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=14 --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=false --azimuth_switch=8 --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=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-23hr42m22s 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 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.03742 for Iteration #2 of Tilt-Series #4. CCMS(rotations) = 1.07921 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 #0.04029 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... Refinement Iteration #2 finished after retrying 2 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1680 Window Size (y) was windowed down to 1680 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)... Creating quality assessment statistics... CCMS(shift) = 0.04161 for Iteration #3 of Tilt-Series #4. CCMS(rotations) = 1.57124 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 #0.05223 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 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1728 Window Size (y) was windowed down to 1728 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)... Creating quality assessment statistics... CCMS(shift) = 0.04523 for Iteration #4 of Tilt-Series #4. CCMS(rotations) = 2.80874 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 #0.07879 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 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1568 Window Size (y) was windowed down to 1568 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)... Creating quality assessment statistics... CCMS(shift) = 0.07136 for Iteration #5 of Tilt-Series #4. CCMS(rotations) = 4.13615 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 #0.1184 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 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 #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)... Creating quality assessment statistics... CCMS(shift) = 0.06981 for Iteration #6 of Tilt-Series #4. CCMS(rotations) = 3.01117 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 #0.09513 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 16 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 896 Window Size (y) was windowed down to 896 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)... 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)... Creating quality assessment statistics... CCMS(shift) = 0.12611 for Iteration #7 of Tilt-Series #4. CCMS(rotations) = 4.30836 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 #0.14922 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 32 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 No Round parameters changed for Iteration #8 of Tilt-Series #4 (tiltseries0004) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #4 (tiltseries0004) fit.azimuth switched from false to true on Iteration #8Refinement 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) = 0.1198 for Iteration #8 of Tilt-Series #4. CCMS(rotations) = 8.83736 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 #0.23665 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 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 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)... 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)... Creating quality assessment statistics... CCMS(shift) = 0.11616 for Iteration #9 of Tilt-Series #4. CCMS(rotations) = 12.60907 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 #0.31026 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 35 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 256 Window Size (y) was windowed down to 256 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)... Refinement failed. Retry #72 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #73 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #74 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #75 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #76 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #77 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #78 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #79 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #80 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #81 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #82 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #83 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #84 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #85 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #86 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #87 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #88 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #89 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #90 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #91 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #92 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #93 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #94 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #95 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #96 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #97 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #98 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #99 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #100 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #101 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #102 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #103 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #104 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #105 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #106 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #107 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #108 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #109 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #110 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #111 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #112 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #113 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #114 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #115 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #116 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #117 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #118 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #119 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #120 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #121 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #122 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #123 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #124 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #125 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #126 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #127 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #128 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #129 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #130 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #131 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #132 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #133 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #134 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #135 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #136 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #137 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #138 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #139 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #140 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #141 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #142 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #143 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #144 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #145 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #146 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #147 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #148 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #149 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #150 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #151 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #152 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #153 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #154 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #155 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #156 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #157 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #158 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #159 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #160 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #161 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #162 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #163 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #164 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #165 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #166 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #167 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #168 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #169 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #170 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #171 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #172 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #173 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #174 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #175 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #176 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #177 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #178 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #179 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #180 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #181 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #182 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #183 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #184 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #185 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #186 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #187 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #188 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #189 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #190 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #191 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #192 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #193 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #194 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #195 with Window Size: (160, 160) (at sampling 8)... Refinement Iteration #10 for Tilt-Series #4 (tiltseries0004) failed after resampling the search area 195 time(s). Window Size (x) was windowed down to 160 Window Size (y) was windowed down to 160 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: 2017yr03m28d-00hr11m11s