++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:06:17 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: P2212_pse14 P2212_pse14_fa -i -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P2212_pse14_fa.res FA and alpha from P2212_pse14_fa.hkl Native data from P2212_pse14.hkl Listing output to P2212_pse14_i.lst Phases output to P2212_pse14_i.phs Revised heavy atom sites output to P2212_pse14_i.hat Revised heavy atom phases output to P2212_pse14_i.pha Poly-Ala trace output to P2212_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 2 21 2 Allowed origin shift code: 4 14 atoms read from file P2212_pse14_fa.res Trimmed to 7 atoms with occupancy > 0.2 11695 Reflections read from file P2212_pse14_fa.hkl 21043 Reflections read from file P2212_pse14.hkl 21026 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003964h^2 -0.000439k^2 -0.000491l^2 +0.000000kl +0.000000hl +0.000000hk 27 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 63 0.000 <= z <= 0.500 92 Point spherical net set up with radius 2.42A 24 Extra Fourier layers will be generated <|E^2-1|> = 0.781 ** Atom coordinates inverted ** 7 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 7 17.14% 0.385 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 16.75% = 0.115 for phases from phiT = phiA + alpha = 0.185 after including heavy atoms = 0.175, Contrast = 0.039, Connect. = 0.534 for dens.mod. cycle 1 = 0.194, Contrast = 0.131, Connect. = 0.614 for dens.mod. cycle 2 = 0.208, Contrast = 0.182, Connect. = 0.638 for dens.mod. cycle 3 = 0.221, Contrast = 0.222, Connect. = 0.653 for dens.mod. cycle 4 = 0.231, Contrast = 0.251, Connect. = 0.664 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 1803 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 244 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 2.526 1.637 0.087 0.356 0.500 0.333 CB 1.353 B: 6 3.596 1.619 0.746 0.365 0.600 0.400 CB 1.096 C: 10 2.936 1.365 0.486 0.216 0.667 0.222 N 1.010 D: 6 2.220 1.467 0.186 0.605 0.800 0.800 CB 0.645 E: 6 2.856 1.520 0.101 0.417 0.800 0.600 N 1.040 F: 8 2.547 1.368 0.494 0.173 0.714 0.143 CB 0.980 6 1.798 1.391 0.417 0.285 0.600 0.400 N 0.866 ? G: 6 2.536 1.453 0.384 0.467 0.600 0.600 CB 0.973 H: 6 2.283 1.318 0.399 0.483 0.800 0.400 CB 0.704 I: 7 2.784 1.198 0.508 0.394 0.667 0.333 N 1.056 J: 6 2.567 1.579 0.565 0.287 0.600 0.600 CB 0.984 K: 8 3.746 1.486 0.187 0.395 0.714 0.429 N 1.255 L: 6 2.309 1.496 0.850 0.112 0.600 0.400 CB 1.016 M: 6 3.239 1.535 0.523 0.285 0.600 0.400 CA 1.316 N: 6 4.526 1.486 0.846 0.318 0.800 0.400 CB 1.128 O: 10 4.117 1.488 0.351 0.299 0.778 0.556 N 1.099 P: 9 2.323 1.216 0.682 0.266 0.625 0.250 N 0.839 Q: 7 3.076 1.415 0.279 0.488 0.833 0.667 CB 0.843 R: 7 4.016 1.340 0.751 0.370 0.833 0.667 N 0.963 6 1.709 1.314 0.979 0.290 0.400 0.400 CB 0.929 ? S: 7 2.848 1.107 0.690 0.345 0.833 0.667 CB 0.883 T: 6 3.321 1.298 0.407 0.493 0.800 0.400 N 1.024 U: 6 2.975 1.352 -0.025 0.502 1.000 0.400 C 1.008 V: 8 3.624 1.362 0.222 0.359 0.857 0.429 N 1.117 W: 6 3.100 1.496 0.206 0.380 0.800 0.400 CB 1.091 105 residues left after pruning, divided into chains as follows: A: 10 B: 7 C: 6 D: 6 E: 7 F: 8 G: 6 H: 6 I: 6 J: 9 K: 6 L: 7 M: 7 N: 6 O: 8 CC for partial structure against native data = 8.82 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.256, Connect. = 0.605 for dens.mod. cycle 1 = 0.281, Contrast = 0.278, Connect. = 0.591 for dens.mod. cycle 2 = 0.281, Contrast = 0.322, Connect. = 0.630 for dens.mod. cycle 3 = 0.281, Contrast = 0.343, Connect. = 0.648 for dens.mod. cycle 4 = 0.281, Contrast = 0.362, Connect. = 0.663 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 498 unique residues taking solvent into account 253 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 7.103 1.991 0.064 0.635 1.000 0.600 CB 1.321 B: 6 4.281 1.920 0.365 0.383 0.600 0.400 CB 1.380 C: 6 9.598 1.819 0.738 0.565 0.800 0.400 CB 1.594 D: 7 3.661 1.611 0.631 0.302 0.667 0.500 O 1.065 E: 6 4.014 1.746 0.402 0.373 0.800 0.600 CB 1.050 F: 6 4.852 1.687 0.075 0.526 0.800 0.200 O 1.458 G: 12 3.002 1.494 0.420 0.287 0.545 0.273 CB 0.995 6 1.979 1.199 0.741 0.349 0.600 0.400 C 0.833 ? H: 7 2.608 1.495 0.400 0.342 0.833 0.333 CB 0.726 I: 6 2.106 1.700 0.238 0.364 0.600 0.400 CB 0.863 J: 8 8.488 1.675 0.755 0.397 1.000 0.429 CB 1.217 K: 10 2.832 1.573 -0.015 0.265 0.778 0.222 CB 1.023 L: 11 4.080 1.734 0.006 0.393 0.600 0.400 CB 1.381 M: 12 4.570 1.635 0.613 0.267 0.818 0.455 CB 0.833 N: 6 2.887 1.234 0.292 0.496 0.800 0.600 CA 1.016 O: 9 2.950 1.433 0.205 0.465 0.875 0.500 CB 0.715 6 1.728 1.593 0.109 0.298 0.600 0.400 CB 0.914 ? 6 1.981 1.234 0.267 0.304 0.800 0.400 O 0.881 ? P: 10 6.243 1.589 0.495 0.393 0.778 0.222 CA 1.262 Using tripeptides from previous cycle as seeds Q: 6 3.097 1.130 0.523 0.630 1.000 0.600 CB 0.712 R: 6 2.788 1.261 1.212 0.445 0.600 0.600 N 0.788 S: 6 5.900 1.879 0.510 0.352 0.800 0.400 N 1.364 80 residues left after pruning, divided into chains as follows: A: 6 B: 6 C: 6 D: 6 E: 8 F: 12 G: 6 H: 9 I: 9 J: 6 K: 6 CC for partial structure against native data = 6.46 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.267, Connect. = 0.612 for dens.mod. cycle 1 = 0.281, Contrast = 0.303, Connect. = 0.607 for dens.mod. cycle 2 = 0.281, Contrast = 0.362, Connect. = 0.651 for dens.mod. cycle 3 = 0.281, Contrast = 0.392, Connect. = 0.673 for dens.mod. cycle 4 = 0.281, Contrast = 0.412, Connect. = 0.687 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 2080 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 258 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 7.064 2.119 0.295 0.450 0.714 0.286 CB 1.434 B: 13 11.911 2.289 0.531 0.301 0.833 0.417 CB 1.470 C: 8 9.353 1.962 0.595 0.460 0.857 0.571 CB 1.372 D: 13 8.454 1.936 0.484 0.246 0.750 0.250 CB 1.518 E: 11 7.902 2.102 0.255 0.302 0.800 0.500 CB 1.476 F: 6 13.757 2.103 0.808 0.454 1.000 0.600 CA 1.696 G: 6 5.777 2.111 0.474 0.382 0.600 0.400 CA 1.568 H: 8 11.365 1.695 0.396 0.838 1.000 0.714 CB 1.356 6 1.795 1.855 -0.245 0.424 0.800 0.600 CB 0.775 ? I: 10 3.076 1.520 0.404 0.229 0.556 0.444 CB 1.185 J: 9 11.037 2.264 0.531 0.346 0.750 0.375 CA 1.774 5 residues pruned to eliminate duplicates K: 6 2.462 1.526 0.288 0.403 0.600 0.200 O 1.033 L: 14 6.717 1.942 0.308 0.403 0.769 0.462 CB 1.056 M: 6 3.946 1.390 0.690 0.383 0.800 0.400 CB 1.064 N: 6 4.373 1.280 0.556 0.719 1.000 0.400 C 0.806 O: 9 2.864 1.358 0.282 0.299 0.875 0.500 CB 0.832 P: 7 7.131 1.736 0.511 0.559 0.833 0.833 CA 1.257 6 residues pruned to eliminate duplicates Q: 13 2.468 1.443 0.150 0.112 0.583 0.083 CB 1.203 R: 13 7.119 1.782 0.180 0.388 0.917 0.583 CB 1.201 Using tripeptides from previous cycle as seeds 117 residues left after pruning, divided into chains as follows: A: 8 B: 13 C: 8 D: 12 E: 11 F: 6 G: 8 H: 10 I: 6 J: 6 K: 9 L: 7 M: 13 CC for partial structure against native data = 10.45 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.300, Connect. = 0.621 for dens.mod. cycle 1 = 0.281, Contrast = 0.352, Connect. = 0.630 for dens.mod. cycle 2 = 0.281, Contrast = 0.413, Connect. = 0.675 for dens.mod. cycle 3 = 0.281, Contrast = 0.432, Connect. = 0.690 for dens.mod. cycle 4 = 0.281, Contrast = 0.446, Connect. = 0.700 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 498 unique residues taking solvent into account 261 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 21 8.859 1.765 0.321 0.362 0.800 0.450 CB 1.233 B: 8 11.089 2.171 0.500 0.535 0.857 0.286 CB 1.451 C: 10 7.941 2.077 0.486 0.286 0.667 0.222 CB 1.636 D: 6 6.183 1.718 0.405 0.681 0.800 0.800 N 1.213 E: 13 8.449 2.216 0.248 0.326 0.833 0.417 CB 1.281 F: 12 6.290 1.789 0.409 0.340 0.818 0.455 CB 1.096 8 1.634 1.592 0.452 0.105 0.571 0.143 CB 0.773 ? G: 12 6.772 2.142 -0.168 0.331 0.909 0.545 CB 1.516 H: 6 3.753 1.866 -0.346 0.539 1.000 0.400 CB 1.324 I: 6 3.606 1.388 0.567 0.607 0.600 0.600 CB 1.116 J: 7 5.174 1.329 0.375 0.843 1.000 0.667 CA 0.860 K: 6 3.991 1.890 0.359 0.288 0.600 0.600 CB 1.470 L: 7 6.515 1.576 0.305 0.595 1.000 0.500 CB 1.181 M: 8 3.180 1.659 0.428 0.071 0.714 0.429 CB 1.242 N: 7 4.447 1.325 0.504 0.608 0.833 0.500 CB 0.987 O: 9 2.508 1.300 0.423 0.262 0.750 0.500 N 0.838 P: 8 3.847 1.375 0.469 0.500 0.714 0.143 CB 1.008 Using tripeptides from previous cycle as seeds Q: 6 5.386 1.777 0.407 0.690 0.600 0.600 CA 1.348 110 residues left after pruning, divided into chains as follows: A: 21 B: 8 C: 10 D: 13 E: 6 F: 12 G: 6 H: 7 I: 8 J: 7 K: 6 L: 6 CC for partial structure against native data = 11.78 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.323, Connect. = 0.622 for dens.mod. cycle 1 = 0.281, Contrast = 0.375, Connect. = 0.630 for dens.mod. cycle 2 = 0.281, Contrast = 0.438, Connect. = 0.676 for dens.mod. cycle 3 = 0.281, Contrast = 0.456, Connect. = 0.692 for dens.mod. cycle 4 = 0.281, Contrast = 0.468, Connect. = 0.703 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 1953 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 258 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 19 13.063 2.102 0.300 0.303 0.833 0.389 CB 1.683 B: 8 5.105 1.892 -0.110 0.396 0.857 0.286 CB 1.493 C: 7 7.720 2.151 0.125 0.480 0.833 0.667 CB 1.594 D: 11 9.493 2.117 0.324 0.280 0.900 0.500 CB 1.527 E: 7 5.208 2.036 0.511 0.297 0.667 0.333 CB 1.301 F: 7 11.692 1.923 0.254 0.818 1.000 0.833 CB 1.500 G: 8 6.248 1.818 0.023 0.490 1.000 0.714 CB 1.283 H: 9 5.163 1.749 0.416 0.210 0.875 0.375 CB 1.186 I: 6 3.833 1.831 0.461 0.488 0.600 0.400 CB 1.081 J: 6 7.145 1.779 0.676 0.808 0.600 0.400 N 1.365 K: 8 7.356 1.977 0.310 0.579 0.857 0.286 CB 1.160 L: 7 5.656 1.313 0.656 0.712 0.833 0.500 CB 1.052 M: 6 2.748 1.404 0.235 0.471 1.000 0.600 CB 0.730 N: 7 4.691 1.335 0.768 0.400 0.833 0.333 C 1.082 6 1.345 1.231 0.497 0.269 0.600 0.200 CB 0.707 ? O: 6 9.419 1.424 0.842 0.831 1.000 1.000 N 1.207 P: 13 3.284 1.510 0.247 0.388 0.667 0.500 CB 0.851 Q: 6 2.673 1.276 0.233 0.299 0.800 0.600 C 1.188 6 1.484 1.329 0.165 0.443 0.400 0.400 CB 1.137 ? Using tripeptides from previous cycle as seeds R: 19 7.812 1.905 0.293 0.188 0.778 0.222 CB 1.398 11 residues pruned to eliminate duplicates 114 residues left after pruning, divided into chains as follows: A: 19 B: 8 C: 7 D: 7 E: 7 F: 8 G: 6 H: 6 I: 8 J: 7 K: 6 L: 6 M: 19 CC for partial structure against native data = 12.36 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.281, Contrast = 0.329, Connect. = 0.626 for dens.mod. cycle 1 = 0.282, Contrast = 0.380, Connect. = 0.633 for dens.mod. cycle 2 = 0.282, Contrast = 0.446, Connect. = 0.679 for dens.mod. cycle 3 = 0.282, Contrast = 0.463, Connect. = 0.693 for dens.mod. cycle 4 = 0.282, Contrast = 0.475, Connect. = 0.705 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.07 - 3.99 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.486 0.548 0.539 0.557 0.505 0.462 0.447 0.414 0.333 0.285 0.643 0.724 0.742 0.763 0.726 0.690 0.677 0.677 0.569 0.495 N 2104 2107 2122 2159 2095 2055 2101 2201 2180 1902 Estimated mean FOM = 0.459 Pseudo-free CC = 50.53 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.6976 0.7500 0.5000 1.0000 53.16 2 0.4503 0.6376 0.5190 0.8814 23.11 3 0.9498 0.5033 0.9818 0.8575 20.98 4 0.8952 0.5054 0.9541 0.7272 18.96 5 0.9553 0.5519 0.8750 0.6736 16.94 6 0.4488 0.5853 0.6226 0.4629 10.32 7 0.6899 0.7295 0.3876 0.3850 9.22 Site x y z h(sig) near old near new 1 0.6971 0.7500 0.5000 53.2 1/0.03 8/2.46 8/2.46 10/2.60 10/2.60 2 0.4509 0.6375 0.5183 23.2 2/0.08 13/2.66 15/5.94 6/10.72 9/12.75 3 0.9518 0.5036 0.9825 21.1 3/0.14 4/4.22 16/4.78 3/5.59 17/5.68 4 0.8954 0.5054 0.9543 19.0 4/0.02 17/2.50 16/2.95 3/4.22 5/9.13 5 0.9550 0.5510 0.8747 17.0 5/0.08 17/7.06 4/9.13 5/9.93 3/10.97 6 0.4505 0.5861 0.6218 10.4 6/0.14 13/8.24 2/10.72 15/12.18 9/19.78 7 0.6901 0.7285 0.3874 9.3 7/0.08 8/9.87 10/10.12 1/10.86 1/10.86 8 0.6977 0.7729 0.4836 -7.1 1/2.46 10/2.29 1/2.46 1/2.46 10/4.52 9 0.5983 0.7500 0.5000 -6.2 1/5.73 1/5.70 1/5.70 10/5.88 10/5.88 10 0.6900 0.7200 0.4935 -6.1 1/2.60 8/2.29 1/2.60 1/2.60 8/4.52 11 0.8784 0.7500 0.5000 -5.5 1/10.43 18/4.28 18/4.28 1/10.45 1/10.45 12 0.9506 0.2813 1.0211 -5.5 3/18.78 12/6.56 3/18.80 16/18.97 3/19.06 13 0.4389 0.6200 0.5406 -5.4 2/2.60 2/2.66 15/7.11 6/8.24 14/14.32 14 0.2897 0.7500 0.5000 -5.4 2/13.27 2/13.29 2/13.29 13/14.32 13/14.32 15 0.5535 0.6426 0.5214 -5.3 2/5.97 2/5.94 13/7.11 9/9.50 9/9.50 16 0.8694 0.4979 0.9801 -5.2 4/2.95 4/2.95 3/4.78 17/5.06 3/10.31 17 0.8979 0.5286 0.9375 -5.1 4/2.49 4/2.50 16/5.06 3/5.68 5/7.06 18 0.9525 0.7500 0.5000 -5.0 1/14.70 11/4.28 11/4.28 1/14.73 1/14.73 Best trace (cycle 5 with CC 12.36%) was saved as P2212_pse14_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 5.0 - Setup, data input and phasing 2.4 - FFTs and peak-searches 5.1 - Sphere of influence 2.8 - Rest of density modification 0.0 - Alpha-helix search 48.8 - Tripeptide search 61.0 - Chain tracing 0.0 - NCS analysis 4.8 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:08:27 Total time: 129.98 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++