++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:17:28 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: P22121_pse14 P22121_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P22121_pse14_fa.res FA and alpha from P22121_pse14_fa.hkl Native data from P22121_pse14.hkl Listing output to P22121_pse14.lst Phases output to P22121_pse14.phs Revised heavy atom sites output to P22121_pse14.hat Revised heavy atom phases output to P22121_pse14.pha Poly-Ala trace output to P22121_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 2 21 21 Allowed origin shift code: 4 14 atoms read from file P22121_pse14_fa.res Trimmed to 13 atoms with occupancy > 0.2 11695 Reflections read from file P22121_pse14_fa.hkl 21043 Reflections read from file P22121_pse14.hkl 21007 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.004007h^2 -0.000438k^2 -0.000495l^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 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|> = 0.781 13 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 13 19.21% 0.250 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 18.78% = 0.123 for phases from phiT = phiA + alpha = 0.188 after including heavy atoms = 0.175, Contrast = 0.029, Connect. = 0.524 for dens.mod. cycle 1 = 0.192, Contrast = 0.089, Connect. = 0.591 for dens.mod. cycle 2 = 0.205, Contrast = 0.120, Connect. = 0.607 for dens.mod. cycle 3 = 0.217, Contrast = 0.149, Connect. = 0.623 for dens.mod. cycle 4 = 0.226, Contrast = 0.172, Connect. = 0.634 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 1835 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 238 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 2.414 1.550 0.346 0.299 0.600 0.400 CB 1.079 B: 14 3.694 1.479 0.236 0.357 0.615 0.385 CB 1.063 C: 10 3.175 1.359 0.203 0.314 0.778 0.444 CB 1.022 D: 8 3.586 1.427 0.417 0.309 0.714 0.571 CB 1.160 6 1.912 1.191 0.304 0.820 1.000 1.000 CB 0.417 ? E: 6 2.873 1.428 0.229 0.287 0.800 0.600 CB 1.161 F: 7 6.100 1.288 0.908 0.659 0.833 0.500 O 1.050 G: 8 2.630 1.519 0.019 0.412 0.571 0.286 CB 1.231 H: 14 3.700 1.335 0.447 0.313 0.692 0.385 CB 0.944 I: 7 2.960 1.281 0.384 0.344 0.833 0.500 N 0.969 J: 7 2.649 1.408 0.718 0.263 0.500 0.500 CB 1.173 K: 9 4.029 1.364 0.439 0.411 0.750 0.500 N 1.062 L: 8 2.781 1.278 0.184 0.427 0.857 0.571 CB 0.874 M: 8 3.905 1.291 0.409 0.524 0.857 0.429 CB 0.925 N: 9 3.261 1.376 0.733 0.305 0.625 0.375 CB 0.962 O: 11 4.918 1.497 0.477 0.351 0.800 0.400 CB 1.033 P: 6 3.431 1.248 0.546 0.453 0.800 0.400 CB 1.044 Q: 8 3.687 1.394 0.177 0.334 0.857 0.571 O 1.189 R: 6 2.890 1.385 0.818 0.259 0.600 0.400 N 1.128 S: 7 2.027 1.472 0.185 0.319 0.667 0.333 CB 0.869 113 residues left after pruning, divided into chains as follows: A: 14 B: 8 C: 8 D: 6 E: 7 F: 13 G: 7 H: 9 I: 8 J: 8 K: 6 L: 11 M: 8 CC for partial structure against native data = 8.64 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.207, Connect. = 0.594 for dens.mod. cycle 1 = 0.281, Contrast = 0.215, Connect. = 0.566 for dens.mod. cycle 2 = 0.281, Contrast = 0.244, Connect. = 0.602 for dens.mod. cycle 3 = 0.281, Contrast = 0.263, Connect. = 0.623 for dens.mod. cycle 4 = 0.281, Contrast = 0.281, Connect. = 0.639 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 2280 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 258 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 6.288 1.523 0.650 0.425 0.857 0.429 N 1.194 B: 10 6.283 1.604 0.793 0.356 0.778 0.556 CB 1.094 C: 9 4.470 1.738 0.255 0.324 0.750 0.500 CB 1.173 D: 9 6.734 1.839 0.924 0.498 0.625 0.500 CB 1.078 E: 6 5.408 1.519 0.012 0.729 1.000 0.600 CB 1.279 F: 6 4.153 1.704 0.512 0.399 0.600 0.600 N 1.336 G: 7 2.341 1.584 0.411 0.246 0.667 0.500 CB 0.860 H: 11 2.765 1.448 0.391 0.198 0.700 0.400 CB 0.888 I: 7 4.364 1.823 0.523 0.339 0.500 0.333 CA 1.530 J: 18 4.570 1.611 0.571 0.200 0.529 0.294 CB 1.181 K: 11 3.402 1.569 0.301 0.422 0.700 0.500 CB 0.816 L: 9 3.706 1.778 0.273 0.298 0.625 0.500 CB 1.160 6 1.337 1.294 0.122 0.287 0.600 0.400 N 0.872 ? M: 6 2.336 1.249 0.071 0.483 0.800 0.400 CB 0.994 N: 10 4.377 1.604 0.329 0.342 0.667 0.444 CB 1.219 6 1.120 1.288 -0.077 0.152 0.800 0.600 N 0.808 ? O: 8 2.739 1.290 0.241 0.388 0.857 0.286 O 0.850 P: 7 5.788 1.368 0.777 0.587 0.833 0.333 CB 1.073 Using tripeptides from previous cycle as seeds Q: 6 2.590 1.240 0.860 0.114 0.800 0.200 CB 1.022 110 residues left after pruning, divided into chains as follows: A: 8 B: 10 C: 9 D: 9 E: 6 F: 6 G: 11 H: 7 I: 15 J: 6 K: 8 L: 8 M: 7 CC for partial structure against native data = 9.83 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.239, Connect. = 0.604 for dens.mod. cycle 1 = 0.281, Contrast = 0.258, Connect. = 0.590 for dens.mod. cycle 2 = 0.281, Contrast = 0.296, Connect. = 0.630 for dens.mod. cycle 3 = 0.281, Contrast = 0.315, Connect. = 0.650 for dens.mod. cycle 4 = 0.281, Contrast = 0.333, Connect. = 0.666 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 2175 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 253 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 7.952 2.401 0.248 0.329 0.625 0.500 CB 1.810 B: 8 5.496 1.850 0.380 0.287 0.714 0.286 CB 1.447 C: 13 5.734 1.741 0.139 0.280 0.750 0.333 CA 1.426 D: 10 8.031 2.021 0.479 0.463 0.778 0.333 CB 1.196 E: 6 3.556 1.560 0.600 0.361 0.600 0.400 CA 1.233 F: 10 8.187 1.715 0.067 0.740 1.000 0.556 CB 1.203 G: 6 3.514 1.672 -0.004 0.419 0.800 0.400 CB 1.283 H: 10 6.107 1.864 0.244 0.442 0.667 0.556 CB 1.397 I: 11 5.383 1.744 0.349 0.424 0.600 0.500 O 1.305 J: 9 4.789 1.905 0.329 0.415 0.625 0.500 CB 1.169 K: 23 6.533 1.880 0.285 0.188 0.591 0.227 CB 1.418 L: 12 3.984 1.570 0.262 0.241 0.727 0.364 CB 1.125 12 residues pruned to eliminate duplicates M: 7 4.111 1.884 0.273 0.370 0.667 0.500 CB 1.206 N: 7 3.642 1.915 0.550 0.386 0.667 0.333 CB 0.848 6 1.714 1.445 0.024 0.299 0.600 0.600 CB 1.080 ? O: 7 2.946 1.366 0.277 0.335 1.000 0.500 CB 0.826 P: 6 2.194 1.457 0.045 0.295 1.000 0.800 CB 0.811 Q: 6 3.013 1.211 1.069 0.373 0.800 0.200 CB 0.770 Using tripeptides from previous cycle as seeds R: 13 5.874 1.757 0.439 0.303 0.750 0.500 CB 1.114 7 residues pruned to eliminate duplicates S: 6 3.524 1.670 0.453 0.394 0.800 0.000 O 0.908 108 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 13 D: 10 E: 6 F: 9 G: 10 H: 7 I: 23 J: 13 CC for partial structure against native data = 9.01 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.261, Connect. = 0.613 for dens.mod. cycle 1 = 0.281, Contrast = 0.286, Connect. = 0.604 for dens.mod. cycle 2 = 0.281, Contrast = 0.328, Connect. = 0.648 for dens.mod. cycle 3 = 0.281, Contrast = 0.344, Connect. = 0.666 for dens.mod. cycle 4 = 0.281, Contrast = 0.359, Connect. = 0.680 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 2129 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 241 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 17 6.667 2.025 0.289 0.375 0.625 0.312 CB 1.168 B: 7 5.243 2.310 0.125 0.340 0.500 0.500 CA 1.961 C: 13 9.575 2.229 0.174 0.278 0.750 0.417 CB 1.808 D: 11 5.879 1.907 -0.095 0.361 0.900 0.500 CB 1.389 E: 10 6.587 2.312 0.114 0.319 0.667 0.444 CB 1.562 F: 9 7.405 1.798 0.531 0.371 0.750 0.500 N 1.456 G: 16 7.638 2.077 0.158 0.273 0.733 0.467 CB 1.446 H: 20 7.493 2.241 0.236 0.194 0.579 0.316 CB 1.544 I: 12 6.364 1.894 0.246 0.326 0.727 0.545 CB 1.354 J: 15 4.426 1.623 0.327 0.197 0.643 0.429 CB 1.226 8 residues pruned to eliminate duplicates K: 10 2.660 1.190 0.487 0.308 0.778 0.556 CB 0.797 Using tripeptides from previous cycle as seeds 101 residues left after pruning, divided into chains as follows: A: 17 B: 7 C: 13 D: 9 E: 9 F: 9 G: 16 H: 21 CC for partial structure against native data = 11.29 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.295, Connect. = 0.609 for dens.mod. cycle 1 = 0.281, Contrast = 0.325, Connect. = 0.610 for dens.mod. cycle 2 = 0.281, Contrast = 0.361, Connect. = 0.651 for dens.mod. cycle 3 = 0.281, Contrast = 0.375, Connect. = 0.671 for dens.mod. cycle 4 = 0.281, Contrast = 0.385, Connect. = 0.684 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 2073 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 255 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 8.696 2.342 0.505 0.315 0.625 0.250 CB 1.712 B: 8 5.914 2.052 0.655 0.314 0.571 0.571 CB 1.415 C: 10 9.287 2.091 0.425 0.330 0.778 0.444 CB 1.609 D: 14 7.247 2.156 0.291 0.274 0.615 0.308 CB 1.515 E: 10 7.514 2.086 0.340 0.305 0.667 0.333 CB 1.669 F: 11 4.806 2.058 0.110 0.237 0.600 0.200 CB 1.506 G: 11 6.921 1.883 0.296 0.367 0.700 0.400 CB 1.479 H: 11 5.905 2.069 0.453 0.271 0.600 0.400 CB 1.344 I: 10 3.317 1.689 0.246 0.316 0.556 0.444 CB 1.158 J: 10 3.898 1.274 0.505 0.314 0.778 0.444 O 1.070 K: 8 2.829 1.327 -0.027 0.496 0.857 0.571 CB 0.970 L: 9 3.099 1.395 0.722 0.341 0.625 0.375 CB 0.868 M: 6 3.540 1.290 0.434 0.545 0.800 0.600 CA 1.024 6 1.223 1.382 0.590 0.205 0.600 0.200 CB 0.589 ? N: 13 5.129 1.624 0.624 0.228 0.750 0.417 CB 1.028 Using tripeptides from previous cycle as seeds O: 9 4.190 1.309 0.495 0.516 0.750 0.500 O 0.993 114 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 10 D: 14 E: 10 F: 11 G: 11 H: 11 I: 8 J: 8 K: 8 L: 6 CC for partial structure against native data = 12.28 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.281, Contrast = 0.299, Connect. = 0.616 for dens.mod. cycle 1 = 0.282, Contrast = 0.330, Connect. = 0.614 for dens.mod. cycle 2 = 0.282, Contrast = 0.376, Connect. = 0.658 for dens.mod. cycle 3 = 0.282, Contrast = 0.390, Connect. = 0.676 for dens.mod. cycle 4 = 0.282, Contrast = 0.398, Connect. = 0.687 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 5.06 - 3.99 - 3.47 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.433 0.570 0.510 0.497 0.487 0.455 0.400 0.353 0.297 0.280 0.553 0.760 0.714 0.702 0.712 0.685 0.633 0.587 0.497 0.473 N 2110 2091 2120 2158 2094 2054 2100 2200 2179 1901 Estimated mean FOM = 0.429 Pseudo-free CC = 47.43 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.2987 0.0667 0.2452 1.0000 28.79 2 0.5523 0.1793 0.2322 0.7753 23.20 3 0.0467 0.1853 0.2618 0.7531 23.00 4 0.6418 0.0751 0.1921 0.6267 20.09 5 0.2923 0.0142 0.1385 0.5777 17.21 6 0.7976 0.0714 0.2157 0.4857 15.39 7 0.4738 0.0463 0.2082 0.4680 16.76 8 0.2940 0.1937 0.2954 0.4361 12.85 9 0.9826 0.0058 0.0741 0.4221 12.46 10 0.2901 0.3198 0.2400 0.4022 11.53 11 0.2683 -0.1033 0.2229 0.3272 10.73 12 0.9223 0.0591 0.1869 0.2749 7.80 13 1.0483 -0.0867 0.1152 0.2501 8.07 Site x y z h(sig) near old near new 1 0.2994 0.0669 0.2446 28.8 1/0.07 17/2.55 15/2.57 18/2.67 22/2.72 2 0.5515 0.1795 0.2323 23.2 2/0.05 14/2.63 4/10.72 6/12.17 22/15.08 3 0.0478 0.1851 0.2618 23.0 3/0.07 19/2.38 23/2.62 20/2.63 13/14.56 4 0.6418 0.0764 0.1921 20.2 4/0.11 7/9.28 6/10.17 2/10.72 21/12.06 5 0.2915 0.0147 0.1386 17.2 5/0.07 16/2.56 18/9.11 15/9.49 1/10.97 6 0.4735 0.0458 0.2095 16.9 7/0.13 18/9.90 4/10.17 15/10.26 22/10.38 7 0.7977 0.0718 0.2157 15.4 6/0.03 21/5.77 13/7.71 4/9.28 20/16.51 8 0.2943 0.1947 0.2960 12.9 8/0.11 22/9.50 17/10.04 10/11.64 1/11.68 9 0.9819 0.0055 0.0734 12.5 9/0.08 12/9.21 13/12.34 9/13.99 7/18.06 10 0.2881 0.3195 0.2402 11.6 10/0.12 8/11.64 19/16.65 3/17.91 20/18.70 11 0.2685 -0.1046 0.2227 10.8 11/0.11 16/11.25 15/12.00 5/12.79 1/14.49 12 1.0464 -0.0843 0.1149 8.3 13/0.23 9/9.21 13/15.46 16/15.99 11/16.49 13 0.9225 0.0571 0.1897 8.0 12/0.31 7/7.71 21/10.95 9/12.34 20/12.63 14 0.5534 0.1872 0.2591 -6.1 2/2.64 2/2.63 4/12.29 6/13.46 8/15.36 15 0.3016 0.0374 0.2363 -5.7 1/2.58 1/2.57 18/3.61 17/4.63 22/5.08 16 0.3028 -0.0151 0.1363 -5.3 5/2.51 5/2.56 15/10.46 18/10.79 11/11.25 17 0.2871 0.0781 0.2684 -5.3 1/2.50 1/2.55 22/2.97 15/4.63 18/4.95 18 0.3077 0.0752 0.2180 -4.9 1/2.73 1/2.67 22/3.61 15/3.61 17/4.95 19 0.0461 0.2109 0.2509 -4.9 3/2.36 3/2.38 20/3.45 23/5.00 8/15.01 20 0.0421 0.1728 0.2366 -4.9 3/2.63 3/2.63 19/3.45 23/3.72 13/12.63 21 0.7976 0.0651 0.2761 -4.9 6/5.77 7/5.77 13/10.95 4/12.06 23/16.38 22 0.3224 0.0946 0.2508 -4.8 1/2.74 1/2.72 17/2.97 18/3.61 15/5.08 23 0.0497 0.1560 0.2726 -4.7 3/2.64 3/2.62 20/3.72 19/5.00 13/13.54 Best trace (cycle 5 with CC 12.28%) was saved as P22121_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 9.9 - Setup, data input and phasing 1.2 - FFTs and peak-searches 4.7 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 51.2 - Tripeptide search 54.9 - Chain tracing 0.0 - NCS analysis 4.9 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:19:35 Total time: 126.95 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++