++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:20:15 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: P212121_pse14 P212121_pse14_fa -i -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P212121_pse14_fa.res FA and alpha from P212121_pse14_fa.hkl Native data from P212121_pse14.hkl Listing output to P212121_pse14_i.lst Phases output to P212121_pse14_i.phs Revised heavy atom sites output to P212121_pse14_i.hat Revised heavy atom phases output to P212121_pse14_i.pha Poly-Ala trace output to P212121_pse14_i.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 invert structure (and space group) -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 0.450 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 refine an unlimited number of heavy atoms Space group: P 21 21 21 Allowed origin shift code: 4 14 atoms read from file P212121_pse14_fa.res Trimmed to 13 atoms with occupancy > 0.2 11695 Reflections read from file P212121_pse14_fa.hkl 21043 Reflections read from file P212121_pse14.hkl 20997 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.004009h^2 -0.000438k^2 -0.000495l^2 +0.000000kl +0.000000hl +0.000000hk 22 Reflections with d > 2.489 and 0 in range 2.489 > d > 2.289 added Density sharpening factor set to 0.32 Fourier grid = 128 x 128 x 32 0.000 <= z <= 0.250 92 Point spherical net set up with radius 2.42A 24 Extra Fourier layers will be generated <|E^2-1|> = 0.780 ** Atom coordinates inverted ** 13 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 13 25.91% 0.174 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 25.58% = 0.154 for phases from phiT = phiA + alpha = 0.220 after including heavy atoms = 0.187, Contrast = 0.057, Connect. = 0.542 for dens.mod. cycle 1 = 0.201, Contrast = 0.157, Connect. = 0.592 for dens.mod. cycle 2 = 0.214, Contrast = 0.222, Connect. = 0.628 for dens.mod. cycle 3 = 0.224, Contrast = 0.263, Connect. = 0.645 for dens.mod. cycle 4 = 0.236, Contrast = 0.297, Connect. = 0.661 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1977 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 277 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 4.764 1.781 0.116 0.425 0.800 0.400 CB 1.448 B: 6 3.201 1.584 0.549 0.331 0.600 0.400 C 1.169 C: 6 2.048 1.266 0.472 0.355 0.800 0.400 CB 0.718 D: 6 3.882 1.500 0.341 0.412 0.800 0.400 CA 1.183 8 1.928 1.385 0.143 0.199 0.571 0.143 N 1.152 ? E: 6 7.172 1.372 0.975 0.737 1.000 0.600 CB 0.957 F: 8 4.013 1.573 0.578 0.217 0.714 0.571 N 1.193 G: 6 4.873 1.486 0.448 0.465 0.800 0.400 CB 1.311 H: 6 3.472 1.426 0.515 0.379 0.800 0.600 CB 1.023 I: 8 3.218 1.336 0.283 0.506 0.857 0.571 CA 0.823 J: 7 5.396 1.402 0.586 0.506 1.000 0.500 N 0.985 K: 9 2.651 1.380 0.576 0.355 0.750 0.500 CB 0.672 L: 6 2.107 1.040 0.422 0.731 0.800 0.600 C 0.647 M: 11 2.894 1.233 0.477 0.272 0.700 0.300 N 0.930 N: 8 3.578 1.455 0.340 0.442 0.714 0.286 CB 1.030 O: 6 2.280 1.613 0.367 0.392 0.600 0.600 CB 0.864 9 1.663 1.230 0.695 0.183 0.750 0.375 CB 0.550 ? 6 1.605 1.442 0.287 0.296 0.600 0.400 CB 0.810 ? P: 9 2.799 1.403 0.332 0.094 0.750 0.250 CB 1.188 6 1.065 1.387 -0.127 0.144 0.600 0.400 N 1.017 ? Q: 8 6.319 1.276 0.631 0.723 0.857 0.714 CB 1.095 R: 12 4.652 1.484 0.327 0.301 0.727 0.455 CB 1.224 10 1.959 1.330 0.009 0.287 0.667 0.222 CB 0.928 ? S: 8 4.475 1.238 0.622 0.714 0.714 0.429 CB 0.972 6 1.994 1.272 0.283 0.573 0.800 0.800 CB 0.636 ? T: 8 3.819 1.372 0.950 0.390 0.571 0.429 CB 1.061 83 residues left after pruning, divided into chains as follows: A: 6 B: 6 C: 6 D: 6 E: 8 F: 11 G: 6 H: 6 I: 8 J: 12 K: 8 CC for partial structure against native data = 7.32 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.250, Connect. = 0.601 for dens.mod. cycle 1 = 0.281, Contrast = 0.276, Connect. = 0.576 for dens.mod. cycle 2 = 0.281, Contrast = 0.335, Connect. = 0.625 for dens.mod. cycle 3 = 0.281, Contrast = 0.364, Connect. = 0.650 for dens.mod. cycle 4 = 0.281, Contrast = 0.390, Connect. = 0.669 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 2210 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 270 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 12.018 2.140 0.437 0.731 0.625 0.500 CB 1.796 B: 8 11.032 1.750 0.644 0.763 1.000 0.857 CB 1.148 C: 8 7.642 2.118 0.249 0.461 0.714 0.571 CA 1.590 D: 9 5.425 1.755 0.192 0.430 0.750 0.500 CB 1.315 E: 8 8.291 1.556 0.481 0.733 1.000 0.286 CA 1.103 F: 8 5.350 1.950 -0.094 0.429 0.857 0.571 CB 1.438 G: 8 4.561 1.980 -0.109 0.376 0.714 0.571 CA 1.561 H: 7 2.545 1.716 0.303 0.284 0.500 0.333 CB 1.185 I: 7 3.921 1.725 0.604 0.286 0.667 0.500 N 1.104 J: 18 6.595 1.716 0.500 0.264 0.647 0.235 CB 1.257 K: 10 5.399 1.902 0.244 0.279 0.667 0.556 CB 1.465 5 residues pruned to eliminate duplicates L: 6 2.587 1.419 0.001 0.416 0.800 0.400 CB 1.112 M: 11 5.496 1.435 0.447 0.421 0.900 0.300 N 1.009 N: 12 2.772 1.527 0.560 0.045 0.636 0.364 CB 1.011 O: 10 2.639 1.627 0.145 0.476 0.556 0.222 CB 0.871 P: 7 3.097 1.382 0.492 0.271 0.833 0.500 CB 0.954 7 1.830 1.261 0.609 0.387 0.667 0.333 CB 0.622 ? Q: 12 3.912 1.474 0.251 0.347 0.727 0.455 CB 1.038 Using tripeptides from previous cycle as seeds 107 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 8 D: 9 E: 8 F: 8 G: 7 H: 13 I: 13 J: 11 K: 6 L: 7 CC for partial structure against native data = 10.79 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.302, Connect. = 0.611 for dens.mod. cycle 1 = 0.281, Contrast = 0.348, Connect. = 0.613 for dens.mod. cycle 2 = 0.281, Contrast = 0.419, Connect. = 0.663 for dens.mod. cycle 3 = 0.281, Contrast = 0.443, Connect. = 0.683 for dens.mod. cycle 4 = 0.281, Contrast = 0.460, Connect. = 0.697 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1976 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 256 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 12.916 1.809 0.695 0.820 1.000 0.667 CB 1.064 B: 7 12.766 1.812 0.899 0.697 0.833 0.333 N 1.518 C: 8 4.248 1.939 -0.032 0.405 0.714 0.429 CB 1.324 D: 6 7.017 2.072 -0.036 0.701 1.000 0.800 CB 1.307 E: 9 9.390 1.868 0.065 0.709 1.000 0.500 CB 1.380 F: 6 2.936 1.738 0.024 0.437 0.600 0.600 N 1.313 G: 8 6.307 1.988 0.214 0.330 0.714 0.429 CB 1.666 H: 10 4.623 1.822 0.504 0.224 0.667 0.333 CB 1.165 I: 9 8.568 1.881 0.524 0.327 0.875 0.500 CB 1.462 J: 13 8.000 1.981 0.208 0.245 0.833 0.417 CB 1.554 8 residues pruned to eliminate duplicates K: 10 3.351 1.691 0.306 0.222 0.667 0.444 CB 1.051 L: 6 4.060 1.474 1.018 0.417 0.800 0.400 N 0.832 M: 10 7.567 1.732 0.915 0.496 0.778 0.556 CB 0.982 N: 8 4.176 1.329 0.218 0.539 0.857 0.571 CB 1.096 O: 6 2.799 1.387 0.945 0.434 0.600 0.400 CB 0.828 6 1.863 1.400 0.854 0.307 0.600 0.400 CB 0.663 ? P: 8 3.772 1.648 0.462 0.415 0.714 0.571 CB 0.906 Q: 6 3.306 1.169 0.685 0.562 0.800 0.600 CA 0.884 R: 8 2.705 1.345 0.083 0.504 0.857 0.571 CB 0.816 S: 6 2.313 1.314 0.167 0.478 0.800 0.800 CA 0.862 T: 6 7.920 1.676 0.114 0.815 1.000 1.000 CB 1.443 6 0.961 1.063 0.627 0.293 0.800 0.400 CB 0.392 ? Using tripeptides from previous cycle as seeds U: 12 8.859 1.918 0.365 0.404 0.727 0.364 CB 1.551 7 residues pruned to eliminate duplicates 95 residues left after pruning, divided into chains as follows: A: 10 B: 7 C: 9 D: 9 E: 12 F: 10 G: 8 H: 6 I: 7 J: 6 K: 11 CC for partial structure against native data = 9.89 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.301, Connect. = 0.614 for dens.mod. cycle 1 = 0.281, Contrast = 0.361, Connect. = 0.622 for dens.mod. cycle 2 = 0.281, Contrast = 0.443, Connect. = 0.677 for dens.mod. cycle 3 = 0.281, Contrast = 0.464, Connect. = 0.693 for dens.mod. cycle 4 = 0.281, Contrast = 0.477, Connect. = 0.704 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1970 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 260 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 7.796 2.218 0.041 0.494 0.833 0.333 CB 1.664 B: 9 8.824 1.934 0.397 0.754 0.875 0.875 N 1.053 C: 10 12.543 2.005 0.317 0.790 1.000 0.556 CB 1.228 D: 6 7.322 2.125 -0.078 0.733 1.000 0.800 CB 1.354 E: 22 11.058 1.796 0.609 0.327 0.714 0.381 CB 1.414 F: 10 4.539 1.844 0.354 0.367 0.444 0.444 N 1.572 G: 6 4.661 1.727 0.337 0.584 0.600 0.600 CB 1.387 H: 13 7.515 1.734 0.391 0.354 0.667 0.500 CB 1.580 I: 8 7.057 2.010 0.430 0.338 0.714 0.571 CB 1.550 6 residues pruned to eliminate duplicates J: 11 5.047 1.566 0.357 0.376 0.800 0.300 O 1.072 K: 12 5.868 1.865 0.283 0.306 0.636 0.455 CB 1.441 L: 7 4.130 1.430 0.408 0.313 0.833 0.500 O 1.236 M: 8 2.621 1.306 0.146 0.360 0.857 0.429 N 0.897 N: 6 2.263 1.414 0.338 0.288 0.600 0.400 N 1.131 O: 6 6.696 1.587 0.518 0.666 0.800 0.800 CB 1.333 P: 8 5.279 1.712 0.476 0.245 0.857 0.571 N 1.236 6 1.295 1.279 0.463 0.378 0.400 0.400 CB 0.882 ? Q: 7 2.355 1.410 0.436 0.494 1.000 0.667 CB 0.477 R: 7 3.243 1.409 0.133 0.438 0.833 0.500 CA 1.061 S: 6 2.245 1.354 0.223 0.626 1.000 0.600 CB 0.538 T: 7 3.694 1.529 0.406 0.347 0.667 0.333 N 1.242 Using tripeptides from previous cycle as seeds U: 13 7.382 1.908 0.465 0.176 0.750 0.167 CB 1.504 9 residues pruned to eliminate duplicates 101 residues left after pruning, divided into chains as follows: A: 7 B: 9 C: 10 D: 6 E: 16 F: 10 G: 11 H: 7 I: 7 J: 7 K: 11 CC for partial structure against native data = 11.48 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.318, Connect. = 0.617 for dens.mod. cycle 1 = 0.281, Contrast = 0.380, Connect. = 0.626 for dens.mod. cycle 2 = 0.281, Contrast = 0.459, Connect. = 0.677 for dens.mod. cycle 3 = 0.281, Contrast = 0.478, Connect. = 0.695 for dens.mod. cycle 4 = 0.281, Contrast = 0.490, Connect. = 0.704 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1907 peaks > 0.5 sigma used to seed fragment search Space for about 500 unique residues taking solvent into account 263 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 6.515 1.956 0.283 0.459 0.625 0.500 CB 1.531 B: 10 5.510 1.960 -0.142 0.599 0.889 0.444 CB 1.118 C: 7 4.699 1.877 0.038 0.619 0.667 0.500 CB 1.320 D: 6 2.570 1.681 0.007 0.338 0.600 0.600 N 1.350 E: 6 9.869 1.678 1.352 0.647 0.800 0.600 N 1.218 F: 8 8.277 2.037 0.397 0.368 0.857 0.571 CB 1.478 G: 10 11.419 1.908 0.504 0.832 0.889 0.778 N 1.120 H: 21 7.209 1.747 0.184 0.287 0.750 0.400 CB 1.322 I: 6 6.448 1.945 0.223 0.689 0.800 0.800 CB 1.274 J: 7 8.475 1.934 0.652 0.299 0.833 0.333 CB 1.626 K: 6 4.637 1.645 1.060 0.360 0.600 0.400 N 1.186 L: 6 2.085 1.391 0.428 0.293 0.800 0.400 CB 0.740 6 1.798 1.210 0.496 0.457 0.800 0.400 CB 0.580 ? M: 9 3.595 1.416 0.302 0.336 0.750 0.250 CB 1.099 N: 9 3.398 1.660 0.614 0.434 0.625 0.500 CB 0.768 O: 15 4.268 1.550 0.619 0.201 0.571 0.286 CB 1.135 7 1.226 1.385 0.772 0.304 0.333 0.333 CB 0.761 ? P: 7 3.063 1.282 0.493 0.575 0.833 0.667 CB 0.730 Q: 8 2.257 1.360 0.151 0.388 0.714 0.714 CA 0.860 R: 6 3.684 1.330 0.244 0.806 0.800 0.800 CB 0.953 Using tripeptides from previous cycle as seeds S: 12 6.816 1.807 0.483 0.275 0.727 0.273 CB 1.362 103 residues left after pruning, divided into chains as follows: A: 9 B: 10 C: 7 D: 6 E: 8 F: 10 G: 12 H: 7 I: 9 J: 7 K: 6 L: 12 CC for partial structure against native data = 11.25 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.281, Contrast = 0.307, Connect. = 0.615 for dens.mod. cycle 1 = 0.282, Contrast = 0.370, Connect. = 0.624 for dens.mod. cycle 2 = 0.282, Contrast = 0.457, Connect. = 0.679 for dens.mod. cycle 3 = 0.282, Contrast = 0.477, Connect. = 0.695 for dens.mod. cycle 4 = 0.282, Contrast = 0.488, Connect. = 0.705 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.06 - 3.98 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.604 0.668 0.637 0.589 0.499 0.443 0.408 0.382 0.367 0.342 0.754 0.851 0.838 0.799 0.721 0.658 0.620 0.620 0.614 0.585 N 2105 2122 2088 2157 2094 2053 2100 2199 2179 1900 Estimated mean FOM = 0.495 Pseudo-free CC = 54.93 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.8015 0.9324 0.7531 1.0000 37.82 2 1.0483 0.8182 0.7691 0.9265 35.32 3 1.0476 0.7676 0.8750 0.5454 22.07 4 0.8928 0.8282 0.7954 0.5353 20.30 5 1.2306 0.7506 0.9106 0.3588 13.42 6 1.0302 0.9476 0.7155 0.3177 12.28 7 1.2196 0.7941 0.8073 0.3139 12.54 8 0.9915 0.6880 0.8794 0.2916 11.12 9 1.2330 0.9898 0.7414 0.2491 8.95 10 0.9746 0.9026 0.7010 0.2387 8.22 11 1.0357 1.0691 0.7694 0.2370 7.54 12 0.8235 1.0911 0.8079 0.2341 8.82 13 1.1406 0.9268 0.6751 0.1740 5.87 Site x y z h(sig) near old near new 1 0.8016 0.9326 0.7530 37.8 1/0.02 17/2.77 14/2.94 18/10.84 4/10.90 2 1.0490 0.8187 0.7691 35.4 2/0.06 19/2.64 16/2.75 15/2.94 20/8.10 3 1.0463 0.7677 0.8743 22.1 3/0.11 20/2.81 8/7.27 15/8.47 16/9.44 4 0.8939 0.8284 0.7949 20.3 4/0.08 18/2.82 15/8.75 19/9.24 2/9.31 5 1.2288 0.7506 0.9108 13.5 5/0.11 6/10.55 3/11.18 20/12.48 8/14.94 6 1.2166 0.7942 0.8068 12.7 7/0.18 16/9.78 15/10.20 2/10.50 5/10.55 7 1.0314 0.9477 0.7148 12.3 6/0.10 11/4.96 13/7.48 19/9.74 12/11.24 8 0.9907 0.6893 0.8799 11.2 8/0.13 3/7.27 20/8.49 16/13.26 15/13.85 9 1.2312 0.9911 0.7422 9.0 9/0.16 13/9.66 7/12.35 12/12.86 11/16.77 10 0.8232 1.0914 0.8079 8.8 12/0.03 14/11.59 12/13.29 1/14.22 17/14.92 11 0.9778 0.9034 0.7016 8.3 10/0.20 7/4.96 19/7.79 13/9.86 2/10.37 12 1.0425 1.0669 0.7707 7.7 11/0.45 7/11.24 9/12.86 10/13.29 11/15.52 13 1.1417 0.9248 0.6787 6.2 13/0.38 7/7.48 9/9.66 11/9.86 19/11.65 14 0.8030 0.9680 0.7519 -6.2 1/2.96 1/2.94 17/3.53 10/11.59 11/12.37 15 1.0452 0.8234 0.7997 -5.7 2/2.94 2/2.94 16/3.79 19/5.06 20/5.88 16 1.0549 0.7869 0.7766 -5.6 2/2.72 2/2.75 15/3.79 19/5.08 20/6.66 17 0.8075 0.9392 0.7247 -5.0 1/2.78 1/2.77 14/3.53 11/10.49 18/11.80 18 0.8882 0.8177 0.7669 -5.0 4/2.85 4/2.82 19/8.73 2/9.28 15/9.59 19 1.0339 0.8367 0.7482 -4.9 2/2.65 2/2.64 15/5.06 16/5.08 11/7.79 20 1.0445 0.7760 0.8457 -4.8 3/2.88 3/2.81 15/5.88 16/6.66 2/8.10 Best trace (cycle 4 with CC 11.48%) was saved as P212121_pse14_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 9.8 - Setup, data input and phasing 1.1 - FFTs and peak-searches 4.7 - Sphere of influence 1.4 - Rest of density modification 0.0 - Alpha-helix search 48.5 - Tripeptide search 58.3 - Chain tracing 0.0 - NCS analysis 4.5 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:22:24 Total time: 128.40 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++