protomo2aligner.py --parallel=True --starting_tlt_file=My_tlt_file --negative=-48 --positive=54 --r1_region_x=2878 --r2_region_x=2878 --r3_region_x=2878 --r4_region_x=2878 --r5_region_x=2878 --r1_region_y=2782 --r2_region_y=2782 --r3_region_y=2782 --r4_region_y=2782 --r5_region_y=2782 --r1_sampling=2 --r2_sampling=1 --r3_sampling=1 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=1414 --r2_mask_width_x=2853 --r3_mask_width_x=2853 --r4_mask_width_x=2853 --r5_mask_width_x=2853 --r1_mask_width_y=1366 --r2_mask_width_y=2757 --r3_mask_width_y=2757 --r4_mask_width_y=2757 --r5_mask_width_y=2757 --r1_lowpass_diameter_x=12.5 --r2_lowpass_diameter_x=6.25 --r3_lowpass_diameter_x=3.125 --r4_lowpass_diameter_x=3.125 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=12.5 --r2_lowpass_diameter_y=6.25 --r3_lowpass_diameter_y=3.125 --r4_lowpass_diameter_y=3.125 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=5107 --r2_highpass_diameter_x=5107 --r3_highpass_diameter_x=5107 --r4_highpass_diameter_x=5107 --r5_highpass_diameter_x=5107 --r1_highpass_diameter_y=5107 --r2_highpass_diameter_y=5107 --r3_highpass_diameter_y=5107 --r4_highpass_diameter_y=5107 --r5_highpass_diameter_y=5107 --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=31 --r2_lowpass_apod_x=16 --r3_lowpass_apod_x=8 --r4_lowpass_apod_x=8 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=31 --r2_lowpass_apod_y=16 --r3_lowpass_apod_y=8 --r4_lowpass_apod_y=8 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=2554 --r2_highpass_apod_x=2554 --r3_highpass_apod_x=2554 --r4_highpass_apod_x=2554 --r5_highpass_apod_x=2554 --r1_highpass_apod_y=2554 --r2_highpass_apod_y=2554 --r3_highpass_apod_y=2554 --r4_highpass_apod_y=2554 --r5_highpass_apod_y=2554 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=15 --r2_iters=10 --r3_iters=0 --r4_iters=0 --r5_iters=0 --preprocessing=true --tilt_azimuth=-79.4 --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=1000 --orientation=true --azimuth=false --azimuth_switch=8 --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=479 --map_size_y=463 --tilt_clip=true --video_type=html5vid --defocus_save=43811 --runname=tiltseries0047dc --rundir=/gpfs/appion/jbrasch/17feb10h/protomo_alignments/tiltseries0047dc --tiltseries=47 --sessionname=17feb10h --pixelsize=1.83586 --dimx=3838 --dimy=3710 --image_file_type=mrc --coarse=False --projectid=282 --expid=3450 --jobtype=protomo node07 Start time: 2017yr03m10d-16hr52m25s Description: Using user-provided tlt file series0047.tlt for Refinement.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #47 lowpass = 12.5 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms) window.lowpass.apodization = { 0.23688516129 0.23688516129 } map.sampling = 2 window.highpass.diameter = { 0.00143791658508 0.00143791658508 } window.highpass.apodization = { 0.00287527016445 0.00287527016445 } window.mask.apodization = { 10 10 } align.mask.width = { 1414 1366 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 694.945679823 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1439 1391 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1414 1366 } reference.body = 694.945679823 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.02077 for Iteration #1 of Tilt-Series #47. CCMS(rotations) = 0.48441 for Iteration #1 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #47. The scaled sum of CCMS values is #0.02007 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.031 for Iteration #2 of Tilt-Series #47. CCMS(rotations) = 0.48745 for Iteration #2 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #47. The scaled sum of CCMS values is #0.02525 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.02774 for Iteration #3 of Tilt-Series #47. CCMS(rotations) = 0.40668 for Iteration #3 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #47. The scaled sum of CCMS values is #0.022 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.0201 for Iteration #4 of Tilt-Series #47. CCMS(rotations) = 0.43582 for Iteration #4 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #47. The scaled sum of CCMS values is #0.01877 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01739 for Iteration #5 of Tilt-Series #47. CCMS(rotations) = 0.32431 for Iteration #5 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #47. The scaled sum of CCMS values is #0.01518 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.02309 for Iteration #6 of Tilt-Series #47. CCMS(rotations) = 0.53416 for Iteration #6 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #47. The scaled sum of CCMS values is #0.02223 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.0164 for Iteration #7 of Tilt-Series #47. CCMS(rotations) = 0.44414 for Iteration #7 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #47. The scaled sum of CCMS values is #0.01708 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #47 fit.azimuth switched from false to true on Iteration #8Creating quality assessment statistics... CCMS(shift) = 0.02442 for Iteration #8 of Tilt-Series #47. CCMS(rotations) = 0.52033 for Iteration #8 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #47. The scaled sum of CCMS values is #0.02262 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.02152 for Iteration #9 of Tilt-Series #47. CCMS(rotations) = 0.54151 for Iteration #9 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #47. The scaled sum of CCMS values is #0.02159 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.02113 for Iteration #10 of Tilt-Series #47. CCMS(rotations) = 0.46679 for Iteration #10 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #47. The scaled sum of CCMS values is #0.0199 for Tilt-Series #47. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... No Round parameters changed for Iteration #11 of Tilt-Series #47 Beginning Refinement Iteration #11, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.02536 for Iteration #11 of Tilt-Series #47. CCMS(rotations) = 0.56947 for Iteration #11 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #47. The scaled sum of CCMS values is #0.02407 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #12, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.02053 for Iteration #12 of Tilt-Series #47. CCMS(rotations) = 0.45532 for Iteration #12 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #47. The scaled sum of CCMS values is #0.01937 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #13, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01856 for Iteration #13 of Tilt-Series #47. CCMS(rotations) = 0.49869 for Iteration #13 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #47. The scaled sum of CCMS values is #0.01925 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #14, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.02154 for Iteration #14 of Tilt-Series #47. CCMS(rotations) = 0.5008 for Iteration #14 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #47. The scaled sum of CCMS values is #0.02079 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #15, Round #1 of Tilt-Series #47 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.03159 for Iteration #15 of Tilt-Series #47. CCMS(rotations) = 0.76778 for Iteration #15 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #47. The scaled sum of CCMS values is #0.03115 for Tilt-Series #47. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... Beginning Refinement Iteration #16, Round #2 of Tilt-Series #47 lowpass = 6.25 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms) window.lowpass.apodization = { 0.2294825 0.2294825 } map.sampling = 1 window.highpass.diameter = { 0.00071895829254 0.00071895829254 } window.highpass.apodization = { 0.00143763508222 0.00143763508222 } window.mask.apodization = { 10 10 } align.mask.width = { 2853 2757 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 1389.89135965 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2878 2782 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2853 2757 } reference.body = 1389.89135965 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.02486 for Iteration #16 of Tilt-Series #47. CCMS(rotations) = 0.54824 for Iteration #16 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #47. The scaled sum of CCMS values is #0.0234 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.02831 for Iteration #17 of Tilt-Series #47. CCMS(rotations) = 0.66283 for Iteration #17 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #47. The scaled sum of CCMS values is #0.02741 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.03333 for Iteration #18 of Tilt-Series #47. CCMS(rotations) = 0.54987 for Iteration #18 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #47. The scaled sum of CCMS values is #0.02766 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.03109 for Iteration #19 of Tilt-Series #47. CCMS(rotations) = 0.55373 for Iteration #19 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #47. The scaled sum of CCMS values is #0.02662 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.02886 for Iteration #20 of Tilt-Series #47. CCMS(rotations) = 0.65186 for Iteration #20 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #47. The scaled sum of CCMS values is #0.02747 for Tilt-Series #47. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... No Round parameters changed for Iteration #21 of Tilt-Series #47 Beginning Refinement Iteration #21, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.03394 for Iteration #21 of Tilt-Series #47. CCMS(rotations) = 0.62621 for Iteration #21 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #47. The scaled sum of CCMS values is #0.02949 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #22, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.02944 for Iteration #22 of Tilt-Series #47. CCMS(rotations) = 0.59609 for Iteration #22 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #47. The scaled sum of CCMS values is #0.02664 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #23, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.03703 for Iteration #23 of Tilt-Series #47. CCMS(rotations) = 0.70628 for Iteration #23 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #47. The scaled sum of CCMS values is #0.03264 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #24, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.02676 for Iteration #24 of Tilt-Series #47. CCMS(rotations) = 0.65181 for Iteration #24 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #47. The scaled sum of CCMS values is #0.02642 for Tilt-Series #47. 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 #47 Beginning Refinement Iteration #25, Round #2 of Tilt-Series #47 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.03774 for Iteration #25 of Tilt-Series #47. CCMS(rotations) = 0.70661 for Iteration #25 of Tilt-Series #47. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #47. The scaled sum of CCMS values is #0.033 for Tilt-Series #47. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Finished Refinement for Tilt-Series #47! 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: 2017yr03m12d-10hr50m23s