protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=2782 --r2_region_x=2782 --r3_region_x=2782 --r4_region_x=2782 --r5_region_x=2782 --r1_region_y=2878 --r2_region_y=2878 --r3_region_y=2878 --r4_region_y=2878 --r5_region_y=2878 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=322 --r2_mask_width_x=670 --r3_mask_width_x=1366 --r4_mask_width_x=2757 --r5_mask_width_x=2757 --r1_mask_width_y=334 --r2_mask_width_y=694 --r3_mask_width_y=1414 --r4_mask_width_y=2853 --r5_mask_width_y=2853 --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=4905 --r2_highpass_diameter_x=4905 --r3_highpass_diameter_x=4905 --r4_highpass_diameter_x=4905 --r5_highpass_diameter_x=4905 --r1_highpass_diameter_y=4905 --r2_highpass_diameter_y=4905 --r3_highpass_diameter_y=4905 --r4_highpass_diameter_y=4905 --r5_highpass_diameter_y=4905 --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=2453 --r2_highpass_apod_x=2453 --r3_highpass_apod_x=2453 --r4_highpass_apod_x=2453 --r5_highpass_apod_x=2453 --r1_highpass_apod_y=2453 --r2_highpass_apod_y=2453 --r3_highpass_apod_y=2453 --r4_highpass_apod_y=2453 --r5_highpass_apod_y=2453 --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=True --azimuth_max_deviation=1 --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=tiltseries0004 --rundir=/gpfs/appion/jbrasch/17mar17a/protomo_alignments/tiltseries0004 --tiltseries=4 --sessionname=17mar17a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=282 --expid=3656 --jobtype=protomo node03 Start time: 2017yr03m28d-13hr35m02s Description: Using Manual alignment for Refinement by copying manual_series0004.tlt to series0004.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 (tiltseries0004) lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00575093170234 0.00575093170234 } window.highpass.apodization = { 0.0114995189564 0.0114995189564 } window.mask.apodization = { 10 10 } align.mask.width = { 322 334 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 50.1311259224 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 347 359 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 322 334 } reference.body = 50.1311259224 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.03006 for Iteration #1 of Tilt-Series #4. CCMS(rotations) = 0.91613 for Iteration #1 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #4. The scaled sum of CCMS values is #0.03335 for Tilt-Series #4. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... The tilt azimuth after iteration #1 deviated from the initial tilt azimuth by 0.653000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #2 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01131 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 0.21757 for Iteration #2 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #4. The scaled sum of CCMS values is #0.01 for Tilt-Series #4. Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... The tilt azimuth after iteration #2 deviated from the initial tilt azimuth by 0.166000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #3 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.01138 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 0.13907 for Iteration #3 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #4. The scaled sum of CCMS values is #0.00847 for Tilt-Series #4. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... The tilt azimuth after iteration #3 deviated from the initial tilt azimuth by 0.225000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #4 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.01074 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 0.13236 for Iteration #4 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #4. The scaled sum of CCMS values is #0.00801 for Tilt-Series #4. Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... The tilt azimuth after iteration #4 deviated from the initial tilt azimuth by 0.127000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #5 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01089 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 0.15185 for Iteration #5 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #4. The scaled sum of CCMS values is #0.00848 for Tilt-Series #4. Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... The tilt azimuth after iteration #5 deviated from the initial tilt azimuth by 0.001000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #6 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01028 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 0.19649 for Iteration #6 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #4. The scaled sum of CCMS values is #0.00907 for Tilt-Series #4. Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... The tilt azimuth after iteration #6 deviated from the initial tilt azimuth by 0.270000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #7 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01227 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 0.14866 for Iteration #7 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #4. The scaled sum of CCMS values is #0.00911 for Tilt-Series #4. Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... The tilt azimuth after iteration #7 deviated from the initial tilt azimuth by 0.169000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #8 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01058 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 0.18918 for Iteration #8 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #4. The scaled sum of CCMS values is #0.00907 for Tilt-Series #4. Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... The tilt azimuth after iteration #8 deviated from the initial tilt azimuth by 0.556000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #9 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01394 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 0.21433 for Iteration #9 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #4. The scaled sum of CCMS values is #0.01125 for Tilt-Series #4. Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... The tilt azimuth after iteration #9 deviated from the initial tilt azimuth by 0.340000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #10 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01077 for Iteration #10 of Tilt-Series #4. CCMS(rotations) = 0.1857 for Iteration #10 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #4. The scaled sum of CCMS values is #0.0091 for Tilt-Series #4. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... The tilt azimuth after iteration #10 deviated from the initial tilt azimuth by 0.471000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 (tiltseries0004) lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.223875555556 0.223875555556 } map.sampling = 4 window.highpass.diameter = { 0.00287546585117 0.00287546585117 } window.highpass.apodization = { 0.00574975947819 0.00574975947819 } window.mask.apodization = { 10 10 } align.mask.width = { 670 694 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 100.262251845 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 695 719 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 670 694 } reference.body = 100.262251845 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01092 for Iteration #11 of Tilt-Series #4. CCMS(rotations) = 0.18341 for Iteration #11 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #4. The scaled sum of CCMS values is #0.00913 for Tilt-Series #4. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... The tilt azimuth after iteration #11 deviated from the initial tilt azimuth by 0.017000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #12 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00379 for Iteration #12 of Tilt-Series #4. CCMS(rotations) = 0.21081 for Iteration #12 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #4. The scaled sum of CCMS values is #0.00611 for Tilt-Series #4. Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... The tilt azimuth after iteration #12 deviated from the initial tilt azimuth by 0.062000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #13 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00475 for Iteration #13 of Tilt-Series #4. CCMS(rotations) = 0.17996 for Iteration #13 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #4. The scaled sum of CCMS values is #0.00597 for Tilt-Series #4. Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... The tilt azimuth after iteration #13 deviated from the initial tilt azimuth by 0.225000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #14 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00456 for Iteration #14 of Tilt-Series #4. CCMS(rotations) = 0.21115 for Iteration #14 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #4. The scaled sum of CCMS values is #0.0065 for Tilt-Series #4. Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... The tilt azimuth after iteration #14 deviated from the initial tilt azimuth by 0.025000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #15 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00458 for Iteration #15 of Tilt-Series #4. CCMS(rotations) = 0.1922 for Iteration #15 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #4. The scaled sum of CCMS values is #0.00614 for Tilt-Series #4. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... The tilt azimuth after iteration #15 deviated from the initial tilt azimuth by 0.283000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #16 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00455 for Iteration #16 of Tilt-Series #4. CCMS(rotations) = 0.2168 for Iteration #16 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #4. The scaled sum of CCMS values is #0.00661 for Tilt-Series #4. Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... The tilt azimuth after iteration #16 deviated from the initial tilt azimuth by 0.033000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #17 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00451 for Iteration #17 of Tilt-Series #4. CCMS(rotations) = 0.18574 for Iteration #17 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #4. The scaled sum of CCMS values is #0.00597 for Tilt-Series #4. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... The tilt azimuth after iteration #17 deviated from the initial tilt azimuth by 0.200000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #18 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.00444 for Iteration #18 of Tilt-Series #4. CCMS(rotations) = 0.21203 for Iteration #18 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #4. The scaled sum of CCMS values is #0.00646 for Tilt-Series #4. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... The tilt azimuth after iteration #18 deviated from the initial tilt azimuth by 0.005000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #19 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00454 for Iteration #19 of Tilt-Series #4. CCMS(rotations) = 0.19725 for Iteration #19 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #4. The scaled sum of CCMS values is #0.00622 for Tilt-Series #4. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... The tilt azimuth after iteration #19 deviated from the initial tilt azimuth by 0.202000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #20 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00445 for Iteration #20 of Tilt-Series #4. CCMS(rotations) = 0.21966 for Iteration #20 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #4. The scaled sum of CCMS values is #0.00662 for Tilt-Series #4. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... The tilt azimuth after iteration #20 deviated from the initial tilt azimuth by 0.010000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #21, Round #3 of Tilt-Series #4 (tiltseries0004) lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.227486451613 0.227486451613 } map.sampling = 2 window.highpass.diameter = { 0.00143773292559 0.00143773292559 } window.highpass.apodization = { 0.00287487973909 0.00287487973909 } window.mask.apodization = { 10 10 } align.mask.width = { 1366 1414 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 200.52450369 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1391 1439 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1366 1414 } reference.body = 200.52450369 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00714 for Iteration #21 of Tilt-Series #4. CCMS(rotations) = 0.16248 for Iteration #21 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #4. The scaled sum of CCMS values is #0.00682 for Tilt-Series #4. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... The tilt azimuth after iteration #21 deviated from the initial tilt azimuth by 0.003000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #22 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00671 for Iteration #22 of Tilt-Series #4. CCMS(rotations) = 0.14683 for Iteration #22 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #4. The scaled sum of CCMS values is #0.00629 for Tilt-Series #4. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... The tilt azimuth after iteration #22 deviated from the initial tilt azimuth by 0.008000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #23 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00527 for Iteration #23 of Tilt-Series #4. CCMS(rotations) = 0.26351 for Iteration #23 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #4. The scaled sum of CCMS values is #0.00791 for Tilt-Series #4. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... The tilt azimuth after iteration #23 deviated from the initial tilt azimuth by 0.026000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #24 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.00532 for Iteration #24 of Tilt-Series #4. CCMS(rotations) = 0.28082 for Iteration #24 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #4. The scaled sum of CCMS values is #0.00827 for Tilt-Series #4. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... The tilt azimuth after iteration #24 deviated from the initial tilt azimuth by 0.070000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #25 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00496 for Iteration #25 of Tilt-Series #4. CCMS(rotations) = 0.1742 for Iteration #25 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #4. The scaled sum of CCMS values is #0.00596 for Tilt-Series #4. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... The tilt azimuth after iteration #25 deviated from the initial tilt azimuth by 0.103000, which is less than the maximum allowed deviation of 1.000000. Beginning Refinement Iteration #26, Round #4 of Tilt-Series #4 (tiltseries0004) lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.2203775 0.2203775 } map.sampling = 1 window.highpass.diameter = { 0.000718866462793 0.000718866462793 } window.highpass.apodization = { 0.00143743986955 0.00143743986955 } window.mask.apodization = { 10 10 } align.mask.width = { 2757 2853 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 401.049007379 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2782 2878 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2757 2853 } reference.body = 401.049007379 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00556 for Iteration #26 of Tilt-Series #4. CCMS(rotations) = 0.33357 for Iteration #26 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #4. The scaled sum of CCMS values is #0.00945 for Tilt-Series #4. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... The tilt azimuth after iteration #26 deviated from the initial tilt azimuth by 0.016000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #27 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00933 for Iteration #27 of Tilt-Series #4. CCMS(rotations) = 0.35226 for Iteration #27 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #4. The scaled sum of CCMS values is #0.01171 for Tilt-Series #4. Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... The tilt azimuth after iteration #27 deviated from the initial tilt azimuth by 0.004000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #28 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00627 for Iteration #28 of Tilt-Series #4. CCMS(rotations) = 0.2625 for Iteration #28 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #4. The scaled sum of CCMS values is #0.00838 for Tilt-Series #4. Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... The tilt azimuth after iteration #28 deviated from the initial tilt azimuth by 0.025000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #29 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00652 for Iteration #29 of Tilt-Series #4. CCMS(rotations) = 0.28913 for Iteration #29 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #4. The scaled sum of CCMS values is #0.00904 for Tilt-Series #4. Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... The tilt azimuth after iteration #29 deviated from the initial tilt azimuth by 0.070000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #30 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00534 for Iteration #30 of Tilt-Series #4. CCMS(rotations) = 0.31489 for Iteration #30 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #4. The scaled sum of CCMS values is #0.00897 for Tilt-Series #4. Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... The tilt azimuth after iteration #30 deviated from the initial tilt azimuth by 0.132000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #31 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 (tiltseries0004) fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00414 for Iteration #31 of Tilt-Series #4. CCMS(rotations) = 0.29187 for Iteration #31 of Tilt-Series #4. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #4. The scaled sum of CCMS values is #0.00791 for Tilt-Series #4. Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... The tilt azimuth after iteration #31 deviated from the initial tilt azimuth by 0.252000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #32 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00553 for Iteration #32 of Tilt-Series #4. CCMS(rotations) = 0.27541 for Iteration #32 of Tilt-Series #4. CCMS(scale) = 0.00152 for Iteration #32 of Tilt-Series #4. The scaled sum of CCMS values is #0.00602 for Tilt-Series #4. Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... The tilt azimuth after iteration #32 deviated from the initial tilt azimuth by 0.018000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #33 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00566 for Iteration #33 of Tilt-Series #4. CCMS(rotations) = 0.26774 for Iteration #33 of Tilt-Series #4. CCMS(scale) = 0.00205 for Iteration #33 of Tilt-Series #4. The scaled sum of CCMS values is #0.00614 for Tilt-Series #4. Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... The tilt azimuth after iteration #33 deviated from the initial tilt azimuth by 0.025000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #34 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00574 for Iteration #34 of Tilt-Series #4. CCMS(rotations) = 0.27282 for Iteration #34 of Tilt-Series #4. CCMS(scale) = 0.0027 for Iteration #34 of Tilt-Series #4. The scaled sum of CCMS values is #0.00645 for Tilt-Series #4. Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... The tilt azimuth after iteration #34 deviated from the initial tilt azimuth by 0.048000, which is less than the maximum allowed deviation of 1.000000. No Round parameters changed for Iteration #35 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00807 for Iteration #35 of Tilt-Series #4. CCMS(rotations) = 0.32549 for Iteration #35 of Tilt-Series #4. CCMS(scale) = 0.00224 for Iteration #35 of Tilt-Series #4. The scaled sum of CCMS values is #0.00778 for Tilt-Series #4. Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... The tilt azimuth after iteration #35 deviated from the initial tilt azimuth by 0.080000, which is less than the maximum allowed deviation of 1.000000.Finished Refinement for Tilt-Series #4 (tiltseries0004)! 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: 2017yr03m29d-12hr21m13s