protomo2aligner.py --parallel=True --starting_tlt_file=Coarse_Iter_2 --r1_region_x=2226 --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 --r5_mask_width_y=2277 --r1_lowpass_diameter_x=50 --r2_lowpass_diameter_x=25 --r3_lowpass_diameter_x=12.5 --r4_lowpass_diameter_x=6.25 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=50 --r2_lowpass_diameter_y=25 --r3_lowpass_diameter_y=12.5 --r4_lowpass_diameter_y=6.25 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=40513 --r2_highpass_diameter_x=40513 --r3_highpass_diameter_x=40513 --r4_highpass_diameter_x=40513 --r5_highpass_diameter_x=40513 --r1_highpass_diameter_y=40513 --r2_highpass_diameter_y=40513 --r3_highpass_diameter_y=40513 --r4_highpass_diameter_y=40513 --r5_highpass_diameter_y=40513 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=125 --r2_lowpass_apod_x=63 --r3_lowpass_apod_x=31 --r4_lowpass_apod_x=16 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=125 --r2_lowpass_apod_y=63 --r3_lowpass_apod_y=31 --r4_lowpass_apod_y=16 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=20257 --r2_highpass_apod_x=20257 --r3_highpass_apod_x=20257 --r4_highpass_apod_x=20257 --r5_highpass_apod_x=20257 --r1_highpass_apod_y=20257 --r2_highpass_apod_y=20257 --r3_highpass_apod_y=20257 --r4_highpass_apod_y=20257 --r5_highpass_apod_y=20257 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=10 --r2_iters=10 --r3_iters=5 --r4_iters=10 --r5_iters=0 --preprocessing=true --azimuth_stability_check=False --azimuth_max_deviation=3 --exclude_images_by_angle_accuracy=0.05 --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 --do_estimation=false --norotations=false --correlation_size_x=160 --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 --translimit=959 --orientation=true --azimuth=true --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true --video_type=html5vid --runname=tiltseries0002 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0002 --tiltseries=2 --sessionname=17mar18a --pixelsize=18.2 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=1 --expid=3662 --jobtype=protomo node03 Start time: 2017yr03m20d-17hr01m15s 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 lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 145.6 Angstroms, Nyquist is 291.2 Angstroms) window.lowpass.apodization = { 2.3296 2.3296 } map.sampling = 8 window.highpass.diameter = { 0.00718781625651 0.00718781625651 } window.highpass.apodization = { 0.0143752776818 0.0143752776818 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 19.4388987984 map.lowpass.diameter = { 5.824 5.824 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 19.4388987984 window.lowpass.diameter = { 5.824 5.824 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.03627 for Iteration #1 of Tilt-Series #2. CCMS(rotations) = 1.55294 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 #0.04919 for Tilt-Series #2. 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 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01132 for Iteration #2 of Tilt-Series #2. CCMS(rotations) = 0.43917 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 #0.01444 for Tilt-Series #2. 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 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00962 for Iteration #3 of Tilt-Series #2. CCMS(rotations) = 0.19049 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 #0.00862 for Tilt-Series #2. 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 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00659 for Iteration #4 of Tilt-Series #2. CCMS(rotations) = 0.2094 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 #0.00748 for Tilt-Series #2. 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 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00653 for Iteration #5 of Tilt-Series #2. CCMS(rotations) = 0.20594 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 #0.00738 for Tilt-Series #2. 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 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00575 for Iteration #6 of Tilt-Series #2. CCMS(rotations) = 0.25629 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 #0.008 for Tilt-Series #2. 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 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00582 for Iteration #7 of Tilt-Series #2. CCMS(rotations) = 0.23185 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 #0.00755 for Tilt-Series #2. 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 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00603 for Iteration #8 of Tilt-Series #2. CCMS(rotations) = 0.20292 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 #0.00707 for Tilt-Series #2. 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 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00579 for Iteration #9 of Tilt-Series #2. CCMS(rotations) = 0.21477 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 #0.00719 for Tilt-Series #2. 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 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #2 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00636 for Iteration #10 of Tilt-Series #2. CCMS(rotations) = 0.24223 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 #0.00802 for Tilt-Series #2. 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 lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 72.8 Angstroms, Nyquist is 145.6 Angstroms) window.lowpass.apodization = { 2.31111111111 2.31111111111 } map.sampling = 4 window.highpass.diameter = { 0.00359390812826 0.00359390812826 } window.highpass.apodization = { 0.00718763884089 0.00718763884089 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 38.8777975967 map.lowpass.diameter = { 5.824 5.824 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 38.8777975967 window.lowpass.diameter = { 5.824 5.824 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00602 for Iteration #11 of Tilt-Series #2. CCMS(rotations) = 0.32858 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 #0.00958 for Tilt-Series #2. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 of Tilt-Series #2 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00224 for Iteration #12 of Tilt-Series #2. CCMS(rotations) = 0.19336 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 #0.00499 for Tilt-Series #2. 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 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00455 for Iteration #13 of Tilt-Series #2. CCMS(rotations) = 0.16317 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 #0.00554 for Tilt-Series #2. 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 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00516 for Iteration #14 of Tilt-Series #2. CCMS(rotations) = 0.19107 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 #0.0064 for Tilt-Series #2. 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 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00522 for Iteration #15 of Tilt-Series #2. CCMS(rotations) = 0.15935 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 #0.0058 for Tilt-Series #2. 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 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00566 for Iteration #16 of Tilt-Series #2. CCMS(rotations) = 0.19758 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 #0.00678 for Tilt-Series #2. 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 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.0057 for Iteration #17 of Tilt-Series #2. CCMS(rotations) = 0.16904 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 #0.00623 for Tilt-Series #2. 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 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00636 for Iteration #18 of Tilt-Series #2. CCMS(rotations) = 0.19423 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 #0.00706 for Tilt-Series #2. 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 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00692 for Iteration #19 of Tilt-Series #2. CCMS(rotations) = 0.18629 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 #0.00718 for Tilt-Series #2. 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 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #2 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00683 for Iteration #20 of Tilt-Series #2. CCMS(rotations) = 0.22462 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 #0.00791 for Tilt-Series #2. 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 lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 36.4 Angstroms, Nyquist is 72.8 Angstroms) window.lowpass.apodization = { 2.34838709677 2.34838709677 } map.sampling = 2 window.highpass.diameter = { 0.00179695406413 0.00179695406413 } window.highpass.apodization = { 0.00359381942045 0.00359381942045 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 77.7555951935 map.lowpass.diameter = { 5.824 5.824 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 77.7555951935 window.lowpass.diameter = { 5.824 5.824 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00663 for Iteration #21 of Tilt-Series #2. CCMS(rotations) = 0.18913 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 #0.0071 for Tilt-Series #2. 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 #2 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #2 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00455 for Iteration #22 of Tilt-Series #2. CCMS(rotations) = 0.19472 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 #0.00617 for Tilt-Series #2. 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 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #2 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00553 for Iteration #23 of Tilt-Series #2. CCMS(rotations) = 0.16036 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 #0.00597 for Tilt-Series #2. 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 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #2 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00579 for Iteration #24 of Tilt-Series #2. CCMS(rotations) = 0.19517 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 #0.0068 for Tilt-Series #2. 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 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #2 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00614 for Iteration #25 of Tilt-Series #2. CCMS(rotations) = 0.15736 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 #0.00622 for Tilt-Series #2. 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 lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 18.2 Angstroms, Nyquist is 36.4 Angstroms) window.lowpass.apodization = { 2.275 2.275 } map.sampling = 1 window.highpass.diameter = { 0.000898477032064 0.000898477032064 } window.highpass.apodization = { 0.00179690971022 0.00179690971022 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 155.511190387 map.lowpass.diameter = { 5.824 5.824 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 155.511190387 window.lowpass.diameter = { 5.824 5.824 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00305 for Iteration #26 of Tilt-Series #2. CCMS(rotations) = 0.13291 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 #0.00419 for Tilt-Series #2. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... No Round parameters changed for Iteration #27 of Tilt-Series #2 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00407 for Iteration #27 of Tilt-Series #2. CCMS(rotations) = 0.10261 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 #0.00409 for Tilt-Series #2. 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 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00259 for Iteration #28 of Tilt-Series #2. CCMS(rotations) = 0.15101 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 #0.00432 for Tilt-Series #2. 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 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.0042 for Iteration #29 of Tilt-Series #2. CCMS(rotations) = 0.14831 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 #0.00507 for Tilt-Series #2. 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 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00361 for Iteration #30 of Tilt-Series #2. CCMS(rotations) = 0.17576 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 #0.00532 for Tilt-Series #2. 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 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #2 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00301 for Iteration #31 of Tilt-Series #2. CCMS(rotations) = 0.142 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 #0.00435 for Tilt-Series #2. 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 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00406 for Iteration #32 of Tilt-Series #2. CCMS(rotations) = 0.10149 for Iteration #32 of Tilt-Series #2. CCMS(scale) = 0.001 for Iteration #32 of Tilt-Series #2. The scaled sum of CCMS values is #0.00304 for Tilt-Series #2. 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 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00365 for Iteration #33 of Tilt-Series #2. CCMS(rotations) = 0.14135 for Iteration #33 of Tilt-Series #2. CCMS(scale) = 0.00109 for Iteration #33 of Tilt-Series #2. The scaled sum of CCMS values is #0.00347 for Tilt-Series #2. 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 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.0024 for Iteration #34 of Tilt-Series #2. CCMS(rotations) = 0.1421 for Iteration #34 of Tilt-Series #2. CCMS(scale) = 0.00102 for Iteration #34 of Tilt-Series #2. The scaled sum of CCMS values is #0.00303 for Tilt-Series #2. 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 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #2 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00456 for Iteration #35 of Tilt-Series #2. CCMS(rotations) = 0.12971 for Iteration #35 of Tilt-Series #2. CCMS(scale) = 0.00084 for Iteration #35 of Tilt-Series #2. The scaled sum of CCMS values is #0.00353 for Tilt-Series #2. 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! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org and include this log file. If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2017yr03m21d-23hr12m31s