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=tiltseries0004 --rundir=/gpfs/appion/vdandey/17mar18a/protomo_alignments/tiltseries0004 --tiltseries=4 --sessionname=17mar18a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=1 --expid=3662 --jobtype=protomo node03 Start time: 2017yr03m20d-16hr28m58s Description: coarse_series0004_iter2.tlt not found, using coarse_series0004.tlt instead...Using Coarse alignment iteration 1 for Refinement by copying coarse_series0004.tlt to series0004.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #4 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 = 47.7004001531 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 = 47.7004001531 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.06401 for Iteration #1 of Tilt-Series #4. CCMS(rotations) = 1.63348 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 #0.06468 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... No Round parameters changed for Iteration #2 of Tilt-Series #4 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.00653 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 0.16216 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 #0.00651 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... No Round parameters changed for Iteration #3 of Tilt-Series #4 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00479 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 0.27003 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 #0.00779 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... No Round parameters changed for Iteration #4 of Tilt-Series #4 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.0043 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 0.20832 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 #0.00631 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... No Round parameters changed for Iteration #5 of Tilt-Series #4 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.00739 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 0.24631 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 #0.00862 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... No Round parameters changed for Iteration #6 of Tilt-Series #4 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00527 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 0.21081 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 #0.00685 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... No Round parameters changed for Iteration #7 of Tilt-Series #4 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.0073 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 0.20076 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 #0.00767 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... No Round parameters changed for Iteration #8 of Tilt-Series #4 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.0055 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 0.21013 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 #0.00695 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... No Round parameters changed for Iteration #9 of Tilt-Series #4 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.0072 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 0.18476 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 #0.00729 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... No Round parameters changed for Iteration #10 of Tilt-Series #4 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #4 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00588 for Iteration #10 of Tilt-Series #4. CCMS(rotations) = 0.21623 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 #0.00727 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... Beginning Refinement Iteration #11, Round #2 of Tilt-Series #4 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 = 95.4008003062 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 = 95.4008003062 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.00914 for Iteration #11 of Tilt-Series #4. CCMS(rotations) = 0.16265 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 #0.00782 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... No Round parameters changed for Iteration #12 of Tilt-Series #4 Beginning Refinement Iteration #12, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00504 for Iteration #12 of Tilt-Series #4. CCMS(rotations) = 0.20767 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 #0.00667 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... No Round parameters changed for Iteration #13 of Tilt-Series #4 Beginning Refinement Iteration #13, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.00507 for Iteration #13 of Tilt-Series #4. CCMS(rotations) = 0.23594 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 #0.00725 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... No Round parameters changed for Iteration #14 of Tilt-Series #4 Beginning Refinement Iteration #14, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00508 for Iteration #14 of Tilt-Series #4. CCMS(rotations) = 0.23055 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 #0.00715 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... No Round parameters changed for Iteration #15 of Tilt-Series #4 Beginning Refinement Iteration #15, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00495 for Iteration #15 of Tilt-Series #4. CCMS(rotations) = 0.18786 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 #0.00623 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... No Round parameters changed for Iteration #16 of Tilt-Series #4 Beginning Refinement Iteration #16, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00817 for Iteration #16 of Tilt-Series #4. CCMS(rotations) = 0.3079 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 #0.01024 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... No Round parameters changed for Iteration #17 of Tilt-Series #4 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.00597 for Iteration #17 of Tilt-Series #4. CCMS(rotations) = 0.14989 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 #0.00598 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... No Round parameters changed for Iteration #18 of Tilt-Series #4 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.0056 for Iteration #18 of Tilt-Series #4. CCMS(rotations) = 0.20346 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 #0.00687 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... No Round parameters changed for Iteration #19 of Tilt-Series #4 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.00605 for Iteration #19 of Tilt-Series #4. CCMS(rotations) = 0.2146 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 #0.00731 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... No Round parameters changed for Iteration #20 of Tilt-Series #4 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #4 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.00567 for Iteration #20 of Tilt-Series #4. CCMS(rotations) = 0.20956 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 #0.00703 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... Beginning Refinement Iteration #21, Round #3 of Tilt-Series #4 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 = 190.801600612 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 = 190.801600612 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.00668 for Iteration #21 of Tilt-Series #4. CCMS(rotations) = 0.23178 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 #0.00798 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... No Round parameters changed for Iteration #22 of Tilt-Series #4 Beginning Refinement Iteration #22, Round #3 of Tilt-Series #4 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.00486 for Iteration #22 of Tilt-Series #4. CCMS(rotations) = 0.18672 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 #0.00617 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... No Round parameters changed for Iteration #23 of Tilt-Series #4 Beginning Refinement Iteration #23, Round #3 of Tilt-Series #4 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00618 for Iteration #23 of Tilt-Series #4. CCMS(rotations) = 0.26363 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 #0.00836 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... No Round parameters changed for Iteration #24 of Tilt-Series #4 Beginning Refinement Iteration #24, Round #3 of Tilt-Series #4 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.0052 for Iteration #24 of Tilt-Series #4. CCMS(rotations) = 0.13109 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 #0.00522 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... No Round parameters changed for Iteration #25 of Tilt-Series #4 Beginning Refinement Iteration #25, Round #3 of Tilt-Series #4 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.00586 for Iteration #25 of Tilt-Series #4. CCMS(rotations) = 0.2408 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 #0.00775 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... Beginning Refinement Iteration #26, Round #4 of Tilt-Series #4 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 = 381.603201225 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 = 381.603201225 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.01061 for Iteration #26 of Tilt-Series #4. CCMS(rotations) = 0.25201 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 #0.01034 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... No Round parameters changed for Iteration #27 of Tilt-Series #4 Beginning Refinement Iteration #27, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.00581 for Iteration #27 of Tilt-Series #4. CCMS(rotations) = 0.11218 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 #0.00515 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... No Round parameters changed for Iteration #28 of Tilt-Series #4 Beginning Refinement Iteration #28, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.00746 for Iteration #28 of Tilt-Series #4. CCMS(rotations) = 0.2498 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 #0.00873 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... No Round parameters changed for Iteration #29 of Tilt-Series #4 Beginning Refinement Iteration #29, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.00638 for Iteration #29 of Tilt-Series #4. CCMS(rotations) = 0.34555 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 #0.0101 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... No Round parameters changed for Iteration #30 of Tilt-Series #4 Beginning Refinement Iteration #30, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.00762 for Iteration #30 of Tilt-Series #4. CCMS(rotations) = 0.18187 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 #0.00745 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... No Round parameters changed for Iteration #31 of Tilt-Series #4 Beginning Refinement Iteration #31, Round #4 of Tilt-Series #4 fit.scale switched from false to true on Iteration #31Creating quality assessment statistics... CCMS(shift) = 0.00679 for Iteration #31 of Tilt-Series #4. CCMS(rotations) = 0.18394 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 #0.00707 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... No Round parameters changed for Iteration #32 of Tilt-Series #4 Beginning Refinement Iteration #32, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00491 for Iteration #32 of Tilt-Series #4. CCMS(rotations) = 0.25328 for Iteration #32 of Tilt-Series #4. CCMS(scale) = 0.00261 for Iteration #32 of Tilt-Series #4. The scaled sum of CCMS values is #0.00588 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... No Round parameters changed for Iteration #33 of Tilt-Series #4 Beginning Refinement Iteration #33, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.00492 for Iteration #33 of Tilt-Series #4. CCMS(rotations) = 0.14129 for Iteration #33 of Tilt-Series #4. CCMS(scale) = 0.00225 for Iteration #33 of Tilt-Series #4. The scaled sum of CCMS values is #0.00427 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... No Round parameters changed for Iteration #34 of Tilt-Series #4 Beginning Refinement Iteration #34, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.00411 for Iteration #34 of Tilt-Series #4. CCMS(rotations) = 0.21814 for Iteration #34 of Tilt-Series #4. CCMS(scale) = 0.00299 for Iteration #34 of Tilt-Series #4. The scaled sum of CCMS values is #0.00527 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... No Round parameters changed for Iteration #35 of Tilt-Series #4 Beginning Refinement Iteration #35, Round #4 of Tilt-Series #4 No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.00474 for Iteration #35 of Tilt-Series #4. CCMS(rotations) = 0.20779 for Iteration #35 of Tilt-Series #4. CCMS(scale) = 0.00267 for Iteration #35 of Tilt-Series #4. The scaled sum of CCMS values is #0.00524 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... Finished Refinement for Tilt-Series #4! 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-04hr18m01s