[ jchase@node15: Wed Sep 28 11:04:44 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true \ --iter_gradient=false --filter=median --kernel_x=5 --kernel_y=5 \ --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=322 --mask_width_y=334 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --defocus_estimate=2 --runname=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --defocus=5 --sessionname=16sep28d --pixelsize=1.76302 \ --dimx=3710 --dimy=3838 --coarse=True --projectid=45 --expid=2667 \ --jobtype=protomo [ jchase@node15: Wed Sep 28 11:11:29 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --tilt_azimuth=-6 --border=100 --clip_low=3.5 --clip_high=3.5 \ --gradient=true --iter_gradient=false --filter=median --kernel_x=5 \ --kernel_y=5 --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=347 --mask_width_y=359 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --amp_contrast_ctf=0.07 --iWidth=20 --DefocusTol=200 --defocus_estimate=2 \ --defocus_min=4 --defocus_max=6 --defocus_difference=0.2 --res_min=10000 \ --res_max=10 --runname=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 11:19:01 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --negative=-44 --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 \ --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 \ --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 \ --r5_mask_apod_y=10 --r1_lowpass_apod_x=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=10 --r2_iters=5 --r3_iters=5 \ --r4_iters=5 --r5_iters=0 --preprocessing=true --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 \ --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 \ --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 \ --do_estimation=false --norotations=false --correlation_size_x=160 \ --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 \ --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 \ --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 \ --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 \ --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 \ --orientation=true --azimuth=true --elevation=false --rotation=true \ --scale=false --logging=true --loglevel=2 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true \ --video_type=html5vid --runname=protomorun1 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/protomorun1 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 11:20:54 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=1500 --lowpass_diameter_x=132 \ --lowpass_diameter_y=132 --lowpass_apod_x=330 --lowpass_apod_y=330 \ --highpass_diameter_x=4905 --highpass_diameter_y=4905 --highpass_apod_x=2453 \ --highpass_apod_y=2453 --corr_mode=mcf --preprocessing=true \ --tilt_azimuth=-6 --border=100 --clip_low=3.5 --clip_high=3.5 \ --gradient=true --iter_gradient=false --filter=median --kernel_x=5 \ --kernel_y=5 --grow=0 --window_area=0.95 --mask_apod_x=10 --mask_apod_y=10 \ --mask_width_x=347 --mask_width_y=359 --correlation_size_x=192 \ --correlation_size_y=192 --peak_search_radius_x=300 --peak_search_radius_y=300 \ --logging=true --loglevel=2 --image_file_type=mrc --gridsearch_limit=2.0 \ --gridsearch_step=0.1 --create_tilt_video=true --create_reconstruction=true \ --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 \ --map_size_y=479 --video_type=html5vid --shift_limit=30 --angle_limit=40 \ --amp_contrast_ctf=0.07 --iWidth=20 --DefocusTol=200 --defocus_estimate=2 \ --defocus_min=6.4 --defocus_max=9.6 --defocus_difference=0.2 \ --res_min=10000 --res_max=10 --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 11:28:03 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=500 --lowpass_diameter_x=132 --lowpass_diameter_y=132 \ --lowpass_apod_x=330 --lowpass_apod_y=330 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-6 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=6.4 --defocus_max=9.6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 11:29:53 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 \ --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 \ --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 \ --r5_mask_apod_y=10 --r1_lowpass_apod_x=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=10 --r2_iters=5 --r3_iters=5 \ --r4_iters=5 --r5_iters=0 --preprocessing=true --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 \ --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 \ --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 \ --do_estimation=false --norotations=false --correlation_size_x=160 \ --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 \ --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 \ --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 \ --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 \ --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 \ --orientation=true --azimuth=true --elevation=false --rotation=true \ --scale=false --logging=true --loglevel=2 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true \ --video_type=html5vid --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 20:02:11 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0003 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0003 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:02:29 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:02:45 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:03:06 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0006 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0006 \ --tiltseries=6 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node16: Wed Sep 28 20:03:32 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0007 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0007 \ --tiltseries=7 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node16: Wed Sep 28 20:04:00 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --dose_presets=False --frame_aligned=True --ctf_correct=False \ --parallel=True --region_x=2782 --region_y=2878 --sampling=8 \ --map_sampling=8 --thickness=400 --lowpass_diameter_x=125 --lowpass_diameter_y=125 \ --lowpass_apod_x=312.5 --lowpass_apod_y=312.5 --highpass_diameter_x=4905 \ --highpass_diameter_y=4905 --highpass_apod_x=2453 --highpass_apod_y=2453 \ --corr_mode=mcf --preprocessing=true --tilt_azimuth=-5 --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --kernel_x=5 --kernel_y=5 --grow=0 --window_area=0.95 \ --mask_apod_x=10 --mask_apod_y=10 --mask_width_x=347 --mask_width_y=359 \ --correlation_size_x=192 --correlation_size_y=192 --peak_search_radius_x=300 \ --peak_search_radius_y=300 --logging=true --loglevel=2 --image_file_type=mrc \ --gridsearch_limit=2.0 --gridsearch_step=0.1 --create_tilt_video=true \ --create_reconstruction=true --show_window_size=true --keep_recons=false \ --slab=true --map_size_x=463 --map_size_y=479 --video_type=html5vid \ --shift_limit=30 --angle_limit=40 --amp_contrast_ctf=0.07 --iWidth=20 \ --DefocusTol=200 --defocus_estimate=2 --defocus_min=4 --defocus_max=6 \ --defocus_difference=0.2 --res_min=10000 --res_max=10 --runname=tiltseries0008 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0008 \ --tiltseries=8 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --coarse=True --projectid=45 --expid=2667 --jobtype=protomo [ jchase@node04: Wed Sep 28 20:08:36 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --negative=-44 --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 \ --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 \ --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 \ --r5_mask_apod_y=10 --r1_lowpass_apod_x=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 \ --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 \ --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 \ --do_estimation=false --norotations=false --correlation_size_x=160 \ --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 \ --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 \ --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 \ --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 \ --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --logging=true --loglevel=2 \ --create_tilt_video=true --create_reconstruction=true --show_window_size=true \ --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 \ --tilt_clip=true --video_type=html5vid --runname=tiltseries0003 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0003 \ --tiltseries=3 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:10:31 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2226 \ --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 \ --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 \ --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 \ --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 \ --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 \ --r5_mask_width_y=2277 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 \ --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 \ --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 \ --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 \ --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 \ --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 \ --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 \ --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 \ --r5_mask_apod_y=10 --r1_lowpass_apod_x=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=1962 \ --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 \ --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 \ --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 \ --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 \ --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 \ --do_estimation=false --norotations=false --correlation_size_x=160 \ --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 \ --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 \ --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 \ --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 \ --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --logging=true --loglevel=2 \ --create_tilt_video=true --create_reconstruction=true --show_window_size=true \ --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 \ --tilt_clip=true --video_type=html5vid --runname=tiltseries0004 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0004 \ --tiltseries=4 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo [ jchase@node15: Wed Sep 28 20:12:00 2016 ] /home/anoble/myami/appion/bin/protomo2aligner.py \ --parallel=True --starting_tlt_file=Coarse --r1_region_x=2782 \ --r2_region_x=2782 --r3_region_x=2782 --r4_region_x=2782 --r5_region_x=2782 \ --r1_region_y=2878 --r2_region_y=2878 --r3_region_y=2878 --r4_region_y=2878 \ --r5_region_y=2878 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 \ --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=400 \ --r1_mask_width_x=322 --r2_mask_width_x=670 --r3_mask_width_x=1366 \ --r4_mask_width_x=2757 --r5_mask_width_x=2757 --r1_mask_width_y=334 \ --r2_mask_width_y=694 --r3_mask_width_y=1414 --r4_mask_width_y=2853 \ --r5_mask_width_y=2853 --r1_lowpass_diameter_x=125 --r2_lowpass_diameter_x=62.5 \ --r3_lowpass_diameter_x=31.25 --r4_lowpass_diameter_x=15.625 \ --r5_lowpass_diameter_x=7.8125 --r1_lowpass_diameter_y=125 \ --r2_lowpass_diameter_y=62.5 --r3_lowpass_diameter_y=31.25 \ --r4_lowpass_diameter_y=15.625 --r5_lowpass_diameter_y=7.8125 \ --r1_highpass_diameter_x=4905 --r2_highpass_diameter_x=4905 \ --r3_highpass_diameter_x=4905 --r4_highpass_diameter_x=4905 \ --r5_highpass_diameter_x=4905 --r1_highpass_diameter_y=4905 \ --r2_highpass_diameter_y=4905 --r3_highpass_diameter_y=4905 \ --r4_highpass_diameter_y=4905 --r5_highpass_diameter_y=4905 \ --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 \ --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 \ --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 \ --r5_mask_apod_y=10 --r1_lowpass_apod_x=313 --r2_lowpass_apod_x=156 \ --r3_lowpass_apod_x=78 --r4_lowpass_apod_x=39 --r5_lowpass_apod_x=20 \ --r1_lowpass_apod_y=313 --r2_lowpass_apod_y=156 --r3_lowpass_apod_y=78 \ --r4_lowpass_apod_y=39 --r5_lowpass_apod_y=20 --r1_highpass_apod_x=2453 \ --r2_highpass_apod_x=2453 --r3_highpass_apod_x=2453 --r4_highpass_apod_x=2453 \ --r5_highpass_apod_x=2453 --r1_highpass_apod_y=2453 --r2_highpass_apod_y=2453 \ --r3_highpass_apod_y=2453 --r4_highpass_apod_y=2453 --r5_highpass_apod_y=2453 \ --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf \ --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 \ --r4_iters=40 --r5_iters=20 --preprocessing=true --border=100 \ --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false \ --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 \ --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 \ --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 \ --do_estimation=false --norotations=false --correlation_size_x=160 \ --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 \ --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 \ --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 \ --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 \ --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 \ --orientation=true --orientation_switch=101 --azimuth=true \ --azimuth_switch=101 --elevation=false --rotation=true --rotation_switch=101 \ --scale=false --scale_switch=81 --logging=true --loglevel=2 \ --create_tilt_video=true --create_reconstruction=true --show_window_size=true \ --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 \ --tilt_clip=true --video_type=html5vid --runname=tiltseries0005 \ --rundir=/gpfs/appion/jchase/16sep28d/protomo_alignments/tiltseries0005 \ --tiltseries=5 --sessionname=16sep28d --pixelsize=1.76302 --dimx=3710 \ --dimy=3838 --image_file_type=mrc --coarse=False --projectid=45 \ --expid=2667 --jobtype=protomo Start time: 2016yr09m28d-20hr12m00s Description: Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 lowpass = 125.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.090122428115 0.090122428115 } map.sampling = 8 window.highpass.diameter = { 0.00575093170234 0.00575093170234 } window.highpass.apodization = { 0.0114995189564 0.0114995189564 } window.mask.apodization = { 10 10 } align.mask.width = { 322 334 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 40.1035010815 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 347 359 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 322 334 } reference.body = 40.1035010815 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0155 for Iteration #1 of Tilt-Series #5. CCMS(rotations) = 0.28688 for Iteration #1 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #5. The scaled sum of CCMS values is #0.01349 for Tilt-Series #5. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... Refinement Iteration #1 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #2 Beginning Refinement Iteration #2, Round #1 No parameters were switched for Iteration #2 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0079 for Iteration #2 of Tilt-Series #5. CCMS(rotations) = 0.20068 for Iteration #2 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #5. The scaled sum of CCMS values is #0.00796 for Tilt-Series #5. Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... Refinement Iteration #2 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #3 Beginning Refinement Iteration #3, Round #1 No parameters were switched for Iteration #3 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00715 for Iteration #3 of Tilt-Series #5. CCMS(rotations) = 0.27122 for Iteration #3 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #5. The scaled sum of CCMS values is #0.009 for Tilt-Series #5. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... Refinement Iteration #3 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #4 Beginning Refinement Iteration #4, Round #1 No parameters were switched for Iteration #4 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00607 for Iteration #4 of Tilt-Series #5. CCMS(rotations) = 0.20061 for Iteration #4 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #5. The scaled sum of CCMS values is #0.00705 for Tilt-Series #5. Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... Refinement Iteration #4 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #5 Beginning Refinement Iteration #5, Round #1 No parameters were switched for Iteration #5 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00334 for Iteration #5 of Tilt-Series #5. CCMS(rotations) = 0.24446 for Iteration #5 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #5. The scaled sum of CCMS values is #0.00656 for Tilt-Series #5. Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... Refinement Iteration #5 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #6 Beginning Refinement Iteration #6, Round #1 No parameters were switched for Iteration #6 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00513 for Iteration #6 of Tilt-Series #5. CCMS(rotations) = 0.25111 for Iteration #6 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #5. The scaled sum of CCMS values is #0.00759 for Tilt-Series #5. Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... Refinement Iteration #6 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #7 Beginning Refinement Iteration #7, Round #1 No parameters were switched for Iteration #7 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.005 for Iteration #7 of Tilt-Series #5. CCMS(rotations) = 0.20032 for Iteration #7 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #5. The scaled sum of CCMS values is #0.0065 for Tilt-Series #5. Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... Refinement Iteration #7 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #8 Beginning Refinement Iteration #8, Round #1 No parameters were switched for Iteration #8 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00451 for Iteration #8 of Tilt-Series #5. CCMS(rotations) = 0.18828 for Iteration #8 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #5. The scaled sum of CCMS values is #0.00602 for Tilt-Series #5. Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... Refinement Iteration #8 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #9 Beginning Refinement Iteration #9, Round #1 No parameters were switched for Iteration #9 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00521 for Iteration #9 of Tilt-Series #5. CCMS(rotations) = 0.22102 for Iteration #9 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #5. The scaled sum of CCMS values is #0.00703 for Tilt-Series #5. Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... Refinement Iteration #9 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #10 Beginning Refinement Iteration #10, Round #1 No parameters were switched for Iteration #10 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00458 for Iteration #10 of Tilt-Series #5. CCMS(rotations) = 0.21371 for Iteration #10 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #5. The scaled sum of CCMS values is #0.00657 for Tilt-Series #5. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... Refinement Iteration #10 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #11 Beginning Refinement Iteration #11, Round #1 No parameters were switched for Iteration #11 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00488 for Iteration #11 of Tilt-Series #5. CCMS(rotations) = 0.17689 for Iteration #11 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #5. The scaled sum of CCMS values is #0.00598 for Tilt-Series #5. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... Refinement Iteration #11 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #12 Beginning Refinement Iteration #12, Round #1 No parameters were switched for Iteration #12 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00413 for Iteration #12 of Tilt-Series #5. CCMS(rotations) = 0.15519 for Iteration #12 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #5. The scaled sum of CCMS values is #0.00517 for Tilt-Series #5. Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... Refinement Iteration #12 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #13 Beginning Refinement Iteration #13, Round #1 No parameters were switched for Iteration #13 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00498 for Iteration #13 of Tilt-Series #5. CCMS(rotations) = 0.17865 for Iteration #13 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #5. The scaled sum of CCMS values is #0.00606 for Tilt-Series #5. Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... Refinement Iteration #13 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #14 Beginning Refinement Iteration #14, Round #1 No parameters were switched for Iteration #14 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0052 for Iteration #14 of Tilt-Series #5. CCMS(rotations) = 0.23342 for Iteration #14 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #5. The scaled sum of CCMS values is #0.00727 for Tilt-Series #5. Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... Refinement Iteration #14 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #15 Beginning Refinement Iteration #15, Round #1 No parameters were switched for Iteration #15 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00566 for Iteration #15 of Tilt-Series #5. CCMS(rotations) = 0.19396 for Iteration #15 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #5. The scaled sum of CCMS values is #0.00671 for Tilt-Series #5. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... Refinement Iteration #15 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #16 Beginning Refinement Iteration #16, Round #1 No parameters were switched for Iteration #16 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00468 for Iteration #16 of Tilt-Series #5. CCMS(rotations) = 0.22754 for Iteration #16 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #5. The scaled sum of CCMS values is #0.00689 for Tilt-Series #5. Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... Refinement Iteration #16 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #17 Beginning Refinement Iteration #17, Round #1 No parameters were switched for Iteration #17 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0043 for Iteration #17 of Tilt-Series #5. CCMS(rotations) = 0.24465 for Iteration #17 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #5. The scaled sum of CCMS values is #0.00705 for Tilt-Series #5. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... Refinement Iteration #17 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #18 Beginning Refinement Iteration #18, Round #1 No parameters were switched for Iteration #18 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.0058 for Iteration #18 of Tilt-Series #5. CCMS(rotations) = 0.23387 for Iteration #18 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #5. The scaled sum of CCMS values is #0.00758 for Tilt-Series #5. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... Refinement Iteration #18 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #19 Beginning Refinement Iteration #19, Round #1 No parameters were switched for Iteration #19 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00335 for Iteration #19 of Tilt-Series #5. CCMS(rotations) = 0.22863 for Iteration #19 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #5. The scaled sum of CCMS values is #0.00625 for Tilt-Series #5. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... Refinement Iteration #19 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 No Round parameters changed for Iteration #20 Beginning Refinement Iteration #20, Round #1 No parameters were switched for Iteration #20 Refinement failed. Retry #1 with Window Size: (2592, 2688) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.00481 for Iteration #20 of Tilt-Series #5. CCMS(rotations) = 0.23175 for Iteration #20 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #5. The scaled sum of CCMS values is #0.00704 for Tilt-Series #5. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Refinement Iteration #20 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2592 Window Size (y) was windowed down to 2688 Beginning Refinement Iteration #21, Round #2 lowpass = 62.5 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 4 window.highpass.diameter = { 0.00287546585117 0.00287546585117 } window.highpass.apodization = { 0.00574975947819 0.00574975947819 } window.mask.apodization = { 10 10 } align.mask.width = { 670 694 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 80.2070021631 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 695 719 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 670 694 } reference.body = 80.2070021631 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00667 for Iteration #21 of Tilt-Series #5. CCMS(rotations) = 0.24447 for Iteration #21 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #5. The scaled sum of CCMS values is #0.00822 for Tilt-Series #5. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... Refinement Iteration #21 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #22 Beginning Refinement Iteration #22, Round #2 No parameters were switched for Iteration #22 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00304 for Iteration #22 of Tilt-Series #5. CCMS(rotations) = 0.19901 for Iteration #22 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #5. The scaled sum of CCMS values is #0.0055 for Tilt-Series #5. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... Refinement Iteration #22 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #23 Beginning Refinement Iteration #23, Round #2 No parameters were switched for Iteration #23 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00362 for Iteration #23 of Tilt-Series #5. CCMS(rotations) = 0.1949 for Iteration #23 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #5. The scaled sum of CCMS values is #0.00571 for Tilt-Series #5. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... Refinement Iteration #23 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #24 Beginning Refinement Iteration #24, Round #2 No parameters were switched for Iteration #24 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00448 for Iteration #24 of Tilt-Series #5. CCMS(rotations) = 0.25684 for Iteration #24 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #5. The scaled sum of CCMS values is #0.00738 for Tilt-Series #5. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... Refinement Iteration #24 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #25 Beginning Refinement Iteration #25, Round #2 No parameters were switched for Iteration #25 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00379 for Iteration #25 of Tilt-Series #5. CCMS(rotations) = 0.19324 for Iteration #25 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #5. The scaled sum of CCMS values is #0.00576 for Tilt-Series #5. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Refinement Iteration #25 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #26 Beginning Refinement Iteration #26, Round #2 No parameters were switched for Iteration #26 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00573 for Iteration #26 of Tilt-Series #5. CCMS(rotations) = 0.22943 for Iteration #26 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #5. The scaled sum of CCMS values is #0.00745 for Tilt-Series #5. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... Refinement Iteration #26 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #27 Beginning Refinement Iteration #27, Round #2 No parameters were switched for Iteration #27 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00422 for Iteration #27 of Tilt-Series #5. CCMS(rotations) = 0.24289 for Iteration #27 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #5. The scaled sum of CCMS values is #0.00697 for Tilt-Series #5. Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... Refinement Iteration #27 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #28 Beginning Refinement Iteration #28, Round #2 No parameters were switched for Iteration #28 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00345 for Iteration #28 of Tilt-Series #5. CCMS(rotations) = 0.21789 for Iteration #28 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #5. The scaled sum of CCMS values is #0.00608 for Tilt-Series #5. Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... Refinement Iteration #28 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #29 Beginning Refinement Iteration #29, Round #2 No parameters were switched for Iteration #29 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00258 for Iteration #29 of Tilt-Series #5. CCMS(rotations) = 0.20911 for Iteration #29 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #5. The scaled sum of CCMS values is #0.00547 for Tilt-Series #5. Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... Refinement Iteration #29 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #30 Beginning Refinement Iteration #30, Round #2 No parameters were switched for Iteration #30 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00355 for Iteration #30 of Tilt-Series #5. CCMS(rotations) = 0.18816 for Iteration #30 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #5. The scaled sum of CCMS values is #0.00554 for Tilt-Series #5. Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... Refinement Iteration #30 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #31 Beginning Refinement Iteration #31, Round #2 No parameters were switched for Iteration #31 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00379 for Iteration #31 of Tilt-Series #5. CCMS(rotations) = 0.23402 for Iteration #31 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #5. The scaled sum of CCMS values is #0.00657 for Tilt-Series #5. Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... Refinement Iteration #31 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #32 Beginning Refinement Iteration #32, Round #2 No parameters were switched for Iteration #32 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00391 for Iteration #32 of Tilt-Series #5. CCMS(rotations) = 0.1906 for Iteration #32 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #32 of Tilt-Series #5. The scaled sum of CCMS values is #0.00577 for Tilt-Series #5. Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... Refinement Iteration #32 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #33 Beginning Refinement Iteration #33, Round #2 No parameters were switched for Iteration #33 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00428 for Iteration #33 of Tilt-Series #5. CCMS(rotations) = 0.18127 for Iteration #33 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #33 of Tilt-Series #5. The scaled sum of CCMS values is #0.00576 for Tilt-Series #5. Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... Refinement Iteration #33 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #34 Beginning Refinement Iteration #34, Round #2 No parameters were switched for Iteration #34 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00466 for Iteration #34 of Tilt-Series #5. CCMS(rotations) = 0.26565 for Iteration #34 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #34 of Tilt-Series #5. The scaled sum of CCMS values is #0.00764 for Tilt-Series #5. Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... Refinement Iteration #34 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #35 Beginning Refinement Iteration #35, Round #2 No parameters were switched for Iteration #35 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00371 for Iteration #35 of Tilt-Series #5. CCMS(rotations) = 0.21988 for Iteration #35 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #35 of Tilt-Series #5. The scaled sum of CCMS values is #0.00625 for Tilt-Series #5. Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... Refinement Iteration #35 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #36 Beginning Refinement Iteration #36, Round #2 No parameters were switched for Iteration #36 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.0036 for Iteration #36 of Tilt-Series #5. CCMS(rotations) = 0.17291 for Iteration #36 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #36 of Tilt-Series #5. The scaled sum of CCMS values is #0.00526 for Tilt-Series #5. Creating Depiction Videos for Iteration #36 in Parallel... Creating Refinement tilt-series video for iteration #36... Generating Refinement reconstruction for iteration #36... Refinement Iteration #36 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #37 Beginning Refinement Iteration #37, Round #2 No parameters were switched for Iteration #37 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00296 for Iteration #37 of Tilt-Series #5. CCMS(rotations) = 0.20835 for Iteration #37 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #37 of Tilt-Series #5. The scaled sum of CCMS values is #0.00564 for Tilt-Series #5. Creating Depiction Videos for Iteration #37 in Parallel... Creating Refinement tilt-series video for iteration #37... Generating Refinement reconstruction for iteration #37... Refinement Iteration #37 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #38 Beginning Refinement Iteration #38, Round #2 No parameters were switched for Iteration #38 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00276 for Iteration #38 of Tilt-Series #5. CCMS(rotations) = 0.22233 for Iteration #38 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #38 of Tilt-Series #5. The scaled sum of CCMS values is #0.00583 for Tilt-Series #5. Creating Depiction Videos for Iteration #38 in Parallel... Creating Refinement tilt-series video for iteration #38... Generating Refinement reconstruction for iteration #38... Refinement Iteration #38 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #39 Beginning Refinement Iteration #39, Round #2 No parameters were switched for Iteration #39 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00471 for Iteration #39 of Tilt-Series #5. CCMS(rotations) = 0.21136 for Iteration #39 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #39 of Tilt-Series #5. The scaled sum of CCMS values is #0.00658 for Tilt-Series #5. Creating Depiction Videos for Iteration #39 in Parallel... Creating Refinement tilt-series video for iteration #39... Generating Refinement reconstruction for iteration #39... Refinement Iteration #39 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #40 Beginning Refinement Iteration #40, Round #2 No parameters were switched for Iteration #40 Refinement failed. Retry #1 with Window Size: (2688, 2744) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.00476 for Iteration #40 of Tilt-Series #5. CCMS(rotations) = 0.22475 for Iteration #40 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #40 of Tilt-Series #5. The scaled sum of CCMS values is #0.00688 for Tilt-Series #5. Creating Depiction Videos for Iteration #40 in Parallel... Creating Refinement tilt-series video for iteration #40... Generating Refinement reconstruction for iteration #40... Refinement Iteration #40 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2688 Window Size (y) was windowed down to 2744 Beginning Refinement Iteration #41, Round #3 lowpass = 31.25 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 2 window.highpass.diameter = { 0.00143773292559 0.00143773292559 } window.highpass.apodization = { 0.00287487973909 0.00287487973909 } window.mask.apodization = { 10 10 } align.mask.width = { 1366 1414 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 160.414004326 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1391 1439 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1366 1414 } reference.body = 160.414004326 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #41 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00677 for Iteration #41 of Tilt-Series #5. CCMS(rotations) = 0.16306 for Iteration #41 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #41 of Tilt-Series #5. The scaled sum of CCMS values is #0.00664 for Tilt-Series #5. Creating Depiction Videos for Iteration #41 in Parallel... Creating Refinement tilt-series video for iteration #41... Generating Refinement reconstruction for iteration #41... Refinement Iteration #41 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #42 Beginning Refinement Iteration #42, Round #3 No parameters were switched for Iteration #42 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00418 for Iteration #42 of Tilt-Series #5. CCMS(rotations) = 0.26751 for Iteration #42 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #42 of Tilt-Series #5. The scaled sum of CCMS values is #0.00744 for Tilt-Series #5. Creating Depiction Videos for Iteration #42 in Parallel... Creating Refinement tilt-series video for iteration #42... Generating Refinement reconstruction for iteration #42... Refinement Iteration #42 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #43 Beginning Refinement Iteration #43, Round #3 No parameters were switched for Iteration #43 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00401 for Iteration #43 of Tilt-Series #5. CCMS(rotations) = 0.28988 for Iteration #43 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #43 of Tilt-Series #5. The scaled sum of CCMS values is #0.0078 for Tilt-Series #5. Creating Depiction Videos for Iteration #43 in Parallel... Creating Refinement tilt-series video for iteration #43... Generating Refinement reconstruction for iteration #43... Refinement Iteration #43 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #44 Beginning Refinement Iteration #44, Round #3 No parameters were switched for Iteration #44 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00439 for Iteration #44 of Tilt-Series #5. CCMS(rotations) = 0.23438 for Iteration #44 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #44 of Tilt-Series #5. The scaled sum of CCMS values is #0.00689 for Tilt-Series #5. Creating Depiction Videos for Iteration #44 in Parallel... Creating Refinement tilt-series video for iteration #44... Generating Refinement reconstruction for iteration #44... Refinement Iteration #44 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #45 Beginning Refinement Iteration #45, Round #3 No parameters were switched for Iteration #45 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00471 for Iteration #45 of Tilt-Series #5. CCMS(rotations) = 0.23681 for Iteration #45 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #45 of Tilt-Series #5. The scaled sum of CCMS values is #0.00709 for Tilt-Series #5. Creating Depiction Videos for Iteration #45 in Parallel... Creating Refinement tilt-series video for iteration #45... Generating Refinement reconstruction for iteration #45... Refinement Iteration #45 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #46 Beginning Refinement Iteration #46, Round #3 No parameters were switched for Iteration #46 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00555 for Iteration #46 of Tilt-Series #5. CCMS(rotations) = 0.28331 for Iteration #46 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #46 of Tilt-Series #5. The scaled sum of CCMS values is #0.00844 for Tilt-Series #5. Creating Depiction Videos for Iteration #46 in Parallel... Creating Refinement tilt-series video for iteration #46... Generating Refinement reconstruction for iteration #46... Refinement Iteration #46 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #47 Beginning Refinement Iteration #47, Round #3 No parameters were switched for Iteration #47 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00419 for Iteration #47 of Tilt-Series #5. CCMS(rotations) = 0.26539 for Iteration #47 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #47 of Tilt-Series #5. The scaled sum of CCMS values is #0.0074 for Tilt-Series #5. Creating Depiction Videos for Iteration #47 in Parallel... Creating Refinement tilt-series video for iteration #47... Generating Refinement reconstruction for iteration #47... Refinement Iteration #47 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #48 Beginning Refinement Iteration #48, Round #3 No parameters were switched for Iteration #48 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00388 for Iteration #48 of Tilt-Series #5. CCMS(rotations) = 0.28464 for Iteration #48 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #48 of Tilt-Series #5. The scaled sum of CCMS values is #0.00763 for Tilt-Series #5. Creating Depiction Videos for Iteration #48 in Parallel... Creating Refinement tilt-series video for iteration #48... Generating Refinement reconstruction for iteration #48... Refinement Iteration #48 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #49 Beginning Refinement Iteration #49, Round #3 No parameters were switched for Iteration #49 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00413 for Iteration #49 of Tilt-Series #5. CCMS(rotations) = 0.32274 for Iteration #49 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #49 of Tilt-Series #5. The scaled sum of CCMS values is #0.00852 for Tilt-Series #5. Creating Depiction Videos for Iteration #49 in Parallel... Creating Refinement tilt-series video for iteration #49... Generating Refinement reconstruction for iteration #49... Refinement Iteration #49 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #50 Beginning Refinement Iteration #50, Round #3 No parameters were switched for Iteration #50 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #50 of Tilt-Series #5. CCMS(rotations) = 0.26315 for Iteration #50 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #50 of Tilt-Series #5. The scaled sum of CCMS values is #0.00705 for Tilt-Series #5. Creating Depiction Videos for Iteration #50 in Parallel... Creating Refinement tilt-series video for iteration #50... Generating Refinement reconstruction for iteration #50... Refinement Iteration #50 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #51 Beginning Refinement Iteration #51, Round #3 No parameters were switched for Iteration #51 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00449 for Iteration #51 of Tilt-Series #5. CCMS(rotations) = 0.32242 for Iteration #51 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #51 of Tilt-Series #5. The scaled sum of CCMS values is #0.00869 for Tilt-Series #5. Creating Depiction Videos for Iteration #51 in Parallel... Creating Refinement tilt-series video for iteration #51... Generating Refinement reconstruction for iteration #51... Refinement Iteration #51 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #52 Beginning Refinement Iteration #52, Round #3 No parameters were switched for Iteration #52 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00384 for Iteration #52 of Tilt-Series #5. CCMS(rotations) = 0.25985 for Iteration #52 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #52 of Tilt-Series #5. The scaled sum of CCMS values is #0.00712 for Tilt-Series #5. Creating Depiction Videos for Iteration #52 in Parallel... Creating Refinement tilt-series video for iteration #52... Generating Refinement reconstruction for iteration #52... Refinement Iteration #52 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #53 Beginning Refinement Iteration #53, Round #3 No parameters were switched for Iteration #53 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00425 for Iteration #53 of Tilt-Series #5. CCMS(rotations) = 0.26268 for Iteration #53 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #53 of Tilt-Series #5. The scaled sum of CCMS values is #0.00738 for Tilt-Series #5. Creating Depiction Videos for Iteration #53 in Parallel... Creating Refinement tilt-series video for iteration #53... Generating Refinement reconstruction for iteration #53... Refinement Iteration #53 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #54 Beginning Refinement Iteration #54, Round #3 No parameters were switched for Iteration #54 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.0041 for Iteration #54 of Tilt-Series #5. CCMS(rotations) = 0.27754 for Iteration #54 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #54 of Tilt-Series #5. The scaled sum of CCMS values is #0.0076 for Tilt-Series #5. Creating Depiction Videos for Iteration #54 in Parallel... Creating Refinement tilt-series video for iteration #54... Generating Refinement reconstruction for iteration #54... Refinement Iteration #54 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #55 Beginning Refinement Iteration #55, Round #3 No parameters were switched for Iteration #55 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00405 for Iteration #55 of Tilt-Series #5. CCMS(rotations) = 0.28848 for Iteration #55 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #55 of Tilt-Series #5. The scaled sum of CCMS values is #0.0078 for Tilt-Series #5. Creating Depiction Videos for Iteration #55 in Parallel... Creating Refinement tilt-series video for iteration #55... Generating Refinement reconstruction for iteration #55... Refinement Iteration #55 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #56 Beginning Refinement Iteration #56, Round #3 No parameters were switched for Iteration #56 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00496 for Iteration #56 of Tilt-Series #5. CCMS(rotations) = 0.2546 for Iteration #56 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #56 of Tilt-Series #5. The scaled sum of CCMS values is #0.00757 for Tilt-Series #5. Creating Depiction Videos for Iteration #56 in Parallel... Creating Refinement tilt-series video for iteration #56... Generating Refinement reconstruction for iteration #56... Refinement Iteration #56 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #57 Beginning Refinement Iteration #57, Round #3 No parameters were switched for Iteration #57 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00403 for Iteration #57 of Tilt-Series #5. CCMS(rotations) = 0.29872 for Iteration #57 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #57 of Tilt-Series #5. The scaled sum of CCMS values is #0.00799 for Tilt-Series #5. Creating Depiction Videos for Iteration #57 in Parallel... Creating Refinement tilt-series video for iteration #57... Generating Refinement reconstruction for iteration #57... Refinement Iteration #57 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #58 Beginning Refinement Iteration #58, Round #3 No parameters were switched for Iteration #58 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00398 for Iteration #58 of Tilt-Series #5. CCMS(rotations) = 0.31756 for Iteration #58 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #58 of Tilt-Series #5. The scaled sum of CCMS values is #0.00834 for Tilt-Series #5. Creating Depiction Videos for Iteration #58 in Parallel... Creating Refinement tilt-series video for iteration #58... Generating Refinement reconstruction for iteration #58... Refinement Iteration #58 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #59 Beginning Refinement Iteration #59, Round #3 No parameters were switched for Iteration #59 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00549 for Iteration #59 of Tilt-Series #5. CCMS(rotations) = 0.26493 for Iteration #59 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #59 of Tilt-Series #5. The scaled sum of CCMS values is #0.00804 for Tilt-Series #5. Creating Depiction Videos for Iteration #59 in Parallel... Creating Refinement tilt-series video for iteration #59... Generating Refinement reconstruction for iteration #59... Refinement Iteration #59 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #60 Beginning Refinement Iteration #60, Round #3 No parameters were switched for Iteration #60 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 2)... Creating quality assessment statistics... CCMS(shift) = 0.00609 for Iteration #60 of Tilt-Series #5. CCMS(rotations) = 0.16428 for Iteration #60 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #60 of Tilt-Series #5. The scaled sum of CCMS values is #0.00633 for Tilt-Series #5. Creating Depiction Videos for Iteration #60 in Parallel... Creating Refinement tilt-series video for iteration #60... Generating Refinement reconstruction for iteration #60... Refinement Iteration #60 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 Beginning Refinement Iteration #61, Round #4 lowpass = 15.625 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.0904112820513 0.0904112820513 } map.sampling = 1 window.highpass.diameter = { 0.000718866462793 0.000718866462793 } window.highpass.apodization = { 0.00143743986955 0.00143743986955 } window.mask.apodization = { 10 10 } align.mask.width = { 2757 2853 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 320.828008652 map.lowpass.diameter = { 0.22566656 0.22566656 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 320.828008652 window.lowpass.diameter = { 0.22566656 0.22566656 } align.correlation.mode = mcf No parameters were switched for Iteration #61 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00645 for Iteration #61 of Tilt-Series #5. CCMS(rotations) = 0.28526 for Iteration #61 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #61 of Tilt-Series #5. The scaled sum of CCMS values is #0.00893 for Tilt-Series #5. Creating Depiction Videos for Iteration #61 in Parallel... Creating Refinement tilt-series video for iteration #61... Generating Refinement reconstruction for iteration #61... Refinement Iteration #61 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #62 Beginning Refinement Iteration #62, Round #4 No parameters were switched for Iteration #62 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00986 for Iteration #62 of Tilt-Series #5. CCMS(rotations) = 0.15556 for Iteration #62 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #62 of Tilt-Series #5. The scaled sum of CCMS values is #0.00804 for Tilt-Series #5. Creating Depiction Videos for Iteration #62 in Parallel... Creating Refinement tilt-series video for iteration #62... Generating Refinement reconstruction for iteration #62... Refinement Iteration #62 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #63 Beginning Refinement Iteration #63, Round #4 No parameters were switched for Iteration #63 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00577 for Iteration #63 of Tilt-Series #5. CCMS(rotations) = 0.37163 for Iteration #63 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #63 of Tilt-Series #5. The scaled sum of CCMS values is #0.01032 for Tilt-Series #5. Creating Depiction Videos for Iteration #63 in Parallel... Creating Refinement tilt-series video for iteration #63... Generating Refinement reconstruction for iteration #63... Refinement Iteration #63 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #64 Beginning Refinement Iteration #64, Round #4 No parameters were switched for Iteration #64 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00894 for Iteration #64 of Tilt-Series #5. CCMS(rotations) = 0.26 for Iteration #64 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #64 of Tilt-Series #5. The scaled sum of CCMS values is #0.00967 for Tilt-Series #5. Creating Depiction Videos for Iteration #64 in Parallel... Creating Refinement tilt-series video for iteration #64... Generating Refinement reconstruction for iteration #64... Refinement Iteration #64 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #65 Beginning Refinement Iteration #65, Round #4 No parameters were switched for Iteration #65 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00706 for Iteration #65 of Tilt-Series #5. CCMS(rotations) = 0.15176 for Iteration #65 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #65 of Tilt-Series #5. The scaled sum of CCMS values is #0.00656 for Tilt-Series #5. Creating Depiction Videos for Iteration #65 in Parallel... Creating Refinement tilt-series video for iteration #65... Generating Refinement reconstruction for iteration #65... Refinement Iteration #65 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #66 Beginning Refinement Iteration #66, Round #4 No parameters were switched for Iteration #66 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00651 for Iteration #66 of Tilt-Series #5. CCMS(rotations) = 0.30009 for Iteration #66 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #66 of Tilt-Series #5. The scaled sum of CCMS values is #0.00926 for Tilt-Series #5. Creating Depiction Videos for Iteration #66 in Parallel... Creating Refinement tilt-series video for iteration #66... Generating Refinement reconstruction for iteration #66... Refinement Iteration #66 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #67 Beginning Refinement Iteration #67, Round #4 No parameters were switched for Iteration #67 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00783 for Iteration #67 of Tilt-Series #5. CCMS(rotations) = 0.39706 for Iteration #67 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #67 of Tilt-Series #5. The scaled sum of CCMS values is #0.01186 for Tilt-Series #5. Creating Depiction Videos for Iteration #67 in Parallel... Creating Refinement tilt-series video for iteration #67... Generating Refinement reconstruction for iteration #67... Refinement Iteration #67 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #68 Beginning Refinement Iteration #68, Round #4 No parameters were switched for Iteration #68 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00532 for Iteration #68 of Tilt-Series #5. CCMS(rotations) = 0.33182 for Iteration #68 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #68 of Tilt-Series #5. The scaled sum of CCMS values is #0.0093 for Tilt-Series #5. Creating Depiction Videos for Iteration #68 in Parallel... Creating Refinement tilt-series video for iteration #68... Generating Refinement reconstruction for iteration #68... Refinement Iteration #68 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #69 Beginning Refinement Iteration #69, Round #4 No parameters were switched for Iteration #69 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00648 for Iteration #69 of Tilt-Series #5. CCMS(rotations) = 0.30635 for Iteration #69 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #69 of Tilt-Series #5. The scaled sum of CCMS values is #0.00937 for Tilt-Series #5. Creating Depiction Videos for Iteration #69 in Parallel... Creating Refinement tilt-series video for iteration #69... Generating Refinement reconstruction for iteration #69... Refinement Iteration #69 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #70 Beginning Refinement Iteration #70, Round #4 No parameters were switched for Iteration #70 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00558 for Iteration #70 of Tilt-Series #5. CCMS(rotations) = 0.25648 for Iteration #70 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #70 of Tilt-Series #5. The scaled sum of CCMS values is #0.00792 for Tilt-Series #5. Creating Depiction Videos for Iteration #70 in Parallel... Creating Refinement tilt-series video for iteration #70... Generating Refinement reconstruction for iteration #70... Refinement Iteration #70 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #71 Beginning Refinement Iteration #71, Round #4 No parameters were switched for Iteration #71 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00834 for Iteration #71 of Tilt-Series #5. CCMS(rotations) = 0.28082 for Iteration #71 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #71 of Tilt-Series #5. The scaled sum of CCMS values is #0.00979 for Tilt-Series #5. Creating Depiction Videos for Iteration #71 in Parallel... Creating Refinement tilt-series video for iteration #71... Generating Refinement reconstruction for iteration #71... Refinement Iteration #71 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #72 Beginning Refinement Iteration #72, Round #4 No parameters were switched for Iteration #72 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00973 for Iteration #72 of Tilt-Series #5. CCMS(rotations) = 0.34074 for Iteration #72 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #72 of Tilt-Series #5. The scaled sum of CCMS values is #0.01168 for Tilt-Series #5. Creating Depiction Videos for Iteration #72 in Parallel... Creating Refinement tilt-series video for iteration #72... Generating Refinement reconstruction for iteration #72... Refinement Iteration #72 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #73 Beginning Refinement Iteration #73, Round #4 No parameters were switched for Iteration #73 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00974 for Iteration #73 of Tilt-Series #5. CCMS(rotations) = 0.31493 for Iteration #73 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #73 of Tilt-Series #5. The scaled sum of CCMS values is #0.01117 for Tilt-Series #5. Creating Depiction Videos for Iteration #73 in Parallel... Creating Refinement tilt-series video for iteration #73... Generating Refinement reconstruction for iteration #73... Refinement Iteration #73 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #74 Beginning Refinement Iteration #74, Round #4 No parameters were switched for Iteration #74 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00994 for Iteration #74 of Tilt-Series #5. CCMS(rotations) = 0.31667 for Iteration #74 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #74 of Tilt-Series #5. The scaled sum of CCMS values is #0.0113 for Tilt-Series #5. Creating Depiction Videos for Iteration #74 in Parallel... Creating Refinement tilt-series video for iteration #74... Generating Refinement reconstruction for iteration #74... Refinement Iteration #74 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #75 Beginning Refinement Iteration #75, Round #4 No parameters were switched for Iteration #75 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00741 for Iteration #75 of Tilt-Series #5. CCMS(rotations) = 0.50933 for Iteration #75 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #75 of Tilt-Series #5. The scaled sum of CCMS values is #0.01389 for Tilt-Series #5. Creating Depiction Videos for Iteration #75 in Parallel... Creating Refinement tilt-series video for iteration #75... Generating Refinement reconstruction for iteration #75... Refinement Iteration #75 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #76 Beginning Refinement Iteration #76, Round #4 No parameters were switched for Iteration #76 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00825 for Iteration #76 of Tilt-Series #5. CCMS(rotations) = 0.23037 for Iteration #76 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #76 of Tilt-Series #5. The scaled sum of CCMS values is #0.00873 for Tilt-Series #5. Creating Depiction Videos for Iteration #76 in Parallel... Creating Refinement tilt-series video for iteration #76... Generating Refinement reconstruction for iteration #76... Refinement Iteration #76 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #77 Beginning Refinement Iteration #77, Round #4 No parameters were switched for Iteration #77 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00439 for Iteration #77 of Tilt-Series #5. CCMS(rotations) = 0.32384 for Iteration #77 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #77 of Tilt-Series #5. The scaled sum of CCMS values is #0.00867 for Tilt-Series #5. Creating Depiction Videos for Iteration #77 in Parallel... Creating Refinement tilt-series video for iteration #77... Generating Refinement reconstruction for iteration #77... Refinement Iteration #77 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #78 Beginning Refinement Iteration #78, Round #4 No parameters were switched for Iteration #78 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00834 for Iteration #78 of Tilt-Series #5. CCMS(rotations) = 0.26072 for Iteration #78 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #78 of Tilt-Series #5. The scaled sum of CCMS values is #0.00938 for Tilt-Series #5. Creating Depiction Videos for Iteration #78 in Parallel... Creating Refinement tilt-series video for iteration #78... Generating Refinement reconstruction for iteration #78... Refinement Iteration #78 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #79 Beginning Refinement Iteration #79, Round #4 No parameters were switched for Iteration #79 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00582 for Iteration #79 of Tilt-Series #5. CCMS(rotations) = 0.32283 for Iteration #79 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #79 of Tilt-Series #5. The scaled sum of CCMS values is #0.00936 for Tilt-Series #5. Creating Depiction Videos for Iteration #79 in Parallel... Creating Refinement tilt-series video for iteration #79... Generating Refinement reconstruction for iteration #79... Refinement Iteration #79 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #80 Beginning Refinement Iteration #80, Round #4 No parameters were switched for Iteration #80 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00771 for Iteration #80 of Tilt-Series #5. CCMS(rotations) = 0.29458 for Iteration #80 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #80 of Tilt-Series #5. The scaled sum of CCMS values is #0.00975 for Tilt-Series #5. Creating Depiction Videos for Iteration #80 in Parallel... Creating Refinement tilt-series video for iteration #80... Generating Refinement reconstruction for iteration #80... Refinement Iteration #80 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #81 Beginning Refinement Iteration #81, Round #4 fit.scale switched from false to true on Iteration #81Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00774 for Iteration #81 of Tilt-Series #5. CCMS(rotations) = 0.31607 for Iteration #81 of Tilt-Series #5. CCMS(scale) = 0.0 for Iteration #81 of Tilt-Series #5. The scaled sum of CCMS values is #0.01019 for Tilt-Series #5. Creating Depiction Videos for Iteration #81 in Parallel... Creating Refinement tilt-series video for iteration #81... Generating Refinement reconstruction for iteration #81... Refinement Iteration #81 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #82 Beginning Refinement Iteration #82, Round #4 No parameters were switched for Iteration #82 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01092 for Iteration #82 of Tilt-Series #5. CCMS(rotations) = 0.27539 for Iteration #82 of Tilt-Series #5. CCMS(scale) = 0.00291 for Iteration #82 of Tilt-Series #5. The scaled sum of CCMS values is #0.00828 for Tilt-Series #5. Creating Depiction Videos for Iteration #82 in Parallel... Creating Refinement tilt-series video for iteration #82... Generating Refinement reconstruction for iteration #82... Refinement Iteration #82 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #83 Beginning Refinement Iteration #83, Round #4 No parameters were switched for Iteration #83 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00621 for Iteration #83 of Tilt-Series #5. CCMS(rotations) = 0.28788 for Iteration #83 of Tilt-Series #5. CCMS(scale) = 0.00526 for Iteration #83 of Tilt-Series #5. The scaled sum of CCMS values is #0.00766 for Tilt-Series #5. Creating Depiction Videos for Iteration #83 in Parallel... Creating Refinement tilt-series video for iteration #83... Generating Refinement reconstruction for iteration #83... Refinement Iteration #83 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #84 Beginning Refinement Iteration #84, Round #4 No parameters were switched for Iteration #84 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00781 for Iteration #84 of Tilt-Series #5. CCMS(rotations) = 0.37897 for Iteration #84 of Tilt-Series #5. CCMS(scale) = 0.00419 for Iteration #84 of Tilt-Series #5. The scaled sum of CCMS values is #0.00905 for Tilt-Series #5. Creating Depiction Videos for Iteration #84 in Parallel... Creating Refinement tilt-series video for iteration #84... Generating Refinement reconstruction for iteration #84... Refinement Iteration #84 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #85 Beginning Refinement Iteration #85, Round #4 No parameters were switched for Iteration #85 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01073 for Iteration #85 of Tilt-Series #5. CCMS(rotations) = 0.24487 for Iteration #85 of Tilt-Series #5. CCMS(scale) = 0.00531 for Iteration #85 of Tilt-Series #5. The scaled sum of CCMS values is #0.00861 for Tilt-Series #5. Creating Depiction Videos for Iteration #85 in Parallel... Creating Refinement tilt-series video for iteration #85... Generating Refinement reconstruction for iteration #85... Refinement Iteration #85 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #86 Beginning Refinement Iteration #86, Round #4 No parameters were switched for Iteration #86 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0077 for Iteration #86 of Tilt-Series #5. CCMS(rotations) = 0.29163 for Iteration #86 of Tilt-Series #5. CCMS(scale) = 0.00412 for Iteration #86 of Tilt-Series #5. The scaled sum of CCMS values is #0.00783 for Tilt-Series #5. Creating Depiction Videos for Iteration #86 in Parallel... Creating Refinement tilt-series video for iteration #86... Generating Refinement reconstruction for iteration #86... Refinement Iteration #86 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #87 Beginning Refinement Iteration #87, Round #4 No parameters were switched for Iteration #87 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01042 for Iteration #87 of Tilt-Series #5. CCMS(rotations) = 0.22379 for Iteration #87 of Tilt-Series #5. CCMS(scale) = 0.00487 for Iteration #87 of Tilt-Series #5. The scaled sum of CCMS values is #0.00808 for Tilt-Series #5. Creating Depiction Videos for Iteration #87 in Parallel... Creating Refinement tilt-series video for iteration #87... Generating Refinement reconstruction for iteration #87... Refinement Iteration #87 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #88 Beginning Refinement Iteration #88, Round #4 No parameters were switched for Iteration #88 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00939 for Iteration #88 of Tilt-Series #5. CCMS(rotations) = 0.27552 for Iteration #88 of Tilt-Series #5. CCMS(scale) = 0.00598 for Iteration #88 of Tilt-Series #5. The scaled sum of CCMS values is #0.0088 for Tilt-Series #5. Creating Depiction Videos for Iteration #88 in Parallel... Creating Refinement tilt-series video for iteration #88... Generating Refinement reconstruction for iteration #88... Refinement Iteration #88 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #89 Beginning Refinement Iteration #89, Round #4 No parameters were switched for Iteration #89 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0087 for Iteration #89 of Tilt-Series #5. CCMS(rotations) = 0.3851 for Iteration #89 of Tilt-Series #5. CCMS(scale) = 0.00561 for Iteration #89 of Tilt-Series #5. The scaled sum of CCMS values is #0.00991 for Tilt-Series #5. Creating Depiction Videos for Iteration #89 in Parallel... Creating Refinement tilt-series video for iteration #89... Generating Refinement reconstruction for iteration #89... Refinement Iteration #89 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #90 Beginning Refinement Iteration #90, Round #4 No parameters were switched for Iteration #90 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01025 for Iteration #90 of Tilt-Series #5. CCMS(rotations) = 0.2026 for Iteration #90 of Tilt-Series #5. CCMS(scale) = 0.00482 for Iteration #90 of Tilt-Series #5. The scaled sum of CCMS values is #0.00772 for Tilt-Series #5. Creating Depiction Videos for Iteration #90 in Parallel... Creating Refinement tilt-series video for iteration #90... Generating Refinement reconstruction for iteration #90... Refinement Iteration #90 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #91 Beginning Refinement Iteration #91, Round #4 No parameters were switched for Iteration #91 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00847 for Iteration #91 of Tilt-Series #5. CCMS(rotations) = 0.30927 for Iteration #91 of Tilt-Series #5. CCMS(scale) = 0.00557 for Iteration #91 of Tilt-Series #5. The scaled sum of CCMS values is #0.0088 for Tilt-Series #5. Creating Depiction Videos for Iteration #91 in Parallel... Creating Refinement tilt-series video for iteration #91... Generating Refinement reconstruction for iteration #91... Refinement Iteration #91 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #92 Beginning Refinement Iteration #92, Round #4 No parameters were switched for Iteration #92 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00841 for Iteration #92 of Tilt-Series #5. CCMS(rotations) = 0.34739 for Iteration #92 of Tilt-Series #5. CCMS(scale) = 0.00477 for Iteration #92 of Tilt-Series #5. The scaled sum of CCMS values is #0.00902 for Tilt-Series #5. Creating Depiction Videos for Iteration #92 in Parallel... Creating Refinement tilt-series video for iteration #92... Generating Refinement reconstruction for iteration #92... Refinement Iteration #92 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #93 Beginning Refinement Iteration #93, Round #4 No parameters were switched for Iteration #93 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01159 for Iteration #93 of Tilt-Series #5. CCMS(rotations) = 0.22603 for Iteration #93 of Tilt-Series #5. CCMS(scale) = 0.00465 for Iteration #93 of Tilt-Series #5. The scaled sum of CCMS values is #0.00843 for Tilt-Series #5. Creating Depiction Videos for Iteration #93 in Parallel... Creating Refinement tilt-series video for iteration #93... Generating Refinement reconstruction for iteration #93... Refinement Iteration #93 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #94 Beginning Refinement Iteration #94, Round #4 No parameters were switched for Iteration #94 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01074 for Iteration #94 of Tilt-Series #5. CCMS(rotations) = 0.20584 for Iteration #94 of Tilt-Series #5. CCMS(scale) = 0.00582 for Iteration #94 of Tilt-Series #5. The scaled sum of CCMS values is #0.00826 for Tilt-Series #5. Creating Depiction Videos for Iteration #94 in Parallel... Creating Refinement tilt-series video for iteration #94... Generating Refinement reconstruction for iteration #94... Refinement Iteration #94 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #95 Beginning Refinement Iteration #95, Round #4 No parameters were switched for Iteration #95 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00913 for Iteration #95 of Tilt-Series #5. CCMS(rotations) = 0.42315 for Iteration #95 of Tilt-Series #5. CCMS(scale) = 0.00548 for Iteration #95 of Tilt-Series #5. The scaled sum of CCMS values is #0.01051 for Tilt-Series #5. Creating Depiction Videos for Iteration #95 in Parallel... Creating Refinement tilt-series video for iteration #95... Generating Refinement reconstruction for iteration #95... Refinement Iteration #95 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #96 Beginning Refinement Iteration #96, Round #4 No parameters were switched for Iteration #96 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01115 for Iteration #96 of Tilt-Series #5. CCMS(rotations) = 0.30726 for Iteration #96 of Tilt-Series #5. CCMS(scale) = 0.00541 for Iteration #96 of Tilt-Series #5. The scaled sum of CCMS values is #0.00962 for Tilt-Series #5. Creating Depiction Videos for Iteration #96 in Parallel... Creating Refinement tilt-series video for iteration #96... Generating Refinement reconstruction for iteration #96... Refinement Iteration #96 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #97 Beginning Refinement Iteration #97, Round #4 No parameters were switched for Iteration #97 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00901 for Iteration #97 of Tilt-Series #5. CCMS(rotations) = 0.28297 for Iteration #97 of Tilt-Series #5. CCMS(scale) = 0.00475 for Iteration #97 of Tilt-Series #5. The scaled sum of CCMS values is #0.00836 for Tilt-Series #5. Creating Depiction Videos for Iteration #97 in Parallel... Creating Refinement tilt-series video for iteration #97... Generating Refinement reconstruction for iteration #97... Refinement Iteration #97 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #98 Beginning Refinement Iteration #98, Round #4 No parameters were switched for Iteration #98 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.00931 for Iteration #98 of Tilt-Series #5. CCMS(rotations) = 0.22504 for Iteration #98 of Tilt-Series #5. CCMS(scale) = 0.00508 for Iteration #98 of Tilt-Series #5. The scaled sum of CCMS values is #0.0078 for Tilt-Series #5. Creating Depiction Videos for Iteration #98 in Parallel... Creating Refinement tilt-series video for iteration #98... Generating Refinement reconstruction for iteration #98... Refinement Iteration #98 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #99 Beginning Refinement Iteration #99, Round #4 No parameters were switched for Iteration #99 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01125 for Iteration #99 of Tilt-Series #5. CCMS(rotations) = 0.44261 for Iteration #99 of Tilt-Series #5. CCMS(scale) = 0.0047 for Iteration #99 of Tilt-Series #5. The scaled sum of CCMS values is #0.01122 for Tilt-Series #5. Creating Depiction Videos for Iteration #99 in Parallel... Creating Refinement tilt-series video for iteration #99... Generating Refinement reconstruction for iteration #99... Refinement Iteration #99 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #100 Beginning Refinement Iteration #100, Round #4 No parameters were switched for Iteration #100 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.011 for Iteration #100 of Tilt-Series #5. CCMS(rotations) = 0.23393 for Iteration #100 of Tilt-Series #5. CCMS(scale) = 0.00612 for Iteration #100 of Tilt-Series #5. The scaled sum of CCMS values is #0.00882 for Tilt-Series #5. Creating Depiction Videos for Iteration #100 in Parallel... Creating Refinement tilt-series video for iteration #100... Generating Refinement reconstruction for iteration #100... Refinement Iteration #100 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 Beginning Refinement Iteration #101, Round #5 lowpass = 7.8125 angstroms Round #5. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.176302 0.176302 } map.sampling = 1 window.highpass.diameter = { 0.000718866462793 0.000718866462793 } window.highpass.apodization = { 0.00143743986955 0.00143743986955 } window.mask.apodization = { 10 10 } align.mask.width = { 2757 2853 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 320.828008652 map.lowpass.diameter = { 0.45133312 0.45133312 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 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 #101Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01645 for Iteration #101 of Tilt-Series #5. CCMS(rotations) = 0.42746 for Iteration #101 of Tilt-Series #5. CCMS(scale) = 0.0066 for Iteration #101 of Tilt-Series #5. The scaled sum of CCMS values is #0.01338 for Tilt-Series #5. Creating Depiction Videos for Iteration #101 in Parallel... Creating Refinement tilt-series video for iteration #101... Generating Refinement reconstruction for iteration #101... Refinement Iteration #101 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #102 Beginning Refinement Iteration #102, Round #5 No parameters were switched for Iteration #102 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01722 for Iteration #102 of Tilt-Series #5. CCMS(rotations) = 0.31582 for Iteration #102 of Tilt-Series #5. CCMS(scale) = 0.00809 for Iteration #102 of Tilt-Series #5. The scaled sum of CCMS values is #0.01265 for Tilt-Series #5. Creating Depiction Videos for Iteration #102 in Parallel... Creating Refinement tilt-series video for iteration #102... Generating Refinement reconstruction for iteration #102... Refinement Iteration #102 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #103 Beginning Refinement Iteration #103, Round #5 No parameters were switched for Iteration #103 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01803 for Iteration #103 of Tilt-Series #5. CCMS(rotations) = 0.45223 for Iteration #103 of Tilt-Series #5. CCMS(scale) = 0.00606 for Iteration #103 of Tilt-Series #5. The scaled sum of CCMS values is #0.01406 for Tilt-Series #5. Creating Depiction Videos for Iteration #103 in Parallel... Creating Refinement tilt-series video for iteration #103... Generating Refinement reconstruction for iteration #103... Refinement Iteration #103 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #104 Beginning Refinement Iteration #104, Round #5 No parameters were switched for Iteration #104 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01547 for Iteration #104 of Tilt-Series #5. CCMS(rotations) = 0.36718 for Iteration #104 of Tilt-Series #5. CCMS(scale) = 0.00648 for Iteration #104 of Tilt-Series #5. The scaled sum of CCMS values is #0.01221 for Tilt-Series #5. Creating Depiction Videos for Iteration #104 in Parallel... Creating Refinement tilt-series video for iteration #104... Generating Refinement reconstruction for iteration #104... Refinement Iteration #104 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #105 Beginning Refinement Iteration #105, Round #5 No parameters were switched for Iteration #105 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01219 for Iteration #105 of Tilt-Series #5. CCMS(rotations) = 0.32568 for Iteration #105 of Tilt-Series #5. CCMS(scale) = 0.00695 for Iteration #105 of Tilt-Series #5. The scaled sum of CCMS values is #0.01072 for Tilt-Series #5. Creating Depiction Videos for Iteration #105 in Parallel... Creating Refinement tilt-series video for iteration #105... Generating Refinement reconstruction for iteration #105... Refinement Iteration #105 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #106 Beginning Refinement Iteration #106, Round #5 No parameters were switched for Iteration #106 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01559 for Iteration #106 of Tilt-Series #5. CCMS(rotations) = 0.40005 for Iteration #106 of Tilt-Series #5. CCMS(scale) = 0.00727 for Iteration #106 of Tilt-Series #5. The scaled sum of CCMS values is #0.01295 for Tilt-Series #5. Creating Depiction Videos for Iteration #106 in Parallel... Creating Refinement tilt-series video for iteration #106... Generating Refinement reconstruction for iteration #106... Refinement Iteration #106 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #107 Beginning Refinement Iteration #107, Round #5 No parameters were switched for Iteration #107 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01272 for Iteration #107 of Tilt-Series #5. CCMS(rotations) = 0.4779 for Iteration #107 of Tilt-Series #5. CCMS(scale) = 0.00666 for Iteration #107 of Tilt-Series #5. The scaled sum of CCMS values is #0.01283 for Tilt-Series #5. Creating Depiction Videos for Iteration #107 in Parallel... Creating Refinement tilt-series video for iteration #107... Generating Refinement reconstruction for iteration #107... Refinement Iteration #107 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #108 Beginning Refinement Iteration #108, Round #5 No parameters were switched for Iteration #108 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01203 for Iteration #108 of Tilt-Series #5. CCMS(rotations) = 0.46231 for Iteration #108 of Tilt-Series #5. CCMS(scale) = 0.00949 for Iteration #108 of Tilt-Series #5. The scaled sum of CCMS values is #0.01334 for Tilt-Series #5. Creating Depiction Videos for Iteration #108 in Parallel... Creating Refinement tilt-series video for iteration #108... Generating Refinement reconstruction for iteration #108... Refinement Iteration #108 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #109 Beginning Refinement Iteration #109, Round #5 No parameters were switched for Iteration #109 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01491 for Iteration #109 of Tilt-Series #5. CCMS(rotations) = 0.34461 for Iteration #109 of Tilt-Series #5. CCMS(scale) = 0.0081 for Iteration #109 of Tilt-Series #5. The scaled sum of CCMS values is #0.01226 for Tilt-Series #5. Creating Depiction Videos for Iteration #109 in Parallel... Creating Refinement tilt-series video for iteration #109... Generating Refinement reconstruction for iteration #109... Refinement Iteration #109 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #110 Beginning Refinement Iteration #110, Round #5 No parameters were switched for Iteration #110 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01701 for Iteration #110 of Tilt-Series #5. CCMS(rotations) = 0.32129 for Iteration #110 of Tilt-Series #5. CCMS(scale) = 0.00831 for Iteration #110 of Tilt-Series #5. The scaled sum of CCMS values is #0.01272 for Tilt-Series #5. Creating Depiction Videos for Iteration #110 in Parallel... Creating Refinement tilt-series video for iteration #110... Generating Refinement reconstruction for iteration #110... Refinement Iteration #110 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #111 Beginning Refinement Iteration #111, Round #5 No parameters were switched for Iteration #111 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.02266 for Iteration #111 of Tilt-Series #5. CCMS(rotations) = 0.25189 for Iteration #111 of Tilt-Series #5. CCMS(scale) = 0.00889 for Iteration #111 of Tilt-Series #5. The scaled sum of CCMS values is #0.01388 for Tilt-Series #5. Creating Depiction Videos for Iteration #111 in Parallel... Creating Refinement tilt-series video for iteration #111... Generating Refinement reconstruction for iteration #111... Refinement Iteration #111 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #112 Beginning Refinement Iteration #112, Round #5 No parameters were switched for Iteration #112 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01614 for Iteration #112 of Tilt-Series #5. CCMS(rotations) = 0.39167 for Iteration #112 of Tilt-Series #5. CCMS(scale) = 0.00985 for Iteration #112 of Tilt-Series #5. The scaled sum of CCMS values is #0.01388 for Tilt-Series #5. Creating Depiction Videos for Iteration #112 in Parallel... Creating Refinement tilt-series video for iteration #112... Generating Refinement reconstruction for iteration #112... Refinement Iteration #112 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #113 Beginning Refinement Iteration #113, Round #5 No parameters were switched for Iteration #113 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01667 for Iteration #113 of Tilt-Series #5. CCMS(rotations) = 0.3305 for Iteration #113 of Tilt-Series #5. CCMS(scale) = 0.01057 for Iteration #113 of Tilt-Series #5. The scaled sum of CCMS values is #0.01348 for Tilt-Series #5. Creating Depiction Videos for Iteration #113 in Parallel... Creating Refinement tilt-series video for iteration #113... Generating Refinement reconstruction for iteration #113... Refinement Iteration #113 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #114 Beginning Refinement Iteration #114, Round #5 No parameters were switched for Iteration #114 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01561 for Iteration #114 of Tilt-Series #5. CCMS(rotations) = 0.31771 for Iteration #114 of Tilt-Series #5. CCMS(scale) = 0.01098 for Iteration #114 of Tilt-Series #5. The scaled sum of CCMS values is #0.0131 for Tilt-Series #5. Creating Depiction Videos for Iteration #114 in Parallel... Creating Refinement tilt-series video for iteration #114... Generating Refinement reconstruction for iteration #114... Refinement Iteration #114 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #115 Beginning Refinement Iteration #115, Round #5 No parameters were switched for Iteration #115 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.02254 for Iteration #115 of Tilt-Series #5. CCMS(rotations) = 0.43739 for Iteration #115 of Tilt-Series #5. CCMS(scale) = 0.01218 for Iteration #115 of Tilt-Series #5. The scaled sum of CCMS values is #0.01741 for Tilt-Series #5. Creating Depiction Videos for Iteration #115 in Parallel... Creating Refinement tilt-series video for iteration #115... Generating Refinement reconstruction for iteration #115... Refinement Iteration #115 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #116 Beginning Refinement Iteration #116, Round #5 No parameters were switched for Iteration #116 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01542 for Iteration #116 of Tilt-Series #5. CCMS(rotations) = 0.23169 for Iteration #116 of Tilt-Series #5. CCMS(scale) = 0.011 for Iteration #116 of Tilt-Series #5. The scaled sum of CCMS values is #0.0119 for Tilt-Series #5. Creating Depiction Videos for Iteration #116 in Parallel... Creating Refinement tilt-series video for iteration #116... Generating Refinement reconstruction for iteration #116... Refinement Iteration #116 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #117 Beginning Refinement Iteration #117, Round #5 No parameters were switched for Iteration #117 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01547 for Iteration #117 of Tilt-Series #5. CCMS(rotations) = 0.31612 for Iteration #117 of Tilt-Series #5. CCMS(scale) = 0.01236 for Iteration #117 of Tilt-Series #5. The scaled sum of CCMS values is #0.01349 for Tilt-Series #5. Creating Depiction Videos for Iteration #117 in Parallel... Creating Refinement tilt-series video for iteration #117... Generating Refinement reconstruction for iteration #117... Refinement Iteration #117 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #118 Beginning Refinement Iteration #118, Round #5 No parameters were switched for Iteration #118 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01335 for Iteration #118 of Tilt-Series #5. CCMS(rotations) = 0.4196 for Iteration #118 of Tilt-Series #5. CCMS(scale) = 0.00981 for Iteration #118 of Tilt-Series #5. The scaled sum of CCMS values is #0.01331 for Tilt-Series #5. Creating Depiction Videos for Iteration #118 in Parallel... Creating Refinement tilt-series video for iteration #118... Generating Refinement reconstruction for iteration #118... Refinement Iteration #118 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #119 Beginning Refinement Iteration #119, Round #5 No parameters were switched for Iteration #119 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0159 for Iteration #119 of Tilt-Series #5. CCMS(rotations) = 0.32934 for Iteration #119 of Tilt-Series #5. CCMS(scale) = 0.00861 for Iteration #119 of Tilt-Series #5. The scaled sum of CCMS values is #0.01256 for Tilt-Series #5. Creating Depiction Videos for Iteration #119 in Parallel... Creating Refinement tilt-series video for iteration #119... Generating Refinement reconstruction for iteration #119... Refinement Iteration #119 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 No Round parameters changed for Iteration #120 Beginning Refinement Iteration #120, Round #5 No parameters were switched for Iteration #120 Refinement failed. Retry #1 with Window Size: (2700, 2744) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.015 for Iteration #120 of Tilt-Series #5. CCMS(rotations) = 0.56206 for Iteration #120 of Tilt-Series #5. CCMS(scale) = 0.00858 for Iteration #120 of Tilt-Series #5. The scaled sum of CCMS values is #0.01535 for Tilt-Series #5. Creating Depiction Videos for Iteration #120 in Parallel... Creating Refinement tilt-series video for iteration #120... Generating Refinement reconstruction for iteration #120... Refinement Iteration #120 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2700 Window Size (y) was windowed down to 2744 Finished Refinement for Tilt-Series #5! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org and include this log file .If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! End time: 2016yr10m03d-20hr27m17s