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/tiltseries0011_thick300 --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=tiltseries0011_thick300 --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=11 --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=300 --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: 2017yr07m25d-11hr22m04s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0011.tlt to series0011.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
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 = 30.0781506686
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 = 30.0781506686
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.04324 for Iteration #1 of Tilt-Series #11.
CCMS(rotations) = 0.57673 for Iteration #1 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #11.
The scaled sum of CCMS values is #0.03315 for iteration 1 of Tilt-Series #11.
Alignment quality for Iteration #1 of Tilt-Series #11 (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 0.114000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.04599 for Iteration #2 of Tilt-Series #11.
CCMS(rotations) = 0.36489 for Iteration #2 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #11.
The scaled sum of CCMS values is #0.03029 for iteration 2 of Tilt-Series #11.
Alignment quality for Iteration #2 of Tilt-Series #11 (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 1.252000, 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 #3 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.04397 for Iteration #3 of Tilt-Series #11.
CCMS(rotations) = 0.25257 for Iteration #3 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #11.
The scaled sum of CCMS values is #0.02703 for iteration 3 of Tilt-Series #11.
Alignment quality for Iteration #3 of Tilt-Series #11 (17jul12a): Okay (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 0.179000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.03932 for Iteration #4 of Tilt-Series #11.
CCMS(rotations) = 0.25401 for Iteration #4 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #11.
The scaled sum of CCMS values is #0.02474 for iteration 4 of Tilt-Series #11.
Alignment quality for Iteration #4 of Tilt-Series #11 (17jul12a): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #11 (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 0.506000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.04334 for Iteration #5 of Tilt-Series #11.
CCMS(rotations) = 0.49725 for Iteration #5 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #11.
The scaled sum of CCMS values is #0.03161 for iteration 5 of Tilt-Series #11.
Alignment quality for Iteration #5 of Tilt-Series #11 (17jul12a): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #11 (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 0.919000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.03485 for Iteration #6 of Tilt-Series #11.
CCMS(rotations) = 0.41229 for Iteration #6 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #11.
The scaled sum of CCMS values is #0.02567 for iteration 6 of Tilt-Series #11.
Alignment quality for Iteration #6 of Tilt-Series #11 (17jul12a): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #11 (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 0.293000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00793 for Iteration #7 of Tilt-Series #11.
CCMS(rotations) = 0.21895 for Iteration #7 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00834 for iteration 7 of Tilt-Series #11.
Alignment quality for Iteration #7 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.053000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00648 for Iteration #8 of Tilt-Series #11.
CCMS(rotations) = 0.10333 for Iteration #8 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0053 for iteration 8 of Tilt-Series #11.
Alignment quality for Iteration #8 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #11 (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 0.253000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.00775 for Iteration #9 of Tilt-Series #11.
CCMS(rotations) = 0.27588 for Iteration #9 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00939 for iteration 9 of Tilt-Series #11.
Alignment quality for Iteration #9 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #11 (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 0.325000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.00666 for Iteration #10 of Tilt-Series #11.
CCMS(rotations) = 0.14339 for Iteration #10 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0062 for iteration 10 of Tilt-Series #11.
Alignment quality for Iteration #10 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #11 (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 0.294000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
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 = 60.1563013371
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 = 60.1563013371
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00828 for Iteration #11 of Tilt-Series #11.
CCMS(rotations) = 0.27499 for Iteration #11 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00964 for iteration 11 of Tilt-Series #11.
Alignment quality for Iteration #11 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #11 (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 0.285000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00622 for Iteration #12 of Tilt-Series #11.
CCMS(rotations) = 0.26368 for Iteration #12 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00838 for iteration 12 of Tilt-Series #11.
Alignment quality for Iteration #12 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #11 (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 0.392000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00591 for Iteration #13 of Tilt-Series #11.
CCMS(rotations) = 0.3031 for Iteration #13 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00902 for iteration 13 of Tilt-Series #11.
Alignment quality for Iteration #13 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #11 (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 0.196000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00621 for Iteration #14 of Tilt-Series #11.
CCMS(rotations) = 0.24732 for Iteration #14 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00805 for iteration 14 of Tilt-Series #11.
Alignment quality for Iteration #14 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #11 (17jul12a): 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 0.494000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00584 for Iteration #15 of Tilt-Series #11.
CCMS(rotations) = 0.32641 for Iteration #15 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00945 for iteration 15 of Tilt-Series #11.
Alignment quality for Iteration #15 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #11 (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 0.273000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00607 for Iteration #16 of Tilt-Series #11.
CCMS(rotations) = 0.27924 for Iteration #16 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00862 for iteration 16 of Tilt-Series #11.
Alignment quality for Iteration #16 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.358000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00564 for Iteration #17 of Tilt-Series #11.
CCMS(rotations) = 0.28073 for Iteration #17 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00844 for iteration 17 of Tilt-Series #11.
Alignment quality for Iteration #17 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.131000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.00608 for Iteration #18 of Tilt-Series #11.
CCMS(rotations) = 0.23129 for Iteration #18 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00767 for iteration 18 of Tilt-Series #11.
Alignment quality for Iteration #18 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #11 (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 0.307000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00565 for Iteration #19 of Tilt-Series #11.
CCMS(rotations) = 0.26743 for Iteration #19 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00817 for iteration 19 of Tilt-Series #11.
Alignment quality for Iteration #19 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.150000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00593 for Iteration #20 of Tilt-Series #11.
CCMS(rotations) = 0.22905 for Iteration #20 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00754 for iteration 20 of Tilt-Series #11.
Alignment quality for Iteration #20 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.266000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #11 (tiltseries0011_thick300)
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 = 120.312602674
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 = 120.312602674
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00776 for Iteration #21 of Tilt-Series #11.
CCMS(rotations) = 0.29969 for Iteration #21 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00987 for iteration 21 of Tilt-Series #11.
Alignment quality for Iteration #21 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #11 (17jul12a): StableCreating 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 0.194000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00553 for Iteration #22 of Tilt-Series #11.
CCMS(rotations) = 0.28729 for Iteration #22 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00851 for iteration 22 of Tilt-Series #11.
Alignment quality for Iteration #22 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #11 (17jul12a): Very StableCreating 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 0.040000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00496 for Iteration #23 of Tilt-Series #11.
CCMS(rotations) = 0.25672 for Iteration #23 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00762 for iteration 23 of Tilt-Series #11.
Alignment quality for Iteration #23 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #11 (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 0.324000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00431 for Iteration #24 of Tilt-Series #11.
CCMS(rotations) = 0.312 for Iteration #24 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0084 for iteration 24 of Tilt-Series #11.
Alignment quality for Iteration #24 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.215000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00469 for Iteration #25 of Tilt-Series #11.
CCMS(rotations) = 0.29504 for Iteration #25 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00825 for iteration 25 of Tilt-Series #11.
Alignment quality for Iteration #25 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #11 (17jul12a): Very 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 0.154000, which is less than the maximum allowed deviation of 1.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
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 = 240.625205348
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 = 240.625205348
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00701 for Iteration #26 of Tilt-Series #11.
CCMS(rotations) = 0.26276 for Iteration #26 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00876 for iteration 26 of Tilt-Series #11.
Alignment quality for Iteration #26 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #11 (17jul12a): Very StableCreating 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 0.068000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00579 for Iteration #27 of Tilt-Series #11.
CCMS(rotations) = 0.29082 for Iteration #27 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00871 for iteration 27 of Tilt-Series #11.
Alignment quality for Iteration #27 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #11 (17jul12a): StableCreating 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 0.123000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00757 for Iteration #28 of Tilt-Series #11.
CCMS(rotations) = 0.26942 for Iteration #28 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00917 for iteration 28 of Tilt-Series #11.
Alignment quality for Iteration #28 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #11 (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 0.188000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01062 for Iteration #29 of Tilt-Series #11.
CCMS(rotations) = 0.43528 for Iteration #29 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #11.
The scaled sum of CCMS values is #0.01401 for iteration 29 of Tilt-Series #11.
Alignment quality for Iteration #29 of Tilt-Series #11 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #11 (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 0.128000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.00616 for Iteration #30 of Tilt-Series #11.
CCMS(rotations) = 0.24225 for Iteration #30 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00793 for iteration 30 of Tilt-Series #11.
Alignment quality for Iteration #30 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #11 (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 0.056000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.0054 for Iteration #31 of Tilt-Series #11.
CCMS(rotations) = 0.3103 for Iteration #31 of Tilt-Series #11.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #11.
The scaled sum of CCMS values is #0.0089 for iteration 31 of Tilt-Series #11.
Alignment quality for Iteration #31 of Tilt-Series #11 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #11 (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 0.251000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00603 for Iteration #32 of Tilt-Series #11.
CCMS(rotations) = 0.21121 for Iteration #32 of Tilt-Series #11.
CCMS(scale) = 0.00123 for Iteration #32 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00523 for iteration 32 of Tilt-Series #11.
Alignment quality for Iteration #32 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #11 (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 0.053000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00619 for Iteration #33 of Tilt-Series #11.
CCMS(rotations) = 0.33532 for Iteration #33 of Tilt-Series #11.
CCMS(scale) = 0.00151 for Iteration #33 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00704 for iteration 33 of Tilt-Series #11.
Alignment quality for Iteration #33 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #11 (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 0.077000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00647 for Iteration #34 of Tilt-Series #11.
CCMS(rotations) = 0.33476 for Iteration #34 of Tilt-Series #11.
CCMS(scale) = 0.00148 for Iteration #34 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00711 for iteration 34 of Tilt-Series #11.
Alignment quality for Iteration #34 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.042000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #11 (tiltseries0011_thick300)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #11 (tiltseries0011_thick300)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.0046 for Iteration #35 of Tilt-Series #11.
CCMS(rotations) = 0.30467 for Iteration #35 of Tilt-Series #11.
CCMS(scale) = 0.00131 for Iteration #35 of Tilt-Series #11.
The scaled sum of CCMS values is #0.00603 for iteration 35 of Tilt-Series #11.
Alignment quality for Iteration #35 of Tilt-Series #11 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #11 (17jul12a): Rock Solid!Creating 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 0.053000, which is less than the maximum allowed deviation of 1.000000.Finished Refinement for Tilt-Series #11 (tiltseries0011_thick300)!
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: 2017yr07m26d-11hr20m53s