protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-40.0 --corr_mode=mcf --rundir=/gpfs/appion/anoble/17dec26e/protomo_alignments/tiltseries0007_thick400 --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=tiltseries0007_thick400 --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=MoreManual --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=7 --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=400 --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=37.0 --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

node05
Start time: 2017yr12m26d-18hr27m15s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0007.tlt to series0007.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
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 = 36.7045509734
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 = 36.7045509734
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0864 for Iteration #1 of Tilt-Series #7.
CCMS(rotations) = 0.36859 for Iteration #1 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7.
The scaled sum of CCMS values is #0.05057 for iteration 1 of Tilt-Series #7.
Alignment quality for Iteration #1 of Tilt-Series #7 (17dec26e): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 78.787879%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02025 for Iteration #2 of Tilt-Series #7.
CCMS(rotations) = 0.11814 for Iteration #2 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01249 for iteration 2 of Tilt-Series #7.
Alignment quality for Iteration #2 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...

No Round parameters changed for Iteration #3 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01159 for Iteration #3 of Tilt-Series #7.
CCMS(rotations) = 0.2348 for Iteration #3 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01049 for iteration 3 of Tilt-Series #7.
Alignment quality for Iteration #3 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...

No Round parameters changed for Iteration #4 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01225 for Iteration #4 of Tilt-Series #7.
CCMS(rotations) = 0.17529 for Iteration #4 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00963 for iteration 4 of Tilt-Series #7.
Alignment quality for Iteration #4 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01262 for Iteration #5 of Tilt-Series #7.
CCMS(rotations) = 0.2097 for Iteration #5 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0105 for iteration 5 of Tilt-Series #7.
Alignment quality for Iteration #5 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01204 for Iteration #6 of Tilt-Series #7.
CCMS(rotations) = 0.22391 for Iteration #6 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0105 for iteration 6 of Tilt-Series #7.
Alignment quality for Iteration #6 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01237 for Iteration #7 of Tilt-Series #7.
CCMS(rotations) = 0.22098 for Iteration #7 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0106 for iteration 7 of Tilt-Series #7.
Alignment quality for Iteration #7 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #7 (17dec26e): StableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...

No Round parameters changed for Iteration #8 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01133 for Iteration #8 of Tilt-Series #7.
CCMS(rotations) = 0.23736 for Iteration #8 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01041 for iteration 8 of Tilt-Series #7.
Alignment quality for Iteration #8 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01187 for Iteration #9 of Tilt-Series #7.
CCMS(rotations) = 0.20747 for Iteration #9 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01009 for iteration 9 of Tilt-Series #7.
Alignment quality for Iteration #9 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #7 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...

No Round parameters changed for Iteration #10 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01069 for Iteration #10 of Tilt-Series #7.
CCMS(rotations) = 0.24785 for Iteration #10 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0103 for iteration 10 of Tilt-Series #7.
Alignment quality for Iteration #10 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #7 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
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 = 73.4091019469
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 = 73.4091019469
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00892 for Iteration #11 of Tilt-Series #7.
CCMS(rotations) = 0.3744 for Iteration #11 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7.
The scaled sum of CCMS values is #0.01195 for iteration 11 of Tilt-Series #7.
Alignment quality for Iteration #11 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00694 for Iteration #12 of Tilt-Series #7.
CCMS(rotations) = 0.26327 for Iteration #12 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00873 for iteration 12 of Tilt-Series #7.
Alignment quality for Iteration #12 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #7 (17dec26e): Very StableCreating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...

No Round parameters changed for Iteration #13 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00697 for Iteration #13 of Tilt-Series #7.
CCMS(rotations) = 0.24026 for Iteration #13 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00829 for iteration 13 of Tilt-Series #7.
Alignment quality for Iteration #13 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #7 (17dec26e): StableCreating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...

No Round parameters changed for Iteration #14 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00747 for Iteration #14 of Tilt-Series #7.
CCMS(rotations) = 0.28326 for Iteration #14 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0094 for iteration 14 of Tilt-Series #7.
Alignment quality for Iteration #14 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00686 for Iteration #15 of Tilt-Series #7.
CCMS(rotations) = 0.2679 for Iteration #15 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00879 for iteration 15 of Tilt-Series #7.
Alignment quality for Iteration #15 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00723 for Iteration #16 of Tilt-Series #7.
CCMS(rotations) = 0.30037 for Iteration #16 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00962 for iteration 16 of Tilt-Series #7.
Alignment quality for Iteration #16 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00674 for Iteration #17 of Tilt-Series #7.
CCMS(rotations) = 0.25019 for Iteration #17 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00838 for iteration 17 of Tilt-Series #7.
Alignment quality for Iteration #17 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00726 for Iteration #18 of Tilt-Series #7.
CCMS(rotations) = 0.28351 for Iteration #18 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0093 for iteration 18 of Tilt-Series #7.
Alignment quality for Iteration #18 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00685 for Iteration #19 of Tilt-Series #7.
CCMS(rotations) = 0.26346 for Iteration #19 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00869 for iteration 19 of Tilt-Series #7.
Alignment quality for Iteration #19 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00709 for Iteration #20 of Tilt-Series #7.
CCMS(rotations) = 0.28528 for Iteration #20 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00925 for iteration 20 of Tilt-Series #7.
Alignment quality for Iteration #20 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)
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 = 146.818203894
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 = 146.818203894
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00756 for Iteration #21 of Tilt-Series #7.
CCMS(rotations) = 0.27458 for Iteration #21 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00927 for iteration 21 of Tilt-Series #7.
Alignment quality for Iteration #21 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00733 for Iteration #22 of Tilt-Series #7.
CCMS(rotations) = 0.22489 for Iteration #22 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00816 for iteration 22 of Tilt-Series #7.
Alignment quality for Iteration #22 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00719 for Iteration #23 of Tilt-Series #7.
CCMS(rotations) = 0.23248 for Iteration #23 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00825 for iteration 23 of Tilt-Series #7.
Alignment quality for Iteration #23 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00708 for Iteration #24 of Tilt-Series #7.
CCMS(rotations) = 0.22568 for Iteration #24 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00805 for iteration 24 of Tilt-Series #7.
Alignment quality for Iteration #24 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00725 for Iteration #25 of Tilt-Series #7.
CCMS(rotations) = 0.22346 for Iteration #25 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7.
The scaled sum of CCMS values is #0.0081 for iteration 25 of Tilt-Series #7.
Alignment quality for Iteration #25 of Tilt-Series #7 (17dec26e): Very Good (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)
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 = 293.636407788
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 = 293.636407788
window.lowpass.diameter = { 0.500979166667 0.500979166667 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00869 for Iteration #26 of Tilt-Series #7.
CCMS(rotations) = 0.12924 for Iteration #26 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00693 for iteration 26 of Tilt-Series #7.
Alignment quality for Iteration #26 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00673 for Iteration #27 of Tilt-Series #7.
CCMS(rotations) = 0.15429 for Iteration #27 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00645 for iteration 27 of Tilt-Series #7.
Alignment quality for Iteration #27 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #7 (17dec26e): StableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...

No Round parameters changed for Iteration #28 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.0066 for Iteration #28 of Tilt-Series #7.
CCMS(rotations) = 0.15697 for Iteration #28 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00644 for iteration 28 of Tilt-Series #7.
Alignment quality for Iteration #28 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #7 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...

No Round parameters changed for Iteration #29 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00769 for Iteration #29 of Tilt-Series #7.
CCMS(rotations) = 0.16569 for Iteration #29 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00716 for iteration 29 of Tilt-Series #7.
Alignment quality for Iteration #29 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00668 for Iteration #30 of Tilt-Series #7.
CCMS(rotations) = 0.17853 for Iteration #30 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00691 for iteration 30 of Tilt-Series #7.
Alignment quality for Iteration #30 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00807 for Iteration #31 of Tilt-Series #7.
CCMS(rotations) = 0.15165 for Iteration #31 of Tilt-Series #7.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00707 for iteration 31 of Tilt-Series #7.
Alignment quality for Iteration #31 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00503 for Iteration #32 of Tilt-Series #7.
CCMS(rotations) = 0.18895 for Iteration #32 of Tilt-Series #7.
CCMS(scale) = 0.00367 for Iteration #32 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00542 for iteration 32 of Tilt-Series #7.
Alignment quality for Iteration #32 of Tilt-Series #7 (17dec26e): Excellent (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #7 (17dec26e): 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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00401 for Iteration #33 of Tilt-Series #7.
CCMS(rotations) = 0.16363 for Iteration #33 of Tilt-Series #7.
CCMS(scale) = 0.00347 for Iteration #33 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00467 for iteration 33 of Tilt-Series #7.
Alignment quality for Iteration #33 of Tilt-Series #7 (17dec26e): Perfection! (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #7 (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 #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.0038 for Iteration #34 of Tilt-Series #7.
CCMS(rotations) = 0.14622 for Iteration #34 of Tilt-Series #7.
CCMS(scale) = 0.0035 for Iteration #34 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00439 for iteration 34 of Tilt-Series #7.
Alignment quality for Iteration #34 of Tilt-Series #7 (17dec26e): Perfection! (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #7 (17dec26e): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #7 (tiltseries0007_thick400)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #7 (tiltseries0007_thick400)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0052 for Iteration #35 of Tilt-Series #7.
CCMS(rotations) = 0.15123 for Iteration #35 of Tilt-Series #7.
CCMS(scale) = 0.00353 for Iteration #35 of Tilt-Series #7.
The scaled sum of CCMS values is #0.00493 for iteration 35 of Tilt-Series #7.
Alignment quality for Iteration #35 of Tilt-Series #7 (17dec26e): Perfection! (confidence: 78.787879%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #7 (17dec26e): Very StableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
Finished Refinement for Tilt-Series #7 (tiltseries0007_thick400)!
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-01hr23m40s