++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:36:21 on 15 Dec 2020 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features" Acta Cryst. D74, 106-116 (Open Access) if SHELXE proves useful. Command line parameters: P43212_visc-standard P43212_visc-standard_fa -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P43212_visc-standard_fa.res FA and alpha from P43212_visc-standard_fa.hkl Native data from P43212_visc-standard.hkl Listing output to P43212_visc-standard.lst Phases output to P43212_visc-standard.phs Revised heavy atom sites output to P43212_visc-standard.hat Revised heavy atom phases output to P43212_visc-standard.pha Poly-Ala trace output to P43212_visc-standard.pdb Summary of parameters to be employed: -a 5 global autotracing cycles -b 5.0 extra B for revised heavy atom sites -B unset just build single beta-strands -c 0.400 fraction of pixels in crossover region -d 0.000 high resolution limit to be applied to input data -D unset do not fuse disulfides for NCS -e unset fill in missing data up to maximum resolution + 0.2 Ang. -f unset read intensity not F from native .hkl file -F 0.800 fractional weight for phases from previous global cycle -g 1.100 solvent gamma flipping factor -G 0.700 FOM threshold for initial tripeptides and chain building -h heavy atoms present in native - use all with occ > 0.2 -i unset no structure inversion -k 4.5 minimum height/sigma for revised heavy atom sites -l 2 space for 2000000 reflections -L 6 minimum number of residues/chain (if more than 3 chains) -m 5 cycles of density modification -n unset do not apply NCS -p unset no phosphate search -q unset no alpha-helix search -r 3.00 map resolution (multiplies maximum indices) -s 0.500 solvent fraction -S 2.42 radius of sphere of influence -t 1.00 time for initial searches (-t6 or more if difficult) -u 500 MB allocatable memory for fragment optimization -v unset density sharpening factor dependent on resolution -w 0.200 weight for experimental phases after cycle 1 -x unset no phase and trace diagnostics -z unset do not optimize heavy atoms -z 0 read heavy atoms from .res Space group: P 43 21 2 Allowed origin shift code: 9 21 atoms read from file P43212_visc-standard_fa.res Trimmed to 17 atoms with occupancy > 0.2 7603 Reflections read from file P43212_visc-standard_fa.hkl 11844 Reflections read from file P43212_visc-standard.hkl 11805 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000242h^2 +0.000242k^2 -0.000707l^2 +0.000000kl +0.000000hl +0.000000hk 4 Reflections with d > 1.902 and 0 in range 1.902 > d > 1.702 added Density sharpening factor set to 1.20 Fourier grid = 128 x 128 x 11 0.000 <= z <= 0.125 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.770 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 17.47% = 0.129 for phases from phiT = phiA + alpha = 0.281 after including heavy atoms = 0.193, Contrast = 0.027, Connect. = 0.516 for dens.mod. cycle 1 = 0.203, Contrast = 0.098, Connect. = 0.561 for dens.mod. cycle 2 = 0.214, Contrast = 0.127, Connect. = 0.580 for dens.mod. cycle 3 = 0.225, Contrast = 0.147, Connect. = 0.584 for dens.mod. cycle 4 = 0.234, Contrast = 0.170, Connect. = 0.590 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 962 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 76 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 8.413 1.516 0.543 0.882 0.667 0.417 CB 1.127 B: 10 8.112 1.534 0.659 0.678 0.889 0.667 CB 1.016 C: 6 3.268 1.372 0.147 0.713 1.000 0.800 CB 0.766 6 1.645 1.234 0.243 0.315 0.800 0.400 N 0.736 ? D: 6 4.388 1.508 0.413 0.466 0.800 0.400 C 1.192 E: 7 2.541 1.073 0.506 0.365 1.000 0.333 N 0.742 6 1.945 0.982 0.564 0.318 1.000 0.600 C 0.692 ? F: 8 3.286 1.234 0.372 0.405 0.857 0.429 CA 0.946 G: 7 2.077 1.246 0.766 0.275 0.667 0.167 CB 0.746 36 residues left after pruning, divided into chains as follows: A: 13 B: 10 C: 6 D: 7 CC for partial structure against native data = 7.51 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.288, Contrast = 0.204, Connect. = 0.544 for dens.mod. cycle 1 = 0.288, Contrast = 0.225, Connect. = 0.504 for dens.mod. cycle 2 = 0.288, Contrast = 0.282, Connect. = 0.553 for dens.mod. cycle 3 = 0.288, Contrast = 0.323, Connect. = 0.585 for dens.mod. cycle 4 = 0.288, Contrast = 0.362, Connect. = 0.612 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 1084 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 76 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 31.345 2.474 0.776 0.807 0.714 0.500 CB 2.043 B: 10 12.615 2.026 0.221 0.805 1.000 0.778 CB 1.302 C: 11 26.343 2.273 0.592 0.892 1.000 0.700 CB 1.654 D: 10 7.071 1.804 0.111 0.345 1.000 0.556 C 1.390 E: 13 16.484 2.139 0.452 0.507 0.917 0.833 CB 1.659 9 residues pruned to eliminate duplicates F: 7 4.471 1.195 0.657 0.557 1.000 1.000 CB 0.872 G: 24 18.860 1.938 0.556 0.562 0.739 0.435 CB 1.662 31 residues pruned to eliminate duplicates H: 15 21.729 2.097 0.554 0.754 0.929 0.714 CB 1.530 15 residues pruned to eliminate duplicates I: 10 9.655 1.503 0.264 0.906 1.000 0.889 CA 1.205 Using tripeptides from previous cycle as seeds 57 residues left after pruning, divided into chains as follows: A: 15 B: 10 C: 7 D: 15 E: 10 CC for partial structure against native data = 17.60 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.288, Contrast = 0.303, Connect. = 0.571 for dens.mod. cycle 1 = 0.288, Contrast = 0.357, Connect. = 0.579 for dens.mod. cycle 2 = 0.288, Contrast = 0.452, Connect. = 0.647 for dens.mod. cycle 3 = 0.288, Contrast = 0.484, Connect. = 0.670 for dens.mod. cycle 4 = 0.288, Contrast = 0.516, Connect. = 0.690 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 918 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 77 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 16 34.914 2.337 0.585 0.867 0.933 0.733 CB 1.907 B: 11 33.117 2.396 0.866 0.907 1.000 0.700 CB 1.665 C: 10 28.069 2.226 0.852 0.879 0.889 0.556 CB 1.852 D: 12 18.174 2.079 0.451 0.814 1.000 0.818 CB 1.382 E: 7 3.928 1.372 0.392 0.349 1.000 0.667 CB 0.989 F: 32 39.265 2.303 0.563 0.637 0.935 0.710 CB 1.843 26 residues pruned to eliminate duplicates G: 10 5.583 1.590 0.250 0.312 1.000 0.444 CA 1.153 Using tripeptides from previous cycle as seeds 72 residues left after pruning, divided into chains as follows: A: 11 B: 12 C: 7 D: 32 E: 10 CC for partial structure against native data = 27.46 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.288, Contrast = 0.333, Connect. = 0.608 for dens.mod. cycle 1 = 0.288, Contrast = 0.408, Connect. = 0.640 for dens.mod. cycle 2 = 0.288, Contrast = 0.531, Connect. = 0.713 for dens.mod. cycle 3 = 0.288, Contrast = 0.550, Connect. = 0.725 for dens.mod. cycle 4 = 0.288, Contrast = 0.570, Connect. = 0.738 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 771 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 70 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 45.227 2.282 1.325 0.896 1.000 0.714 CB 1.632 B: 16 41.033 2.334 0.866 0.919 1.000 0.800 CB 1.715 C: 11 19.547 2.122 0.583 0.852 0.900 0.800 CB 1.513 D: 11 25.103 2.306 0.585 0.832 1.000 0.800 CB 1.630 E: 16 7.659 1.702 0.437 0.370 0.867 0.533 CB 1.072 F: 43 44.898 2.280 0.709 0.576 0.929 0.643 CB 1.780 27 residues pruned to eliminate duplicates G: 46 47.242 2.320 0.651 0.598 0.933 0.711 CB 1.793 48 residues pruned to eliminate duplicates H: 34 36.353 2.208 0.608 0.697 0.939 0.818 CB 1.586 33 residues pruned to eliminate duplicates I: 35 44.684 2.192 0.907 0.682 0.971 0.824 CB 1.598 34 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 85 residues left after pruning, divided into chains as follows: A: 41 B: 44 CC for partial structure against native data = 36.94 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.288, Contrast = 0.342, Connect. = 0.636 for dens.mod. cycle 1 = 0.288, Contrast = 0.423, Connect. = 0.677 for dens.mod. cycle 2 = 0.288, Contrast = 0.544, Connect. = 0.740 for dens.mod. cycle 3 = 0.288, Contrast = 0.556, Connect. = 0.746 for dens.mod. cycle 4 = 0.288, Contrast = 0.575, Connect. = 0.753 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 722 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 79 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 44.422 2.348 1.051 0.894 1.000 0.786 CB 1.768 B: 16 29.463 2.184 1.216 0.849 0.867 0.733 CB 1.345 C: 10 24.961 2.261 0.595 0.914 1.000 0.778 CB 1.632 D: 11 25.482 2.136 0.766 0.884 1.000 0.800 CB 1.544 E: 28 27.263 2.125 0.609 0.445 1.000 0.630 CB 1.623 11 residues pruned to eliminate duplicates F: 29 27.865 2.207 0.701 0.439 0.893 0.571 CB 1.673 29 residues pruned to eliminate duplicates G: 44 48.542 2.304 0.940 0.605 0.907 0.698 CB 1.653 43 residues pruned to eliminate duplicates H: 20 17.444 2.087 0.330 0.380 1.000 0.684 CB 1.639 Using tripeptides from previous cycle as seeds 87 residues left after pruning, divided into chains as follows: A: 15 B: 10 C: 45 D: 17 CC for partial structure against native data = 36.50 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.288, Contrast = 0.349, Connect. = 0.642 for dens.mod. cycle 1 = 0.289, Contrast = 0.431, Connect. = 0.684 for dens.mod. cycle 2 = 0.289, Contrast = 0.548, Connect. = 0.742 for dens.mod. cycle 3 = 0.289, Contrast = 0.558, Connect. = 0.750 for dens.mod. cycle 4 = 0.289, Contrast = 0.577, Connect. = 0.756 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 3.80 - 2.97 - 2.58 - 2.34 - 2.17 - 2.03 - 1.93 - 1.84 - 1.77 - 1.71 0.575 0.663 0.684 0.686 0.711 0.735 0.728 0.657 0.562 0.519 0.745 0.822 0.841 0.838 0.886 0.921 0.920 0.890 0.831 0.799 N 1183 1196 1195 1173 1166 1263 1139 1251 1144 1095 Estimated mean FOM = 0.654 Pseudo-free CC = 69.79 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.7320 0.8829 0.1104 16.0000 17.12 2 0.6714 0.9557 0.2460 11.5360 15.19 3 0.5707 0.8352 -0.1719 10.9440 14.08 4 0.6586 0.9359 0.2013 10.8384 12.90 5 0.6397 0.7757 -0.0519 10.5072 14.27 6 0.4312 0.8278 -0.2043 10.2736 14.34 7 0.4362 0.8013 -0.1720 9.8752 14.70 8 0.6808 1.0929 0.2333 9.4688 15.67 9 0.6499 0.8049 -0.0186 9.2272 10.68 10 0.6553 1.0970 0.2733 8.0240 10.93 11 0.6835 0.8893 0.3183 6.7472 3.73 12 0.5109 0.7113 0.1337 6.6352 5.37 13 0.5685 0.7266 0.2768 4.6944 1.57 14 0.6228 0.9045 -0.2078 4.4000 4.46 15 0.7016 0.8818 0.1692 4.3088 3.61 16 0.6083 0.6763 0.1043 3.5680 1.61 17 0.6160 0.5247 0.1271 3.4592 1.92 Site x y z h(sig) near old near new 1 0.7336 0.8817 0.1121 17.4 1/0.15 7/7.35 3/8.67 10/9.91 8/11.99 2 0.6830 1.0912 0.2372 16.4 8/0.26 9/2.07 3/9.18 5/9.70 7/10.21 3 0.6721 0.9520 0.2418 15.8 2/0.31 7/2.11 1/8.67 2/9.18 9/9.63 4 0.4388 0.8039 -0.1718 15.3 7/0.24 5/2.14 6/9.08 9/9.71 13/9.76 5 0.4308 0.8246 -0.2049 14.8 6/0.21 4/2.14 9/8.09 6/9.48 2/9.70 6 0.5725 0.8383 -0.1733 14.8 3/0.25 11/2.05 13/2.10 8/8.32 10/8.93 7 0.6630 0.9391 0.2028 14.6 4/0.37 3/2.11 1/7.35 2/10.21 9/10.83 8 0.6417 0.7772 -0.0526 14.6 5/0.17 10/2.22 13/6.41 11/7.22 6/8.32 9 0.6622 1.0969 0.2691 13.5 10/0.49 2/2.07 5/8.09 3/9.63 4/9.71 10 0.6517 0.8039 -0.0273 13.0 9/0.43 8/2.22 13/7.32 11/7.40 6/8.93 11 0.5840 0.8491 -0.1358 11.2 3/2.12 6/2.05 13/2.43 8/7.22 10/7.40 12 0.5075 0.7125 0.1345 5.5 12/0.24 8/13.18 10/13.57 1/14.00 13/15.93 13 0.5862 0.8140 -0.1519 -4.6 3/1.97 6/2.10 11/2.43 8/6.41 10/7.32 Best trace (cycle 4 with CC 36.94%) was saved as P43212_visc-standard.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 0.6 - FFTs and peak-searches 1.6 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 45.9 - Tripeptide search 26.9 - Chain tracing 0.0 - NCS analysis 2.2 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:37:38 Total time: 77.48 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++