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/tiltseries0016_thick150 --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=tiltseries0016_thick150 --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=Coarse_Iter_2 --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=16 --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=150 --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

node30
Start time: 2017yr09m14d-19hr12m09s
Description: 
coarse_series0016_iter2.tlt not found, using coarse_series0016.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0016.tlt to series0016.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
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 = 11.0871269834
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 = 11.0871269834
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0181 for Iteration #1 of Tilt-Series #16.
CCMS(rotations) = 0.57207 for Iteration #1 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #16.
The scaled sum of CCMS values is #0.02049 for iteration 1 of Tilt-Series #16.
Alignment quality for Iteration #1 of Tilt-Series #16 (17sep08r): Okay (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel...
Creating Refinement tilt-series video for iteration #1...
Generating Refinement reconstruction for iteration #1...
The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01847 for Iteration #2 of Tilt-Series #16.
CCMS(rotations) = 0.55633 for Iteration #2 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #16.
The scaled sum of CCMS values is #0.02036 for iteration 2 of Tilt-Series #16.
Alignment quality for Iteration #2 of Tilt-Series #16 (17sep08r): 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 0.323000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01692 for Iteration #3 of Tilt-Series #16.
CCMS(rotations) = 0.54892 for Iteration #3 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01944 for iteration 3 of Tilt-Series #16.
Alignment quality for Iteration #3 of Tilt-Series #16 (17sep08r): 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 1.218000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.03321 for Iteration #4 of Tilt-Series #16.
CCMS(rotations) = 0.89989 for Iteration #4 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0346 for iteration 4 of Tilt-Series #16.
Alignment quality for Iteration #4 of Tilt-Series #16 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #16 (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 2.045000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.03461 for Iteration #5 of Tilt-Series #16.
CCMS(rotations) = 1.068 for Iteration #5 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #16.
The scaled sum of CCMS values is #0.03866 for iteration 5 of Tilt-Series #16.
Alignment quality for Iteration #5 of Tilt-Series #16 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #16 (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 3.380000, which is greater than the maximum allowed deviation of 3.000000.Changing the tilt azimuth back to the initial tilt azimuth of -96.000000 for the next iteration.
No Round parameters changed for Iteration #6 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.03212 for Iteration #6 of Tilt-Series #16.
CCMS(rotations) = 0.75045 for Iteration #6 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #16.
The scaled sum of CCMS values is #0.03107 for iteration 6 of Tilt-Series #16.
Alignment quality for Iteration #6 of Tilt-Series #16 (17sep08r): Bad (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #16 (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 1.663000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.02073 for Iteration #7 of Tilt-Series #16.
CCMS(rotations) = 0.54176 for Iteration #7 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0212 for iteration 7 of Tilt-Series #16.
Alignment quality for Iteration #7 of Tilt-Series #16 (17sep08r): Okay (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #16 (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 1.345000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #8 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.01916 for Iteration #8 of Tilt-Series #16.
CCMS(rotations) = 0.40399 for Iteration #8 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01766 for iteration 8 of Tilt-Series #16.
Alignment quality for Iteration #8 of Tilt-Series #16 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #16 (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 0.781000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.01538 for Iteration #9 of Tilt-Series #16.
CCMS(rotations) = 0.36827 for Iteration #9 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01506 for iteration 9 of Tilt-Series #16.
Alignment quality for Iteration #9 of Tilt-Series #16 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #16 (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 0.248000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.01225 for Iteration #10 of Tilt-Series #16.
CCMS(rotations) = 0.32274 for Iteration #10 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01258 for iteration 10 of Tilt-Series #16.
Alignment quality for Iteration #10 of Tilt-Series #16 (17sep08r): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #16 (17sep08r): Rock Solid!Creating 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 0.134000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
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 = 22.1742539668
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 = 22.1742539668
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Creating quality assessment statistics...
CCMS(shift) = 0.01042 for Iteration #11 of Tilt-Series #16.
CCMS(rotations) = 0.23094 for Iteration #11 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00983 for iteration 11 of Tilt-Series #16.
Alignment quality for Iteration #11 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #16 (17sep08r): 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 0.032000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #12 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #12
Creating quality assessment statistics...
CCMS(shift) = 0.00998 for Iteration #12 of Tilt-Series #16.
CCMS(rotations) = 0.21922 for Iteration #12 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00937 for iteration 12 of Tilt-Series #16.
Alignment quality for Iteration #12 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #16 (17sep08r): 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 0.440000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #13 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #13
Creating quality assessment statistics...
CCMS(shift) = 0.00871 for Iteration #13 of Tilt-Series #16.
CCMS(rotations) = 0.2173 for Iteration #13 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0087 for iteration 13 of Tilt-Series #16.
Alignment quality for Iteration #13 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #16 (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 0.588000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #14 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #14
Creating quality assessment statistics...
CCMS(shift) = 0.00814 for Iteration #14 of Tilt-Series #16.
CCMS(rotations) = 0.2371 for Iteration #14 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00881 for iteration 14 of Tilt-Series #16.
Alignment quality for Iteration #14 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #16 (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 0.504000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #15 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #15
Creating quality assessment statistics...
CCMS(shift) = 0.00819 for Iteration #15 of Tilt-Series #16.
CCMS(rotations) = 0.237 for Iteration #15 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00883 for iteration 15 of Tilt-Series #16.
Alignment quality for Iteration #15 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #16 (17sep08r): 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 0.575000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #16 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #16
Creating quality assessment statistics...
CCMS(shift) = 0.00749 for Iteration #16 of Tilt-Series #16.
CCMS(rotations) = 0.20624 for Iteration #16 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00787 for iteration 16 of Tilt-Series #16.
Alignment quality for Iteration #16 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #16 (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 0.656000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #17 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #17
Creating quality assessment statistics...
CCMS(shift) = 0.00625 for Iteration #17 of Tilt-Series #16.
CCMS(rotations) = 0.17738 for Iteration #17 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00667 for iteration 17 of Tilt-Series #16.
Alignment quality for Iteration #17 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #16 (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 0.835000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #18 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #18
Creating quality assessment statistics...
CCMS(shift) = 0.0059 for Iteration #18 of Tilt-Series #16.
CCMS(rotations) = 0.2134 for Iteration #18 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00722 for iteration 18 of Tilt-Series #16.
Alignment quality for Iteration #18 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #16 (17sep08r): Very StableCreating 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 0.873000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #19 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #19
Creating quality assessment statistics...
CCMS(shift) = 0.00521 for Iteration #19 of Tilt-Series #16.
CCMS(rotations) = 0.1939 for Iteration #19 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00648 for iteration 19 of Tilt-Series #16.
Alignment quality for Iteration #19 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #16 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel...
Creating Refinement tilt-series video for iteration #19...
Generating Refinement reconstruction for iteration #19...
The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.780000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #20 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #20
Creating quality assessment statistics...
CCMS(shift) = 0.00566 for Iteration #20 of Tilt-Series #16.
CCMS(rotations) = 0.21047 for Iteration #20 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00704 for iteration 20 of Tilt-Series #16.
Alignment quality for Iteration #20 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #16 (17sep08r): StableCreating 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 0.955000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #21, Round #3 of Tilt-Series #16 (tiltseries0016_thick150)
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 = 44.3485079335
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 = 44.3485079335
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Creating quality assessment statistics...
CCMS(shift) = 0.00633 for Iteration #21 of Tilt-Series #16.
CCMS(rotations) = 0.24232 for Iteration #21 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00801 for iteration 21 of Tilt-Series #16.
Alignment quality for Iteration #21 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #16 (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 0.764000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #22 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #22
Creating quality assessment statistics...
CCMS(shift) = 0.00577 for Iteration #22 of Tilt-Series #16.
CCMS(rotations) = 0.1696 for Iteration #22 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00628 for iteration 22 of Tilt-Series #16.
Alignment quality for Iteration #22 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #16 (17sep08r): Rock Solid!Creating 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 0.848000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #23 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #23
Creating quality assessment statistics...
CCMS(shift) = 0.00558 for Iteration #23 of Tilt-Series #16.
CCMS(rotations) = 0.15712 for Iteration #23 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00593 for iteration 23 of Tilt-Series #16.
Alignment quality for Iteration #23 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #16 (17sep08r): Very StableCreating 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 0.783000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #24 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #24
Creating quality assessment statistics...
CCMS(shift) = 0.00617 for Iteration #24 of Tilt-Series #16.
CCMS(rotations) = 0.20061 for Iteration #24 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0071 for iteration 24 of Tilt-Series #16.
Alignment quality for Iteration #24 of Tilt-Series #16 (17sep08r): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #16 (17sep08r): Very 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 0.628000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #25 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #25
Creating quality assessment statistics...
CCMS(shift) = 0.00794 for Iteration #25 of Tilt-Series #16.
CCMS(rotations) = 0.19162 for Iteration #25 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0078 for iteration 25 of Tilt-Series #16.
Alignment quality for Iteration #25 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #16 (17sep08r): 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 0.711000, which is less than the maximum allowed deviation of 3.000000.
Beginning Refinement Iteration #26, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
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 = 88.697015867
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 = 88.697015867
window.lowpass.diameter = { 0.7488 0.7488 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Creating quality assessment statistics...
CCMS(shift) = 0.00668 for Iteration #26 of Tilt-Series #16.
CCMS(rotations) = 0.2238 for Iteration #26 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00782 for iteration 26 of Tilt-Series #16.
Alignment quality for Iteration #26 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #16 (17sep08r): Very StableCreating Depiction Videos for Iteration #26 in Parallel...
Creating Refinement tilt-series video for iteration #26...
Generating Refinement reconstruction for iteration #26...
The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 0.646000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #27 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #27
Creating quality assessment statistics...
CCMS(shift) = 0.00693 for Iteration #27 of Tilt-Series #16.
CCMS(rotations) = 0.32182 for Iteration #27 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0099 for iteration 27 of Tilt-Series #16.
Alignment quality for Iteration #27 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #16 (17sep08r): Rock Solid!Creating 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 0.629000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #28 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #28
Creating quality assessment statistics...
CCMS(shift) = 0.00814 for Iteration #28 of Tilt-Series #16.
CCMS(rotations) = 0.2624 for Iteration #28 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00932 for iteration 28 of Tilt-Series #16.
Alignment quality for Iteration #28 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #16 (17sep08r): UnstableCreating Depiction Videos for Iteration #28 in Parallel...
Creating Refinement tilt-series video for iteration #28...
Generating Refinement reconstruction for iteration #28...
The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 0.620000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #29 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #29
Creating quality assessment statistics...
CCMS(shift) = 0.00737 for Iteration #29 of Tilt-Series #16.
CCMS(rotations) = 0.26693 for Iteration #29 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00902 for iteration 29 of Tilt-Series #16.
Alignment quality for Iteration #29 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #16 (17sep08r): Rock Solid!Creating 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 0.615000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #30 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #30
Creating quality assessment statistics...
CCMS(shift) = 0.01038 for Iteration #30 of Tilt-Series #16.
CCMS(rotations) = 0.25329 for Iteration #30 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #16.
The scaled sum of CCMS values is #0.01026 for iteration 30 of Tilt-Series #16.
Alignment quality for Iteration #30 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #16 (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 0.366000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #31 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
fit.scale switched from false to true on Iteration #31Creating quality assessment statistics...
CCMS(shift) = 0.00649 for Iteration #31 of Tilt-Series #16.
CCMS(rotations) = 0.29271 for Iteration #31 of Tilt-Series #16.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0091 for iteration 31 of Tilt-Series #16.
Alignment quality for Iteration #31 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #16 (17sep08r): Very StableCreating 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 0.263000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #32 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #32
Creating quality assessment statistics...
CCMS(shift) = 0.00773 for Iteration #32 of Tilt-Series #16.
CCMS(rotations) = 0.34343 for Iteration #32 of Tilt-Series #16.
CCMS(scale) = 0.00187 for Iteration #32 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00778 for iteration 32 of Tilt-Series #16.
Alignment quality for Iteration #32 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #16 (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 0.036000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #33 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #33
Creating quality assessment statistics...
CCMS(shift) = 0.00631 for Iteration #33 of Tilt-Series #16.
CCMS(rotations) = 0.34779 for Iteration #33 of Tilt-Series #16.
CCMS(scale) = 0.0029 for Iteration #33 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00771 for iteration 33 of Tilt-Series #16.
Alignment quality for Iteration #33 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #16 (17sep08r): 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 0.076000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #34 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #34
Creating quality assessment statistics...
CCMS(shift) = 0.00832 for Iteration #34 of Tilt-Series #16.
CCMS(rotations) = 0.28696 for Iteration #34 of Tilt-Series #16.
CCMS(scale) = 0.003 for Iteration #34 of Tilt-Series #16.
The scaled sum of CCMS values is #0.0076 for iteration 34 of Tilt-Series #16.
Alignment quality for Iteration #34 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #16 (17sep08r): 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 0.000000, which is less than the maximum allowed deviation of 3.000000.
No Round parameters changed for Iteration #35 of Tilt-Series #16 (tiltseries0016_thick150)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #16 (tiltseries0016_thick150)
No parameters were switched for Iteration #35
Creating quality assessment statistics...
CCMS(shift) = 0.00853 for Iteration #35 of Tilt-Series #16.
CCMS(rotations) = 0.27535 for Iteration #35 of Tilt-Series #16.
CCMS(scale) = 0.00371 for Iteration #35 of Tilt-Series #16.
The scaled sum of CCMS values is #0.00775 for iteration 35 of Tilt-Series #16.
Alignment quality for Iteration #35 of Tilt-Series #16 (17sep08r): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #16 (17sep08r): Rock Solid!Creating Depiction Videos for Iteration #35 in Parallel...
Creating Refinement tilt-series video for iteration #35...
Generating Refinement reconstruction for iteration #35...
The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.133000, which is less than the maximum allowed deviation of 3.000000.Finished Refinement for Tilt-Series #16 (tiltseries0016_thick150)!
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-16hr58m19s