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/tiltseries0004_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=2097.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=3051 --r1_region_y=969 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=2097.0 --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=969 --r2_region_x=3051 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1049.0 --defocus_ang_positive=90 --r5_mask_width_x=3026 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=2097.0 --r3_highpass_apod_x=1049.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=737 --r2_mask_width_y=218 --r5_region_x=3051 --r5_region_y=969 --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=2097.0 --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=944 --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=1049.0 --runname=tiltseries0004_thick50 --r1_highpass_diameter_x=2097.0 --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=3026 --r4_mask_width_y=944 --r5_highpass_apod_y=1049.0 --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=1049.0 --r1_highpass_apod_x=1049.0 --r2_highpass_apod_x=1049.0 --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=4 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=459 --r3_mask_width_x=1500 --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=2097.0 --r4_highpass_diameter_x=2097.0 --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=2097.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1049.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=2097.0 --defocus_max=0 --r4_region_y=969 --r4_region_x=3051 --r5_kernel_y=5 --r3_region_x=3051 --r3_region_y=969 --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=2097.0 --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=1049.0 --r4_highpass_apod_y=1049.0 --azimuth=true --r1_mask_width_y=109 --r1_mask_width_x=356 --jobtype=protomo

node39
Start time: 2018yr01m23d-17hr12m25s
Description: 
Using Imod Coarse alignment for Refinement by copying imod_coarse_series0004.tlt to series0004.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_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 = { 0.0165129613734 0.0165129613734 }
window.highpass.apodization = { 0.0330101811249 0.0330101811249 }
window.mask.apodization = { 10 10 }
align.mask.width = { 356 109 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 3.16098782024
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 381 121 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 356 109 }
reference.body = 3.16098782024
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.02186 for Iteration #1 of Tilt-Series #4.
CCMS(rotations) = 0.51277 for Iteration #1 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4.
The scaled sum of CCMS values is #0.02118 for iteration 1 of Tilt-Series #4.
Alignment quality for Iteration #1 of Tilt-Series #4 (17dec26e): Okay (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00563 for Iteration #2 of Tilt-Series #4.
CCMS(rotations) = 0.06409 for Iteration #2 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0041 for iteration 2 of Tilt-Series #4.
Alignment quality for Iteration #2 of Tilt-Series #4 (17dec26e): Perfection! (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.0057 for Iteration #3 of Tilt-Series #4.
CCMS(rotations) = 0.07686 for Iteration #3 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00439 for iteration 3 of Tilt-Series #4.
Alignment quality for Iteration #3 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00591 for Iteration #4 of Tilt-Series #4.
CCMS(rotations) = 0.07963 for Iteration #4 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00455 for iteration 4 of Tilt-Series #4.
Alignment quality for Iteration #4 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00576 for Iteration #5 of Tilt-Series #4.
CCMS(rotations) = 0.09493 for Iteration #5 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00478 for iteration 5 of Tilt-Series #4.
Alignment quality for Iteration #5 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (17dec26e): Rock Solid!Creating 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00662 for Iteration #6 of Tilt-Series #4.
CCMS(rotations) = 0.09599 for Iteration #6 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00523 for iteration 6 of Tilt-Series #4.
Alignment quality for Iteration #6 of Tilt-Series #4 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #7 of Tilt-Series #4.
CCMS(rotations) = 0.10802 for Iteration #7 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00526 for iteration 7 of Tilt-Series #4.
Alignment quality for Iteration #7 of Tilt-Series #4 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #8 of Tilt-Series #4.
CCMS(rotations) = 0.10048 for Iteration #8 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00502 for iteration 8 of Tilt-Series #4.
Alignment quality for Iteration #8 of Tilt-Series #4 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (17dec26e): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00601 for Iteration #9 of Tilt-Series #4.
CCMS(rotations) = 0.09448 for Iteration #9 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0049 for iteration 9 of Tilt-Series #4.
Alignment quality for Iteration #9 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (17dec26e): Very StableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00612 for Iteration #10 of Tilt-Series #4.
CCMS(rotations) = 0.10106 for Iteration #10 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00508 for iteration 10 of Tilt-Series #4.
Alignment quality for Iteration #10 of Tilt-Series #4 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (17dec26e): StableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004_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 = { 0.0082564806867 0.0082564806867 }
window.highpass.apodization = { 0.0165050905624 0.0165050905624 }
window.mask.apodization = { 10 10 }
align.mask.width = { 737 218 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 6.32197564049
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 762 242 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 737 218 }
reference.body = 6.32197564049
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00476 for Iteration #11 of Tilt-Series #4.
CCMS(rotations) = 0.08846 for Iteration #11 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00415 for iteration 11 of Tilt-Series #4.
Alignment quality for Iteration #11 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00345 for Iteration #12 of Tilt-Series #4.
CCMS(rotations) = 0.05185 for Iteration #12 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00276 for iteration 12 of Tilt-Series #4.
Alignment quality for Iteration #12 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (17dec26e): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0035 for Iteration #13 of Tilt-Series #4.
CCMS(rotations) = 0.05712 for Iteration #13 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00289 for iteration 13 of Tilt-Series #4.
Alignment quality for Iteration #13 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00338 for Iteration #14 of Tilt-Series #4.
CCMS(rotations) = 0.05424 for Iteration #14 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00277 for iteration 14 of Tilt-Series #4.
Alignment quality for Iteration #14 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00365 for Iteration #15 of Tilt-Series #4.
CCMS(rotations) = 0.05953 for Iteration #15 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00302 for iteration 15 of Tilt-Series #4.
Alignment quality for Iteration #15 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00347 for Iteration #16 of Tilt-Series #4.
CCMS(rotations) = 0.05325 for Iteration #16 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0028 for iteration 16 of Tilt-Series #4.
Alignment quality for Iteration #16 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00363 for Iteration #17 of Tilt-Series #4.
CCMS(rotations) = 0.0587 for Iteration #17 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00299 for iteration 17 of Tilt-Series #4.
Alignment quality for Iteration #17 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00344 for Iteration #18 of Tilt-Series #4.
CCMS(rotations) = 0.05415 for Iteration #18 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0028 for iteration 18 of Tilt-Series #4.
Alignment quality for Iteration #18 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00367 for Iteration #19 of Tilt-Series #4.
CCMS(rotations) = 0.05783 for Iteration #19 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00299 for iteration 19 of Tilt-Series #4.
Alignment quality for Iteration #19 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00345 for Iteration #20 of Tilt-Series #4.
CCMS(rotations) = 0.05477 for Iteration #20 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00282 for iteration 20 of Tilt-Series #4.
Alignment quality for Iteration #20 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (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 #4 (tiltseries0004_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 = { 0.00412824034335 0.00412824034335 }
window.highpass.apodization = { 0.00825254528122 0.00825254528122 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1500 459 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 12.643951281
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1525 484 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1500 459 }
reference.body = 12.643951281
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00351 for Iteration #21 of Tilt-Series #4.
CCMS(rotations) = 0.06401 for Iteration #21 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00303 for iteration 21 of Tilt-Series #4.
Alignment quality for Iteration #21 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00315 for Iteration #22 of Tilt-Series #4.
CCMS(rotations) = 0.06156 for Iteration #22 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0028 for iteration 22 of Tilt-Series #4.
Alignment quality for Iteration #22 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (17dec26e): 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00301 for Iteration #23 of Tilt-Series #4.
CCMS(rotations) = 0.05478 for Iteration #23 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0026 for iteration 23 of Tilt-Series #4.
Alignment quality for Iteration #23 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00312 for Iteration #24 of Tilt-Series #4.
CCMS(rotations) = 0.05698 for Iteration #24 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0027 for iteration 24 of Tilt-Series #4.
Alignment quality for Iteration #24 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00326 for Iteration #25 of Tilt-Series #4.
CCMS(rotations) = 0.05545 for Iteration #25 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00274 for iteration 25 of Tilt-Series #4.
Alignment quality for Iteration #25 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (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 #4 (tiltseries0004_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 = { 0.00206412017167 0.00206412017167 }
window.highpass.apodization = { 0.00412627264061 0.00412627264061 }
window.mask.apodization = { 10 10 }
align.mask.width = { 3026 944 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 25.2879025619
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 3051 969 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 3026 944 }
reference.body = 25.2879025619
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00428 for Iteration #26 of Tilt-Series #4.
CCMS(rotations) = 0.07791 for Iteration #26 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0037 for iteration 26 of Tilt-Series #4.
Alignment quality for Iteration #26 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00523 for Iteration #27 of Tilt-Series #4.
CCMS(rotations) = 0.13606 for Iteration #27 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00534 for iteration 27 of Tilt-Series #4.
Alignment quality for Iteration #27 of Tilt-Series #4 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00447 for Iteration #28 of Tilt-Series #4.
CCMS(rotations) = 0.07953 for Iteration #28 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00383 for iteration 28 of Tilt-Series #4.
Alignment quality for Iteration #28 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00434 for Iteration #29 of Tilt-Series #4.
CCMS(rotations) = 0.09778 for Iteration #29 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00412 for iteration 29 of Tilt-Series #4.
Alignment quality for Iteration #29 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (17dec26e): Very StableCreating 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00461 for Iteration #30 of Tilt-Series #4.
CCMS(rotations) = 0.09378 for Iteration #30 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00418 for iteration 30 of Tilt-Series #4.
Alignment quality for Iteration #30 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0046 for Iteration #31 of Tilt-Series #4.
CCMS(rotations) = 0.09429 for Iteration #31 of Tilt-Series #4.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00418 for iteration 31 of Tilt-Series #4.
Alignment quality for Iteration #31 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (17dec26e): StableCreating 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00328 for Iteration #32 of Tilt-Series #4.
CCMS(rotations) = 0.07549 for Iteration #32 of Tilt-Series #4.
CCMS(scale) = 0.00197 for Iteration #32 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00276 for iteration 32 of Tilt-Series #4.
Alignment quality for Iteration #32 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00313 for Iteration #33 of Tilt-Series #4.
CCMS(rotations) = 0.08577 for Iteration #33 of Tilt-Series #4.
CCMS(scale) = 0.00157 for Iteration #33 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00271 for iteration 33 of Tilt-Series #4.
Alignment quality for Iteration #33 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00328 for Iteration #34 of Tilt-Series #4.
CCMS(rotations) = 0.08392 for Iteration #34 of Tilt-Series #4.
CCMS(scale) = 0.00201 for Iteration #34 of Tilt-Series #4.
The scaled sum of CCMS values is #0.00288 for iteration 34 of Tilt-Series #4.
Alignment quality for Iteration #34 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (17dec26e): Very 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 #4 (tiltseries0004_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0031 for Iteration #35 of Tilt-Series #4.
CCMS(rotations) = 0.07797 for Iteration #35 of Tilt-Series #4.
CCMS(scale) = 0.00159 for Iteration #35 of Tilt-Series #4.
The scaled sum of CCMS values is #0.0026 for iteration 35 of Tilt-Series #4.
Alignment quality for Iteration #35 of Tilt-Series #4 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (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 #4 (tiltseries0004_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: 2018yr01m23d-21hr00m39s