protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=1484 --r2_region_x=1484 --r3_region_x=1484 --r4_region_x=1484 --r5_region_x=1484 --r1_region_y=1535 --r2_region_y=1535 --r3_region_y=1535 --r4_region_y=1535 --r5_region_y=1535 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=160 --r2_mask_width_x=346 --r3_mask_width_x=717 --r4_mask_width_x=1459 --r5_mask_width_x=1459 --r1_mask_width_y=166 --r2_mask_width_y=358 --r3_mask_width_y=742 --r4_mask_width_y=1510 --r5_mask_width_y=1510 --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=2616 --r2_highpass_diameter_x=2616 --r3_highpass_diameter_x=2616 --r4_highpass_diameter_x=2616 --r5_highpass_diameter_x=2616 --r1_highpass_diameter_y=2616 --r2_highpass_diameter_y=2616 --r3_highpass_diameter_y=2616 --r4_highpass_diameter_y=2616 --r5_highpass_diameter_y=2616 --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=1308 --r2_highpass_apod_x=1308 --r3_highpass_apod_x=1308 --r4_highpass_apod_x=1308 --r5_highpass_apod_x=1308 --r1_highpass_apod_y=1308 --r2_highpass_apod_y=1308 --r3_highpass_apod_y=1308 --r4_highpass_apod_y=1308 --r5_highpass_apod_y=1308 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=14 --r2_iters=10 --r3_iters=5 --r4_iters=10 --r5_iters=0 --preprocessing=true --azimuth_stability_check=False --azimuth_max_deviation=3 --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

node03
Start time: 2017yr03m27d-23hr49m28s
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 = { 0.0107829969419 0.0107829969419 }
window.highpass.apodization = { 0.0215659938838 0.0215659938838 }
window.mask.apodization = { 10 10 }
align.mask.width = { 160 166 }
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 = { 185 191 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 160 166 }
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) = 0.03585 for Iteration #1 of Tilt-Series #6.
CCMS(rotations) = 0.88526 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 #0.03563 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...

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.04261 for Iteration #2 of Tilt-Series #6.
CCMS(rotations) = 2.08274 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 #0.06296 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...
Refinement Iteration #2 finished after retrying 1 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 1344
Window Size (y) was windowed down to 1344

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.06269 for Iteration #3 of Tilt-Series #6.
CCMS(rotations) = 1.552 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 #0.06238 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...
Refinement Iteration #3 finished after retrying 15 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 720
Window Size (y) was windowed down to 720

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.21648 for Iteration #4 of Tilt-Series #6.
CCMS(rotations) = 1.42149 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 #0.13667 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...
Refinement Iteration #4 finished after retrying 26 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 336
Window Size (y) was windowed down to 336

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.14757 for Iteration #5 of Tilt-Series #6.
CCMS(rotations) = 2.54047 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 #0.12459 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...
Refinement Iteration #5 finished after retrying 26 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 336
Window Size (y) was windowed down to 336

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.20033 for Iteration #6 of Tilt-Series #6.
CCMS(rotations) = 7.48279 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 #0.24982 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...
Refinement Iteration #6 finished after retrying 32 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 192
Window Size (y) was windowed down to 192

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.27953 for Iteration #7 of Tilt-Series #6.
CCMS(rotations) = 9.58355 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 #0.33143 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...
Refinement Iteration #7 finished after retrying 32 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 192
Window Size (y) was windowed down to 192

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.153 for Iteration #8 of Tilt-Series #6.
CCMS(rotations) = 11.28883 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 #0.30227 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...
Refinement Iteration #8 finished after retrying 28 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 288
Window Size (y) was windowed down to 288

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.23393 for Iteration #9 of Tilt-Series #6.
CCMS(rotations) = 13.18986 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 #0.38076 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...
Refinement Iteration #9 finished after retrying 32 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 192
Window Size (y) was windowed down to 192

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
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #33 with Window Size: (160, 160) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.34524 for Iteration #10 of Tilt-Series #6.
CCMS(rotations) = 14.73059 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 #0.46723 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...
Refinement Iteration #10 finished after retrying 33 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 160
Window Size (y) was windowed down to 160

No Round parameters changed for Iteration #11 of Tilt-Series #6 (tiltseries0006)

Beginning Refinement Iteration #11, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #11
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #33 with Window Size: (160, 160) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.37173 for Iteration #11 of Tilt-Series #6.
CCMS(rotations) = 17.54969 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 #0.53686 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...
Refinement Iteration #11 finished after retrying 33 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 160
Window Size (y) was windowed down to 160

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

Beginning Refinement Iteration #12, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #12
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #33 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #34 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #35 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #36 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #37 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #38 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #39 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #40 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #41 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #42 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #43 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #44 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #45 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #46 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #47 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #48 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #49 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #50 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #51 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #52 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #53 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #54 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #55 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #56 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #57 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #58 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #59 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #60 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #61 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #62 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #63 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #64 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #65 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #66 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #67 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #68 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #69 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #70 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #71 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #72 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #73 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #74 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #75 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #76 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #77 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #78 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #79 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #80 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #81 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #82 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #83 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #84 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #85 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #86 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #87 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #88 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #89 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #90 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #91 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #92 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #93 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #94 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #95 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #96 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #97 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #98 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #99 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #100 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #101 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #102 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #103 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #104 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #105 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #106 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #107 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #108 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #109 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #110 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #111 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #112 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #113 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #114 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #115 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #116 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #117 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #118 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #119 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #120 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #121 with Window Size: (448, 448) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.09241 for Iteration #12 of Tilt-Series #6.
CCMS(rotations) = 17.09692 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 #0.38814 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...
Refinement Iteration #12 finished after retrying 121 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 448
Window Size (y) was windowed down to 448

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

Beginning Refinement Iteration #13, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #13
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.11031 for Iteration #13 of Tilt-Series #6.
CCMS(rotations) = 18.22761 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 #0.41971 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...
Refinement Iteration #13 finished after retrying 21 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 480
Window Size (y) was windowed down to 480

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

Beginning Refinement Iteration #14, Round #1 of Tilt-Series #6 (tiltseries0006)
No parameters were switched for Iteration #14
Refinement failed. Retry #1 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #2 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #3 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #4 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #5 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #6 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #7 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #8 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #9 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #10 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #11 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #12 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #13 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #14 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #15 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #16 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #17 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #18 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #19 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #20 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #21 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #22 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #23 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #24 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #25 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #26 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #27 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #28 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #29 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #30 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #31 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #32 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #33 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #34 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #35 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #36 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #37 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #38 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #39 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #40 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #41 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #42 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #43 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #44 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #45 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #46 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #47 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #48 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #49 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #50 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #51 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #52 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #53 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #54 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #55 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #56 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #57 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #58 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #59 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #60 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #61 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #62 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #63 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #64 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #65 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #66 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #67 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #68 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #69 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #70 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #71 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #72 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #73 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #74 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #75 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #76 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #77 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #78 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #79 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #80 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #81 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #82 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #83 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #84 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #85 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #86 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #87 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #88 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #89 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #90 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #91 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #92 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #93 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #94 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #95 with Window Size: (256, 256) (at sampling 8)...
Refinement failed. Retry #96 with Window Size: (240, 240) (at sampling 8)...
Refinement failed. Retry #97 with Window Size: (224, 224) (at sampling 8)...
Refinement failed. Retry #98 with Window Size: (192, 192) (at sampling 8)...
Refinement failed. Retry #99 with Window Size: (160, 160) (at sampling 8)...
Refinement failed. Retry #100 with Window Size: (1344, 1344) (at sampling 8)...
Refinement failed. Retry #101 with Window Size: (1296, 1296) (at sampling 8)...
Refinement failed. Retry #102 with Window Size: (1280, 1280) (at sampling 8)...
Refinement failed. Retry #103 with Window Size: (1200, 1200) (at sampling 8)...
Refinement failed. Retry #104 with Window Size: (1152, 1152) (at sampling 8)...
Refinement failed. Retry #105 with Window Size: (1120, 1120) (at sampling 8)...
Refinement failed. Retry #106 with Window Size: (1024, 1024) (at sampling 8)...
Refinement failed. Retry #107 with Window Size: (1008, 1008) (at sampling 8)...
Refinement failed. Retry #108 with Window Size: (960, 960) (at sampling 8)...
Refinement failed. Retry #109 with Window Size: (896, 896) (at sampling 8)...
Refinement failed. Retry #110 with Window Size: (864, 864) (at sampling 8)...
Refinement failed. Retry #111 with Window Size: (800, 800) (at sampling 8)...
Refinement failed. Retry #112 with Window Size: (784, 784) (at sampling 8)...
Refinement failed. Retry #113 with Window Size: (768, 768) (at sampling 8)...
Refinement failed. Retry #114 with Window Size: (720, 720) (at sampling 8)...
Refinement failed. Retry #115 with Window Size: (672, 672) (at sampling 8)...
Refinement failed. Retry #116 with Window Size: (640, 640) (at sampling 8)...
Refinement failed. Retry #117 with Window Size: (576, 576) (at sampling 8)...
Refinement failed. Retry #118 with Window Size: (560, 560) (at sampling 8)...
Refinement failed. Retry #119 with Window Size: (512, 512) (at sampling 8)...
Refinement failed. Retry #120 with Window Size: (480, 480) (at sampling 8)...
Refinement failed. Retry #121 with Window Size: (448, 448) (at sampling 8)...
Refinement failed. Retry #122 with Window Size: (432, 432) (at sampling 8)...
Refinement failed. Retry #123 with Window Size: (400, 400) (at sampling 8)...
Refinement failed. Retry #124 with Window Size: (384, 384) (at sampling 8)...
Refinement failed. Retry #125 with Window Size: (336, 336) (at sampling 8)...
Refinement failed. Retry #126 with Window Size: (320, 320) (at sampling 8)...
Refinement failed. Retry #127 with Window Size: (288, 288) (at sampling 8)...
Refinement failed. Retry #128 with Window Size: (256, 256) (at sampling 8)...
Creating quality assessment statistics...
CCMS(shift) = 0.21794 for Iteration #14 of Tilt-Series #6.
CCMS(rotations) = 19.14147 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 #0.4918 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...
Refinement Iteration #14 finished after retrying 128 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 256
Window Size (y) was windowed down to 256

Beginning Refinement Iteration #15, 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 = { 0.00539149847095 0.00539149847095 }
window.highpass.apodization = { 0.0107829969419 0.0107829969419 }
window.mask.apodization = { 10 10 }
align.mask.width = { 346 358 }
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 = { 371 383 }
preprocess.mask.kernel = { 5 5 }
window.mask.width = { 346 358 }
reference.body = 100.262251845
window.lowpass.diameter = { 0.5641664 0.5641664 }
align.correlation.mode = mcf
No parameters were switched for Iteration #15
Refinement failed. Retry #1 with Window Size: (1400, 1440) (at sampling 4)...
Refinement failed. Retry #2 with Window Size: (1344, 1400) (at sampling 4)...
Refinement failed. Retry #3 with Window Size: (1296, 1344) (at sampling 4)...
Refinement failed. Retry #4 with Window Size: (1280, 1296) (at sampling 4)...
Refinement failed. Retry #5 with Window Size: (1200, 1280) (at sampling 4)...
Refinement failed. Retry #6 with Window Size: (1176, 1200) (at sampling 4)...
Refinement failed. Retry #7 with Window Size: (1152, 1176) (at sampling 4)...
Refinement failed. Retry #8 with Window Size: (1120, 1152) (at sampling 4)...
Refinement failed. Retry #9 with Window Size: (1080, 1120) (at sampling 4)...
Refinement failed. Retry #10 with Window Size: (1024, 1080) (at sampling 4)...
Refinement failed. Retry #11 with Window Size: (1008, 1024) (at sampling 4)...
Refinement failed. Retry #12 with Window Size: (1000, 1008) (at sampling 4)...
Refinement failed. Retry #13 with Window Size: (960, 1000) (at sampling 4)...
Refinement failed. Retry #14 with Window Size: (896, 960) (at sampling 4)...
Refinement failed. Retry #15 with Window Size: (864, 896) (at sampling 4)...
Refinement failed. Retry #16 with Window Size: (840, 864) (at sampling 4)...
Refinement failed. Retry #17 with Window Size: (800, 840) (at sampling 4)...
Refinement failed. Retry #18 with Window Size: (784, 800) (at sampling 4)...
Refinement failed. Retry #19 with Window Size: (768, 784) (at sampling 4)...
Refinement failed. Retry #20 with Window Size: (720, 768) (at sampling 4)...
Refinement failed. Retry #21 with Window Size: (672, 720) (at sampling 4)...
Refinement failed. Retry #22 with Window Size: (648, 672) (at sampling 4)...
Refinement failed. Retry #23 with Window Size: (640, 648) (at sampling 4)...
Refinement failed. Retry #24 with Window Size: (600, 640) (at sampling 4)...
Refinement failed. Retry #25 with Window Size: (576, 600) (at sampling 4)...
Refinement failed. Retry #26 with Window Size: (560, 576) (at sampling 4)...
Refinement failed. Retry #27 with Window Size: (512, 560) (at sampling 4)...
Refinement failed. Retry #28 with Window Size: (504, 512) (at sampling 4)...
Refinement failed. Retry #29 with Window Size: (480, 504) (at sampling 4)...
Refinement failed. Retry #30 with Window Size: (448, 480) (at sampling 4)...
Refinement failed. Retry #31 with Window Size: (432, 448) (at sampling 4)...
Refinement failed. Retry #32 with Window Size: (400, 432) (at sampling 4)...
Refinement failed. Retry #33 with Window Size: (392, 400) (at sampling 4)...
Refinement failed. Retry #34 with Window Size: (384, 392) (at sampling 4)...
Refinement failed. Retry #35 with Window Size: (360, 384) (at sampling 4)...
Refinement failed. Retry #36 with Window Size: (336, 360) (at sampling 4)...
Refinement failed. Retry #37 with Window Size: (320, 336) (at sampling 4)...
Refinement failed. Retry #38 with Window Size: (288, 320) (at sampling 4)...
Refinement failed. Retry #39 with Window Size: (280, 288) (at sampling 4)...
Refinement failed. Retry #40 with Window Size: (256, 280) (at sampling 4)...
Refinement failed. Retry #41 with Window Size: (240, 256) (at sampling 4)...
Refinement failed. Retry #42 with Window Size: (224, 240) (at sampling 4)...
Refinement failed. Retry #43 with Window Size: (216, 224) (at sampling 4)...
Refinement failed. Retry #44 with Window Size: (200, 216) (at sampling 4)...
Refinement failed. Retry #45 with Window Size: (192, 200) (at sampling 4)...
Refinement failed. Retry #46 with Window Size: (168, 192) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.2008 for Iteration #15 of Tilt-Series #6.
CCMS(rotations) = 19.54704 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 #0.49134 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...
Refinement Iteration #15 finished after retrying 46 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 168
Window Size (y) was windowed down to 192

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: (1400, 1440) (at sampling 4)...
Refinement failed. Retry #2 with Window Size: (1344, 1400) (at sampling 4)...
Refinement failed. Retry #3 with Window Size: (1296, 1344) (at sampling 4)...
Refinement failed. Retry #4 with Window Size: (1280, 1296) (at sampling 4)...
Refinement failed. Retry #5 with Window Size: (1200, 1280) (at sampling 4)...
Refinement failed. Retry #6 with Window Size: (1176, 1200) (at sampling 4)...
Refinement failed. Retry #7 with Window Size: (1152, 1176) (at sampling 4)...
Refinement failed. Retry #8 with Window Size: (1120, 1152) (at sampling 4)...
Refinement failed. Retry #9 with Window Size: (1080, 1120) (at sampling 4)...
Refinement failed. Retry #10 with Window Size: (1024, 1080) (at sampling 4)...
Refinement failed. Retry #11 with Window Size: (1008, 1024) (at sampling 4)...
Refinement failed. Retry #12 with Window Size: (1000, 1008) (at sampling 4)...
Refinement failed. Retry #13 with Window Size: (960, 1000) (at sampling 4)...
Refinement failed. Retry #14 with Window Size: (896, 960) (at sampling 4)...
Refinement failed. Retry #15 with Window Size: (864, 896) (at sampling 4)...
Refinement failed. Retry #16 with Window Size: (840, 864) (at sampling 4)...
Refinement failed. Retry #17 with Window Size: (800, 840) (at sampling 4)...
Refinement failed. Retry #18 with Window Size: (784, 800) (at sampling 4)...
Refinement failed. Retry #19 with Window Size: (768, 784) (at sampling 4)...
Refinement failed. Retry #20 with Window Size: (720, 768) (at sampling 4)...
Refinement failed. Retry #21 with Window Size: (672, 720) (at sampling 4)...
Refinement failed. Retry #22 with Window Size: (648, 672) (at sampling 4)...
Refinement failed. Retry #23 with Window Size: (640, 648) (at sampling 4)...
Refinement failed. Retry #24 with Window Size: (600, 640) (at sampling 4)...
Refinement failed. Retry #25 with Window Size: (576, 600) (at sampling 4)...
Refinement failed. Retry #26 with Window Size: (560, 576) (at sampling 4)...
Refinement failed. Retry #27 with Window Size: (512, 560) (at sampling 4)...
Refinement failed. Retry #28 with Window Size: (504, 512) (at sampling 4)...
Refinement failed. Retry #29 with Window Size: (480, 504) (at sampling 4)...
Refinement failed. Retry #30 with Window Size: (448, 480) (at sampling 4)...
Refinement failed. Retry #31 with Window Size: (432, 448) (at sampling 4)...
Refinement failed. Retry #32 with Window Size: (400, 432) (at sampling 4)...
Refinement failed. Retry #33 with Window Size: (392, 400) (at sampling 4)...
Refinement failed. Retry #34 with Window Size: (384, 392) (at sampling 4)...
Refinement failed. Retry #35 with Window Size: (360, 384) (at sampling 4)...
Refinement failed. Retry #36 with Window Size: (336, 360) (at sampling 4)...
Refinement failed. Retry #37 with Window Size: (320, 336) (at sampling 4)...
Refinement failed. Retry #38 with Window Size: (288, 320) (at sampling 4)...
Refinement failed. Retry #39 with Window Size: (280, 288) (at sampling 4)...
Refinement failed. Retry #40 with Window Size: (256, 280) (at sampling 4)...
Refinement failed. Retry #41 with Window Size: (240, 256) (at sampling 4)...
Refinement failed. Retry #42 with Window Size: (224, 240) (at sampling 4)...
Refinement failed. Retry #43 with Window Size: (216, 224) (at sampling 4)...
Refinement failed. Retry #44 with Window Size: (200, 216) (at sampling 4)...
Refinement failed. Retry #45 with Window Size: (192, 200) (at sampling 4)...
Refinement failed. Retry #46 with Window Size: (168, 192) (at sampling 4)...
Refinement failed. Retry #47 with Window Size: (160, 168) (at sampling 4)...
Refinement failed. Retry #48 with Window Size: (144, 160) (at sampling 4)...
Refinement failed. Retry #49 with Window Size: (128, 144) (at sampling 4)...
Refinement failed. Retry #50 with Window Size: (120, 128) (at sampling 4)...
Refinement failed. Retry #51 with Window Size: (112, 120) (at sampling 4)...
Refinement failed. Retry #52 with Window Size: (96, 112) (at sampling 4)...
Creating quality assessment statistics...
CCMS(shift) = 0.51529 for Iteration #16 of Tilt-Series #6.
CCMS(rotations) = 17.69081 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 #0.61146 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...
Refinement Iteration #16 finished after retrying 52 time(s) due to the sampled search area being too small.
Window Size (x) was windowed down to 96
Window Size (y) was windowed down to 112

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: (1400, 1440) (at sampling 4)...
Refinement failed. Retry #2 with Window Size: (1344, 1400) (at sampling 4)...
Refinement failed. Retry #3 with Window Size: (1296, 1344) (at sampling 4)...
Refinement failed. Retry #4 with Window Size: (1280, 1296) (at sampling 4)...
Refinement failed. Retry #5 with Window Size: (1200, 1280) (at sampling 4)...
Refinement failed. Retry #6 with Window Size: (1176, 1200) (at sampling 4)...
Refinement failed. Retry #7 with Window Size: (1152, 1176) (at sampling 4)...
Refinement failed. Retry #8 with Window Size: (1120, 1152) (at sampling 4)...
Refinement failed. Retry #9 with Window Size: (1080, 1120) (at sampling 4)...
Refinement failed. Retry #10 with Window Size: (1024, 1080) (at sampling 4)...
Refinement failed. Retry #11 with Window Size: (1008, 1024) (at sampling 4)...
Refinement failed. Retry #12 with Window Size: (1000, 1008) (at sampling 4)...
Refinement failed. Retry #13 with Window Size: (960, 1000) (at sampling 4)...
Refinement failed. Retry #14 with Window Size: (896, 960) (at sampling 4)...
Refinement failed. Retry #15 with Window Size: (864, 896) (at sampling 4)...
Refinement failed. Retry #16 with Window Size: (840, 864) (at sampling 4)...
Refinement failed. Retry #17 with Window Size: (800, 840) (at sampling 4)...
Refinement failed. Retry #18 with Window Size: (784, 800) (at sampling 4)...
Refinement failed. Retry #19 with Window Size: (768, 784) (at sampling 4)...
Refinement failed. Retry #20 with Window Size: (720, 768) (at sampling 4)...
Refinement failed. Retry #21 with Window Size: (672, 720) (at sampling 4)...
Refinement failed. Retry #22 with Window Size: (648, 672) (at sampling 4)...
Refinement failed. Retry #23 with Window Size: (640, 648) (at sampling 4)...
Refinement failed. Retry #24 with Window Size: (600, 640) (at sampling 4)...
Refinement failed. Retry #25 with Window Size: (576, 600) (at sampling 4)...
Refinement failed. Retry #26 with Window Size: (560, 576) (at sampling 4)...
Refinement failed. Retry #27 with Window Size: (512, 560) (at sampling 4)...
Refinement failed. Retry #28 with Window Size: (504, 512) (at sampling 4)...
Refinement failed. Retry #29 with Window Size: (480, 504) (at sampling 4)...
Refinement failed. Retry #30 with Window Size: (448, 480) (at sampling 4)...
Refinement failed. Retry #31 with Window Size: (432, 448) (at sampling 4)...
Refinement failed. Retry #32 with Window Size: (400, 432) (at sampling 4)...
Refinement failed. Retry #33 with Window Size: (392, 400) (at sampling 4)...
Refinement failed. Retry #34 with Window Size: (384, 392) (at sampling 4)...
Refinement failed. Retry #35 with Window Size: (360, 384) (at sampling 4)...
Refinement failed. Retry #36 with Window Size: (336, 360) (at sampling 4)...
Refinement failed. Retry #37 with Window Size: (320, 336) (at sampling 4)...
Refinement failed. Retry #38 with Window Size: (288, 320) (at sampling 4)...
Refinement failed. Retry #39 with Window Size: (280, 288) (at sampling 4)...
Refinement failed. Retry #40 with Window Size: (256, 280) (at sampling 4)...
Refinement failed. Retry #41 with Window Size: (240, 256) (at sampling 4)...
Refinement failed. Retry #42 with Window Size: (224, 240) (at sampling 4)...
Refinement failed. Retry #43 with Window Size: (216, 224) (at sampling 4)...
Refinement failed. Retry #44 with Window Size: (200, 216) (at sampling 4)...
Refinement failed. Retry #45 with Window Size: (192, 200) (at sampling 4)...
Refinement failed. Retry #46 with Window Size: (168, 192) (at sampling 4)...
Refinement failed. Retry #47 with Window Size: (160, 168) (at sampling 4)...
Refinement failed. Retry #48 with Window Size: (144, 160) (at sampling 4)...
Refinement failed. Retry #49 with Window Size: (128, 144) (at sampling 4)...
Refinement failed. Retry #50 with Window Size: (120, 128) (at sampling 4)...
Refinement failed. Retry #51 with Window Size: (112, 120) (at sampling 4)...
Refinement failed. Retry #52 with Window Size: (96, 112) (at sampling 4)...
Refinement failed. Retry #53 with Window Size: (80, 96) (at sampling 4)...
Refinement failed. Retry #54 with Window Size: (1400, 1400) (at sampling 4)...
Refinement failed. Retry #55 with Window Size: (1344, 1344) (at sampling 4)...
Refinement failed. Retry #56 with Window Size: (1296, 1296) (at sampling 4)...
Refinement failed. Retry #57 with Window Size: (1280, 1280) (at sampling 4)...
Refinement failed. Retry #58 with Window Size: (1200, 1200) (at sampling 4)...
Refinement failed. Retry #59 with Window Size: (1176, 1176) (at sampling 4)...
Refinement failed. Retry #60 with Window Size: (1152, 1152) (at sampling 4)...
Refinement failed. Retry #61 with Window Size: (1120, 1120) (at sampling 4)...
Refinement failed. Retry #62 with Window Size: (1080, 1080) (at sampling 4)...
Refinement failed. Retry #63 with Window Size: (1024, 1024) (at sampling 4)...
Refinement failed. Retry #64 with Window Size: (1008, 1008) (at sampling 4)...
Refinement failed. Retry #65 with Window Size: (1000, 1000) (at sampling 4)...
Refinement failed. Retry #66 with Window Size: (960, 960) (at sampling 4)...
Refinement failed. Retry #67 with Window Size: (896, 896) (at sampling 4)...
Refinement failed. Retry #68 with Window Size: (864, 864) (at sampling 4)...
Refinement failed. Retry #69 with Window Size: (840, 840) (at sampling 4)...
Refinement failed. Retry #70 with Window Size: (800, 800) (at sampling 4)...
Refinement failed. Retry #71 with Window Size: (784, 784) (at sampling 4)...
Refinement failed. Retry #72 with Window Size: (768, 768) (at sampling 4)...
Refinement failed. Retry #73 with Window Size: (720, 720) (at sampling 4)...
Refinement failed. Retry #74 with Window Size: (672, 672) (at sampling 4)...
Refinement failed. Retry #75 with Window Size: (648, 648) (at sampling 4)...
Refinement failed. Retry #76 with Window Size: (640, 640) (at sampling 4)...
Refinement failed. Retry #77 with Window Size: (600, 600) (at sampling 4)...
Refinement failed. Retry #78 with Window Size: (576, 576) (at sampling 4)...
Refinement failed. Retry #79 with Window Size: (560, 560) (at sampling 4)...
Refinement failed. Retry #80 with Window Size: (512, 512) (at sampling 4)...
Refinement failed. Retry #81 with Window Size: (504, 504) (at sampling 4)...
Refinement failed. Retry #82 with Window Size: (480, 480) (at sampling 4)...
Refinement failed. Retry #83 with Window Size: (448, 448) (at sampling 4)...
Refinement failed. Retry #84 with Window Size: (432, 432) (at sampling 4)...
Refinement failed. Retry #85 with Window Size: (400, 400) (at sampling 4)...
Refinement failed. Retry #86 with Window Size: (392, 392) (at sampling 4)...
Refinement failed. Retry #87 with Window Size: (384, 384) (at sampling 4)...
Refinement failed. Retry #88 with Window Size: (360, 360) (at sampling 4)...
Refinement failed. Retry #89 with Window Size: (336, 336) (at sampling 4)...
Refinement failed. Retry #90 with Window Size: (320, 320) (at sampling 4)...
Refinement failed. Retry #91 with Window Size: (288, 288) (at sampling 4)...
Refinement failed. Retry #92 with Window Size: (280, 280) (at sampling 4)...
Refinement failed. Retry #93 with Window Size: (256, 256) (at sampling 4)...
Refinement failed. Retry #94 with Window Size: (240, 240) (at sampling 4)...
Refinement failed. Retry #95 with Window Size: (224, 224) (at sampling 4)...
Refinement failed. Retry #96 with Window Size: (216, 216) (at sampling 4)...
Refinement failed. Retry #97 with Window Size: (200, 200) (at sampling 4)...
Refinement failed. Retry #98 with Window Size: (192, 192) (at sampling 4)...
Refinement failed. Retry #99 with Window Size: (168, 168) (at sampling 4)...
Refinement failed. Retry #100 with Window Size: (160, 160) (at sampling 4)...
Refinement failed. Retry #101 with Window Size: (144, 144) (at sampling 4)...
Refinement failed. Retry #102 with Window Size: (128, 128) (at sampling 4)...
Refinement failed. Retry #103 with Window Size: (120, 120) (at sampling 4)...
Refinement failed. Retry #104 with Window Size: (112, 112) (at sampling 4)...
Refinement failed. Retry #105 with Window Size: (96, 96) (at sampling 4)...
Refinement failed. Retry #106 with Window Size: (80, 80) (at sampling 4)...
Refinement failed. Retry #107 with Window Size: (1400, 1400) (at sampling 4)...
Refinement failed. Retry #108 with Window Size: (1344, 1344) (at sampling 4)...
Refinement failed. Retry #109 with Window Size: (1296, 1296) (at sampling 4)...
Refinement failed. Retry #110 with Window Size: (1280, 1280) (at sampling 4)...
Refinement failed. Retry #111 with Window Size: (1200, 1200) (at sampling 4)...
Refinement failed. Retry #112 with Window Size: (1176, 1176) (at sampling 4)...
Refinement failed. Retry #113 with Window Size: (1152, 1152) (at sampling 4)...
Refinement failed. Retry #114 with Window Size: (1120, 1120) (at sampling 4)...
Refinement failed. Retry #115 with Window Size: (1080, 1080) (at sampling 4)...
Refinement failed. Retry #116 with Window Size: (1024, 1024) (at sampling 4)...
Refinement failed. Retry #117 with Window Size: (1008, 1008) (at sampling 4)...
Refinement failed. Retry #118 with Window Size: (1000, 1000) (at sampling 4)...
Refinement failed. Retry #119 with Window Size: (960, 960) (at sampling 4)...
Refinement failed. Retry #120 with Window Size: (896, 896) (at sampling 4)...
Refinement failed. Retry #121 with Window Size: (864, 864) (at sampling 4)...
Refinement failed. Retry #122 with Window Size: (840, 840) (at sampling 4)...
Refinement failed. Retry #123 with Window Size: (800, 800) (at sampling 4)...
Refinement failed. Retry #124 with Window Size: (784, 784) (at sampling 4)...
Refinement failed. Retry #125 with Window Size: (768, 768) (at sampling 4)...
Refinement failed. Retry #126 with Window Size: (720, 720) (at sampling 4)...
Refinement failed. Retry #127 with Window Size: (672, 672) (at sampling 4)...
Refinement failed. Retry #128 with Window Size: (648, 648) (at sampling 4)...
Refinement failed. Retry #129 with Window Size: (640, 640) (at sampling 4)...
Refinement failed. Retry #130 with Window Size: (600, 600) (at sampling 4)...
Refinement failed. Retry #131 with Window Size: (576, 576) (at sampling 4)...
Refinement failed. Retry #132 with Window Size: (560, 560) (at sampling 4)...
Refinement failed. Retry #133 with Window Size: (512, 512) (at sampling 4)...
Refinement failed. Retry #134 with Window Size: (504, 504) (at sampling 4)...
Refinement failed. Retry #135 with Window Size: (480, 480) (at sampling 4)...
Refinement failed. Retry #136 with Window Size: (448, 448) (at sampling 4)...
Refinement failed. Retry #137 with Window Size: (432, 432) (at sampling 4)...
Refinement failed. Retry #138 with Window Size: (400, 400) (at sampling 4)...
Refinement failed. Retry #139 with Window Size: (392, 392) (at sampling 4)...
Refinement failed. Retry #140 with Window Size: (384, 384) (at sampling 4)...
Refinement failed. Retry #141 with Window Size: (360, 360) (at sampling 4)...
Refinement failed. Retry #142 with Window Size: (336, 336) (at sampling 4)...
Refinement failed. Retry #143 with Window Size: (320, 320) (at sampling 4)...
Refinement failed. Retry #144 with Window Size: (288, 288) (at sampling 4)...
Refinement failed. Retry #145 with Window Size: (280, 280) (at sampling 4)...
Refinement failed. Retry #146 with Window Size: (256, 256) (at sampling 4)...
Refinement failed. Retry #147 with Window Size: (240, 240) (at sampling 4)...
Refinement failed. Retry #148 with Window Size: (224, 224) (at sampling 4)...
Refinement failed. Retry #149 with Window Size: (216, 216) (at sampling 4)...
Refinement failed. Retry #150 with Window Size: (200, 200) (at sampling 4)...
Refinement failed. Retry #151 with Window Size: (192, 192) (at sampling 4)...
Refinement failed. Retry #152 with Window Size: (168, 168) (at sampling 4)...
Refinement failed. Retry #153 with Window Size: (160, 160) (at sampling 4)...
Refinement failed. Retry #154 with Window Size: (144, 144) (at sampling 4)...
Refinement failed. Retry #155 with Window Size: (128, 128) (at sampling 4)...
Refinement failed. Retry #156 with Window Size: (120, 120) (at sampling 4)...
Refinement failed. Retry #157 with Window Size: (112, 112) (at sampling 4)...
Refinement failed. Retry #158 with Window Size: (96, 96) (at sampling 4)...
Refinement failed. Retry #159 with Window Size: (80, 80) (at sampling 4)...
Refinement failed. Retry #160 with Window Size: (1400, 1400) (at sampling 4)...
Refinement failed. Retry #161 with Window Size: (1344, 1344) (at sampling 4)...
Refinement failed. Retry #162 with Window Size: (1296, 1296) (at sampling 4)...
Refinement failed. Retry #163 with Window Size: (1280, 1280) (at sampling 4)...
Refinement failed. Retry #164 with Window Size: (1200, 1200) (at sampling 4)...
Refinement failed. Retry #165 with Window Size: (1176, 1176) (at sampling 4)...
Refinement failed. Retry #166 with Window Size: (1152, 1152) (at sampling 4)...
Refinement failed. Retry #167 with Window Size: (1120, 1120) (at sampling 4)...
Refinement failed. Retry #168 with Window Size: (1080, 1080) (at sampling 4)...
Refinement failed. Retry #169 with Window Size: (1024, 1024) (at sampling 4)...
Refinement failed. Retry #170 with Window Size: (1008, 1008) (at sampling 4)...
Refinement failed. Retry #171 with Window Size: (1000, 1000) (at sampling 4)...
Refinement failed. Retry #172 with Window Size: (960, 960) (at sampling 4)...
Refinement failed. Retry #173 with Window Size: (896, 896) (at sampling 4)...
Refinement failed. Retry #174 with Window Size: (864, 864) (at sampling 4)...
Refinement failed. Retry #175 with Window Size: (840, 840) (at sampling 4)...
Refinement failed. Retry #176 with Window Size: (800, 800) (at sampling 4)...
Refinement failed. Retry #177 with Window Size: (784, 784) (at sampling 4)...
Refinement failed. Retry #178 with Window Size: (768, 768) (at sampling 4)...
Refinement failed. Retry #179 with Window Size: (720, 720) (at sampling 4)...
Refinement failed. Retry #180 with Window Size: (672, 672) (at sampling 4)...
Refinement failed. Retry #181 with Window Size: (648, 648) (at sampling 4)...
Refinement failed. Retry #182 with Window Size: (640, 640) (at sampling 4)...
Refinement failed. Retry #183 with Window Size: (600, 600) (at sampling 4)...
Refinement failed. Retry #184 with Window Size: (576, 576) (at sampling 4)...
Refinement failed. Retry #185 with Window Size: (560, 560) (at sampling 4)...
Refinement failed. Retry #186 with Window Size: (512, 512) (at sampling 4)...
Refinement failed. Retry #187 with Window Size: (504, 504) (at sampling 4)...
Refinement failed. Retry #188 with Window Size: (480, 480) (at sampling 4)...
Refinement failed. Retry #189 with Window Size: (448, 448) (at sampling 4)...
Refinement failed. Retry #190 with Window Size: (432, 432) (at sampling 4)...
Refinement failed. Retry #191 with Window Size: (400, 400) (at sampling 4)...
Refinement failed. Retry #192 with Window Size: (392, 392) (at sampling 4)...
Refinement failed. Retry #193 with Window Size: (384, 384) (at sampling 4)...
Refinement failed. Retry #194 with Window Size: (360, 360) (at sampling 4)...
Refinement failed. Retry #195 with Window Size: (336, 336) (at sampling 4)...
Refinement failed. Retry #196 with Window Size: (320, 320) (at sampling 4)...
Refinement failed. Retry #197 with Window Size: (288, 288) (at sampling 4)...
Refinement failed. Retry #198 with Window Size: (280, 280) (at sampling 4)...
Refinement failed. Retry #199 with Window Size: (256, 256) (at sampling 4)...
Refinement failed. Retry #200 with Window Size: (240, 240) (at sampling 4)...
Refinement failed. Retry #201 with Window Size: (224, 224) (at sampling 4)...
Refinement failed. Retry #202 with Window Size: (216, 216) (at sampling 4)...
Refinement failed. Retry #203 with Window Size: (200, 200) (at sampling 4)...
Refinement failed. Retry #204 with Window Size: (192, 192) (at sampling 4)...
Refinement failed. Retry #205 with Window Size: (168, 168) (at sampling 4)...
Refinement failed. Retry #206 with Window Size: (160, 160) (at sampling 4)...
Refinement failed. Retry #207 with Window Size: (144, 144) (at sampling 4)...
Refinement failed. Retry #208 with Window Size: (128, 128) (at sampling 4)...
Refinement failed. Retry #209 with Window Size: (120, 120) (at sampling 4)...
Refinement failed. Retry #210 with Window Size: (112, 112) (at sampling 4)...
Refinement failed. Retry #211 with Window Size: (96, 96) (at sampling 4)...
Refinement failed. Retry #212 with Window Size: (80, 80) (at sampling 4)...
Refinement failed. Retry #213 with Window Size: (1400, 1400) (at sampling 4)...
Refinement failed. Retry #214 with Window Size: (1344, 1344) (at sampling 4)...
Refinement failed. Retry #215 with Window Size: (1296, 1296) (at sampling 4)...
Refinement failed. Retry #216 with Window Size: (1280, 1280) (at sampling 4)...
Refinement failed. Retry #217 with Window Size: (1200, 1200) (at sampling 4)...
Refinement failed. Retry #218 with Window Size: (1176, 1176) (at sampling 4)...
Refinement failed. Retry #219 with Window Size: (1152, 1152) (at sampling 4)...
Refinement failed. Retry #220 with Window Size: (1120, 1120) (at sampling 4)...
Refinement failed. Retry #221 with Window Size: (1080, 1080) (at sampling 4)...
Refinement failed. Retry #222 with Window Size: (1024, 1024) (at sampling 4)...
Refinement failed. Retry #223 with Window Size: (1008, 1008) (at sampling 4)...
Refinement failed. Retry #224 with Window Size: (1000, 1000) (at sampling 4)...
Refinement failed. Retry #225 with Window Size: (960, 960) (at sampling 4)...
Refinement failed. Retry #226 with Window Size: (896, 896) (at sampling 4)...
Refinement failed. Retry #227 with Window Size: (864, 864) (at sampling 4)...
Refinement failed. Retry #228 with Window Size: (840, 840) (at sampling 4)...
Refinement failed. Retry #229 with Window Size: (800, 800) (at sampling 4)...
Refinement failed. Retry #230 with Window Size: (784, 784) (at sampling 4)...
Refinement failed. Retry #231 with Window Size: (768, 768) (at sampling 4)...
Refinement failed. Retry #232 with Window Size: (720, 720) (at sampling 4)...
Refinement failed. Retry #233 with Window Size: (672, 672) (at sampling 4)...
Refinement failed. Retry #234 with Window Size: (648, 648) (at sampling 4)...
Refinement failed. Retry #235 with Window Size: (640, 640) (at sampling 4)...
Refinement failed. Retry #236 with Window Size: (600, 600) (at sampling 4)...
Refinement failed. Retry #237 with Window Size: (576, 576) (at sampling 4)...
Refinement failed. Retry #238 with Window Size: (560, 560) (at sampling 4)...
Refinement failed. Retry #239 with Window Size: (512, 512) (at sampling 4)...
Refinement failed. Retry #240 with Window Size: (504, 504) (at sampling 4)...
Refinement failed. Retry #241 with Window Size: (480, 480) (at sampling 4)...
Refinement failed. Retry #242 with Window Size: (448, 448) (at sampling 4)...
Refinement failed. Retry #243 with Window Size: (432, 432) (at sampling 4)...
Refinement failed. Retry #244 with Window Size: (400, 400) (at sampling 4)...
Refinement failed. Retry #245 with Window Size: (392, 392) (at sampling 4)...
Refinement failed. Retry #246 with Window Size: (384, 384) (at sampling 4)...
Refinement failed. Retry #247 with Window Size: (360, 360) (at sampling 4)...
Refinement failed. Retry #248 with Window Size: (336, 336) (at sampling 4)...
Refinement failed. Retry #249 with Window Size: (320, 320) (at sampling 4)...
Refinement failed. Retry #250 with Window Size: (288, 288) (at sampling 4)...
Refinement failed. Retry #251 with Window Size: (280, 280) (at sampling 4)...
Refinement failed. Retry #252 with Window Size: (256, 256) (at sampling 4)...
Refinement failed. Retry #253 with Window Size: (240, 240) (at sampling 4)...
Refinement failed. Retry #254 with Window Size: (224, 224) (at sampling 4)...
Refinement failed. Retry #255 with Window Size: (216, 216) (at sampling 4)...
Refinement failed. Retry #256 with Window Size: (200, 200) (at sampling 4)...
Refinement failed. Retry #257 with Window Size: (192, 192) (at sampling 4)...
Refinement failed. Retry #258 with Window Size: (168, 168) (at sampling 4)...
Refinement failed. Retry #259 with Window Size: (160, 160) (at sampling 4)...
Refinement failed. Retry #260 with Window Size: (144, 144) (at sampling 4)...
Refinement failed. Retry #261 with Window Size: (128, 128) (at sampling 4)...
Refinement failed. Retry #262 with Window Size: (120, 120) (at sampling 4)...
Refinement failed. Retry #263 with Window Size: (112, 112) (at sampling 4)...
Refinement failed. Retry #264 with Window Size: (96, 96) (at sampling 4)...
Refinement failed. Retry #265 with Window Size: (80, 80) (at sampling 4)...
Refinement Iteration #17 for Tilt-Series #6 (tiltseries0006) failed after resampling the search area 265 time(s).
Window Size (x) was windowed down to 80
Window Size (y) was windowed down to 80
Put values less than these into the corresponding parameter boxes on the Protomo Refinement Appion webpage and try again.
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: 2017yr03m28d-00hr19m16s