[ 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 [ jchase@node16: Wed Sep 28 20:17:27 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Initial --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=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node16: Thu Sep 29 17:07:12 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 --negative=-34 --positive=44 [ jchase@node16: Thu Sep 29 17:10:36 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 --negative=-34 --positive=44 [ jchase@node16: Thu Sep 29 17:11:59 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 --negative=-34 --positive=44 [ jchase@node16: Thu Sep 29 17:13:57 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Initial --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=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo --negative=-22 --positive=32 [ jchase@node16: Thu Sep 29 17:18:12 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Initial --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=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo --negative=-20 --positive=32 [ jchase@node16: Thu Sep 29 17:20:13 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Initial --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=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo --negative=-17 --positive=32 [ jchase@node16: Thu Sep 29 17:22:36 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Initial --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=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo --negative=-17 --positive=32 Start time: 2016yr09m29d-17hr22m36s 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 = { 0.00718866462793 0.00718866462793 } window.highpass.apodization = { 0.0143773292559 0.0143773292559 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 31.8268214849 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 31.8268214849 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01207 for Iteration #1 of Tilt-Series #8. CCMS(rotations) = 0.43014 for Iteration #1 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #8. The scaled sum of CCMS values is #0.01464 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01058 for Iteration #2 of Tilt-Series #8. CCMS(rotations) = 0.29146 for Iteration #2 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #8. The scaled sum of CCMS values is #0.01112 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01003 for Iteration #3 of Tilt-Series #8. CCMS(rotations) = 0.29605 for Iteration #3 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #8. The scaled sum of CCMS values is #0.01093 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00908 for Iteration #4 of Tilt-Series #8. CCMS(rotations) = 0.26489 for Iteration #4 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #8. The scaled sum of CCMS values is #0.00984 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01101 for Iteration #5 of Tilt-Series #8. CCMS(rotations) = 0.31934 for Iteration #5 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #8. The scaled sum of CCMS values is #0.01189 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00896 for Iteration #6 of Tilt-Series #8. CCMS(rotations) = 0.2905 for Iteration #6 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #8. The scaled sum of CCMS values is #0.01029 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01064 for Iteration #7 of Tilt-Series #8. CCMS(rotations) = 0.2771 for Iteration #7 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #8. The scaled sum of CCMS values is #0.01086 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00916 for Iteration #8 of Tilt-Series #8. CCMS(rotations) = 0.24148 for Iteration #8 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #8. The scaled sum of CCMS values is #0.00941 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01034 for Iteration #9 of Tilt-Series #8. CCMS(rotations) = 0.26599 for Iteration #9 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #8. The scaled sum of CCMS values is #0.01049 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00901 for Iteration #10 of Tilt-Series #8. CCMS(rotations) = 0.28554 for Iteration #10 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #8. The scaled sum of CCMS values is #0.01022 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00965 for Iteration #11 of Tilt-Series #8. CCMS(rotations) = 0.27297 for Iteration #11 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #8. The scaled sum of CCMS values is #0.01029 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00865 for Iteration #12 of Tilt-Series #8. CCMS(rotations) = 0.27937 for Iteration #12 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #8. The scaled sum of CCMS values is #0.00991 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0105 for Iteration #13 of Tilt-Series #8. CCMS(rotations) = 0.26237 for Iteration #13 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #8. The scaled sum of CCMS values is #0.0105 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00808 for Iteration #14 of Tilt-Series #8. CCMS(rotations) = 0.23215 for Iteration #14 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #8. The scaled sum of CCMS values is #0.00868 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01032 for Iteration #15 of Tilt-Series #8. CCMS(rotations) = 0.28742 for Iteration #15 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #8. The scaled sum of CCMS values is #0.01091 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.009 for Iteration #16 of Tilt-Series #8. CCMS(rotations) = 0.2323 for Iteration #16 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #8. The scaled sum of CCMS values is #0.00915 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01056 for Iteration #17 of Tilt-Series #8. CCMS(rotations) = 0.27557 for Iteration #17 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #8. The scaled sum of CCMS values is #0.01079 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00944 for Iteration #18 of Tilt-Series #8. CCMS(rotations) = 0.28506 for Iteration #18 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #8. The scaled sum of CCMS values is #0.01042 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.01069 for Iteration #19 of Tilt-Series #8. CCMS(rotations) = 0.202 for Iteration #19 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #8. The scaled sum of CCMS values is #0.00939 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00881 for Iteration #20 of Tilt-Series #8. CCMS(rotations) = 0.28211 for Iteration #20 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #8. The scaled sum of CCMS values is #0.01005 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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 = { 0.00359433231397 0.00359433231397 } window.highpass.apodization = { 0.00718866462793 0.00718866462793 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 63.6536429699 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 63.6536429699 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: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00836 for Iteration #21 of Tilt-Series #8. CCMS(rotations) = 0.12058 for Iteration #21 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #8. The scaled sum of CCMS values is #0.00659 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00412 for Iteration #22 of Tilt-Series #8. CCMS(rotations) = 0.05588 for Iteration #22 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #8. The scaled sum of CCMS values is #0.00318 for Tilt-Series #8. 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 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 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: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00371 for Iteration #23 of Tilt-Series #8. CCMS(rotations) = 0.10279 for Iteration #23 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #8. The scaled sum of CCMS values is #0.00391 for Tilt-Series #8. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... Refinement Iteration #23 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #24 Beginning Refinement Iteration #24, Round #2 No parameters were switched for Iteration #24 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00381 for Iteration #24 of Tilt-Series #8. CCMS(rotations) = 0.10933 for Iteration #24 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #8. The scaled sum of CCMS values is #0.00409 for Tilt-Series #8. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... Refinement Iteration #24 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #25 Beginning Refinement Iteration #25, Round #2 No parameters were switched for Iteration #25 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #25 of Tilt-Series #8. CCMS(rotations) = 0.09269 for Iteration #25 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #8. The scaled sum of CCMS values is #0.00364 for Tilt-Series #8. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Refinement Iteration #25 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #26 Beginning Refinement Iteration #26, Round #2 No parameters were switched for Iteration #26 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00372 for Iteration #26 of Tilt-Series #8. CCMS(rotations) = 0.10896 for Iteration #26 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #8. The scaled sum of CCMS values is #0.00404 for Tilt-Series #8. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... Refinement Iteration #26 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #27 Beginning Refinement Iteration #27, Round #2 No parameters were switched for Iteration #27 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00407 for Iteration #27 of Tilt-Series #8. CCMS(rotations) = 0.08043 for Iteration #27 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #8. The scaled sum of CCMS values is #0.00364 for Tilt-Series #8. Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... Refinement Iteration #27 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #28 Beginning Refinement Iteration #28, Round #2 No parameters were switched for Iteration #28 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00446 for Iteration #28 of Tilt-Series #8. CCMS(rotations) = 0.12387 for Iteration #28 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #8. The scaled sum of CCMS values is #0.00471 for Tilt-Series #8. Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... Refinement Iteration #28 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #29 Beginning Refinement Iteration #29, Round #2 No parameters were switched for Iteration #29 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00377 for Iteration #29 of Tilt-Series #8. CCMS(rotations) = 0.08812 for Iteration #29 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #8. The scaled sum of CCMS values is #0.00365 for Tilt-Series #8. Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... Refinement Iteration #29 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #30 Beginning Refinement Iteration #30, Round #2 No parameters were switched for Iteration #30 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00431 for Iteration #30 of Tilt-Series #8. CCMS(rotations) = 0.10611 for Iteration #30 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #8. The scaled sum of CCMS values is #0.00428 for Tilt-Series #8. Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... Refinement Iteration #30 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #31 Beginning Refinement Iteration #31, Round #2 No parameters were switched for Iteration #31 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00304 for Iteration #31 of Tilt-Series #8. CCMS(rotations) = 0.08879 for Iteration #31 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #8. The scaled sum of CCMS values is #0.0033 for Tilt-Series #8. Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... Refinement Iteration #31 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #32 Beginning Refinement Iteration #32, Round #2 No parameters were switched for Iteration #32 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00469 for Iteration #32 of Tilt-Series #8. CCMS(rotations) = 0.12654 for Iteration #32 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #32 of Tilt-Series #8. The scaled sum of CCMS values is #0.00488 for Tilt-Series #8. Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... Refinement Iteration #32 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #33 Beginning Refinement Iteration #33, Round #2 No parameters were switched for Iteration #33 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00348 for Iteration #33 of Tilt-Series #8. CCMS(rotations) = 0.10419 for Iteration #33 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #33 of Tilt-Series #8. The scaled sum of CCMS values is #0.00382 for Tilt-Series #8. Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... Refinement Iteration #33 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #34 Beginning Refinement Iteration #34, Round #2 No parameters were switched for Iteration #34 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00448 for Iteration #34 of Tilt-Series #8. CCMS(rotations) = 0.11019 for Iteration #34 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #34 of Tilt-Series #8. The scaled sum of CCMS values is #0.00444 for Tilt-Series #8. Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... Refinement Iteration #34 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #35 Beginning Refinement Iteration #35, Round #2 No parameters were switched for Iteration #35 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00306 for Iteration #35 of Tilt-Series #8. CCMS(rotations) = 0.10047 for Iteration #35 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #35 of Tilt-Series #8. The scaled sum of CCMS values is #0.00354 for Tilt-Series #8. Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... Refinement Iteration #35 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #36 Beginning Refinement Iteration #36, Round #2 No parameters were switched for Iteration #36 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.0037 for Iteration #36 of Tilt-Series #8. CCMS(rotations) = 0.07621 for Iteration #36 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #36 of Tilt-Series #8. The scaled sum of CCMS values is #0.00337 for Tilt-Series #8. Creating Depiction Videos for Iteration #36 in Parallel... Creating Refinement tilt-series video for iteration #36... Generating Refinement reconstruction for iteration #36... Refinement Iteration #36 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #37 Beginning Refinement Iteration #37, Round #2 No parameters were switched for Iteration #37 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00307 for Iteration #37 of Tilt-Series #8. CCMS(rotations) = 0.07688 for Iteration #37 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #37 of Tilt-Series #8. The scaled sum of CCMS values is #0.00307 for Tilt-Series #8. Creating Depiction Videos for Iteration #37 in Parallel... Creating Refinement tilt-series video for iteration #37... Generating Refinement reconstruction for iteration #37... Refinement Iteration #37 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #38 Beginning Refinement Iteration #38, Round #2 No parameters were switched for Iteration #38 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00421 for Iteration #38 of Tilt-Series #8. CCMS(rotations) = 0.12333 for Iteration #38 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #38 of Tilt-Series #8. The scaled sum of CCMS values is #0.00457 for Tilt-Series #8. Creating Depiction Videos for Iteration #38 in Parallel... Creating Refinement tilt-series video for iteration #38... Generating Refinement reconstruction for iteration #38... Refinement Iteration #38 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #39 Beginning Refinement Iteration #39, Round #2 No parameters were switched for Iteration #39 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00407 for Iteration #39 of Tilt-Series #8. CCMS(rotations) = 0.0859 for Iteration #39 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #39 of Tilt-Series #8. The scaled sum of CCMS values is #0.00376 for Tilt-Series #8. Creating Depiction Videos for Iteration #39 in Parallel... Creating Refinement tilt-series video for iteration #39... Generating Refinement reconstruction for iteration #39... Refinement Iteration #39 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 No Round parameters changed for Iteration #40 Beginning Refinement Iteration #40, Round #2 No parameters were switched for Iteration #40 Refinement failed. Retry #1 with Window Size: (2048, 2160) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (2016, 2048) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00506 for Iteration #40 of Tilt-Series #8. CCMS(rotations) = 0.10257 for Iteration #40 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #40 of Tilt-Series #8. The scaled sum of CCMS values is #0.00458 for Tilt-Series #8. Creating Depiction Videos for Iteration #40 in Parallel... Creating Refinement tilt-series video for iteration #40... Generating Refinement reconstruction for iteration #40... Refinement Iteration #40 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2048 Beginning Refinement Iteration #41, Round #3 lowpass = 31.25 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 2 window.highpass.diameter = { 0.00179716615698 0.00179716615698 } window.highpass.apodization = { 0.00359433231397 0.00359433231397 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 127.30728594 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 127.30728594 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #41 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.0045 for Iteration #41 of Tilt-Series #8. CCMS(rotations) = 0.11367 for Iteration #41 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #41 of Tilt-Series #8. The scaled sum of CCMS values is #0.00453 for Tilt-Series #8. Creating Depiction Videos for Iteration #41 in Parallel... Creating Refinement tilt-series video for iteration #41... Generating Refinement reconstruction for iteration #41... Refinement Iteration #41 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #42 Beginning Refinement Iteration #42, Round #3 No parameters were switched for Iteration #42 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00454 for Iteration #42 of Tilt-Series #8. CCMS(rotations) = 0.12636 for Iteration #42 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #42 of Tilt-Series #8. The scaled sum of CCMS values is #0.0048 for Tilt-Series #8. Creating Depiction Videos for Iteration #42 in Parallel... Creating Refinement tilt-series video for iteration #42... Generating Refinement reconstruction for iteration #42... Refinement Iteration #42 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #43 Beginning Refinement Iteration #43, Round #3 No parameters were switched for Iteration #43 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00457 for Iteration #43 of Tilt-Series #8. CCMS(rotations) = 0.20753 for Iteration #43 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #43 of Tilt-Series #8. The scaled sum of CCMS values is #0.00643 for Tilt-Series #8. Creating Depiction Videos for Iteration #43 in Parallel... Creating Refinement tilt-series video for iteration #43... Generating Refinement reconstruction for iteration #43... Refinement Iteration #43 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #44 Beginning Refinement Iteration #44, Round #3 No parameters were switched for Iteration #44 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00428 for Iteration #44 of Tilt-Series #8. CCMS(rotations) = 0.14871 for Iteration #44 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #44 of Tilt-Series #8. The scaled sum of CCMS values is #0.00511 for Tilt-Series #8. Creating Depiction Videos for Iteration #44 in Parallel... Creating Refinement tilt-series video for iteration #44... Generating Refinement reconstruction for iteration #44... Refinement Iteration #44 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #45 Beginning Refinement Iteration #45, Round #3 No parameters were switched for Iteration #45 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00453 for Iteration #45 of Tilt-Series #8. CCMS(rotations) = 0.18367 for Iteration #45 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #45 of Tilt-Series #8. The scaled sum of CCMS values is #0.00594 for Tilt-Series #8. Creating Depiction Videos for Iteration #45 in Parallel... Creating Refinement tilt-series video for iteration #45... Generating Refinement reconstruction for iteration #45... Refinement Iteration #45 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #46 Beginning Refinement Iteration #46, Round #3 No parameters were switched for Iteration #46 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00395 for Iteration #46 of Tilt-Series #8. CCMS(rotations) = 0.09797 for Iteration #46 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #46 of Tilt-Series #8. The scaled sum of CCMS values is #0.00394 for Tilt-Series #8. Creating Depiction Videos for Iteration #46 in Parallel... Creating Refinement tilt-series video for iteration #46... Generating Refinement reconstruction for iteration #46... Refinement Iteration #46 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #47 Beginning Refinement Iteration #47, Round #3 No parameters were switched for Iteration #47 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00506 for Iteration #47 of Tilt-Series #8. CCMS(rotations) = 0.08121 for Iteration #47 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #47 of Tilt-Series #8. The scaled sum of CCMS values is #0.00415 for Tilt-Series #8. Creating Depiction Videos for Iteration #47 in Parallel... Creating Refinement tilt-series video for iteration #47... Generating Refinement reconstruction for iteration #47... Refinement Iteration #47 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #48 Beginning Refinement Iteration #48, Round #3 No parameters were switched for Iteration #48 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00412 for Iteration #48 of Tilt-Series #8. CCMS(rotations) = 0.15687 for Iteration #48 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #48 of Tilt-Series #8. The scaled sum of CCMS values is #0.0052 for Tilt-Series #8. Creating Depiction Videos for Iteration #48 in Parallel... Creating Refinement tilt-series video for iteration #48... Generating Refinement reconstruction for iteration #48... Refinement Iteration #48 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #49 Beginning Refinement Iteration #49, Round #3 No parameters were switched for Iteration #49 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00485 for Iteration #49 of Tilt-Series #8. CCMS(rotations) = 0.22104 for Iteration #49 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #49 of Tilt-Series #8. The scaled sum of CCMS values is #0.00685 for Tilt-Series #8. Creating Depiction Videos for Iteration #49 in Parallel... Creating Refinement tilt-series video for iteration #49... Generating Refinement reconstruction for iteration #49... Refinement Iteration #49 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #50 Beginning Refinement Iteration #50, Round #3 No parameters were switched for Iteration #50 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.0049 for Iteration #50 of Tilt-Series #8. CCMS(rotations) = 0.12293 for Iteration #50 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #50 of Tilt-Series #8. The scaled sum of CCMS values is #0.00491 for Tilt-Series #8. Creating Depiction Videos for Iteration #50 in Parallel... Creating Refinement tilt-series video for iteration #50... Generating Refinement reconstruction for iteration #50... Refinement Iteration #50 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #51 Beginning Refinement Iteration #51, Round #3 No parameters were switched for Iteration #51 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00393 for Iteration #51 of Tilt-Series #8. CCMS(rotations) = 0.10946 for Iteration #51 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #51 of Tilt-Series #8. The scaled sum of CCMS values is #0.00416 for Tilt-Series #8. Creating Depiction Videos for Iteration #51 in Parallel... Creating Refinement tilt-series video for iteration #51... Generating Refinement reconstruction for iteration #51... Refinement Iteration #51 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #52 Beginning Refinement Iteration #52, Round #3 No parameters were switched for Iteration #52 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00415 for Iteration #52 of Tilt-Series #8. CCMS(rotations) = 0.15977 for Iteration #52 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #52 of Tilt-Series #8. The scaled sum of CCMS values is #0.00527 for Tilt-Series #8. Creating Depiction Videos for Iteration #52 in Parallel... Creating Refinement tilt-series video for iteration #52... Generating Refinement reconstruction for iteration #52... Refinement Iteration #52 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #53 Beginning Refinement Iteration #53, Round #3 No parameters were switched for Iteration #53 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00397 for Iteration #53 of Tilt-Series #8. CCMS(rotations) = 0.22909 for Iteration #53 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #53 of Tilt-Series #8. The scaled sum of CCMS values is #0.00657 for Tilt-Series #8. Creating Depiction Videos for Iteration #53 in Parallel... Creating Refinement tilt-series video for iteration #53... Generating Refinement reconstruction for iteration #53... Refinement Iteration #53 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #54 Beginning Refinement Iteration #54, Round #3 No parameters were switched for Iteration #54 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00457 for Iteration #54 of Tilt-Series #8. CCMS(rotations) = 0.1372 for Iteration #54 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #54 of Tilt-Series #8. The scaled sum of CCMS values is #0.00503 for Tilt-Series #8. Creating Depiction Videos for Iteration #54 in Parallel... Creating Refinement tilt-series video for iteration #54... Generating Refinement reconstruction for iteration #54... Refinement Iteration #54 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #55 Beginning Refinement Iteration #55, Round #3 No parameters were switched for Iteration #55 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00515 for Iteration #55 of Tilt-Series #8. CCMS(rotations) = 0.09334 for Iteration #55 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #55 of Tilt-Series #8. The scaled sum of CCMS values is #0.00444 for Tilt-Series #8. Creating Depiction Videos for Iteration #55 in Parallel... Creating Refinement tilt-series video for iteration #55... Generating Refinement reconstruction for iteration #55... Refinement Iteration #55 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #56 Beginning Refinement Iteration #56, Round #3 No parameters were switched for Iteration #56 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #56 of Tilt-Series #8. CCMS(rotations) = 0.08828 for Iteration #56 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #56 of Tilt-Series #8. The scaled sum of CCMS values is #0.00386 for Tilt-Series #8. Creating Depiction Videos for Iteration #56 in Parallel... Creating Refinement tilt-series video for iteration #56... Generating Refinement reconstruction for iteration #56... Refinement Iteration #56 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #57 Beginning Refinement Iteration #57, Round #3 No parameters were switched for Iteration #57 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.0035 for Iteration #57 of Tilt-Series #8. CCMS(rotations) = 0.11468 for Iteration #57 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #57 of Tilt-Series #8. The scaled sum of CCMS values is #0.00404 for Tilt-Series #8. Creating Depiction Videos for Iteration #57 in Parallel... Creating Refinement tilt-series video for iteration #57... Generating Refinement reconstruction for iteration #57... Refinement Iteration #57 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #58 Beginning Refinement Iteration #58, Round #3 No parameters were switched for Iteration #58 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00547 for Iteration #58 of Tilt-Series #8. CCMS(rotations) = 0.21299 for Iteration #58 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #58 of Tilt-Series #8. The scaled sum of CCMS values is #0.007 for Tilt-Series #8. Creating Depiction Videos for Iteration #58 in Parallel... Creating Refinement tilt-series video for iteration #58... Generating Refinement reconstruction for iteration #58... Refinement Iteration #58 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #59 Beginning Refinement Iteration #59, Round #3 No parameters were switched for Iteration #59 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00509 for Iteration #59 of Tilt-Series #8. CCMS(rotations) = 0.08266 for Iteration #59 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #59 of Tilt-Series #8. The scaled sum of CCMS values is #0.0042 for Tilt-Series #8. Creating Depiction Videos for Iteration #59 in Parallel... Creating Refinement tilt-series video for iteration #59... Generating Refinement reconstruction for iteration #59... Refinement Iteration #59 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #60 Beginning Refinement Iteration #60, Round #3 No parameters were switched for Iteration #60 Refinement failed. Retry #1 with Window Size: (2100, 2240) (at sampling 2)... Refinement failed. Retry #2 with Window Size: (2048, 2160) (at sampling 2)... Refinement failed. Retry #3 with Window Size: (2016, 2100) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00505 for Iteration #60 of Tilt-Series #8. CCMS(rotations) = 0.1546 for Iteration #60 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #60 of Tilt-Series #8. The scaled sum of CCMS values is #0.00562 for Tilt-Series #8. Creating Depiction Videos for Iteration #60 in Parallel... Creating Refinement tilt-series video for iteration #60... Generating Refinement reconstruction for iteration #60... Refinement Iteration #60 finished after retrying 3 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 Beginning Refinement Iteration #61, Round #4 lowpass = 15.625 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 254.61457188 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 254.61457188 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #61 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00587 for Iteration #61 of Tilt-Series #8. CCMS(rotations) = 0.08531 for Iteration #61 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #61 of Tilt-Series #8. The scaled sum of CCMS values is #0.00464 for Tilt-Series #8. Creating Depiction Videos for Iteration #61 in Parallel... Creating Refinement tilt-series video for iteration #61... Generating Refinement reconstruction for iteration #61... Refinement Iteration #61 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #62 Beginning Refinement Iteration #62, Round #4 No parameters were switched for Iteration #62 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00663 for Iteration #62 of Tilt-Series #8. CCMS(rotations) = 0.1704 for Iteration #62 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #62 of Tilt-Series #8. The scaled sum of CCMS values is #0.00672 for Tilt-Series #8. Creating Depiction Videos for Iteration #62 in Parallel... Creating Refinement tilt-series video for iteration #62... Generating Refinement reconstruction for iteration #62... Refinement Iteration #62 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #63 Beginning Refinement Iteration #63, Round #4 No parameters were switched for Iteration #63 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0056 for Iteration #63 of Tilt-Series #8. CCMS(rotations) = 0.28023 for Iteration #63 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #63 of Tilt-Series #8. The scaled sum of CCMS values is #0.0084 for Tilt-Series #8. Creating Depiction Videos for Iteration #63 in Parallel... Creating Refinement tilt-series video for iteration #63... Generating Refinement reconstruction for iteration #63... Refinement Iteration #63 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #64 Beginning Refinement Iteration #64, Round #4 No parameters were switched for Iteration #64 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00528 for Iteration #64 of Tilt-Series #8. CCMS(rotations) = 0.21181 for Iteration #64 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #64 of Tilt-Series #8. The scaled sum of CCMS values is #0.00687 for Tilt-Series #8. Creating Depiction Videos for Iteration #64 in Parallel... Creating Refinement tilt-series video for iteration #64... Generating Refinement reconstruction for iteration #64... Refinement Iteration #64 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #65 Beginning Refinement Iteration #65, Round #4 No parameters were switched for Iteration #65 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00622 for Iteration #65 of Tilt-Series #8. CCMS(rotations) = 0.26409 for Iteration #65 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #65 of Tilt-Series #8. The scaled sum of CCMS values is #0.00839 for Tilt-Series #8. Creating Depiction Videos for Iteration #65 in Parallel... Creating Refinement tilt-series video for iteration #65... Generating Refinement reconstruction for iteration #65... Refinement Iteration #65 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #66 Beginning Refinement Iteration #66, Round #4 No parameters were switched for Iteration #66 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00451 for Iteration #66 of Tilt-Series #8. CCMS(rotations) = 0.29601 for Iteration #66 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #66 of Tilt-Series #8. The scaled sum of CCMS values is #0.00817 for Tilt-Series #8. Creating Depiction Videos for Iteration #66 in Parallel... Creating Refinement tilt-series video for iteration #66... Generating Refinement reconstruction for iteration #66... Refinement Iteration #66 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #67 Beginning Refinement Iteration #67, Round #4 No parameters were switched for Iteration #67 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00682 for Iteration #67 of Tilt-Series #8. CCMS(rotations) = 0.18868 for Iteration #67 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #67 of Tilt-Series #8. The scaled sum of CCMS values is #0.00718 for Tilt-Series #8. Creating Depiction Videos for Iteration #67 in Parallel... Creating Refinement tilt-series video for iteration #67... Generating Refinement reconstruction for iteration #67... Refinement Iteration #67 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #68 Beginning Refinement Iteration #68, Round #4 No parameters were switched for Iteration #68 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00546 for Iteration #68 of Tilt-Series #8. CCMS(rotations) = 0.3055 for Iteration #68 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #68 of Tilt-Series #8. The scaled sum of CCMS values is #0.00884 for Tilt-Series #8. Creating Depiction Videos for Iteration #68 in Parallel... Creating Refinement tilt-series video for iteration #68... Generating Refinement reconstruction for iteration #68... Refinement Iteration #68 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #69 Beginning Refinement Iteration #69, Round #4 No parameters were switched for Iteration #69 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00481 for Iteration #69 of Tilt-Series #8. CCMS(rotations) = 0.29924 for Iteration #69 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #69 of Tilt-Series #8. The scaled sum of CCMS values is #0.00839 for Tilt-Series #8. Creating Depiction Videos for Iteration #69 in Parallel... Creating Refinement tilt-series video for iteration #69... Generating Refinement reconstruction for iteration #69... Refinement Iteration #69 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #70 Beginning Refinement Iteration #70, Round #4 No parameters were switched for Iteration #70 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00514 for Iteration #70 of Tilt-Series #8. CCMS(rotations) = 0.24928 for Iteration #70 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #70 of Tilt-Series #8. The scaled sum of CCMS values is #0.00755 for Tilt-Series #8. Creating Depiction Videos for Iteration #70 in Parallel... Creating Refinement tilt-series video for iteration #70... Generating Refinement reconstruction for iteration #70... Refinement Iteration #70 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #71 Beginning Refinement Iteration #71, Round #4 No parameters were switched for Iteration #71 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00631 for Iteration #71 of Tilt-Series #8. CCMS(rotations) = 0.26216 for Iteration #71 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #71 of Tilt-Series #8. The scaled sum of CCMS values is #0.0084 for Tilt-Series #8. Creating Depiction Videos for Iteration #71 in Parallel... Creating Refinement tilt-series video for iteration #71... Generating Refinement reconstruction for iteration #71... Refinement Iteration #71 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #72 Beginning Refinement Iteration #72, Round #4 No parameters were switched for Iteration #72 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00559 for Iteration #72 of Tilt-Series #8. CCMS(rotations) = 0.24181 for Iteration #72 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #72 of Tilt-Series #8. The scaled sum of CCMS values is #0.00763 for Tilt-Series #8. Creating Depiction Videos for Iteration #72 in Parallel... Creating Refinement tilt-series video for iteration #72... Generating Refinement reconstruction for iteration #72... Refinement Iteration #72 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #73 Beginning Refinement Iteration #73, Round #4 No parameters were switched for Iteration #73 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00517 for Iteration #73 of Tilt-Series #8. CCMS(rotations) = 0.25861 for Iteration #73 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #73 of Tilt-Series #8. The scaled sum of CCMS values is #0.00776 for Tilt-Series #8. Creating Depiction Videos for Iteration #73 in Parallel... Creating Refinement tilt-series video for iteration #73... Generating Refinement reconstruction for iteration #73... Refinement Iteration #73 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #74 Beginning Refinement Iteration #74, Round #4 No parameters were switched for Iteration #74 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00479 for Iteration #74 of Tilt-Series #8. CCMS(rotations) = 0.21438 for Iteration #74 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #74 of Tilt-Series #8. The scaled sum of CCMS values is #0.00668 for Tilt-Series #8. Creating Depiction Videos for Iteration #74 in Parallel... Creating Refinement tilt-series video for iteration #74... Generating Refinement reconstruction for iteration #74... Refinement Iteration #74 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #75 Beginning Refinement Iteration #75, Round #4 No parameters were switched for Iteration #75 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00567 for Iteration #75 of Tilt-Series #8. CCMS(rotations) = 0.22702 for Iteration #75 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #75 of Tilt-Series #8. The scaled sum of CCMS values is #0.00737 for Tilt-Series #8. Creating Depiction Videos for Iteration #75 in Parallel... Creating Refinement tilt-series video for iteration #75... Generating Refinement reconstruction for iteration #75... Refinement Iteration #75 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #76 Beginning Refinement Iteration #76, Round #4 No parameters were switched for Iteration #76 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00526 for Iteration #76 of Tilt-Series #8. CCMS(rotations) = 0.29268 for Iteration #76 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #76 of Tilt-Series #8. The scaled sum of CCMS values is #0.00848 for Tilt-Series #8. Creating Depiction Videos for Iteration #76 in Parallel... Creating Refinement tilt-series video for iteration #76... Generating Refinement reconstruction for iteration #76... Refinement Iteration #76 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #77 Beginning Refinement Iteration #77, Round #4 No parameters were switched for Iteration #77 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00527 for Iteration #77 of Tilt-Series #8. CCMS(rotations) = 0.19286 for Iteration #77 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #77 of Tilt-Series #8. The scaled sum of CCMS values is #0.00649 for Tilt-Series #8. Creating Depiction Videos for Iteration #77 in Parallel... Creating Refinement tilt-series video for iteration #77... Generating Refinement reconstruction for iteration #77... Refinement Iteration #77 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #78 Beginning Refinement Iteration #78, Round #4 No parameters were switched for Iteration #78 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00679 for Iteration #78 of Tilt-Series #8. CCMS(rotations) = 0.20685 for Iteration #78 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #78 of Tilt-Series #8. The scaled sum of CCMS values is #0.00753 for Tilt-Series #8. Creating Depiction Videos for Iteration #78 in Parallel... Creating Refinement tilt-series video for iteration #78... Generating Refinement reconstruction for iteration #78... Refinement Iteration #78 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #79 Beginning Refinement Iteration #79, Round #4 No parameters were switched for Iteration #79 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00569 for Iteration #79 of Tilt-Series #8. CCMS(rotations) = 0.27505 for Iteration #79 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #79 of Tilt-Series #8. The scaled sum of CCMS values is #0.00835 for Tilt-Series #8. Creating Depiction Videos for Iteration #79 in Parallel... Creating Refinement tilt-series video for iteration #79... Generating Refinement reconstruction for iteration #79... Refinement Iteration #79 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #80 Beginning Refinement Iteration #80, Round #4 No parameters were switched for Iteration #80 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00522 for Iteration #80 of Tilt-Series #8. CCMS(rotations) = 0.26535 for Iteration #80 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #80 of Tilt-Series #8. The scaled sum of CCMS values is #0.00792 for Tilt-Series #8. Creating Depiction Videos for Iteration #80 in Parallel... Creating Refinement tilt-series video for iteration #80... Generating Refinement reconstruction for iteration #80... Refinement Iteration #80 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #81 Beginning Refinement Iteration #81, Round #4 fit.scale switched from false to true on Iteration #81Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00549 for Iteration #81 of Tilt-Series #8. CCMS(rotations) = 0.25333 for Iteration #81 of Tilt-Series #8. CCMS(scale) = 0.0 for Iteration #81 of Tilt-Series #8. The scaled sum of CCMS values is #0.00781 for Tilt-Series #8. Creating Depiction Videos for Iteration #81 in Parallel... Creating Refinement tilt-series video for iteration #81... Generating Refinement reconstruction for iteration #81... Refinement Iteration #81 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #82 Beginning Refinement Iteration #82, Round #4 No parameters were switched for Iteration #82 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00421 for Iteration #82 of Tilt-Series #8. CCMS(rotations) = 0.24378 for Iteration #82 of Tilt-Series #8. CCMS(scale) = 0.00222 for Iteration #82 of Tilt-Series #8. The scaled sum of CCMS values is #0.00539 for Tilt-Series #8. Creating Depiction Videos for Iteration #82 in Parallel... Creating Refinement tilt-series video for iteration #82... Generating Refinement reconstruction for iteration #82... Refinement Iteration #82 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #83 Beginning Refinement Iteration #83, Round #4 No parameters were switched for Iteration #83 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00382 for Iteration #83 of Tilt-Series #8. CCMS(rotations) = 0.27599 for Iteration #83 of Tilt-Series #8. CCMS(scale) = 0.00218 for Iteration #83 of Tilt-Series #8. The scaled sum of CCMS values is #0.00568 for Tilt-Series #8. Creating Depiction Videos for Iteration #83 in Parallel... Creating Refinement tilt-series video for iteration #83... Generating Refinement reconstruction for iteration #83... Refinement Iteration #83 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #84 Beginning Refinement Iteration #84, Round #4 No parameters were switched for Iteration #84 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00538 for Iteration #84 of Tilt-Series #8. CCMS(rotations) = 0.33912 for Iteration #84 of Tilt-Series #8. CCMS(scale) = 0.00205 for Iteration #84 of Tilt-Series #8. The scaled sum of CCMS values is #0.007 for Tilt-Series #8. Creating Depiction Videos for Iteration #84 in Parallel... Creating Refinement tilt-series video for iteration #84... Generating Refinement reconstruction for iteration #84... Refinement Iteration #84 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #85 Beginning Refinement Iteration #85, Round #4 No parameters were switched for Iteration #85 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00437 for Iteration #85 of Tilt-Series #8. CCMS(rotations) = 0.32912 for Iteration #85 of Tilt-Series #8. CCMS(scale) = 0.00208 for Iteration #85 of Tilt-Series #8. The scaled sum of CCMS values is #0.00654 for Tilt-Series #8. Creating Depiction Videos for Iteration #85 in Parallel... Creating Refinement tilt-series video for iteration #85... Generating Refinement reconstruction for iteration #85... Refinement Iteration #85 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #86 Beginning Refinement Iteration #86, Round #4 No parameters were switched for Iteration #86 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00442 for Iteration #86 of Tilt-Series #8. CCMS(rotations) = 0.29361 for Iteration #86 of Tilt-Series #8. CCMS(scale) = 0.00181 for Iteration #86 of Tilt-Series #8. The scaled sum of CCMS values is #0.00599 for Tilt-Series #8. Creating Depiction Videos for Iteration #86 in Parallel... Creating Refinement tilt-series video for iteration #86... Generating Refinement reconstruction for iteration #86... Refinement Iteration #86 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #87 Beginning Refinement Iteration #87, Round #4 No parameters were switched for Iteration #87 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00446 for Iteration #87 of Tilt-Series #8. CCMS(rotations) = 0.24619 for Iteration #87 of Tilt-Series #8. CCMS(scale) = 0.00237 for Iteration #87 of Tilt-Series #8. The scaled sum of CCMS values is #0.00556 for Tilt-Series #8. Creating Depiction Videos for Iteration #87 in Parallel... Creating Refinement tilt-series video for iteration #87... Generating Refinement reconstruction for iteration #87... Refinement Iteration #87 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #88 Beginning Refinement Iteration #88, Round #4 No parameters were switched for Iteration #88 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #88 of Tilt-Series #8. CCMS(rotations) = 0.30939 for Iteration #88 of Tilt-Series #8. CCMS(scale) = 0.00238 for Iteration #88 of Tilt-Series #8. The scaled sum of CCMS values is #0.00631 for Tilt-Series #8. Creating Depiction Videos for Iteration #88 in Parallel... Creating Refinement tilt-series video for iteration #88... Generating Refinement reconstruction for iteration #88... Refinement Iteration #88 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #89 Beginning Refinement Iteration #89, Round #4 No parameters were switched for Iteration #89 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00564 for Iteration #89 of Tilt-Series #8. CCMS(rotations) = 0.38625 for Iteration #89 of Tilt-Series #8. CCMS(scale) = 0.00237 for Iteration #89 of Tilt-Series #8. The scaled sum of CCMS values is #0.00782 for Tilt-Series #8. Creating Depiction Videos for Iteration #89 in Parallel... Creating Refinement tilt-series video for iteration #89... Generating Refinement reconstruction for iteration #89... Refinement Iteration #89 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #90 Beginning Refinement Iteration #90, Round #4 No parameters were switched for Iteration #90 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0061 for Iteration #90 of Tilt-Series #8. CCMS(rotations) = 0.23021 for Iteration #90 of Tilt-Series #8. CCMS(scale) = 0.00296 for Iteration #90 of Tilt-Series #8. The scaled sum of CCMS values is #0.00609 for Tilt-Series #8. Creating Depiction Videos for Iteration #90 in Parallel... Creating Refinement tilt-series video for iteration #90... Generating Refinement reconstruction for iteration #90... Refinement Iteration #90 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #91 Beginning Refinement Iteration #91, Round #4 No parameters were switched for Iteration #91 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00566 for Iteration #91 of Tilt-Series #8. CCMS(rotations) = 0.22558 for Iteration #91 of Tilt-Series #8. CCMS(scale) = 0.00224 for Iteration #91 of Tilt-Series #8. The scaled sum of CCMS values is #0.00564 for Tilt-Series #8. Creating Depiction Videos for Iteration #91 in Parallel... Creating Refinement tilt-series video for iteration #91... Generating Refinement reconstruction for iteration #91... Refinement Iteration #91 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #92 Beginning Refinement Iteration #92, Round #4 No parameters were switched for Iteration #92 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00621 for Iteration #92 of Tilt-Series #8. CCMS(rotations) = 0.29514 for Iteration #92 of Tilt-Series #8. CCMS(scale) = 0.00264 for Iteration #92 of Tilt-Series #8. The scaled sum of CCMS values is #0.00689 for Tilt-Series #8. Creating Depiction Videos for Iteration #92 in Parallel... Creating Refinement tilt-series video for iteration #92... Generating Refinement reconstruction for iteration #92... Refinement Iteration #92 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #93 Beginning Refinement Iteration #93, Round #4 No parameters were switched for Iteration #93 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00569 for Iteration #93 of Tilt-Series #8. CCMS(rotations) = 0.30529 for Iteration #93 of Tilt-Series #8. CCMS(scale) = 0.00296 for Iteration #93 of Tilt-Series #8. The scaled sum of CCMS values is #0.00695 for Tilt-Series #8. Creating Depiction Videos for Iteration #93 in Parallel... Creating Refinement tilt-series video for iteration #93... Generating Refinement reconstruction for iteration #93... Refinement Iteration #93 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #94 Beginning Refinement Iteration #94, Round #4 No parameters were switched for Iteration #94 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00541 for Iteration #94 of Tilt-Series #8. CCMS(rotations) = 0.32536 for Iteration #94 of Tilt-Series #8. CCMS(scale) = 0.00287 for Iteration #94 of Tilt-Series #8. The scaled sum of CCMS values is #0.0071 for Tilt-Series #8. Creating Depiction Videos for Iteration #94 in Parallel... Creating Refinement tilt-series video for iteration #94... Generating Refinement reconstruction for iteration #94... Refinement Iteration #94 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #95 Beginning Refinement Iteration #95, Round #4 No parameters were switched for Iteration #95 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00378 for Iteration #95 of Tilt-Series #8. CCMS(rotations) = 0.31949 for Iteration #95 of Tilt-Series #8. CCMS(scale) = 0.00208 for Iteration #95 of Tilt-Series #8. The scaled sum of CCMS values is #0.00621 for Tilt-Series #8. Creating Depiction Videos for Iteration #95 in Parallel... Creating Refinement tilt-series video for iteration #95... Generating Refinement reconstruction for iteration #95... Refinement Iteration #95 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #96 Beginning Refinement Iteration #96, Round #4 No parameters were switched for Iteration #96 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00552 for Iteration #96 of Tilt-Series #8. CCMS(rotations) = 0.38457 for Iteration #96 of Tilt-Series #8. CCMS(scale) = 0.00201 for Iteration #96 of Tilt-Series #8. The scaled sum of CCMS values is #0.00764 for Tilt-Series #8. Creating Depiction Videos for Iteration #96 in Parallel... Creating Refinement tilt-series video for iteration #96... Generating Refinement reconstruction for iteration #96... Refinement Iteration #96 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #97 Beginning Refinement Iteration #97, Round #4 No parameters were switched for Iteration #97 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0053 for Iteration #97 of Tilt-Series #8. CCMS(rotations) = 0.30401 for Iteration #97 of Tilt-Series #8. CCMS(scale) = 0.00181 for Iteration #97 of Tilt-Series #8. The scaled sum of CCMS values is #0.00642 for Tilt-Series #8. Creating Depiction Videos for Iteration #97 in Parallel... Creating Refinement tilt-series video for iteration #97... Generating Refinement reconstruction for iteration #97... Refinement Iteration #97 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #98 Beginning Refinement Iteration #98, Round #4 No parameters were switched for Iteration #98 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00362 for Iteration #98 of Tilt-Series #8. CCMS(rotations) = 0.21355 for Iteration #98 of Tilt-Series #8. CCMS(scale) = 0.00226 for Iteration #98 of Tilt-Series #8. The scaled sum of CCMS values is #0.00481 for Tilt-Series #8. Creating Depiction Videos for Iteration #98 in Parallel... Creating Refinement tilt-series video for iteration #98... Generating Refinement reconstruction for iteration #98... Refinement Iteration #98 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #99 Beginning Refinement Iteration #99, Round #4 No parameters were switched for Iteration #99 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00435 for Iteration #99 of Tilt-Series #8. CCMS(rotations) = 0.22971 for Iteration #99 of Tilt-Series #8. CCMS(scale) = 0.00212 for Iteration #99 of Tilt-Series #8. The scaled sum of CCMS values is #0.00522 for Tilt-Series #8. Creating Depiction Videos for Iteration #99 in Parallel... Creating Refinement tilt-series video for iteration #99... Generating Refinement reconstruction for iteration #99... Refinement Iteration #99 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #100 Beginning Refinement Iteration #100, Round #4 No parameters were switched for Iteration #100 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00469 for Iteration #100 of Tilt-Series #8. CCMS(rotations) = 0.24533 for Iteration #100 of Tilt-Series #8. CCMS(scale) = 0.0021 for Iteration #100 of Tilt-Series #8. The scaled sum of CCMS values is #0.00553 for Tilt-Series #8. Creating Depiction Videos for Iteration #100 in Parallel... Creating Refinement tilt-series video for iteration #100... Generating Refinement reconstruction for iteration #100... Refinement Iteration #100 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 Beginning Refinement Iteration #101, Round #5 lowpass = 7.8125 angstroms Round #5. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.176302 0.176302 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 254.61457188 map.lowpass.diameter = { 0.45133312 0.45133312 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 254.61457188 window.lowpass.diameter = { 0.45133312 0.45133312 } align.correlation.mode = pcf fit.rotation switched from true to false on Iteration #101fit.azimuth switched from true to false on Iteration #101fit.orientation switched from true to false on Iteration #101Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01045 for Iteration #101 of Tilt-Series #8. CCMS(rotations) = 0.23634 for Iteration #101 of Tilt-Series #8. CCMS(scale) = 0.00228 for Iteration #101 of Tilt-Series #8. The scaled sum of CCMS values is #0.00739 for Tilt-Series #8. Creating Depiction Videos for Iteration #101 in Parallel... Creating Refinement tilt-series video for iteration #101... Generating Refinement reconstruction for iteration #101... Refinement Iteration #101 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #102 Beginning Refinement Iteration #102, Round #5 No parameters were switched for Iteration #102 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01219 for Iteration #102 of Tilt-Series #8. CCMS(rotations) = 0.24595 for Iteration #102 of Tilt-Series #8. CCMS(scale) = 0.00382 for Iteration #102 of Tilt-Series #8. The scaled sum of CCMS values is #0.00862 for Tilt-Series #8. Creating Depiction Videos for Iteration #102 in Parallel... Creating Refinement tilt-series video for iteration #102... Generating Refinement reconstruction for iteration #102... Refinement Iteration #102 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #103 Beginning Refinement Iteration #103, Round #5 No parameters were switched for Iteration #103 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00852 for Iteration #103 of Tilt-Series #8. CCMS(rotations) = 0.24319 for Iteration #103 of Tilt-Series #8. CCMS(scale) = 0.00451 for Iteration #103 of Tilt-Series #8. The scaled sum of CCMS values is #0.00759 for Tilt-Series #8. Creating Depiction Videos for Iteration #103 in Parallel... Creating Refinement tilt-series video for iteration #103... Generating Refinement reconstruction for iteration #103... Refinement Iteration #103 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #104 Beginning Refinement Iteration #104, Round #5 No parameters were switched for Iteration #104 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01169 for Iteration #104 of Tilt-Series #8. CCMS(rotations) = 0.34931 for Iteration #104 of Tilt-Series #8. CCMS(scale) = 0.00717 for Iteration #104 of Tilt-Series #8. The scaled sum of CCMS values is #0.01095 for Tilt-Series #8. Creating Depiction Videos for Iteration #104 in Parallel... Creating Refinement tilt-series video for iteration #104... Generating Refinement reconstruction for iteration #104... Refinement Iteration #104 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #105 Beginning Refinement Iteration #105, Round #5 No parameters were switched for Iteration #105 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01246 for Iteration #105 of Tilt-Series #8. CCMS(rotations) = 0.45251 for Iteration #105 of Tilt-Series #8. CCMS(scale) = 0.00619 for Iteration #105 of Tilt-Series #8. The scaled sum of CCMS values is #0.01225 for Tilt-Series #8. Creating Depiction Videos for Iteration #105 in Parallel... Creating Refinement tilt-series video for iteration #105... Generating Refinement reconstruction for iteration #105... Refinement Iteration #105 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #106 Beginning Refinement Iteration #106, Round #5 No parameters were switched for Iteration #106 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00909 for Iteration #106 of Tilt-Series #8. CCMS(rotations) = 0.58064 for Iteration #106 of Tilt-Series #8. CCMS(scale) = 0.00699 for Iteration #106 of Tilt-Series #8. The scaled sum of CCMS values is #0.0131 for Tilt-Series #8. Creating Depiction Videos for Iteration #106 in Parallel... Creating Refinement tilt-series video for iteration #106... Generating Refinement reconstruction for iteration #106... Refinement Iteration #106 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #107 Beginning Refinement Iteration #107, Round #5 No parameters were switched for Iteration #107 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01088 for Iteration #107 of Tilt-Series #8. CCMS(rotations) = 0.65776 for Iteration #107 of Tilt-Series #8. CCMS(scale) = 0.00889 for Iteration #107 of Tilt-Series #8. The scaled sum of CCMS values is #0.01536 for Tilt-Series #8. Creating Depiction Videos for Iteration #107 in Parallel... Creating Refinement tilt-series video for iteration #107... Generating Refinement reconstruction for iteration #107... Refinement Iteration #107 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #108 Beginning Refinement Iteration #108, Round #5 No parameters were switched for Iteration #108 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01152 for Iteration #108 of Tilt-Series #8. CCMS(rotations) = 0.89381 for Iteration #108 of Tilt-Series #8. CCMS(scale) = 0.0106 for Iteration #108 of Tilt-Series #8. The scaled sum of CCMS values is #0.01929 for Tilt-Series #8. Creating Depiction Videos for Iteration #108 in Parallel... Creating Refinement tilt-series video for iteration #108... Generating Refinement reconstruction for iteration #108... Refinement Iteration #108 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #109 Beginning Refinement Iteration #109, Round #5 No parameters were switched for Iteration #109 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01143 for Iteration #109 of Tilt-Series #8. CCMS(rotations) = 0.8919 for Iteration #109 of Tilt-Series #8. CCMS(scale) = 0.01187 for Iteration #109 of Tilt-Series #8. The scaled sum of CCMS values is #0.01966 for Tilt-Series #8. Creating Depiction Videos for Iteration #109 in Parallel... Creating Refinement tilt-series video for iteration #109... Generating Refinement reconstruction for iteration #109... Refinement Iteration #109 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #110 Beginning Refinement Iteration #110, Round #5 No parameters were switched for Iteration #110 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01326 for Iteration #110 of Tilt-Series #8. CCMS(rotations) = 0.90712 for Iteration #110 of Tilt-Series #8. CCMS(scale) = 0.01254 for Iteration #110 of Tilt-Series #8. The scaled sum of CCMS values is #0.0207 for Tilt-Series #8. Creating Depiction Videos for Iteration #110 in Parallel... Creating Refinement tilt-series video for iteration #110... Generating Refinement reconstruction for iteration #110... Refinement Iteration #110 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #111 Beginning Refinement Iteration #111, Round #5 No parameters were switched for Iteration #111 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01241 for Iteration #111 of Tilt-Series #8. CCMS(rotations) = 1.01684 for Iteration #111 of Tilt-Series #8. CCMS(scale) = 0.01334 for Iteration #111 of Tilt-Series #8. The scaled sum of CCMS values is #0.02214 for Tilt-Series #8. Creating Depiction Videos for Iteration #111 in Parallel... Creating Refinement tilt-series video for iteration #111... Generating Refinement reconstruction for iteration #111... Refinement Iteration #111 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #112 Beginning Refinement Iteration #112, Round #5 No parameters were switched for Iteration #112 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01322 for Iteration #112 of Tilt-Series #8. CCMS(rotations) = 1.00524 for Iteration #112 of Tilt-Series #8. CCMS(scale) = 0.01502 for Iteration #112 of Tilt-Series #8. The scaled sum of CCMS values is #0.02282 for Tilt-Series #8. Creating Depiction Videos for Iteration #112 in Parallel... Creating Refinement tilt-series video for iteration #112... Generating Refinement reconstruction for iteration #112... Refinement Iteration #112 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #113 Beginning Refinement Iteration #113, Round #5 No parameters were switched for Iteration #113 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01623 for Iteration #113 of Tilt-Series #8. CCMS(rotations) = 0.8774 for Iteration #113 of Tilt-Series #8. CCMS(scale) = 0.01623 for Iteration #113 of Tilt-Series #8. The scaled sum of CCMS values is #0.02252 for Tilt-Series #8. Creating Depiction Videos for Iteration #113 in Parallel... Creating Refinement tilt-series video for iteration #113... Generating Refinement reconstruction for iteration #113... Refinement Iteration #113 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #114 Beginning Refinement Iteration #114, Round #5 No parameters were switched for Iteration #114 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01047 for Iteration #114 of Tilt-Series #8. CCMS(rotations) = 0.95779 for Iteration #114 of Tilt-Series #8. CCMS(scale) = 0.01961 for Iteration #114 of Tilt-Series #8. The scaled sum of CCMS values is #0.0228 for Tilt-Series #8. Creating Depiction Videos for Iteration #114 in Parallel... Creating Refinement tilt-series video for iteration #114... Generating Refinement reconstruction for iteration #114... Refinement Iteration #114 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #115 Beginning Refinement Iteration #115, Round #5 No parameters were switched for Iteration #115 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01181 for Iteration #115 of Tilt-Series #8. CCMS(rotations) = 0.99384 for Iteration #115 of Tilt-Series #8. CCMS(scale) = 0.02128 for Iteration #115 of Tilt-Series #8. The scaled sum of CCMS values is #0.02428 for Tilt-Series #8. Creating Depiction Videos for Iteration #115 in Parallel... Creating Refinement tilt-series video for iteration #115... Generating Refinement reconstruction for iteration #115... Refinement Iteration #115 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #116 Beginning Refinement Iteration #116, Round #5 No parameters were switched for Iteration #116 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Creating quality assessment statistics...