[ 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 Start time: 2016yr09m28d-20hr10m31s Description: Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 lowpass = 125.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.090122428115 0.090122428115 } map.sampling = 8 window.highpass.diameter = { 0.00718866462793 0.00718866462793 } window.highpass.apodization = { 0.0143773292559 0.0143773292559 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 40.1035010815 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 40.1035010815 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.01757 for Iteration #1 of Tilt-Series #4. CCMS(rotations) = 0.53161 for Iteration #1 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4. The scaled sum of CCMS values is #0.01942 for Tilt-Series #4. 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) = 0.01088 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 0.20854 for Iteration #2 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4. The scaled sum of CCMS values is #0.00961 for Tilt-Series #4. 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) = 0.00783 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 0.21461 for Iteration #3 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4. The scaled sum of CCMS values is #0.00821 for Tilt-Series #4. 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) = 0.00862 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 0.18655 for Iteration #4 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4. The scaled sum of CCMS values is #0.00804 for Tilt-Series #4. 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) = 0.01198 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 0.23723 for Iteration #5 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4. The scaled sum of CCMS values is #0.01073 for Tilt-Series #4. 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) = 0.00661 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 0.3306 for Iteration #6 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4. The scaled sum of CCMS values is #0.00992 for Tilt-Series #4. 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) = 0.00611 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 0.33549 for Iteration #7 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4. The scaled sum of CCMS values is #0.00976 for Tilt-Series #4. 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) = 0.00957 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 0.26714 for Iteration #8 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4. The scaled sum of CCMS values is #0.01013 for Tilt-Series #4. 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) = 0.0066 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 0.23226 for Iteration #9 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4. The scaled sum of CCMS values is #0.00794 for Tilt-Series #4. 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) = 0.00671 for Iteration #10 of Tilt-Series #4. CCMS(rotations) = 0.21317 for Iteration #10 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4. The scaled sum of CCMS values is #0.00762 for Tilt-Series #4. 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) = 0.00773 for Iteration #11 of Tilt-Series #4. CCMS(rotations) = 0.24909 for Iteration #11 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4. The scaled sum of CCMS values is #0.00885 for Tilt-Series #4. 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) = 0.00957 for Iteration #12 of Tilt-Series #4. CCMS(rotations) = 0.17986 for Iteration #12 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4. The scaled sum of CCMS values is #0.00838 for Tilt-Series #4. 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) = 0.00876 for Iteration #13 of Tilt-Series #4. CCMS(rotations) = 0.24928 for Iteration #13 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4. The scaled sum of CCMS values is #0.00937 for Tilt-Series #4. 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) = 0.00669 for Iteration #14 of Tilt-Series #4. CCMS(rotations) = 0.18054 for Iteration #14 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4. The scaled sum of CCMS values is #0.00696 for Tilt-Series #4. 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) = 0.01129 for Iteration #15 of Tilt-Series #4. CCMS(rotations) = 0.24833 for Iteration #15 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4. The scaled sum of CCMS values is #0.01061 for Tilt-Series #4. 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) = 0.01127 for Iteration #16 of Tilt-Series #4. CCMS(rotations) = 0.23277 for Iteration #16 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4. The scaled sum of CCMS values is #0.01029 for Tilt-Series #4. 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) = 0.00622 for Iteration #17 of Tilt-Series #4. CCMS(rotations) = 0.15549 for Iteration #17 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4. The scaled sum of CCMS values is #0.00622 for Tilt-Series #4. 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) = 0.00843 for Iteration #18 of Tilt-Series #4. CCMS(rotations) = 0.14573 for Iteration #18 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4. The scaled sum of CCMS values is #0.00713 for Tilt-Series #4. 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) = 0.00773 for Iteration #19 of Tilt-Series #4. CCMS(rotations) = 0.19831 for Iteration #19 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4. The scaled sum of CCMS values is #0.00783 for Tilt-Series #4. 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) = 0.00613 for Iteration #20 of Tilt-Series #4. CCMS(rotations) = 0.15655 for Iteration #20 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4. The scaled sum of CCMS values is #0.00619 for Tilt-Series #4. 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 = { 0.00359433231397 0.00359433231397 } window.highpass.apodization = { 0.00718866462793 0.00718866462793 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 80.2070021631 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 80.2070021631 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.01146 for Iteration #21 of Tilt-Series #4. CCMS(rotations) = 0.24752 for Iteration #21 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4. The scaled sum of CCMS values is #0.01068 for Tilt-Series #4. 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) = 0.00572 for Iteration #22 of Tilt-Series #4. CCMS(rotations) = 0.14831 for Iteration #22 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4. The scaled sum of CCMS values is #0.00583 for Tilt-Series #4. 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) = 0.00528 for Iteration #23 of Tilt-Series #4. CCMS(rotations) = 0.16243 for Iteration #23 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4. The scaled sum of CCMS values is #0.00589 for Tilt-Series #4. 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) = 0.00551 for Iteration #24 of Tilt-Series #4. CCMS(rotations) = 0.20416 for Iteration #24 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4. The scaled sum of CCMS values is #0.00684 for Tilt-Series #4. 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) = 0.00507 for Iteration #25 of Tilt-Series #4. CCMS(rotations) = 0.16187 for Iteration #25 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4. The scaled sum of CCMS values is #0.00577 for Tilt-Series #4. 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) = 0.00498 for Iteration #26 of Tilt-Series #4. CCMS(rotations) = 0.16241 for Iteration #26 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4. The scaled sum of CCMS values is #0.00574 for Tilt-Series #4. 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) = 0.00518 for Iteration #27 of Tilt-Series #4. CCMS(rotations) = 0.15843 for Iteration #27 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4. The scaled sum of CCMS values is #0.00576 for Tilt-Series #4. 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) = 0.0053 for Iteration #28 of Tilt-Series #4. CCMS(rotations) = 0.2055 for Iteration #28 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4. The scaled sum of CCMS values is #0.00676 for Tilt-Series #4. 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) = 0.00484 for Iteration #29 of Tilt-Series #4. CCMS(rotations) = 0.23855 for Iteration #29 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4. The scaled sum of CCMS values is #0.00719 for Tilt-Series #4. 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) = 0.00413 for Iteration #30 of Tilt-Series #4. CCMS(rotations) = 0.22935 for Iteration #30 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4. The scaled sum of CCMS values is #0.00665 for Tilt-Series #4. 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) = 0.00527 for Iteration #31 of Tilt-Series #4. CCMS(rotations) = 0.21116 for Iteration #31 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4. The scaled sum of CCMS values is #0.00686 for Tilt-Series #4. 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) = 0.00466 for Iteration #32 of Tilt-Series #4. CCMS(rotations) = 0.2892 for Iteration #32 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #32 of Tilt-Series #4. The scaled sum of CCMS values is #0.00811 for Tilt-Series #4. 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) = 0.00478 for Iteration #33 of Tilt-Series #4. CCMS(rotations) = 0.30021 for Iteration #33 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #33 of Tilt-Series #4. The scaled sum of CCMS values is #0.00839 for Tilt-Series #4. 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) = 0.00503 for Iteration #34 of Tilt-Series #4. CCMS(rotations) = 0.26665 for Iteration #34 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #34 of Tilt-Series #4. The scaled sum of CCMS values is #0.00785 for Tilt-Series #4. 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) = 0.00518 for Iteration #35 of Tilt-Series #4. CCMS(rotations) = 0.23173 for Iteration #35 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #35 of Tilt-Series #4. The scaled sum of CCMS values is #0.00722 for Tilt-Series #4. 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) = 0.00419 for Iteration #36 of Tilt-Series #4. CCMS(rotations) = 0.2168 for Iteration #36 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #36 of Tilt-Series #4. The scaled sum of CCMS values is #0.00643 for Tilt-Series #4. 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) = 0.00561 for Iteration #37 of Tilt-Series #4. CCMS(rotations) = 0.15228 for Iteration #37 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #37 of Tilt-Series #4. The scaled sum of CCMS values is #0.00585 for Tilt-Series #4. 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) = 0.00362 for Iteration #38 of Tilt-Series #4. CCMS(rotations) = 0.26811 for Iteration #38 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #38 of Tilt-Series #4. The scaled sum of CCMS values is #0.00717 for Tilt-Series #4. 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) = 0.00491 for Iteration #39 of Tilt-Series #4. CCMS(rotations) = 0.24734 for Iteration #39 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #39 of Tilt-Series #4. The scaled sum of CCMS values is #0.0074 for Tilt-Series #4. 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) = 0.00407 for Iteration #40 of Tilt-Series #4. CCMS(rotations) = 0.22336 for Iteration #40 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #40 of Tilt-Series #4. The scaled sum of CCMS values is #0.0065 for Tilt-Series #4. 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 = { 0.00179716615698 0.00179716615698 } window.highpass.apodization = { 0.00359433231397 0.00359433231397 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 160.414004326 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 160.414004326 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #41 Creating quality assessment statistics... CCMS(shift) = 0.00827 for Iteration #41 of Tilt-Series #4. CCMS(rotations) = 0.20871 for Iteration #41 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #41 of Tilt-Series #4. The scaled sum of CCMS values is #0.00831 for Tilt-Series #4. 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) = 0.00669 for Iteration #42 of Tilt-Series #4. CCMS(rotations) = 0.29516 for Iteration #42 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #42 of Tilt-Series #4. The scaled sum of CCMS values is #0.00925 for Tilt-Series #4. 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) = 0.00904 for Iteration #43 of Tilt-Series #4. CCMS(rotations) = 0.27847 for Iteration #43 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #43 of Tilt-Series #4. The scaled sum of CCMS values is #0.01009 for Tilt-Series #4. 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) = 0.00927 for Iteration #44 of Tilt-Series #4. CCMS(rotations) = 0.19832 for Iteration #44 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #44 of Tilt-Series #4. The scaled sum of CCMS values is #0.0086 for Tilt-Series #4. 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) = 0.00801 for Iteration #45 of Tilt-Series #4. CCMS(rotations) = 0.24498 for Iteration #45 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #45 of Tilt-Series #4. The scaled sum of CCMS values is #0.00891 for Tilt-Series #4. 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) = 0.00782 for Iteration #46 of Tilt-Series #4. CCMS(rotations) = 0.23635 for Iteration #46 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #46 of Tilt-Series #4. The scaled sum of CCMS values is #0.00864 for Tilt-Series #4. 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) = 0.00807 for Iteration #47 of Tilt-Series #4. CCMS(rotations) = 0.27058 for Iteration #47 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #47 of Tilt-Series #4. The scaled sum of CCMS values is #0.00945 for Tilt-Series #4. 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) = 0.00721 for Iteration #48 of Tilt-Series #4. CCMS(rotations) = 0.30017 for Iteration #48 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #48 of Tilt-Series #4. The scaled sum of CCMS values is #0.00961 for Tilt-Series #4. 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) = 0.00457 for Iteration #49 of Tilt-Series #4. CCMS(rotations) = 0.23234 for Iteration #49 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #49 of Tilt-Series #4. The scaled sum of CCMS values is #0.00693 for Tilt-Series #4. 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) = 0.00711 for Iteration #50 of Tilt-Series #4. CCMS(rotations) = 0.27887 for Iteration #50 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #50 of Tilt-Series #4. The scaled sum of CCMS values is #0.00913 for Tilt-Series #4. 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) = 0.00605 for Iteration #51 of Tilt-Series #4. CCMS(rotations) = 0.25316 for Iteration #51 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #51 of Tilt-Series #4. The scaled sum of CCMS values is #0.00809 for Tilt-Series #4. 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) = 0.00721 for Iteration #52 of Tilt-Series #4. CCMS(rotations) = 0.17957 for Iteration #52 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #52 of Tilt-Series #4. The scaled sum of CCMS values is #0.0072 for Tilt-Series #4. 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) = 0.01142 for Iteration #53 of Tilt-Series #4. CCMS(rotations) = 0.25484 for Iteration #53 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #53 of Tilt-Series #4. The scaled sum of CCMS values is #0.01081 for Tilt-Series #4. 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) = 0.00641 for Iteration #54 of Tilt-Series #4. CCMS(rotations) = 0.2526 for Iteration #54 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #54 of Tilt-Series #4. The scaled sum of CCMS values is #0.00826 for Tilt-Series #4. 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) = 0.00645 for Iteration #55 of Tilt-Series #4. CCMS(rotations) = 0.20903 for Iteration #55 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #55 of Tilt-Series #4. The scaled sum of CCMS values is #0.0074 for Tilt-Series #4. 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) = 0.00517 for Iteration #56 of Tilt-Series #4. CCMS(rotations) = 0.23996 for Iteration #56 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #56 of Tilt-Series #4. The scaled sum of CCMS values is #0.00739 for Tilt-Series #4. 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) = 0.00873 for Iteration #57 of Tilt-Series #4. CCMS(rotations) = 0.25557 for Iteration #57 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #57 of Tilt-Series #4. The scaled sum of CCMS values is #0.00948 for Tilt-Series #4. 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) = 0.00719 for Iteration #58 of Tilt-Series #4. CCMS(rotations) = 0.23516 for Iteration #58 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #58 of Tilt-Series #4. The scaled sum of CCMS values is #0.0083 for Tilt-Series #4. 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) = 0.0054 for Iteration #59 of Tilt-Series #4. CCMS(rotations) = 0.20015 for Iteration #59 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #59 of Tilt-Series #4. The scaled sum of CCMS values is #0.0067 for Tilt-Series #4. 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) = 0.00826 for Iteration #60 of Tilt-Series #4. CCMS(rotations) = 0.19855 for Iteration #60 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #60 of Tilt-Series #4. The scaled sum of CCMS values is #0.0081 for Tilt-Series #4. 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 = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 320.828008652 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 320.828008652 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #61 Creating quality assessment statistics... CCMS(shift) = 0.00967 for Iteration #61 of Tilt-Series #4. CCMS(rotations) = 0.26597 for Iteration #61 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #61 of Tilt-Series #4. The scaled sum of CCMS values is #0.01015 for Tilt-Series #4. 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) = 0.00825 for Iteration #62 of Tilt-Series #4. CCMS(rotations) = 0.31933 for Iteration #62 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #62 of Tilt-Series #4. The scaled sum of CCMS values is #0.01051 for Tilt-Series #4. 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) = 0.0093 for Iteration #63 of Tilt-Series #4. CCMS(rotations) = 0.39881 for Iteration #63 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #63 of Tilt-Series #4. The scaled sum of CCMS values is #0.01263 for Tilt-Series #4. 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) = 0.01022 for Iteration #64 of Tilt-Series #4. CCMS(rotations) = 0.40577 for Iteration #64 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #64 of Tilt-Series #4. The scaled sum of CCMS values is #0.01322 for Tilt-Series #4. 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) = 0.00919 for Iteration #65 of Tilt-Series #4. CCMS(rotations) = 0.29592 for Iteration #65 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #65 of Tilt-Series #4. The scaled sum of CCMS values is #0.01051 for Tilt-Series #4. 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) = 0.00916 for Iteration #66 of Tilt-Series #4. CCMS(rotations) = 0.28105 for Iteration #66 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #66 of Tilt-Series #4. The scaled sum of CCMS values is #0.0102 for Tilt-Series #4. 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) = 0.00753 for Iteration #67 of Tilt-Series #4. CCMS(rotations) = 0.34484 for Iteration #67 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #67 of Tilt-Series #4. The scaled sum of CCMS values is #0.01066 for Tilt-Series #4. 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) = 0.0095 for Iteration #68 of Tilt-Series #4. CCMS(rotations) = 0.25365 for Iteration #68 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #68 of Tilt-Series #4. The scaled sum of CCMS values is #0.00982 for Tilt-Series #4. 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) = 0.00877 for Iteration #69 of Tilt-Series #4. CCMS(rotations) = 0.32577 for Iteration #69 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #69 of Tilt-Series #4. The scaled sum of CCMS values is #0.0109 for Tilt-Series #4. 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) = 0.00807 for Iteration #70 of Tilt-Series #4. CCMS(rotations) = 0.23979 for Iteration #70 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #70 of Tilt-Series #4. The scaled sum of CCMS values is #0.00883 for Tilt-Series #4. 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) = 0.00901 for Iteration #71 of Tilt-Series #4. CCMS(rotations) = 0.30126 for Iteration #71 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #71 of Tilt-Series #4. The scaled sum of CCMS values is #0.01053 for Tilt-Series #4. 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) = 0.00778 for Iteration #72 of Tilt-Series #4. CCMS(rotations) = 0.26184 for Iteration #72 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #72 of Tilt-Series #4. The scaled sum of CCMS values is #0.00913 for Tilt-Series #4. 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) = 0.00843 for Iteration #73 of Tilt-Series #4. CCMS(rotations) = 0.30526 for Iteration #73 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #73 of Tilt-Series #4. The scaled sum of CCMS values is #0.01032 for Tilt-Series #4. 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) = 0.00841 for Iteration #74 of Tilt-Series #4. CCMS(rotations) = 0.34458 for Iteration #74 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #74 of Tilt-Series #4. The scaled sum of CCMS values is #0.0111 for Tilt-Series #4. 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) = 0.00767 for Iteration #75 of Tilt-Series #4. CCMS(rotations) = 0.32909 for Iteration #75 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #75 of Tilt-Series #4. The scaled sum of CCMS values is #0.01042 for Tilt-Series #4. 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) = 0.0094 for Iteration #76 of Tilt-Series #4. CCMS(rotations) = 0.28913 for Iteration #76 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #76 of Tilt-Series #4. The scaled sum of CCMS values is #0.01048 for Tilt-Series #4. 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) = 0.00899 for Iteration #77 of Tilt-Series #4. CCMS(rotations) = 0.25834 for Iteration #77 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #77 of Tilt-Series #4. The scaled sum of CCMS values is #0.00966 for Tilt-Series #4. 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) = 0.00735 for Iteration #78 of Tilt-Series #4. CCMS(rotations) = 0.27312 for Iteration #78 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #78 of Tilt-Series #4. The scaled sum of CCMS values is #0.00914 for Tilt-Series #4. 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) = 0.00853 for Iteration #79 of Tilt-Series #4. CCMS(rotations) = 0.29422 for Iteration #79 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #79 of Tilt-Series #4. The scaled sum of CCMS values is #0.01015 for Tilt-Series #4. 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) = 0.00872 for Iteration #80 of Tilt-Series #4. CCMS(rotations) = 0.34429 for Iteration #80 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #80 of Tilt-Series #4. The scaled sum of CCMS values is #0.01125 for Tilt-Series #4. 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) = 0.00741 for Iteration #81 of Tilt-Series #4. CCMS(rotations) = 0.39405 for Iteration #81 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #81 of Tilt-Series #4. The scaled sum of CCMS values is #0.01158 for Tilt-Series #4. 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) = 0.0099 for Iteration #82 of Tilt-Series #4. CCMS(rotations) = 0.31315 for Iteration #82 of Tilt-Series #4. CCMS(scale) = 0.00333 for Iteration #82 of Tilt-Series #4. The scaled sum of CCMS values is #0.00858 for Tilt-Series #4. 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) = 0.00874 for Iteration #83 of Tilt-Series #4. CCMS(rotations) = 0.33645 for Iteration #83 of Tilt-Series #4. CCMS(scale) = 0.00495 for Iteration #83 of Tilt-Series #4. The scaled sum of CCMS values is #0.00905 for Tilt-Series #4. 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) = 0.00782 for Iteration #84 of Tilt-Series #4. CCMS(rotations) = 0.33458 for Iteration #84 of Tilt-Series #4. CCMS(scale) = 0.00516 for Iteration #84 of Tilt-Series #4. The scaled sum of CCMS values is #0.00879 for Tilt-Series #4. 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) = 0.00831 for Iteration #85 of Tilt-Series #4. CCMS(rotations) = 0.32179 for Iteration #85 of Tilt-Series #4. CCMS(scale) = 0.00446 for Iteration #85 of Tilt-Series #4. The scaled sum of CCMS values is #0.00855 for Tilt-Series #4. 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) = 0.00806 for Iteration #86 of Tilt-Series #4. CCMS(rotations) = 0.35652 for Iteration #86 of Tilt-Series #4. CCMS(scale) = 0.00452 for Iteration #86 of Tilt-Series #4. The scaled sum of CCMS values is #0.00895 for Tilt-Series #4. 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) = 0.00845 for Iteration #87 of Tilt-Series #4. CCMS(rotations) = 0.36471 for Iteration #87 of Tilt-Series #4. CCMS(scale) = 0.00478 for Iteration #87 of Tilt-Series #4. The scaled sum of CCMS values is #0.00927 for Tilt-Series #4. 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) = 0.00795 for Iteration #88 of Tilt-Series #4. CCMS(rotations) = 0.34471 for Iteration #88 of Tilt-Series #4. CCMS(scale) = 0.00343 for Iteration #88 of Tilt-Series #4. The scaled sum of CCMS values is #0.00839 for Tilt-Series #4. 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) = 0.00811 for Iteration #89 of Tilt-Series #4. CCMS(rotations) = 0.25232 for Iteration #89 of Tilt-Series #4. CCMS(scale) = 0.00459 for Iteration #89 of Tilt-Series #4. The scaled sum of CCMS values is #0.0076 for Tilt-Series #4. 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) = 0.00778 for Iteration #90 of Tilt-Series #4. CCMS(rotations) = 0.29611 for Iteration #90 of Tilt-Series #4. CCMS(scale) = 0.00429 for Iteration #90 of Tilt-Series #4. The scaled sum of CCMS values is #0.00797 for Tilt-Series #4. 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) = 0.00967 for Iteration #91 of Tilt-Series #4. CCMS(rotations) = 0.30814 for Iteration #91 of Tilt-Series #4. CCMS(scale) = 0.00513 for Iteration #91 of Tilt-Series #4. The scaled sum of CCMS values is #0.00904 for Tilt-Series #4. 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) = 0.00844 for Iteration #92 of Tilt-Series #4. CCMS(rotations) = 0.30534 for Iteration #92 of Tilt-Series #4. CCMS(scale) = 0.00486 for Iteration #92 of Tilt-Series #4. The scaled sum of CCMS values is #0.00851 for Tilt-Series #4. 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) = 0.00712 for Iteration #93 of Tilt-Series #4. CCMS(rotations) = 0.27401 for Iteration #93 of Tilt-Series #4. CCMS(scale) = 0.0055 for Iteration #93 of Tilt-Series #4. The scaled sum of CCMS values is #0.00786 for Tilt-Series #4. 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) = 0.008 for Iteration #94 of Tilt-Series #4. CCMS(rotations) = 0.40464 for Iteration #94 of Tilt-Series #4. CCMS(scale) = 0.00512 for Iteration #94 of Tilt-Series #4. The scaled sum of CCMS values is #0.00977 for Tilt-Series #4. 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) = 0.01037 for Iteration #95 of Tilt-Series #4. CCMS(rotations) = 0.33237 for Iteration #95 of Tilt-Series #4. CCMS(scale) = 0.00592 for Iteration #95 of Tilt-Series #4. The scaled sum of CCMS values is #0.00986 for Tilt-Series #4. 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) = 0.01052 for Iteration #96 of Tilt-Series #4. CCMS(rotations) = 0.29727 for Iteration #96 of Tilt-Series #4. CCMS(scale) = 0.00566 for Iteration #96 of Tilt-Series #4. The scaled sum of CCMS values is #0.00936 for Tilt-Series #4. 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) = 0.00899 for Iteration #97 of Tilt-Series #4. CCMS(rotations) = 0.35592 for Iteration #97 of Tilt-Series #4. CCMS(scale) = 0.00567 for Iteration #97 of Tilt-Series #4. The scaled sum of CCMS values is #0.00963 for Tilt-Series #4. 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) = 0.00927 for Iteration #98 of Tilt-Series #4. CCMS(rotations) = 0.31459 for Iteration #98 of Tilt-Series #4. CCMS(scale) = 0.00414 for Iteration #98 of Tilt-Series #4. The scaled sum of CCMS values is #0.00866 for Tilt-Series #4. 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) = 0.00825 for Iteration #99 of Tilt-Series #4. CCMS(rotations) = 0.26569 for Iteration #99 of Tilt-Series #4. CCMS(scale) = 0.00519 for Iteration #99 of Tilt-Series #4. The scaled sum of CCMS values is #0.00802 for Tilt-Series #4. 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) = 0.00889 for Iteration #100 of Tilt-Series #4. CCMS(rotations) = 0.2765 for Iteration #100 of Tilt-Series #4. CCMS(scale) = 0.00418 for Iteration #100 of Tilt-Series #4. The scaled sum of CCMS values is #0.00805 for Tilt-Series #4. 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 = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 320.828008652 map.lowpass.diameter = { 0.45133312 0.45133312 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 320.828008652 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) = 0.00989 for Iteration #101 of Tilt-Series #4. CCMS(rotations) = 0.35333 for Iteration #101 of Tilt-Series #4. CCMS(scale) = 0.00454 for Iteration #101 of Tilt-Series #4. The scaled sum of CCMS values is #0.00952 for Tilt-Series #4. 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) = 0.01362 for Iteration #102 of Tilt-Series #4. CCMS(rotations) = 0.42373 for Iteration #102 of Tilt-Series #4. CCMS(scale) = 0.00645 for Iteration #102 of Tilt-Series #4. The scaled sum of CCMS values is #0.01234 for Tilt-Series #4. 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) = 0.01908 for Iteration #103 of Tilt-Series #4. CCMS(rotations) = 0.42774 for Iteration #103 of Tilt-Series #4. CCMS(scale) = 0.00995 for Iteration #103 of Tilt-Series #4. The scaled sum of CCMS values is #0.01538 for Tilt-Series #4. 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) = 0.02094 for Iteration #104 of Tilt-Series #4. CCMS(rotations) = 0.39768 for Iteration #104 of Tilt-Series #4. CCMS(scale) = 0.01256 for Iteration #104 of Tilt-Series #4. The scaled sum of CCMS values is #0.01647 for Tilt-Series #4. 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) = 0.01969 for Iteration #105 of Tilt-Series #4. CCMS(rotations) = 0.4234 for Iteration #105 of Tilt-Series #4. CCMS(scale) = 0.01272 for Iteration #105 of Tilt-Series #4. The scaled sum of CCMS values is #0.01645 for Tilt-Series #4. 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) = 0.01833 for Iteration #106 of Tilt-Series #4. CCMS(rotations) = 0.51058 for Iteration #106 of Tilt-Series #4. CCMS(scale) = 0.01156 for Iteration #106 of Tilt-Series #4. The scaled sum of CCMS values is #0.01677 for Tilt-Series #4. 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) = 0.01565 for Iteration #107 of Tilt-Series #4. CCMS(rotations) = 0.4043 for Iteration #107 of Tilt-Series #4. CCMS(scale) = 0.01103 for Iteration #107 of Tilt-Series #4. The scaled sum of CCMS values is #0.01428 for Tilt-Series #4. 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) = 0.0141 for Iteration #108 of Tilt-Series #4. CCMS(rotations) = 0.46697 for Iteration #108 of Tilt-Series #4. CCMS(scale) = 0.01071 for Iteration #108 of Tilt-Series #4. The scaled sum of CCMS values is #0.0145 for Tilt-Series #4. 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) = 0.02339 for Iteration #109 of Tilt-Series #4. CCMS(rotations) = 0.4059 for Iteration #109 of Tilt-Series #4. CCMS(scale) = 0.01124 for Iteration #109 of Tilt-Series #4. The scaled sum of CCMS values is #0.01696 for Tilt-Series #4. 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) = 0.01463 for Iteration #110 of Tilt-Series #4. CCMS(rotations) = 0.33737 for Iteration #110 of Tilt-Series #4. CCMS(scale) = 0.01385 for Iteration #110 of Tilt-Series #4. The scaled sum of CCMS values is #0.01399 for Tilt-Series #4. 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) = 0.01692 for Iteration #111 of Tilt-Series #4. CCMS(rotations) = 0.29858 for Iteration #111 of Tilt-Series #4. CCMS(scale) = 0.01373 for Iteration #111 of Tilt-Series #4. The scaled sum of CCMS values is #0.0142 for Tilt-Series #4. 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) = 0.01149 for Iteration #112 of Tilt-Series #4. CCMS(rotations) = 0.31454 for Iteration #112 of Tilt-Series #4. CCMS(scale) = 0.01185 for Iteration #112 of Tilt-Series #4. The scaled sum of CCMS values is #0.01197 for Tilt-Series #4. 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) = 0.01313 for Iteration #113 of Tilt-Series #4. CCMS(rotations) = 0.33321 for Iteration #113 of Tilt-Series #4. CCMS(scale) = 0.01195 for Iteration #113 of Tilt-Series #4. The scaled sum of CCMS values is #0.01281 for Tilt-Series #4. 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 Creating quality assessment statistics... CCMS(shift) = 0.01361 for Iteration #114 of Tilt-Series #4. CCMS(rotations) = 0.30839 for Iteration #114 of Tilt-Series #4. CCMS(scale) = 0.01403 for Iteration #114 of Tilt-Series #4. The scaled sum of CCMS values is #0.01333 for Tilt-Series #4. Creating Depiction Videos for Iteration #114 in Parallel... Creating Refinement tilt-series video for iteration #114... Generating Refinement reconstruction for iteration #114... No Round parameters changed for Iteration #115 Beginning Refinement Iteration #115, Round #5 No parameters were switched for Iteration #115 Creating quality assessment statistics... CCMS(shift) = 0.01985 for Iteration #115 of Tilt-Series #4. CCMS(rotations) = 0.44732 for Iteration #115 of Tilt-Series #4. CCMS(scale) = 0.01608 for Iteration #115 of Tilt-Series #4. The scaled sum of CCMS values is #0.01794 for Tilt-Series #4. Creating Depiction Videos for Iteration #115 in Parallel... Creating Refinement tilt-series video for iteration #115... Generating Refinement reconstruction for iteration #115... No Round parameters changed for Iteration #116 Beginning Refinement Iteration #116, Round #5 No parameters were switched for Iteration #116 Creating quality assessment statistics... CCMS(shift) = 0.0175 for Iteration #116 of Tilt-Series #4. CCMS(rotations) = 0.53265 for Iteration #116 of Tilt-Series #4. CCMS(scale) = 0.01814 for Iteration #116 of Tilt-Series #4. The scaled sum of CCMS values is #0.01898 for Tilt-Series #4. Creating Depiction Videos for Iteration #116 in Parallel... Creating Refinement tilt-series video for iteration #116... Generating Refinement reconstruction for iteration #116... No Round parameters changed for Iteration #117 Beginning Refinement Iteration #117, Round #5 No parameters were switched for Iteration #117 Creating quality assessment statistics... CCMS(shift) = 0.01429 for Iteration #117 of Tilt-Series #4. CCMS(rotations) = 0.57442 for Iteration #117 of Tilt-Series #4. CCMS(scale) = 0.01855 for Iteration #117 of Tilt-Series #4. The scaled sum of CCMS values is #0.01861 for Tilt-Series #4. Creating Depiction Videos for Iteration #117 in Parallel... Creating Refinement tilt-series video for iteration #117... Generating Refinement reconstruction for iteration #117... No Round parameters changed for Iteration #118 Beginning Refinement Iteration #118, Round #5 No parameters were switched for Iteration #118 Creating quality assessment statistics... CCMS(shift) = 0.01434 for Iteration #118 of Tilt-Series #4. CCMS(rotations) = 0.43803 for Iteration #118 of Tilt-Series #4. CCMS(scale) = 0.01973 for Iteration #118 of Tilt-Series #4. The scaled sum of CCMS values is #0.0172 for Tilt-Series #4. Creating Depiction Videos for Iteration #118 in Parallel... Creating Refinement tilt-series video for iteration #118... Generating Refinement reconstruction for iteration #118... No Round parameters changed for Iteration #119 Beginning Refinement Iteration #119, Round #5 No parameters were switched for Iteration #119 Creating quality assessment statistics... CCMS(shift) = 0.01583 for Iteration #119 of Tilt-Series #4. CCMS(rotations) = 0.36551 for Iteration #119 of Tilt-Series #4. CCMS(scale) = 0.02241 for Iteration #119 of Tilt-Series #4. The scaled sum of CCMS values is #0.01762 for Tilt-Series #4. Creating Depiction Videos for Iteration #119 in Parallel... Creating Refinement tilt-series video for iteration #119... Generating Refinement reconstruction for iteration #119... No Round parameters changed for Iteration #120 Beginning Refinement Iteration #120, Round #5 No parameters were switched for Iteration #120 Creating quality assessment statistics... CCMS(shift) = 0.01722 for Iteration #120 of Tilt-Series #4. CCMS(rotations) = 0.69218 for Iteration #120 of Tilt-Series #4. CCMS(scale) = 0.02346 for Iteration #120 of Tilt-Series #4. The scaled sum of CCMS values is #0.02279 for Tilt-Series #4. Creating Depiction Videos for Iteration #120 in Parallel... Creating Refinement tilt-series video for iteration #120... Generating Refinement reconstruction for iteration #120... Finished Refinement for Tilt-Series #4! 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: 2016yr10m02d-00hr19m44s