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/anoble/17oct05c/protomo_alignments/tiltseries0002_thick50 --r1_peak_search_radius_y=300.0 --r1_peak_search_radius_x=300.0 --serialem_stack= --r3_highpass_diameter_x=4015.0 --r4_lowpass_diameter_x=6.25 --filename_prefix= --r4_cmdiameter_x=100.0 --r4_cmdiameter_y=100.0 --r1_region_x=1855 --r1_region_y=1919 --cmdiameter_y=100.0 --r2_corr_mode=mcf --r5_highpass_diameter_x=4015.0 --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=1919 --r2_region_x=1855 --r3_mask_apod_y=10 --video_type=html5vid --rotation=true --r2_highpass_apod_y=2008.0 --defocus_ang_positive=90 --r5_mask_width_x=1830 --frame_aligned=True --image_file_type=mrc --r3_highpass_diameter_y=4015.0 --r3_highpass_apod_x=2008.0 --r5_cmdiameter_y=100.0 --r5_cmdiameter_x=100.0 --r2_mask_width_x=438 --r2_mask_width_y=454 --r5_region_x=1855 --r5_region_y=1919 --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=False --r1_highpass_diameter_y=4015.0 --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=1894 --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=2008.0 --runname=tiltseries0002_thick50 --r1_highpass_diameter_x=4015.0 --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=1830 --r4_mask_width_y=1894 --r5_highpass_apod_y=2008.0 --logging=true --DefocusTol=200 --filter=median --sessionname=17oct05c --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=2008.0 --r1_highpass_apod_x=2008.0 --r2_highpass_apod_x=2008.0 --sampling=8 --starting_tlt_file=Coarse_Iter_2 --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=2 --r5_corr_mode=pcf --change_refimg=False --r3_mask_width_y=934 --r3_mask_width_x=902 --map_sampling=8 --dose_c=2.81 --exclude_images_by_angle_accuracy=0.05 --gridsearch_step=0.1 --coarse=False --r2_iters=10 --region_y=512 --r4_highpass_diameter_y=4015.0 --r4_highpass_diameter_x=4015.0 --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=4015.0 --r2_mask_apod_y=10 --r2_mask_apod_x=10 --desired_ref_tilt_angle=0.0 --r5_highpass_apod_x=2008.0 --defocus_save=0 --protomo_outdir=out --r5_highpass_diameter_y=4015.0 --defocus_max=0 --r4_region_y=1919 --r4_region_x=1855 --r5_kernel_y=5 --r3_region_x=1855 --r3_region_y=1919 --r4_body=0 --serialem_mdoc= --r2_peak_search_radius_x=300.0 --r2_peak_search_radius_y=300.0 --thickness=50 --expid=5089 --r2_body=0 --orientation=true --do_estimation=false --iter_gradient=false --projectid=304 --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=2.16423 --link=False --r2_highpass_diameter_x=4015.0 --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=3.0 --tilt_clip=true --r4_highpass_apod_x=2008.0 --r4_highpass_apod_y=2008.0 --azimuth=true --r1_mask_width_y=214 --r1_mask_width_x=206 --jobtype=protomo node39 Start time: 2017yr10m05d-11hr02m55s Description: coarse_series0002_iter2.tlt not found, using coarse_series0002.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0002.tlt to series0002.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 17.31384 Angstroms, Nyquist is 34.62768 Angstroms) window.lowpass.apodization = { 0.27702144 0.27702144 } map.sampling = 8 window.highpass.diameter = { 0.00862457783313 0.00862457783313 } window.highpass.apodization = { 0.0172448605578 0.0172448605578 } window.mask.apodization = { 10 10 } align.mask.width = { 206 214 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 3.71540793829 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 231 239 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 206 214 } reference.body = 3.71540793829 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.07588 for Iteration #1 of Tilt-Series #2. CCMS(rotations) = 0.89247 for Iteration #1 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #2. The scaled sum of CCMS values is #0.05579 for iteration 1 of Tilt-Series #2. Alignment quality for Iteration #1 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.00375 for Iteration #2 of Tilt-Series #2. CCMS(rotations) = 0.08218 for Iteration #2 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #2. The scaled sum of CCMS values is #0.00352 for iteration 2 of Tilt-Series #2. Alignment quality for Iteration #2 of Tilt-Series #2 (17oct05c): Perfection! (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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.0038 for Iteration #3 of Tilt-Series #2. CCMS(rotations) = 0.07861 for Iteration #3 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #2. The scaled sum of CCMS values is #0.00347 for iteration 3 of Tilt-Series #2. Alignment quality for Iteration #3 of Tilt-Series #2 (17oct05c): Perfection! (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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00374 for Iteration #4 of Tilt-Series #2. CCMS(rotations) = 0.06785 for Iteration #4 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #2. The scaled sum of CCMS values is #0.00323 for iteration 4 of Tilt-Series #2. Alignment quality for Iteration #4 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #4 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00368 for Iteration #5 of Tilt-Series #2. CCMS(rotations) = 0.07147 for Iteration #5 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #2. The scaled sum of CCMS values is #0.00327 for iteration 5 of Tilt-Series #2. Alignment quality for Iteration #5 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #5 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00381 for Iteration #6 of Tilt-Series #2. CCMS(rotations) = 0.07158 for Iteration #6 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #2. The scaled sum of CCMS values is #0.00334 for iteration 6 of Tilt-Series #2. Alignment quality for Iteration #6 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #6 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00369 for Iteration #7 of Tilt-Series #2. CCMS(rotations) = 0.07016 for Iteration #7 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #2. The scaled sum of CCMS values is #0.00325 for iteration 7 of Tilt-Series #2. Alignment quality for Iteration #7 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #7 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00382 for Iteration #8 of Tilt-Series #2. CCMS(rotations) = 0.07098 for Iteration #8 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #2. The scaled sum of CCMS values is #0.00333 for iteration 8 of Tilt-Series #2. Alignment quality for Iteration #8 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #8 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00379 for Iteration #9 of Tilt-Series #2. CCMS(rotations) = 0.07308 for Iteration #9 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #2. The scaled sum of CCMS values is #0.00336 for iteration 9 of Tilt-Series #2. Alignment quality for Iteration #9 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #9 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00376 for Iteration #10 of Tilt-Series #2. CCMS(rotations) = 0.0736 for Iteration #10 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #2. The scaled sum of CCMS values is #0.00335 for iteration 10 of Tilt-Series #2. Alignment quality for Iteration #10 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #10 of Tilt-Series #2 (17oct05c): Rock Solid!Creating 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 #2 (tiltseries0002_thick50) lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 8.65692 Angstroms, Nyquist is 17.31384 Angstroms) window.lowpass.apodization = { 0.274822857143 0.274822857143 } map.sampling = 4 window.highpass.diameter = { 0.00431228891656 0.00431228891656 } window.highpass.apodization = { 0.00862243027888 0.00862243027888 } window.mask.apodization = { 10 10 } align.mask.width = { 438 454 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 7.43081587659 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 463 479 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 438 454 } reference.body = 7.43081587659 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00358 for Iteration #11 of Tilt-Series #2. CCMS(rotations) = 0.06252 for Iteration #11 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #2. The scaled sum of CCMS values is #0.00304 for iteration 11 of Tilt-Series #2. Alignment quality for Iteration #11 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #11 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00313 for Iteration #12 of Tilt-Series #2. CCMS(rotations) = 0.0926 for Iteration #12 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #2. The scaled sum of CCMS values is #0.00341 for iteration 12 of Tilt-Series #2. Alignment quality for Iteration #12 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #12 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00326 for Iteration #13 of Tilt-Series #2. CCMS(rotations) = 0.10096 for Iteration #13 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #2. The scaled sum of CCMS values is #0.00365 for iteration 13 of Tilt-Series #2. Alignment quality for Iteration #13 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #13 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.0031 for Iteration #14 of Tilt-Series #2. CCMS(rotations) = 0.09595 for Iteration #14 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #2. The scaled sum of CCMS values is #0.00347 for iteration 14 of Tilt-Series #2. Alignment quality for Iteration #14 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #14 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00324 for Iteration #15 of Tilt-Series #2. CCMS(rotations) = 0.09921 for Iteration #15 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #2. The scaled sum of CCMS values is #0.0036 for iteration 15 of Tilt-Series #2. Alignment quality for Iteration #15 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #15 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00311 for Iteration #16 of Tilt-Series #2. CCMS(rotations) = 0.09568 for Iteration #16 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #2. The scaled sum of CCMS values is #0.00347 for iteration 16 of Tilt-Series #2. Alignment quality for Iteration #16 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #16 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00321 for Iteration #17 of Tilt-Series #2. CCMS(rotations) = 0.10218 for Iteration #17 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #2. The scaled sum of CCMS values is #0.00365 for iteration 17 of Tilt-Series #2. Alignment quality for Iteration #17 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #17 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00308 for Iteration #18 of Tilt-Series #2. CCMS(rotations) = 0.09576 for Iteration #18 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #2. The scaled sum of CCMS values is #0.00345 for iteration 18 of Tilt-Series #2. Alignment quality for Iteration #18 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #18 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00319 for Iteration #19 of Tilt-Series #2. CCMS(rotations) = 0.1006 for Iteration #19 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #2. The scaled sum of CCMS values is #0.00361 for iteration 19 of Tilt-Series #2. Alignment quality for Iteration #19 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #19 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00308 for Iteration #20 of Tilt-Series #2. CCMS(rotations) = 0.09995 for Iteration #20 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #2. The scaled sum of CCMS values is #0.00354 for iteration 20 of Tilt-Series #2. Alignment quality for Iteration #20 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #20 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 4.32846 Angstroms, Nyquist is 8.65692 Angstroms) window.lowpass.apodization = { 0.279255483871 0.279255483871 } map.sampling = 2 window.highpass.diameter = { 0.00215614445828 0.00215614445828 } window.highpass.apodization = { 0.00431121513944 0.00431121513944 } window.mask.apodization = { 10 10 } align.mask.width = { 902 934 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 14.8616317532 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 927 959 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 902 934 } reference.body = 14.8616317532 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00357 for Iteration #21 of Tilt-Series #2. CCMS(rotations) = 0.10033 for Iteration #21 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #2. The scaled sum of CCMS values is #0.00379 for iteration 21 of Tilt-Series #2. Alignment quality for Iteration #21 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #21 of Tilt-Series #2 (17oct05c): StableCreating 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00343 for Iteration #22 of Tilt-Series #2. CCMS(rotations) = 0.07909 for Iteration #22 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #2. The scaled sum of CCMS values is #0.0033 for iteration 22 of Tilt-Series #2. Alignment quality for Iteration #22 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #22 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00346 for Iteration #23 of Tilt-Series #2. CCMS(rotations) = 0.08745 for Iteration #23 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #2. The scaled sum of CCMS values is #0.00348 for iteration 23 of Tilt-Series #2. Alignment quality for Iteration #23 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #23 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.0035 for Iteration #24 of Tilt-Series #2. CCMS(rotations) = 0.08827 for Iteration #24 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #2. The scaled sum of CCMS values is #0.00352 for iteration 24 of Tilt-Series #2. Alignment quality for Iteration #24 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #24 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00331 for Iteration #25 of Tilt-Series #2. CCMS(rotations) = 0.07926 for Iteration #25 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #2. The scaled sum of CCMS values is #0.00324 for iteration 25 of Tilt-Series #2. Alignment quality for Iteration #25 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #25 of Tilt-Series #2 (17oct05c): 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 #2 (tiltseries0002_thick50) lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 2.16423 Angstroms, Nyquist is 4.32846 Angstroms) window.lowpass.apodization = { 0.27052875 0.27052875 } map.sampling = 1 window.highpass.diameter = { 0.00107807222914 0.00107807222914 } window.highpass.apodization = { 0.00215560756972 0.00215560756972 } window.mask.apodization = { 10 10 } align.mask.width = { 1830 1894 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 29.7232635064 map.lowpass.diameter = { 0.6925536 0.6925536 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1855 1919 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1830 1894 } reference.body = 29.7232635064 window.lowpass.diameter = { 0.6925536 0.6925536 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00297 for Iteration #26 of Tilt-Series #2. CCMS(rotations) = 0.12273 for Iteration #26 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #2. The scaled sum of CCMS values is #0.00394 for iteration 26 of Tilt-Series #2. Alignment quality for Iteration #26 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #26 of Tilt-Series #2 (17oct05c): StableCreating 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 #2 (tiltseries0002_thick50) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00283 for Iteration #27 of Tilt-Series #2. CCMS(rotations) = 0.06206 for Iteration #27 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #2. The scaled sum of CCMS values is #0.00266 for iteration 27 of Tilt-Series #2. Alignment quality for Iteration #27 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #27 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... No Round parameters changed for Iteration #28 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00259 for Iteration #28 of Tilt-Series #2. CCMS(rotations) = 0.09437 for Iteration #28 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #2. The scaled sum of CCMS values is #0.00318 for iteration 28 of Tilt-Series #2. Alignment quality for Iteration #28 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #28 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... No Round parameters changed for Iteration #29 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00265 for Iteration #29 of Tilt-Series #2. CCMS(rotations) = 0.07965 for Iteration #29 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #2. The scaled sum of CCMS values is #0.00292 for iteration 29 of Tilt-Series #2. Alignment quality for Iteration #29 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #29 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... No Round parameters changed for Iteration #30 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00254 for Iteration #30 of Tilt-Series #2. CCMS(rotations) = 0.07879 for Iteration #30 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #2. The scaled sum of CCMS values is #0.00284 for iteration 30 of Tilt-Series #2. Alignment quality for Iteration #30 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #30 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... No Round parameters changed for Iteration #31 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00266 for Iteration #31 of Tilt-Series #2. CCMS(rotations) = 0.07291 for Iteration #31 of Tilt-Series #2. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #2. The scaled sum of CCMS values is #0.00279 for iteration 31 of Tilt-Series #2. Alignment quality for Iteration #31 of Tilt-Series #2 (17oct05c): Perfection! (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #31 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... No Round parameters changed for Iteration #32 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00184 for Iteration #32 of Tilt-Series #2. CCMS(rotations) = 0.08262 for Iteration #32 of Tilt-Series #2. CCMS(scale) = 0.00119 for Iteration #32 of Tilt-Series #2. The scaled sum of CCMS values is #0.00211 for iteration 32 of Tilt-Series #2. Alignment quality for Iteration #32 of Tilt-Series #2 (17oct05c): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #32 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... No Round parameters changed for Iteration #33 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00179 for Iteration #33 of Tilt-Series #2. CCMS(rotations) = 0.08467 for Iteration #33 of Tilt-Series #2. CCMS(scale) = 0.00123 for Iteration #33 of Tilt-Series #2. The scaled sum of CCMS values is #0.00214 for iteration 33 of Tilt-Series #2. Alignment quality for Iteration #33 of Tilt-Series #2 (17oct05c): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #33 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... No Round parameters changed for Iteration #34 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00179 for Iteration #34 of Tilt-Series #2. CCMS(rotations) = 0.08393 for Iteration #34 of Tilt-Series #2. CCMS(scale) = 0.00123 for Iteration #34 of Tilt-Series #2. The scaled sum of CCMS values is #0.00212 for iteration 34 of Tilt-Series #2. Alignment quality for Iteration #34 of Tilt-Series #2 (17oct05c): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #34 of Tilt-Series #2 (17oct05c): Rock Solid!Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... No Round parameters changed for Iteration #35 of Tilt-Series #2 (tiltseries0002_thick50) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 (tiltseries0002_thick50) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00192 for Iteration #35 of Tilt-Series #2. CCMS(rotations) = 0.08155 for Iteration #35 of Tilt-Series #2. CCMS(scale) = 0.00126 for Iteration #35 of Tilt-Series #2. The scaled sum of CCMS values is #0.00215 for iteration 35 of Tilt-Series #2. Alignment quality for Iteration #35 of Tilt-Series #2 (17oct05c): Suspiciously Perfect... (confidence: 100.000000%)Tilt model stability (with respect to the last 3 iterations) at Iteration #35 of Tilt-Series #2 (17oct05c): Rock Solid!Creating 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 #2 (tiltseries0002_thick50)! 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: 2017yr10m05d-18hr21m19s