protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=2226 --r2_region_x=2226 --r3_region_x=2226 --r4_region_x=2226 --r5_region_x=2226 --r1_region_y=2302 --r2_region_y=2302 --r3_region_y=2302 --r4_region_y=2302 --r5_region_y=2302 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=500 --r1_mask_width_x=253 --r2_mask_width_x=531 --r3_mask_width_x=1088 --r4_mask_width_x=2201 --r5_mask_width_x=2201 --r1_mask_width_y=262 --r2_mask_width_y=550 --r3_mask_width_y=1126 --r4_mask_width_y=2277 --r5_mask_width_y=2277 --r1_lowpass_diameter_x=50 --r2_lowpass_diameter_x=25 --r3_lowpass_diameter_x=12.5 --r4_lowpass_diameter_x=6.25 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=50 --r2_lowpass_diameter_y=25 --r3_lowpass_diameter_y=12.5 --r4_lowpass_diameter_y=6.25 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=3924 --r2_highpass_diameter_x=3924 --r3_highpass_diameter_x=3924 --r4_highpass_diameter_x=3924 --r5_highpass_diameter_x=3924 --r1_highpass_diameter_y=3924 --r2_highpass_diameter_y=3924 --r3_highpass_diameter_y=3924 --r4_highpass_diameter_y=3924 --r5_highpass_diameter_y=3924 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=125 --r2_lowpass_apod_x=63 --r3_lowpass_apod_x=31 --r4_lowpass_apod_x=16 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=125 --r2_lowpass_apod_y=63 --r3_lowpass_apod_y=31 --r4_lowpass_apod_y=16 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=1962 --r2_highpass_apod_x=1962 --r3_highpass_apod_x=1962 --r4_highpass_apod_x=1962 --r5_highpass_apod_x=1962 --r1_highpass_apod_y=1962 --r2_highpass_apod_y=1962 --r3_highpass_apod_y=1962 --r4_highpass_apod_y=1962 --r5_highpass_apod_y=1962 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=20 --r2_iters=20 --r3_iters=20 --r4_iters=40 --r5_iters=20 --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=81 --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=tiltseries0003 --rundir=/gpfs/appion/jbrasch/17mar17a/protomo_alignments/tiltseries0003 --tiltseries=3 --sessionname=17mar17a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=282 --expid=3656 --jobtype=protomo node05 Start time: 2017yr03m24d-14hr10m18s Description: Using Manual alignment for Refinement by copying manual_series0003.tlt to series0003.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #3 (tiltseries0003) lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00718866462793 0.00718866462793 } window.highpass.apodization = { 0.0143773292559 0.0143773292559 } window.mask.apodization = { 10 10 } align.mask.width = { 253 262 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 50.1311259224 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 278 287 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 253 262 } reference.body = 50.1311259224 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.0469 for Iteration #1 of Tilt-Series #3. CCMS(rotations) = 0.77763 for Iteration #1 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #3. The scaled sum of CCMS values is #0.039 for Tilt-Series #3. 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 #3 (tiltseries0003) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.05148 for Iteration #2 of Tilt-Series #3. CCMS(rotations) = 1.00158 for Iteration #2 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #3. The scaled sum of CCMS values is #0.04577 for Tilt-Series #3. 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 #3 (tiltseries0003) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.04783 for Iteration #3 of Tilt-Series #3. CCMS(rotations) = 0.84232 for Iteration #3 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #3. The scaled sum of CCMS values is #0.04076 for Tilt-Series #3. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... No Round parameters changed for Iteration #4 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #4, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.04643 for Iteration #4 of Tilt-Series #3. CCMS(rotations) = 0.8409 for Iteration #4 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #3. The scaled sum of CCMS values is #0.04003 for Tilt-Series #3. Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #5, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.03981 for Iteration #5 of Tilt-Series #3. CCMS(rotations) = 0.68065 for Iteration #5 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #3. The scaled sum of CCMS values is #0.03352 for Tilt-Series #3. Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #6, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.01352 for Iteration #6 of Tilt-Series #3. CCMS(rotations) = 0.20257 for Iteration #6 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #3. The scaled sum of CCMS values is #0.01081 for Tilt-Series #3. Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #7, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.01066 for Iteration #7 of Tilt-Series #3. CCMS(rotations) = 0.259 for Iteration #7 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #3. The scaled sum of CCMS values is #0.01051 for Tilt-Series #3. Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #8, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.01206 for Iteration #8 of Tilt-Series #3. CCMS(rotations) = 0.27658 for Iteration #8 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #3. The scaled sum of CCMS values is #0.01156 for Tilt-Series #3. Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... No Round parameters changed for Iteration #9 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #9, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01146 for Iteration #9 of Tilt-Series #3. CCMS(rotations) = 0.25899 for Iteration #9 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #3. The scaled sum of CCMS values is #0.01091 for Tilt-Series #3. Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... No Round parameters changed for Iteration #10 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #10, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.01104 for Iteration #10 of Tilt-Series #3. CCMS(rotations) = 0.28414 for Iteration #10 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #3. The scaled sum of CCMS values is #0.0112 for Tilt-Series #3. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... No Round parameters changed for Iteration #11 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #11, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01203 for Iteration #11 of Tilt-Series #3. CCMS(rotations) = 0.31734 for Iteration #11 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #3. The scaled sum of CCMS values is #0.01236 for Tilt-Series #3. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #12, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.01201 for Iteration #12 of Tilt-Series #3. CCMS(rotations) = 0.30811 for Iteration #12 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #3. The scaled sum of CCMS values is #0.01217 for Tilt-Series #3. Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #13, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01387 for Iteration #13 of Tilt-Series #3. CCMS(rotations) = 0.28139 for Iteration #13 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #3. The scaled sum of CCMS values is #0.01256 for Tilt-Series #3. Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... No Round parameters changed for Iteration #14 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #14, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.01375 for Iteration #14 of Tilt-Series #3. CCMS(rotations) = 0.29118 for Iteration #14 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #3. The scaled sum of CCMS values is #0.0127 for Tilt-Series #3. Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #15, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.01388 for Iteration #15 of Tilt-Series #3. CCMS(rotations) = 0.23231 for Iteration #15 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #3. The scaled sum of CCMS values is #0.01159 for Tilt-Series #3. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... No Round parameters changed for Iteration #16 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #16, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.01411 for Iteration #16 of Tilt-Series #3. CCMS(rotations) = 0.2775 for Iteration #16 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #3. The scaled sum of CCMS values is #0.0126 for Tilt-Series #3. Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... No Round parameters changed for Iteration #17 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #17, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.01484 for Iteration #17 of Tilt-Series #3. CCMS(rotations) = 0.29671 for Iteration #17 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #3. The scaled sum of CCMS values is #0.01335 for Tilt-Series #3. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... No Round parameters changed for Iteration #18 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #18, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.0142 for Iteration #18 of Tilt-Series #3. CCMS(rotations) = 0.3493 for Iteration #18 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #3. The scaled sum of CCMS values is #0.01409 for Tilt-Series #3. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #19, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.01531 for Iteration #19 of Tilt-Series #3. CCMS(rotations) = 0.23505 for Iteration #19 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #3. The scaled sum of CCMS values is #0.01236 for Tilt-Series #3. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #20, Round #1 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.01513 for Iteration #20 of Tilt-Series #3. CCMS(rotations) = 0.39413 for Iteration #20 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #3. The scaled sum of CCMS values is #0.01545 for Tilt-Series #3. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... Beginning Refinement Iteration #21, Round #2 of Tilt-Series #3 (tiltseries0003) lowpass = 25.0 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 4, pixelsize is 7.05208 Angstroms, Nyquist is 14.10416 Angstroms) window.lowpass.apodization = { 0.223875555556 0.223875555556 } map.sampling = 4 window.highpass.diameter = { 0.00359433231397 0.00359433231397 } window.highpass.apodization = { 0.00718866462793 0.00718866462793 } window.mask.apodization = { 10 10 } align.mask.width = { 531 550 } sampling = 4 align.mask.apodization = { 10 10 } map.body = 100.262251845 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 556 575 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 531 550 } reference.body = 100.262251845 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.01084 for Iteration #21 of Tilt-Series #3. CCMS(rotations) = 0.31253 for Iteration #21 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #3. The scaled sum of CCMS values is #0.01167 for Tilt-Series #3. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... No Round parameters changed for Iteration #22 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #22, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.01468 for Iteration #22 of Tilt-Series #3. CCMS(rotations) = 0.30295 for Iteration #22 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #3. The scaled sum of CCMS values is #0.0134 for Tilt-Series #3. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... No Round parameters changed for Iteration #23 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #23, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.00851 for Iteration #23 of Tilt-Series #3. CCMS(rotations) = 0.28963 for Iteration #23 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #3. The scaled sum of CCMS values is #0.01005 for Tilt-Series #3. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... No Round parameters changed for Iteration #24 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #24, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.01038 for Iteration #24 of Tilt-Series #3. CCMS(rotations) = 0.24073 for Iteration #24 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #3. The scaled sum of CCMS values is #0.01 for Tilt-Series #3. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... No Round parameters changed for Iteration #25 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #25, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.01179 for Iteration #25 of Tilt-Series #3. CCMS(rotations) = 0.26435 for Iteration #25 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #3. The scaled sum of CCMS values is #0.01118 for Tilt-Series #3. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... No Round parameters changed for Iteration #26 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #26, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #26 Creating quality assessment statistics... CCMS(shift) = 0.00946 for Iteration #26 of Tilt-Series #3. CCMS(rotations) = 0.19366 for Iteration #26 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #26 of Tilt-Series #3. The scaled sum of CCMS values is #0.0086 for Tilt-Series #3. Creating Depiction Videos for Iteration #26 in Parallel... Creating Refinement tilt-series video for iteration #26... Generating Refinement reconstruction for iteration #26... No Round parameters changed for Iteration #27 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #27, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #27 Creating quality assessment statistics... CCMS(shift) = 0.01332 for Iteration #27 of Tilt-Series #3. CCMS(rotations) = 0.18072 for Iteration #27 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #27 of Tilt-Series #3. The scaled sum of CCMS values is #0.01028 for Tilt-Series #3. Creating Depiction Videos for Iteration #27 in Parallel... Creating Refinement tilt-series video for iteration #27... Generating Refinement reconstruction for iteration #27... No Round parameters changed for Iteration #28 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #28, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #28 Creating quality assessment statistics... CCMS(shift) = 0.01436 for Iteration #28 of Tilt-Series #3. CCMS(rotations) = 0.24454 for Iteration #28 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #28 of Tilt-Series #3. The scaled sum of CCMS values is #0.01207 for Tilt-Series #3. Creating Depiction Videos for Iteration #28 in Parallel... Creating Refinement tilt-series video for iteration #28... Generating Refinement reconstruction for iteration #28... No Round parameters changed for Iteration #29 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #29, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #29 Creating quality assessment statistics... CCMS(shift) = 0.01501 for Iteration #29 of Tilt-Series #3. CCMS(rotations) = 0.26129 for Iteration #29 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #29 of Tilt-Series #3. The scaled sum of CCMS values is #0.01273 for Tilt-Series #3. Creating Depiction Videos for Iteration #29 in Parallel... Creating Refinement tilt-series video for iteration #29... Generating Refinement reconstruction for iteration #29... No Round parameters changed for Iteration #30 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #30, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #30 Creating quality assessment statistics... CCMS(shift) = 0.01191 for Iteration #30 of Tilt-Series #3. CCMS(rotations) = 0.22262 for Iteration #30 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #30 of Tilt-Series #3. The scaled sum of CCMS values is #0.01041 for Tilt-Series #3. Creating Depiction Videos for Iteration #30 in Parallel... Creating Refinement tilt-series video for iteration #30... Generating Refinement reconstruction for iteration #30... No Round parameters changed for Iteration #31 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #31, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #31 Creating quality assessment statistics... CCMS(shift) = 0.01026 for Iteration #31 of Tilt-Series #3. CCMS(rotations) = 0.24862 for Iteration #31 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #31 of Tilt-Series #3. The scaled sum of CCMS values is #0.0101 for Tilt-Series #3. Creating Depiction Videos for Iteration #31 in Parallel... Creating Refinement tilt-series video for iteration #31... Generating Refinement reconstruction for iteration #31... No Round parameters changed for Iteration #32 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #32, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #32 Creating quality assessment statistics... CCMS(shift) = 0.00808 for Iteration #32 of Tilt-Series #3. CCMS(rotations) = 0.21888 for Iteration #32 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #32 of Tilt-Series #3. The scaled sum of CCMS values is #0.00842 for Tilt-Series #3. Creating Depiction Videos for Iteration #32 in Parallel... Creating Refinement tilt-series video for iteration #32... Generating Refinement reconstruction for iteration #32... No Round parameters changed for Iteration #33 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #33, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #33 Creating quality assessment statistics... CCMS(shift) = 0.01111 for Iteration #33 of Tilt-Series #3. CCMS(rotations) = 0.21201 for Iteration #33 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #33 of Tilt-Series #3. The scaled sum of CCMS values is #0.00979 for Tilt-Series #3. Creating Depiction Videos for Iteration #33 in Parallel... Creating Refinement tilt-series video for iteration #33... Generating Refinement reconstruction for iteration #33... No Round parameters changed for Iteration #34 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #34, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #34 Creating quality assessment statistics... CCMS(shift) = 0.01025 for Iteration #34 of Tilt-Series #3. CCMS(rotations) = 0.22686 for Iteration #34 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #34 of Tilt-Series #3. The scaled sum of CCMS values is #0.00966 for Tilt-Series #3. Creating Depiction Videos for Iteration #34 in Parallel... Creating Refinement tilt-series video for iteration #34... Generating Refinement reconstruction for iteration #34... No Round parameters changed for Iteration #35 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #35, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #35 Creating quality assessment statistics... CCMS(shift) = 0.01319 for Iteration #35 of Tilt-Series #3. CCMS(rotations) = 0.18897 for Iteration #35 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #35 of Tilt-Series #3. The scaled sum of CCMS values is #0.01038 for Tilt-Series #3. Creating Depiction Videos for Iteration #35 in Parallel... Creating Refinement tilt-series video for iteration #35... Generating Refinement reconstruction for iteration #35... No Round parameters changed for Iteration #36 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #36, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #36 Creating quality assessment statistics... CCMS(shift) = 0.01231 for Iteration #36 of Tilt-Series #3. CCMS(rotations) = 0.20002 for Iteration #36 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #36 of Tilt-Series #3. The scaled sum of CCMS values is #0.01015 for Tilt-Series #3. Creating Depiction Videos for Iteration #36 in Parallel... Creating Refinement tilt-series video for iteration #36... Generating Refinement reconstruction for iteration #36... No Round parameters changed for Iteration #37 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #37, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #37 Creating quality assessment statistics... CCMS(shift) = 0.00927 for Iteration #37 of Tilt-Series #3. CCMS(rotations) = 0.31363 for Iteration #37 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #37 of Tilt-Series #3. The scaled sum of CCMS values is #0.01091 for Tilt-Series #3. Creating Depiction Videos for Iteration #37 in Parallel... Creating Refinement tilt-series video for iteration #37... Generating Refinement reconstruction for iteration #37... No Round parameters changed for Iteration #38 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #38, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #38 Creating quality assessment statistics... CCMS(shift) = 0.01027 for Iteration #38 of Tilt-Series #3. CCMS(rotations) = 0.36204 for Iteration #38 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #38 of Tilt-Series #3. The scaled sum of CCMS values is #0.01237 for Tilt-Series #3. Creating Depiction Videos for Iteration #38 in Parallel... Creating Refinement tilt-series video for iteration #38... Generating Refinement reconstruction for iteration #38... No Round parameters changed for Iteration #39 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #39, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #39 Creating quality assessment statistics... CCMS(shift) = 0.00925 for Iteration #39 of Tilt-Series #3. CCMS(rotations) = 0.34005 for Iteration #39 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #39 of Tilt-Series #3. The scaled sum of CCMS values is #0.01142 for Tilt-Series #3. Creating Depiction Videos for Iteration #39 in Parallel... Creating Refinement tilt-series video for iteration #39... Generating Refinement reconstruction for iteration #39... No Round parameters changed for Iteration #40 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #40, Round #2 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #40 Creating quality assessment statistics... CCMS(shift) = 0.00977 for Iteration #40 of Tilt-Series #3. CCMS(rotations) = 0.30507 for Iteration #40 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #40 of Tilt-Series #3. The scaled sum of CCMS values is #0.01099 for Tilt-Series #3. Creating Depiction Videos for Iteration #40 in Parallel... Creating Refinement tilt-series video for iteration #40... Generating Refinement reconstruction for iteration #40... Beginning Refinement Iteration #41, Round #3 of Tilt-Series #3 (tiltseries0003) lowpass = 12.5 angstroms Round #3. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.52604 Angstroms, Nyquist is 7.05208 Angstroms) window.lowpass.apodization = { 0.227486451613 0.227486451613 } map.sampling = 2 window.highpass.diameter = { 0.00179716615698 0.00179716615698 } window.highpass.apodization = { 0.00359433231397 0.00359433231397 } window.mask.apodization = { 10 10 } align.mask.width = { 1088 1126 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 200.52450369 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1113 1151 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1088 1126 } reference.body = 200.52450369 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #41 Creating quality assessment statistics... CCMS(shift) = 0.01127 for Iteration #41 of Tilt-Series #3. CCMS(rotations) = 0.30724 for Iteration #41 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #41 of Tilt-Series #3. The scaled sum of CCMS values is #0.01178 for Tilt-Series #3. Creating Depiction Videos for Iteration #41 in Parallel... Creating Refinement tilt-series video for iteration #41... Generating Refinement reconstruction for iteration #41... No Round parameters changed for Iteration #42 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #42, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #42 Creating quality assessment statistics... CCMS(shift) = 0.01754 for Iteration #42 of Tilt-Series #3. CCMS(rotations) = 0.35908 for Iteration #42 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #42 of Tilt-Series #3. The scaled sum of CCMS values is #0.01595 for Tilt-Series #3. Creating Depiction Videos for Iteration #42 in Parallel... Creating Refinement tilt-series video for iteration #42... Generating Refinement reconstruction for iteration #42... No Round parameters changed for Iteration #43 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #43, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #43 Creating quality assessment statistics... CCMS(shift) = 0.01432 for Iteration #43 of Tilt-Series #3. CCMS(rotations) = 0.45336 for Iteration #43 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #43 of Tilt-Series #3. The scaled sum of CCMS values is #0.01623 for Tilt-Series #3. Creating Depiction Videos for Iteration #43 in Parallel... Creating Refinement tilt-series video for iteration #43... Generating Refinement reconstruction for iteration #43... No Round parameters changed for Iteration #44 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #44, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #44 Creating quality assessment statistics... CCMS(shift) = 0.0108 for Iteration #44 of Tilt-Series #3. CCMS(rotations) = 0.56536 for Iteration #44 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #44 of Tilt-Series #3. The scaled sum of CCMS values is #0.01671 for Tilt-Series #3. Creating Depiction Videos for Iteration #44 in Parallel... Creating Refinement tilt-series video for iteration #44... Generating Refinement reconstruction for iteration #44... No Round parameters changed for Iteration #45 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #45, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #45 Creating quality assessment statistics... CCMS(shift) = 0.0076 for Iteration #45 of Tilt-Series #3. CCMS(rotations) = 0.29506 for Iteration #45 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #45 of Tilt-Series #3. The scaled sum of CCMS values is #0.0097 for Tilt-Series #3. Creating Depiction Videos for Iteration #45 in Parallel... Creating Refinement tilt-series video for iteration #45... Generating Refinement reconstruction for iteration #45... No Round parameters changed for Iteration #46 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #46, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #46 Creating quality assessment statistics... CCMS(shift) = 0.01019 for Iteration #46 of Tilt-Series #3. CCMS(rotations) = 0.37 for Iteration #46 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #46 of Tilt-Series #3. The scaled sum of CCMS values is #0.01249 for Tilt-Series #3. Creating Depiction Videos for Iteration #46 in Parallel... Creating Refinement tilt-series video for iteration #46... Generating Refinement reconstruction for iteration #46... No Round parameters changed for Iteration #47 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #47, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #47 Creating quality assessment statistics... CCMS(shift) = 0.01142 for Iteration #47 of Tilt-Series #3. CCMS(rotations) = 0.17592 for Iteration #47 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #47 of Tilt-Series #3. The scaled sum of CCMS values is #0.00923 for Tilt-Series #3. Creating Depiction Videos for Iteration #47 in Parallel... Creating Refinement tilt-series video for iteration #47... Generating Refinement reconstruction for iteration #47... No Round parameters changed for Iteration #48 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #48, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #48 Creating quality assessment statistics... CCMS(shift) = 0.00993 for Iteration #48 of Tilt-Series #3. CCMS(rotations) = 0.27927 for Iteration #48 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #48 of Tilt-Series #3. The scaled sum of CCMS values is #0.01055 for Tilt-Series #3. Creating Depiction Videos for Iteration #48 in Parallel... Creating Refinement tilt-series video for iteration #48... Generating Refinement reconstruction for iteration #48... No Round parameters changed for Iteration #49 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #49, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #49 Creating quality assessment statistics... CCMS(shift) = 0.0097 for Iteration #49 of Tilt-Series #3. CCMS(rotations) = 0.27958 for Iteration #49 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #49 of Tilt-Series #3. The scaled sum of CCMS values is #0.01044 for Tilt-Series #3. Creating Depiction Videos for Iteration #49 in Parallel... Creating Refinement tilt-series video for iteration #49... Generating Refinement reconstruction for iteration #49... No Round parameters changed for Iteration #50 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #50, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #50 Creating quality assessment statistics... CCMS(shift) = 0.00845 for Iteration #50 of Tilt-Series #3. CCMS(rotations) = 0.37541 for Iteration #50 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #50 of Tilt-Series #3. The scaled sum of CCMS values is #0.01173 for Tilt-Series #3. Creating Depiction Videos for Iteration #50 in Parallel... Creating Refinement tilt-series video for iteration #50... Generating Refinement reconstruction for iteration #50... No Round parameters changed for Iteration #51 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #51, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #51 Creating quality assessment statistics... CCMS(shift) = 0.00821 for Iteration #51 of Tilt-Series #3. CCMS(rotations) = 0.38265 for Iteration #51 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #51 of Tilt-Series #3. The scaled sum of CCMS values is #0.01176 for Tilt-Series #3. Creating Depiction Videos for Iteration #51 in Parallel... Creating Refinement tilt-series video for iteration #51... Generating Refinement reconstruction for iteration #51... No Round parameters changed for Iteration #52 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #52, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #52 Creating quality assessment statistics... CCMS(shift) = 0.00793 for Iteration #52 of Tilt-Series #3. CCMS(rotations) = 0.36105 for Iteration #52 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #52 of Tilt-Series #3. The scaled sum of CCMS values is #0.01119 for Tilt-Series #3. Creating Depiction Videos for Iteration #52 in Parallel... Creating Refinement tilt-series video for iteration #52... Generating Refinement reconstruction for iteration #52... No Round parameters changed for Iteration #53 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #53, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #53 Creating quality assessment statistics... CCMS(shift) = 0.00781 for Iteration #53 of Tilt-Series #3. CCMS(rotations) = 0.34867 for Iteration #53 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #53 of Tilt-Series #3. The scaled sum of CCMS values is #0.01088 for Tilt-Series #3. Creating Depiction Videos for Iteration #53 in Parallel... Creating Refinement tilt-series video for iteration #53... Generating Refinement reconstruction for iteration #53... No Round parameters changed for Iteration #54 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #54, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #54 Creating quality assessment statistics... CCMS(shift) = 0.00891 for Iteration #54 of Tilt-Series #3. CCMS(rotations) = 0.29342 for Iteration #54 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #54 of Tilt-Series #3. The scaled sum of CCMS values is #0.01033 for Tilt-Series #3. Creating Depiction Videos for Iteration #54 in Parallel... Creating Refinement tilt-series video for iteration #54... Generating Refinement reconstruction for iteration #54... No Round parameters changed for Iteration #55 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #55, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #55 Creating quality assessment statistics... CCMS(shift) = 0.01016 for Iteration #55 of Tilt-Series #3. CCMS(rotations) = 0.25236 for Iteration #55 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #55 of Tilt-Series #3. The scaled sum of CCMS values is #0.01013 for Tilt-Series #3. Creating Depiction Videos for Iteration #55 in Parallel... Creating Refinement tilt-series video for iteration #55... Generating Refinement reconstruction for iteration #55... No Round parameters changed for Iteration #56 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #56, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #56 Creating quality assessment statistics... CCMS(shift) = 0.009 for Iteration #56 of Tilt-Series #3. CCMS(rotations) = 0.32812 for Iteration #56 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #56 of Tilt-Series #3. The scaled sum of CCMS values is #0.01106 for Tilt-Series #3. Creating Depiction Videos for Iteration #56 in Parallel... Creating Refinement tilt-series video for iteration #56... Generating Refinement reconstruction for iteration #56... No Round parameters changed for Iteration #57 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #57, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #57 Creating quality assessment statistics... CCMS(shift) = 0.01126 for Iteration #57 of Tilt-Series #3. CCMS(rotations) = 0.30411 for Iteration #57 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #57 of Tilt-Series #3. The scaled sum of CCMS values is #0.01171 for Tilt-Series #3. Creating Depiction Videos for Iteration #57 in Parallel... Creating Refinement tilt-series video for iteration #57... Generating Refinement reconstruction for iteration #57... No Round parameters changed for Iteration #58 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #58, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #58 Creating quality assessment statistics... CCMS(shift) = 0.01071 for Iteration #58 of Tilt-Series #3. CCMS(rotations) = 0.32366 for Iteration #58 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #58 of Tilt-Series #3. The scaled sum of CCMS values is #0.01183 for Tilt-Series #3. Creating Depiction Videos for Iteration #58 in Parallel... Creating Refinement tilt-series video for iteration #58... Generating Refinement reconstruction for iteration #58... No Round parameters changed for Iteration #59 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #59, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #59 Creating quality assessment statistics... CCMS(shift) = 0.00792 for Iteration #59 of Tilt-Series #3. CCMS(rotations) = 0.32002 for Iteration #59 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #59 of Tilt-Series #3. The scaled sum of CCMS values is #0.01036 for Tilt-Series #3. Creating Depiction Videos for Iteration #59 in Parallel... Creating Refinement tilt-series video for iteration #59... Generating Refinement reconstruction for iteration #59... No Round parameters changed for Iteration #60 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #60, Round #3 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #60 Creating quality assessment statistics... CCMS(shift) = 0.00836 for Iteration #60 of Tilt-Series #3. CCMS(rotations) = 0.28901 for Iteration #60 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #60 of Tilt-Series #3. The scaled sum of CCMS values is #0.00996 for Tilt-Series #3. Creating Depiction Videos for Iteration #60 in Parallel... Creating Refinement tilt-series video for iteration #60... Generating Refinement reconstruction for iteration #60... Beginning Refinement Iteration #61, Round #4 of Tilt-Series #3 (tiltseries0003) lowpass = 6.25 angstroms Round #4. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.2203775 0.2203775 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 401.049007379 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 401.049007379 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #61 Creating quality assessment statistics... CCMS(shift) = 0.01669 for Iteration #61 of Tilt-Series #3. CCMS(rotations) = 0.26425 for Iteration #61 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #61 of Tilt-Series #3. The scaled sum of CCMS values is #0.01363 for Tilt-Series #3. Creating Depiction Videos for Iteration #61 in Parallel... Creating Refinement tilt-series video for iteration #61... Generating Refinement reconstruction for iteration #61... No Round parameters changed for Iteration #62 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #62, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #62 Creating quality assessment statistics... CCMS(shift) = 0.0176 for Iteration #62 of Tilt-Series #3. CCMS(rotations) = 0.32917 for Iteration #62 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #62 of Tilt-Series #3. The scaled sum of CCMS values is #0.01538 for Tilt-Series #3. Creating Depiction Videos for Iteration #62 in Parallel... Creating Refinement tilt-series video for iteration #62... Generating Refinement reconstruction for iteration #62... No Round parameters changed for Iteration #63 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #63, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #63 Creating quality assessment statistics... CCMS(shift) = 0.01603 for Iteration #63 of Tilt-Series #3. CCMS(rotations) = 0.28593 for Iteration #63 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #63 of Tilt-Series #3. The scaled sum of CCMS values is #0.01374 for Tilt-Series #3. Creating Depiction Videos for Iteration #63 in Parallel... Creating Refinement tilt-series video for iteration #63... Generating Refinement reconstruction for iteration #63... No Round parameters changed for Iteration #64 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #64, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #64 Creating quality assessment statistics... CCMS(shift) = 0.01362 for Iteration #64 of Tilt-Series #3. CCMS(rotations) = 0.42084 for Iteration #64 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #64 of Tilt-Series #3. The scaled sum of CCMS values is #0.01523 for Tilt-Series #3. Creating Depiction Videos for Iteration #64 in Parallel... Creating Refinement tilt-series video for iteration #64... Generating Refinement reconstruction for iteration #64... No Round parameters changed for Iteration #65 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #65, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #65 Creating quality assessment statistics... CCMS(shift) = 0.01611 for Iteration #65 of Tilt-Series #3. CCMS(rotations) = 0.39489 for Iteration #65 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #65 of Tilt-Series #3. The scaled sum of CCMS values is #0.01595 for Tilt-Series #3. Creating Depiction Videos for Iteration #65 in Parallel... Creating Refinement tilt-series video for iteration #65... Generating Refinement reconstruction for iteration #65... No Round parameters changed for Iteration #66 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #66, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #66 Creating quality assessment statistics... CCMS(shift) = 0.01756 for Iteration #66 of Tilt-Series #3. CCMS(rotations) = 0.38665 for Iteration #66 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #66 of Tilt-Series #3. The scaled sum of CCMS values is #0.01651 for Tilt-Series #3. Creating Depiction Videos for Iteration #66 in Parallel... Creating Refinement tilt-series video for iteration #66... Generating Refinement reconstruction for iteration #66... No Round parameters changed for Iteration #67 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #67, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #67 Creating quality assessment statistics... CCMS(shift) = 0.01537 for Iteration #67 of Tilt-Series #3. CCMS(rotations) = 0.33509 for Iteration #67 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #67 of Tilt-Series #3. The scaled sum of CCMS values is #0.01439 for Tilt-Series #3. Creating Depiction Videos for Iteration #67 in Parallel... Creating Refinement tilt-series video for iteration #67... Generating Refinement reconstruction for iteration #67... No Round parameters changed for Iteration #68 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #68, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #68 Creating quality assessment statistics... CCMS(shift) = 0.01416 for Iteration #68 of Tilt-Series #3. CCMS(rotations) = 0.27123 for Iteration #68 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #68 of Tilt-Series #3. The scaled sum of CCMS values is #0.0125 for Tilt-Series #3. Creating Depiction Videos for Iteration #68 in Parallel... Creating Refinement tilt-series video for iteration #68... Generating Refinement reconstruction for iteration #68... No Round parameters changed for Iteration #69 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #69, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #69 Creating quality assessment statistics... CCMS(shift) = 0.0126 for Iteration #69 of Tilt-Series #3. CCMS(rotations) = 0.28507 for Iteration #69 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #69 of Tilt-Series #3. The scaled sum of CCMS values is #0.012 for Tilt-Series #3. Creating Depiction Videos for Iteration #69 in Parallel... Creating Refinement tilt-series video for iteration #69... Generating Refinement reconstruction for iteration #69... No Round parameters changed for Iteration #70 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #70, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #70 Creating quality assessment statistics... CCMS(shift) = 0.01607 for Iteration #70 of Tilt-Series #3. CCMS(rotations) = 0.41902 for Iteration #70 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #70 of Tilt-Series #3. The scaled sum of CCMS values is #0.01642 for Tilt-Series #3. Creating Depiction Videos for Iteration #70 in Parallel... Creating Refinement tilt-series video for iteration #70... Generating Refinement reconstruction for iteration #70... No Round parameters changed for Iteration #71 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #71, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #71 Creating quality assessment statistics... CCMS(shift) = 0.01307 for Iteration #71 of Tilt-Series #3. CCMS(rotations) = 0.35487 for Iteration #71 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #71 of Tilt-Series #3. The scaled sum of CCMS values is #0.01363 for Tilt-Series #3. Creating Depiction Videos for Iteration #71 in Parallel... Creating Refinement tilt-series video for iteration #71... Generating Refinement reconstruction for iteration #71... No Round parameters changed for Iteration #72 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #72, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #72 Creating quality assessment statistics... CCMS(shift) = 0.01478 for Iteration #72 of Tilt-Series #3. CCMS(rotations) = 0.39092 for Iteration #72 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #72 of Tilt-Series #3. The scaled sum of CCMS values is #0.01521 for Tilt-Series #3. Creating Depiction Videos for Iteration #72 in Parallel... Creating Refinement tilt-series video for iteration #72... Generating Refinement reconstruction for iteration #72... No Round parameters changed for Iteration #73 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #73, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #73 Creating quality assessment statistics... CCMS(shift) = 0.01388 for Iteration #73 of Tilt-Series #3. CCMS(rotations) = 0.31902 for Iteration #73 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #73 of Tilt-Series #3. The scaled sum of CCMS values is #0.01332 for Tilt-Series #3. Creating Depiction Videos for Iteration #73 in Parallel... Creating Refinement tilt-series video for iteration #73... Generating Refinement reconstruction for iteration #73... No Round parameters changed for Iteration #74 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #74, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #74 Creating quality assessment statistics... CCMS(shift) = 0.01186 for Iteration #74 of Tilt-Series #3. CCMS(rotations) = 0.35338 for Iteration #74 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #74 of Tilt-Series #3. The scaled sum of CCMS values is #0.013 for Tilt-Series #3. Creating Depiction Videos for Iteration #74 in Parallel... Creating Refinement tilt-series video for iteration #74... Generating Refinement reconstruction for iteration #74... No Round parameters changed for Iteration #75 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #75, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #75 Creating quality assessment statistics... CCMS(shift) = 0.01511 for Iteration #75 of Tilt-Series #3. CCMS(rotations) = 0.2601 for Iteration #75 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #75 of Tilt-Series #3. The scaled sum of CCMS values is #0.01276 for Tilt-Series #3. Creating Depiction Videos for Iteration #75 in Parallel... Creating Refinement tilt-series video for iteration #75... Generating Refinement reconstruction for iteration #75... No Round parameters changed for Iteration #76 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #76, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #76 Creating quality assessment statistics... CCMS(shift) = 0.01436 for Iteration #76 of Tilt-Series #3. CCMS(rotations) = 0.26843 for Iteration #76 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #76 of Tilt-Series #3. The scaled sum of CCMS values is #0.01255 for Tilt-Series #3. Creating Depiction Videos for Iteration #76 in Parallel... Creating Refinement tilt-series video for iteration #76... Generating Refinement reconstruction for iteration #76... No Round parameters changed for Iteration #77 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #77, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #77 Creating quality assessment statistics... CCMS(shift) = 0.01554 for Iteration #77 of Tilt-Series #3. CCMS(rotations) = 0.31008 for Iteration #77 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #77 of Tilt-Series #3. The scaled sum of CCMS values is #0.01397 for Tilt-Series #3. Creating Depiction Videos for Iteration #77 in Parallel... Creating Refinement tilt-series video for iteration #77... Generating Refinement reconstruction for iteration #77... No Round parameters changed for Iteration #78 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #78, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #78 Creating quality assessment statistics... CCMS(shift) = 0.02028 for Iteration #78 of Tilt-Series #3. CCMS(rotations) = 0.37657 for Iteration #78 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #78 of Tilt-Series #3. The scaled sum of CCMS values is #0.01767 for Tilt-Series #3. Creating Depiction Videos for Iteration #78 in Parallel... Creating Refinement tilt-series video for iteration #78... Generating Refinement reconstruction for iteration #78... No Round parameters changed for Iteration #79 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #79, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #79 Creating quality assessment statistics... CCMS(shift) = 0.01814 for Iteration #79 of Tilt-Series #3. CCMS(rotations) = 0.33281 for Iteration #79 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #79 of Tilt-Series #3. The scaled sum of CCMS values is #0.01573 for Tilt-Series #3. Creating Depiction Videos for Iteration #79 in Parallel... Creating Refinement tilt-series video for iteration #79... Generating Refinement reconstruction for iteration #79... No Round parameters changed for Iteration #80 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #80, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #80 Creating quality assessment statistics... CCMS(shift) = 0.01727 for Iteration #80 of Tilt-Series #3. CCMS(rotations) = 0.33079 for Iteration #80 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #80 of Tilt-Series #3. The scaled sum of CCMS values is #0.01525 for Tilt-Series #3. Creating Depiction Videos for Iteration #80 in Parallel... Creating Refinement tilt-series video for iteration #80... Generating Refinement reconstruction for iteration #80... No Round parameters changed for Iteration #81 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #81, Round #4 of Tilt-Series #3 (tiltseries0003) fit.scale switched from false to true on Iteration #81Creating quality assessment statistics... CCMS(shift) = 0.01412 for Iteration #81 of Tilt-Series #3. CCMS(rotations) = 0.39091 for Iteration #81 of Tilt-Series #3. CCMS(scale) = 0.0 for Iteration #81 of Tilt-Series #3. The scaled sum of CCMS values is #0.01488 for Tilt-Series #3. Creating Depiction Videos for Iteration #81 in Parallel... Creating Refinement tilt-series video for iteration #81... Generating Refinement reconstruction for iteration #81... No Round parameters changed for Iteration #82 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #82, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #82 Creating quality assessment statistics... CCMS(shift) = 0.01113 for Iteration #82 of Tilt-Series #3. CCMS(rotations) = 0.32017 for Iteration #82 of Tilt-Series #3. CCMS(scale) = 0.00566 for Iteration #82 of Tilt-Series #3. The scaled sum of CCMS values is #0.00986 for Tilt-Series #3. Creating Depiction Videos for Iteration #82 in Parallel... Creating Refinement tilt-series video for iteration #82... Generating Refinement reconstruction for iteration #82... No Round parameters changed for Iteration #83 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #83, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #83 Creating quality assessment statistics... CCMS(shift) = 0.01162 for Iteration #83 of Tilt-Series #3. CCMS(rotations) = 0.2831 for Iteration #83 of Tilt-Series #3. CCMS(scale) = 0.0076 for Iteration #83 of Tilt-Series #3. The scaled sum of CCMS values is #0.01018 for Tilt-Series #3. Creating Depiction Videos for Iteration #83 in Parallel... Creating Refinement tilt-series video for iteration #83... Generating Refinement reconstruction for iteration #83... No Round parameters changed for Iteration #84 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #84, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #84 Creating quality assessment statistics... CCMS(shift) = 0.01309 for Iteration #84 of Tilt-Series #3. CCMS(rotations) = 0.38036 for Iteration #84 of Tilt-Series #3. CCMS(scale) = 0.00804 for Iteration #84 of Tilt-Series #3. The scaled sum of CCMS values is #0.01211 for Tilt-Series #3. Creating Depiction Videos for Iteration #84 in Parallel... Creating Refinement tilt-series video for iteration #84... Generating Refinement reconstruction for iteration #84... No Round parameters changed for Iteration #85 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #85, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #85 Creating quality assessment statistics... CCMS(shift) = 0.01939 for Iteration #85 of Tilt-Series #3. CCMS(rotations) = 0.41905 for Iteration #85 of Tilt-Series #3. CCMS(scale) = 0.00894 for Iteration #85 of Tilt-Series #3. The scaled sum of CCMS values is #0.01503 for Tilt-Series #3. Creating Depiction Videos for Iteration #85 in Parallel... Creating Refinement tilt-series video for iteration #85... Generating Refinement reconstruction for iteration #85... No Round parameters changed for Iteration #86 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #86, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #86 Creating quality assessment statistics... CCMS(shift) = 0.01402 for Iteration #86 of Tilt-Series #3. CCMS(rotations) = 0.54898 for Iteration #86 of Tilt-Series #3. CCMS(scale) = 0.01029 for Iteration #86 of Tilt-Series #3. The scaled sum of CCMS values is #0.01542 for Tilt-Series #3. Creating Depiction Videos for Iteration #86 in Parallel... Creating Refinement tilt-series video for iteration #86... Generating Refinement reconstruction for iteration #86... No Round parameters changed for Iteration #87 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #87, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #87 Creating quality assessment statistics... CCMS(shift) = 0.01126 for Iteration #87 of Tilt-Series #3. CCMS(rotations) = 0.40543 for Iteration #87 of Tilt-Series #3. CCMS(scale) = 0.00704 for Iteration #87 of Tilt-Series #3. The scaled sum of CCMS values is #0.0115 for Tilt-Series #3. Creating Depiction Videos for Iteration #87 in Parallel... Creating Refinement tilt-series video for iteration #87... Generating Refinement reconstruction for iteration #87... No Round parameters changed for Iteration #88 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #88, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #88 Creating quality assessment statistics... CCMS(shift) = 0.02054 for Iteration #88 of Tilt-Series #3. CCMS(rotations) = 0.37517 for Iteration #88 of Tilt-Series #3. CCMS(scale) = 0.00905 for Iteration #88 of Tilt-Series #3. The scaled sum of CCMS values is #0.01487 for Tilt-Series #3. Creating Depiction Videos for Iteration #88 in Parallel... Creating Refinement tilt-series video for iteration #88... Generating Refinement reconstruction for iteration #88... No Round parameters changed for Iteration #89 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #89, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #89 Creating quality assessment statistics... CCMS(shift) = 0.01217 for Iteration #89 of Tilt-Series #3. CCMS(rotations) = 0.46601 for Iteration #89 of Tilt-Series #3. CCMS(scale) = 0.01077 for Iteration #89 of Tilt-Series #3. The scaled sum of CCMS values is #0.01386 for Tilt-Series #3. Creating Depiction Videos for Iteration #89 in Parallel... Creating Refinement tilt-series video for iteration #89... Generating Refinement reconstruction for iteration #89... No Round parameters changed for Iteration #90 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #90, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #90 Creating quality assessment statistics... CCMS(shift) = 0.01513 for Iteration #90 of Tilt-Series #3. CCMS(rotations) = 0.57679 for Iteration #90 of Tilt-Series #3. CCMS(scale) = 0.00985 for Iteration #90 of Tilt-Series #3. The scaled sum of CCMS values is #0.01602 for Tilt-Series #3. Creating Depiction Videos for Iteration #90 in Parallel... Creating Refinement tilt-series video for iteration #90... Generating Refinement reconstruction for iteration #90... No Round parameters changed for Iteration #91 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #91, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #91 Creating quality assessment statistics... CCMS(shift) = 0.01597 for Iteration #91 of Tilt-Series #3. CCMS(rotations) = 0.68873 for Iteration #91 of Tilt-Series #3. CCMS(scale) = 0.00701 for Iteration #91 of Tilt-Series #3. The scaled sum of CCMS values is #0.01684 for Tilt-Series #3. Creating Depiction Videos for Iteration #91 in Parallel... Creating Refinement tilt-series video for iteration #91... Generating Refinement reconstruction for iteration #91... No Round parameters changed for Iteration #92 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #92, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #92 Creating quality assessment statistics... CCMS(shift) = 0.01252 for Iteration #92 of Tilt-Series #3. CCMS(rotations) = 0.55382 for Iteration #92 of Tilt-Series #3. CCMS(scale) = 0.0083 for Iteration #92 of Tilt-Series #3. The scaled sum of CCMS values is #0.01432 for Tilt-Series #3. Creating Depiction Videos for Iteration #92 in Parallel... Creating Refinement tilt-series video for iteration #92... Generating Refinement reconstruction for iteration #92... No Round parameters changed for Iteration #93 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #93, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #93 Creating quality assessment statistics... CCMS(shift) = 0.0111 for Iteration #93 of Tilt-Series #3. CCMS(rotations) = 0.50391 for Iteration #93 of Tilt-Series #3. CCMS(scale) = 0.00645 for Iteration #93 of Tilt-Series #3. The scaled sum of CCMS values is #0.01257 for Tilt-Series #3. Creating Depiction Videos for Iteration #93 in Parallel... Creating Refinement tilt-series video for iteration #93... Generating Refinement reconstruction for iteration #93... No Round parameters changed for Iteration #94 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #94, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #94 Creating quality assessment statistics... CCMS(shift) = 0.01926 for Iteration #94 of Tilt-Series #3. CCMS(rotations) = 0.36257 for Iteration #94 of Tilt-Series #3. CCMS(scale) = 0.00559 for Iteration #94 of Tilt-Series #3. The scaled sum of CCMS values is #0.01312 for Tilt-Series #3. Creating Depiction Videos for Iteration #94 in Parallel... Creating Refinement tilt-series video for iteration #94... Generating Refinement reconstruction for iteration #94... No Round parameters changed for Iteration #95 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #95, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #95 Creating quality assessment statistics... CCMS(shift) = 0.01177 for Iteration #95 of Tilt-Series #3. CCMS(rotations) = 0.40477 for Iteration #95 of Tilt-Series #3. CCMS(scale) = 0.00609 for Iteration #95 of Tilt-Series #3. The scaled sum of CCMS values is #0.01135 for Tilt-Series #3. Creating Depiction Videos for Iteration #95 in Parallel... Creating Refinement tilt-series video for iteration #95... Generating Refinement reconstruction for iteration #95... No Round parameters changed for Iteration #96 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #96, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #96 Creating quality assessment statistics... CCMS(shift) = 0.01864 for Iteration #96 of Tilt-Series #3. CCMS(rotations) = 0.4412 for Iteration #96 of Tilt-Series #3. CCMS(scale) = 0.00685 for Iteration #96 of Tilt-Series #3. The scaled sum of CCMS values is #0.01438 for Tilt-Series #3. Creating Depiction Videos for Iteration #96 in Parallel... Creating Refinement tilt-series video for iteration #96... Generating Refinement reconstruction for iteration #96... No Round parameters changed for Iteration #97 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #97, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #97 Creating quality assessment statistics... CCMS(shift) = 0.02421 for Iteration #97 of Tilt-Series #3. CCMS(rotations) = 0.38129 for Iteration #97 of Tilt-Series #3. CCMS(scale) = 0.0092 for Iteration #97 of Tilt-Series #3. The scaled sum of CCMS values is #0.01622 for Tilt-Series #3. Creating Depiction Videos for Iteration #97 in Parallel... Creating Refinement tilt-series video for iteration #97... Generating Refinement reconstruction for iteration #97... No Round parameters changed for Iteration #98 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #98, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #98 Creating quality assessment statistics... CCMS(shift) = 0.01768 for Iteration #98 of Tilt-Series #3. CCMS(rotations) = 0.64775 for Iteration #98 of Tilt-Series #3. CCMS(scale) = 0.00738 for Iteration #98 of Tilt-Series #3. The scaled sum of CCMS values is #0.01699 for Tilt-Series #3. Creating Depiction Videos for Iteration #98 in Parallel... Creating Refinement tilt-series video for iteration #98... Generating Refinement reconstruction for iteration #98... No Round parameters changed for Iteration #99 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #99, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #99 Creating quality assessment statistics... CCMS(shift) = 0.02197 for Iteration #99 of Tilt-Series #3. CCMS(rotations) = 0.52519 for Iteration #99 of Tilt-Series #3. CCMS(scale) = 0.0054 for Iteration #99 of Tilt-Series #3. The scaled sum of CCMS values is #0.01613 for Tilt-Series #3. Creating Depiction Videos for Iteration #99 in Parallel... Creating Refinement tilt-series video for iteration #99... Generating Refinement reconstruction for iteration #99... No Round parameters changed for Iteration #100 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #100, Round #4 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #100 Creating quality assessment statistics... CCMS(shift) = 0.02195 for Iteration #100 of Tilt-Series #3. CCMS(rotations) = 0.31774 for Iteration #100 of Tilt-Series #3. CCMS(scale) = 0.01062 for Iteration #100 of Tilt-Series #3. The scaled sum of CCMS values is #0.01509 for Tilt-Series #3. Creating Depiction Videos for Iteration #100 in Parallel... Creating Refinement tilt-series video for iteration #100... Generating Refinement reconstruction for iteration #100... Beginning Refinement Iteration #101, Round #5 of Tilt-Series #3 (tiltseries0003) lowpass = 3.125 angstroms Round #5. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.76302 Angstroms, Nyquist is 3.52604 Angstroms) window.lowpass.apodization = { 0.440755 0.440755 } map.sampling = 1 window.highpass.diameter = { 0.000898583078491 0.000898583078491 } window.highpass.apodization = { 0.00179716615698 0.00179716615698 } window.mask.apodization = { 10 10 } align.mask.width = { 2201 2277 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 401.049007379 map.lowpass.diameter = { 1.1283328 1.1283328 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2226 2302 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2201 2277 } reference.body = 401.049007379 window.lowpass.diameter = { 1.1283328 1.1283328 } align.correlation.mode = pcf No parameters were switched for Iteration #101 Creating quality assessment statistics... CCMS(shift) = 0.02185 for Iteration #101 of Tilt-Series #3. CCMS(rotations) = 0.60043 for Iteration #101 of Tilt-Series #3. CCMS(scale) = 0.00669 for Iteration #101 of Tilt-Series #3. The scaled sum of CCMS values is #0.01752 for Tilt-Series #3. Creating Depiction Videos for Iteration #101 in Parallel... Creating Refinement tilt-series video for iteration #101... Generating Refinement reconstruction for iteration #101... No Round parameters changed for Iteration #102 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #102, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #102 Creating quality assessment statistics... CCMS(shift) = 0.02082 for Iteration #102 of Tilt-Series #3. CCMS(rotations) = 0.7247 for Iteration #102 of Tilt-Series #3. CCMS(scale) = 0.0116 for Iteration #102 of Tilt-Series #3. The scaled sum of CCMS values is #0.02047 for Tilt-Series #3. Creating Depiction Videos for Iteration #102 in Parallel... Creating Refinement tilt-series video for iteration #102... Generating Refinement reconstruction for iteration #102... No Round parameters changed for Iteration #103 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #103, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #103 Creating quality assessment statistics... CCMS(shift) = 0.02248 for Iteration #103 of Tilt-Series #3. CCMS(rotations) = 0.77528 for Iteration #103 of Tilt-Series #3. CCMS(scale) = 0.01303 for Iteration #103 of Tilt-Series #3. The scaled sum of CCMS values is #0.02218 for Tilt-Series #3. Creating Depiction Videos for Iteration #103 in Parallel... Creating Refinement tilt-series video for iteration #103... Generating Refinement reconstruction for iteration #103... No Round parameters changed for Iteration #104 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #104, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #104 Creating quality assessment statistics... CCMS(shift) = 0.0207 for Iteration #104 of Tilt-Series #3. CCMS(rotations) = 0.92426 for Iteration #104 of Tilt-Series #3. CCMS(scale) = 0.01627 for Iteration #104 of Tilt-Series #3. The scaled sum of CCMS values is #0.02465 for Tilt-Series #3. Creating Depiction Videos for Iteration #104 in Parallel... Creating Refinement tilt-series video for iteration #104... Generating Refinement reconstruction for iteration #104... No Round parameters changed for Iteration #105 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #105, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #105 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.02644 for Iteration #105 of Tilt-Series #3. CCMS(rotations) = 0.53593 for Iteration #105 of Tilt-Series #3. CCMS(scale) = 0.02222 for Iteration #105 of Tilt-Series #3. The scaled sum of CCMS values is #0.02336 for Tilt-Series #3. Creating Depiction Videos for Iteration #105 in Parallel... Creating Refinement tilt-series video for iteration #105... Generating Refinement reconstruction for iteration #105... Refinement Iteration #105 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #106 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #106, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #106 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.03958 for Iteration #106 of Tilt-Series #3. CCMS(rotations) = 1.10305 for Iteration #106 of Tilt-Series #3. CCMS(scale) = 0.02439 for Iteration #106 of Tilt-Series #3. The scaled sum of CCMS values is #0.03603 for Tilt-Series #3. Creating Depiction Videos for Iteration #106 in Parallel... Creating Refinement tilt-series video for iteration #106... Generating Refinement reconstruction for iteration #106... Refinement Iteration #106 finished after retrying 4 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2016 Window Size (y) was windowed down to 2100 No Round parameters changed for Iteration #107 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #107, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #107 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.01959 for Iteration #107 of Tilt-Series #3. CCMS(rotations) = 1.2407 for Iteration #107 of Tilt-Series #3. CCMS(scale) = 0.02426 for Iteration #107 of Tilt-Series #3. The scaled sum of CCMS values is #0.03116 for Tilt-Series #3. Creating Depiction Videos for Iteration #107 in Parallel... Creating Refinement tilt-series video for iteration #107... Generating Refinement reconstruction for iteration #107... Refinement Iteration #107 finished after retrying 1 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 2100 Window Size (y) was windowed down to 2250 No Round parameters changed for Iteration #108 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #108, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #108 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.02196 for Iteration #108 of Tilt-Series #3. CCMS(rotations) = 1.04733 for Iteration #108 of Tilt-Series #3. CCMS(scale) = 0.03115 for Iteration #108 of Tilt-Series #3. The scaled sum of CCMS values is #0.03167 for Tilt-Series #3. Creating Depiction Videos for Iteration #108 in Parallel... Creating Refinement tilt-series video for iteration #108... Generating Refinement reconstruction for iteration #108... Refinement Iteration #108 finished after retrying 13 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1750 Window Size (y) was windowed down to 1800 No Round parameters changed for Iteration #109 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #109, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #109 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.0255 for Iteration #109 of Tilt-Series #3. CCMS(rotations) = 0.8313 for Iteration #109 of Tilt-Series #3. CCMS(scale) = 0.0363 for Iteration #109 of Tilt-Series #3. The scaled sum of CCMS values is #0.03168 for Tilt-Series #3. Creating Depiction Videos for Iteration #109 in Parallel... Creating Refinement tilt-series video for iteration #109... Generating Refinement reconstruction for iteration #109... Refinement Iteration #109 finished after retrying 22 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1470 Window Size (y) was windowed down to 1536 No Round parameters changed for Iteration #110 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #110, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #110 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.03715 for Iteration #110 of Tilt-Series #3. CCMS(rotations) = 1.15454 for Iteration #110 of Tilt-Series #3. CCMS(scale) = 0.03739 for Iteration #110 of Tilt-Series #3. The scaled sum of CCMS values is #0.04024 for Tilt-Series #3. Creating Depiction Videos for Iteration #110 in Parallel... Creating Refinement tilt-series video for iteration #110... Generating Refinement reconstruction for iteration #110... Refinement Iteration #110 finished after retrying 32 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1250 Window Size (y) was windowed down to 1296 No Round parameters changed for Iteration #111 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #111, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #111 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.04041 for Iteration #111 of Tilt-Series #3. CCMS(rotations) = 1.36113 for Iteration #111 of Tilt-Series #3. CCMS(scale) = 0.03661 for Iteration #111 of Tilt-Series #3. The scaled sum of CCMS values is #0.04382 for Tilt-Series #3. Creating Depiction Videos for Iteration #111 in Parallel... Creating Refinement tilt-series video for iteration #111... Generating Refinement reconstruction for iteration #111... Refinement Iteration #111 finished after retrying 55 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 756 Window Size (y) was windowed down to 800 No Round parameters changed for Iteration #112 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #112, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #112 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.04695 for Iteration #112 of Tilt-Series #3. CCMS(rotations) = 2.14224 for Iteration #112 of Tilt-Series #3. CCMS(scale) = 0.05204 for Iteration #112 of Tilt-Series #3. The scaled sum of CCMS values is #0.06156 for Tilt-Series #3. Creating Depiction Videos for Iteration #112 in Parallel... Creating Refinement tilt-series video for iteration #112... Generating Refinement reconstruction for iteration #112... Refinement Iteration #112 finished after retrying 58 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 700 Window Size (y) was windowed down to 756 No Round parameters changed for Iteration #113 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #113, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #113 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.04291 for Iteration #113 of Tilt-Series #3. CCMS(rotations) = 2.43283 for Iteration #113 of Tilt-Series #3. CCMS(scale) = 0.06468 for Iteration #113 of Tilt-Series #3. The scaled sum of CCMS values is #0.0683 for Tilt-Series #3. Creating Depiction Videos for Iteration #113 in Parallel... Creating Refinement tilt-series video for iteration #113... Generating Refinement reconstruction for iteration #113... Refinement Iteration #113 finished after retrying 57 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 720 Window Size (y) was windowed down to 768 No Round parameters changed for Iteration #114 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #114, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #114 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.03946 for Iteration #114 of Tilt-Series #3. CCMS(rotations) = 3.22242 for Iteration #114 of Tilt-Series #3. CCMS(scale) = 0.06879 for Iteration #114 of Tilt-Series #3. The scaled sum of CCMS values is #0.07905 for Tilt-Series #3. Creating Depiction Videos for Iteration #114 in Parallel... Creating Refinement tilt-series video for iteration #114... Generating Refinement reconstruction for iteration #114... Refinement Iteration #114 finished after retrying 54 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 768 Window Size (y) was windowed down to 810 No Round parameters changed for Iteration #115 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #115, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #115 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Refinement failed. Retry #63 with Window Size: (630, 672) (at sampling 1)... Refinement failed. Retry #64 with Window Size: (600, 648) (at sampling 1)... Refinement failed. Retry #65 with Window Size: (588, 640) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.04518 for Iteration #115 of Tilt-Series #3. CCMS(rotations) = 4.07633 for Iteration #115 of Tilt-Series #3. CCMS(scale) = 0.05852 for Iteration #115 of Tilt-Series #3. The scaled sum of CCMS values is #0.08892 for Tilt-Series #3. Creating Depiction Videos for Iteration #115 in Parallel... Creating Refinement tilt-series video for iteration #115... Generating Refinement reconstruction for iteration #115... Refinement Iteration #115 finished after retrying 65 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 588 Window Size (y) was windowed down to 640 No Round parameters changed for Iteration #116 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #116, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #116 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Refinement failed. Retry #63 with Window Size: (630, 672) (at sampling 1)... Refinement failed. Retry #64 with Window Size: (600, 648) (at sampling 1)... Refinement failed. Retry #65 with Window Size: (588, 640) (at sampling 1)... Refinement failed. Retry #66 with Window Size: (576, 630) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.04623 for Iteration #116 of Tilt-Series #3. CCMS(rotations) = 4.60266 for Iteration #116 of Tilt-Series #3. CCMS(scale) = 0.06661 for Iteration #116 of Tilt-Series #3. The scaled sum of CCMS values is #0.09898 for Tilt-Series #3. Creating Depiction Videos for Iteration #116 in Parallel... Creating Refinement tilt-series video for iteration #116... Generating Refinement reconstruction for iteration #116... Refinement Iteration #116 finished after retrying 66 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 576 Window Size (y) was windowed down to 630 No Round parameters changed for Iteration #117 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #117, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #117 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Refinement failed. Retry #63 with Window Size: (630, 672) (at sampling 1)... Refinement failed. Retry #64 with Window Size: (600, 648) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.06238 for Iteration #117 of Tilt-Series #3. CCMS(rotations) = 4.71086 for Iteration #117 of Tilt-Series #3. CCMS(scale) = 0.07423 for Iteration #117 of Tilt-Series #3. The scaled sum of CCMS values is #0.10835 for Tilt-Series #3. Creating Depiction Videos for Iteration #117 in Parallel... Creating Refinement tilt-series video for iteration #117... Generating Refinement reconstruction for iteration #117... Refinement Iteration #117 finished after retrying 64 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 600 Window Size (y) was windowed down to 648 No Round parameters changed for Iteration #118 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #118, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #118 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Refinement failed. Retry #63 with Window Size: (630, 672) (at sampling 1)... Refinement failed. Retry #64 with Window Size: (600, 648) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.03488 for Iteration #118 of Tilt-Series #3. CCMS(rotations) = 4.76359 for Iteration #118 of Tilt-Series #3. CCMS(scale) = 0.08905 for Iteration #118 of Tilt-Series #3. The scaled sum of CCMS values is #0.10483 for Tilt-Series #3. Creating Depiction Videos for Iteration #118 in Parallel... Creating Refinement tilt-series video for iteration #118... Generating Refinement reconstruction for iteration #118... Refinement Iteration #118 finished after retrying 64 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 600 Window Size (y) was windowed down to 648 No Round parameters changed for Iteration #119 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #119, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #119 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.02902 for Iteration #119 of Tilt-Series #3. CCMS(rotations) = 3.11432 for Iteration #119 of Tilt-Series #3. CCMS(scale) = 0.07085 for Iteration #119 of Tilt-Series #3. The scaled sum of CCMS values is #0.07481 for Tilt-Series #3. Creating Depiction Videos for Iteration #119 in Parallel... Creating Refinement tilt-series video for iteration #119... Generating Refinement reconstruction for iteration #119... Refinement Iteration #119 finished after retrying 62 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 640 Window Size (y) was windowed down to 686 No Round parameters changed for Iteration #120 of Tilt-Series #3 (tiltseries0003) Beginning Refinement Iteration #120, Round #5 of Tilt-Series #3 (tiltseries0003) No parameters were switched for Iteration #120 Refinement failed. Retry #1 with Window Size: (2100, 2250) (at sampling 1)... Refinement failed. Retry #2 with Window Size: (2058, 2240) (at sampling 1)... Refinement failed. Retry #3 with Window Size: (2048, 2160) (at sampling 1)... Refinement failed. Retry #4 with Window Size: (2016, 2100) (at sampling 1)... Refinement failed. Retry #5 with Window Size: (2000, 2058) (at sampling 1)... Refinement failed. Retry #6 with Window Size: (1960, 2048) (at sampling 1)... Refinement failed. Retry #7 with Window Size: (1944, 2016) (at sampling 1)... Refinement failed. Retry #8 with Window Size: (1920, 2000) (at sampling 1)... Refinement failed. Retry #9 with Window Size: (1890, 1960) (at sampling 1)... Refinement failed. Retry #10 with Window Size: (1800, 1944) (at sampling 1)... Refinement failed. Retry #11 with Window Size: (1792, 1920) (at sampling 1)... Refinement failed. Retry #12 with Window Size: (1764, 1890) (at sampling 1)... Refinement failed. Retry #13 with Window Size: (1750, 1800) (at sampling 1)... Refinement failed. Retry #14 with Window Size: (1728, 1792) (at sampling 1)... Refinement failed. Retry #15 with Window Size: (1680, 1764) (at sampling 1)... Refinement failed. Retry #16 with Window Size: (1620, 1750) (at sampling 1)... Refinement failed. Retry #17 with Window Size: (1600, 1728) (at sampling 1)... Refinement failed. Retry #18 with Window Size: (1568, 1680) (at sampling 1)... Refinement failed. Retry #19 with Window Size: (1536, 1620) (at sampling 1)... Refinement failed. Retry #20 with Window Size: (1512, 1600) (at sampling 1)... Refinement failed. Retry #21 with Window Size: (1500, 1568) (at sampling 1)... Refinement failed. Retry #22 with Window Size: (1470, 1536) (at sampling 1)... Refinement failed. Retry #23 with Window Size: (1458, 1512) (at sampling 1)... Refinement failed. Retry #24 with Window Size: (1440, 1500) (at sampling 1)... Refinement failed. Retry #25 with Window Size: (1400, 1470) (at sampling 1)... Refinement failed. Retry #26 with Window Size: (1372, 1458) (at sampling 1)... Refinement failed. Retry #27 with Window Size: (1350, 1440) (at sampling 1)... Refinement failed. Retry #28 with Window Size: (1344, 1400) (at sampling 1)... Refinement failed. Retry #29 with Window Size: (1296, 1372) (at sampling 1)... Refinement failed. Retry #30 with Window Size: (1280, 1350) (at sampling 1)... Refinement failed. Retry #31 with Window Size: (1260, 1344) (at sampling 1)... Refinement failed. Retry #32 with Window Size: (1250, 1296) (at sampling 1)... Refinement failed. Retry #33 with Window Size: (1200, 1280) (at sampling 1)... Refinement failed. Retry #34 with Window Size: (1176, 1260) (at sampling 1)... Refinement failed. Retry #35 with Window Size: (1152, 1250) (at sampling 1)... Refinement failed. Retry #36 with Window Size: (1134, 1200) (at sampling 1)... Refinement failed. Retry #37 with Window Size: (1120, 1176) (at sampling 1)... Refinement failed. Retry #38 with Window Size: (1080, 1152) (at sampling 1)... Refinement failed. Retry #39 with Window Size: (1050, 1134) (at sampling 1)... Refinement failed. Retry #40 with Window Size: (1024, 1120) (at sampling 1)... Refinement failed. Retry #41 with Window Size: (1008, 1080) (at sampling 1)... Refinement failed. Retry #42 with Window Size: (1000, 1050) (at sampling 1)... Refinement failed. Retry #43 with Window Size: (980, 1024) (at sampling 1)... Refinement failed. Retry #44 with Window Size: (972, 1008) (at sampling 1)... Refinement failed. Retry #45 with Window Size: (960, 1000) (at sampling 1)... Refinement failed. Retry #46 with Window Size: (900, 980) (at sampling 1)... Refinement failed. Retry #47 with Window Size: (896, 972) (at sampling 1)... Refinement failed. Retry #48 with Window Size: (882, 960) (at sampling 1)... Refinement failed. Retry #49 with Window Size: (864, 900) (at sampling 1)... Refinement failed. Retry #50 with Window Size: (840, 896) (at sampling 1)... Refinement failed. Retry #51 with Window Size: (810, 882) (at sampling 1)... Refinement failed. Retry #52 with Window Size: (800, 864) (at sampling 1)... Refinement failed. Retry #53 with Window Size: (784, 840) (at sampling 1)... Refinement failed. Retry #54 with Window Size: (768, 810) (at sampling 1)... Refinement failed. Retry #55 with Window Size: (756, 800) (at sampling 1)... Refinement failed. Retry #56 with Window Size: (750, 784) (at sampling 1)... Refinement failed. Retry #57 with Window Size: (720, 768) (at sampling 1)... Refinement failed. Retry #58 with Window Size: (700, 756) (at sampling 1)... Refinement failed. Retry #59 with Window Size: (686, 750) (at sampling 1)... Refinement failed. Retry #60 with Window Size: (672, 720) (at sampling 1)... Refinement failed. Retry #61 with Window Size: (648, 700) (at sampling 1)... Refinement failed. Retry #62 with Window Size: (640, 686) (at sampling 1)... Refinement failed. Retry #63 with Window Size: (630, 672) (at sampling 1)... Refinement failed. Retry #64 with Window Size: (600, 648) (at sampling 1)... Creating quality assessment statistics... CCMS(shift) = 0.05928 for Iteration #120 of Tilt-Series #3. CCMS(rotations) = 5.30701 for Iteration #120 of Tilt-Series #3. CCMS(scale) = 0.08451 for Iteration #120 of Tilt-Series #3. The scaled sum of CCMS values is #0.11869 for Tilt-Series #3. Creating Depiction Videos for Iteration #120 in Parallel... Creating Refinement tilt-series video for iteration #120... Generating Refinement reconstruction for iteration #120... Refinement Iteration #120 finished after retrying 64 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 600 Window Size (y) was windowed down to 648 Finished Refinement for Tilt-Series #3 (tiltseries0003)! 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-11hr11m07s