[ 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 Start time: 2016yr09m29d-17hr11m59s Description: Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 lowpass = 125.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.090122428115 0.090122428115 } map.sampling = 8 window.highpass.diameter = { 0.00575093170234 0.00575093170234 } window.highpass.apodization = { 0.0114995189564 0.0114995189564 } window.mask.apodization = { 10 10 } align.mask.width = { 322 334 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 36.489440962 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 347 359 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 322 334 } reference.body = 36.489440962 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.02406 for Iteration #1 of Tilt-Series #7. CCMS(rotations) = 0.28557 for Iteration #1 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #7. The scaled sum of CCMS values is #0.01774 for Tilt-Series #7. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... No Round parameters changed for Iteration #2 Beginning Refinement Iteration #2, Round #1 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.00829 for Iteration #2 of Tilt-Series #7. CCMS(rotations) = 0.28141 for Iteration #2 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #7. The scaled sum of CCMS values is #0.00977 for Tilt-Series #7. Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... No Round parameters changed for Iteration #3 Beginning Refinement Iteration #3, Round #1 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00741 for Iteration #3 of Tilt-Series #7. CCMS(rotations) = 0.23769 for Iteration #3 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #7. The scaled sum of CCMS values is #0.00846 for Tilt-Series #7. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... No Round parameters changed for Iteration #4 Beginning Refinement Iteration #4, Round #1 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00857 for Iteration #4 of Tilt-Series #7. CCMS(rotations) = 0.14945 for Iteration #4 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #7. The scaled sum of CCMS values is #0.00727 for Tilt-Series #7. Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 Beginning Refinement Iteration #5, Round #1 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00857 for Iteration #5 of Tilt-Series #7. CCMS(rotations) = 0.20486 for Iteration #5 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #7. The scaled sum of CCMS values is #0.00838 for Tilt-Series #7. Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 Beginning Refinement Iteration #6, Round #1 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00781 for Iteration #6 of Tilt-Series #7. CCMS(rotations) = 0.18266 for Iteration #6 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #7. The scaled sum of CCMS values is #0.00756 for Tilt-Series #7. Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 Beginning Refinement Iteration #7, Round #1 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00793 for Iteration #7 of Tilt-Series #7. CCMS(rotations) = 0.24438 for Iteration #7 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #7. The scaled sum of CCMS values is #0.00885 for Tilt-Series #7. Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 Beginning Refinement Iteration #8, Round #1 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00755 for Iteration #8 of Tilt-Series #7. CCMS(rotations) = 0.14301 for Iteration #8 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #7. The scaled sum of CCMS values is #0.00664 for Tilt-Series #7. Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... No Round parameters changed for Iteration #9 Beginning Refinement Iteration #9, Round #1 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00813 for Iteration #9 of Tilt-Series #7. CCMS(rotations) = 0.25916 for Iteration #9 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #7. The scaled sum of CCMS values is #0.00925 for Tilt-Series #7. Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... No Round parameters changed for Iteration #10 Beginning Refinement Iteration #10, Round #1 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00844 for Iteration #10 of Tilt-Series #7. CCMS(rotations) = 0.21699 for Iteration #10 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #7. The scaled sum of CCMS values is #0.00856 for Tilt-Series #7. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... No Round parameters changed for Iteration #11 Beginning Refinement Iteration #11, Round #1 No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00934 for Iteration #11 of Tilt-Series #7. CCMS(rotations) = 0.16603 for Iteration #11 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #7. The scaled sum of CCMS values is #0.00799 for Tilt-Series #7. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 Beginning Refinement Iteration #12, Round #1 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00712 for Iteration #12 of Tilt-Series #7. CCMS(rotations) = 0.25582 for Iteration #12 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #7. The scaled sum of CCMS values is #0.00868 for Tilt-Series #7. Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 Beginning Refinement Iteration #13, Round #1 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00848 for Iteration #13 of Tilt-Series #7. CCMS(rotations) = 0.25625 for Iteration #13 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #7. The scaled sum of CCMS values is #0.00937 for Tilt-Series #7. Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... No Round parameters changed for Iteration #14 Beginning Refinement Iteration #14, Round #1 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00641 for Iteration #14 of Tilt-Series #7. CCMS(rotations) = 0.19014 for Iteration #14 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #7. The scaled sum of CCMS values is #0.00701 for Tilt-Series #7. Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 Beginning Refinement Iteration #15, Round #1 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00774 for Iteration #15 of Tilt-Series #7. CCMS(rotations) = 0.28121 for Iteration #15 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #7. The scaled sum of CCMS values is #0.00949 for Tilt-Series #7. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... No Round parameters changed for Iteration #16 Beginning Refinement Iteration #16, Round #1 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00866 for Iteration #16 of Tilt-Series #7. CCMS(rotations) = 0.13809 for Iteration #16 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #7. The scaled sum of CCMS values is #0.00709 for Tilt-Series #7. Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... No Round parameters changed for Iteration #17 Beginning Refinement Iteration #17, Round #1 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00861 for Iteration #17 of Tilt-Series #7. CCMS(rotations) = 0.24771 for Iteration #17 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #7. The scaled sum of CCMS values is #0.00926 for Tilt-Series #7. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... No Round parameters changed for Iteration #18 Beginning Refinement Iteration #18, Round #1 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.0072 for Iteration #18 of Tilt-Series #7. CCMS(rotations) = 0.19545 for Iteration #18 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #7. The scaled sum of CCMS values is #0.00751 for Tilt-Series #7. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 Beginning Refinement Iteration #19, Round #1 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00822 for Iteration #19 of Tilt-Series #7. CCMS(rotations) = 0.27177 for Iteration #19 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #7. The scaled sum of CCMS values is #0.00955 for Tilt-Series #7. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 Beginning Refinement Iteration #20, Round #1 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00625 for Iteration #20 of Tilt-Series #7. CCMS(rotations) = 0.20592 for Iteration #20 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #7. The scaled sum of CCMS values is #0.00725 for Tilt-Series #7. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Beginning Refinement Iteration #21, Round #2 lowpass = 62.5 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 4 window.highpass.diameter = { 0.00287546585117 0.00287546585117 } window.highpass.apodization = { 0.00574975947819 0.00574975947819 } window.mask.apodization = { 10 10 } align.mask.width = { 670 694 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 72.978881924 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 695 719 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 670 694 } reference.body = 72.978881924 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.0154 for Iteration #21 of Tilt-Series #7. CCMS(rotations) = 0.36036 for Iteration #21 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #7. The scaled sum of CCMS values is #0.01491 for Tilt-Series #7. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... No Round parameters changed for Iteration #22 Beginning Refinement Iteration #22, Round #2 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00426 for Iteration #22 of Tilt-Series #7. CCMS(rotations) = 0.12131 for Iteration #22 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #7. The scaled sum of CCMS values is #0.00455 for Tilt-Series #7. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... No Round parameters changed for Iteration #23 Beginning Refinement Iteration #23, Round #2 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00405 for Iteration #23 of Tilt-Series #7. CCMS(rotations) = 0.2122 for Iteration #23 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #7. The scaled sum of CCMS values is #0.00627 for Tilt-Series #7. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... No Round parameters changed for Iteration #24 Beginning Refinement Iteration #24, Round #2 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00525 for Iteration #24 of Tilt-Series #7. CCMS(rotations) = 0.20574 for Iteration #24 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #7. The scaled sum of CCMS values is #0.00674 for Tilt-Series #7. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... No Round parameters changed for Iteration #25 Beginning Refinement Iteration #25, Round #2 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00438 for Iteration #25 of Tilt-Series #7. CCMS(rotations) = 0.18261 for Iteration #25 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #7. The scaled sum of CCMS values is #0.00584 for Tilt-Series #7. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... No Round parameters changed for Iteration #26 Beginning Refinement Iteration #26, Round #2 No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00424 for Iteration #26 of Tilt-Series #7. CCMS(rotations) = 0.20254 for Iteration #26 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #7. The scaled sum of CCMS values is #0.00617 for Tilt-Series #7. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... No Round parameters changed for Iteration #27 Beginning Refinement Iteration #27, Round #2 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00436 for Iteration #27 of Tilt-Series #7. CCMS(rotations) = 0.13186 for Iteration #27 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #7. The scaled sum of CCMS values is #0.00482 for Tilt-Series #7. Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... No Round parameters changed for Iteration #28 Beginning Refinement Iteration #28, Round #2 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00453 for Iteration #28 of Tilt-Series #7. CCMS(rotations) = 0.19536 for Iteration #28 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #7. The scaled sum of CCMS values is #0.00617 for Tilt-Series #7. Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... No Round parameters changed for Iteration #29 Beginning Refinement Iteration #29, Round #2 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00453 for Iteration #29 of Tilt-Series #7. CCMS(rotations) = 0.13984 for Iteration #29 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #7. The scaled sum of CCMS values is #0.00506 for Tilt-Series #7. Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... No Round parameters changed for Iteration #30 Beginning Refinement Iteration #30, Round #2 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00399 for Iteration #30 of Tilt-Series #7. CCMS(rotations) = 0.09509 for Iteration #30 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #7. The scaled sum of CCMS values is #0.0039 for Tilt-Series #7. Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... No Round parameters changed for Iteration #31 Beginning Refinement Iteration #31, Round #2 No parameters were switched for Iteration #31 Creating quality assessment statistics... CCMS(shift) = 0.00561 for Iteration #31 of Tilt-Series #7. CCMS(rotations) = 0.16411 for Iteration #31 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #7. The scaled sum of CCMS values is #0.00609 for Tilt-Series #7. Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... No Round parameters changed for Iteration #32 Beginning Refinement Iteration #32, Round #2 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00406 for Iteration #32 of Tilt-Series #7. CCMS(rotations) = 0.12976 for Iteration #32 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #32 of Tilt-Series #7. The scaled sum of CCMS values is #0.00462 for Tilt-Series #7. Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... No Round parameters changed for Iteration #33 Beginning Refinement Iteration #33, Round #2 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00465 for Iteration #33 of Tilt-Series #7. CCMS(rotations) = 0.12037 for Iteration #33 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #33 of Tilt-Series #7. The scaled sum of CCMS values is #0.00473 for Tilt-Series #7. Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... No Round parameters changed for Iteration #34 Beginning Refinement Iteration #34, Round #2 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00437 for Iteration #34 of Tilt-Series #7. CCMS(rotations) = 0.14892 for Iteration #34 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #34 of Tilt-Series #7. The scaled sum of CCMS values is #0.00516 for Tilt-Series #7. Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... No Round parameters changed for Iteration #35 Beginning Refinement Iteration #35, Round #2 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00488 for Iteration #35 of Tilt-Series #7. CCMS(rotations) = 0.09507 for Iteration #35 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #35 of Tilt-Series #7. The scaled sum of CCMS values is #0.00434 for Tilt-Series #7. Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... No Round parameters changed for Iteration #36 Beginning Refinement Iteration #36, Round #2 No parameters were switched for Iteration #36 Creating quality assessment statistics... CCMS(shift) = 0.00448 for Iteration #36 of Tilt-Series #7. CCMS(rotations) = 0.16586 for Iteration #36 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #36 of Tilt-Series #7. The scaled sum of CCMS values is #0.00556 for Tilt-Series #7. Creating Depiction Videos for Iteration #36 in Parallel... Creating Refinement tilt-series video for iteration #36... Generating Refinement reconstruction for iteration #36... No Round parameters changed for Iteration #37 Beginning Refinement Iteration #37, Round #2 No parameters were switched for Iteration #37 Creating quality assessment statistics... CCMS(shift) = 0.0048 for Iteration #37 of Tilt-Series #7. CCMS(rotations) = 0.10167 for Iteration #37 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #37 of Tilt-Series #7. The scaled sum of CCMS values is #0.00443 for Tilt-Series #7. Creating Depiction Videos for Iteration #37 in Parallel... Creating Refinement tilt-series video for iteration #37... Generating Refinement reconstruction for iteration #37... No Round parameters changed for Iteration #38 Beginning Refinement Iteration #38, Round #2 No parameters were switched for Iteration #38 Creating quality assessment statistics... CCMS(shift) = 0.00476 for Iteration #38 of Tilt-Series #7. CCMS(rotations) = 0.21678 for Iteration #38 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #38 of Tilt-Series #7. The scaled sum of CCMS values is #0.00672 for Tilt-Series #7. Creating Depiction Videos for Iteration #38 in Parallel... Creating Refinement tilt-series video for iteration #38... Generating Refinement reconstruction for iteration #38... No Round parameters changed for Iteration #39 Beginning Refinement Iteration #39, Round #2 No parameters were switched for Iteration #39 Creating quality assessment statistics... CCMS(shift) = 0.00488 for Iteration #39 of Tilt-Series #7. CCMS(rotations) = 0.09463 for Iteration #39 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #39 of Tilt-Series #7. The scaled sum of CCMS values is #0.00433 for Tilt-Series #7. Creating Depiction Videos for Iteration #39 in Parallel... Creating Refinement tilt-series video for iteration #39... Generating Refinement reconstruction for iteration #39... No Round parameters changed for Iteration #40 Beginning Refinement Iteration #40, Round #2 No parameters were switched for Iteration #40 Creating quality assessment statistics... CCMS(shift) = 0.00424 for Iteration #40 of Tilt-Series #7. CCMS(rotations) = 0.15844 for Iteration #40 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #40 of Tilt-Series #7. The scaled sum of CCMS values is #0.00529 for Tilt-Series #7. Creating Depiction Videos for Iteration #40 in Parallel... Creating Refinement tilt-series video for iteration #40... Generating Refinement reconstruction for iteration #40... 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 = { 0.00143773292559 0.00143773292559 } window.highpass.apodization = { 0.00287487973909 0.00287487973909 } window.mask.apodization = { 10 10 } align.mask.width = { 1366 1414 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 145.957763848 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1391 1439 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1366 1414 } reference.body = 145.957763848 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #41 Creating quality assessment statistics... CCMS(shift) = 0.0058 for Iteration #41 of Tilt-Series #7. CCMS(rotations) = 0.2371 for Iteration #41 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #41 of Tilt-Series #7. The scaled sum of CCMS values is #0.00764 for Tilt-Series #7. Creating Depiction Videos for Iteration #41 in Parallel... Creating Refinement tilt-series video for iteration #41... Generating Refinement reconstruction for iteration #41... No Round parameters changed for Iteration #42 Beginning Refinement Iteration #42, Round #3 No parameters were switched for Iteration #42 Creating quality assessment statistics... CCMS(shift) = 0.00566 for Iteration #42 of Tilt-Series #7. CCMS(rotations) = 0.13699 for Iteration #42 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #42 of Tilt-Series #7. The scaled sum of CCMS values is #0.00557 for Tilt-Series #7. Creating Depiction Videos for Iteration #42 in Parallel... Creating Refinement tilt-series video for iteration #42... Generating Refinement reconstruction for iteration #42... No Round parameters changed for Iteration #43 Beginning Refinement Iteration #43, Round #3 No parameters were switched for Iteration #43 Creating quality assessment statistics... CCMS(shift) = 0.00536 for Iteration #43 of Tilt-Series #7. CCMS(rotations) = 0.15183 for Iteration #43 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #43 of Tilt-Series #7. The scaled sum of CCMS values is #0.00572 for Tilt-Series #7. Creating Depiction Videos for Iteration #43 in Parallel... Creating Refinement tilt-series video for iteration #43... Generating Refinement reconstruction for iteration #43... No Round parameters changed for Iteration #44 Beginning Refinement Iteration #44, Round #3 No parameters were switched for Iteration #44 Creating quality assessment statistics... CCMS(shift) = 0.00442 for Iteration #44 of Tilt-Series #7. CCMS(rotations) = 0.11184 for Iteration #44 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #44 of Tilt-Series #7. The scaled sum of CCMS values is #0.00444 for Tilt-Series #7. Creating Depiction Videos for Iteration #44 in Parallel... Creating Refinement tilt-series video for iteration #44... Generating Refinement reconstruction for iteration #44... No Round parameters changed for Iteration #45 Beginning Refinement Iteration #45, Round #3 No parameters were switched for Iteration #45 Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #45 of Tilt-Series #7. CCMS(rotations) = 0.1636 for Iteration #45 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #45 of Tilt-Series #7. The scaled sum of CCMS values is #0.00536 for Tilt-Series #7. Creating Depiction Videos for Iteration #45 in Parallel... Creating Refinement tilt-series video for iteration #45... Generating Refinement reconstruction for iteration #45... No Round parameters changed for Iteration #46 Beginning Refinement Iteration #46, Round #3 No parameters were switched for Iteration #46 Creating quality assessment statistics... CCMS(shift) = 0.00431 for Iteration #46 of Tilt-Series #7. CCMS(rotations) = 0.17789 for Iteration #46 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #46 of Tilt-Series #7. The scaled sum of CCMS values is #0.00571 for Tilt-Series #7. Creating Depiction Videos for Iteration #46 in Parallel... Creating Refinement tilt-series video for iteration #46... Generating Refinement reconstruction for iteration #46... No Round parameters changed for Iteration #47 Beginning Refinement Iteration #47, Round #3 No parameters were switched for Iteration #47 Creating quality assessment statistics... CCMS(shift) = 0.00507 for Iteration #47 of Tilt-Series #7. CCMS(rotations) = 0.11083 for Iteration #47 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #47 of Tilt-Series #7. The scaled sum of CCMS values is #0.00475 for Tilt-Series #7. Creating Depiction Videos for Iteration #47 in Parallel... Creating Refinement tilt-series video for iteration #47... Generating Refinement reconstruction for iteration #47... No Round parameters changed for Iteration #48 Beginning Refinement Iteration #48, Round #3 No parameters were switched for Iteration #48 Creating quality assessment statistics... CCMS(shift) = 0.00445 for Iteration #48 of Tilt-Series #7. CCMS(rotations) = 0.16939 for Iteration #48 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #48 of Tilt-Series #7. The scaled sum of CCMS values is #0.00561 for Tilt-Series #7. Creating Depiction Videos for Iteration #48 in Parallel... Creating Refinement tilt-series video for iteration #48... Generating Refinement reconstruction for iteration #48... No Round parameters changed for Iteration #49 Beginning Refinement Iteration #49, Round #3 No parameters were switched for Iteration #49 Creating quality assessment statistics... CCMS(shift) = 0.00431 for Iteration #49 of Tilt-Series #7. CCMS(rotations) = 0.14862 for Iteration #49 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #49 of Tilt-Series #7. The scaled sum of CCMS values is #0.00513 for Tilt-Series #7. Creating Depiction Videos for Iteration #49 in Parallel... Creating Refinement tilt-series video for iteration #49... Generating Refinement reconstruction for iteration #49... No Round parameters changed for Iteration #50 Beginning Refinement Iteration #50, Round #3 No parameters were switched for Iteration #50 Creating quality assessment statistics... CCMS(shift) = 0.00406 for Iteration #50 of Tilt-Series #7. CCMS(rotations) = 0.13773 for Iteration #50 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #50 of Tilt-Series #7. The scaled sum of CCMS values is #0.00479 for Tilt-Series #7. Creating Depiction Videos for Iteration #50 in Parallel... Creating Refinement tilt-series video for iteration #50... Generating Refinement reconstruction for iteration #50... No Round parameters changed for Iteration #51 Beginning Refinement Iteration #51, Round #3 No parameters were switched for Iteration #51 Creating quality assessment statistics... CCMS(shift) = 0.00441 for Iteration #51 of Tilt-Series #7. CCMS(rotations) = 0.11776 for Iteration #51 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #51 of Tilt-Series #7. The scaled sum of CCMS values is #0.00456 for Tilt-Series #7. Creating Depiction Videos for Iteration #51 in Parallel... Creating Refinement tilt-series video for iteration #51... Generating Refinement reconstruction for iteration #51... No Round parameters changed for Iteration #52 Beginning Refinement Iteration #52, Round #3 No parameters were switched for Iteration #52 Creating quality assessment statistics... CCMS(shift) = 0.00427 for Iteration #52 of Tilt-Series #7. CCMS(rotations) = 0.13995 for Iteration #52 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #52 of Tilt-Series #7. The scaled sum of CCMS values is #0.00493 for Tilt-Series #7. Creating Depiction Videos for Iteration #52 in Parallel... Creating Refinement tilt-series video for iteration #52... Generating Refinement reconstruction for iteration #52... No Round parameters changed for Iteration #53 Beginning Refinement Iteration #53, Round #3 No parameters were switched for Iteration #53 Creating quality assessment statistics... CCMS(shift) = 0.00428 for Iteration #53 of Tilt-Series #7. CCMS(rotations) = 0.13857 for Iteration #53 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #53 of Tilt-Series #7. The scaled sum of CCMS values is #0.00491 for Tilt-Series #7. Creating Depiction Videos for Iteration #53 in Parallel... Creating Refinement tilt-series video for iteration #53... Generating Refinement reconstruction for iteration #53... No Round parameters changed for Iteration #54 Beginning Refinement Iteration #54, Round #3 No parameters were switched for Iteration #54 Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #54 of Tilt-Series #7. CCMS(rotations) = 0.14043 for Iteration #54 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #54 of Tilt-Series #7. The scaled sum of CCMS values is #0.00459 for Tilt-Series #7. Creating Depiction Videos for Iteration #54 in Parallel... Creating Refinement tilt-series video for iteration #54... Generating Refinement reconstruction for iteration #54... No Round parameters changed for Iteration #55 Beginning Refinement Iteration #55, Round #3 No parameters were switched for Iteration #55 Creating quality assessment statistics... CCMS(shift) = 0.00423 for Iteration #55 of Tilt-Series #7. CCMS(rotations) = 0.13968 for Iteration #55 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #55 of Tilt-Series #7. The scaled sum of CCMS values is #0.00491 for Tilt-Series #7. Creating Depiction Videos for Iteration #55 in Parallel... Creating Refinement tilt-series video for iteration #55... Generating Refinement reconstruction for iteration #55... No Round parameters changed for Iteration #56 Beginning Refinement Iteration #56, Round #3 No parameters were switched for Iteration #56 Creating quality assessment statistics... CCMS(shift) = 0.00405 for Iteration #56 of Tilt-Series #7. CCMS(rotations) = 0.17569 for Iteration #56 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #56 of Tilt-Series #7. The scaled sum of CCMS values is #0.00554 for Tilt-Series #7. Creating Depiction Videos for Iteration #56 in Parallel... Creating Refinement tilt-series video for iteration #56... Generating Refinement reconstruction for iteration #56... No Round parameters changed for Iteration #57 Beginning Refinement Iteration #57, Round #3 No parameters were switched for Iteration #57 Creating quality assessment statistics... CCMS(shift) = 0.00406 for Iteration #57 of Tilt-Series #7. CCMS(rotations) = 0.12516 for Iteration #57 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #57 of Tilt-Series #7. The scaled sum of CCMS values is #0.00454 for Tilt-Series #7. Creating Depiction Videos for Iteration #57 in Parallel... Creating Refinement tilt-series video for iteration #57... Generating Refinement reconstruction for iteration #57... No Round parameters changed for Iteration #58 Beginning Refinement Iteration #58, Round #3 No parameters were switched for Iteration #58 Creating quality assessment statistics... CCMS(shift) = 0.00351 for Iteration #58 of Tilt-Series #7. CCMS(rotations) = 0.13485 for Iteration #58 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #58 of Tilt-Series #7. The scaled sum of CCMS values is #0.00445 for Tilt-Series #7. Creating Depiction Videos for Iteration #58 in Parallel... Creating Refinement tilt-series video for iteration #58... Generating Refinement reconstruction for iteration #58... No Round parameters changed for Iteration #59 Beginning Refinement Iteration #59, Round #3 No parameters were switched for Iteration #59 Creating quality assessment statistics... CCMS(shift) = 0.0042 for Iteration #59 of Tilt-Series #7. CCMS(rotations) = 0.14142 for Iteration #59 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #59 of Tilt-Series #7. The scaled sum of CCMS values is #0.00493 for Tilt-Series #7. Creating Depiction Videos for Iteration #59 in Parallel... Creating Refinement tilt-series video for iteration #59... Generating Refinement reconstruction for iteration #59... No Round parameters changed for Iteration #60 Beginning Refinement Iteration #60, Round #3 No parameters were switched for Iteration #60 Creating quality assessment statistics... CCMS(shift) = 0.00401 for Iteration #60 of Tilt-Series #7. CCMS(rotations) = 0.15503 for Iteration #60 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #60 of Tilt-Series #7. The scaled sum of CCMS values is #0.00511 for Tilt-Series #7. Creating Depiction Videos for Iteration #60 in Parallel... Creating Refinement tilt-series video for iteration #60... Generating Refinement reconstruction for iteration #60... 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 = { 0.000718866462793 0.000718866462793 } window.highpass.apodization = { 0.00143743986955 0.00143743986955 } window.mask.apodization = { 10 10 } align.mask.width = { 2757 2853 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 291.915527696 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 291.915527696 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #61 Creating quality assessment statistics... CCMS(shift) = 0.0096 for Iteration #61 of Tilt-Series #7. CCMS(rotations) = 0.3837 for Iteration #61 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #61 of Tilt-Series #7. The scaled sum of CCMS values is #0.01247 for Tilt-Series #7. Creating Depiction Videos for Iteration #61 in Parallel... Creating Refinement tilt-series video for iteration #61... Generating Refinement reconstruction for iteration #61... No Round parameters changed for Iteration #62 Beginning Refinement Iteration #62, Round #4 No parameters were switched for Iteration #62 Creating quality assessment statistics... CCMS(shift) = 0.00441 for Iteration #62 of Tilt-Series #7. CCMS(rotations) = 0.16542 for Iteration #62 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #62 of Tilt-Series #7. The scaled sum of CCMS values is #0.00551 for Tilt-Series #7. Creating Depiction Videos for Iteration #62 in Parallel... Creating Refinement tilt-series video for iteration #62... Generating Refinement reconstruction for iteration #62... No Round parameters changed for Iteration #63 Beginning Refinement Iteration #63, Round #4 No parameters were switched for Iteration #63 Creating quality assessment statistics... CCMS(shift) = 0.00461 for Iteration #63 of Tilt-Series #7. CCMS(rotations) = 0.13131 for Iteration #63 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #63 of Tilt-Series #7. The scaled sum of CCMS values is #0.00493 for Tilt-Series #7. Creating Depiction Videos for Iteration #63 in Parallel... Creating Refinement tilt-series video for iteration #63... Generating Refinement reconstruction for iteration #63... No Round parameters changed for Iteration #64 Beginning Refinement Iteration #64, Round #4 No parameters were switched for Iteration #64 Creating quality assessment statistics... CCMS(shift) = 0.00412 for Iteration #64 of Tilt-Series #7. CCMS(rotations) = 0.17569 for Iteration #64 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #64 of Tilt-Series #7. The scaled sum of CCMS values is #0.00558 for Tilt-Series #7. Creating Depiction Videos for Iteration #64 in Parallel... Creating Refinement tilt-series video for iteration #64... Generating Refinement reconstruction for iteration #64... No Round parameters changed for Iteration #65 Beginning Refinement Iteration #65, Round #4 No parameters were switched for Iteration #65 Creating quality assessment statistics... CCMS(shift) = 0.00478 for Iteration #65 of Tilt-Series #7. CCMS(rotations) = 0.17707 for Iteration #65 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #65 of Tilt-Series #7. The scaled sum of CCMS values is #0.00593 for Tilt-Series #7. Creating Depiction Videos for Iteration #65 in Parallel... Creating Refinement tilt-series video for iteration #65... Generating Refinement reconstruction for iteration #65... No Round parameters changed for Iteration #66 Beginning Refinement Iteration #66, Round #4 No parameters were switched for Iteration #66 Creating quality assessment statistics... CCMS(shift) = 0.00501 for Iteration #66 of Tilt-Series #7. CCMS(rotations) = 0.18542 for Iteration #66 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #66 of Tilt-Series #7. The scaled sum of CCMS values is #0.00622 for Tilt-Series #7. Creating Depiction Videos for Iteration #66 in Parallel... Creating Refinement tilt-series video for iteration #66... Generating Refinement reconstruction for iteration #66... No Round parameters changed for Iteration #67 Beginning Refinement Iteration #67, Round #4 No parameters were switched for Iteration #67 Creating quality assessment statistics... CCMS(shift) = 0.00443 for Iteration #67 of Tilt-Series #7. CCMS(rotations) = 0.16139 for Iteration #67 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #67 of Tilt-Series #7. The scaled sum of CCMS values is #0.00545 for Tilt-Series #7. Creating Depiction Videos for Iteration #67 in Parallel... Creating Refinement tilt-series video for iteration #67... Generating Refinement reconstruction for iteration #67... No Round parameters changed for Iteration #68 Beginning Refinement Iteration #68, Round #4 No parameters were switched for Iteration #68 Creating quality assessment statistics... CCMS(shift) = 0.004 for Iteration #68 of Tilt-Series #7. CCMS(rotations) = 0.17914 for Iteration #68 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #68 of Tilt-Series #7. The scaled sum of CCMS values is #0.00558 for Tilt-Series #7. Creating Depiction Videos for Iteration #68 in Parallel... Creating Refinement tilt-series video for iteration #68... Generating Refinement reconstruction for iteration #68... No Round parameters changed for Iteration #69 Beginning Refinement Iteration #69, Round #4 No parameters were switched for Iteration #69 Creating quality assessment statistics... CCMS(shift) = 0.00474 for Iteration #69 of Tilt-Series #7. CCMS(rotations) = 0.18002 for Iteration #69 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #69 of Tilt-Series #7. The scaled sum of CCMS values is #0.00597 for Tilt-Series #7. Creating Depiction Videos for Iteration #69 in Parallel... Creating Refinement tilt-series video for iteration #69... Generating Refinement reconstruction for iteration #69... No Round parameters changed for Iteration #70 Beginning Refinement Iteration #70, Round #4 No parameters were switched for Iteration #70 Creating quality assessment statistics... CCMS(shift) = 0.00423 for Iteration #70 of Tilt-Series #7. CCMS(rotations) = 0.18215 for Iteration #70 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #70 of Tilt-Series #7. The scaled sum of CCMS values is #0.00576 for Tilt-Series #7. Creating Depiction Videos for Iteration #70 in Parallel... Creating Refinement tilt-series video for iteration #70... Generating Refinement reconstruction for iteration #70... No Round parameters changed for Iteration #71 Beginning Refinement Iteration #71, Round #4 No parameters were switched for Iteration #71 Creating quality assessment statistics... CCMS(shift) = 0.00334 for Iteration #71 of Tilt-Series #7. CCMS(rotations) = 0.18256 for Iteration #71 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #71 of Tilt-Series #7. The scaled sum of CCMS values is #0.00532 for Tilt-Series #7. Creating Depiction Videos for Iteration #71 in Parallel... Creating Refinement tilt-series video for iteration #71... Generating Refinement reconstruction for iteration #71... No Round parameters changed for Iteration #72 Beginning Refinement Iteration #72, Round #4 No parameters were switched for Iteration #72 Creating quality assessment statistics... CCMS(shift) = 0.00406 for Iteration #72 of Tilt-Series #7. CCMS(rotations) = 0.18073 for Iteration #72 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #72 of Tilt-Series #7. The scaled sum of CCMS values is #0.00565 for Tilt-Series #7. Creating Depiction Videos for Iteration #72 in Parallel... Creating Refinement tilt-series video for iteration #72... Generating Refinement reconstruction for iteration #72... No Round parameters changed for Iteration #73 Beginning Refinement Iteration #73, Round #4 No parameters were switched for Iteration #73 Creating quality assessment statistics... CCMS(shift) = 0.00508 for Iteration #73 of Tilt-Series #7. CCMS(rotations) = 0.15091 for Iteration #73 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #73 of Tilt-Series #7. The scaled sum of CCMS values is #0.00556 for Tilt-Series #7. Creating Depiction Videos for Iteration #73 in Parallel... Creating Refinement tilt-series video for iteration #73... Generating Refinement reconstruction for iteration #73... No Round parameters changed for Iteration #74 Beginning Refinement Iteration #74, Round #4 No parameters were switched for Iteration #74 Creating quality assessment statistics... CCMS(shift) = 0.00516 for Iteration #74 of Tilt-Series #7. CCMS(rotations) = 0.18223 for Iteration #74 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #74 of Tilt-Series #7. The scaled sum of CCMS values is #0.00622 for Tilt-Series #7. Creating Depiction Videos for Iteration #74 in Parallel... Creating Refinement tilt-series video for iteration #74... Generating Refinement reconstruction for iteration #74... No Round parameters changed for Iteration #75 Beginning Refinement Iteration #75, Round #4 No parameters were switched for Iteration #75 Creating quality assessment statistics... CCMS(shift) = 0.00417 for Iteration #75 of Tilt-Series #7. CCMS(rotations) = 0.15347 for Iteration #75 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #75 of Tilt-Series #7. The scaled sum of CCMS values is #0.00515 for Tilt-Series #7. Creating Depiction Videos for Iteration #75 in Parallel... Creating Refinement tilt-series video for iteration #75... Generating Refinement reconstruction for iteration #75... No Round parameters changed for Iteration #76 Beginning Refinement Iteration #76, Round #4 No parameters were switched for Iteration #76 Creating quality assessment statistics... CCMS(shift) = 0.00473 for Iteration #76 of Tilt-Series #7. CCMS(rotations) = 0.15854 for Iteration #76 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #76 of Tilt-Series #7. The scaled sum of CCMS values is #0.00554 for Tilt-Series #7. Creating Depiction Videos for Iteration #76 in Parallel... Creating Refinement tilt-series video for iteration #76... Generating Refinement reconstruction for iteration #76... No Round parameters changed for Iteration #77 Beginning Refinement Iteration #77, Round #4 No parameters were switched for Iteration #77 Creating quality assessment statistics... CCMS(shift) = 0.00467 for Iteration #77 of Tilt-Series #7. CCMS(rotations) = 0.14083 for Iteration #77 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #77 of Tilt-Series #7. The scaled sum of CCMS values is #0.00515 for Tilt-Series #7. Creating Depiction Videos for Iteration #77 in Parallel... Creating Refinement tilt-series video for iteration #77... Generating Refinement reconstruction for iteration #77... No Round parameters changed for Iteration #78 Beginning Refinement Iteration #78, Round #4 No parameters were switched for Iteration #78 Creating quality assessment statistics... CCMS(shift) = 0.00431 for Iteration #78 of Tilt-Series #7. CCMS(rotations) = 0.21223 for Iteration #78 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #78 of Tilt-Series #7. The scaled sum of CCMS values is #0.0064 for Tilt-Series #7. Creating Depiction Videos for Iteration #78 in Parallel... Creating Refinement tilt-series video for iteration #78... Generating Refinement reconstruction for iteration #78... No Round parameters changed for Iteration #79 Beginning Refinement Iteration #79, Round #4 No parameters were switched for Iteration #79 Creating quality assessment statistics... CCMS(shift) = 0.00395 for Iteration #79 of Tilt-Series #7. CCMS(rotations) = 0.17478 for Iteration #79 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #79 of Tilt-Series #7. The scaled sum of CCMS values is #0.00547 for Tilt-Series #7. Creating Depiction Videos for Iteration #79 in Parallel... Creating Refinement tilt-series video for iteration #79... Generating Refinement reconstruction for iteration #79... No Round parameters changed for Iteration #80 Beginning Refinement Iteration #80, Round #4 No parameters were switched for Iteration #80 Creating quality assessment statistics... CCMS(shift) = 0.00373 for Iteration #80 of Tilt-Series #7. CCMS(rotations) = 0.11037 for Iteration #80 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #80 of Tilt-Series #7. The scaled sum of CCMS values is #0.00407 for Tilt-Series #7. Creating Depiction Videos for Iteration #80 in Parallel... Creating Refinement tilt-series video for iteration #80... Generating Refinement reconstruction for iteration #80... No Round parameters changed for Iteration #81 Beginning Refinement Iteration #81, Round #4 fit.scale switched from false to true on Iteration #81Creating quality assessment statistics... CCMS(shift) = 0.00344 for Iteration #81 of Tilt-Series #7. CCMS(rotations) = 0.15628 for Iteration #81 of Tilt-Series #7. CCMS(scale) = 0.0 for Iteration #81 of Tilt-Series #7. The scaled sum of CCMS values is #0.00485 for Tilt-Series #7. Creating Depiction Videos for Iteration #81 in Parallel... Creating Refinement tilt-series video for iteration #81... Generating Refinement reconstruction for iteration #81... No Round parameters changed for Iteration #82 Beginning Refinement Iteration #82, Round #4 No parameters were switched for Iteration #82 Creating quality assessment statistics... CCMS(shift) = 0.00294 for Iteration #82 of Tilt-Series #7. CCMS(rotations) = 0.18208 for Iteration #82 of Tilt-Series #7. CCMS(scale) = 0.0013 for Iteration #82 of Tilt-Series #7. The scaled sum of CCMS values is #0.00384 for Tilt-Series #7. Creating Depiction Videos for Iteration #82 in Parallel... Creating Refinement tilt-series video for iteration #82... Generating Refinement reconstruction for iteration #82... No Round parameters changed for Iteration #83 Beginning Refinement Iteration #83, Round #4 No parameters were switched for Iteration #83 Creating quality assessment statistics... CCMS(shift) = 0.00436 for Iteration #83 of Tilt-Series #7. CCMS(rotations) = 0.18077 for Iteration #83 of Tilt-Series #7. CCMS(scale) = 0.00175 for Iteration #83 of Tilt-Series #7. The scaled sum of CCMS values is #0.00445 for Tilt-Series #7. Creating Depiction Videos for Iteration #83 in Parallel... Creating Refinement tilt-series video for iteration #83... Generating Refinement reconstruction for iteration #83... No Round parameters changed for Iteration #84 Beginning Refinement Iteration #84, Round #4 No parameters were switched for Iteration #84 Creating quality assessment statistics... CCMS(shift) = 0.00413 for Iteration #84 of Tilt-Series #7. CCMS(rotations) = 0.19246 for Iteration #84 of Tilt-Series #7. CCMS(scale) = 0.00184 for Iteration #84 of Tilt-Series #7. The scaled sum of CCMS values is #0.00455 for Tilt-Series #7. Creating Depiction Videos for Iteration #84 in Parallel... Creating Refinement tilt-series video for iteration #84... Generating Refinement reconstruction for iteration #84... No Round parameters changed for Iteration #85 Beginning Refinement Iteration #85, Round #4 No parameters were switched for Iteration #85 Creating quality assessment statistics... CCMS(shift) = 0.00401 for Iteration #85 of Tilt-Series #7. CCMS(rotations) = 0.17427 for Iteration #85 of Tilt-Series #7. CCMS(scale) = 0.00207 for Iteration #85 of Tilt-Series #7. The scaled sum of CCMS values is #0.00435 for Tilt-Series #7. Creating Depiction Videos for Iteration #85 in Parallel... Creating Refinement tilt-series video for iteration #85... Generating Refinement reconstruction for iteration #85... No Round parameters changed for Iteration #86 Beginning Refinement Iteration #86, Round #4 No parameters were switched for Iteration #86 Creating quality assessment statistics... CCMS(shift) = 0.00527 for Iteration #86 of Tilt-Series #7. CCMS(rotations) = 0.18127 for Iteration #86 of Tilt-Series #7. CCMS(scale) = 0.00161 for Iteration #86 of Tilt-Series #7. The scaled sum of CCMS values is #0.00471 for Tilt-Series #7. Creating Depiction Videos for Iteration #86 in Parallel... Creating Refinement tilt-series video for iteration #86... Generating Refinement reconstruction for iteration #86... No Round parameters changed for Iteration #87 Beginning Refinement Iteration #87, Round #4 No parameters were switched for Iteration #87 Creating quality assessment statistics... CCMS(shift) = 0.00388 for Iteration #87 of Tilt-Series #7. CCMS(rotations) = 0.19417 for Iteration #87 of Tilt-Series #7. CCMS(scale) = 0.00211 for Iteration #87 of Tilt-Series #7. The scaled sum of CCMS values is #0.00459 for Tilt-Series #7. Creating Depiction Videos for Iteration #87 in Parallel... Creating Refinement tilt-series video for iteration #87... Generating Refinement reconstruction for iteration #87... No Round parameters changed for Iteration #88 Beginning Refinement Iteration #88, Round #4 No parameters were switched for Iteration #88 Creating quality assessment statistics... CCMS(shift) = 0.00314 for Iteration #88 of Tilt-Series #7. CCMS(rotations) = 0.18096 for Iteration #88 of Tilt-Series #7. CCMS(scale) = 0.00184 for Iteration #88 of Tilt-Series #7. The scaled sum of CCMS values is #0.00407 for Tilt-Series #7. Creating Depiction Videos for Iteration #88 in Parallel... Creating Refinement tilt-series video for iteration #88... Generating Refinement reconstruction for iteration #88... No Round parameters changed for Iteration #89 Beginning Refinement Iteration #89, Round #4 No parameters were switched for Iteration #89 Creating quality assessment statistics... CCMS(shift) = 0.00339 for Iteration #89 of Tilt-Series #7. CCMS(rotations) = 0.16031 for Iteration #89 of Tilt-Series #7. CCMS(scale) = 0.00175 for Iteration #89 of Tilt-Series #7. The scaled sum of CCMS values is #0.00385 for Tilt-Series #7. Creating Depiction Videos for Iteration #89 in Parallel... Creating Refinement tilt-series video for iteration #89... Generating Refinement reconstruction for iteration #89... No Round parameters changed for Iteration #90 Beginning Refinement Iteration #90, Round #4 No parameters were switched for Iteration #90 Creating quality assessment statistics... CCMS(shift) = 0.00255 for Iteration #90 of Tilt-Series #7. CCMS(rotations) = 0.15218 for Iteration #90 of Tilt-Series #7. CCMS(scale) = 0.00191 for Iteration #90 of Tilt-Series #7. The scaled sum of CCMS values is #0.00352 for Tilt-Series #7. Creating Depiction Videos for Iteration #90 in Parallel... Creating Refinement tilt-series video for iteration #90... Generating Refinement reconstruction for iteration #90... No Round parameters changed for Iteration #91 Beginning Refinement Iteration #91, Round #4 No parameters were switched for Iteration #91 Creating quality assessment statistics... CCMS(shift) = 0.00442 for Iteration #91 of Tilt-Series #7. CCMS(rotations) = 0.16985 for Iteration #91 of Tilt-Series #7. CCMS(scale) = 0.00157 for Iteration #91 of Tilt-Series #7. The scaled sum of CCMS values is #0.00426 for Tilt-Series #7. Creating Depiction Videos for Iteration #91 in Parallel... Creating Refinement tilt-series video for iteration #91... Generating Refinement reconstruction for iteration #91... No Round parameters changed for Iteration #92 Beginning Refinement Iteration #92, Round #4 No parameters were switched for Iteration #92 Creating quality assessment statistics... CCMS(shift) = 0.00333 for Iteration #92 of Tilt-Series #7. CCMS(rotations) = 0.21158 for Iteration #92 of Tilt-Series #7. CCMS(scale) = 0.00155 for Iteration #92 of Tilt-Series #7. The scaled sum of CCMS values is #0.00445 for Tilt-Series #7. Creating Depiction Videos for Iteration #92 in Parallel... Creating Refinement tilt-series video for iteration #92... Generating Refinement reconstruction for iteration #92... No Round parameters changed for Iteration #93 Beginning Refinement Iteration #93, Round #4 No parameters were switched for Iteration #93 Creating quality assessment statistics... CCMS(shift) = 0.0042 for Iteration #93 of Tilt-Series #7. CCMS(rotations) = 0.17647 for Iteration #93 of Tilt-Series #7. CCMS(scale) = 0.00162 for Iteration #93 of Tilt-Series #7. The scaled sum of CCMS values is #0.00429 for Tilt-Series #7. Creating Depiction Videos for Iteration #93 in Parallel... Creating Refinement tilt-series video for iteration #93... Generating Refinement reconstruction for iteration #93... No Round parameters changed for Iteration #94 Beginning Refinement Iteration #94, Round #4 No parameters were switched for Iteration #94 Creating quality assessment statistics... CCMS(shift) = 0.0041 for Iteration #94 of Tilt-Series #7. CCMS(rotations) = 0.18711 for Iteration #94 of Tilt-Series #7. CCMS(scale) = 0.00189 for Iteration #94 of Tilt-Series #7. The scaled sum of CCMS values is #0.00449 for Tilt-Series #7. Creating Depiction Videos for Iteration #94 in Parallel... Creating Refinement tilt-series video for iteration #94... Generating Refinement reconstruction for iteration #94... No Round parameters changed for Iteration #95 Beginning Refinement Iteration #95, Round #4 No parameters were switched for Iteration #95 Creating quality assessment statistics... CCMS(shift) = 0.00338 for Iteration #95 of Tilt-Series #7. CCMS(rotations) = 0.13891 for Iteration #95 of Tilt-Series #7. CCMS(scale) = 0.00187 for Iteration #95 of Tilt-Series #7. The scaled sum of CCMS values is #0.0036 for Tilt-Series #7. Creating Depiction Videos for Iteration #95 in Parallel... Creating Refinement tilt-series video for iteration #95... Generating Refinement reconstruction for iteration #95... No Round parameters changed for Iteration #96 Beginning Refinement Iteration #96, Round #4 No parameters were switched for Iteration #96 Creating quality assessment statistics... CCMS(shift) = 0.00415 for Iteration #96 of Tilt-Series #7. CCMS(rotations) = 0.18601 for Iteration #96 of Tilt-Series #7. CCMS(scale) = 0.00213 for Iteration #96 of Tilt-Series #7. The scaled sum of CCMS values is #0.00457 for Tilt-Series #7. Creating Depiction Videos for Iteration #96 in Parallel... Creating Refinement tilt-series video for iteration #96... Generating Refinement reconstruction for iteration #96... No Round parameters changed for Iteration #97 Beginning Refinement Iteration #97, Round #4 No parameters were switched for Iteration #97 Creating quality assessment statistics... CCMS(shift) = 0.00402 for Iteration #97 of Tilt-Series #7. CCMS(rotations) = 0.18823 for Iteration #97 of Tilt-Series #7. CCMS(scale) = 0.00176 for Iteration #97 of Tilt-Series #7. The scaled sum of CCMS values is #0.00444 for Tilt-Series #7. Creating Depiction Videos for Iteration #97 in Parallel... Creating Refinement tilt-series video for iteration #97... Generating Refinement reconstruction for iteration #97... No Round parameters changed for Iteration #98 Beginning Refinement Iteration #98, Round #4 No parameters were switched for Iteration #98 Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #98 of Tilt-Series #7. CCMS(rotations) = 0.14013 for Iteration #98 of Tilt-Series #7. CCMS(scale) = 0.00147 for Iteration #98 of Tilt-Series #7. The scaled sum of CCMS values is #0.00375 for Tilt-Series #7. Creating Depiction Videos for Iteration #98 in Parallel... Creating Refinement tilt-series video for iteration #98... Generating Refinement reconstruction for iteration #98... No Round parameters changed for Iteration #99 Beginning Refinement Iteration #99, Round #4 No parameters were switched for Iteration #99 Creating quality assessment statistics... CCMS(shift) = 0.0042 for Iteration #99 of Tilt-Series #7. CCMS(rotations) = 0.21373 for Iteration #99 of Tilt-Series #7. CCMS(scale) = 0.00191 for Iteration #99 of Tilt-Series #7. The scaled sum of CCMS values is #0.00488 for Tilt-Series #7. Creating Depiction Videos for Iteration #99 in Parallel... Creating Refinement tilt-series video for iteration #99... Generating Refinement reconstruction for iteration #99... No Round parameters changed for Iteration #100 Beginning Refinement Iteration #100, Round #4 No parameters were switched for Iteration #100 Creating quality assessment statistics... CCMS(shift) = 0.00353 for Iteration #100 of Tilt-Series #7. CCMS(rotations) = 0.19616 for Iteration #100 of Tilt-Series #7. CCMS(scale) = 0.00178 for Iteration #100 of Tilt-Series #7. The scaled sum of CCMS values is #0.00439 for Tilt-Series #7. Creating Depiction Videos for Iteration #100 in Parallel... Creating Refinement tilt-series video for iteration #100... Generating Refinement reconstruction for iteration #100... 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 = { 0.000718866462793 0.000718866462793 } window.highpass.apodization = { 0.00143743986955 0.00143743986955 } window.mask.apodization = { 10 10 } align.mask.width = { 2757 2853 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 291.915527696 map.lowpass.diameter = { 0.45133312 0.45133312 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 291.915527696 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 #101Creating quality assessment statistics... CCMS(shift) = 0.0101 for Iteration #101 of Tilt-Series #7. CCMS(rotations) = 0.13908 for Iteration #101 of Tilt-Series #7. CCMS(scale) = 0.00197 for Iteration #101 of Tilt-Series #7. The scaled sum of CCMS values is #0.00588 for Tilt-Series #7. Creating Depiction Videos for Iteration #101 in Parallel... Creating Refinement tilt-series video for iteration #101... Generating Refinement reconstruction for iteration #101... No Round parameters changed for Iteration #102 Beginning Refinement Iteration #102, Round #5 No parameters were switched for Iteration #102 Creating quality assessment statistics... CCMS(shift) = 0.0089 for Iteration #102 of Tilt-Series #7. CCMS(rotations) = 0.19988 for Iteration #102 of Tilt-Series #7. CCMS(scale) = 0.00342 for Iteration #102 of Tilt-Series #7. The scaled sum of CCMS values is #0.00677 for Tilt-Series #7. Creating Depiction Videos for Iteration #102 in Parallel... Creating Refinement tilt-series video for iteration #102... Generating Refinement reconstruction for iteration #102... No Round parameters changed for Iteration #103 Beginning Refinement Iteration #103, Round #5 No parameters were switched for Iteration #103 Creating quality assessment statistics... CCMS(shift) = 0.00949 for Iteration #103 of Tilt-Series #7. CCMS(rotations) = 0.2049 for Iteration #103 of Tilt-Series #7. CCMS(scale) = 0.00383 for Iteration #103 of Tilt-Series #7. The scaled sum of CCMS values is #0.00717 for Tilt-Series #7. Creating Depiction Videos for Iteration #103 in Parallel... Creating Refinement tilt-series video for iteration #103... Generating Refinement reconstruction for iteration #103... No Round parameters changed for Iteration #104 Beginning Refinement Iteration #104, Round #5 No parameters were switched for Iteration #104 Creating quality assessment statistics... CCMS(shift) = 0.0122 for Iteration #104 of Tilt-Series #7. CCMS(rotations) = 0.31705 for Iteration #104 of Tilt-Series #7. CCMS(scale) = 0.00457 for Iteration #104 of Tilt-Series #7. The scaled sum of CCMS values is #0.00982 for Tilt-Series #7. Creating Depiction Videos for Iteration #104 in Parallel... Creating Refinement tilt-series video for iteration #104... Generating Refinement reconstruction for iteration #104... No Round parameters changed for Iteration #105 Beginning Refinement Iteration #105, Round #5 No parameters were switched for Iteration #105 Creating quality assessment statistics... CCMS(shift) = 0.01471 for Iteration #105 of Tilt-Series #7. CCMS(rotations) = 0.3615 for Iteration #105 of Tilt-Series #7. CCMS(scale) = 0.00574 for Iteration #105 of Tilt-Series #7. The scaled sum of CCMS values is #0.01164 for Tilt-Series #7. Creating Depiction Videos for Iteration #105 in Parallel... Creating Refinement tilt-series video for iteration #105... Generating Refinement reconstruction for iteration #105... No Round parameters changed for Iteration #106 Beginning Refinement Iteration #106, Round #5 No parameters were switched for Iteration #106 Creating quality assessment statistics... CCMS(shift) = 0.01403 for Iteration #106 of Tilt-Series #7. CCMS(rotations) = 0.46283 for Iteration #106 of Tilt-Series #7. CCMS(scale) = 0.00609 for Iteration #106 of Tilt-Series #7. The scaled sum of CCMS values is #0.01288 for Tilt-Series #7. Creating Depiction Videos for Iteration #106 in Parallel... Creating Refinement tilt-series video for iteration #106... Generating Refinement reconstruction for iteration #106... No Round parameters changed for Iteration #107 Beginning Refinement Iteration #107, Round #5 No parameters were switched for Iteration #107 Creating quality assessment statistics... CCMS(shift) = 0.0121 for Iteration #107 of Tilt-Series #7. CCMS(rotations) = 0.59088 for Iteration #107 of Tilt-Series #7. CCMS(scale) = 0.00937 for Iteration #107 of Tilt-Series #7. The scaled sum of CCMS values is #0.01503 for Tilt-Series #7. Creating Depiction Videos for Iteration #107 in Parallel... Creating Refinement tilt-series video for iteration #107... Generating Refinement reconstruction for iteration #107... No Round parameters changed for Iteration #108 Beginning Refinement Iteration #108, Round #5 No parameters were switched for Iteration #108 Creating quality assessment statistics... CCMS(shift) = 0.01334 for Iteration #108 of Tilt-Series #7. CCMS(rotations) = 0.65158 for Iteration #108 of Tilt-Series #7. CCMS(scale) = 0.01231 for Iteration #108 of Tilt-Series #7. The scaled sum of CCMS values is #0.01724 for Tilt-Series #7. Creating Depiction Videos for Iteration #108 in Parallel... Creating Refinement tilt-series video for iteration #108... Generating Refinement reconstruction for iteration #108... No Round parameters changed for Iteration #109 Beginning Refinement Iteration #109, Round #5 No parameters were switched for Iteration #109 Creating quality assessment statistics... CCMS(shift) = 0.01392 for Iteration #109 of Tilt-Series #7. CCMS(rotations) = 0.85237 for Iteration #109 of Tilt-Series #7. CCMS(scale) = 0.01332 for Iteration #109 of Tilt-Series #7. The scaled sum of CCMS values is #0.02044 for Tilt-Series #7. Creating Depiction Videos for Iteration #109 in Parallel... Creating Refinement tilt-series video for iteration #109... Generating Refinement reconstruction for iteration #109... No Round parameters changed for Iteration #110 Beginning Refinement Iteration #110, Round #5 No parameters were switched for Iteration #110 Creating quality assessment statistics... CCMS(shift) = 0.01157 for Iteration #110 of Tilt-Series #7. CCMS(rotations) = 0.74893 for Iteration #110 of Tilt-Series #7. CCMS(scale) = 0.01533 for Iteration #110 of Tilt-Series #7. The scaled sum of CCMS values is #0.01895 for Tilt-Series #7. Creating Depiction Videos for Iteration #110 in Parallel... Creating Refinement tilt-series video for iteration #110... Generating Refinement reconstruction for iteration #110... No Round parameters changed for Iteration #111 Beginning Refinement Iteration #111, Round #5 No parameters were switched for Iteration #111 Creating quality assessment statistics... CCMS(shift) = 0.01468 for Iteration #111 of Tilt-Series #7. CCMS(rotations) = 0.79982 for Iteration #111 of Tilt-Series #7. CCMS(scale) = 0.01697 for Iteration #111 of Tilt-Series #7. The scaled sum of CCMS values is #0.02121 for Tilt-Series #7. Creating Depiction Videos for Iteration #111 in Parallel... Creating Refinement tilt-series video for iteration #111... Generating Refinement reconstruction for iteration #111... No Round parameters changed for Iteration #112 Beginning Refinement Iteration #112, Round #5 No parameters were switched for Iteration #112 Creating quality assessment statistics... CCMS(shift) = 0.01466 for Iteration #112 of Tilt-Series #7. CCMS(rotations) = 0.76362 for Iteration #112 of Tilt-Series #7. CCMS(scale) = 0.01957 for Iteration #112 of Tilt-Series #7. The scaled sum of CCMS values is #0.02159 for Tilt-Series #7. Creating Depiction Videos for Iteration #112 in Parallel... Creating Refinement tilt-series video for iteration #112... Generating Refinement reconstruction for iteration #112... No Round parameters changed for Iteration #113 Beginning Refinement Iteration #113, Round #5 No parameters were switched for Iteration #113 Creating quality assessment statistics... CCMS(shift) = 0.01283 for Iteration #113 of Tilt-Series #7. CCMS(rotations) = 0.93316 for Iteration #113 of Tilt-Series #7. CCMS(scale) = 0.02083 for Iteration #113 of Tilt-Series #7. The scaled sum of CCMS values is #0.02367 for Tilt-Series #7. Creating Depiction Videos for Iteration #113 in Parallel... Creating Refinement tilt-series video for iteration #113... Generating Refinement reconstruction for iteration #113... 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: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01426 for Iteration #114 of Tilt-Series #7. CCMS(rotations) = 1.59015 for Iteration #114 of Tilt-Series #7. CCMS(scale) = 0.0368 for Iteration #114 of Tilt-Series #7. The scaled sum of CCMS values is #0.03822 for Tilt-Series #7. 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 2592 Window Size (y) was windowed down to 2646 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: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01413 for Iteration #115 of Tilt-Series #7. CCMS(rotations) = 1.76878 for Iteration #115 of Tilt-Series #7. CCMS(scale) = 0.04158 for Iteration #115 of Tilt-Series #7. The scaled sum of CCMS values is #0.04215 for Tilt-Series #7. 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 14 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2250 Window Size (y) was windowed down to 2268 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: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (2240, 2250) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (2160, 2240) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (2100, 2160) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (2058, 2100) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (2048, 2058) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (2016, 2048) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (2000, 2016) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1960, 2000) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1944, 1960) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1920, 1944) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1890, 1920) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1800, 1890) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1792, 1800) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1764, 1792) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1750, 1764) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1728, 1750) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1680, 1728) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01933 for Iteration #116 of Tilt-Series #7. CCMS(rotations) = 1.63619 for Iteration #116 of Tilt-Series #7. CCMS(scale) = 0.04629 for Iteration #116 of Tilt-Series #7. The scaled sum of CCMS values is #0.04369 for Tilt-Series #7. Creating Depiction Videos for Iteration #116 in Parallel... Creating Refinement tilt-series video for iteration #116... Generating Refinement reconstruction for iteration #116... Refinement Iteration #116 finished after retrying 31 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1680 Window Size (y) was windowed down to 1728 No Round parameters changed for Iteration #117 Beginning Refinement Iteration #117, Round #5 No parameters were switched for Iteration #117 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (2240, 2250) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (2160, 2240) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (2100, 2160) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (2058, 2100) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (2048, 2058) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (2016, 2048) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (2000, 2016) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1960, 2000) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1944, 1960) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1920, 1944) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1890, 1920) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1800, 1890) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1792, 1800) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1764, 1792) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1750, 1764) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1728, 1750) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1680, 1728) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0173 for Iteration #117 of Tilt-Series #7. CCMS(rotations) = 1.375 for Iteration #117 of Tilt-Series #7. CCMS(scale) = 0.04565 for Iteration #117 of Tilt-Series #7. The scaled sum of CCMS values is #0.03932 for Tilt-Series #7. Creating Depiction Videos for Iteration #117 in Parallel... Creating Refinement tilt-series video for iteration #117... Generating Refinement reconstruction for iteration #117... Refinement Iteration #117 finished after retrying 31 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1680 Window Size (y) was windowed down to 1728 No Round parameters changed for Iteration #118 Beginning Refinement Iteration #118, Round #5 No parameters were switched for Iteration #118 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (2240, 2250) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (2160, 2240) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (2100, 2160) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (2058, 2100) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (2048, 2058) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (2016, 2048) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (2000, 2016) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1960, 2000) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1944, 1960) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1920, 1944) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1890, 1920) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01665 for Iteration #118 of Tilt-Series #7. CCMS(rotations) = 1.33619 for Iteration #118 of Tilt-Series #7. CCMS(scale) = 0.04683 for Iteration #118 of Tilt-Series #7. The scaled sum of CCMS values is #0.03898 for Tilt-Series #7. Creating Depiction Videos for Iteration #118 in Parallel... Creating Refinement tilt-series video for iteration #118... Generating Refinement reconstruction for iteration #118... Refinement Iteration #118 finished after retrying 25 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1890 Window Size (y) was windowed down to 1920 No Round parameters changed for Iteration #119 Beginning Refinement Iteration #119, Round #5 No parameters were switched for Iteration #119 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (2240, 2250) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (2160, 2240) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (2100, 2160) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (2058, 2100) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (2048, 2058) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (2016, 2048) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (2000, 2016) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1960, 2000) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1944, 1960) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1920, 1944) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1890, 1920) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1800, 1890) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1792, 1800) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1764, 1792) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1750, 1764) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1728, 1750) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1680, 1728) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1620, 1680) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1600, 1620) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1568, 1600) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1536, 1568) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0143 for Iteration #119 of Tilt-Series #7. CCMS(rotations) = 1.37728 for Iteration #119 of Tilt-Series #7. CCMS(scale) = 0.04372 for Iteration #119 of Tilt-Series #7. The scaled sum of CCMS values is #0.0377 for Tilt-Series #7. Creating Depiction Videos for Iteration #119 in Parallel... Creating Refinement tilt-series video for iteration #119... Generating Refinement reconstruction for iteration #119... Refinement Iteration #119 finished after retrying 35 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1536 Window Size (y) was windowed down to 1568 No Round parameters changed for Iteration #120 Beginning Refinement Iteration #120, Round #5 No parameters were switched for Iteration #120 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2688, 2700) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2646, 2688) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2592, 2646) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2560, 2592) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (2520, 2560) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (2500, 2520) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (2450, 2500) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (2430, 2450) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (2400, 2430) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (2352, 2400) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (2304, 2352) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (2268, 2304) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (2250, 2268) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (2240, 2250) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (2160, 2240) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (2100, 2160) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (2058, 2100) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (2048, 2058) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (2016, 2048) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (2000, 2016) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1960, 2000) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1944, 1960) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1920, 1944) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1890, 1920) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1800, 1890) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1792, 1800) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1764, 1792) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1750, 1764) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1728, 1750) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1680, 1728) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1620, 1680) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1600, 1620) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1568, 1600) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1536, 1568) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1512, 1536) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1500, 1512) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1470, 1500) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1458, 1470) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1440, 1458) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1400, 1440) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1372, 1400) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (1350, 1372) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (1344, 1350) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (1296, 1344) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (1280, 1296) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (1260, 1280) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (1250, 1260) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (1200, 1250) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (1176, 1200) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (1152, 1176) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01513 for Iteration #120 of Tilt-Series #7. CCMS(rotations) = 1.58798 for Iteration #120 of Tilt-Series #7. CCMS(scale) = 0.04561 for Iteration #120 of Tilt-Series #7. The scaled sum of CCMS values is #0.04142 for Tilt-Series #7. Creating Depiction Videos for Iteration #120 in Parallel... Creating Refinement tilt-series video for iteration #120... Generating Refinement reconstruction for iteration #120... Refinement Iteration #120 finished after retrying 51 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1152 Window Size (y) was windowed down to 1176 Finished Refinement for Tilt-Series #7! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org and include this log file .If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! End time: 2016yr10m03d-16hr28m11s