[ jchase@node15: Wed Sep 28 11:04:44 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true \ --iter_gradient=false --filter=median --kernel_x=5 --kernel_y=5 \ --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=322 --mask_width_y=334 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --defocus_estimate=2 --runname=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --defocus=5 --sessionname=16sep28d --pixelsize=1.76302 \ --dimx=3710 --dimy=3838 --coarse=True --projectid=45 --expid=2667 \ --jobtype=protomo [ jchase@node15: Wed Sep 28 11:11:29 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --tilt_azimuth=-6 --border=100 --clip_low=3.5 --clip_high=3.5 \ --gradient=true --iter_gradient=false --filter=median --kernel_x=5 \ --kernel_y=5 --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=347 --mask_width_y=359 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --amp_contrast_ctf=0.07 --iWidth=20 --DefocusTol=200 --defocus_estimate=2 \ --defocus_min=4 --defocus_max=6 --defocus_difference=0.2 --res_min=10000 \ --res_max=10 --runname=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 11:19:01 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --negative=-44 --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --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=5 --r3_iters=5 \ --r4_iters=5 --r5_iters=0 --preprocessing=true --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 \ --orientation=true --azimuth=true --elevation=false --rotation=true \ --scale=false --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=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 11:20:54 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --tilt_azimuth=-6 --border=100 --clip_low=3.5 --clip_high=3.5 \ --gradient=true --iter_gradient=false --filter=median --kernel_x=5 \ --kernel_y=5 --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=347 --mask_width_y=359 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --amp_contrast_ctf=0.07 --iWidth=20 --DefocusTol=200 --defocus_estimate=2 \ --defocus_min=6.4 --defocus_max=9.6 --defocus_difference=0.2 \ --res_min=10000 --res_max=10 --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 11:28:03 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=500 --lowpass_diameter_x=132 --lowpass_diameter_y=132 \ --lowpass_apod_x=330 --lowpass_apod_y=330 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-6 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=6.4 --defocus_max=9.6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 11:29:53 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --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=5 --r3_iters=5 \ --r4_iters=5 --r5_iters=0 --preprocessing=true --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 \ --orientation=true --azimuth=true --elevation=false --rotation=true \ --scale=false --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=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 20:02:11 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0003 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0003 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:02:29 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:02:45 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:03:06 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0006 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0006 \ --tiltseries=6 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node16: Wed Sep 28 20:03:32 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0007 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0007 \ --tiltseries=7 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node16: Wed Sep 28 20:04:00 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 20:08:36 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --negative=-44 --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --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 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --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=tiltseries0003 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0003 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:10:31 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --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 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --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=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:12:00 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --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=400 \ --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=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --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=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --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 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --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=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:13:49 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --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 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --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/jchase/16sep28d/protomo_alignments/tiltseries0006 \ --tiltseries=6 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node16: Wed Sep 28 20:15:51 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --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=400 \ --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=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --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=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --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=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --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 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --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=tiltseries0007 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0007 \ --tiltseries=7 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo Start time: 2016yr09m28d-20hr15m51s Description: Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 lowpass = 125.0 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 = { 0.090122428115 0.090122428115 } 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 = 40.1042008914 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 347 359 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 322 334 } reference.body = 40.1042008914 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.05508 for Iteration #1 of Tilt-Series #7. CCMS(rotations) = 1.42806 for Iteration #1 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7. The scaled sum of CCMS values is #0.0561 for Tilt-Series #7. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... Refinement Iteration #1 finished after retrying 18 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1440 Window Size (y) was windowed down to 1536 No Round parameters changed for Iteration #2 Beginning Refinement Iteration #2, Round #1 No parameters were switched for Iteration #2 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (448, 480) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (432, 448) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (400, 432) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (384, 400) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (336, 384) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (320, 336) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (288, 320) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (256, 288) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (240, 256) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (224, 240) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (192, 224) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (160, 192) (at sampling 8)... Refinement failed. Retry #52 with Window Size: (2592, 2592) (at sampling 8)... Refinement failed. Retry #53 with Window Size: (2560, 2560) (at sampling 8)... Refinement failed. Retry #54 with Window Size: (2400, 2400) (at sampling 8)... Refinement failed. Retry #55 with Window Size: (2352, 2352) (at sampling 8)... Refinement failed. Retry #56 with Window Size: (2304, 2304) (at sampling 8)... Refinement failed. Retry #57 with Window Size: (2240, 2240) (at sampling 8)... Refinement failed. Retry #58 with Window Size: (2160, 2160) (at sampling 8)... Refinement failed. Retry #59 with Window Size: (2048, 2048) (at sampling 8)... Refinement failed. Retry #60 with Window Size: (2016, 2016) (at sampling 8)... Refinement failed. Retry #61 with Window Size: (2000, 2000) (at sampling 8)... Refinement failed. Retry #62 with Window Size: (1920, 1920) (at sampling 8)... Refinement failed. Retry #63 with Window Size: (1792, 1792) (at sampling 8)... Refinement failed. Retry #64 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #65 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #66 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #67 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #68 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #69 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #70 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #71 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #72 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #73 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #74 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #75 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #76 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #77 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #78 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #79 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #80 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #81 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #82 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #83 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #84 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #85 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #86 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #87 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #88 with Window Size: (560, 560) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.09583 for Iteration #2 of Tilt-Series #7. CCMS(rotations) = 0.91012 for Iteration #2 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7. The scaled sum of CCMS values is #0.06612 for Tilt-Series #7. 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 88 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 560 Window Size (y) was windowed down to 560 No Round parameters changed for Iteration #3 Beginning Refinement Iteration #3, Round #1 No parameters were switched for Iteration #3 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07204 for Iteration #3 of Tilt-Series #7. CCMS(rotations) = 1.59914 for Iteration #3 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7. The scaled sum of CCMS values is #0.06801 for Tilt-Series #7. 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 37 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 560 Window Size (y) was windowed down to 576 No Round parameters changed for Iteration #4 Beginning Refinement Iteration #4, Round #1 No parameters were switched for Iteration #4 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07632 for Iteration #4 of Tilt-Series #7. CCMS(rotations) = 1.57185 for Iteration #4 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7. The scaled sum of CCMS values is #0.06959 for Tilt-Series #7. 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 33 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 768 No Round parameters changed for Iteration #5 Beginning Refinement Iteration #5, Round #1 No parameters were switched for Iteration #5 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07676 for Iteration #5 of Tilt-Series #7. CCMS(rotations) = 2.04988 for Iteration #5 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7. The scaled sum of CCMS values is #0.07938 for Tilt-Series #7. 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 23 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1152 Window Size (y) was windowed down to 1200 No Round parameters changed for Iteration #6 Beginning Refinement Iteration #6, Round #1 No parameters were switched for Iteration #6 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.06439 for Iteration #6 of Tilt-Series #7. CCMS(rotations) = 1.84993 for Iteration #6 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7. The scaled sum of CCMS values is #0.06919 for Tilt-Series #7. 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 22 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1200 Window Size (y) was windowed down to 1280 No Round parameters changed for Iteration #7 Beginning Refinement Iteration #7, Round #1 No parameters were switched for Iteration #7 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.06234 for Iteration #7 of Tilt-Series #7. CCMS(rotations) = 2.35864 for Iteration #7 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7. The scaled sum of CCMS values is #0.07834 for Tilt-Series #7. 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 22 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1200 Window Size (y) was windowed down to 1280 No Round parameters changed for Iteration #8 Beginning Refinement Iteration #8, Round #1 No parameters were switched for Iteration #8 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.14586 for Iteration #8 of Tilt-Series #7. CCMS(rotations) = 1.74345 for Iteration #8 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7. The scaled sum of CCMS values is #0.1078 for Tilt-Series #7. 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 39 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 512 No Round parameters changed for Iteration #9 Beginning Refinement Iteration #9, Round #1 No parameters were switched for Iteration #9 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.10953 for Iteration #9 of Tilt-Series #7. CCMS(rotations) = 3.44627 for Iteration #9 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7. The scaled sum of CCMS values is #0.12369 for Tilt-Series #7. 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 39 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 512 No Round parameters changed for Iteration #10 Beginning Refinement Iteration #10, Round #1 No parameters were switched for Iteration #10 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07238 for Iteration #10 of Tilt-Series #7. CCMS(rotations) = 3.15266 for Iteration #10 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7. The scaled sum of CCMS values is #0.09925 for Tilt-Series #7. 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 720 Window Size (y) was windowed down to 768 No Round parameters changed for Iteration #11 Beginning Refinement Iteration #11, Round #1 No parameters were switched for Iteration #11 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.13046 for Iteration #11 of Tilt-Series #7. CCMS(rotations) = 2.78599 for Iteration #11 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7. The scaled sum of CCMS values is #0.12095 for Tilt-Series #7. 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 35 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 640 Window Size (y) was windowed down to 672 No Round parameters changed for Iteration #12 Beginning Refinement Iteration #12, Round #1 No parameters were switched for Iteration #12 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.11297 for Iteration #12 of Tilt-Series #7. CCMS(rotations) = 2.28113 for Iteration #12 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7. The scaled sum of CCMS values is #0.10211 for Tilt-Series #7. 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 36 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 576 Window Size (y) was windowed down to 640 No Round parameters changed for Iteration #13 Beginning Refinement Iteration #13, Round #1 No parameters were switched for Iteration #13 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (448, 480) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (432, 448) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (400, 432) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (384, 400) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (336, 384) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (320, 336) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (288, 320) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (256, 288) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (240, 256) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (224, 240) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (192, 224) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (160, 192) (at sampling 8)... Refinement failed. Retry #52 with Window Size: (2592, 2592) (at sampling 8)... Refinement failed. Retry #53 with Window Size: (2560, 2560) (at sampling 8)... Refinement failed. Retry #54 with Window Size: (2400, 2400) (at sampling 8)... Refinement failed. Retry #55 with Window Size: (2352, 2352) (at sampling 8)... Refinement failed. Retry #56 with Window Size: (2304, 2304) (at sampling 8)... Refinement failed. Retry #57 with Window Size: (2240, 2240) (at sampling 8)... Refinement failed. Retry #58 with Window Size: (2160, 2160) (at sampling 8)... Refinement failed. Retry #59 with Window Size: (2048, 2048) (at sampling 8)... Refinement failed. Retry #60 with Window Size: (2016, 2016) (at sampling 8)... Refinement failed. Retry #61 with Window Size: (2000, 2000) (at sampling 8)... Refinement failed. Retry #62 with Window Size: (1920, 1920) (at sampling 8)... Refinement failed. Retry #63 with Window Size: (1792, 1792) (at sampling 8)... Refinement failed. Retry #64 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #65 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #66 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #67 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #68 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #69 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #70 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #71 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #72 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #73 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #74 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #75 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #76 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #77 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #78 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #79 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #80 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #81 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #82 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #83 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #84 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #85 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #86 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #87 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #88 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #89 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #90 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #91 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #92 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #93 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #94 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #95 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #96 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #97 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #98 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #99 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #100 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #101 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #102 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #103 with Window Size: (2592, 2592) (at sampling 8)... Refinement failed. Retry #104 with Window Size: (2560, 2560) (at sampling 8)... Refinement failed. Retry #105 with Window Size: (2400, 2400) (at sampling 8)... Refinement failed. Retry #106 with Window Size: (2352, 2352) (at sampling 8)... Refinement failed. Retry #107 with Window Size: (2304, 2304) (at sampling 8)... Refinement failed. Retry #108 with Window Size: (2240, 2240) (at sampling 8)... Refinement failed. Retry #109 with Window Size: (2160, 2160) (at sampling 8)... Refinement failed. Retry #110 with Window Size: (2048, 2048) (at sampling 8)... Refinement failed. Retry #111 with Window Size: (2016, 2016) (at sampling 8)... Refinement failed. Retry #112 with Window Size: (2000, 2000) (at sampling 8)... Refinement failed. Retry #113 with Window Size: (1920, 1920) (at sampling 8)... Refinement failed. Retry #114 with Window Size: (1792, 1792) (at sampling 8)... Refinement failed. Retry #115 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #116 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #117 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #118 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #119 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #120 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #121 with Window Size: (1344, 1344) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07181 for Iteration #13 of Tilt-Series #7. CCMS(rotations) = 2.20594 for Iteration #13 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7. The scaled sum of CCMS values is #0.08003 for Tilt-Series #7. 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 121 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 #14 Beginning Refinement Iteration #14, Round #1 No parameters were switched for Iteration #14 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.08297 for Iteration #14 of Tilt-Series #7. CCMS(rotations) = 2.17983 for Iteration #14 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7. The scaled sum of CCMS values is #0.08508 for Tilt-Series #7. 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 14 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1680 Window Size (y) was windowed down to 1728 No Round parameters changed for Iteration #15 Beginning Refinement Iteration #15, Round #1 No parameters were switched for Iteration #15 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.04656 for Iteration #15 of Tilt-Series #7. CCMS(rotations) = 1.76532 for Iteration #15 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7. The scaled sum of CCMS values is #0.05859 for Tilt-Series #7. 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 15 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1600 Window Size (y) was windowed down to 1680 No Round parameters changed for Iteration #16 Beginning Refinement Iteration #16, Round #1 No parameters were switched for Iteration #16 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.05604 for Iteration #16 of Tilt-Series #7. CCMS(rotations) = 3.36783 for Iteration #16 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7. The scaled sum of CCMS values is #0.09538 for Tilt-Series #7. 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 29 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 864 Window Size (y) was windowed down to 896 No Round parameters changed for Iteration #17 Beginning Refinement Iteration #17, Round #1 No parameters were switched for Iteration #17 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.12534 for Iteration #17 of Tilt-Series #7. CCMS(rotations) = 1.48273 for Iteration #17 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7. The scaled sum of CCMS values is #0.09232 for Tilt-Series #7. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... Refinement Iteration #17 finished after retrying 37 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 560 Window Size (y) was windowed down to 576 No Round parameters changed for Iteration #18 Beginning Refinement Iteration #18, Round #1 No parameters were switched for Iteration #18 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.13471 for Iteration #18 of Tilt-Series #7. CCMS(rotations) = 2.54736 for Iteration #18 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7. The scaled sum of CCMS values is #0.1183 for Tilt-Series #7. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... Refinement Iteration #18 finished after retrying 39 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 512 No Round parameters changed for Iteration #19 Beginning Refinement Iteration #19, Round #1 No parameters were switched for Iteration #19 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (448, 480) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (432, 448) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (400, 432) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (384, 400) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (336, 384) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (320, 336) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (288, 320) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (256, 288) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (240, 256) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.17449 for Iteration #19 of Tilt-Series #7. CCMS(rotations) = 3.2399 for Iteration #19 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7. The scaled sum of CCMS values is #0.15204 for Tilt-Series #7. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... Refinement Iteration #19 finished after retrying 48 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 240 Window Size (y) was windowed down to 256 No Round parameters changed for Iteration #20 Beginning Refinement Iteration #20, Round #1 No parameters were switched for Iteration #20 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2560, 2592) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (2400, 2560) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (2352, 2400) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (2304, 2352) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (2240, 2304) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (2160, 2240) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (2048, 2160) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (2016, 2048) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (2000, 2016) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1920, 2000) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1792, 1920) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1728, 1792) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1680, 1728) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (1600, 1680) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (1568, 1600) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (1536, 1568) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (1440, 1536) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (1344, 1440) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (1296, 1344) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (1280, 1296) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (1200, 1280) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (1152, 1200) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (1120, 1152) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (1024, 1120) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (1008, 1024) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (960, 1008) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (896, 960) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (864, 896) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (800, 864) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (784, 800) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (768, 784) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (720, 768) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (672, 720) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (640, 672) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (576, 640) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (560, 576) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (512, 560) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (480, 512) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (448, 480) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (432, 448) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (400, 432) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (384, 400) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (336, 384) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (320, 336) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (288, 320) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (256, 288) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (240, 256) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (224, 240) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (192, 224) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (160, 192) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.41243 for Iteration #20 of Tilt-Series #7. CCMS(rotations) = 28.4543 for Iteration #20 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7. The scaled sum of CCMS values is #0.7753 for Tilt-Series #7. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Refinement Iteration #20 finished after retrying 51 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 192 Beginning Refinement Iteration #21, Round #2 lowpass = 62.5 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 = { 0.0904112820513 0.0904112820513 } 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 = 80.2084017828 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 695 719 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 670 694 } reference.body = 80.2084017828 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2592, 2688) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (2560, 2592) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (2520, 2560) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (2400, 2520) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (2352, 2400) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (2304, 2352) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (2240, 2304) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (2160, 2240) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (2016, 2048) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (2000, 2016) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1960, 2000) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1944, 1960) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1920, 1944) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1800, 1920) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1792, 1800) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1728, 1792) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1680, 1728) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1600, 1680) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (1568, 1600) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (1536, 1568) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (1512, 1536) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (1440, 1512) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (1400, 1440) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (1344, 1400) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (1296, 1344) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (1280, 1296) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (1200, 1280) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (1176, 1200) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (1152, 1176) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (1120, 1152) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (1080, 1120) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (1024, 1080) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (1008, 1024) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (1000, 1008) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (960, 1000) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (896, 960) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (864, 896) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (840, 864) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (800, 840) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (784, 800) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (768, 784) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (720, 768) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (672, 720) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (648, 672) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (640, 648) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (600, 640) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (576, 600) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (560, 576) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (512, 560) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (504, 512) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (480, 504) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (448, 480) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (432, 448) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (400, 432) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (392, 400) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (384, 392) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (360, 384) (at sampling 4)... Refinement failed. Retry #60 with Window Size: (336, 360) (at sampling 4)... Refinement failed. Retry #61 with Window Size: (320, 336) (at sampling 4)... Refinement failed. Retry #62 with Window Size: (288, 320) (at sampling 4)... Refinement failed. Retry #63 with Window Size: (280, 288) (at sampling 4)... Refinement failed. Retry #64 with Window Size: (256, 280) (at sampling 4)... Refinement failed. Retry #65 with Window Size: (240, 256) (at sampling 4)... Refinement failed. Retry #66 with Window Size: (224, 240) (at sampling 4)... Refinement failed. Retry #67 with Window Size: (216, 224) (at sampling 4)... Refinement failed. Retry #68 with Window Size: (200, 216) (at sampling 4)... Refinement failed. Retry #69 with Window Size: (192, 200) (at sampling 4)... Refinement failed. Retry #70 with Window Size: (168, 192) (at sampling 4)... Refinement failed. Retry #71 with Window Size: (160, 168) (at sampling 4)... Refinement failed. Retry #72 with Window Size: (144, 160) (at sampling 4)... Refinement failed. Retry #73 with Window Size: (128, 144) (at sampling 4)... Refinement failed. Retry #74 with Window Size: (120, 128) (at sampling 4)... Refinement failed. Retry #75 with Window Size: (112, 120) (at sampling 4)... Refinement failed. Retry #76 with Window Size: (96, 112) (at sampling 4)... Refinement failed. Retry #77 with Window Size: (80, 96) (at sampling 4)... Refinement failed. Retry #78 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #79 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #80 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #81 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #82 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #83 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #84 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #85 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #86 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #87 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #88 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #89 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #90 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #91 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #92 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #93 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #94 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #95 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #96 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #97 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #98 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #99 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #100 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #101 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #102 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #103 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #104 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #105 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #106 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #107 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #108 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #109 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #110 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #111 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #112 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #113 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #114 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #115 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #116 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #117 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #118 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #119 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #120 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #121 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #122 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #123 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #124 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #125 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #126 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #127 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #128 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #129 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #130 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #131 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #132 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #133 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #134 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #135 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #136 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #137 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #138 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #139 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #140 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #141 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #142 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #143 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #144 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #145 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #146 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #147 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #148 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #149 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #150 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #151 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #152 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #153 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #154 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #155 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #156 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #157 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #158 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #159 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #160 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #161 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #162 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #163 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #164 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #165 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #166 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #167 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #168 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #169 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #170 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #171 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #172 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #173 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #174 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #175 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #176 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #177 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #178 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #179 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #180 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #181 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #182 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #183 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #184 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #185 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #186 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #187 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #188 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #189 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #190 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #191 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #192 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #193 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #194 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #195 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #196 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #197 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #198 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #199 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #200 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #201 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #202 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #203 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #204 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #205 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #206 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #207 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #208 with Window Size: (448, 448) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.06286 for Iteration #21 of Tilt-Series #7. CCMS(rotations) = 21.21088 for Iteration #21 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7. The scaled sum of CCMS values is #0.45565 for Tilt-Series #7. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... Refinement Iteration #21 finished after retrying 208 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 #22 Beginning Refinement Iteration #22, Round #2 No parameters were switched for Iteration #22 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2592, 2688) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (2560, 2592) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (2520, 2560) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (2400, 2520) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (2352, 2400) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (2304, 2352) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (2240, 2304) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (2160, 2240) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (2016, 2048) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (2000, 2016) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1960, 2000) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1944, 1960) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1920, 1944) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1800, 1920) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1792, 1800) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1728, 1792) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1680, 1728) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1600, 1680) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (1568, 1600) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (1536, 1568) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (1512, 1536) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (1440, 1512) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (1400, 1440) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (1344, 1400) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (1296, 1344) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (1280, 1296) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (1200, 1280) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (1176, 1200) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (1152, 1176) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (1120, 1152) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (1080, 1120) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (1024, 1080) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (1008, 1024) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (1000, 1008) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (960, 1000) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (896, 960) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (864, 896) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (840, 864) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (800, 840) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (784, 800) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (768, 784) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (720, 768) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (672, 720) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (648, 672) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (640, 648) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (600, 640) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (576, 600) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (560, 576) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (512, 560) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (504, 512) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (480, 504) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (448, 480) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (432, 448) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (400, 432) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (392, 400) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (384, 392) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (360, 384) (at sampling 4)... Refinement failed. Retry #60 with Window Size: (336, 360) (at sampling 4)... Refinement failed. Retry #61 with Window Size: (320, 336) (at sampling 4)... Refinement failed. Retry #62 with Window Size: (288, 320) (at sampling 4)... Refinement failed. Retry #63 with Window Size: (280, 288) (at sampling 4)... Refinement failed. Retry #64 with Window Size: (256, 280) (at sampling 4)... Refinement failed. Retry #65 with Window Size: (240, 256) (at sampling 4)... Refinement failed. Retry #66 with Window Size: (224, 240) (at sampling 4)... Refinement failed. Retry #67 with Window Size: (216, 224) (at sampling 4)... Refinement failed. Retry #68 with Window Size: (200, 216) (at sampling 4)... Refinement failed. Retry #69 with Window Size: (192, 200) (at sampling 4)... Refinement failed. Retry #70 with Window Size: (168, 192) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.14703 for Iteration #22 of Tilt-Series #7. CCMS(rotations) = 20.42412 for Iteration #22 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7. The scaled sum of CCMS values is #0.482 for Tilt-Series #7. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... Refinement Iteration #22 finished after retrying 70 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 #23 Beginning Refinement Iteration #23, Round #2 No parameters were switched for Iteration #23 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2592, 2688) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (2560, 2592) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (2520, 2560) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (2400, 2520) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (2352, 2400) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (2304, 2352) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (2240, 2304) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (2160, 2240) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (2016, 2048) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (2000, 2016) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1960, 2000) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1944, 1960) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1920, 1944) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1800, 1920) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1792, 1800) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1728, 1792) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1680, 1728) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1600, 1680) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (1568, 1600) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (1536, 1568) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (1512, 1536) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (1440, 1512) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (1400, 1440) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (1344, 1400) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (1296, 1344) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (1280, 1296) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (1200, 1280) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (1176, 1200) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (1152, 1176) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (1120, 1152) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (1080, 1120) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (1024, 1080) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (1008, 1024) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (1000, 1008) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (960, 1000) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (896, 960) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (864, 896) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (840, 864) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (800, 840) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (784, 800) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (768, 784) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (720, 768) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (672, 720) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (648, 672) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (640, 648) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (600, 640) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (576, 600) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (560, 576) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (512, 560) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (504, 512) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (480, 504) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (448, 480) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (432, 448) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (400, 432) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (392, 400) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (384, 392) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (360, 384) (at sampling 4)... Refinement failed. Retry #60 with Window Size: (336, 360) (at sampling 4)... Refinement failed. Retry #61 with Window Size: (320, 336) (at sampling 4)... Refinement failed. Retry #62 with Window Size: (288, 320) (at sampling 4)... Refinement failed. Retry #63 with Window Size: (280, 288) (at sampling 4)... Refinement failed. Retry #64 with Window Size: (256, 280) (at sampling 4)... Refinement failed. Retry #65 with Window Size: (240, 256) (at sampling 4)... Refinement failed. Retry #66 with Window Size: (224, 240) (at sampling 4)... Refinement failed. Retry #67 with Window Size: (216, 224) (at sampling 4)... Refinement failed. Retry #68 with Window Size: (200, 216) (at sampling 4)... Refinement failed. Retry #69 with Window Size: (192, 200) (at sampling 4)... Refinement failed. Retry #70 with Window Size: (168, 192) (at sampling 4)... Refinement failed. Retry #71 with Window Size: (160, 168) (at sampling 4)... Refinement failed. Retry #72 with Window Size: (144, 160) (at sampling 4)... Refinement failed. Retry #73 with Window Size: (128, 144) (at sampling 4)... Refinement failed. Retry #74 with Window Size: (120, 128) (at sampling 4)... Refinement failed. Retry #75 with Window Size: (112, 120) (at sampling 4)... Refinement failed. Retry #76 with Window Size: (96, 112) (at sampling 4)... Refinement failed. Retry #77 with Window Size: (80, 96) (at sampling 4)... Refinement failed. Retry #78 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #79 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #80 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #81 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #82 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #83 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #84 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #85 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #86 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #87 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #88 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #89 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #90 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #91 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #92 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #93 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #94 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #95 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #96 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #97 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #98 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #99 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #100 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #101 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #102 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #103 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #104 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #105 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #106 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #107 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #108 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #109 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #110 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #111 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #112 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #113 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #114 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #115 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #116 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #117 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #118 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #119 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #120 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #121 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #122 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #123 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #124 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #125 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #126 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #127 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #128 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #129 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #130 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #131 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #132 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #133 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #134 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #135 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #136 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #137 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #138 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #139 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #140 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #141 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #142 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #143 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #144 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #145 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #146 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #147 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #148 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #149 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #150 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #151 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #152 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #153 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #154 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #155 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #156 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #157 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #158 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #159 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #160 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #161 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #162 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #163 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #164 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #165 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #166 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #167 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #168 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #169 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #170 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #171 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #172 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #173 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #174 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #175 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #176 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #177 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #178 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #179 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #180 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #181 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #182 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #183 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #184 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #185 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #186 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #187 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #188 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #189 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #190 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #191 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #192 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #193 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #194 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #195 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #196 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #197 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #198 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #199 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #200 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #201 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #202 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #203 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #204 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #205 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #206 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #207 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #208 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #209 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #210 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #211 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #212 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #213 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #214 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #215 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #216 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #217 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #218 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #219 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #220 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #221 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #222 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #223 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #224 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #225 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #226 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #227 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #228 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #229 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #230 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #231 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #232 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #233 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #234 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #235 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #236 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #237 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #238 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #239 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #240 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #241 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #242 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #243 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #244 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #245 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #246 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #247 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #248 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #249 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #250 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #251 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #252 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #253 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #254 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #255 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #256 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #257 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #258 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #259 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #260 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #261 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #262 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #263 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #264 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #265 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #266 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #267 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #268 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #269 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #270 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #271 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #272 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #273 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #274 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #275 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #276 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #277 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #278 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #279 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #280 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #281 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #282 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #283 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #284 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #285 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #286 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #287 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #288 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #289 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #290 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #291 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #292 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #293 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #294 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #295 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #296 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #297 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #298 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #299 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #300 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #301 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #302 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #303 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #304 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #305 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #306 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #307 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #308 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #309 with Window Size: (2688, 2688) (at sampling 4)... Refinement failed. Retry #310 with Window Size: (2592, 2592) (at sampling 4)... Refinement failed. Retry #311 with Window Size: (2560, 2560) (at sampling 4)... Refinement failed. Retry #312 with Window Size: (2520, 2520) (at sampling 4)... Refinement failed. Retry #313 with Window Size: (2400, 2400) (at sampling 4)... Refinement failed. Retry #314 with Window Size: (2352, 2352) (at sampling 4)... Refinement failed. Retry #315 with Window Size: (2304, 2304) (at sampling 4)... Refinement failed. Retry #316 with Window Size: (2240, 2240) (at sampling 4)... Refinement failed. Retry #317 with Window Size: (2160, 2160) (at sampling 4)... Refinement failed. Retry #318 with Window Size: (2048, 2048) (at sampling 4)... Refinement failed. Retry #319 with Window Size: (2016, 2016) (at sampling 4)... Refinement failed. Retry #320 with Window Size: (2000, 2000) (at sampling 4)... Refinement failed. Retry #321 with Window Size: (1960, 1960) (at sampling 4)... Refinement failed. Retry #322 with Window Size: (1944, 1944) (at sampling 4)... Refinement failed. Retry #323 with Window Size: (1920, 1920) (at sampling 4)... Refinement failed. Retry #324 with Window Size: (1800, 1800) (at sampling 4)... Refinement failed. Retry #325 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #326 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #327 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #328 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #329 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #330 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #331 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #332 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #333 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #334 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #335 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #336 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #337 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #338 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #339 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #340 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #341 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #342 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #343 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #344 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #345 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #346 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #347 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #348 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #349 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #350 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #351 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #352 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #353 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #354 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #355 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #356 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #357 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #358 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #359 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #360 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #361 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #362 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #363 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #364 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #365 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #366 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #367 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #368 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #369 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #370 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #371 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #372 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #373 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #374 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #375 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #376 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #377 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #378 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #379 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #380 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #381 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #382 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #383 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #384 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #385 with Window Size: (80, 80) (at sampling 4)... Refinement Iteration #23 for Tilt-Series #7 failed after resampling the search area 385 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! End time: 2016yr09m28d-21hr45m17s