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/17may19b/protomo_alignments/tiltseries0005_thick200 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4087.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2302 --r1_region_y=2226 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4087.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=2226 --r2_region_x=2302 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2044.0 --defocus_ang_positive=90 --r5_mask_width_x=2277 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4087.0 --r3_highpass_apod_x=2044.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=550 --r2_mask_width_y=531 --r5_region_x=2302 --r5_region_y=2226 --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=6.25 --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=4087.0 --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=2201 --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=2044.0 --runname=tiltseries0005_thick200 --r1_highpass_diameter_x=4087.0 --r2_lowpass_diameter_y=25.0 --map_size_y=463 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --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=2277 --r4_mask_width_y=2201 --logging=true --DefocusTol=200 --filter=median --sessionname=17may19b --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=2044.0 --r1_highpass_apod_x=2044.0 --r2_highpass_apod_x=2044.0 --sampling=8 --starting_tlt_file=MoreManual --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --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=5 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=1088 --r3_mask_width_x=1126 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4087.0 --r4_highpass_diameter_x=4087.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4087.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2044.0 --r5_highpass_apod_x=2044.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4087.0 --defocus_max=0 --r4_region_y=2226 --r4_region_x=2302 --r5_kernel_y=5 --r3_region_x=2302 --r3_region_y=2226 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=200 --expid=4066 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=479 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.83586 --link=False --r2_highpass_diameter_x=4087.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --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=25.0 --dimx=3838 --dimy=3710 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --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=2044.0 --r4_highpass_apod_y=2044.0 --azimuth=true --r1_mask_width_y=253 --r1_mask_width_x=262 --jobtype=protomo

node36
Start time: 2017yr06m21d-12hr48m00s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0005.tlt to series0005.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.68688 Angstroms, Nyquist is 29.37376 Angstroms)
window.lowpass.apodization = { 0.23499008 0.23499008 }
map.sampling = 8
window.highpass.diameter = { 0.00718712013702 0.00718712013702 }
window.highpass.apodization = { 0.0143707240705 0.0143707240705 }
window.mask.apodization = { 10 10 }
align.mask.width = { 262 253 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 19.2581891099
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 287 278 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 262 253 }
reference.body = 19.2581891099
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0608 for Iteration #1 of Tilt-Series #5.
CCMS(rotations) = 1.82343 for Iteration #1 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5.
The scaled sum of CCMS values is #0.06687 for iteration 1 of Tilt-Series #5.
Alignment quality for Iteration #1 of Tilt-Series #5 (17may19b): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...

No Round parameters changed for Iteration #2 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.05713 for Iteration #2 of Tilt-Series #5.
CCMS(rotations) = 1.79389 for Iteration #2 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5.
The scaled sum of CCMS values is #0.06444 for iteration 2 of Tilt-Series #5.
Alignment quality for Iteration #2 of Tilt-Series #5 (17may19b): Bad (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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.06391 for Iteration #3 of Tilt-Series #5.
CCMS(rotations) = 1.61065 for Iteration #3 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5.
The scaled sum of CCMS values is #0.06417 for iteration 3 of Tilt-Series #5.
Alignment quality for Iteration #3 of Tilt-Series #5 (17may19b): Bad (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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.05096 for Iteration #4 of Tilt-Series #5.
CCMS(rotations) = 1.55892 for Iteration #4 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5.
The scaled sum of CCMS values is #0.05666 for iteration 4 of Tilt-Series #5.
Alignment quality for Iteration #4 of Tilt-Series #5 (17may19b): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.03609 for Iteration #5 of Tilt-Series #5.
CCMS(rotations) = 1.5182 for Iteration #5 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5.
The scaled sum of CCMS values is #0.04841 for iteration 5 of Tilt-Series #5.
Alignment quality for Iteration #5 of Tilt-Series #5 (17may19b): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.02415 for Iteration #6 of Tilt-Series #5.
CCMS(rotations) = 1.0996 for Iteration #6 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5.
The scaled sum of CCMS values is #0.03407 for iteration 6 of Tilt-Series #5.
Alignment quality for Iteration #6 of Tilt-Series #5 (17may19b): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01177 for Iteration #7 of Tilt-Series #5.
CCMS(rotations) = 0.53648 for Iteration #7 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01661 for iteration 7 of Tilt-Series #5.
Alignment quality for Iteration #7 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.0118 for Iteration #8 of Tilt-Series #5.
CCMS(rotations) = 0.48433 for Iteration #8 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01559 for iteration 8 of Tilt-Series #5.
Alignment quality for Iteration #8 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01166 for Iteration #9 of Tilt-Series #5.
CCMS(rotations) = 0.4517 for Iteration #9 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01486 for iteration 9 of Tilt-Series #5.
Alignment quality for Iteration #9 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01796 for Iteration #10 of Tilt-Series #5.
CCMS(rotations) = 0.45018 for Iteration #10 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01798 for iteration 10 of Tilt-Series #5.
Alignment quality for Iteration #10 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.34344 Angstroms, Nyquist is 14.68688 Angstroms)
window.lowpass.apodization = { 0.233125079365 0.233125079365 }
map.sampling = 4
window.highpass.diameter = { 0.00359356006851 0.00359356006851 }
window.highpass.apodization = { 0.00718536203523 0.00718536203523 }
window.mask.apodization = { 10 10 }
align.mask.width = { 550 531 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 38.5163782198
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 575 556 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 550 531 }
reference.body = 38.5163782198
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01632 for Iteration #11 of Tilt-Series #5.
CCMS(rotations) = 0.39525 for Iteration #11 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01607 for iteration 11 of Tilt-Series #5.
Alignment quality for Iteration #11 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #5 (17may19b): StableCreating 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00948 for Iteration #12 of Tilt-Series #5.
CCMS(rotations) = 0.43475 for Iteration #12 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01344 for iteration 12 of Tilt-Series #5.
Alignment quality for Iteration #12 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00628 for Iteration #13 of Tilt-Series #5.
CCMS(rotations) = 0.62206 for Iteration #13 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01558 for iteration 13 of Tilt-Series #5.
Alignment quality for Iteration #13 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00556 for Iteration #14 of Tilt-Series #5.
CCMS(rotations) = 0.62134 for Iteration #14 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01521 for iteration 14 of Tilt-Series #5.
Alignment quality for Iteration #14 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00574 for Iteration #15 of Tilt-Series #5.
CCMS(rotations) = 0.59667 for Iteration #15 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0148 for iteration 15 of Tilt-Series #5.
Alignment quality for Iteration #15 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00511 for Iteration #16 of Tilt-Series #5.
CCMS(rotations) = 0.60953 for Iteration #16 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01474 for iteration 16 of Tilt-Series #5.
Alignment quality for Iteration #16 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00572 for Iteration #17 of Tilt-Series #5.
CCMS(rotations) = 0.59166 for Iteration #17 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01469 for iteration 17 of Tilt-Series #5.
Alignment quality for Iteration #17 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00553 for Iteration #18 of Tilt-Series #5.
CCMS(rotations) = 0.61195 for Iteration #18 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5.
The scaled sum of CCMS values is #0.015 for iteration 18 of Tilt-Series #5.
Alignment quality for Iteration #18 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.0062 for Iteration #19 of Tilt-Series #5.
CCMS(rotations) = 0.57986 for Iteration #19 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0147 for iteration 19 of Tilt-Series #5.
Alignment quality for Iteration #19 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00546 for Iteration #20 of Tilt-Series #5.
CCMS(rotations) = 0.59733 for Iteration #20 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01468 for iteration 20 of Tilt-Series #5.
Alignment quality for Iteration #20 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms)
window.lowpass.apodization = { 0.23688516129 0.23688516129 }
map.sampling = 2
window.highpass.diameter = { 0.00179678003425 0.00179678003425 }
window.highpass.apodization = { 0.00359268101761 0.00359268101761 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1126 1088 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 77.0327564397
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1151 1113 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1126 1088 }
reference.body = 77.0327564397
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00829 for Iteration #21 of Tilt-Series #5.
CCMS(rotations) = 0.65506 for Iteration #21 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01725 for iteration 21 of Tilt-Series #5.
Alignment quality for Iteration #21 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00642 for Iteration #22 of Tilt-Series #5.
CCMS(rotations) = 0.62193 for Iteration #22 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01565 for iteration 22 of Tilt-Series #5.
Alignment quality for Iteration #22 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #5 (17may19b): UnstableCreating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...

No Round parameters changed for Iteration #23 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00681 for Iteration #23 of Tilt-Series #5.
CCMS(rotations) = 0.56737 for Iteration #23 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01475 for iteration 23 of Tilt-Series #5.
Alignment quality for Iteration #23 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00727 for Iteration #24 of Tilt-Series #5.
CCMS(rotations) = 0.55112 for Iteration #24 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01466 for iteration 24 of Tilt-Series #5.
Alignment quality for Iteration #24 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00655 for Iteration #25 of Tilt-Series #5.
CCMS(rotations) = 0.5702 for Iteration #25 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01468 for iteration 25 of Tilt-Series #5.
Alignment quality for Iteration #25 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms)
window.lowpass.apodization = { 0.2294825 0.2294825 }
map.sampling = 1
window.highpass.diameter = { 0.000898390017127 0.000898390017127 }
window.highpass.apodization = { 0.00179634050881 0.00179634050881 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2277 2201 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 154.065512879
map.lowpass.diameter = { 0.5874752 0.5874752 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2302 2226 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2277 2201 }
reference.body = 154.065512879
window.lowpass.diameter = { 0.5874752 0.5874752 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01704 for Iteration #26 of Tilt-Series #5.
CCMS(rotations) = 0.83565 for Iteration #26 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02523 for iteration 26 of Tilt-Series #5.
Alignment quality for Iteration #26 of Tilt-Series #5 (17may19b): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00866 for Iteration #27 of Tilt-Series #5.
CCMS(rotations) = 0.76465 for Iteration #27 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01963 for iteration 27 of Tilt-Series #5.
Alignment quality for Iteration #27 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00992 for Iteration #28 of Tilt-Series #5.
CCMS(rotations) = 0.80663 for Iteration #28 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02109 for iteration 28 of Tilt-Series #5.
Alignment quality for Iteration #28 of Tilt-Series #5 (17may19b): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #29 of Tilt-Series #5.
CCMS(rotations) = 0.8267 for Iteration #29 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02067 for iteration 29 of Tilt-Series #5.
Alignment quality for Iteration #29 of Tilt-Series #5 (17may19b): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00735 for Iteration #30 of Tilt-Series #5.
CCMS(rotations) = 0.8498 for Iteration #30 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02067 for iteration 30 of Tilt-Series #5.
Alignment quality for Iteration #30 of Tilt-Series #5 (17may19b): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00689 for Iteration #31 of Tilt-Series #5.
CCMS(rotations) = 0.88348 for Iteration #31 of Tilt-Series #5.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5.
The scaled sum of CCMS values is #0.02111 for iteration 31 of Tilt-Series #5.
Alignment quality for Iteration #31 of Tilt-Series #5 (17may19b): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00742 for Iteration #32 of Tilt-Series #5.
CCMS(rotations) = 0.91457 for Iteration #32 of Tilt-Series #5.
CCMS(scale) = 0.00309 for Iteration #32 of Tilt-Series #5.
The scaled sum of CCMS values is #0.0157 for iteration 32 of Tilt-Series #5.
Alignment quality for Iteration #32 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00853 for Iteration #33 of Tilt-Series #5.
CCMS(rotations) = 0.88596 for Iteration #33 of Tilt-Series #5.
CCMS(scale) = 0.00395 for Iteration #33 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01597 for iteration 33 of Tilt-Series #5.
Alignment quality for Iteration #33 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #5 (17may19b): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...

No Round parameters changed for Iteration #34 of Tilt-Series #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00934 for Iteration #34 of Tilt-Series #5.
CCMS(rotations) = 0.86316 for Iteration #34 of Tilt-Series #5.
CCMS(scale) = 0.00438 for Iteration #34 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01608 for iteration 34 of Tilt-Series #5.
Alignment quality for Iteration #34 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #5 (tiltseries0005_thick200)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01099 for Iteration #35 of Tilt-Series #5.
CCMS(rotations) = 0.80838 for Iteration #35 of Tilt-Series #5.
CCMS(scale) = 0.0039 for Iteration #35 of Tilt-Series #5.
The scaled sum of CCMS values is #0.01574 for iteration 35 of Tilt-Series #5.
Alignment quality for Iteration #35 of Tilt-Series #5 (17may19b): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #5 (17may19b): 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 #5 (tiltseries0005_thick200)!
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: 2017yr06m22d-00hr51m46s