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/anoble/17sep08r/protomo_alignments/tiltseries0018_thick250 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=5211.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2227 --r1_region_y=2990 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=5211.0 --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=2990 --r2_region_x=2227 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2606.0 --defocus_ang_positive=90 --r5_mask_width_x=2202 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=5211.0 --r3_highpass_apod_x=2606.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=531 --r2_mask_width_y=722 --r5_region_x=2227 --r5_region_y=2990 --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=5211.0 --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=2965 --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=2606.0 --runname=tiltseries0018_thick250 --r1_highpass_diameter_x=5211.0 --r2_lowpass_diameter_y=25.0 --map_size_y=623 --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=2202 --r4_mask_width_y=2965 --r5_highpass_apod_y=2606.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17sep08r --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=2606.0 --r1_highpass_apod_x=2606.0 --r2_highpass_apod_x=2606.0 --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=18 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1470 --r3_mask_width_x=1088 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=5211.0 --r4_highpass_diameter_x=5211.0 --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=5211.0 --tilt_azimuth=-96.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2606.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=5211.0 --defocus_max=0 --r4_region_y=2990 --r4_region_x=2227 --r5_kernel_y=5 --r3_region_x=2227 --r3_region_y=2990 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=250 --expid=4896 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --max_correction=999999 --map_size_x=464 --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=2.34 --link=False --r2_highpass_diameter_x=5211.0 --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=1246.0 --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=3712 --dimy=4984 --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=3.0 --tilt_clip=true --r4_highpass_apod_x=2606.0 --r4_highpass_apod_y=2606.0 --azimuth=true --r1_mask_width_y=348 --r1_mask_width_x=253 --jobtype=protomo

node07
Start time: 2017yr09m14d-19hr19m33s
Description: 
Using More Manual alignment for Refinement by copying more_manual_series0018.tlt to series0018.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
lowpass = 50.0 Angstroms

Round #1. Parameters in Protomo units:
(Note: At binned by 8, pixelsize is 18.72 Angstroms, Nyquist is 37.44 Angstroms)
window.lowpass.apodization = { 0.29952 0.29952 }
map.sampling = 8
window.highpass.diameter = { 0.00718480138169 0.00718480138169 }
window.highpass.apodization = { 0.0143668457406 0.0143668457406 }
window.mask.apodization = { 10 10 }
align.mask.width = { 253 348 }
sampling = 8
align.mask.apodization = { 10 10 }
map.body = 18.335026253
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 278 373 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 253 348 }
reference.body = 18.335026253
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.03765 for Iteration #1 of Tilt-Series #18.
CCMS(rotations) = 1.02351 for Iteration #1 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03929 for iteration 1 of Tilt-Series #18.
Alignment quality for Iteration #1 of Tilt-Series #18 (17sep08r): 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 0.639000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.03705 for Iteration #2 of Tilt-Series #18.
CCMS(rotations) = 1.00435 for Iteration #2 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03861 for iteration 2 of Tilt-Series #18.
Alignment quality for Iteration #2 of Tilt-Series #18 (17sep08r): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel...
Creating Refinement tilt-series video for iteration #2...
Generating Refinement reconstruction for iteration #2...
The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.900000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.03675 for Iteration #3 of Tilt-Series #18.
CCMS(rotations) = 0.88293 for Iteration #3 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03604 for iteration 3 of Tilt-Series #18.
Alignment quality for Iteration #3 of Tilt-Series #18 (17sep08r): Bad (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 1.021000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.0452 for Iteration #4 of Tilt-Series #18.
CCMS(rotations) = 0.80189 for Iteration #4 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03864 for iteration 4 of Tilt-Series #18.
Alignment quality for Iteration #4 of Tilt-Series #18 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #18 (17sep08r): 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 1.154000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.04146 for Iteration #5 of Tilt-Series #18.
CCMS(rotations) = 0.76451 for Iteration #5 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03602 for iteration 5 of Tilt-Series #18.
Alignment quality for Iteration #5 of Tilt-Series #18 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #18 (17sep08r): 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 1.292000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #6 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.03866 for Iteration #6 of Tilt-Series #18.
CCMS(rotations) = 0.6967 for Iteration #6 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #18.
The scaled sum of CCMS values is #0.03326 for iteration 6 of Tilt-Series #18.
Alignment quality for Iteration #6 of Tilt-Series #18 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #18 (17sep08r): 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 1.853000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.03479 for Iteration #7 of Tilt-Series #18.
CCMS(rotations) = 0.42544 for Iteration #7 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0259 for iteration 7 of Tilt-Series #18.
Alignment quality for Iteration #7 of Tilt-Series #18 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #18 (17sep08r): 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 1.380000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.03019 for Iteration #8 of Tilt-Series #18.
CCMS(rotations) = 0.37379 for Iteration #8 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #18.
The scaled sum of CCMS values is #0.02257 for iteration 8 of Tilt-Series #18.
Alignment quality for Iteration #8 of Tilt-Series #18 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #18 (17sep08r): 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 1.475000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01542 for Iteration #9 of Tilt-Series #18.
CCMS(rotations) = 0.31521 for Iteration #9 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01402 for iteration 9 of Tilt-Series #18.
Alignment quality for Iteration #9 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #18 (17sep08r): 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 1.001000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01468 for Iteration #10 of Tilt-Series #18.
CCMS(rotations) = 0.37901 for Iteration #10 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01492 for iteration 10 of Tilt-Series #18.
Alignment quality for Iteration #10 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #18 (17sep08r): 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 0.923000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
lowpass = 25.0 angstroms

Round #2. Parameters in Protomo units:
(Note: At binned by 4, pixelsize is 9.36 Angstroms, Nyquist is 18.72 Angstroms)
window.lowpass.apodization = { 0.297142857143 0.297142857143 }
map.sampling = 4
window.highpass.diameter = { 0.00359240069085 0.00359240069085 }
window.highpass.apodization = { 0.0071834228703 0.0071834228703 }
window.mask.apodization = { 10 10 }
align.mask.width = { 531 722 }
sampling = 4
align.mask.apodization = { 10 10 }
map.body = 36.670052506
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 556 747 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 531 722 }
reference.body = 36.670052506
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01157 for Iteration #11 of Tilt-Series #18.
CCMS(rotations) = 0.34961 for Iteration #11 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01278 for iteration 11 of Tilt-Series #18.
Alignment quality for Iteration #11 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #18 (17sep08r): Very StableCreating Depiction Videos for Iteration #11 in Parallel...
Creating Refinement tilt-series video for iteration #11...
Generating Refinement reconstruction for iteration #11...
The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 1.422000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00717 for Iteration #12 of Tilt-Series #18.
CCMS(rotations) = 0.20958 for Iteration #12 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #18.
The scaled sum of CCMS values is #0.00778 for iteration 12 of Tilt-Series #18.
Alignment quality for Iteration #12 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #18 (17sep08r): StableCreating 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 1.168000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00802 for Iteration #13 of Tilt-Series #18.
CCMS(rotations) = 0.30463 for Iteration #13 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0101 for iteration 13 of Tilt-Series #18.
Alignment quality for Iteration #13 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #18 (17sep08r): 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 1.153000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.01215 for Iteration #14 of Tilt-Series #18.
CCMS(rotations) = 0.31098 for Iteration #14 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01229 for iteration 14 of Tilt-Series #18.
Alignment quality for Iteration #14 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #18 (17sep08r): 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 1.183000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.01023 for Iteration #15 of Tilt-Series #18.
CCMS(rotations) = 0.32429 for Iteration #15 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0116 for iteration 15 of Tilt-Series #18.
Alignment quality for Iteration #15 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #18 (17sep08r): 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 1.076000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00898 for Iteration #16 of Tilt-Series #18.
CCMS(rotations) = 0.30946 for Iteration #16 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01068 for iteration 16 of Tilt-Series #18.
Alignment quality for Iteration #16 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #18 (17sep08r): 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 1.201000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00825 for Iteration #17 of Tilt-Series #18.
CCMS(rotations) = 0.31446 for Iteration #17 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01041 for iteration 17 of Tilt-Series #18.
Alignment quality for Iteration #17 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #18 (17sep08r): 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 0.893000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.01005 for Iteration #18 of Tilt-Series #18.
CCMS(rotations) = 0.27674 for Iteration #18 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01056 for iteration 18 of Tilt-Series #18.
Alignment quality for Iteration #18 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #18 (17sep08r): 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 1.042000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00854 for Iteration #19 of Tilt-Series #18.
CCMS(rotations) = 0.23049 for Iteration #19 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #18.
The scaled sum of CCMS values is #0.00888 for iteration 19 of Tilt-Series #18.
Alignment quality for Iteration #19 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #18 (17sep08r): 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 0.813000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00756 for Iteration #20 of Tilt-Series #18.
CCMS(rotations) = 0.21804 for Iteration #20 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #18.
The scaled sum of CCMS values is #0.00814 for iteration 20 of Tilt-Series #18.
Alignment quality for Iteration #20 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #18 (17sep08r): 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 1.137000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #18 (tiltseries0018_thick250)
lowpass = 12.5 angstroms

Round #3. Parameters in Protomo units:
(Note: At binned by 2, pixelsize is 4.68 Angstroms, Nyquist is 9.36 Angstroms)
window.lowpass.apodization = { 0.301935483871 0.301935483871 }
map.sampling = 2
window.highpass.diameter = { 0.00179620034542 0.00179620034542 }
window.highpass.apodization = { 0.00359171143515 0.00359171143515 }
window.mask.apodization = { 10 10 }
align.mask.width = { 1088 1470 }
sampling = 2
align.mask.apodization = { 10 10 }
map.body = 73.3401050119
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 1113 1495 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 1088 1470 }
reference.body = 73.3401050119
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00945 for Iteration #21 of Tilt-Series #18.
CCMS(rotations) = 0.36431 for Iteration #21 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01201 for iteration 21 of Tilt-Series #18.
Alignment quality for Iteration #21 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #18 (17sep08r): 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 0.749000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.01307 for Iteration #22 of Tilt-Series #18.
CCMS(rotations) = 0.33197 for Iteration #22 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01317 for iteration 22 of Tilt-Series #18.
Alignment quality for Iteration #22 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #18 (17sep08r): 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 0.993000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00884 for Iteration #23 of Tilt-Series #18.
CCMS(rotations) = 0.37081 for Iteration #23 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01183 for iteration 23 of Tilt-Series #18.
Alignment quality for Iteration #23 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #18 (17sep08r): 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 0.915000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.01022 for Iteration #24 of Tilt-Series #18.
CCMS(rotations) = 0.28901 for Iteration #24 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01089 for iteration 24 of Tilt-Series #18.
Alignment quality for Iteration #24 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #18 (17sep08r): 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 1.123000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00835 for Iteration #25 of Tilt-Series #18.
CCMS(rotations) = 0.20639 for Iteration #25 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #18.
The scaled sum of CCMS values is #0.0083 for iteration 25 of Tilt-Series #18.
Alignment quality for Iteration #25 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #18 (17sep08r): Rock Solid!Creating 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 1.038000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
lowpass = 6.25 angstroms

Round #4. Parameters in Protomo units:
(Note: At binned by 1, pixelsize is 2.34 Angstroms, Nyquist is 4.68 Angstroms)
window.lowpass.apodization = { 0.2925 0.2925 }
map.sampling = 1
window.highpass.diameter = { 0.000898100172712 0.000898100172712 }
window.highpass.apodization = { 0.00179585571757 0.00179585571757 }
window.mask.apodization = { 10 10 }
align.mask.width = { 2202 2965 }
sampling = 1
align.mask.apodization = { 10 10 }
map.body = 146.680210024
map.lowpass.diameter = { 0.7488 0.7488 }
align.peaksearch.radius = { 300.0 300.0 }
window.size = { 2227 2990 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 2202 2965 }
reference.body = 146.680210024
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.01003 for Iteration #26 of Tilt-Series #18.
CCMS(rotations) = 0.3003 for Iteration #26 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01102 for iteration 26 of Tilt-Series #18.
Alignment quality for Iteration #26 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #18 (17sep08r): 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 0.862000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.0104 for Iteration #27 of Tilt-Series #18.
CCMS(rotations) = 0.30325 for Iteration #27 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01126 for iteration 27 of Tilt-Series #18.
Alignment quality for Iteration #27 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #18 (17sep08r): 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 1.190000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.01006 for Iteration #28 of Tilt-Series #18.
CCMS(rotations) = 0.33598 for Iteration #28 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01175 for iteration 28 of Tilt-Series #18.
Alignment quality for Iteration #28 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #18 (17sep08r): 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 0.585000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.01091 for Iteration #29 of Tilt-Series #18.
CCMS(rotations) = 0.34498 for Iteration #29 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01236 for iteration 29 of Tilt-Series #18.
Alignment quality for Iteration #29 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #18 (17sep08r): 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 0.684000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01153 for Iteration #30 of Tilt-Series #18.
CCMS(rotations) = 0.4121 for Iteration #30 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01401 for iteration 30 of Tilt-Series #18.
Alignment quality for Iteration #30 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #18 (17sep08r): 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 0.286000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.012 for Iteration #31 of Tilt-Series #18.
CCMS(rotations) = 0.43808 for Iteration #31 of Tilt-Series #18.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01476 for iteration 31 of Tilt-Series #18.
Alignment quality for Iteration #31 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #18 (17sep08r): 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 0.078000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.01006 for Iteration #32 of Tilt-Series #18.
CCMS(rotations) = 0.54796 for Iteration #32 of Tilt-Series #18.
CCMS(scale) = 0.00417 for Iteration #32 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01205 for iteration 32 of Tilt-Series #18.
Alignment quality for Iteration #32 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #18 (17sep08r): Rock Solid!Creating 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 0.005000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00976 for Iteration #33 of Tilt-Series #18.
CCMS(rotations) = 0.58367 for Iteration #33 of Tilt-Series #18.
CCMS(scale) = 0.00462 for Iteration #33 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01258 for iteration 33 of Tilt-Series #18.
Alignment quality for Iteration #33 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #18 (17sep08r): StableCreating 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 0.271000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00876 for Iteration #34 of Tilt-Series #18.
CCMS(rotations) = 0.55071 for Iteration #34 of Tilt-Series #18.
CCMS(scale) = 0.00548 for Iteration #34 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01209 for iteration 34 of Tilt-Series #18.
Alignment quality for Iteration #34 of Tilt-Series #18 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #18 (17sep08r): StableCreating 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 0.212000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #18 (tiltseries0018_thick250)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #18 (tiltseries0018_thick250)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.01157 for Iteration #35 of Tilt-Series #18.
CCMS(rotations) = 0.56299 for Iteration #35 of Tilt-Series #18.
CCMS(scale) = 0.00645 for Iteration #35 of Tilt-Series #18.
The scaled sum of CCMS values is #0.01351 for iteration 35 of Tilt-Series #18.
Alignment quality for Iteration #35 of Tilt-Series #18 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #18 (17sep08r): Very StableCreating 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 0.047000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #18 (tiltseries0018_thick250)!
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: 2017yr09m15d-15hr49m55s