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=500 --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 --r5_mask_width_y=2277 --r1_lowpass_diameter_x=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=3924 --r2_highpass_diameter_x=3924 --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=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=1962 --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=10 --r2_iters=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=tiltseries0009 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0009 --tiltseries=9 --sessionname=17mar18a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=1 --expid=3662 --jobtype=protomo node04 Start time: 2017yr03m20d-18hr34m57s Description: coarse_series0009_iter2.tlt not found, using coarse_series0009.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0009.tlt to series0009.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #9 lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00718866462793 0.00718866462793 } window.highpass.apodization = { 0.0143773292559 0.0143773292559 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 47.6996506649 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 47.6996506649 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.04381 for Iteration #1 of Tilt-Series #9. CCMS(rotations) = 1.5652 for Iteration #1 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #9. The scaled sum of CCMS values is #0.05321 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01773 for Iteration #2 of Tilt-Series #9. CCMS(rotations) = 0.41245 for Iteration #2 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #9. The scaled sum of CCMS values is #0.01711 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00596 for Iteration #3 of Tilt-Series #9. CCMS(rotations) = 0.17503 for Iteration #3 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #9. The scaled sum of CCMS values is #0.00648 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00544 for Iteration #4 of Tilt-Series #9. CCMS(rotations) = 0.19006 for Iteration #4 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #9. The scaled sum of CCMS values is #0.00652 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00617 for Iteration #5 of Tilt-Series #9. CCMS(rotations) = 0.15048 for Iteration #5 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #9. The scaled sum of CCMS values is #0.0061 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00656 for Iteration #6 of Tilt-Series #9. CCMS(rotations) = 0.16363 for Iteration #6 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #9. The scaled sum of CCMS values is #0.00655 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.00594 for Iteration #7 of Tilt-Series #9. CCMS(rotations) = 0.15462 for Iteration #7 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #9. The scaled sum of CCMS values is #0.00606 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.00597 for Iteration #8 of Tilt-Series #9. CCMS(rotations) = 0.08346 for Iteration #8 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #9. The scaled sum of CCMS values is #0.00465 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.00573 for Iteration #9 of Tilt-Series #9. CCMS(rotations) = 0.13225 for Iteration #9 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #9. The scaled sum of CCMS values is #0.00551 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #9 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.0072 for Iteration #10 of Tilt-Series #9. CCMS(rotations) = 0.17832 for Iteration #10 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #9. The scaled sum of CCMS values is #0.00716 for Tilt-Series #9. 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 #9 lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.223875555556 0.223875555556 } map.sampling = 4 window.highpass.diameter = { 0.00359433231397 0.00359433231397 } window.highpass.apodization = { 0.00718866462793 0.00718866462793 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 95.3993013298 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 95.3993013298 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.0043 for Iteration #11 of Tilt-Series #9. CCMS(rotations) = 0.12404 for Iteration #11 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #9. The scaled sum of CCMS values is #0.00463 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00442 for Iteration #12 of Tilt-Series #9. CCMS(rotations) = 0.16459 for Iteration #12 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #9. The scaled sum of CCMS values is #0.0055 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00419 for Iteration #13 of Tilt-Series #9. CCMS(rotations) = 0.12288 for Iteration #13 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #9. The scaled sum of CCMS values is #0.00455 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00402 for Iteration #14 of Tilt-Series #9. CCMS(rotations) = 0.09686 for Iteration #14 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #9. The scaled sum of CCMS values is #0.00395 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00393 for Iteration #15 of Tilt-Series #9. CCMS(rotations) = 0.16248 for Iteration #15 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #9. The scaled sum of CCMS values is #0.00522 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00352 for Iteration #16 of Tilt-Series #9. CCMS(rotations) = 0.0861 for Iteration #16 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #9. The scaled sum of CCMS values is #0.00348 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00438 for Iteration #17 of Tilt-Series #9. CCMS(rotations) = 0.17986 for Iteration #17 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #9. The scaled sum of CCMS values is #0.00579 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.0038 for Iteration #18 of Tilt-Series #9. CCMS(rotations) = 0.08281 for Iteration #18 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #9. The scaled sum of CCMS values is #0.00356 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00396 for Iteration #19 of Tilt-Series #9. CCMS(rotations) = 0.17249 for Iteration #19 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #9. The scaled sum of CCMS values is #0.00543 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #9 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00343 for Iteration #20 of Tilt-Series #9. CCMS(rotations) = 0.07724 for Iteration #20 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #9. The scaled sum of CCMS values is #0.00326 for Tilt-Series #9. 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 #9 lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.227486451613 0.227486451613 } map.sampling = 2 window.highpass.diameter = { 0.00179716615698 0.00179716615698 } window.highpass.apodization = { 0.00359433231397 0.00359433231397 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 190.79860266 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 190.79860266 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00464 for Iteration #21 of Tilt-Series #9. CCMS(rotations) = 0.14643 for Iteration #21 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #9. The scaled sum of CCMS values is #0.00525 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #9 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00374 for Iteration #22 of Tilt-Series #9. CCMS(rotations) = 0.13032 for Iteration #22 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #9. The scaled sum of CCMS values is #0.00447 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #9 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00448 for Iteration #23 of Tilt-Series #9. CCMS(rotations) = 0.21957 for Iteration #23 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #9. The scaled sum of CCMS values is #0.00663 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #9 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00486 for Iteration #24 of Tilt-Series #9. CCMS(rotations) = 0.06 for Iteration #24 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #9. The scaled sum of CCMS values is #0.00363 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #9 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00342 for Iteration #25 of Tilt-Series #9. CCMS(rotations) = 0.14097 for Iteration #25 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #9. The scaled sum of CCMS values is #0.00453 for Tilt-Series #9. 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 #9 lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.2203775 0.2203775 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 381.597205319 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 381.597205319 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00656 for Iteration #26 of Tilt-Series #9. CCMS(rotations) = 0.22282 for Iteration #26 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #9. The scaled sum of CCMS values is #0.00774 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00751 for Iteration #27 of Tilt-Series #9. CCMS(rotations) = 0.20645 for Iteration #27 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #9. The scaled sum of CCMS values is #0.00789 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.0076 for Iteration #28 of Tilt-Series #9. CCMS(rotations) = 0.15562 for Iteration #28 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #9. The scaled sum of CCMS values is #0.00691 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00674 for Iteration #29 of Tilt-Series #9. CCMS(rotations) = 0.26617 for Iteration #29 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #9. The scaled sum of CCMS values is #0.00869 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00722 for Iteration #30 of Tilt-Series #9. CCMS(rotations) = 0.2636 for Iteration #30 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #9. The scaled sum of CCMS values is #0.00888 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #9 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00845 for Iteration #31 of Tilt-Series #9. CCMS(rotations) = 0.17581 for Iteration #31 of Tilt-Series #9. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #9. The scaled sum of CCMS values is #0.00774 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00649 for Iteration #32 of Tilt-Series #9. CCMS(rotations) = 0.15932 for Iteration #32 of Tilt-Series #9. CCMS(scale) = 0.00335 for Iteration #32 of Tilt-Series #9. The scaled sum of CCMS values is #0.00541 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.0052 for Iteration #33 of Tilt-Series #9. CCMS(rotations) = 0.21939 for Iteration #33 of Tilt-Series #9. CCMS(scale) = 0.0025 for Iteration #33 of Tilt-Series #9. The scaled sum of CCMS values is #0.00549 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00594 for Iteration #34 of Tilt-Series #9. CCMS(rotations) = 0.21335 for Iteration #34 of Tilt-Series #9. CCMS(scale) = 0.00244 for Iteration #34 of Tilt-Series #9. The scaled sum of CCMS values is #0.00564 for Tilt-Series #9. 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 #9 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #9 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00889 for Iteration #35 of Tilt-Series #9. CCMS(rotations) = 0.16597 for Iteration #35 of Tilt-Series #9. CCMS(scale) = 0.00241 for Iteration #35 of Tilt-Series #9. The scaled sum of CCMS values is #0.00598 for Tilt-Series #9. 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 #9! 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-06hr34m25s