protomo2aligner.py --my_tlt=False --r3_iters=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --negative_recon=-90.0 --corr_mode=mcf --rundir=/gpfs/appion/jbrasch/17jul12d/protomo_alignments/tiltseries0067_thick400 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4905.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2782 --r1_region_y=2878 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4905.0 --r4_lowpass_apod_y=16.0 --r4_lowpass_apod_x=16.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=31.0 --r3_lowpass_apod_y=31.0 --manual_alignment_finished=False --r5_body=0 --r2_region_y=2878 --r2_region_x=2782 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2453.0 --defocus_ang_positive=90 --r5_mask_width_x=2757 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4905.0 --r3_highpass_apod_x=2453.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=670 --r2_mask_width_y=694 --azimuth_switch=27 --r5_region_x=2782 --r5_region_y=2878 --highpass_diameter_y=0.001 --highpass_diameter_x=0.001 --create_reconstruction=true --r5_mask_apod_x=10 --r5_mask_apod_y=10 --r4_lowpass_diameter_y=6.25 --r1_body=0 --r1_mask_apod_x=10 --defocus_difference=0.2 --correlation_size_y=160 --correlation_size_x=160 --r2_cmdiameter_x=100.0 --r2_cmdiameter_y=100.0 --gridsearch_limit=2.0 --azimuth_stability_check=True --r1_highpass_diameter_y=4905.0 --r4_kernel_x=5 --r4_kernel_y=5 --amp_contrast_defocus=0.07 --peak_search_radius_x=100.0 --peak_search_radius_y=100.0 --r5_mask_width_y=2853 --window_area=0.95 --r1_corr_mode=mcf --gradient=true --create_tilt_video=true --mask_apod_y=10 --r5_peak_search_radius_y=300.0 --exclude_images_by_angle= --r3_mask_apod_x=10 --r2_sampling=4 --norotations=false --r3_highpass_apod_y=2453.0 --runname=tiltseries0067_thick400 --r1_highpass_diameter_x=4905.0 --r2_lowpass_diameter_y=25.0 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=3.125 --r5_lowpass_diameter_x=3.125 --max_shift=999999 --cachedir=cache --clip_high=3.5 --grow=0 --r3_cmdiameter_y=100.0 --r3_cmdiameter_x=100.0 --keep_recons=false --r4_mask_width_x=2757 --r4_mask_width_y=2853 --logging=true --DefocusTol=200 --filter=median --sessionname=17jul12d --commit=False --r1_kernel_y=5 --r1_kernel_x=5 --dose_presets=False --mask_apod_x=10 --r4_corr_mode=mcf --show_window_size=true --defocus_estimate=False --r4_iters=10 --amp_contrast_ctf=0.07 --r1_highpass_apod_y=2453.0 --r1_highpass_apod_x=2453.0 --r2_highpass_apod_x=2453.0 --sampling=8 --starting_tlt_file=Coarse_Iter_1 --r5_lowpass_apod_x=8.0 --r5_lowpass_apod_y=8.0 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=50.0 --r1_lowpass_diameter_x=50.0 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --exclude_images=999999 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --thr_low=0 --parallel=True --tiltseries=67 --r5_corr_mode=pcf --coarse=False --r3_mask_width_y=1414 --r3_mask_width_x=1366 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4905.0 --r4_highpass_diameter_x=4905.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=125.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=4905.0 --tilt_azimuth=5.3 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --r5_highpass_apod_y=2453.0 --r5_highpass_apod_x=2453.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4905.0 --defocus_max=0 --r4_region_y=2878 --r4_region_x=2782 --r5_kernel_y=5 --r3_region_x=2782 --r3_region_y=2878 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=400 --expid=4384 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=282 --max_correction=999999 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=12.5 --r3_lowpass_diameter_x=12.5 --mask_width_y=1024 --positive_recon=90.0 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.76302 --link=False --r2_highpass_diameter_x=4905.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=63.0 --r5_kernel_x=5 --r2_lowpass_apod_x=63.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=959.0 --iters=1 --r5_peak_search_radius_x=300.0 --r1_iters=10 --r1_cmdiameter_x=100.0 --preprocessing=true --scale=false --iWidth=20 --r2_lowpass_diameter_x=25.0 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=125.0 --region_x=512 --manual_alignment=False --loglevel=2 --restart_cycle=0 --dose_a=0.245 --lowpass_apod_y=0.05 --lowpass_apod_x=0.05 --kernel_x=3 --kernel_y=3 --clip_low=3.5 --azimuth_max_deviation=1.0 --tilt_clip=true --r4_highpass_apod_x=2453.0 --r4_highpass_apod_y=2453.0 --azimuth=false --r1_mask_width_y=334 --r1_mask_width_x=322 --jobtype=protomo node27 Start time: 2017yr07m25d-16hr22m41s Description: Using Coarse alignment iteration 1 for Refinement by copying coarse_series0067.tlt to series0067.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) lowpass = 50.0 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 = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00575093170234 0.00575093170234 } window.highpass.apodization = { 0.0114995189564 0.0114995189564 } window.mask.apodization = { 10 10 } align.mask.width = { 322 334 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 40.1042008914 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 347 359 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 322 334 } reference.body = 40.1042008914 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.04598 for Iteration #1 of Tilt-Series #67. CCMS(rotations) = 1.96729 for Iteration #1 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #67. The scaled sum of CCMS values is #0.06234 for iteration 1 of Tilt-Series #67. Alignment quality for Iteration #1 of Tilt-Series #67 (17jul12d): Bad - 1st iteration is always bad because the geometry has not yet been estimated (confidence: 100.000000%)Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #2 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.0179 for Iteration #2 of Tilt-Series #67. CCMS(rotations) = 0.82589 for Iteration #2 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #67. The scaled sum of CCMS values is #0.02547 for iteration 2 of Tilt-Series #67. Alignment quality for Iteration #2 of Tilt-Series #67 (17jul12d): Okay (confidence: 100.000000%)Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #3 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01254 for Iteration #3 of Tilt-Series #67. CCMS(rotations) = 0.5984 for Iteration #3 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #67. The scaled sum of CCMS values is #0.01824 for iteration 3 of Tilt-Series #67. Alignment quality for Iteration #3 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #4 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01342 for Iteration #4 of Tilt-Series #67. CCMS(rotations) = 0.36776 for Iteration #4 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #67. The scaled sum of CCMS values is #0.01406 for iteration 4 of Tilt-Series #67. Alignment quality for Iteration #4 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... The tilt azimuth after iteration #4 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #5 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01205 for Iteration #5 of Tilt-Series #67. CCMS(rotations) = 0.5495 for Iteration #5 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #67. The scaled sum of CCMS values is #0.01702 for iteration 5 of Tilt-Series #67. Alignment quality for Iteration #5 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... The tilt azimuth after iteration #5 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #6 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.0085 for Iteration #6 of Tilt-Series #67. CCMS(rotations) = 0.4771 for Iteration #6 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #67. The scaled sum of CCMS values is #0.01379 for iteration 6 of Tilt-Series #67. Alignment quality for Iteration #6 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #7 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01311 for Iteration #7 of Tilt-Series #67. CCMS(rotations) = 0.36171 for Iteration #7 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #67. The scaled sum of CCMS values is #0.01379 for iteration 7 of Tilt-Series #67. Alignment quality for Iteration #7 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #8 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00884 for Iteration #8 of Tilt-Series #67. CCMS(rotations) = 0.46355 for Iteration #8 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #67. The scaled sum of CCMS values is #0.01369 for iteration 8 of Tilt-Series #67. Alignment quality for Iteration #8 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #67 (17jul12d): Very StableCreating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... The tilt azimuth after iteration #8 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #9 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01075 for Iteration #9 of Tilt-Series #67. CCMS(rotations) = 0.42729 for Iteration #9 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #67. The scaled sum of CCMS values is #0.01392 for iteration 9 of Tilt-Series #67. Alignment quality for Iteration #9 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #67 (17jul12d): Very StableCreating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #10 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00917 for Iteration #10 of Tilt-Series #67. CCMS(rotations) = 0.43741 for Iteration #10 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #67. The scaled sum of CCMS values is #0.01333 for iteration 10 of Tilt-Series #67. Alignment quality for Iteration #10 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #67 (17jul12d): Rock Solid!Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #11, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) lowpass = 25.0 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 = { 0.223875555556 0.223875555556 } map.sampling = 4 window.highpass.diameter = { 0.00287546585117 0.00287546585117 } window.highpass.apodization = { 0.00574975947819 0.00574975947819 } window.mask.apodization = { 10 10 } align.mask.width = { 670 694 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 80.2084017828 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 695 719 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 670 694 } reference.body = 80.2084017828 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01282 for Iteration #11 of Tilt-Series #67. CCMS(rotations) = 0.30201 for Iteration #11 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #67. The scaled sum of CCMS values is #0.01245 for iteration 11 of Tilt-Series #67. Alignment quality for Iteration #11 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #67 (17jul12d): Rock Solid!Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #12 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.01016 for Iteration #12 of Tilt-Series #67. CCMS(rotations) = 0.17721 for Iteration #12 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #67. The scaled sum of CCMS values is #0.00863 for iteration 12 of Tilt-Series #67. Alignment quality for Iteration #12 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #13 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.0073 for Iteration #13 of Tilt-Series #67. CCMS(rotations) = 0.22698 for Iteration #13 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #67. The scaled sum of CCMS values is #0.00819 for iteration 13 of Tilt-Series #67. Alignment quality for Iteration #13 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #67 (17jul12d): StableCreating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... The tilt azimuth after iteration #13 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #14 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.0077 for Iteration #14 of Tilt-Series #67. CCMS(rotations) = 0.29311 for Iteration #14 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #67. The scaled sum of CCMS values is #0.00971 for iteration 14 of Tilt-Series #67. Alignment quality for Iteration #14 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #67 (17jul12d): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #15 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.0074 for Iteration #15 of Tilt-Series #67. CCMS(rotations) = 0.24022 for Iteration #15 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #67. The scaled sum of CCMS values is #0.0085 for iteration 15 of Tilt-Series #67. Alignment quality for Iteration #15 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #67 (17jul12d): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #16 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.0087 for Iteration #16 of Tilt-Series #67. CCMS(rotations) = 0.27441 for Iteration #16 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #67. The scaled sum of CCMS values is #0.00984 for iteration 16 of Tilt-Series #67. Alignment quality for Iteration #16 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #67 (17jul12d): Very StableCreating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #17 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00702 for Iteration #17 of Tilt-Series #67. CCMS(rotations) = 0.26421 for Iteration #17 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #67. The scaled sum of CCMS values is #0.00879 for iteration 17 of Tilt-Series #67. Alignment quality for Iteration #17 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #18 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00838 for Iteration #18 of Tilt-Series #67. CCMS(rotations) = 0.27509 for Iteration #18 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #67. The scaled sum of CCMS values is #0.00969 for iteration 18 of Tilt-Series #67. Alignment quality for Iteration #18 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #67 (17jul12d): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #19 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00747 for Iteration #19 of Tilt-Series #67. CCMS(rotations) = 0.31092 for Iteration #19 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #67. The scaled sum of CCMS values is #0.00995 for iteration 19 of Tilt-Series #67. Alignment quality for Iteration #19 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #67 (17jul12d): StableCreating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #20 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00927 for Iteration #20 of Tilt-Series #67. CCMS(rotations) = 0.26802 for Iteration #20 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #67. The scaled sum of CCMS values is #0.01 for iteration 20 of Tilt-Series #67. Alignment quality for Iteration #20 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #21, Round #3 of Tilt-Series #67 (tiltseries0067_thick400) lowpass = 12.5 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 = { 0.227486451613 0.227486451613 } 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 = 160.416803566 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1391 1439 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1366 1414 } reference.body = 160.416803566 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.01096 for Iteration #21 of Tilt-Series #67. CCMS(rotations) = 0.36188 for Iteration #21 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #67. The scaled sum of CCMS values is #0.01272 for iteration 21 of Tilt-Series #67. Alignment quality for Iteration #21 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... The tilt azimuth after iteration #21 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #22 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00775 for Iteration #22 of Tilt-Series #67. CCMS(rotations) = 0.12251 for Iteration #22 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #67. The scaled sum of CCMS values is #0.00633 for iteration 22 of Tilt-Series #67. Alignment quality for Iteration #22 of Tilt-Series #67 (17jul12d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #23 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00783 for Iteration #23 of Tilt-Series #67. CCMS(rotations) = 0.31577 for Iteration #23 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #67. The scaled sum of CCMS values is #0.01023 for iteration 23 of Tilt-Series #67. Alignment quality for Iteration #23 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #24 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00906 for Iteration #24 of Tilt-Series #67. CCMS(rotations) = 0.17229 for Iteration #24 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #67. The scaled sum of CCMS values is #0.00798 for iteration 24 of Tilt-Series #67. Alignment quality for Iteration #24 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #25 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00709 for Iteration #25 of Tilt-Series #67. CCMS(rotations) = 0.25315 for Iteration #25 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #67. The scaled sum of CCMS values is #0.00861 for iteration 25 of Tilt-Series #67. Alignment quality for Iteration #25 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #26, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) lowpass = 6.25 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 = { 0.2203775 0.2203775 } 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 = 320.833607131 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 320.833607131 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00947 for Iteration #26 of Tilt-Series #67. CCMS(rotations) = 0.32976 for Iteration #26 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #67. The scaled sum of CCMS values is #0.01133 for iteration 26 of Tilt-Series #67. Alignment quality for Iteration #26 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #27 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) fit.azimuth switched from false to true on Iteration #27Creating quality assessment statistics... CCMS(shift) = 0.00879 for Iteration #27 of Tilt-Series #67. CCMS(rotations) = 0.41061 for Iteration #27 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #67. The scaled sum of CCMS values is #0.01261 for iteration 27 of Tilt-Series #67. Alignment quality for Iteration #27 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #67 (17jul12d): Very StableCreating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... The tilt azimuth after iteration #27 deviated from the initial tilt azimuth by 0.750000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #28 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01557 for Iteration #28 of Tilt-Series #67. CCMS(rotations) = 0.15812 for Iteration #28 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #67. The scaled sum of CCMS values is #0.01095 for iteration 28 of Tilt-Series #67. Alignment quality for Iteration #28 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 0.012000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #29 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01599 for Iteration #29 of Tilt-Series #67. CCMS(rotations) = 0.54869 for Iteration #29 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #67. The scaled sum of CCMS values is #0.01897 for iteration 29 of Tilt-Series #67. Alignment quality for Iteration #29 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 0.651000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #30 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01132 for Iteration #30 of Tilt-Series #67. CCMS(rotations) = 0.23513 for Iteration #30 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #67. The scaled sum of CCMS values is #0.01036 for iteration 30 of Tilt-Series #67. Alignment quality for Iteration #30 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 0.579000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #31 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00862 for Iteration #31 of Tilt-Series #67. CCMS(rotations) = 0.45509 for Iteration #31 of Tilt-Series #67. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #67. The scaled sum of CCMS values is #0.01341 for iteration 31 of Tilt-Series #67. Alignment quality for Iteration #31 of Tilt-Series #67 (17jul12d): Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 0.731000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #32 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00708 for Iteration #32 of Tilt-Series #67. CCMS(rotations) = 0.31049 for Iteration #32 of Tilt-Series #67. CCMS(scale) = 0.00268 for Iteration #32 of Tilt-Series #67. The scaled sum of CCMS values is #0.00739 for iteration 32 of Tilt-Series #67. Alignment quality for Iteration #32 of Tilt-Series #67 (17jul12d): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... The tilt azimuth after iteration #32 deviated from the initial tilt azimuth by 0.750000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #33 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00817 for Iteration #33 of Tilt-Series #67. CCMS(rotations) = 0.43676 for Iteration #33 of Tilt-Series #67. CCMS(scale) = 0.00249 for Iteration #33 of Tilt-Series #67. The scaled sum of CCMS values is #0.00938 for iteration 33 of Tilt-Series #67. Alignment quality for Iteration #33 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 1.022000, which is greater than the maximum allowed deviation of 1.000000.Changing the tilt azimuth back to the initial tilt azimuth of 5.300000 for the next iteration. No Round parameters changed for Iteration #34 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01616 for Iteration #34 of Tilt-Series #67. CCMS(rotations) = 0.44776 for Iteration #34 of Tilt-Series #67. CCMS(scale) = 0.00212 for Iteration #34 of Tilt-Series #67. The scaled sum of CCMS values is #0.01206 for iteration 34 of Tilt-Series #67. Alignment quality for Iteration #34 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #35 of Tilt-Series #67 (tiltseries0067_thick400) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #67 (tiltseries0067_thick400) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.01634 for Iteration #35 of Tilt-Series #67. CCMS(rotations) = 0.211 for Iteration #35 of Tilt-Series #67. CCMS(scale) = 0.00212 for Iteration #35 of Tilt-Series #67. The scaled sum of CCMS values is #0.00897 for iteration 35 of Tilt-Series #67. Alignment quality for Iteration #35 of Tilt-Series #67 (17jul12d): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #67 (17jul12d): UnstableCreating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.000000, which is less than the maximum allowed deviation of 1.000000.Finished Refinement for Tilt-Series #67 (tiltseries0067_thick400)! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org explaining the issue and include this log file. If everything worked beautifully and you publish, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2017yr07m26d-15hr08m49s