.0 --r2_highpass_apod_x=1801.0 --sampling=8 --starting_tlt_file=Imod_Coarse --r5_lowpass_apod_x=11.0 --r5_lowpass_apod_y=11.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=69.12 --r1_lowpass_diameter_x=69.12 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=3 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=807 --r3_mask_width_x=1435 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3601.0 --r4_highpass_diameter_x=3601.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=173.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3601.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1801.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3601.0 --defocus_max=0 --r4_region_y=1664 --r4_region_x=2920 --r5_kernel_y=5 --r3_region_x=2920 --r3_region_y=1664 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=5636 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=1 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=17.28 --r3_lowpass_diameter_x=17.28 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=2.16423 --link=False --r2_highpass_diameter_x=3601.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=86.0 --r5_kernel_x=5 --r2_lowpass_apod_x=86.0 --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=34.56 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=173.0 --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=1801.0 --r4_highpass_apod_y=1801.0 --azimuth=true --r1_mask_width_y=187 --r1_mask_width_x=340 --jobtype=protomo --from_multirefine=True

node15
Start time: 2018yr01m23d-18hr52m20s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 69.12 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms)
window.lowpass.apodization = { 0.20016 0.20016 }
align.translimit = 47.125e0
map.sampling = 8
window.highpass.diameter = { 0.0096161288531 0.0096161288531 }
window.highpass.apodization = { 0.0192269183787 0.0192269183787 }
window.mask.apodization = { 10 10 }
align.mask.width = { 340 187 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 3.33418041878
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 365 208 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 340 187 }
reference.body = 3.33418041878
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.09223 for Iteration #1 of Tilt-Series #3.
CCMS(rotations) = 0.10634 for Iteration #1 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3.
The scaled sum of CCMS values is #0.04824 for iteration 1 of Tilt-Series #3.
Alignment quality for Iteration #1 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #2 of Tilt-Series #3.
CCMS(rotations) = 0.1471 for Iteration #2 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00502 for iteration 2 of Tilt-Series #3.
Alignment quality for Iteration #2 of Tilt-Series #3 (17dec26e): Excellent (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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00481 for Iteration #3 of Tilt-Series #3.
CCMS(rotations) = 0.10049 for Iteration #3 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00441 for iteration 3 of Tilt-Series #3.
Alignment quality for Iteration #3 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #4 of Tilt-Series #3.
CCMS(rotations) = 0.16671 for Iteration #4 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00538 for iteration 4 of Tilt-Series #3.
Alignment quality for Iteration #4 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00475 for Iteration #5 of Tilt-Series #3.
CCMS(rotations) = 0.11382 for Iteration #5 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00465 for iteration 5 of Tilt-Series #3.
Alignment quality for Iteration #5 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00422 for Iteration #6 of Tilt-Series #3.
CCMS(rotations) = 0.17878 for Iteration #6 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00568 for iteration 6 of Tilt-Series #3.
Alignment quality for Iteration #6 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00482 for Iteration #7 of Tilt-Series #3.
CCMS(rotations) = 0.11254 for Iteration #7 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00466 for iteration 7 of Tilt-Series #3.
Alignment quality for Iteration #7 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00416 for Iteration #8 of Tilt-Series #3.
CCMS(rotations) = 0.17553 for Iteration #8 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00559 for iteration 8 of Tilt-Series #3.
Alignment quality for Iteration #8 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #3 (17dec26e): UnstableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00481 for Iteration #9 of Tilt-Series #3.
CCMS(rotations) = 0.11525 for Iteration #9 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00471 for iteration 9 of Tilt-Series #3.
Alignment quality for Iteration #9 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #3 (17dec26e): UnstableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00413 for Iteration #10 of Tilt-Series #3.
CCMS(rotations) = 0.17821 for Iteration #10 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00563 for iteration 10 of Tilt-Series #3.
Alignment quality for Iteration #10 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)
lowpass = 34.56 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
align.translimit = 94.25e0
map.sampling = 4
window.highpass.diameter = { 0.00480806442655 0.00480806442655 }
window.highpass.apodization = { 0.00961345918934 0.00961345918934 }
window.mask.apodization = { 10 10 }
align.mask.width = { 705 391 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 6.66836083756
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 730 416 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 705 391 }
reference.body = 6.66836083756
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00429 for Iteration #11 of Tilt-Series #3.
CCMS(rotations) = 0.10832 for Iteration #11 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00431 for iteration 11 of Tilt-Series #3.
Alignment quality for Iteration #11 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00443 for Iteration #12 of Tilt-Series #3.
CCMS(rotations) = 0.1721 for Iteration #12 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00566 for iteration 12 of Tilt-Series #3.
Alignment quality for Iteration #12 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #13 of Tilt-Series #3.
CCMS(rotations) = 0.1325 for Iteration #13 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00487 for iteration 13 of Tilt-Series #3.
Alignment quality for Iteration #13 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00436 for Iteration #14 of Tilt-Series #3.
CCMS(rotations) = 0.14529 for Iteration #14 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00508 for iteration 14 of Tilt-Series #3.
Alignment quality for Iteration #14 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00434 for Iteration #15 of Tilt-Series #3.
CCMS(rotations) = 0.15278 for Iteration #15 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00523 for iteration 15 of Tilt-Series #3.
Alignment quality for Iteration #15 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00435 for Iteration #16 of Tilt-Series #3.
CCMS(rotations) = 0.15041 for Iteration #16 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00518 for iteration 16 of Tilt-Series #3.
Alignment quality for Iteration #16 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00436 for Iteration #17 of Tilt-Series #3.
CCMS(rotations) = 0.14877 for Iteration #17 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00515 for iteration 17 of Tilt-Series #3.
Alignment quality for Iteration #17 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00435 for Iteration #18 of Tilt-Series #3.
CCMS(rotations) = 0.14923 for Iteration #18 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00516 for iteration 18 of Tilt-Series #3.
Alignment quality for Iteration #18 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00432 for Iteration #19 of Tilt-Series #3.
CCMS(rotations) = 0.15066 for Iteration #19 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00517 for iteration 19 of Tilt-Series #3.
Alignment quality for Iteration #19 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00435 for Iteration #20 of Tilt-Series #3.
CCMS(rotations) = 0.14899 for Iteration #20 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00515 for iteration 20 of Tilt-Series #3.
Alignment quality for Iteration #20 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)
lowpass = 17.28 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms)
window.lowpass.apodization = { 0.20132372093 0.20132372093 }
align.translimit = 188.5e0
map.sampling = 2
window.highpass.diameter = { 0.00240403221327 0.00240403221327 }
window.highpass.apodization = { 0.00480672959467 0.00480672959467 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1435 807 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 13.3367216751
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1460 832 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1435 807 }
reference.body = 13.3367216751
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00379 for Iteration #21 of Tilt-Series #3.
CCMS(rotations) = 0.14437 for Iteration #21 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00478 for iteration 21 of Tilt-Series #3.
Alignment quality for Iteration #21 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00456 for Iteration #22 of Tilt-Series #3.
CCMS(rotations) = 0.10376 for Iteration #22 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00436 for iteration 22 of Tilt-Series #3.
Alignment quality for Iteration #22 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00444 for Iteration #23 of Tilt-Series #3.
CCMS(rotations) = 0.14259 for Iteration #23 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00507 for iteration 23 of Tilt-Series #3.
Alignment quality for Iteration #23 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #3 (17dec26e): Very StableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00432 for Iteration #24 of Tilt-Series #3.
CCMS(rotations) = 0.10856 for Iteration #24 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00433 for iteration 24 of Tilt-Series #3.
Alignment quality for Iteration #24 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #3 (17dec26e): Very 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00458 for Iteration #25 of Tilt-Series #3.
CCMS(rotations) = 0.13948 for Iteration #25 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00508 for iteration 25 of Tilt-Series #3.
Alignment quality for Iteration #25 of Tilt-Series #3 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)
lowpass = 8.64 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms)
window.lowpass.apodization = { 0.196748181818 0.196748181818 }
align.translimit = 377.0e0
map.sampling = 1
window.highpass.diameter = { 0.00120201610664 0.00120201610664 }
window.highpass.apodization = { 0.00240336479733 0.00240336479733 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2895 1639 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 26.6734433503
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2920 1664 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2895 1639 }
reference.body = 26.6734433503
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00402 for Iteration #26 of Tilt-Series #3.
CCMS(rotations) = 0.14826 for Iteration #26 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00497 for iteration 26 of Tilt-Series #3.
Alignment quality for Iteration #26 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.004 for Iteration #27 of Tilt-Series #3.
CCMS(rotations) = 0.12331 for Iteration #27 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00447 for iteration 27 of Tilt-Series #3.
Alignment quality for Iteration #27 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #3 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00402 for Iteration #28 of Tilt-Series #3.
CCMS(rotations) = 0.12704 for Iteration #28 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00455 for iteration 28 of Tilt-Series #3.
Alignment quality for Iteration #28 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #29 of Tilt-Series #3.
CCMS(rotations) = 0.11916 for Iteration #29 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00443 for iteration 29 of Tilt-Series #3.
Alignment quality for Iteration #29 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00391 for Iteration #30 of Tilt-Series #3.
CCMS(rotations) = 0.13553 for Iteration #30 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00466 for iteration 30 of Tilt-Series #3.
Alignment quality for Iteration #30 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00397 for Iteration #31 of Tilt-Series #3.
CCMS(rotations) = 0.13848 for Iteration #31 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00476 for iteration 31 of Tilt-Series #3.
Alignment quality for Iteration #31 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #32 of Tilt-Series #3.
CCMS(rotations) = 0.12299 for Iteration #32 of Tilt-Series #3.
CCMS(scale) = 0.00163 for Iteration #32 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0034 for iteration 32 of Tilt-Series #3.
Alignment quality for Iteration #32 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00366 for Iteration #33 of Tilt-Series #3.
CCMS(rotations) = 0.14048 for Iteration #33 of Tilt-Series #3.
CCMS(scale) = 0.00179 for Iteration #33 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00369 for iteration 33 of Tilt-Series #3.
Alignment quality for Iteration #33 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #3 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00363 for Iteration #34 of Tilt-Series #3.
CCMS(rotations) = 0.14757 for Iteration #34 of Tilt-Series #3.
CCMS(scale) = 0.00179 for Iteration #34 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00377 for iteration 34 of Tilt-Series #3.
Alignment quality for Iteration #34 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00367 for Iteration #35 of Tilt-Series #3.
CCMS(rotations) = 0.15335 for Iteration #35 of Tilt-Series #3.
CCMS(scale) = 0.0019 for Iteration #35 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0039 for iteration 35 of Tilt-Series #3.
Alignment quality for Iteration #35 of Tilt-Series #3 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #3 (17dec26e): 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 #3 (tiltseries0003_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: 2018yr01m24d-01hr45m48s