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/tiltseries0014_thick350 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=8.64 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --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=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --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=4015.0 --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=1894 --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=2008.0 --runname=tiltseries0014_thick350 --r1_highpass_diameter_x=4015.0 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --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=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --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=14 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=934 --r3_mask_width_x=902 --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=4015.0 --r4_highpass_diameter_x=4015.0 --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=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=350 --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=4015.0 --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=959.0 --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=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo

node45
Start time: 2017yr12m26d-20hr31m44s
Description: 
coarse_series0014_iter2.tlt not found, using coarse_series0014.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0014.tlt to series0014.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
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 }
map.sampling = 8
window.highpass.diameter = { 0.00862457783313 0.00862457783313 }
window.highpass.apodization = { 0.0172448605578 0.0172448605578 }
window.mask.apodization = { 10 10 }
align.mask.width = { 206 214 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 28.5814034321
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 231 239 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 206 214 }
reference.body = 28.5814034321
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03042 for Iteration #1 of Tilt-Series #14.
CCMS(rotations) = 0.39176 for Iteration #1 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #14.
The scaled sum of CCMS values is #0.02305 for iteration 1 of Tilt-Series #14.
Alignment quality for Iteration #1 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01535 for Iteration #2 of Tilt-Series #14.
CCMS(rotations) = 0.21741 for Iteration #2 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01202 for iteration 2 of Tilt-Series #14.
Alignment quality for Iteration #2 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01117 for Iteration #3 of Tilt-Series #14.
CCMS(rotations) = 0.19227 for Iteration #3 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00943 for iteration 3 of Tilt-Series #14.
Alignment quality for Iteration #3 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01113 for Iteration #4 of Tilt-Series #14.
CCMS(rotations) = 0.21077 for Iteration #4 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00978 for iteration 4 of Tilt-Series #14.
Alignment quality for Iteration #4 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #14 (17dec26e): Very StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01065 for Iteration #5 of Tilt-Series #14.
CCMS(rotations) = 0.23753 for Iteration #5 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01007 for iteration 5 of Tilt-Series #14.
Alignment quality for Iteration #5 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #14 (17dec26e): StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01096 for Iteration #6 of Tilt-Series #14.
CCMS(rotations) = 0.2668 for Iteration #6 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01081 for iteration 6 of Tilt-Series #14.
Alignment quality for Iteration #6 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #14 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...

No Round parameters changed for Iteration #7 of Tilt-Series #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01115 for Iteration #7 of Tilt-Series #14.
CCMS(rotations) = 0.27532 for Iteration #7 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01108 for iteration 7 of Tilt-Series #14.
Alignment quality for Iteration #7 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01141 for Iteration #8 of Tilt-Series #14.
CCMS(rotations) = 0.28753 for Iteration #8 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01146 for iteration 8 of Tilt-Series #14.
Alignment quality for Iteration #8 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #14 (17dec26e): Rock Solid!Creating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01155 for Iteration #9 of Tilt-Series #14.
CCMS(rotations) = 0.29057 for Iteration #9 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01159 for iteration 9 of Tilt-Series #14.
Alignment quality for Iteration #9 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0119 for Iteration #10 of Tilt-Series #14.
CCMS(rotations) = 0.29858 for Iteration #10 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01192 for iteration 10 of Tilt-Series #14.
Alignment quality for Iteration #10 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)
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 }
map.sampling = 4
window.highpass.diameter = { 0.00431228891656 0.00431228891656 }
window.highpass.apodization = { 0.00862243027888 0.00862243027888 }
window.mask.apodization = { 10 10 }
align.mask.width = { 438 454 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 57.1628068643
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 463 479 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 438 454 }
reference.body = 57.1628068643
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01684 for Iteration #11 of Tilt-Series #14.
CCMS(rotations) = 0.38067 for Iteration #11 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01603 for iteration 11 of Tilt-Series #14.
Alignment quality for Iteration #11 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.0106 for Iteration #12 of Tilt-Series #14.
CCMS(rotations) = 0.44891 for Iteration #12 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01428 for iteration 12 of Tilt-Series #14.
Alignment quality for Iteration #12 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00929 for Iteration #13 of Tilt-Series #14.
CCMS(rotations) = 0.5045 for Iteration #13 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01474 for iteration 13 of Tilt-Series #14.
Alignment quality for Iteration #13 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00791 for Iteration #14 of Tilt-Series #14.
CCMS(rotations) = 0.43275 for Iteration #14 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01261 for iteration 14 of Tilt-Series #14.
Alignment quality for Iteration #14 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #14 (17dec26e): Very StableCreating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...

No Round parameters changed for Iteration #15 of Tilt-Series #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00881 for Iteration #15 of Tilt-Series #14.
CCMS(rotations) = 0.50843 for Iteration #15 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01457 for iteration 15 of Tilt-Series #14.
Alignment quality for Iteration #15 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00837 for Iteration #16 of Tilt-Series #14.
CCMS(rotations) = 0.42258 for Iteration #16 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01264 for iteration 16 of Tilt-Series #14.
Alignment quality for Iteration #16 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #14 (17dec26e): StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...

No Round parameters changed for Iteration #17 of Tilt-Series #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00856 for Iteration #17 of Tilt-Series #14.
CCMS(rotations) = 0.50025 for Iteration #17 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01429 for iteration 17 of Tilt-Series #14.
Alignment quality for Iteration #17 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00813 for Iteration #18 of Tilt-Series #14.
CCMS(rotations) = 0.41511 for Iteration #18 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01237 for iteration 18 of Tilt-Series #14.
Alignment quality for Iteration #18 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00859 for Iteration #19 of Tilt-Series #14.
CCMS(rotations) = 0.49555 for Iteration #19 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #14.
The scaled sum of CCMS values is #0.0142 for iteration 19 of Tilt-Series #14.
Alignment quality for Iteration #19 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #14 (17dec26e): Very StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00846 for Iteration #20 of Tilt-Series #14.
CCMS(rotations) = 0.4108 for Iteration #20 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01244 for iteration 20 of Tilt-Series #14.
Alignment quality for Iteration #20 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #14 (17dec26e): StableCreating 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 #14 (tiltseries0014_thick350)
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 }
map.sampling = 2
window.highpass.diameter = { 0.00215614445828 0.00215614445828 }
window.highpass.apodization = { 0.00431121513944 0.00431121513944 }
window.mask.apodization = { 10 10 }
align.mask.width = { 902 934 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 114.325613729
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 927 959 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 902 934 }
reference.body = 114.325613729
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00994 for Iteration #21 of Tilt-Series #14.
CCMS(rotations) = 0.45584 for Iteration #21 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01409 for iteration 21 of Tilt-Series #14.
Alignment quality for Iteration #21 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00949 for Iteration #22 of Tilt-Series #14.
CCMS(rotations) = 0.43014 for Iteration #22 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01335 for iteration 22 of Tilt-Series #14.
Alignment quality for Iteration #22 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01007 for Iteration #23 of Tilt-Series #14.
CCMS(rotations) = 0.40989 for Iteration #23 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01323 for iteration 23 of Tilt-Series #14.
Alignment quality for Iteration #23 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #14 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...

No Round parameters changed for Iteration #24 of Tilt-Series #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00847 for Iteration #24 of Tilt-Series #14.
CCMS(rotations) = 0.39345 for Iteration #24 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01211 for iteration 24 of Tilt-Series #14.
Alignment quality for Iteration #24 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #14 (17dec26e): 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00934 for Iteration #25 of Tilt-Series #14.
CCMS(rotations) = 0.44632 for Iteration #25 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #14.
The scaled sum of CCMS values is #0.0136 for iteration 25 of Tilt-Series #14.
Alignment quality for Iteration #25 of Tilt-Series #14 (17dec26e): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)
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 }
map.sampling = 1
window.highpass.diameter = { 0.00107807222914 0.00107807222914 }
window.highpass.apodization = { 0.00215560756972 0.00215560756972 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1830 1894 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 228.651227457
map.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1855 1919 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1830 1894 }
reference.body = 228.651227457
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01901 for Iteration #26 of Tilt-Series #14.
CCMS(rotations) = 0.07436 for Iteration #26 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01099 for iteration 26 of Tilt-Series #14.
Alignment quality for Iteration #26 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00948 for Iteration #27 of Tilt-Series #14.
CCMS(rotations) = 0.32737 for Iteration #27 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #14.
The scaled sum of CCMS values is #0.01129 for iteration 27 of Tilt-Series #14.
Alignment quality for Iteration #27 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00782 for Iteration #28 of Tilt-Series #14.
CCMS(rotations) = 0.196 for Iteration #28 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00783 for iteration 28 of Tilt-Series #14.
Alignment quality for Iteration #28 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #14 (17dec26e): StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00691 for Iteration #29 of Tilt-Series #14.
CCMS(rotations) = 0.16385 for Iteration #29 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00673 for iteration 29 of Tilt-Series #14.
Alignment quality for Iteration #29 of Tilt-Series #14 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00787 for Iteration #30 of Tilt-Series #14.
CCMS(rotations) = 0.19154 for Iteration #30 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00777 for iteration 30 of Tilt-Series #14.
Alignment quality for Iteration #30 of Tilt-Series #14 (17dec26e): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00712 for Iteration #31 of Tilt-Series #14.
CCMS(rotations) = 0.18638 for Iteration #31 of Tilt-Series #14.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00729 for iteration 31 of Tilt-Series #14.
Alignment quality for Iteration #31 of Tilt-Series #14 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #14 (17dec26e): Very 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #32 of Tilt-Series #14.
CCMS(rotations) = 0.17286 for Iteration #32 of Tilt-Series #14.
CCMS(scale) = 0.00145 for Iteration #32 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00506 for iteration 32 of Tilt-Series #14.
Alignment quality for Iteration #32 of Tilt-Series #14 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #14 (17dec26e): Very StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #33 of Tilt-Series #14.
CCMS(rotations) = 0.16835 for Iteration #33 of Tilt-Series #14.
CCMS(scale) = 0.0016 for Iteration #33 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00514 for iteration 33 of Tilt-Series #14.
Alignment quality for Iteration #33 of Tilt-Series #14 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #14 (17dec26e): StableCreating 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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00712 for Iteration #34 of Tilt-Series #14.
CCMS(rotations) = 0.14677 for Iteration #34 of Tilt-Series #14.
CCMS(scale) = 0.00159 for Iteration #34 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00486 for iteration 34 of Tilt-Series #14.
Alignment quality for Iteration #34 of Tilt-Series #14 (17dec26e): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #14 (tiltseries0014_thick350)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00642 for Iteration #35 of Tilt-Series #14.
CCMS(rotations) = 0.18868 for Iteration #35 of Tilt-Series #14.
CCMS(scale) = 0.00185 for Iteration #35 of Tilt-Series #14.
The scaled sum of CCMS values is #0.00527 for iteration 35 of Tilt-Series #14.
Alignment quality for Iteration #35 of Tilt-Series #14 (17dec26e): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #14 (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 #14 (tiltseries0014_thick350)!
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: 2017yr12m27d-02hr33m17s