protomo2aligner.py --my_tlt=False --r5_kernel_x=5 --r5_iters=0 --r4_mask_apod_y=10 --r4_mask_apod_x=10 --corr_mode=mcf --rundir=/gpfs/appion/anoble/18mar12b/protomo_alignments/tiltseries0004_thick125 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=3071.0 --r4_lowpass_diameter_x=5.32 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=2307 --r1_region_y=2399 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=3071.0 --r4_lowpass_apod_y=13.0 --r4_lowpass_apod_x=13.0 --r3_kernel_y=5 --r3_kernel_x=5 --r3_lowpass_apod_x=27.0 --r3_lowpass_apod_y=27.0 --manual_alignment_finished=False --r5_body=0 --runname=tiltseries0004_thick125 --r2_region_y=2399 --r2_region_x=2307 --r2_sampling=4 --video_type=html5vid --rotation=true --r2_highpass_apod_y=1536.0 --defocus_ang_positive=90 --r5_mask_width_x=2282 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=3071.0 --r3_highpass_apod_x=1536.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=551 --r2_mask_width_y=574 --r5_region_x=2307 --r5_region_y=2399 --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=5.32 --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=False --r1_highpass_diameter_y=3071.0 --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=2374 --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 --r3_mask_apod_y=10 --norotations=false --r3_highpass_apod_y=1536.0 --r3_iters=5 --r1_highpass_diameter_x=3071.0 --r2_lowpass_diameter_y=21.28 --map_size_y=479 --map_size_z=200 --r5_lowpass_diameter_y=2.66 --r5_lowpass_diameter_x=2.66 --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=2282 --r4_mask_width_y=2374 --r5_highpass_apod_y=1536.0 --logging=true --DefocusTol=200 --filter=median --sessionname=18mar12b --exclude_images=999999 --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=1536.0 --r1_highpass_apod_x=1536.0 --r2_highpass_apod_x=1536.0 --sampling=8 --starting_tlt_file=Coarse_Iter_1 --r5_lowpass_apod_x=7.0 --r5_lowpass_apod_y=7.0 --dose_c=2.81 --r1_cmdiameter_y=100.0 --further_alignment=False --r1_lowpass_diameter_y=42.56 --r1_lowpass_diameter_x=42.56 --r4_sampling=1 --res_max=10 --r1_mask_apod_y=10 --res_min=10000 --scale_switch=31 --dose_b=-1.665 --positive=90.0 --r3_peak_search_radius_y=300.0 --r3_peak_search_radius_x=300.0 --negative=-90.0 --parallel=True --tiltseries=4 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=1174 --r3_mask_width_x=1128 --map_sampling=8 --thr_low=0 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=3071.0 --r4_highpass_diameter_x=3071.0 --mask_width_x=1024 --highpass_apod_x=0.002 --binning=true --r1_lowpass_apod_y=106.0 --thr_high=999999 --r5_sampling=1 --highpass_apod_y=0.002 --defocus_min=0 --r1_sampling=8 --ctf_correct=False --r2_highpass_diameter_y=3071.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=1536.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=3071.0 --defocus_max=0 --r4_region_y=2399 --r4_region_x=2307 --r5_kernel_y=5 --r3_region_x=2307 --r3_region_y=2399 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=125 --expid=6268 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=340 --map_size_x=463 --r3_body=0 --r3_lowpass_diameter_y=10.64 --r3_lowpass_diameter_x=10.64 --mask_width_y=1024 --max_correction=999999 --elevation=false --r2_kernel_x=5 --r2_kernel_y=5 --slab=true --pixelsize=1.331 --link=False --r2_highpass_diameter_x=3071.0 --lowpass_diameter_x=0.5 --lowpass_diameter_y=0.5 --defocus=3 --border=100 --r3_corr_mode=mcf --r2_lowpass_apod_y=53.0 --exclude_images_by_angle_accuracy=0.05 --r2_lowpass_apod_x=53.0 --defocus_ang_negative=-90 --r3_sampling=2 --description= --make_searchable=True --translimit=377.0 --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=21.28 --dimx=3710 --dimy=3838 --r4_peak_search_radius_x=300.0 --r4_peak_search_radius_y=300.0 --r1_lowpass_apod_x=106.0 --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=3.0 --tilt_clip=true --r4_highpass_apod_x=1536.0 --r4_highpass_apod_y=1536.0 --azimuth=true --r1_mask_width_y=274 --r1_mask_width_x=263 --jobtype=protomo --from_multirefine=True node07 Start time: 2018yr03m12d-12hr25m52s Description: Using alignment .tlt file as determined by protomo2multirefine.py.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) lowpass = 42.56 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 10.648 Angstroms, Nyquist is 21.296 Angstroms) window.lowpass.apodization = { 0.200905660377 0.200905660377 } align.translimit = 47.125e0 map.sampling = 8 window.highpass.diameter = { 0.00693454900684 0.00693454900684 } window.highpass.apodization = { 0.0138645833333 0.0138645833333 } window.mask.apodization = { 10 10 } align.mask.width = { 263 274 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 16.6021582187 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 288 299 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 263 274 } reference.body = 16.6021582187 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.06584 for Iteration #1 of Tilt-Series #4. CCMS(rotations) = 0.2381 for Iteration #1 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4. The scaled sum of CCMS values is #0.03768 for iteration 1 of Tilt-Series #4. Alignment quality for Iteration #1 of Tilt-Series #4 (18mar12b): 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... No Round parameters changed for Iteration #2 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.00674 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 0.15699 for Iteration #2 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4. The scaled sum of CCMS values is #0.00651 for iteration 2 of Tilt-Series #4. Alignment quality for Iteration #2 of Tilt-Series #4 (18mar12b): Excellent (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... No Round parameters changed for Iteration #3 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00631 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 0.16949 for Iteration #3 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4. The scaled sum of CCMS values is #0.00655 for iteration 3 of Tilt-Series #4. Alignment quality for Iteration #3 of Tilt-Series #4 (18mar12b): Excellent (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... No Round parameters changed for Iteration #4 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00725 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 0.17134 for Iteration #4 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4. The scaled sum of CCMS values is #0.00705 for iteration 4 of Tilt-Series #4. Alignment quality for Iteration #4 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #4 (18mar12b): StableCreating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00577 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 0.15813 for Iteration #5 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4. The scaled sum of CCMS values is #0.00605 for iteration 5 of Tilt-Series #4. Alignment quality for Iteration #5 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00803 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 0.18399 for Iteration #6 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4. The scaled sum of CCMS values is #0.0077 for iteration 6 of Tilt-Series #4. Alignment quality for Iteration #6 of Tilt-Series #4 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00578 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 0.1536 for Iteration #7 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4. The scaled sum of CCMS values is #0.00596 for iteration 7 of Tilt-Series #4. Alignment quality for Iteration #7 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.0077 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 0.18347 for Iteration #8 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4. The scaled sum of CCMS values is #0.00752 for iteration 8 of Tilt-Series #4. Alignment quality for Iteration #8 of Tilt-Series #4 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... No Round parameters changed for Iteration #9 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00591 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 0.15961 for Iteration #9 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4. The scaled sum of CCMS values is #0.00615 for iteration 9 of Tilt-Series #4. Alignment quality for Iteration #9 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... No Round parameters changed for Iteration #10 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00809 for Iteration #10 of Tilt-Series #4. CCMS(rotations) = 0.18504 for Iteration #10 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4. The scaled sum of CCMS values is #0.00774 for iteration 10 of Tilt-Series #4. Alignment quality for Iteration #10 of Tilt-Series #4 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #4 (18mar12b): StableCreating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) lowpass = 21.28 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 5.324 Angstroms, Nyquist is 10.648 Angstroms) window.lowpass.apodization = { 0.200905660377 0.200905660377 } align.translimit = 94.25e0 map.sampling = 4 window.highpass.diameter = { 0.00346727450342 0.00346727450342 } window.highpass.apodization = { 0.00693229166667 0.00693229166667 } window.mask.apodization = { 10 10 } align.mask.width = { 551 574 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 33.2043164374 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 576 599 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 551 574 } reference.body = 33.2043164374 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00664 for Iteration #11 of Tilt-Series #4. CCMS(rotations) = 0.09817 for Iteration #11 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4. The scaled sum of CCMS values is #0.00528 for iteration 11 of Tilt-Series #4. Alignment quality for Iteration #11 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #4 (18mar12b): StableCreating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00595 for Iteration #12 of Tilt-Series #4. CCMS(rotations) = 0.13439 for Iteration #12 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4. The scaled sum of CCMS values is #0.00566 for iteration 12 of Tilt-Series #4. Alignment quality for Iteration #12 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00568 for Iteration #13 of Tilt-Series #4. CCMS(rotations) = 0.13575 for Iteration #13 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4. The scaled sum of CCMS values is #0.00556 for iteration 13 of Tilt-Series #4. Alignment quality for Iteration #13 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... No Round parameters changed for Iteration #14 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00591 for Iteration #14 of Tilt-Series #4. CCMS(rotations) = 0.13639 for Iteration #14 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4. The scaled sum of CCMS values is #0.00568 for iteration 14 of Tilt-Series #4. Alignment quality for Iteration #14 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00567 for Iteration #15 of Tilt-Series #4. CCMS(rotations) = 0.12971 for Iteration #15 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4. The scaled sum of CCMS values is #0.00543 for iteration 15 of Tilt-Series #4. Alignment quality for Iteration #15 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... No Round parameters changed for Iteration #16 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.0056 for Iteration #16 of Tilt-Series #4. CCMS(rotations) = 0.14595 for Iteration #16 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4. The scaled sum of CCMS values is #0.00572 for iteration 16 of Tilt-Series #4. Alignment quality for Iteration #16 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... No Round parameters changed for Iteration #17 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00558 for Iteration #17 of Tilt-Series #4. CCMS(rotations) = 0.13422 for Iteration #17 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4. The scaled sum of CCMS values is #0.00547 for iteration 17 of Tilt-Series #4. Alignment quality for Iteration #17 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... No Round parameters changed for Iteration #18 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00579 for Iteration #18 of Tilt-Series #4. CCMS(rotations) = 0.13979 for Iteration #18 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4. The scaled sum of CCMS values is #0.00569 for iteration 18 of Tilt-Series #4. Alignment quality for Iteration #18 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00554 for Iteration #19 of Tilt-Series #4. CCMS(rotations) = 0.1474 for Iteration #19 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4. The scaled sum of CCMS values is #0.00572 for iteration 19 of Tilt-Series #4. Alignment quality for Iteration #19 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #4 (18mar12b): Very StableCreating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00572 for Iteration #20 of Tilt-Series #4. CCMS(rotations) = 0.13567 for Iteration #20 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4. The scaled sum of CCMS values is #0.00557 for iteration 20 of Tilt-Series #4. Alignment quality for Iteration #20 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Beginning Refinement Iteration #21, Round #3 of Tilt-Series #4 (tiltseries0004_thick125) lowpass = 10.64 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 2.662 Angstroms, Nyquist is 5.324 Angstroms) window.lowpass.apodization = { 0.197185185185 0.197185185185 } align.translimit = 188.5e0 map.sampling = 2 window.highpass.diameter = { 0.00173363725171 0.00173363725171 } window.highpass.apodization = { 0.00346614583333 0.00346614583333 } window.mask.apodization = { 10 10 } align.mask.width = { 1128 1174 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 66.4086328748 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1153 1199 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1128 1174 } reference.body = 66.4086328748 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00534 for Iteration #21 of Tilt-Series #4. CCMS(rotations) = 0.12641 for Iteration #21 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4. The scaled sum of CCMS values is #0.0052 for iteration 21 of Tilt-Series #4. Alignment quality for Iteration #21 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... No Round parameters changed for Iteration #22 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00545 for Iteration #22 of Tilt-Series #4. CCMS(rotations) = 0.14527 for Iteration #22 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4. The scaled sum of CCMS values is #0.00563 for iteration 22 of Tilt-Series #4. Alignment quality for Iteration #22 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... No Round parameters changed for Iteration #23 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00611 for Iteration #23 of Tilt-Series #4. CCMS(rotations) = 0.13364 for Iteration #23 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4. The scaled sum of CCMS values is #0.00573 for iteration 23 of Tilt-Series #4. Alignment quality for Iteration #23 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... No Round parameters changed for Iteration #24 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00583 for Iteration #24 of Tilt-Series #4. CCMS(rotations) = 0.12715 for Iteration #24 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4. The scaled sum of CCMS values is #0.00546 for iteration 24 of Tilt-Series #4. Alignment quality for Iteration #24 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... No Round parameters changed for Iteration #25 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00547 for Iteration #25 of Tilt-Series #4. CCMS(rotations) = 0.1478 for Iteration #25 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4. The scaled sum of CCMS values is #0.00569 for iteration 25 of Tilt-Series #4. Alignment quality for Iteration #25 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #4 (18mar12b): Rock Solid!Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Beginning Refinement Iteration #26, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) lowpass = 5.32 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.331 Angstroms, Nyquist is 2.662 Angstroms) window.lowpass.apodization = { 0.204769230769 0.204769230769 } align.translimit = 377.0e0 map.sampling = 1 window.highpass.diameter = { 0.000866818625855 0.000866818625855 } window.highpass.apodization = { 0.00173307291667 0.00173307291667 } window.mask.apodization = { 10 10 } align.mask.width = { 2282 2374 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 132.81726575 map.lowpass.diameter = { 0.50037593985 0.50037593985 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2307 2399 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2282 2374 } reference.body = 132.81726575 window.lowpass.diameter = { 0.50037593985 0.50037593985 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00632 for Iteration #26 of Tilt-Series #4. CCMS(rotations) = 0.28116 for Iteration #26 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4. The scaled sum of CCMS values is #0.00878 for iteration 26 of Tilt-Series #4. Alignment quality for Iteration #26 of Tilt-Series #4 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... No Round parameters changed for Iteration #27 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00817 for Iteration #27 of Tilt-Series #4. CCMS(rotations) = 0.26818 for Iteration #27 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4. The scaled sum of CCMS values is #0.00945 for iteration 27 of Tilt-Series #4. Alignment quality for Iteration #27 of Tilt-Series #4 (18mar12b): Very Good (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... No Round parameters changed for Iteration #28 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00738 for Iteration #28 of Tilt-Series #4. CCMS(rotations) = 0.17715 for Iteration #28 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4. The scaled sum of CCMS values is #0.00723 for iteration 28 of Tilt-Series #4. Alignment quality for Iteration #28 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... No Round parameters changed for Iteration #29 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00711 for Iteration #29 of Tilt-Series #4. CCMS(rotations) = 0.17878 for Iteration #29 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4. The scaled sum of CCMS values is #0.00713 for iteration 29 of Tilt-Series #4. Alignment quality for Iteration #29 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... No Round parameters changed for Iteration #30 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00607 for Iteration #30 of Tilt-Series #4. CCMS(rotations) = 0.17015 for Iteration #30 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4. The scaled sum of CCMS values is #0.00644 for iteration 30 of Tilt-Series #4. Alignment quality for Iteration #30 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... No Round parameters changed for Iteration #31 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00734 for Iteration #31 of Tilt-Series #4. CCMS(rotations) = 0.18227 for Iteration #31 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4. The scaled sum of CCMS values is #0.00732 for iteration 31 of Tilt-Series #4. Alignment quality for Iteration #31 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... No Round parameters changed for Iteration #32 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00478 for Iteration #32 of Tilt-Series #4. CCMS(rotations) = 0.16787 for Iteration #32 of Tilt-Series #4. CCMS(scale) = 0.00254 for Iteration #32 of Tilt-Series #4. The scaled sum of CCMS values is #0.00468 for iteration 32 of Tilt-Series #4. Alignment quality for Iteration #32 of Tilt-Series #4 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... No Round parameters changed for Iteration #33 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00556 for Iteration #33 of Tilt-Series #4. CCMS(rotations) = 0.20956 for Iteration #33 of Tilt-Series #4. CCMS(scale) = 0.00245 for Iteration #33 of Tilt-Series #4. The scaled sum of CCMS values is #0.00546 for iteration 33 of Tilt-Series #4. Alignment quality for Iteration #33 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... No Round parameters changed for Iteration #34 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.0053 for Iteration #34 of Tilt-Series #4. CCMS(rotations) = 0.1731 for Iteration #34 of Tilt-Series #4. CCMS(scale) = 0.00267 for Iteration #34 of Tilt-Series #4. The scaled sum of CCMS values is #0.00496 for iteration 34 of Tilt-Series #4. Alignment quality for Iteration #34 of Tilt-Series #4 (18mar12b): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... No Round parameters changed for Iteration #35 of Tilt-Series #4 (tiltseries0004_thick125) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004_thick125) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00933 for Iteration #35 of Tilt-Series #4. CCMS(rotations) = 0.20006 for Iteration #35 of Tilt-Series #4. CCMS(scale) = 0.00227 for Iteration #35 of Tilt-Series #4. The scaled sum of CCMS values is #0.00653 for iteration 35 of Tilt-Series #4. Alignment quality for Iteration #35 of Tilt-Series #4 (18mar12b): Excellent (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #4 (18mar12b): UnstableCreating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... Finished Refinement for Tilt-Series #4 (tiltseries0004_thick125)! 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: 2018yr03m13d-01hr51m24s