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/17jul12d/protomo_alignments/tiltseries0070_thick500 --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=tiltseries0070_thick500 --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=17jul12d --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=Coarse_Iter_1 --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=70 --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=500 --expid=4384 --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

node05
Start time: 2017yr07m24d-17hr53m04s
Description: 
Using Coarse alignment iteration 1 for Refinement by copying coarse_series0070.tlt to series0070.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
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 = 50.1302511143
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 = 50.1302511143
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.07062 for Iteration #1 of Tilt-Series #70.
CCMS(rotations) = 1.78569 for Iteration #1 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #70.
The scaled sum of CCMS values is #0.07102 for iteration 1 of Tilt-Series #70.
Alignment quality for Iteration #1 of Tilt-Series #70 (17jul12d): 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 1.259000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01986 for Iteration #2 of Tilt-Series #70.
CCMS(rotations) = 0.41237 for Iteration #2 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01818 for iteration 2 of Tilt-Series #70.
Alignment quality for Iteration #2 of Tilt-Series #70 (17jul12d): Good (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 0.748000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01979 for Iteration #3 of Tilt-Series #70.
CCMS(rotations) = 0.38123 for Iteration #3 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01752 for iteration 3 of Tilt-Series #70.
Alignment quality for Iteration #3 of Tilt-Series #70 (17jul12d): 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 1.106000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01642 for Iteration #4 of Tilt-Series #70.
CCMS(rotations) = 0.43578 for Iteration #4 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01692 for iteration 4 of Tilt-Series #70.
Alignment quality for Iteration #4 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #70 (17jul12d): 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 1.173000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.01886 for Iteration #5 of Tilt-Series #70.
CCMS(rotations) = 0.42147 for Iteration #5 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01786 for iteration 5 of Tilt-Series #70.
Alignment quality for Iteration #5 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #70 (17jul12d): 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 0.754000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.01916 for Iteration #6 of Tilt-Series #70.
CCMS(rotations) = 0.49952 for Iteration #6 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01957 for iteration 6 of Tilt-Series #70.
Alignment quality for Iteration #6 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #70 (17jul12d): 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 1.195000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.01717 for Iteration #7 of Tilt-Series #70.
CCMS(rotations) = 0.52118 for Iteration #7 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01901 for iteration 7 of Tilt-Series #70.
Alignment quality for Iteration #7 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #70 (17jul12d): 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 1.240000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01815 for Iteration #8 of Tilt-Series #70.
CCMS(rotations) = 0.4998 for Iteration #8 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01907 for iteration 8 of Tilt-Series #70.
Alignment quality for Iteration #8 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #70 (17jul12d): 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 1.239000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01739 for Iteration #9 of Tilt-Series #70.
CCMS(rotations) = 0.47992 for Iteration #9 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01829 for iteration 9 of Tilt-Series #70.
Alignment quality for Iteration #9 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #70 (17jul12d): 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 1.223000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01872 for Iteration #10 of Tilt-Series #70.
CCMS(rotations) = 0.48815 for Iteration #10 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01912 for iteration 10 of Tilt-Series #70.
Alignment quality for Iteration #10 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #70 (17jul12d): 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 1.284000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
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 = 100.260502229
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 = 100.260502229
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01994 for Iteration #11 of Tilt-Series #70.
CCMS(rotations) = 0.63161 for Iteration #11 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #70.
The scaled sum of CCMS values is #0.0226 for iteration 11 of Tilt-Series #70.
Alignment quality for Iteration #11 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #70 (17jul12d): 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 1.851000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.01577 for Iteration #12 of Tilt-Series #70.
CCMS(rotations) = 0.57528 for Iteration #12 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01939 for iteration 12 of Tilt-Series #70.
Alignment quality for Iteration #12 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #70 (17jul12d): 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 1.706000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.01532 for Iteration #13 of Tilt-Series #70.
CCMS(rotations) = 0.58607 for Iteration #13 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01938 for iteration 13 of Tilt-Series #70.
Alignment quality for Iteration #13 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #70 (17jul12d): 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 1.709000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01651 for Iteration #14 of Tilt-Series #70.
CCMS(rotations) = 0.60647 for Iteration #14 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02038 for iteration 14 of Tilt-Series #70.
Alignment quality for Iteration #14 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #70 (17jul12d): Very StableCreating Depiction Videos for Iteration #14 in Parallel...
Creating Refinement tilt-series video for iteration #14...
Generating Refinement reconstruction for iteration #14...
The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 1.780000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01515 for Iteration #15 of Tilt-Series #70.
CCMS(rotations) = 0.59023 for Iteration #15 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01938 for iteration 15 of Tilt-Series #70.
Alignment quality for Iteration #15 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #70 (17jul12d): Rock Solid!Creating 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 1.861000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.01538 for Iteration #16 of Tilt-Series #70.
CCMS(rotations) = 0.53492 for Iteration #16 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01839 for iteration 16 of Tilt-Series #70.
Alignment quality for Iteration #16 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #70 (17jul12d): Very StableCreating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...
The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 1.738000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.01582 for Iteration #17 of Tilt-Series #70.
CCMS(rotations) = 0.54213 for Iteration #17 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01875 for iteration 17 of Tilt-Series #70.
Alignment quality for Iteration #17 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #70 (17jul12d): 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 1.692000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0146 for Iteration #18 of Tilt-Series #70.
CCMS(rotations) = 0.5454 for Iteration #18 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01821 for iteration 18 of Tilt-Series #70.
Alignment quality for Iteration #18 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #70 (17jul12d): 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 1.629000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.01567 for Iteration #19 of Tilt-Series #70.
CCMS(rotations) = 0.53003 for Iteration #19 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01844 for iteration 19 of Tilt-Series #70.
Alignment quality for Iteration #19 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #70 (17jul12d): 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 1.518000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.01518 for Iteration #20 of Tilt-Series #70.
CCMS(rotations) = 0.53816 for Iteration #20 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01836 for iteration 20 of Tilt-Series #70.
Alignment quality for Iteration #20 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #70 (17jul12d): 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 1.529000, which is less than the maximum allowed deviation of 2.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #70 (tiltseries0070_thick500)
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 = 200.521004457
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 = 200.521004457
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.01668 for Iteration #21 of Tilt-Series #70.
CCMS(rotations) = 0.65269 for Iteration #21 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02139 for iteration 21 of Tilt-Series #70.
Alignment quality for Iteration #21 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #70 (17jul12d): 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 1.909000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01796 for Iteration #22 of Tilt-Series #70.
CCMS(rotations) = 0.58701 for Iteration #22 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02072 for iteration 22 of Tilt-Series #70.
Alignment quality for Iteration #22 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #70 (17jul12d): 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 1.791000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.01946 for Iteration #23 of Tilt-Series #70.
CCMS(rotations) = 0.66153 for Iteration #23 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02296 for iteration 23 of Tilt-Series #70.
Alignment quality for Iteration #23 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #70 (17jul12d): Rock Solid!Creating 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 2.003000, which is greater than the maximum allowed deviation of 2.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration.
No Round parameters changed for Iteration #24 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.02065 for Iteration #24 of Tilt-Series #70.
CCMS(rotations) = 0.53186 for Iteration #24 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02096 for iteration 24 of Tilt-Series #70.
Alignment quality for Iteration #24 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #70 (17jul12d): StableCreating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...
The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 1.818000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.01638 for Iteration #25 of Tilt-Series #70.
CCMS(rotations) = 0.6711 for Iteration #25 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02161 for iteration 25 of Tilt-Series #70.
Alignment quality for Iteration #25 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #70 (17jul12d): 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 2.011000, which is greater than the maximum allowed deviation of 2.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
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 = 401.042008914
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 = 401.042008914
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.02409 for Iteration #26 of Tilt-Series #70.
CCMS(rotations) = 0.55449 for Iteration #26 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02313 for iteration 26 of Tilt-Series #70.
Alignment quality for Iteration #26 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #70 (17jul12d): 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 1.468000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.01871 for Iteration #27 of Tilt-Series #70.
CCMS(rotations) = 0.53578 for Iteration #27 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02007 for iteration 27 of Tilt-Series #70.
Alignment quality for Iteration #27 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #70 (17jul12d): 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 1.567000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.02406 for Iteration #28 of Tilt-Series #70.
CCMS(rotations) = 0.59697 for Iteration #28 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02397 for iteration 28 of Tilt-Series #70.
Alignment quality for Iteration #28 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #70 (17jul12d): 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 1.918000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01915 for Iteration #29 of Tilt-Series #70.
CCMS(rotations) = 0.6197 for Iteration #29 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02197 for iteration 29 of Tilt-Series #70.
Alignment quality for Iteration #29 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #70 (17jul12d): 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 1.987000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01867 for Iteration #30 of Tilt-Series #70.
CCMS(rotations) = 0.60075 for Iteration #30 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #70.
The scaled sum of CCMS values is #0.02135 for iteration 30 of Tilt-Series #70.
Alignment quality for Iteration #30 of Tilt-Series #70 (17jul12d): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #70 (17jul12d): 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 2.079000, which is greater than the maximum allowed deviation of 2.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration.
No Round parameters changed for Iteration #31 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.01919 for Iteration #31 of Tilt-Series #70.
CCMS(rotations) = 0.39142 for Iteration #31 of Tilt-Series #70.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01743 for iteration 31 of Tilt-Series #70.
Alignment quality for Iteration #31 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #70 (17jul12d): 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 1.243000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00927 for Iteration #32 of Tilt-Series #70.
CCMS(rotations) = 0.39478 for Iteration #32 of Tilt-Series #70.
CCMS(scale) = 0.00827 for Iteration #32 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01111 for iteration 32 of Tilt-Series #70.
Alignment quality for Iteration #32 of Tilt-Series #70 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #70 (17jul12d): 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 1.291000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.01111 for Iteration #33 of Tilt-Series #70.
CCMS(rotations) = 0.46553 for Iteration #33 of Tilt-Series #70.
CCMS(scale) = 0.00841 for Iteration #33 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01271 for iteration 33 of Tilt-Series #70.
Alignment quality for Iteration #33 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #70 (17jul12d): 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 1.468000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.01142 for Iteration #34 of Tilt-Series #70.
CCMS(rotations) = 0.52468 for Iteration #34 of Tilt-Series #70.
CCMS(scale) = 0.00756 for Iteration #34 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01332 for iteration 34 of Tilt-Series #70.
Alignment quality for Iteration #34 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #70 (17jul12d): 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 1.653000, which is less than the maximum allowed deviation of 2.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #70 (tiltseries0070_thick500)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #70 (tiltseries0070_thick500)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01603 for Iteration #35 of Tilt-Series #70.
CCMS(rotations) = 0.6281 for Iteration #35 of Tilt-Series #70.
CCMS(scale) = 0.0085 for Iteration #35 of Tilt-Series #70.
The scaled sum of CCMS values is #0.01655 for iteration 35 of Tilt-Series #70.
Alignment quality for Iteration #35 of Tilt-Series #70 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #70 (17jul12d): 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 2.000000, which is less than the maximum allowed deviation of 2.000000.Finished Refinement for Tilt-Series #70 (tiltseries0070_thick500)!
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-20hr32m24s