protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/18mar12b/protomo_alignments/tiltseries0003_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3076.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2482 --r1_region_y=2311 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3076.0 --r4_lowpass_apod_y=13.0 --r4_lowpass_apod_x=13.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=27.0 --r3_lowpass_apod_y=27.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0003_thick50 --r2_region_y=2311 --r2_region_x=2482 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1538.0 --defocus_ang_positive=90 --r5_mask_width_x=2457 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3076.0 --r3_highpass_apod_x=1538.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=595 --r2_mask_width_y=552 --r5_region_x=2482 --r5_region_y=2311 --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=5.32 --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=3076.0 --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=2286 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1538.0 --r3_iters=5 --r1_highpass_diameter_x=3076.0 --r2_lowpass_diameter_y=21.28 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=2.66 --r5_lowpass_diameter_x=2.66 --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=2457 --r4_mask_width_y=2286 --r5_highpass_apod_y=1538.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar12b --exclude_images=999999 --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=1538.0 --r1_highpass_apod_x=1538.0 --r2_highpass_apod_x=1538.0 --sampling=8 --starting_tlt_file=Imod_Coarse --r5_lowpass_apod_x=7.0 --r5_lowpass_apod_y=7.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=42.56 --r1_lowpass_diameter_x=42.56 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=3 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1130 --r3_mask_width_x=1216 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3076.0 --r4_highpass_diameter_x=3076.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=106.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3076.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1538.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3076.0 --defocus_max=0 --r4_region_y=2311 --r4_region_x=2482 --r5_kernel_y=5 --r3_region_x=2482 --r3_region_y=2311 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=6268 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=340 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=10.64 --r3_lowpass_diameter_x=10.64 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.331 --link=False --r2_highpass_diameter_x=3076.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=53.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=53.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=21.28 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=106.0 --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=1538.0 --r4_highpass_apod_y=1538.0 --azimuth=true --r1_mask_width_y=263 --r1_mask_width_x=285 --jobtype=protomo --from_multirefine=True

node03
Start time: 2018yr03m12d-11hr39m36s
Description: 
Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 42.56 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 10.648 Angstroms, Nyquist is 21.296 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 47.125e0
map.sampling = 8
window.highpass.diameter = { 0.00692327698309 0.00692327698309 }
window.highpass.apodization = { 0.0138465539662 0.0138465539662 }
window.mask.apodization = { 10 10 }
align.mask.width = { 285 263 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 6.64086328748
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 310 288 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 285 263 }
reference.body = 6.64086328748
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.06254 for Iteration #1 of Tilt-Series #3.
CCMS(rotations) = 0.20898 for Iteration #1 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3.
The scaled sum of CCMS values is #0.03545 for iteration 1 of Tilt-Series #3.
Alignment quality for Iteration #1 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.00738 for Iteration #2 of Tilt-Series #3.
CCMS(rotations) = 0.23104 for Iteration #2 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00831 for iteration 2 of Tilt-Series #3.
Alignment quality for Iteration #2 of Tilt-Series #3 (18mar12b): Very Good (confidence: 96.774194%)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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.00402 for Iteration #3 of Tilt-Series #3.
CCMS(rotations) = 0.19569 for Iteration #3 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00592 for iteration 3 of Tilt-Series #3.
Alignment quality for Iteration #3 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.00392 for Iteration #4 of Tilt-Series #3.
CCMS(rotations) = 0.1996 for Iteration #4 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00595 for iteration 4 of Tilt-Series #3.
Alignment quality for Iteration #4 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #3 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...

No Round parameters changed for Iteration #5 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00409 for Iteration #5 of Tilt-Series #3.
CCMS(rotations) = 0.19383 for Iteration #5 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00592 for iteration 5 of Tilt-Series #3.
Alignment quality for Iteration #5 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #3 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...

No Round parameters changed for Iteration #6 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.00362 for Iteration #6 of Tilt-Series #3.
CCMS(rotations) = 0.19034 for Iteration #6 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00562 for iteration 6 of Tilt-Series #3.
Alignment quality for Iteration #6 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00443 for Iteration #7 of Tilt-Series #3.
CCMS(rotations) = 0.19174 for Iteration #7 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00605 for iteration 7 of Tilt-Series #3.
Alignment quality for Iteration #7 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00372 for Iteration #8 of Tilt-Series #3.
CCMS(rotations) = 0.18214 for Iteration #8 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00551 for iteration 8 of Tilt-Series #3.
Alignment quality for Iteration #8 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #3 (18mar12b): StableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...

No Round parameters changed for Iteration #9 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00446 for Iteration #9 of Tilt-Series #3.
CCMS(rotations) = 0.19574 for Iteration #9 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00615 for iteration 9 of Tilt-Series #3.
Alignment quality for Iteration #9 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00367 for Iteration #10 of Tilt-Series #3.
CCMS(rotations) = 0.17868 for Iteration #10 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00541 for iteration 10 of Tilt-Series #3.
Alignment quality for Iteration #10 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #3 (18mar12b): StableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...

Beginning Refinement Iteration #11, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
lowpass = 21.28 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 5.324 Angstroms, Nyquist is 10.648 Angstroms)
window.lowpass.apodization = { 0.200905660377 0.200905660377 }
align.translimit = 94.25e0
map.sampling = 4
window.highpass.diameter = { 0.00346163849155 0.00346163849155 }
window.highpass.apodization = { 0.00692327698309 0.00692327698309 }
window.mask.apodization = { 10 10 }
align.mask.width = { 595 552 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 13.281726575
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 620 577 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 595 552 }
reference.body = 13.281726575
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00344 for Iteration #11 of Tilt-Series #3.
CCMS(rotations) = 0.18489 for Iteration #11 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00542 for iteration 11 of Tilt-Series #3.
Alignment quality for Iteration #11 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #3 (18mar12b): Rock Solid!Creating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00318 for Iteration #12 of Tilt-Series #3.
CCMS(rotations) = 0.17478 for Iteration #12 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00508 for iteration 12 of Tilt-Series #3.
Alignment quality for Iteration #12 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #3 (18mar12b): Rock Solid!Creating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00297 for Iteration #13 of Tilt-Series #3.
CCMS(rotations) = 0.1842 for Iteration #13 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00517 for iteration 13 of Tilt-Series #3.
Alignment quality for Iteration #13 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00305 for Iteration #14 of Tilt-Series #3.
CCMS(rotations) = 0.17871 for Iteration #14 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0051 for iteration 14 of Tilt-Series #3.
Alignment quality for Iteration #14 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00316 for Iteration #15 of Tilt-Series #3.
CCMS(rotations) = 0.17314 for Iteration #15 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00504 for iteration 15 of Tilt-Series #3.
Alignment quality for Iteration #15 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0032 for Iteration #16 of Tilt-Series #3.
CCMS(rotations) = 0.1861 for Iteration #16 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00532 for iteration 16 of Tilt-Series #3.
Alignment quality for Iteration #16 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00313 for Iteration #17 of Tilt-Series #3.
CCMS(rotations) = 0.17247 for Iteration #17 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00502 for iteration 17 of Tilt-Series #3.
Alignment quality for Iteration #17 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00307 for Iteration #18 of Tilt-Series #3.
CCMS(rotations) = 0.17894 for Iteration #18 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00511 for iteration 18 of Tilt-Series #3.
Alignment quality for Iteration #18 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00307 for Iteration #19 of Tilt-Series #3.
CCMS(rotations) = 0.17303 for Iteration #19 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3.
The scaled sum of CCMS values is #0.005 for iteration 19 of Tilt-Series #3.
Alignment quality for Iteration #19 of Tilt-Series #3 (18mar12b): Perfection! (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00311 for Iteration #20 of Tilt-Series #3.
CCMS(rotations) = 0.18091 for Iteration #20 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00517 for iteration 20 of Tilt-Series #3.
Alignment quality for Iteration #20 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)
lowpass = 10.64 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 2.662 Angstroms, Nyquist is 5.324 Angstroms)
window.lowpass.apodization = { 0.197185185185 0.197185185185 }
align.translimit = 188.5e0
map.sampling = 2
window.highpass.diameter = { 0.00173081924577 0.00173081924577 }
window.highpass.apodization = { 0.00346163849155 0.00346163849155 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1216 1130 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 26.5634531499
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1241 1155 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1216 1130 }
reference.body = 26.5634531499
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00374 for Iteration #21 of Tilt-Series #3.
CCMS(rotations) = 0.21056 for Iteration #21 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00608 for iteration 21 of Tilt-Series #3.
Alignment quality for Iteration #21 of Tilt-Series #3 (18mar12b): Excellent (confidence: 96.774194%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00621 for Iteration #22 of Tilt-Series #3.
CCMS(rotations) = 0.21394 for Iteration #22 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00739 for iteration 22 of Tilt-Series #3.
Alignment quality for Iteration #22 of Tilt-Series #3 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00661 for Iteration #23 of Tilt-Series #3.
CCMS(rotations) = 0.30587 for Iteration #23 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00942 for iteration 23 of Tilt-Series #3.
Alignment quality for Iteration #23 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #3 (18mar12b): Very StableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00612 for Iteration #24 of Tilt-Series #3.
CCMS(rotations) = 0.32296 for Iteration #24 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00952 for iteration 24 of Tilt-Series #3.
Alignment quality for Iteration #24 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #3 (18mar12b): UnstableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...

No Round parameters changed for Iteration #25 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.0055 for Iteration #25 of Tilt-Series #3.
CCMS(rotations) = 0.31485 for Iteration #25 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00905 for iteration 25 of Tilt-Series #3.
Alignment quality for Iteration #25 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)
lowpass = 5.32 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.331 Angstroms, Nyquist is 2.662 Angstroms)
window.lowpass.apodization = { 0.204769230769 0.204769230769 }
align.translimit = 377.0e0
map.sampling = 1
window.highpass.diameter = { 0.000865409622887 0.000865409622887 }
window.highpass.apodization = { 0.00173081924577 0.00173081924577 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2457 2286 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 53.1269062999
map.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2482 2311 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2457 2286 }
reference.body = 53.1269062999
window.lowpass.diameter = { 0.50037593985 0.50037593985 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00838 for Iteration #26 of Tilt-Series #3.
CCMS(rotations) = 0.2285 for Iteration #26 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00876 for iteration 26 of Tilt-Series #3.
Alignment quality for Iteration #26 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00815 for Iteration #27 of Tilt-Series #3.
CCMS(rotations) = 0.27595 for Iteration #27 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00959 for iteration 27 of Tilt-Series #3.
Alignment quality for Iteration #27 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #3 (18mar12b): Rock Solid!Creating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00743 for Iteration #28 of Tilt-Series #3.
CCMS(rotations) = 0.30131 for Iteration #28 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00974 for iteration 28 of Tilt-Series #3.
Alignment quality for Iteration #28 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00727 for Iteration #29 of Tilt-Series #3.
CCMS(rotations) = 0.29742 for Iteration #29 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00958 for iteration 29 of Tilt-Series #3.
Alignment quality for Iteration #29 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #3 (18mar12b): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...

No Round parameters changed for Iteration #30 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00783 for Iteration #30 of Tilt-Series #3.
CCMS(rotations) = 0.26601 for Iteration #30 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00924 for iteration 30 of Tilt-Series #3.
Alignment quality for Iteration #30 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #3 (18mar12b): Very StableCreating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00776 for Iteration #31 of Tilt-Series #3.
CCMS(rotations) = 0.27819 for Iteration #31 of Tilt-Series #3.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00944 for iteration 31 of Tilt-Series #3.
Alignment quality for Iteration #31 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #3 (18mar12b): UnstableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...

No Round parameters changed for Iteration #32 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.0072 for Iteration #32 of Tilt-Series #3.
CCMS(rotations) = 0.27832 for Iteration #32 of Tilt-Series #3.
CCMS(scale) = 0.00229 for Iteration #32 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00687 for iteration 32 of Tilt-Series #3.
Alignment quality for Iteration #32 of Tilt-Series #3 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #3 (18mar12b): Rock Solid!Creating 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00815 for Iteration #33 of Tilt-Series #3.
CCMS(rotations) = 0.31245 for Iteration #33 of Tilt-Series #3.
CCMS(scale) = 0.00258 for Iteration #33 of Tilt-Series #3.
The scaled sum of CCMS values is #0.00774 for iteration 33 of Tilt-Series #3.
Alignment quality for Iteration #33 of Tilt-Series #3 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00638 for Iteration #34 of Tilt-Series #3.
CCMS(rotations) = 0.29653 for Iteration #34 of Tilt-Series #3.
CCMS(scale) = 0.00397 for Iteration #34 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0074 for iteration 34 of Tilt-Series #3.
Alignment quality for Iteration #34 of Tilt-Series #3 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #3 (18mar12b): StableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...

No Round parameters changed for Iteration #35 of Tilt-Series #3 (tiltseries0003_thick50)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #3 (tiltseries0003_thick50)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00768 for Iteration #35 of Tilt-Series #3.
CCMS(rotations) = 0.23761 for Iteration #35 of Tilt-Series #3.
CCMS(scale) = 0.005 for Iteration #35 of Tilt-Series #3.
The scaled sum of CCMS values is #0.0074 for iteration 35 of Tilt-Series #3.
Alignment quality for Iteration #35 of Tilt-Series #3 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #3 (18mar12b): 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 #3 (tiltseries0003_thick50)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file.
If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2018yr03m13d-02hr52m23s