protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=2782 --r2_region_x=2782 --r3_region_x=2782 --r4_region_x=2782 --r5_region_x=2782 --r1_region_y=2878 --r2_region_y=2878 --r3_region_y=2878 --r4_region_y=2878 --r5_region_y=2878 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=322 --r2_mask_width_x=670 --r3_mask_width_x=1366 --r4_mask_width_x=2757 --r5_mask_width_x=2757 --r1_mask_width_y=334 --r2_mask_width_y=694 --r3_mask_width_y=1414 --r4_mask_width_y=2853 --r5_mask_width_y=2853 --r1_lowpass_diameter_x=50 --r2_lowpass_diameter_x=25 --r3_lowpass_diameter_x=12.5 --r4_lowpass_diameter_x=6.25 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=50 --r2_lowpass_diameter_y=25 --r3_lowpass_diameter_y=12.5 --r4_lowpass_diameter_y=6.25 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=4905 --r2_highpass_diameter_x=4905 --r3_highpass_diameter_x=4905 --r4_highpass_diameter_x=4905 --r5_highpass_diameter_x=4905 --r1_highpass_diameter_y=4905 --r2_highpass_diameter_y=4905 --r3_highpass_diameter_y=4905 --r4_highpass_diameter_y=4905 --r5_highpass_diameter_y=4905 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=125 --r2_lowpass_apod_x=63 --r3_lowpass_apod_x=31 --r4_lowpass_apod_x=16 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=125 --r2_lowpass_apod_y=63 --r3_lowpass_apod_y=31 --r4_lowpass_apod_y=16 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=2453 --r2_highpass_apod_x=2453 --r3_highpass_apod_x=2453 --r4_highpass_apod_x=2453 --r5_highpass_apod_x=2453 --r1_highpass_apod_y=2453 --r2_highpass_apod_y=2453 --r3_highpass_apod_y=2453 --r4_highpass_apod_y=2453 --r5_highpass_apod_y=2453 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=10 --r2_iters=10 --r3_iters=5 --r4_iters=10 --r5_iters=0 --preprocessing=true --azimuth_stability_check=True --azimuth_max_deviation=1 --exclude_images_by_angle_accuracy=0.05 --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 --do_estimation=false --norotations=false --correlation_size_x=160 --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 --translimit=959 --orientation=true --azimuth=true --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true --video_type=html5vid --runname=tiltseries0006 --rundir=/gpfs/appion/jbrasch/17mar17a/protomo_alignments/tiltseries0006 --tiltseries=6 --sessionname=17mar17a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=282 --expid=3656 --jobtype=protomo

node05
Start time: 2017yr03m28d-13hr40m55s
Description: 
Using Manual alignment for Refinement by copying manual_series0006.tlt to series0006.tlt.Starting Protomo alignment

Beginning Refinements

Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006)
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 = 50.1311259224
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 = 50.1311259224
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #1
Creating quality assessment statistics...
CCMS(shift) = 0.0175 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 0.26975 for Iteration #1 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01415 for Tilt-Series #6.
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 0.140000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #2 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #2
Creating quality assessment statistics...
CCMS(shift) = 0.01674 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 0.29257 for Iteration #2 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01422 for Tilt-Series #6.
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 0.043000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #3 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #3
Creating quality assessment statistics...
CCMS(shift) = 0.01692 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 0.31993 for Iteration #3 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01486 for Tilt-Series #6.
Creating Depiction Videos for Iteration #3 in Parallel...
Creating Refinement tilt-series video for iteration #3...
Generating Refinement reconstruction for iteration #3...
The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.055000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #4 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #4, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #4
Creating quality assessment statistics...
CCMS(shift) = 0.01538 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 0.31204 for Iteration #4 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01393 for Tilt-Series #6.
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 0.143000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #5 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #5, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #5
Creating quality assessment statistics...
CCMS(shift) = 0.0287 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 0.43585 for Iteration #5 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02307 for Tilt-Series #6.
Creating 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 1.009000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.
No Round parameters changed for Iteration #6 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #6, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #6
Creating quality assessment statistics...
CCMS(shift) = 0.0227 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 0.29958 for Iteration #6 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01734 for Tilt-Series #6.
Creating Depiction Videos for Iteration #6 in Parallel...
Creating Refinement tilt-series video for iteration #6...
Generating Refinement reconstruction for iteration #6...
The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.326000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #7 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #7, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #7
Creating quality assessment statistics...
CCMS(shift) = 0.02778 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 0.54375 for Iteration #7 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02477 for Tilt-Series #6.
Creating Depiction Videos for Iteration #7 in Parallel...
Creating Refinement tilt-series video for iteration #7...
Generating Refinement reconstruction for iteration #7...
The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 1.241000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.
No Round parameters changed for Iteration #8 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #8, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #8
Creating quality assessment statistics...
CCMS(shift) = 0.02623 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 0.48438 for Iteration #8 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0228 for Tilt-Series #6.
Creating 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 0.773000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #9 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #9, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #9
Creating quality assessment statistics...
CCMS(shift) = 0.02004 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 0.2935 for Iteration #9 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01589 for Tilt-Series #6.
Creating 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 0.289000, which is less than the maximum allowed deviation of 1.000000.
No Round parameters changed for Iteration #10 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #10, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #10
Creating quality assessment statistics...
CCMS(shift) = 0.02733 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 0.4379 for Iteration #10 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02242 for Tilt-Series #6.
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 1.236000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.
Beginning Refinement Iteration #11, Round #2 of Tilt-Series #6 (tiltseries0006)
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 = 100.262251845
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 = 100.262251845
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #11
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01649 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 0.40816 for Iteration #11 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01641 for Tilt-Series #6.
Creating 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 0.958000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #11 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #12 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #12, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #12
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01541 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 0.40562 for Iteration #12 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01582 for Tilt-Series #6.
Creating Depiction Videos for Iteration #12 in Parallel...
Creating Refinement tilt-series video for iteration #12...
Generating Refinement reconstruction for iteration #12...
The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 0.791000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #12 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #13 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #13, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #13
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.02084 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 0.4296 for Iteration #13 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01901 for Tilt-Series #6.
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 0.965000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #13 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #14 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #14, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #14
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01906 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 0.46697 for Iteration #14 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01887 for Tilt-Series #6.
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 0.571000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #14 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #15 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #15, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #15
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.0233 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 0.48082 for Iteration #15 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02127 for Tilt-Series #6.
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 0.715000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #15 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #16 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #16, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #16
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01675 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 0.61931 for Iteration #16 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02076 for Tilt-Series #6.
Creating Depiction Videos for Iteration #16 in Parallel...
Creating Refinement tilt-series video for iteration #16...
Generating Refinement reconstruction for iteration #16...
The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.680000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #16 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #17 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #17, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #17
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.02897 for Iteration #17 of Tilt-Series #6.
CCMS(rotations) = 0.44078 for Iteration #17 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0233 for Tilt-Series #6.
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 1.083000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.Refinement Iteration #17 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #18 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #18, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #18
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01809 for Iteration #18 of Tilt-Series #6.
CCMS(rotations) = 0.17856 for Iteration #18 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01262 for Tilt-Series #6.
Creating Depiction Videos for Iteration #18 in Parallel...
Creating Refinement tilt-series video for iteration #18...
Generating Refinement reconstruction for iteration #18...
The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 0.253000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #18 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #19 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #19, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #19
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01639 for Iteration #19 of Tilt-Series #6.
CCMS(rotations) = 0.19953 for Iteration #19 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01218 for Tilt-Series #6.
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 0.017000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #19 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #20 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #20, Round #2 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #20
Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.01402 for Iteration #20 of Tilt-Series #6.
CCMS(rotations) = 0.21285 for Iteration #20 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01127 for Tilt-Series #6.
Creating Depiction Videos for Iteration #20 in Parallel...
Creating Refinement tilt-series video for iteration #20...
Generating Refinement reconstruction for iteration #20...
The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 0.017000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #20 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2688
Window Size (y) was windowed down to 2744

Beginning Refinement Iteration #21, Round #3 of Tilt-Series #6 (tiltseries0006)
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 = 200.52450369
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 = 200.52450369
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #21
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)...
Creating quality assessment statistics...
CCMS(shift) = 0.01351 for Iteration #21 of Tilt-Series #6.
CCMS(rotations) = 0.38212 for Iteration #21 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0144 for Tilt-Series #6.
Creating 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 0.173000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #21 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #22 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #22, Round #3 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #22
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)...
Creating quality assessment statistics...
CCMS(shift) = 0.01573 for Iteration #22 of Tilt-Series #6.
CCMS(rotations) = 0.5709 for Iteration #22 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01928 for Tilt-Series #6.
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 0.491000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #22 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #23 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #23, Round #3 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #23
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)...
Creating quality assessment statistics...
CCMS(shift) = 0.01851 for Iteration #23 of Tilt-Series #6.
CCMS(rotations) = 0.70131 for Iteration #23 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02328 for Tilt-Series #6.
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 0.113000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #23 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #24 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #24, Round #3 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #24
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)...
Creating quality assessment statistics...
CCMS(shift) = 0.01716 for Iteration #24 of Tilt-Series #6.
CCMS(rotations) = 0.45101 for Iteration #24 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #6.
The scaled sum of CCMS values is #0.0176 for Tilt-Series #6.
Creating Depiction Videos for Iteration #24 in Parallel...
Creating Refinement tilt-series video for iteration #24...
Generating Refinement reconstruction for iteration #24...
The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.003000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #24 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #25 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #25, Round #3 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #25
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)...
Creating quality assessment statistics...
CCMS(shift) = 0.02221 for Iteration #25 of Tilt-Series #6.
CCMS(rotations) = 0.43281 for Iteration #25 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01976 for Tilt-Series #6.
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 0.101000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #25 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

Beginning Refinement Iteration #26, Round #4 of Tilt-Series #6 (tiltseries0006)
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 = 401.049007379
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 = 401.049007379
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #26
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.0245 for Iteration #26 of Tilt-Series #6.
CCMS(rotations) = 0.52657 for Iteration #26 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02278 for Tilt-Series #6.
Creating 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 0.098000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #26 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #27 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #27, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #27
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01881 for Iteration #27 of Tilt-Series #6.
CCMS(rotations) = 0.47028 for Iteration #27 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01881 for Tilt-Series #6.
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 0.968000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #27 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #28 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #28, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #28
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.02073 for Iteration #28 of Tilt-Series #6.
CCMS(rotations) = 0.56402 for Iteration #28 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02164 for Tilt-Series #6.
Creating 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 0.415000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #28 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #29 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #29, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #29
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.02233 for Iteration #29 of Tilt-Series #6.
CCMS(rotations) = 0.65084 for Iteration #29 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02418 for Tilt-Series #6.
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 1.618000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.Refinement Iteration #29 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #30 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #30, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #30
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.0273 for Iteration #30 of Tilt-Series #6.
CCMS(rotations) = 0.56756 for Iteration #30 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #6.
The scaled sum of CCMS values is #0.025 for Tilt-Series #6.
Creating 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 0.879000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #30 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #31 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #31, Round #4 of Tilt-Series #6 (tiltseries0006)
fit.scale switched from false to true on Iteration #31Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01817 for Iteration #31 of Tilt-Series #6.
CCMS(rotations) = 0.60805 for Iteration #31 of Tilt-Series #6.
CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #6.
The scaled sum of CCMS values is #0.02125 for Tilt-Series #6.
Creating Depiction Videos for Iteration #31 in Parallel...
Creating Refinement tilt-series video for iteration #31...
Generating Refinement reconstruction for iteration #31...
The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 1.471000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.Refinement Iteration #31 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #32 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #32, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #32
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01759 for Iteration #32 of Tilt-Series #6.
CCMS(rotations) = 0.50692 for Iteration #32 of Tilt-Series #6.
CCMS(scale) = 0.0063 for Iteration #32 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01472 for Tilt-Series #6.
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 0.489000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #32 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #33 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #33, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #33
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01788 for Iteration #33 of Tilt-Series #6.
CCMS(rotations) = 0.60639 for Iteration #33 of Tilt-Series #6.
CCMS(scale) = 0.0063 for Iteration #33 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01614 for Tilt-Series #6.
Creating 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 1.007000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of -174.700000 for the next iteration.Refinement Iteration #33 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #34 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #34, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #34
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.02447 for Iteration #34 of Tilt-Series #6.
CCMS(rotations) = 0.52438 for Iteration #34 of Tilt-Series #6.
CCMS(scale) = 0.0063 for Iteration #34 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01725 for Tilt-Series #6.
Creating Depiction Videos for Iteration #34 in Parallel...
Creating Refinement tilt-series video for iteration #34...
Generating Refinement reconstruction for iteration #34...
The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 0.258000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #34 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744

No Round parameters changed for Iteration #35 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #35, Round #4 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #35
Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)...
Creating quality assessment statistics...
CCMS(shift) = 0.01661 for Iteration #35 of Tilt-Series #6.
CCMS(rotations) = 0.41825 for Iteration #35 of Tilt-Series #6.
CCMS(scale) = 0.0063 for Iteration #35 of Tilt-Series #6.
The scaled sum of CCMS values is #0.01321 for Tilt-Series #6.
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 0.584000, which is less than the maximum allowed deviation of 1.000000.Refinement Iteration #35 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 2700
Window Size (y) was windowed down to 2744
Finished Refinement for Tilt-Series #6 (tiltseries0006)!
Did everything blow up and now you're yelling at your computer screen?
If so, kindly email Alex at anoble@nysbc.org and include this log file.
If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations

End time: 2017yr03m29d-20hr22m12s