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/tiltseries0010_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=tiltseries0010_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=10 --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

node38
Start time: 2017yr07m24d-16hr09m37s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0010.tlt to series0010.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #10 (tiltseries0010_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 = 40.1042008914
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 = 40.1042008914
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03598 for Iteration #1 of Tilt-Series #10.
CCMS(rotations) = 1.26249 for Iteration #1 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #10.
The scaled sum of CCMS values is #0.04324 for iteration 1 of Tilt-Series #10.
Alignment quality for Iteration #1 of Tilt-Series #10 (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 0.615000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.02394 for Iteration #2 of Tilt-Series #10.
CCMS(rotations) = 0.82427 for Iteration #2 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #10.
The scaled sum of CCMS values is #0.02846 for iteration 2 of Tilt-Series #10.
Alignment quality for Iteration #2 of Tilt-Series #10 (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 0.169000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01339 for Iteration #3 of Tilt-Series #10.
CCMS(rotations) = 0.36608 for Iteration #3 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01402 for iteration 3 of Tilt-Series #10.
Alignment quality for Iteration #3 of Tilt-Series #10 (17jul12a): 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 0.121000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01698 for Iteration #4 of Tilt-Series #10.
CCMS(rotations) = 0.15136 for Iteration #4 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01152 for iteration 4 of Tilt-Series #10.
Alignment quality for Iteration #4 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #10 (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 0.409000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01311 for Iteration #5 of Tilt-Series #10.
CCMS(rotations) = 0.37804 for Iteration #5 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01412 for iteration 5 of Tilt-Series #10.
Alignment quality for Iteration #5 of Tilt-Series #10 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #10 (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 0.435000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.0092 for Iteration #6 of Tilt-Series #10.
CCMS(rotations) = 0.20505 for Iteration #6 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #10.
The scaled sum of CCMS values is #0.0087 for iteration 6 of Tilt-Series #10.
Alignment quality for Iteration #6 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #10 (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 0.553000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.00997 for Iteration #7 of Tilt-Series #10.
CCMS(rotations) = 0.24687 for Iteration #7 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00992 for iteration 7 of Tilt-Series #10.
Alignment quality for Iteration #7 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #10 (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 0.426000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.00944 for Iteration #8 of Tilt-Series #10.
CCMS(rotations) = 0.28595 for Iteration #8 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01044 for iteration 8 of Tilt-Series #10.
Alignment quality for Iteration #8 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #10 (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 0.497000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01043 for Iteration #9 of Tilt-Series #10.
CCMS(rotations) = 0.25412 for Iteration #9 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #10.
The scaled sum of CCMS values is #0.0103 for iteration 9 of Tilt-Series #10.
Alignment quality for Iteration #9 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #10 (17jul12a): Very StableCreating 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 0.567000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.0091 for Iteration #10 of Tilt-Series #10.
CCMS(rotations) = 0.22021 for Iteration #10 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00895 for iteration 10 of Tilt-Series #10.
Alignment quality for Iteration #10 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #10 (17jul12a): StableCreating 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 0.456000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #10 (tiltseries0010_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 = 80.2084017828
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 = 80.2084017828
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.00991 for Iteration #11 of Tilt-Series #10.
CCMS(rotations) = 0.12759 for Iteration #11 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00751 for iteration 11 of Tilt-Series #10.
Alignment quality for Iteration #11 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #10 (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 0.228000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01167 for Iteration #12 of Tilt-Series #10.
CCMS(rotations) = 0.16036 for Iteration #12 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00904 for iteration 12 of Tilt-Series #10.
Alignment quality for Iteration #12 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #10 (17jul12a): UnstableCreating 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 0.149000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01183 for Iteration #13 of Tilt-Series #10.
CCMS(rotations) = 0.16977 for Iteration #13 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00931 for iteration 13 of Tilt-Series #10.
Alignment quality for Iteration #13 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #10 (17jul12a): UnstableCreating 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 0.025000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01191 for Iteration #14 of Tilt-Series #10.
CCMS(rotations) = 0.17611 for Iteration #14 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00948 for iteration 14 of Tilt-Series #10.
Alignment quality for Iteration #14 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #10 (17jul12a): Rock Solid!Creating 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 0.106000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.011 for Iteration #15 of Tilt-Series #10.
CCMS(rotations) = 0.16535 for Iteration #15 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00881 for iteration 15 of Tilt-Series #10.
Alignment quality for Iteration #15 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #10 (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 0.093000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.0123 for Iteration #16 of Tilt-Series #10.
CCMS(rotations) = 0.24594 for Iteration #16 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01107 for iteration 16 of Tilt-Series #10.
Alignment quality for Iteration #16 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #10 (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 0.336000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01185 for Iteration #17 of Tilt-Series #10.
CCMS(rotations) = 0.15097 for Iteration #17 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00895 for iteration 17 of Tilt-Series #10.
Alignment quality for Iteration #17 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #10 (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 0.221000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01178 for Iteration #18 of Tilt-Series #10.
CCMS(rotations) = 0.1856 for Iteration #18 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #10.
The scaled sum of CCMS values is #0.0096 for iteration 18 of Tilt-Series #10.
Alignment quality for Iteration #18 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #10 (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 0.224000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01022 for Iteration #19 of Tilt-Series #10.
CCMS(rotations) = 0.167 for Iteration #19 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00845 for iteration 19 of Tilt-Series #10.
Alignment quality for Iteration #19 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #10 (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 0.175000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01199 for Iteration #20 of Tilt-Series #10.
CCMS(rotations) = 0.22868 for Iteration #20 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01057 for iteration 20 of Tilt-Series #10.
Alignment quality for Iteration #20 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #10 (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 0.184000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #10 (tiltseries0010_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 = 160.416803566
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 = 160.416803566
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01199 for Iteration #21 of Tilt-Series #10.
CCMS(rotations) = 0.1698 for Iteration #21 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00939 for iteration 21 of Tilt-Series #10.
Alignment quality for Iteration #21 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #10 (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 0.283000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01008 for Iteration #22 of Tilt-Series #10.
CCMS(rotations) = 0.19183 for Iteration #22 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00888 for iteration 22 of Tilt-Series #10.
Alignment quality for Iteration #22 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #10 (17jul12a): 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 0.405000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01529 for Iteration #23 of Tilt-Series #10.
CCMS(rotations) = 0.32397 for Iteration #23 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01413 for iteration 23 of Tilt-Series #10.
Alignment quality for Iteration #23 of Tilt-Series #10 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #10 (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 0.369000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01208 for Iteration #24 of Tilt-Series #10.
CCMS(rotations) = 0.20242 for Iteration #24 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01009 for iteration 24 of Tilt-Series #10.
Alignment quality for Iteration #24 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #10 (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 0.143000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01325 for Iteration #25 of Tilt-Series #10.
CCMS(rotations) = 0.19868 for Iteration #25 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #10.
The scaled sum of CCMS values is #0.0106 for iteration 25 of Tilt-Series #10.
Alignment quality for Iteration #25 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #10 (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 0.367000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #10 (tiltseries0010_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 = 320.833607131
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 = 320.833607131
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01332 for Iteration #26 of Tilt-Series #10.
CCMS(rotations) = 0.27131 for Iteration #26 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01209 for iteration 26 of Tilt-Series #10.
Alignment quality for Iteration #26 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #10 (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 0.122000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0149 for Iteration #27 of Tilt-Series #10.
CCMS(rotations) = 0.34014 for Iteration #27 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01425 for iteration 27 of Tilt-Series #10.
Alignment quality for Iteration #27 of Tilt-Series #10 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #10 (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 0.664000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01118 for Iteration #28 of Tilt-Series #10.
CCMS(rotations) = 0.39258 for Iteration #28 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01344 for iteration 28 of Tilt-Series #10.
Alignment quality for Iteration #28 of Tilt-Series #10 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #10 (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 0.205000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.0082 for Iteration #29 of Tilt-Series #10.
CCMS(rotations) = 0.28289 for Iteration #29 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00976 for iteration 29 of Tilt-Series #10.
Alignment quality for Iteration #29 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #10 (17jul12a): Very StableCreating 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 0.354000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01195 for Iteration #30 of Tilt-Series #10.
CCMS(rotations) = 0.27342 for Iteration #30 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01145 for iteration 30 of Tilt-Series #10.
Alignment quality for Iteration #30 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #10 (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 0.405000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01069 for Iteration #31 of Tilt-Series #10.
CCMS(rotations) = 0.44581 for Iteration #31 of Tilt-Series #10.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01426 for iteration 31 of Tilt-Series #10.
Alignment quality for Iteration #31 of Tilt-Series #10 (17jul12a): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #10 (17jul12a): Rock Solid!Creating 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 0.545000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00933 for Iteration #32 of Tilt-Series #10.
CCMS(rotations) = 0.3434 for Iteration #32 of Tilt-Series #10.
CCMS(scale) = 0.00258 for Iteration #32 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00855 for iteration 32 of Tilt-Series #10.
Alignment quality for Iteration #32 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #10 (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 0.256000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01335 for Iteration #33 of Tilt-Series #10.
CCMS(rotations) = 0.34455 for Iteration #33 of Tilt-Series #10.
CCMS(scale) = 0.00363 for Iteration #33 of Tilt-Series #10.
The scaled sum of CCMS values is #0.01025 for iteration 33 of Tilt-Series #10.
Alignment quality for Iteration #33 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #10 (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 0.418000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00831 for Iteration #34 of Tilt-Series #10.
CCMS(rotations) = 0.25034 for Iteration #34 of Tilt-Series #10.
CCMS(scale) = 0.00289 for Iteration #34 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00707 for iteration 34 of Tilt-Series #10.
Alignment quality for Iteration #34 of Tilt-Series #10 (17jul12a): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #10 (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 0.282000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #10 (tiltseries0010_thick400)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #10 (tiltseries0010_thick400)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01397 for Iteration #35 of Tilt-Series #10.
CCMS(rotations) = 0.2526 for Iteration #35 of Tilt-Series #10.
CCMS(scale) = 0.00317 for Iteration #35 of Tilt-Series #10.
The scaled sum of CCMS values is #0.00908 for iteration 35 of Tilt-Series #10.
Alignment quality for Iteration #35 of Tilt-Series #10 (17jul12a): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #10 (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 0.275000, which is less than the maximum allowed deviation of 2.000000.Finished Refinement for Tilt-Series #10 (tiltseries0010_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-19hr23m45s