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/jbrasch/17jul12a/protomo_alignments/tiltseries0012_thick400 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4905.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2782 --r1_region_y=2878 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4905.0 --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=2878 --r2_region_x=2782 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2453.0 --defocus_ang_positive=90 --r5_mask_width_x=2757 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4905.0 --r3_highpass_apod_x=2453.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=670 --r2_mask_width_y=694 --r5_region_x=2782 --r5_region_y=2878 --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=True --r1_highpass_diameter_y=4905.0 --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=2853 --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=2453.0 --runname=tiltseries0012_thick400 --r1_highpass_diameter_x=4905.0 --r2_lowpass_diameter_y=25.0 --map_size_y=479 --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=2757 --r4_mask_width_y=2853 --logging=true --DefocusTol=200 --filter=median --sessionname=17jul12a --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=2453.0 --r1_highpass_apod_x=2453.0 --r2_highpass_apod_x=2453.0 --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=12 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=1414 --r3_mask_width_x=1366 --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=4905.0 --r4_highpass_diameter_x=4905.0 --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=4905.0 --tilt_azimuth=5.3 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2453.0 --r5_highpass_apod_x=2453.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4905.0 --defocus_max=0 --r4_region_y=2878 --r4_region_x=2782 --r5_kernel_y=5 --r3_region_x=2782 --r3_region_y=2878 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=400 --expid=4381 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --max_correction=999999 --map_size_x=463 --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=1.76302 --link=False --r2_highpass_diameter_x=4905.0 --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=3710 --dimy=3838 --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=2.0 --tilt_clip=true --r4_highpass_apod_x=2453.0 --r4_highpass_apod_y=2453.0 --azimuth=true --r1_mask_width_y=334 --r1_mask_width_x=322 --jobtype=protomo

node30
Start time: 2017yr07m24d-15hr48m22s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0012.tlt to series0012.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms)
window.lowpass.apodization = { 0.22566656 0.22566656 }
map.sampling = 8
window.highpass.diameter = { 0.00575093170234 0.00575093170234 }
window.highpass.apodization = { 0.0114995189564 0.0114995189564 }
window.mask.apodization = { 10 10 }
align.mask.width = { 322 334 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 40.1049007379
map.lowpass.diameter = { 0.5641664 0.5641664 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 347 359 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 322 334 }
reference.body = 40.1049007379
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.05351 for Iteration #1 of Tilt-Series #12.
CCMS(rotations) = 2.32061 for Iteration #1 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #12.
The scaled sum of CCMS values is #0.07317 for iteration 1 of Tilt-Series #12.
Alignment quality for Iteration #1 of Tilt-Series #12 (17jul12a): 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...
The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.951000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04444 for Iteration #2 of Tilt-Series #12.
CCMS(rotations) = 1.64386 for Iteration #2 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #12.
The scaled sum of CCMS values is #0.0551 for iteration 2 of Tilt-Series #12.
Alignment quality for Iteration #2 of Tilt-Series #12 (17jul12a): 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...
The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.211000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.05055 for Iteration #3 of Tilt-Series #12.
CCMS(rotations) = 1.34979 for Iteration #3 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #12.
The scaled sum of CCMS values is #0.05227 for iteration 3 of Tilt-Series #12.
Alignment quality for Iteration #3 of Tilt-Series #12 (17jul12a): 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...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.457000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.04076 for Iteration #4 of Tilt-Series #12.
CCMS(rotations) = 1.27563 for Iteration #4 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #12.
The scaled sum of CCMS values is #0.04589 for iteration 4 of Tilt-Series #12.
Alignment quality for Iteration #4 of Tilt-Series #12 (17jul12a): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #4 in Parallel...
Creating Refinement tilt-series video for iteration #4...
Generating Refinement reconstruction for iteration #4...
The tilt azimuth after iteration #4 deviated from the initial tilt azimuth by 0.725000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.03568 for Iteration #5 of Tilt-Series #12.
CCMS(rotations) = 0.99304 for Iteration #5 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #12.
The scaled sum of CCMS values is #0.0377 for iteration 5 of Tilt-Series #12.
Alignment quality for Iteration #5 of Tilt-Series #12 (17jul12a): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #5 in Parallel...
Creating Refinement tilt-series video for iteration #5...
Generating Refinement reconstruction for iteration #5...
The tilt azimuth after iteration #5 deviated from the initial tilt azimuth by 0.246000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01776 for Iteration #6 of Tilt-Series #12.
CCMS(rotations) = 0.59332 for Iteration #6 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #12.
The scaled sum of CCMS values is #0.02075 for iteration 6 of Tilt-Series #12.
Alignment quality for Iteration #6 of Tilt-Series #12 (17jul12a): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...
The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.344000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01516 for Iteration #7 of Tilt-Series #12.
CCMS(rotations) = 0.52712 for Iteration #7 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01812 for iteration 7 of Tilt-Series #12.
Alignment quality for Iteration #7 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...
The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 0.001000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01135 for Iteration #8 of Tilt-Series #12.
CCMS(rotations) = 0.37072 for Iteration #8 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01309 for iteration 8 of Tilt-Series #12.
Alignment quality for Iteration #8 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #8 in Parallel...
Creating Refinement tilt-series video for iteration #8...
Generating Refinement reconstruction for iteration #8...
The tilt azimuth after iteration #8 deviated from the initial tilt azimuth by 0.727000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00986 for Iteration #9 of Tilt-Series #12.
CCMS(rotations) = 0.39059 for Iteration #9 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01274 for iteration 9 of Tilt-Series #12.
Alignment quality for Iteration #9 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #9 in Parallel...
Creating Refinement tilt-series video for iteration #9...
Generating Refinement reconstruction for iteration #9...
The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.742000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01034 for Iteration #10 of Tilt-Series #12.
CCMS(rotations) = 0.39122 for Iteration #10 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #12.
The scaled sum of CCMS values is #0.013 for iteration 10 of Tilt-Series #12.
Alignment quality for Iteration #10 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #10 in Parallel...
Creating Refinement tilt-series video for iteration #10...
Generating Refinement reconstruction for iteration #10...
The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 0.574000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms)
window.lowpass.apodization = { 0.223875555556 0.223875555556 }
map.sampling = 4
window.highpass.diameter = { 0.00287546585117 0.00287546585117 }
window.highpass.apodization = { 0.00574975947819 0.00574975947819 }
window.mask.apodization = { 10 10 }
align.mask.width = { 670 694 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 80.2098014758
map.lowpass.diameter = { 0.5641664 0.5641664 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 695 719 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 670 694 }
reference.body = 80.2098014758
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01319 for Iteration #11 of Tilt-Series #12.
CCMS(rotations) = 0.40895 for Iteration #11 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01477 for iteration 11 of Tilt-Series #12.
Alignment quality for Iteration #11 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...
The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 0.096000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01214 for Iteration #12 of Tilt-Series #12.
CCMS(rotations) = 0.29191 for Iteration #12 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01191 for iteration 12 of Tilt-Series #12.
Alignment quality for Iteration #12 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #12 (17jul12a): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...
The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 0.064000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01237 for Iteration #13 of Tilt-Series #12.
CCMS(rotations) = 0.23775 for Iteration #13 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01094 for iteration 13 of Tilt-Series #12.
Alignment quality for Iteration #13 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #12 (17jul12a): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel...
Creating Refinement tilt-series video for iteration #13...
Generating Refinement reconstruction for iteration #13...
The tilt azimuth after iteration #13 deviated from the initial tilt azimuth by 0.181000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.0131 for Iteration #14 of Tilt-Series #12.
CCMS(rotations) = 0.25048 for Iteration #14 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01156 for iteration 14 of Tilt-Series #12.
Alignment quality for Iteration #14 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...
The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 0.122000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01267 for Iteration #15 of Tilt-Series #12.
CCMS(rotations) = 0.24001 for Iteration #15 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01114 for iteration 15 of Tilt-Series #12.
Alignment quality for Iteration #15 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #15 in Parallel...
Creating Refinement tilt-series video for iteration #15...
Generating Refinement reconstruction for iteration #15...
The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 0.214000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01248 for Iteration #16 of Tilt-Series #12.
CCMS(rotations) = 0.27216 for Iteration #16 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01168 for iteration 16 of Tilt-Series #12.
Alignment quality for Iteration #16 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...
The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.080000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01207 for Iteration #17 of Tilt-Series #12.
CCMS(rotations) = 0.2252 for Iteration #17 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01054 for iteration 17 of Tilt-Series #12.
Alignment quality for Iteration #17 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #17 in Parallel...
Creating Refinement tilt-series video for iteration #17...
Generating Refinement reconstruction for iteration #17...
The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 0.166000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01179 for Iteration #18 of Tilt-Series #12.
CCMS(rotations) = 0.25226 for Iteration #18 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01094 for iteration 18 of Tilt-Series #12.
Alignment quality for Iteration #18 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #12 (17jul12a): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...
The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 0.017000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01137 for Iteration #19 of Tilt-Series #12.
CCMS(rotations) = 0.21224 for Iteration #19 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00993 for iteration 19 of Tilt-Series #12.
Alignment quality for Iteration #19 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...
The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.277000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01361 for Iteration #20 of Tilt-Series #12.
CCMS(rotations) = 0.26962 for Iteration #20 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #12.
The scaled sum of CCMS values is #0.0122 for iteration 20 of Tilt-Series #12.
Alignment quality for Iteration #20 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...
The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 0.155000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #12 (tiltseries0012_thick400)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms)
window.lowpass.apodization = { 0.227486451613 0.227486451613 }
map.sampling = 2
window.highpass.diameter = { 0.00143773292559 0.00143773292559 }
window.highpass.apodization = { 0.00287487973909 0.00287487973909 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1366 1414 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 160.419602952
map.lowpass.diameter = { 0.5641664 0.5641664 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1391 1439 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1366 1414 }
reference.body = 160.419602952
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01281 for Iteration #21 of Tilt-Series #12.
CCMS(rotations) = 0.22447 for Iteration #21 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01089 for iteration 21 of Tilt-Series #12.
Alignment quality for Iteration #21 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #21 in Parallel...
Creating Refinement tilt-series video for iteration #21...
Generating Refinement reconstruction for iteration #21...
The tilt azimuth after iteration #21 deviated from the initial tilt azimuth by 0.048000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01182 for Iteration #22 of Tilt-Series #12.
CCMS(rotations) = 0.31979 for Iteration #22 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01231 for iteration 22 of Tilt-Series #12.
Alignment quality for Iteration #22 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #12 (17jul12a): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel...
Creating Refinement tilt-series video for iteration #22...
Generating Refinement reconstruction for iteration #22...
The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 0.281000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01305 for Iteration #23 of Tilt-Series #12.
CCMS(rotations) = 0.27625 for Iteration #23 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01205 for iteration 23 of Tilt-Series #12.
Alignment quality for Iteration #23 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #23 in Parallel...
Creating Refinement tilt-series video for iteration #23...
Generating Refinement reconstruction for iteration #23...
The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 0.253000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01098 for Iteration #24 of Tilt-Series #12.
CCMS(rotations) = 0.27377 for Iteration #24 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01097 for iteration 24 of Tilt-Series #12.
Alignment quality for Iteration #24 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...
The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.334000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01309 for Iteration #25 of Tilt-Series #12.
CCMS(rotations) = 0.27034 for Iteration #25 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01195 for iteration 25 of Tilt-Series #12.
Alignment quality for Iteration #25 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #25 in Parallel...
Creating Refinement tilt-series video for iteration #25...
Generating Refinement reconstruction for iteration #25...
The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 0.428000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms)
window.lowpass.apodization = { 0.2203775 0.2203775 }
map.sampling = 1
window.highpass.diameter = { 0.000718866462793 0.000718866462793 }
window.highpass.apodization = { 0.00143743986955 0.00143743986955 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2757 2853 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 320.839205903
map.lowpass.diameter = { 0.5641664 0.5641664 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2782 2878 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2757 2853 }
reference.body = 320.839205903
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01472 for Iteration #26 of Tilt-Series #12.
CCMS(rotations) = 0.36931 for Iteration #26 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01475 for iteration 26 of Tilt-Series #12.
Alignment quality for Iteration #26 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...
The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 0.519000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01225 for Iteration #27 of Tilt-Series #12.
CCMS(rotations) = 0.27481 for Iteration #27 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01162 for iteration 27 of Tilt-Series #12.
Alignment quality for Iteration #27 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #27 in Parallel...
Creating Refinement tilt-series video for iteration #27...
Generating Refinement reconstruction for iteration #27...
The tilt azimuth after iteration #27 deviated from the initial tilt azimuth by 0.453000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01591 for Iteration #28 of Tilt-Series #12.
CCMS(rotations) = 0.3261 for Iteration #28 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01448 for iteration 28 of Tilt-Series #12.
Alignment quality for Iteration #28 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #12 (17jul12a): Very StableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...
The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 0.454000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01437 for Iteration #29 of Tilt-Series #12.
CCMS(rotations) = 0.23721 for Iteration #29 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01193 for iteration 29 of Tilt-Series #12.
Alignment quality for Iteration #29 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #29 in Parallel...
Creating Refinement tilt-series video for iteration #29...
Generating Refinement reconstruction for iteration #29...
The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 0.515000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01154 for Iteration #30 of Tilt-Series #12.
CCMS(rotations) = 0.32529 for Iteration #30 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01228 for iteration 30 of Tilt-Series #12.
Alignment quality for Iteration #30 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #30 in Parallel...
Creating Refinement tilt-series video for iteration #30...
Generating Refinement reconstruction for iteration #30...
The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 0.019000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0111 for Iteration #31 of Tilt-Series #12.
CCMS(rotations) = 0.23952 for Iteration #31 of Tilt-Series #12.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01034 for iteration 31 of Tilt-Series #12.
Alignment quality for Iteration #31 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #12 (17jul12a): StableCreating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...
The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 0.103000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01202 for Iteration #32 of Tilt-Series #12.
CCMS(rotations) = 0.26859 for Iteration #32 of Tilt-Series #12.
CCMS(scale) = 0.00347 for Iteration #32 of Tilt-Series #12.
The scaled sum of CCMS values is #0.00874 for iteration 32 of Tilt-Series #12.
Alignment quality for Iteration #32 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #32 in Parallel...
Creating Refinement tilt-series video for iteration #32...
Generating Refinement reconstruction for iteration #32...
The tilt azimuth after iteration #32 deviated from the initial tilt azimuth by 0.669000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01485 for Iteration #33 of Tilt-Series #12.
CCMS(rotations) = 0.28862 for Iteration #33 of Tilt-Series #12.
CCMS(scale) = 0.00472 for Iteration #33 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01037 for iteration 33 of Tilt-Series #12.
Alignment quality for Iteration #33 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #33 in Parallel...
Creating Refinement tilt-series video for iteration #33...
Generating Refinement reconstruction for iteration #33...
The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 0.798000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.0159 for Iteration #34 of Tilt-Series #12.
CCMS(rotations) = 0.23895 for Iteration #34 of Tilt-Series #12.
CCMS(scale) = 0.0059 for Iteration #34 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01045 for iteration 34 of Tilt-Series #12.
Alignment quality for Iteration #34 of Tilt-Series #12 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...
The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 0.491000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #12 (tiltseries0012_thick400)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #12 (tiltseries0012_thick400)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.02193 for Iteration #35 of Tilt-Series #12.
CCMS(rotations) = 0.33218 for Iteration #35 of Tilt-Series #12.
CCMS(scale) = 0.00569 for Iteration #35 of Tilt-Series #12.
The scaled sum of CCMS values is #0.01363 for iteration 35 of Tilt-Series #12.
Alignment quality for Iteration #35 of Tilt-Series #12 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #12 (17jul12a): UnstableCreating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.354000, which is less than the maximum allowed deviation of 2.000000.Finished Refinement for Tilt-Series #12 (tiltseries0012_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: 2017yr07m25d-19hr31m54s