protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=1855 --r2_region_x=1855 --r3_region_x=1855 --r4_region_x=1855 --r5_region_x=1855 --r1_region_y=1919 --r2_region_y=1919 --r3_region_y=1919 --r4_region_y=1919 --r5_region_y=1919 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=206 --r2_mask_width_x=438 --r3_mask_width_x=902 --r4_mask_width_x=1830 --r5_mask_width_x=1830 --r1_mask_width_y=214 --r2_mask_width_y=454 --r3_mask_width_y=934 --r4_mask_width_y=1894 --r5_mask_width_y=1894 --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=3270 --r2_highpass_diameter_x=3270 --r3_highpass_diameter_x=3270 --r4_highpass_diameter_x=3270 --r5_highpass_diameter_x=3270 --r1_highpass_diameter_y=3270 --r2_highpass_diameter_y=3270 --r3_highpass_diameter_y=3270 --r4_highpass_diameter_y=3270 --r5_highpass_diameter_y=3270 --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=1635 --r2_highpass_apod_x=1635 --r3_highpass_apod_x=1635 --r4_highpass_apod_x=1635 --r5_highpass_apod_x=1635 --r1_highpass_apod_y=1635 --r2_highpass_apod_y=1635 --r3_highpass_apod_y=1635 --r4_highpass_apod_y=1635 --r5_highpass_apod_y=1635 --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/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: 2017yr03m27d-13hr46m25s 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 = { 0.00862639755352 0.00862639755352 } window.highpass.apodization = { 0.017252795107 0.017252795107 } window.mask.apodization = { 10 10 } align.mask.width = { 206 214 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 150.393377767 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 231 239 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 206 214 } reference.body = 150.393377767 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.0371 for Iteration #1 of Tilt-Series #4. CCMS(rotations) = 0.59795 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 #0.03051 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 (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) = 0.03118 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 0.87236 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 #0.03304 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 (tiltseries0004) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #4 (tiltseries0004) No parameters were switched for Iteration #3 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.15437 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 3.61784 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 #0.14954 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... Refinement Iteration #3 finished after retrying 28 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 448 Window Size (y) was windowed down to 448 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.19703 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 6.37444 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 #0.226 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... Refinement Iteration #4 finished after retrying 33 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 320 Window Size (y) was windowed down to 320 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (160, 160) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.46625 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 9.04056 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 #0.41394 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... Refinement Iteration #5 finished after retrying 39 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 160 Window Size (y) was windowed down to 160 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #52 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #53 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #54 with Window Size: (960, 960) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.04298 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 10.4649 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 #0.23079 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... Refinement Iteration #6 finished after retrying 54 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 960 Window Size (y) was windowed down to 960 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.03901 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 11.19746 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 #0.24346 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... Refinement Iteration #7 finished after retrying 17 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 864 Window Size (y) was windowed down to 864 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.1073 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 11.46073 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 #0.28287 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... Refinement Iteration #8 finished after retrying 18 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 800 Window Size (y) was windowed down to 800 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.05653 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 8.55242 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 #0.19931 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... Refinement Iteration #9 finished after retrying 18 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 800 Window Size (y) was windowed down to 800 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #52 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #53 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #54 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #55 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #56 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #57 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #58 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #59 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #60 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #61 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #62 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #63 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #64 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #65 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #66 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #67 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #68 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #69 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #70 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #71 with Window Size: (336, 336) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.20861 for Iteration #10 of Tilt-Series #4. CCMS(rotations) = 9.17351 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 #0.28778 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... Refinement Iteration #10 finished after retrying 71 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 336 Window Size (y) was windowed down to 336 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 = { 0.00431319877676 0.00431319877676 } window.highpass.apodization = { 0.00862639755352 0.00862639755352 } window.mask.apodization = { 10 10 } align.mask.width = { 438 454 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 300.786755534 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 463 479 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 438 454 } reference.body = 300.786755534 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #11 Refinement failed. Retry #1 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (112, 112) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.582 for Iteration #11 of Tilt-Series #4. CCMS(rotations) = 16.36824 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 #0.61837 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... Refinement Iteration #11 finished after retrying 59 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 112 Window Size (y) was windowed down to 112 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 Refinement failed. Retry #1 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #60 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #61 with Window Size: (80, 80) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.50168 for Iteration #12 of Tilt-Series #4. CCMS(rotations) = 23.25253 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 #0.71589 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... Refinement Iteration #12 finished after retrying 61 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 80 Window Size (y) was windowed down to 80 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 Refinement failed. Retry #1 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (160, 160) (at sampling 4)... Creating quality assessment statistics... CCMS(shift) = 0.33086 for Iteration #13 of Tilt-Series #4. CCMS(rotations) = 18.96966 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 #0.54482 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... Refinement Iteration #13 finished after retrying 55 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 160 Window Size (y) was windowed down to 160 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 Refinement failed. Retry #1 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #2 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #3 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #4 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #5 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #6 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #7 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #8 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #9 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #10 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #11 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #12 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #13 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #14 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #15 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #16 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #17 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #18 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #19 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #20 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #21 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #22 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #23 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #24 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #25 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #26 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #27 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #28 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #29 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #30 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #31 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #32 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #33 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #34 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #35 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #36 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #37 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #38 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #39 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #40 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #41 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #42 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #43 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #44 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #45 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #46 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #47 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #48 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #49 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #50 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #51 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #52 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #53 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #54 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #55 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #56 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #57 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #58 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #59 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #60 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #61 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #62 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #63 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #64 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #65 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #66 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #67 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #68 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #69 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #70 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #71 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #72 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #73 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #74 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #75 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #76 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #77 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #78 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #79 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #80 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #81 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #82 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #83 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #84 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #85 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #86 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #87 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #88 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #89 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #90 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #91 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #92 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #93 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #94 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #95 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #96 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #97 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #98 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #99 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #100 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #101 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #102 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #103 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #104 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #105 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #106 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #107 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #108 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #109 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #110 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #111 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #112 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #113 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #114 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #115 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #116 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #117 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #118 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #119 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #120 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #121 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #122 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #123 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #124 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #125 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #126 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #127 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #128 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #129 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #130 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #131 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #132 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #133 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #134 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #135 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #136 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #137 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #138 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #139 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #140 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #141 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #142 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #143 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #144 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #145 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #146 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #147 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #148 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #149 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #150 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #151 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #152 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #153 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #154 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #155 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #156 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #157 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #158 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #159 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #160 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #161 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #162 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #163 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #164 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #165 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #166 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #167 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #168 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #169 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #170 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #171 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #172 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #173 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #174 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #175 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #176 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #177 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #178 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #179 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #180 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #181 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #182 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #183 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #184 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #185 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #186 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #187 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #188 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #189 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #190 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #191 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #192 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #193 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #194 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #195 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #196 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #197 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #198 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #199 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #200 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #201 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #202 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #203 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #204 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #205 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #206 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #207 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #208 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #209 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #210 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #211 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #212 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #213 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #214 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #215 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #216 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #217 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #218 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #219 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #220 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #221 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #222 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #223 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #224 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #225 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #226 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #227 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #228 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #229 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #230 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #231 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #232 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #233 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #234 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #235 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #236 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #237 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #238 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #239 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #240 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #241 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #242 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #243 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #244 with Window Size: (80, 80) (at sampling 4)... Refinement failed. Retry #245 with Window Size: (1792, 1792) (at sampling 4)... Refinement failed. Retry #246 with Window Size: (1728, 1728) (at sampling 4)... Refinement failed. Retry #247 with Window Size: (1680, 1680) (at sampling 4)... Refinement failed. Retry #248 with Window Size: (1600, 1600) (at sampling 4)... Refinement failed. Retry #249 with Window Size: (1568, 1568) (at sampling 4)... Refinement failed. Retry #250 with Window Size: (1536, 1536) (at sampling 4)... Refinement failed. Retry #251 with Window Size: (1512, 1512) (at sampling 4)... Refinement failed. Retry #252 with Window Size: (1440, 1440) (at sampling 4)... Refinement failed. Retry #253 with Window Size: (1400, 1400) (at sampling 4)... Refinement failed. Retry #254 with Window Size: (1344, 1344) (at sampling 4)... Refinement failed. Retry #255 with Window Size: (1296, 1296) (at sampling 4)... Refinement failed. Retry #256 with Window Size: (1280, 1280) (at sampling 4)... Refinement failed. Retry #257 with Window Size: (1200, 1200) (at sampling 4)... Refinement failed. Retry #258 with Window Size: (1176, 1176) (at sampling 4)... Refinement failed. Retry #259 with Window Size: (1152, 1152) (at sampling 4)... Refinement failed. Retry #260 with Window Size: (1120, 1120) (at sampling 4)... Refinement failed. Retry #261 with Window Size: (1080, 1080) (at sampling 4)... Refinement failed. Retry #262 with Window Size: (1024, 1024) (at sampling 4)... Refinement failed. Retry #263 with Window Size: (1008, 1008) (at sampling 4)... Refinement failed. Retry #264 with Window Size: (1000, 1000) (at sampling 4)... Refinement failed. Retry #265 with Window Size: (960, 960) (at sampling 4)... Refinement failed. Retry #266 with Window Size: (896, 896) (at sampling 4)... Refinement failed. Retry #267 with Window Size: (864, 864) (at sampling 4)... Refinement failed. Retry #268 with Window Size: (840, 840) (at sampling 4)... Refinement failed. Retry #269 with Window Size: (800, 800) (at sampling 4)... Refinement failed. Retry #270 with Window Size: (784, 784) (at sampling 4)... Refinement failed. Retry #271 with Window Size: (768, 768) (at sampling 4)... Refinement failed. Retry #272 with Window Size: (720, 720) (at sampling 4)... Refinement failed. Retry #273 with Window Size: (672, 672) (at sampling 4)... Refinement failed. Retry #274 with Window Size: (648, 648) (at sampling 4)... Refinement failed. Retry #275 with Window Size: (640, 640) (at sampling 4)... Refinement failed. Retry #276 with Window Size: (600, 600) (at sampling 4)... Refinement failed. Retry #277 with Window Size: (576, 576) (at sampling 4)... Refinement failed. Retry #278 with Window Size: (560, 560) (at sampling 4)... Refinement failed. Retry #279 with Window Size: (512, 512) (at sampling 4)... Refinement failed. Retry #280 with Window Size: (504, 504) (at sampling 4)... Refinement failed. Retry #281 with Window Size: (480, 480) (at sampling 4)... Refinement failed. Retry #282 with Window Size: (448, 448) (at sampling 4)... Refinement failed. Retry #283 with Window Size: (432, 432) (at sampling 4)... Refinement failed. Retry #284 with Window Size: (400, 400) (at sampling 4)... Refinement failed. Retry #285 with Window Size: (392, 392) (at sampling 4)... Refinement failed. Retry #286 with Window Size: (384, 384) (at sampling 4)... Refinement failed. Retry #287 with Window Size: (360, 360) (at sampling 4)... Refinement failed. Retry #288 with Window Size: (336, 336) (at sampling 4)... Refinement failed. Retry #289 with Window Size: (320, 320) (at sampling 4)... Refinement failed. Retry #290 with Window Size: (288, 288) (at sampling 4)... Refinement failed. Retry #291 with Window Size: (280, 280) (at sampling 4)... Refinement failed. Retry #292 with Window Size: (256, 256) (at sampling 4)... Refinement failed. Retry #293 with Window Size: (240, 240) (at sampling 4)... Refinement failed. Retry #294 with Window Size: (224, 224) (at sampling 4)... Refinement failed. Retry #295 with Window Size: (216, 216) (at sampling 4)... Refinement failed. Retry #296 with Window Size: (200, 200) (at sampling 4)... Refinement failed. Retry #297 with Window Size: (192, 192) (at sampling 4)... Refinement failed. Retry #298 with Window Size: (168, 168) (at sampling 4)... Refinement failed. Retry #299 with Window Size: (160, 160) (at sampling 4)... Refinement failed. Retry #300 with Window Size: (144, 144) (at sampling 4)... Refinement failed. Retry #301 with Window Size: (128, 128) (at sampling 4)... Refinement failed. Retry #302 with Window Size: (120, 120) (at sampling 4)... Refinement failed. Retry #303 with Window Size: (112, 112) (at sampling 4)... Refinement failed. Retry #304 with Window Size: (96, 96) (at sampling 4)... Refinement failed. Retry #305 with Window Size: (80, 80) (at sampling 4)... Refinement Iteration #14 for Tilt-Series #4 (tiltseries0004) failed after resampling the search area 305 time(s). Window Size (x) was windowed down to 80 Window Size (y) was windowed down to 80 Put values less than these into the corresponding parameter boxes on the Protomo Refinement Appion webpage and try again. 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: 2017yr03m27d-14hr47m35s