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/tiltseries0013_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=tiltseries0013_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=13 --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=1.0 --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

node39
Start time: 2017yr07m27d-12hr18m29s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0013.tlt to series0013.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #13 (tiltseries0013_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) = 0.04193 for Iteration #1 of Tilt-Series #13.
CCMS(rotations) = 0.43128 for Iteration #1 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #13.
The scaled sum of CCMS values is #0.02959 for iteration 1 of Tilt-Series #13.
Alignment quality for Iteration #1 of Tilt-Series #13 (17jul12a): Okay (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...
The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.646000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02496 for Iteration #2 of Tilt-Series #13.
CCMS(rotations) = 0.41346 for Iteration #2 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #13.
The scaled sum of CCMS values is #0.02075 for iteration 2 of Tilt-Series #13.
Alignment quality for Iteration #2 of Tilt-Series #13 (17jul12a): Okay (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 0.826000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01239 for Iteration #3 of Tilt-Series #13.
CCMS(rotations) = 0.29077 for Iteration #3 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01201 for iteration 3 of Tilt-Series #13.
Alignment quality for Iteration #3 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.192000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01122 for Iteration #4 of Tilt-Series #13.
CCMS(rotations) = 0.27131 for Iteration #4 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01104 for iteration 4 of Tilt-Series #13.
Alignment quality for Iteration #4 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #13 (17jul12a): Rock Solid!Creating 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 0.320000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.00913 for Iteration #5 of Tilt-Series #13.
CCMS(rotations) = 0.24229 for Iteration #5 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00941 for iteration 5 of Tilt-Series #13.
Alignment quality for Iteration #5 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #13 (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 0.020000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01109 for Iteration #6 of Tilt-Series #13.
CCMS(rotations) = 0.31946 for Iteration #6 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01193 for iteration 6 of Tilt-Series #13.
Alignment quality for Iteration #6 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.210000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00875 for Iteration #7 of Tilt-Series #13.
CCMS(rotations) = 0.23752 for Iteration #7 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00913 for iteration 7 of Tilt-Series #13.
Alignment quality for Iteration #7 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #13 (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 0.060000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01277 for Iteration #8 of Tilt-Series #13.
CCMS(rotations) = 0.22679 for Iteration #8 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01092 for iteration 8 of Tilt-Series #13.
Alignment quality for Iteration #8 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #13 (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 0.406000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01002 for Iteration #9 of Tilt-Series #13.
CCMS(rotations) = 0.24777 for Iteration #9 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00997 for iteration 9 of Tilt-Series #13.
Alignment quality for Iteration #9 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #13 (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 0.119000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01111 for Iteration #10 of Tilt-Series #13.
CCMS(rotations) = 0.22425 for Iteration #10 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01004 for iteration 10 of Tilt-Series #13.
Alignment quality for Iteration #10 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #13 (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 0.327000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #13 (tiltseries0013_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) = 0.00695 for Iteration #11 of Tilt-Series #13.
CCMS(rotations) = 0.25812 for Iteration #11 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00864 for iteration 11 of Tilt-Series #13.
Alignment quality for Iteration #11 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.211000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00658 for Iteration #12 of Tilt-Series #13.
CCMS(rotations) = 0.21098 for Iteration #12 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00751 for iteration 12 of Tilt-Series #13.
Alignment quality for Iteration #12 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #13 (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 0.271000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.0088 for Iteration #13 of Tilt-Series #13.
CCMS(rotations) = 0.20458 for Iteration #13 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00849 for iteration 13 of Tilt-Series #13.
Alignment quality for Iteration #13 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #13 (17jul12a): Very StableCreating 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 0.239000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01101 for Iteration #14 of Tilt-Series #13.
CCMS(rotations) = 0.27289 for Iteration #14 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01096 for iteration 14 of Tilt-Series #13.
Alignment quality for Iteration #14 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.344000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00842 for Iteration #15 of Tilt-Series #13.
CCMS(rotations) = 0.30032 for Iteration #15 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01022 for iteration 15 of Tilt-Series #13.
Alignment quality for Iteration #15 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #13 (17jul12a): Very 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 0.517000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00826 for Iteration #16 of Tilt-Series #13.
CCMS(rotations) = 0.32071 for Iteration #16 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01054 for iteration 16 of Tilt-Series #13.
Alignment quality for Iteration #16 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.426000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01263 for Iteration #17 of Tilt-Series #13.
CCMS(rotations) = 0.24208 for Iteration #17 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01116 for iteration 17 of Tilt-Series #13.
Alignment quality for Iteration #17 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.492000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0129 for Iteration #18 of Tilt-Series #13.
CCMS(rotations) = 0.26144 for Iteration #18 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01168 for iteration 18 of Tilt-Series #13.
Alignment quality for Iteration #18 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.566000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00871 for Iteration #19 of Tilt-Series #13.
CCMS(rotations) = 0.18722 for Iteration #19 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #13.
The scaled sum of CCMS values is #0.0081 for iteration 19 of Tilt-Series #13.
Alignment quality for Iteration #19 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.435000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00855 for Iteration #20 of Tilt-Series #13.
CCMS(rotations) = 0.24448 for Iteration #20 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00917 for iteration 20 of Tilt-Series #13.
Alignment quality for Iteration #20 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.493000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #13 (tiltseries0013_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) = 0.01002 for Iteration #21 of Tilt-Series #13.
CCMS(rotations) = 0.17341 for Iteration #21 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00848 for iteration 21 of Tilt-Series #13.
Alignment quality for Iteration #21 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #13 (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 0.077000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00885 for Iteration #22 of Tilt-Series #13.
CCMS(rotations) = 0.19175 for Iteration #22 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00826 for iteration 22 of Tilt-Series #13.
Alignment quality for Iteration #22 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.204000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01079 for Iteration #23 of Tilt-Series #13.
CCMS(rotations) = 0.16115 for Iteration #23 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00862 for iteration 23 of Tilt-Series #13.
Alignment quality for Iteration #23 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #13 (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 0.086000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00836 for Iteration #24 of Tilt-Series #13.
CCMS(rotations) = 0.24795 for Iteration #24 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00914 for iteration 24 of Tilt-Series #13.
Alignment quality for Iteration #24 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.267000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01112 for Iteration #25 of Tilt-Series #13.
CCMS(rotations) = 0.25386 for Iteration #25 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01064 for iteration 25 of Tilt-Series #13.
Alignment quality for Iteration #25 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.597000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #13 (tiltseries0013_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) = 0.01224 for Iteration #26 of Tilt-Series #13.
CCMS(rotations) = 0.4475 for Iteration #26 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01507 for iteration 26 of Tilt-Series #13.
Alignment quality for Iteration #26 of Tilt-Series #13 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #13 (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 0.326000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01396 for Iteration #27 of Tilt-Series #13.
CCMS(rotations) = 0.57044 for Iteration #27 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01839 for iteration 27 of Tilt-Series #13.
Alignment quality for Iteration #27 of Tilt-Series #13 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #13 (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 0.159000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01137 for Iteration #28 of Tilt-Series #13.
CCMS(rotations) = 0.25862 for Iteration #28 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01086 for iteration 28 of Tilt-Series #13.
Alignment quality for Iteration #28 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.361000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01534 for Iteration #29 of Tilt-Series #13.
CCMS(rotations) = 0.44397 for Iteration #29 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01655 for iteration 29 of Tilt-Series #13.
Alignment quality for Iteration #29 of Tilt-Series #13 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #13 (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 1.026000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration.
No Round parameters changed for Iteration #30 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01215 for Iteration #30 of Tilt-Series #13.
CCMS(rotations) = 0.38541 for Iteration #30 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01379 for iteration 30 of Tilt-Series #13.
Alignment quality for Iteration #30 of Tilt-Series #13 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #13 (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 0.024000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01462 for Iteration #31 of Tilt-Series #13.
CCMS(rotations) = 0.47694 for Iteration #31 of Tilt-Series #13.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01685 for iteration 31 of Tilt-Series #13.
Alignment quality for Iteration #31 of Tilt-Series #13 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #13 (17jul12a): UnstableCreating 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 0.300000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01223 for Iteration #32 of Tilt-Series #13.
CCMS(rotations) = 0.41965 for Iteration #32 of Tilt-Series #13.
CCMS(scale) = 0.00411 for Iteration #32 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01104 for iteration 32 of Tilt-Series #13.
Alignment quality for Iteration #32 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #13 (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 0.917000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.0186 for Iteration #33 of Tilt-Series #13.
CCMS(rotations) = 0.2814 for Iteration #33 of Tilt-Series #13.
CCMS(scale) = 0.00331 for Iteration #33 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01105 for iteration 33 of Tilt-Series #13.
Alignment quality for Iteration #33 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #13 (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 0.949000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01353 for Iteration #34 of Tilt-Series #13.
CCMS(rotations) = 0.27821 for Iteration #34 of Tilt-Series #13.
CCMS(scale) = 0.00447 for Iteration #34 of Tilt-Series #13.
The scaled sum of CCMS values is #0.00971 for iteration 34 of Tilt-Series #13.
Alignment quality for Iteration #34 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #13 (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 1.437000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration.
No Round parameters changed for Iteration #35 of Tilt-Series #13 (tiltseries0013_thick400)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #13 (tiltseries0013_thick400)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01962 for Iteration #35 of Tilt-Series #13.
CCMS(rotations) = 0.23182 for Iteration #35 of Tilt-Series #13.
CCMS(scale) = 0.00559 for Iteration #35 of Tilt-Series #13.
The scaled sum of CCMS values is #0.01149 for iteration 35 of Tilt-Series #13.
Alignment quality for Iteration #35 of Tilt-Series #13 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #13 (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 0.739000, which is less than the maximum allowed deviation of 1.000000.Finished Refinement for Tilt-Series #13 (tiltseries0013_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: 2017yr07m28d-17hr19m37s