++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:11:56 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: P21212_pse14 P21212_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P21212_pse14_fa.res FA and alpha from P21212_pse14_fa.hkl Native data from P21212_pse14.hkl Listing output to P21212_pse14.lst Phases output to P21212_pse14.phs Revised heavy atom sites output to P21212_pse14.hat Revised heavy atom phases output to P21212_pse14.pha Poly-Ala trace output to P21212_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 21 2 Allowed origin shift code: 4 14 atoms read from file P21212_pse14_fa.res 11695 Reflections read from file P21212_pse14_fa.hkl 21043 Reflections read from file P21212_pse14.hkl 21016 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003948h^2 -0.000442k^2 -0.000489l^2 +0.000000kl +0.000000hl +0.000000hk 24 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 14 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 14 18.45% 0.208 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 18.26% = 0.120 for phases from phiT = phiA + alpha = 0.192 after including heavy atoms = 0.171, Contrast = 0.032, Connect. = 0.537 for dens.mod. cycle 1 = 0.190, Contrast = 0.086, Connect. = 0.592 for dens.mod. cycle 2 = 0.205, Contrast = 0.113, Connect. = 0.606 for dens.mod. cycle 3 = 0.218, Contrast = 0.141, Connect. = 0.620 for dens.mod. cycle 4 = 0.230, Contrast = 0.165, Connect. = 0.632 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 13 heavy atoms with Occ*Z > 0.30 added to NOGO map 1917 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: 6 2.799 1.418 0.416 0.610 1.000 0.400 CB 0.562 B: 7 5.786 1.285 0.463 0.795 1.000 0.833 CB 0.971 C: 10 3.082 1.233 0.624 0.321 0.667 0.444 N 0.937 D: 6 3.471 1.310 0.266 0.388 1.000 0.400 O 1.054 6 1.590 1.259 0.434 0.408 0.800 0.400 CB 0.542 ? E: 7 3.573 1.267 0.410 0.686 0.833 0.333 CB 0.827 F: 11 3.446 1.279 0.472 0.319 0.800 0.400 CB 0.883 G: 7 2.838 1.093 0.398 0.398 1.000 0.500 CB 0.844 H: 6 6.074 1.557 0.508 0.459 1.000 0.600 CB 1.206 I: 6 3.039 1.516 0.237 0.359 0.800 0.400 CB 1.055 J: 9 5.285 1.176 0.587 0.779 1.000 0.375 CB 0.783 K: 8 3.781 1.488 0.676 0.359 0.714 0.286 CB 0.934 L: 10 3.443 1.189 0.397 0.455 0.889 0.667 CB 0.814 M: 7 2.728 1.146 0.243 0.530 0.833 0.667 O 0.911 N: 6 3.442 1.023 0.685 0.598 1.000 0.600 CB 0.813 O: 8 3.493 1.422 0.160 0.236 1.000 0.571 CB 1.087 P: 6 3.218 1.330 0.661 0.598 0.600 0.400 N 0.989 Q: 7 3.224 1.429 -0.081 0.402 1.000 0.333 CB 1.110 104 residues left after pruning, divided into chains as follows: A: 7 B: 10 C: 6 D: 7 E: 7 F: 6 G: 9 H: 8 I: 10 J: 7 K: 6 L: 8 M: 6 N: 7 CC for partial structure against native data = 7.93 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.210, Connect. = 0.587 for dens.mod. cycle 1 = 0.281, Contrast = 0.215, Connect. = 0.557 for dens.mod. cycle 2 = 0.281, Contrast = 0.238, Connect. = 0.590 for dens.mod. cycle 3 = 0.281, Contrast = 0.257, Connect. = 0.611 for dens.mod. cycle 4 = 0.281, Contrast = 0.276, Connect. = 0.629 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 13 heavy atoms with Occ*Z > 0.30 added to NOGO map 2374 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 232 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 6.045 2.115 0.187 0.314 0.714 0.429 CB 1.566 B: 7 8.209 1.854 0.271 0.667 0.833 0.500 CB 1.463 C: 9 2.085 1.789 0.214 0.232 0.500 0.250 CB 0.928 D: 9 5.114 1.735 0.223 0.613 0.750 0.250 CB 1.022 E: 6 4.393 1.807 0.208 0.373 1.000 0.400 CB 1.031 F: 6 2.442 1.264 0.119 0.404 1.000 0.600 N 0.854 G: 15 4.900 1.549 0.268 0.317 0.786 0.429 CB 1.040 H: 6 5.758 1.592 0.165 0.815 0.800 0.600 CB 1.319 I: 8 4.198 1.797 -0.134 0.213 1.000 0.571 CA 1.430 J: 8 4.061 1.436 0.287 0.526 0.714 0.429 N 1.132 6 1.574 1.413 0.236 0.342 0.400 0.200 CB 1.196 ? 6 1.918 1.218 0.266 0.299 0.800 0.800 N 0.870 ? 7 1.855 1.218 0.398 0.397 0.667 0.500 CB 0.743 ? K: 10 2.706 1.275 0.227 0.266 0.667 0.222 O 1.129 L: 9 4.278 1.804 0.411 0.268 0.625 0.375 CB 1.238 9 residues pruned to eliminate duplicates M: 6 2.997 0.976 0.374 0.794 1.000 0.600 O 0.773 N: 8 3.421 1.293 0.555 0.274 0.857 0.571 CB 0.970 O: 7 2.240 1.184 0.567 0.380 0.833 0.333 CB 0.672 6 1.931 1.370 0.239 0.297 0.800 0.600 CB 0.798 ? 8 1.853 1.119 0.076 0.499 0.714 0.286 CB 0.815 ? Using tripeptides from previous cycle as seeds P: 6 4.310 1.638 0.150 0.401 1.000 0.400 CB 1.136 91 residues left after pruning, divided into chains as follows: A: 8 B: 7 C: 9 D: 15 E: 6 F: 8 G: 8 H: 9 I: 9 J: 6 K: 6 CC for partial structure against native data = 7.90 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.262, Connect. = 0.594 for dens.mod. cycle 1 = 0.281, Contrast = 0.281, Connect. = 0.580 for dens.mod. cycle 2 = 0.281, Contrast = 0.311, Connect. = 0.618 for dens.mod. cycle 3 = 0.281, Contrast = 0.328, Connect. = 0.640 for dens.mod. cycle 4 = 0.281, Contrast = 0.343, Connect. = 0.657 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 13 heavy atoms with Occ*Z > 0.30 added to NOGO map 2249 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 242 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 11.642 1.849 0.412 0.781 0.875 0.500 CA 1.407 B: 10 5.865 1.926 0.266 0.273 0.778 0.222 CB 1.334 C: 9 5.764 2.036 0.193 0.293 0.625 0.250 CB 1.692 D: 7 9.039 2.116 0.547 0.533 0.667 0.500 CB 1.636 E: 8 3.719 1.883 0.033 0.211 0.714 0.714 CB 1.423 7 1.934 1.376 0.593 0.369 0.500 0.333 CB 0.829 ? F: 6 7.100 1.796 0.337 0.781 1.000 0.800 N 1.032 G: 9 4.468 1.769 0.124 0.338 0.750 0.250 CB 1.263 H: 8 3.652 1.626 0.706 0.237 0.714 0.429 CA 0.946 I: 9 4.141 1.801 0.010 0.364 0.750 0.625 CB 1.243 J: 7 3.237 1.626 0.391 0.344 0.667 0.500 CB 1.038 K: 7 3.342 1.452 0.746 0.315 0.667 0.500 CB 0.990 L: 8 3.665 1.307 0.373 0.397 0.857 0.571 CB 1.004 7 1.846 1.225 0.742 0.558 0.667 0.333 CB 0.501 ? M: 16 6.078 1.644 0.531 0.358 0.867 0.400 CB 0.838 N: 6 3.139 1.321 0.323 0.477 0.800 0.600 CB 1.028 O: 7 3.117 1.294 0.450 0.248 0.833 0.333 N 1.088 P: 6 5.059 1.390 0.713 0.678 0.800 0.600 CB 1.008 Q: 6 4.002 1.526 0.799 0.315 0.800 0.600 CB 1.000 R: 7 2.734 1.254 0.648 0.402 0.667 0.500 CB 0.899 Using tripeptides from previous cycle as seeds 98 residues left after pruning, divided into chains as follows: A: 9 B: 10 C: 7 D: 8 E: 6 F: 9 G: 7 H: 8 I: 8 J: 7 K: 6 L: 6 M: 7 CC for partial structure against native data = 9.78 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.265, Connect. = 0.603 for dens.mod. cycle 1 = 0.281, Contrast = 0.293, Connect. = 0.597 for dens.mod. cycle 2 = 0.281, Contrast = 0.331, Connect. = 0.637 for dens.mod. cycle 3 = 0.281, Contrast = 0.351, Connect. = 0.658 for dens.mod. cycle 4 = 0.281, Contrast = 0.366, Connect. = 0.673 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 13 heavy atoms with Occ*Z > 0.30 added to NOGO map 2162 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 237 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 9.446 2.187 0.569 0.603 0.625 0.500 CB 1.411 B: 8 10.331 1.985 0.113 0.774 0.857 0.714 CB 1.619 C: 9 12.760 2.029 0.430 0.681 0.875 0.500 CB 1.504 D: 7 3.734 2.092 0.053 0.367 0.500 0.333 CB 1.596 E: 9 8.254 1.857 0.364 0.305 1.000 0.500 CB 1.432 F: 9 4.051 2.139 0.121 0.182 0.625 0.625 CB 1.400 G: 8 10.534 2.117 0.841 0.431 0.714 0.429 CB 1.537 H: 8 3.157 1.809 -0.040 0.371 0.714 0.571 CB 1.104 I: 11 7.372 1.664 0.291 0.456 0.800 0.400 CA 1.418 J: 7 3.174 1.855 0.083 0.390 0.500 0.333 CA 1.450 K: 9 2.915 1.538 0.195 0.444 0.750 0.500 CB 0.792 L: 6 4.177 1.732 0.153 0.602 0.800 0.600 CB 1.061 M: 6 3.743 1.382 0.830 0.287 0.800 0.600 CA 1.051 N: 6 2.737 1.194 0.419 0.666 0.800 0.800 N 0.774 O: 10 2.298 1.228 0.350 0.240 0.667 0.556 N 0.936 P: 7 4.903 1.710 0.093 0.243 1.000 0.833 CA 1.442 Q: 10 6.540 2.008 -0.003 0.426 0.667 0.444 CB 1.762 8 residues pruned to eliminate duplicates R: 8 4.059 1.577 0.600 0.377 0.857 0.429 CB 0.809 S: 8 4.966 1.375 0.550 0.481 0.857 0.571 O 1.047 6 1.527 1.371 0.581 0.361 1.000 0.600 CB 0.366 ? T: 7 2.101 1.281 0.457 0.169 0.667 0.333 CA 1.031 Using tripeptides from previous cycle as seeds U: 9 6.933 2.266 0.032 0.266 0.750 0.375 CA 1.826 9 residues pruned to eliminate duplicates V: 6 5.923 1.810 0.662 0.563 1.000 0.600 CB 0.829 96 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 9 D: 9 E: 9 F: 6 G: 6 H: 8 I: 7 J: 13 K: 6 L: 6 CC for partial structure against native data = 8.43 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.280, Connect. = 0.606 for dens.mod. cycle 1 = 0.281, Contrast = 0.316, Connect. = 0.603 for dens.mod. cycle 2 = 0.281, Contrast = 0.359, Connect. = 0.647 for dens.mod. cycle 3 = 0.281, Contrast = 0.375, Connect. = 0.666 for dens.mod. cycle 4 = 0.281, Contrast = 0.388, Connect. = 0.681 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 13 heavy atoms with Occ*Z > 0.30 added to NOGO map 2148 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 224 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 14.550 2.025 0.540 0.816 0.875 0.625 CB 1.432 B: 10 12.113 2.142 0.671 0.700 0.556 0.556 CB 1.692 C: 8 13.325 2.222 0.439 0.861 1.000 0.857 CB 1.157 D: 8 3.416 1.869 0.218 0.239 0.857 0.571 CB 0.896 E: 7 13.427 2.006 0.760 0.788 0.833 0.667 CA 1.446 F: 12 7.656 1.811 0.378 0.453 0.727 0.364 CB 1.335 G: 11 6.182 1.816 0.448 0.254 0.700 0.400 CB 1.409 H: 10 4.976 1.604 0.341 0.323 0.778 0.556 CB 1.204 I: 7 7.487 1.814 0.431 0.590 0.833 0.500 CB 1.296 J: 8 3.130 1.340 0.382 0.361 0.714 0.286 CB 1.039 K: 6 4.448 1.294 0.460 0.479 1.000 0.600 CB 1.076 L: 7 3.057 1.208 0.947 0.406 0.667 0.333 CB 0.878 6 0.881 1.248 -0.327 0.284 0.800 0.400 CB 0.747 ? M: 8 2.304 1.125 0.520 0.632 0.714 0.571 CB 0.630 N: 20 3.918 1.532 0.373 0.287 0.684 0.316 CB 0.793 O: 11 2.441 1.451 0.023 0.417 0.800 0.700 CB 0.709 6 1.926 1.487 0.210 0.151 0.800 0.800 CB 0.919 ? Using tripeptides from previous cycle as seeds P: 11 7.682 1.644 0.862 0.323 0.800 0.100 CB 1.206 119 residues left after pruning, divided into chains as follows: A: 9 B: 10 C: 8 D: 8 E: 7 F: 12 G: 9 H: 7 I: 6 J: 6 K: 7 L: 7 M: 6 N: 8 O: 9 CC for partial structure against native data = 10.68 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.281, Contrast = 0.285, Connect. = 0.609 for dens.mod. cycle 1 = 0.282, Contrast = 0.323, Connect. = 0.608 for dens.mod. cycle 2 = 0.282, Contrast = 0.370, Connect. = 0.651 for dens.mod. cycle 3 = 0.282, Contrast = 0.385, Connect. = 0.669 for dens.mod. cycle 4 = 0.282, Contrast = 0.397, Connect. = 0.683 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 0.554 0.601 0.563 0.476 0.439 0.431 0.348 0.222 0.224 0.212 0.728 0.803 0.785 0.694 0.642 0.657 0.556 0.371 0.366 0.360 N 2112 2094 2121 2158 2095 2054 2101 2200 2180 1901 Estimated mean FOM = 0.408 Pseudo-free CC = 45.14 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.4487 0.5924 0.0042 1.0000 23.67 2 0.7008 0.7430 -0.1269 0.9276 22.37 3 0.2045 0.6584 -0.4802 0.9238 21.56 4 0.4489 0.5437 -0.4993 0.8713 20.34 5 0.1981 0.7065 0.0197 0.8462 19.43 6 0.3523 0.6988 0.0459 0.7307 19.34 7 0.1937 0.6821 -0.3671 0.5698 12.88 8 0.2202 0.5771 -0.0319 0.4711 11.69 9 0.2158 0.4070 -0.4762 0.3762 8.22 10 0.5423 0.7525 0.1808 0.3643 7.78 11 0.5142 0.9097 0.2276 0.3484 8.88 12 0.2727 0.4820 -0.2427 0.3396 8.96 13 0.4723 0.6447 0.1235 0.3269 8.60 14 0.4339 0.5713 -0.1215 0.2076 3.28 Site x y z h(sig) near old near new 1 0.4487 0.5926 0.0044 23.7 1/0.02 5/11.21 11/12.04 8/13.72 1/16.46 2 0.7021 0.7427 -0.1262 22.5 2/0.11 6/10.93 5/12.46 11/18.24 13/20.19 3 0.2045 0.6587 -0.4804 21.6 3/0.04 7/10.89 14/16.07 4/17.06 12/20.92 4 0.4471 0.5431 -0.5003 20.5 4/0.15 3/17.06 12/17.56 12/19.91 7/22.45 5 0.3504 0.6993 0.0454 19.7 6/0.12 6/9.05 11/11.17 1/11.21 2/12.46 6 0.1994 0.7059 0.0204 19.4 5/0.11 5/9.05 2/10.93 8/11.87 1/17.24 7 0.1946 0.6824 -0.3679 12.9 7/0.09 14/10.48 3/10.89 9/18.50 13/20.68 8 0.2196 0.5767 -0.0320 11.7 8/0.05 6/11.87 1/13.72 5/14.64 2/21.25 9 0.5124 0.9100 0.2295 9.0 11/0.20 13/13.88 10/17.53 10/17.56 7/18.50 10 0.2730 0.4821 -0.2422 9.0 12/0.05 9/17.53 9/17.56 7/20.96 8/21.69 11 0.4722 0.6429 0.1224 8.7 13/0.18 5/11.17 13/11.40 1/12.04 2/18.24 12 0.2179 0.4068 -0.4752 8.3 9/0.15 14/17.22 4/17.56 4/19.91 3/20.92 13 0.5410 0.7540 0.1793 7.7 10/0.20 11/11.40 9/13.88 5/17.42 2/20.19 14 0.1994 0.8086 -0.3733 -5.1 7/10.52 7/10.48 3/16.07 12/17.22 13/21.22 Best trace (cycle 5 with CC 10.68%) was saved as P21212_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 10.8 - Setup, data input and phasing 2.3 - FFTs and peak-searches 5.2 - Sphere of influence 0.7 - Rest of density modification 0.0 - Alpha-helix search 52.9 - Tripeptide search 56.2 - Chain tracing 0.0 - NCS analysis 5.0 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:14:10 Total time: 133.15 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++