++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:09:07 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: P2122_pse14 P2122_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P2122_pse14_fa.res FA and alpha from P2122_pse14_fa.hkl Native data from P2122_pse14.hkl Listing output to P2122_pse14.lst Phases output to P2122_pse14.phs Revised heavy atom sites output to P2122_pse14.hat Revised heavy atom phases output to P2122_pse14.pha Poly-Ala trace output to P2122_pse14.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 0.450 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 2 2 Allowed origin shift code: 4 14 atoms read from file P2122_pse14_fa.res Trimmed to 12 atoms with occupancy > 0.2 11695 Reflections read from file P2122_pse14_fa.hkl 21043 Reflections read from file P2122_pse14.hkl 21033 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003986h^2 -0.000437k^2 -0.000492l^2 +0.000000kl +0.000000hl +0.000000hk 25 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 12 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 12 19.07% 0.253 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 18.71% = 0.122 for phases from phiT = phiA + alpha = 0.198 after including heavy atoms = 0.179, Contrast = 0.034, Connect. = 0.526 for dens.mod. cycle 1 = 0.196, Contrast = 0.119, Connect. = 0.603 for dens.mod. cycle 2 = 0.211, Contrast = 0.167, Connect. = 0.626 for dens.mod. cycle 3 = 0.222, Contrast = 0.206, Connect. = 0.644 for dens.mod. cycle 4 = 0.232, Contrast = 0.236, Connect. = 0.655 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 1877 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 2.212 1.424 0.120 0.357 0.667 0.333 CB 0.992 B: 7 2.327 1.501 0.387 0.244 0.667 0.333 CB 0.920 C: 8 2.706 1.331 0.348 0.382 0.714 0.429 CB 0.905 D: 7 2.745 1.445 0.226 0.369 0.833 0.500 CB 0.873 E: 10 5.376 1.501 0.384 0.367 0.778 0.556 CB 1.280 F: 6 3.967 1.630 0.164 0.390 0.800 0.600 CB 1.313 G: 6 2.051 1.193 0.114 0.384 0.800 0.600 C 0.975 H: 6 5.145 1.474 0.531 0.478 0.800 0.400 N 1.303 I: 7 2.110 1.302 0.395 0.127 0.667 0.333 N 1.135 9 1.458 1.254 0.752 0.269 0.500 0.500 CB 0.610 ? J: 6 4.412 1.263 0.757 0.653 0.800 0.800 CB 0.964 K: 8 3.926 1.343 0.157 0.403 1.000 0.286 CB 1.058 L: 7 2.482 1.192 0.223 0.474 0.833 0.667 O 0.856 M: 11 2.889 1.369 0.382 0.271 0.600 0.500 CB 1.044 N: 6 3.445 1.387 0.461 0.539 1.000 0.400 CB 0.732 O: 16 2.707 1.378 0.707 0.191 0.600 0.333 CB 0.717 6 1.437 1.261 -0.136 0.316 0.800 0.600 CB 0.903 ? P: 6 2.930 1.332 0.452 0.348 1.000 0.600 CB 0.799 85 residues left after pruning, divided into chains as follows: A: 7 B: 8 C: 7 D: 8 E: 6 F: 6 G: 6 H: 7 I: 6 J: 7 K: 11 L: 6 CC for partial structure against native data = 7.01 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.239, Connect. = 0.594 for dens.mod. cycle 1 = 0.281, Contrast = 0.263, Connect. = 0.576 for dens.mod. cycle 2 = 0.281, Contrast = 0.304, Connect. = 0.617 for dens.mod. cycle 3 = 0.281, Contrast = 0.328, Connect. = 0.639 for dens.mod. cycle 4 = 0.281, Contrast = 0.350, Connect. = 0.656 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2265 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 229 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 8.721 1.762 0.505 0.599 0.857 0.571 CB 1.320 B: 9 6.125 1.629 0.738 0.394 0.750 0.375 CB 1.140 C: 9 6.193 1.842 0.497 0.378 0.625 0.375 CB 1.447 D: 8 6.096 1.505 0.684 0.542 0.857 0.571 CB 1.018 6 0.413 1.713 -0.364 0.386 0.800 0.600 CB 0.239 ? E: 11 4.861 1.667 0.462 0.356 0.700 0.200 CB 1.053 6 1.844 0.988 -0.010 0.627 1.000 0.800 N 0.747 ? F: 10 4.784 1.730 0.631 0.438 0.667 0.333 CB 0.904 6 1.626 1.413 -0.100 0.354 0.600 0.600 N 1.116 ? G: 7 2.976 1.786 0.877 0.083 0.667 0.333 CB 0.932 H: 6 2.719 1.699 -0.172 0.300 0.800 0.600 CB 1.351 I: 10 6.924 1.783 0.356 0.510 0.778 0.333 CB 1.215 J: 9 3.391 1.445 -0.025 0.502 0.875 0.250 CB 0.971 K: 6 2.183 1.544 0.331 0.100 0.800 0.200 CB 0.989 L: 8 3.233 1.246 0.524 0.246 0.857 0.429 CB 1.006 6 1.584 1.153 0.552 0.448 0.600 0.400 O 0.696 ? M: 7 4.674 1.506 0.599 0.368 0.833 0.167 N 1.095 N: 10 2.998 1.300 0.281 0.295 0.667 0.444 O 1.132 Using tripeptides from previous cycle as seeds 6 1.691 1.328 0.341 0.186 0.600 0.200 O 1.031 ? O: 9 3.422 1.724 0.214 0.109 0.750 0.250 CA 1.267 6 1.465 1.266 0.413 0.197 0.600 0.400 O 0.876 ? P: 6 3.655 1.347 0.983 0.205 0.800 0.600 CB 1.085 98 residues left after pruning, divided into chains as follows: A: 8 B: 9 C: 9 D: 8 E: 11 F: 10 G: 10 H: 6 I: 8 J: 7 K: 6 L: 6 CC for partial structure against native data = 8.92 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.284, Connect. = 0.602 for dens.mod. cycle 1 = 0.281, Contrast = 0.319, Connect. = 0.595 for dens.mod. cycle 2 = 0.281, Contrast = 0.372, Connect. = 0.642 for dens.mod. cycle 3 = 0.281, Contrast = 0.396, Connect. = 0.664 for dens.mod. cycle 4 = 0.281, Contrast = 0.414, Connect. = 0.678 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2182 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 239 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 7.669 1.843 0.592 0.398 0.833 0.333 CA 1.426 B: 9 5.449 1.478 0.305 0.414 0.875 0.375 CB 1.249 C: 6 3.766 1.969 0.279 0.314 0.600 0.400 CB 1.369 D: 7 3.148 1.541 0.460 0.245 1.000 0.500 CB 0.767 E: 6 5.070 1.831 -0.052 0.481 1.000 0.600 N 1.331 F: 10 3.163 1.583 0.438 0.096 0.667 0.333 CB 1.166 G: 8 3.120 1.849 0.366 0.205 0.714 0.714 CB 0.927 H: 8 3.877 1.612 0.123 0.427 0.714 0.429 CB 1.222 I: 6 4.544 1.356 0.671 0.700 0.600 0.600 N 1.245 J: 7 2.619 1.376 0.951 0.324 0.833 0.333 CB 0.580 K: 6 4.166 1.560 0.632 0.573 0.800 0.600 CB 0.852 6 1.393 1.441 0.502 0.303 0.400 0.400 N 0.896 ? L: 10 4.095 1.528 0.536 0.360 0.667 0.333 CB 1.015 M: 6 3.939 1.932 -0.125 0.331 0.800 0.600 O 1.568 N: 13 4.787 1.496 0.518 0.312 0.667 0.417 CB 1.124 6 1.798 1.694 0.244 0.267 0.400 0.000 CB 1.244 ? O: 8 3.693 1.635 0.338 0.317 0.714 0.714 CB 1.094 P: 14 5.002 1.494 0.414 0.288 0.769 0.385 CB 1.084 Q: 6 3.806 1.249 0.077 0.795 1.000 0.800 O 0.978 R: 6 4.988 1.516 0.664 0.485 0.800 0.600 N 1.121 S: 8 2.909 1.481 0.303 0.370 0.714 0.571 CB 0.916 Using tripeptides from previous cycle as seeds 86 residues left after pruning, divided into chains as follows: A: 7 B: 9 C: 6 D: 7 E: 6 F: 8 G: 10 H: 13 I: 6 J: 6 K: 8 CC for partial structure against native data = 9.21 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.309, Connect. = 0.606 for dens.mod. cycle 1 = 0.281, Contrast = 0.352, Connect. = 0.611 for dens.mod. cycle 2 = 0.281, Contrast = 0.405, Connect. = 0.655 for dens.mod. cycle 3 = 0.281, Contrast = 0.427, Connect. = 0.675 for dens.mod. cycle 4 = 0.281, Contrast = 0.443, Connect. = 0.688 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 2035 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 229 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 11.843 2.346 0.603 0.370 0.833 0.500 CB 1.773 B: 9 5.043 1.860 0.352 0.357 0.750 0.375 CB 1.104 C: 8 2.451 1.860 0.202 0.196 0.714 0.429 CB 0.834 D: 6 2.240 1.829 0.555 0.247 0.400 0.400 CA 1.178 E: 8 6.103 1.960 0.213 0.308 0.714 0.286 CB 1.680 F: 6 5.919 2.027 0.463 0.389 0.600 0.600 O 1.673 G: 6 8.314 1.900 0.788 0.478 0.800 0.600 CB 1.399 6 1.429 1.535 0.430 0.478 0.600 0.600 CB 0.496 ? H: 9 3.742 1.428 0.774 0.251 0.750 0.500 CB 0.927 I: 11 2.505 1.669 0.310 0.234 0.600 0.400 CB 0.823 8 1.685 1.835 0.022 0.229 0.429 0.286 CB 1.086 ? J: 6 8.134 1.785 0.327 0.602 1.000 0.800 CA 1.393 K: 6 4.128 1.686 0.857 0.471 0.600 0.600 CB 1.012 L: 6 3.620 1.391 0.407 0.441 0.800 0.800 CB 1.100 M: 6 2.731 1.747 0.376 0.299 0.600 0.400 CB 1.059 6 1.730 1.240 0.394 0.298 0.800 0.400 N 0.701 ? 6 1.245 1.153 0.783 0.314 0.600 0.400 CB 0.555 ? N: 15 3.811 1.844 0.294 0.198 0.571 0.214 CB 1.071 6 residues pruned to eliminate duplicates O: 6 2.730 1.272 0.489 0.334 0.800 0.400 N 0.966 6 0.443 1.197 0.429 0.289 0.800 0.400 CB 0.183 ? P: 7 2.575 1.300 0.146 0.424 0.833 0.333 CB 0.917 Using tripeptides from previous cycle as seeds 98 residues left after pruning, divided into chains as follows: A: 7 B: 9 C: 8 D: 6 E: 6 F: 9 G: 7 H: 6 I: 6 J: 6 K: 15 L: 6 M: 7 CC for partial structure against native data = 11.60 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.327, Connect. = 0.616 for dens.mod. cycle 1 = 0.281, Contrast = 0.376, Connect. = 0.621 for dens.mod. cycle 2 = 0.281, Contrast = 0.439, Connect. = 0.667 for dens.mod. cycle 3 = 0.281, Contrast = 0.460, Connect. = 0.685 for dens.mod. cycle 4 = 0.281, Contrast = 0.473, Connect. = 0.697 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 11 heavy atoms with Occ*Z > 0.30 added to NOGO map 1979 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 234 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 7.093 1.997 0.413 0.259 0.714 0.286 CA 1.753 B: 11 5.523 1.870 0.178 0.237 0.700 0.400 CA 1.537 C: 13 6.128 1.965 0.248 0.311 0.667 0.417 CB 1.335 D: 7 4.540 1.901 0.251 0.333 0.833 0.333 CB 1.122 E: 6 2.559 1.976 0.079 0.299 0.600 0.400 CB 1.119 F: 6 6.525 1.853 0.619 0.790 1.000 0.600 CB 0.754 G: 6 4.377 1.948 -0.298 0.522 1.000 1.000 CB 1.399 H: 26 12.504 1.828 0.578 0.338 0.760 0.480 CB 1.362 11 residues pruned to eliminate duplicates I: 8 3.625 1.729 0.479 0.265 0.714 0.286 CB 0.981 J: 15 3.556 1.717 0.271 0.198 0.571 0.214 CB 1.092 K: 7 10.372 1.917 0.591 0.451 1.000 0.500 CB 1.461 L: 7 7.112 1.190 1.095 0.702 1.000 0.667 N 0.969 M: 7 4.104 1.670 0.200 0.333 0.833 0.500 CB 1.205 6 1.473 1.294 0.091 0.438 0.600 0.600 N 0.829 ? N: 6 2.091 1.400 0.521 0.298 0.600 0.400 N 0.917 O: 11 3.586 1.386 0.115 0.313 0.800 0.400 N 1.128 P: 11 6.183 1.577 0.591 0.309 0.900 0.400 CB 1.071 Q: 8 2.400 1.358 0.341 0.266 0.714 0.286 N 0.911 Using tripeptides from previous cycle as seeds 110 residues left after pruning, divided into chains as follows: A: 8 B: 11 C: 6 D: 6 E: 28 F: 7 G: 14 H: 7 I: 7 J: 7 K: 9 CC for partial structure against native data = 11.76 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.281, Contrast = 0.332, Connect. = 0.621 for dens.mod. cycle 1 = 0.281, Contrast = 0.386, Connect. = 0.630 for dens.mod. cycle 2 = 0.282, Contrast = 0.456, Connect. = 0.677 for dens.mod. cycle 3 = 0.282, Contrast = 0.474, Connect. = 0.694 for dens.mod. cycle 4 = 0.282, Contrast = 0.486, Connect. = 0.704 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.07 - 3.99 - 3.47 - 3.15 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.548 0.610 0.556 0.524 0.525 0.515 0.485 0.422 0.346 0.308 0.721 0.802 0.762 0.727 0.742 0.753 0.723 0.690 0.592 0.529 N 2106 2109 2123 2075 2180 2055 2102 2201 2180 1902 Estimated mean FOM = 0.485 Pseudo-free CC = 53.68 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.0895 0.4344 0.2310 1.0000 25.05 2 0.0919 0.4844 0.1258 0.9300 24.81 3 -0.0639 0.8164 0.2547 0.8931 21.40 4 0.1663 0.6822 0.2495 0.8181 23.38 5 0.2350 0.4205 0.2073 0.6529 17.10 6 0.1361 0.9977 0.4060 0.5532 15.28 7 0.1898 0.9264 0.2699 0.5525 15.40 8 0.1646 0.3502 0.2949 0.5172 13.87 9 0.0261 0.9266 0.2995 0.4322 9.54 10 0.1009 0.1782 0.2304 0.4033 9.21 11 0.1420 0.2961 0.2097 0.3356 7.98 12 -0.0083 0.6553 0.1731 0.2525 4.56 Site x y z h(sig) near old near new 1 0.0908 0.4339 0.2313 25.0 1/0.09 12/2.76 15/8.60 5/8.75 8/10.14 2 0.0922 0.4850 0.1259 24.8 2/0.05 12/8.16 1/10.88 5/12.53 15/14.08 3 0.1664 0.6816 0.2496 23.4 4/0.05 15/10.84 8/10.90 5/10.96 11/11.91 4 -0.0632 0.8163 0.2551 21.2 3/0.06 9/11.40 14/15.68 3/17.33 6/17.38 5 0.2360 0.4209 0.2073 17.1 5/0.06 15/2.64 12/8.70 1/8.75 8/10.91 6 0.1911 0.9275 0.2695 15.5 7/0.12 9/9.78 13/12.86 7/14.62 10/15.22 7 0.1347 0.9966 0.4067 15.4 6/0.14 9/13.23 6/14.62 6/17.63 13/21.07 8 0.1661 0.3507 0.2947 13.9 8/0.09 11/9.22 15/9.75 1/10.14 3/10.90 9 0.0288 0.9270 0.2992 9.6 9/0.16 6/9.78 4/11.40 7/13.23 6/20.36 10 0.1037 0.1791 0.2308 9.3 10/0.18 13/4.80 11/10.11 6/15.22 8/15.89 11 0.1394 0.2964 0.2117 8.1 11/0.24 8/9.22 10/10.11 13/10.23 5/11.74 12 0.0885 0.4427 0.2034 -5.1 1/2.72 1/2.76 2/8.16 5/8.70 15/9.25 13 0.1639 0.1902 0.2643 -4.9 10/4.96 10/4.80 11/10.23 6/12.86 8/13.62 14 -0.0054 0.6582 0.1719 4.7 12/0.32 3/12.51 4/15.68 2/16.04 5/17.20 15 0.2398 0.4302 0.2338 -4.7 5/2.66 5/2.64 1/8.60 12/9.25 8/9.75 Best trace (cycle 5 with CC 11.76%) was saved as P2122_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 9.1 - Setup, data input and phasing 2.3 - FFTs and peak-searches 5.1 - Sphere of influence 0.6 - Rest of density modification 0.0 - Alpha-helix search 49.7 - Tripeptide search 58.0 - Chain tracing 0.0 - NCS analysis 4.4 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:11:17 Total time: 129.38 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++