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/tiltseries0001_thick275 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3716.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2810 --r1_region_y=1717 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3716.0 --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=1717 --r2_region_x=2810 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1858.0 --defocus_ang_positive=90 --r5_mask_width_x=2785 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3716.0 --r3_highpass_apod_x=1858.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=677 --r2_mask_width_y=404 --r5_region_x=2810 --r5_region_y=1717 --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=3716.0 --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=1692 --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=1858.0 --runname=tiltseries0001_thick275 --r1_highpass_diameter_x=3716.0 --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=2785 --r4_mask_width_y=1692 --r5_highpass_apod_y=1858.0 --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=1858.0 --r1_highpass_apod_x=1858.0 --r2_highpass_apod_x=1858.0 --sampling=8 --starting_tlt_file=Manual --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=1 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=833 --r3_mask_width_x=1380 --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=3716.0 --r4_highpass_diameter_x=3716.0 --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=3716.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1858.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3716.0 --defocus_max=0 --r4_region_y=1717 --r4_region_x=2810 --r5_kernel_y=5 --r3_region_x=2810 --r3_region_y=1717 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=275 --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=3716.0 --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=1858.0 --r4_highpass_apod_y=1858.0 --azimuth=true --r1_mask_width_y=193 --r1_mask_width_x=326 --jobtype=protomo --from_multirefine=True

node48
Start time: 2018yr01m25d-19hr06m51s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
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 = { 0.00931853606028 0.00931853606028 }
window.highpass.apodization = { 0.0186370721206 0.0186370721206 }
window.mask.apodization = { 10 10 }
align.mask.width = { 326 193 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 22.4568169824
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 351 214 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 326 193 }
reference.body = 22.4568169824
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.01592 for Iteration #1 of Tilt-Series #1.
CCMS(rotations) = 0.28725 for Iteration #1 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #1.
The scaled sum of CCMS values is #0.01371 for iteration 1 of Tilt-Series #1.
Alignment quality for Iteration #1 of Tilt-Series #1 (17dec26e): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00806 for Iteration #2 of Tilt-Series #1.
CCMS(rotations) = 0.20621 for Iteration #2 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00815 for iteration 2 of Tilt-Series #1.
Alignment quality for Iteration #2 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #3 of Tilt-Series #1.
CCMS(rotations) = 0.26634 for Iteration #3 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00876 for iteration 3 of Tilt-Series #1.
Alignment quality for Iteration #3 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00663 for Iteration #4 of Tilt-Series #1.
CCMS(rotations) = 0.27242 for Iteration #4 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00876 for iteration 4 of Tilt-Series #1.
Alignment quality for Iteration #4 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00601 for Iteration #5 of Tilt-Series #1.
CCMS(rotations) = 0.23726 for Iteration #5 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00775 for iteration 5 of Tilt-Series #1.
Alignment quality for Iteration #5 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00637 for Iteration #6 of Tilt-Series #1.
CCMS(rotations) = 0.28626 for Iteration #6 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00891 for iteration 6 of Tilt-Series #1.
Alignment quality for Iteration #6 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #1 (17dec26e): StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00673 for Iteration #7 of Tilt-Series #1.
CCMS(rotations) = 0.27803 for Iteration #7 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00892 for iteration 7 of Tilt-Series #1.
Alignment quality for Iteration #7 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00644 for Iteration #8 of Tilt-Series #1.
CCMS(rotations) = 0.26449 for Iteration #8 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00851 for iteration 8 of Tilt-Series #1.
Alignment quality for Iteration #8 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #9 of Tilt-Series #1.
CCMS(rotations) = 0.25983 for Iteration #9 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00805 for iteration 9 of Tilt-Series #1.
Alignment quality for Iteration #9 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #10 of Tilt-Series #1.
CCMS(rotations) = 0.26879 for Iteration #10 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00819 for iteration 10 of Tilt-Series #1.
Alignment quality for Iteration #10 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)
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 = { 0.00465926803014 0.00465926803014 }
window.highpass.apodization = { 0.00931853606028 0.00931853606028 }
window.mask.apodization = { 10 10 }
align.mask.width = { 677 404 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 44.9136339648
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 702 429 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 677 404 }
reference.body = 44.9136339648
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00954 for Iteration #11 of Tilt-Series #1.
CCMS(rotations) = 0.09203 for Iteration #11 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00661 for iteration 11 of Tilt-Series #1.
Alignment quality for Iteration #11 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #1 (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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00498 for Iteration #12 of Tilt-Series #1.
CCMS(rotations) = 0.1593 for Iteration #12 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00568 for iteration 12 of Tilt-Series #1.
Alignment quality for Iteration #12 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00568 for Iteration #13 of Tilt-Series #1.
CCMS(rotations) = 0.28425 for Iteration #13 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00852 for iteration 13 of Tilt-Series #1.
Alignment quality for Iteration #13 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #14 of Tilt-Series #1.
CCMS(rotations) = 0.20658 for Iteration #14 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00665 for iteration 14 of Tilt-Series #1.
Alignment quality for Iteration #14 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00448 for Iteration #15 of Tilt-Series #1.
CCMS(rotations) = 0.16431 for Iteration #15 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00552 for iteration 15 of Tilt-Series #1.
Alignment quality for Iteration #15 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...

No Round parameters changed for Iteration #16 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00637 for Iteration #16 of Tilt-Series #1.
CCMS(rotations) = 0.19269 for Iteration #16 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00704 for iteration 16 of Tilt-Series #1.
Alignment quality for Iteration #16 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00491 for Iteration #17 of Tilt-Series #1.
CCMS(rotations) = 0.18967 for Iteration #17 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00625 for iteration 17 of Tilt-Series #1.
Alignment quality for Iteration #17 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00634 for Iteration #18 of Tilt-Series #1.
CCMS(rotations) = 0.18183 for Iteration #18 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00681 for iteration 18 of Tilt-Series #1.
Alignment quality for Iteration #18 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00505 for Iteration #19 of Tilt-Series #1.
CCMS(rotations) = 0.19518 for Iteration #19 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00643 for iteration 19 of Tilt-Series #1.
Alignment quality for Iteration #19 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00618 for Iteration #20 of Tilt-Series #1.
CCMS(rotations) = 0.18002 for Iteration #20 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00669 for iteration 20 of Tilt-Series #1.
Alignment quality for Iteration #20 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)
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 = { 0.00232963401507 0.00232963401507 }
window.highpass.apodization = { 0.00465926803014 0.00465926803014 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1380 833 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 89.8272679296
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1405 858 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1380 833 }
reference.body = 89.8272679296
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00446 for Iteration #21 of Tilt-Series #1.
CCMS(rotations) = 0.15915 for Iteration #21 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00541 for iteration 21 of Tilt-Series #1.
Alignment quality for Iteration #21 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.0038 for Iteration #22 of Tilt-Series #1.
CCMS(rotations) = 0.11622 for Iteration #22 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00423 for iteration 22 of Tilt-Series #1.
Alignment quality for Iteration #22 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.0033 for Iteration #23 of Tilt-Series #1.
CCMS(rotations) = 0.09579 for Iteration #23 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00357 for iteration 23 of Tilt-Series #1.
Alignment quality for Iteration #23 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00335 for Iteration #24 of Tilt-Series #1.
CCMS(rotations) = 0.11218 for Iteration #24 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00392 for iteration 24 of Tilt-Series #1.
Alignment quality for Iteration #24 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #1 (17dec26e): UnstableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00368 for Iteration #25 of Tilt-Series #1.
CCMS(rotations) = 0.09848 for Iteration #25 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00381 for iteration 25 of Tilt-Series #1.
Alignment quality for Iteration #25 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)
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 = { 0.00116481700753 0.00116481700753 }
window.highpass.apodization = { 0.00232963401507 0.00232963401507 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2785 1692 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 179.654535859
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2810 1717 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2785 1692 }
reference.body = 179.654535859
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00496 for Iteration #26 of Tilt-Series #1.
CCMS(rotations) = 0.35971 for Iteration #26 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00967 for iteration 26 of Tilt-Series #1.
Alignment quality for Iteration #26 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00422 for Iteration #27 of Tilt-Series #1.
CCMS(rotations) = 0.21459 for Iteration #27 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #1.
The scaled sum of CCMS values is #0.0064 for iteration 27 of Tilt-Series #1.
Alignment quality for Iteration #27 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00408 for Iteration #28 of Tilt-Series #1.
CCMS(rotations) = 0.34632 for Iteration #28 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00897 for iteration 28 of Tilt-Series #1.
Alignment quality for Iteration #28 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00381 for Iteration #29 of Tilt-Series #1.
CCMS(rotations) = 0.20091 for Iteration #29 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00592 for iteration 29 of Tilt-Series #1.
Alignment quality for Iteration #29 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00386 for Iteration #30 of Tilt-Series #1.
CCMS(rotations) = 0.33783 for Iteration #30 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00868 for iteration 30 of Tilt-Series #1.
Alignment quality for Iteration #30 of Tilt-Series #1 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00364 for Iteration #31 of Tilt-Series #1.
CCMS(rotations) = 0.21204 for Iteration #31 of Tilt-Series #1.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00606 for iteration 31 of Tilt-Series #1.
Alignment quality for Iteration #31 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #32 of Tilt-Series #1.
CCMS(rotations) = 0.3357 for Iteration #32 of Tilt-Series #1.
CCMS(scale) = 0.00089 for Iteration #32 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00599 for iteration 32 of Tilt-Series #1.
Alignment quality for Iteration #32 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00345 for Iteration #33 of Tilt-Series #1.
CCMS(rotations) = 0.21958 for Iteration #33 of Tilt-Series #1.
CCMS(scale) = 0.00095 for Iteration #33 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00439 for iteration 33 of Tilt-Series #1.
Alignment quality for Iteration #33 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00361 for Iteration #34 of Tilt-Series #1.
CCMS(rotations) = 0.36414 for Iteration #34 of Tilt-Series #1.
CCMS(scale) = 0.00086 for Iteration #34 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00634 for iteration 34 of Tilt-Series #1.
Alignment quality for Iteration #34 of Tilt-Series #1 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #1 (tiltseries0001_thick275)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00348 for Iteration #35 of Tilt-Series #1.
CCMS(rotations) = 0.22008 for Iteration #35 of Tilt-Series #1.
CCMS(scale) = 0.00086 for Iteration #35 of Tilt-Series #1.
The scaled sum of CCMS values is #0.00438 for iteration 35 of Tilt-Series #1.
Alignment quality for Iteration #35 of Tilt-Series #1 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #1 (17dec26e): 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 #1 (tiltseries0001_thick275)!
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: 2018yr01m26d-02hr39m58s