++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:01:07 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: P222_pse14 P222_pse14_fa -i -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P222_pse14_fa.res FA and alpha from P222_pse14_fa.hkl Native data from P222_pse14.hkl Listing output to P222_pse14_i.lst Phases output to P222_pse14_i.phs Revised heavy atom sites output to P222_pse14_i.hat Revised heavy atom phases output to P222_pse14_i.pha Poly-Ala trace output to P222_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 2 2 Allowed origin shift code: 4 14 atoms read from file P222_pse14_fa.res Trimmed to 5 atoms with occupancy > 0.2 11695 Reflections read from file P222_pse14_fa.hkl 21043 Reflections read from file P222_pse14.hkl 21043 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003974h^2 -0.000438k^2 -0.000491l^2 +0.000000kl +0.000000hl +0.000000hk 28 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|> = 0.782 ** Atom coordinates inverted ** 5 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 5 12.58% 0.702 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 12.45% = 0.098 for phases from phiT = phiA + alpha = 0.195 after including heavy atoms = 0.163, Contrast = 0.045, Connect. = 0.527 for dens.mod. cycle 1 = 0.191, Contrast = 0.159, Connect. = 0.631 for dens.mod. cycle 2 = 0.207, Contrast = 0.211, Connect. = 0.650 for dens.mod. cycle 3 = 0.221, Contrast = 0.244, Connect. = 0.662 for dens.mod. cycle 4 = 0.231, Contrast = 0.268, Connect. = 0.671 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 5 heavy atoms with Occ*Z > 0.30 added to NOGO map 1764 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 241 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 4.218 1.463 0.716 0.649 1.000 1.000 CB 0.654 B: 6 2.181 1.278 0.779 0.561 0.400 0.400 CB 1.011 C: 7 5.894 1.444 1.039 0.426 0.833 0.500 CB 1.059 D: 8 3.381 1.410 0.425 0.344 0.714 0.429 N 1.056 E: 6 2.948 1.458 -0.044 0.441 0.800 0.800 CA 1.257 F: 6 3.033 1.392 0.254 0.484 0.800 0.400 CB 0.987 G: 8 3.912 1.418 1.138 0.442 0.714 0.571 CB 0.725 H: 7 3.126 1.244 0.671 0.402 0.833 0.500 CB 0.817 I: 6 2.148 1.336 0.304 0.293 0.600 0.400 CA 1.160 J: 9 7.170 1.267 1.015 0.481 1.000 0.375 CB 1.012 K: 6 2.573 1.467 0.317 0.448 0.800 0.600 N 0.785 L: 7 2.320 1.260 0.110 0.681 0.667 0.667 C 0.860 M: 8 3.130 1.460 0.339 0.453 0.714 0.429 CB 0.889 N: 6 3.148 1.351 0.316 0.275 1.000 0.400 N 1.023 O: 8 3.644 1.244 0.416 0.474 0.857 0.429 CB 0.937 P: 11 3.219 1.264 0.295 0.551 0.800 0.400 CB 0.739 Q: 6 3.116 1.443 0.307 0.527 0.800 0.600 CB 0.899 R: 7 3.161 1.319 0.543 0.395 1.000 0.500 CB 0.708 6 1.640 1.435 -0.300 0.322 0.800 0.400 CB 1.110 ? S: 6 2.150 1.422 0.133 0.325 0.800 0.400 CB 0.905 T: 7 3.316 1.375 0.101 0.457 0.833 0.333 N 1.122 U: 8 3.130 1.395 0.504 0.374 0.857 0.429 CB 0.752 6 1.499 1.399 0.247 0.374 0.800 0.600 CB 0.550 ? V: 6 4.253 1.338 0.806 0.483 0.800 0.400 CB 1.001 92 residues left after pruning, divided into chains as follows: A: 7 B: 6 C: 6 D: 6 E: 8 F: 6 G: 9 H: 6 I: 7 J: 6 K: 8 L: 11 M: 6 CC for partial structure against native data = 8.02 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.265, Connect. = 0.608 for dens.mod. cycle 1 = 0.281, Contrast = 0.284, Connect. = 0.588 for dens.mod. cycle 2 = 0.281, Contrast = 0.322, Connect. = 0.626 for dens.mod. cycle 3 = 0.281, Contrast = 0.343, Connect. = 0.644 for dens.mod. cycle 4 = 0.281, Contrast = 0.356, Connect. = 0.655 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 5 heavy atoms with Occ*Z > 0.30 added to NOGO map 2354 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 254 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 5.984 1.983 0.561 0.313 0.857 0.571 CB 1.050 B: 7 9.442 2.245 -0.011 0.713 0.833 0.667 CB 1.718 C: 7 6.237 1.737 0.507 0.491 0.833 0.333 CB 1.178 D: 10 5.552 1.833 0.340 0.267 0.667 0.444 CB 1.474 E: 7 2.298 1.514 0.441 0.374 0.500 0.333 CB 0.984 F: 11 6.769 1.842 0.554 0.398 0.700 0.600 CB 1.190 G: 12 3.376 1.532 0.292 0.390 0.727 0.545 CB 0.794 H: 7 4.739 1.759 0.235 0.514 1.000 0.333 CB 0.878 I: 10 15.620 1.848 0.643 0.624 1.000 0.333 N 1.526 J: 10 6.547 1.798 0.428 0.289 0.778 0.444 N 1.386 K: 7 6.455 1.819 0.442 0.581 0.833 0.667 CB 1.115 6 1.920 1.377 0.196 0.460 0.600 0.400 CB 0.905 ? L: 7 5.212 1.792 0.276 0.246 0.833 0.500 CB 1.497 M: 10 6.516 1.279 0.886 0.643 0.889 0.444 CB 0.886 N: 6 2.907 1.390 -0.042 0.360 1.000 0.600 CB 1.134 O: 10 4.382 1.471 0.166 0.553 0.778 0.444 CB 1.040 P: 8 4.563 1.385 0.664 0.479 0.714 0.571 CB 1.071 Q: 7 4.366 1.673 0.471 0.377 0.667 0.500 CA 1.239 9 1.648 1.522 0.142 0.383 0.750 0.500 CB 0.506 ? R: 8 2.218 1.266 0.366 0.326 0.571 0.286 CB 1.027 S: 11 2.629 1.452 0.078 0.189 0.700 0.400 CB 1.101 11 residues pruned to eliminate duplicates 6 1.644 1.317 0.044 0.300 0.800 0.400 CB 0.836 ? Using tripeptides from previous cycle as seeds T: 6 2.840 1.391 0.742 0.489 0.800 0.800 CB 0.662 U: 8 5.541 1.819 0.265 0.303 0.714 0.571 O 1.586 89 residues left after pruning, divided into chains as follows: A: 7 B: 7 C: 11 D: 10 E: 10 F: 7 G: 7 H: 6 I: 8 J: 8 K: 8 CC for partial structure against native data = 10.52 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.326, Connect. = 0.609 for dens.mod. cycle 1 = 0.281, Contrast = 0.359, Connect. = 0.610 for dens.mod. cycle 2 = 0.281, Contrast = 0.400, Connect. = 0.648 for dens.mod. cycle 3 = 0.281, Contrast = 0.418, Connect. = 0.665 for dens.mod. cycle 4 = 0.281, Contrast = 0.432, Connect. = 0.679 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 5 heavy atoms with Occ*Z > 0.30 added to NOGO map 2179 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 220 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 7.513 1.977 0.512 0.392 0.625 0.375 CB 1.593 B: 9 9.062 2.307 0.188 0.336 0.750 0.750 CB 1.865 C: 8 10.008 2.136 0.290 0.639 0.857 0.571 CB 1.405 D: 7 5.312 1.793 0.526 0.341 0.667 0.500 CB 1.414 E: 6 5.578 2.120 0.091 0.488 0.800 0.600 O 1.364 F: 6 4.432 1.608 0.381 0.497 0.800 0.800 CB 1.120 G: 6 2.031 1.693 0.379 0.561 0.800 0.400 CB 0.459 H: 6 3.562 1.620 0.375 0.485 0.600 0.600 CB 1.210 I: 8 5.376 1.886 0.700 0.296 0.571 0.286 CB 1.393 6 1.575 1.413 0.394 0.406 0.800 0.600 CB 0.493 ? J: 9 4.328 1.680 0.451 0.300 0.625 0.625 CB 1.256 K: 6 2.002 1.239 0.198 0.441 0.600 0.400 O 1.069 L: 6 3.812 1.267 0.343 0.812 1.000 0.800 CA 0.764 M: 7 2.223 1.844 0.137 0.282 0.667 0.500 CB 0.831 N: 7 5.438 1.488 0.419 0.522 0.833 0.667 C 1.234 O: 11 7.769 1.413 0.815 0.722 0.800 0.400 CB 0.979 7 1.876 1.633 0.001 0.137 0.500 0.333 O 1.472 ? P: 6 3.767 1.630 0.196 0.442 0.800 0.200 CB 1.147 Using tripeptides from previous cycle as seeds 84 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 6 D: 6 E: 6 F: 6 G: 6 H: 8 I: 6 J: 6 K: 6 L: 11 CC for partial structure against native data = 8.75 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.349, Connect. = 0.618 for dens.mod. cycle 1 = 0.281, Contrast = 0.395, Connect. = 0.617 for dens.mod. cycle 2 = 0.281, Contrast = 0.441, Connect. = 0.657 for dens.mod. cycle 3 = 0.281, Contrast = 0.453, Connect. = 0.674 for dens.mod. cycle 4 = 0.281, Contrast = 0.464, Connect. = 0.687 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 5 heavy atoms with Occ*Z > 0.30 added to NOGO map 2120 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 213 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 8.320 2.080 0.482 0.338 0.600 0.300 CB 1.696 B: 12 7.419 1.967 0.413 0.204 0.727 0.273 CB 1.571 C: 10 2.440 1.777 0.057 0.273 0.667 0.444 CB 0.840 D: 12 9.245 2.196 0.429 0.275 0.727 0.455 CB 1.575 E: 10 6.152 1.965 0.133 0.274 0.778 0.333 CB 1.529 F: 9 3.492 1.697 0.489 0.306 0.625 0.500 CB 0.970 G: 7 2.680 1.902 0.596 0.246 0.333 0.333 CB 1.450 6 1.845 1.884 0.169 0.313 0.400 0.400 CB 1.152 ? H: 13 11.164 1.723 0.658 0.425 0.833 0.667 CB 1.463 I: 6 3.193 1.862 0.194 0.746 1.000 0.400 CB 0.515 J: 6 4.867 1.516 0.042 0.660 1.000 0.600 CB 1.188 K: 9 2.582 1.375 0.614 0.243 0.625 0.375 CB 0.886 L: 8 4.244 1.434 0.125 0.409 0.857 0.286 CB 1.277 6 1.892 0.920 1.276 0.260 0.800 0.400 N 0.664 ? M: 6 7.628 1.486 0.598 0.718 1.000 0.800 CB 1.180 9 1.251 1.510 0.447 0.187 0.375 0.250 CB 0.786 ? N: 7 2.379 1.889 0.319 0.221 0.500 0.500 CB 1.081 7 residues pruned to eliminate duplicates O: 10 3.873 1.472 0.129 0.378 0.778 0.222 N 1.138 6 1.894 1.641 0.267 0.288 0.800 0.600 CB 0.646 ? Using tripeptides from previous cycle as seeds P: 6 2.099 1.879 -0.168 0.418 0.600 0.400 CB 1.090 83 residues left after pruning, divided into chains as follows: A: 11 B: 12 C: 12 D: 13 E: 6 F: 9 G: 8 H: 6 I: 6 CC for partial structure against native data = 9.56 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.365, Connect. = 0.618 for dens.mod. cycle 1 = 0.281, Contrast = 0.414, Connect. = 0.626 for dens.mod. cycle 2 = 0.281, Contrast = 0.458, Connect. = 0.667 for dens.mod. cycle 3 = 0.281, Contrast = 0.470, Connect. = 0.682 for dens.mod. cycle 4 = 0.281, Contrast = 0.476, Connect. = 0.692 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 5 heavy atoms with Occ*Z > 0.30 added to NOGO map 2058 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 215 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 10.871 2.555 0.611 0.400 0.800 0.400 CB 1.640 B: 14 11.947 2.218 0.579 0.333 0.769 0.385 CB 1.477 C: 6 4.963 2.042 -0.014 0.416 0.800 0.600 N 1.504 D: 14 11.282 1.980 0.533 0.485 0.846 0.615 CB 1.236 6 residues pruned to eliminate duplicates E: 14 6.192 2.007 0.019 0.319 0.846 0.462 CB 1.212 F: 10 5.943 1.610 0.228 0.449 0.778 0.222 CA 1.357 8 1.737 1.480 0.639 0.214 0.429 0.286 CB 0.885 ? 6 1.828 1.712 0.769 0.208 0.400 0.200 CB 0.953 ? G: 7 6.739 1.522 0.866 0.724 0.833 0.333 CB 0.950 H: 7 3.083 1.795 -0.062 0.453 0.833 0.333 O 0.941 I: 7 4.610 1.467 0.620 0.473 1.000 0.333 CB 0.813 J: 7 3.805 1.267 0.882 0.362 0.833 0.500 CB 0.906 K: 8 4.403 1.286 0.818 0.363 0.857 0.714 CB 0.963 L: 6 3.715 1.453 0.778 0.350 0.800 0.600 CB 0.945 M: 7 4.619 1.664 0.766 0.340 0.833 0.667 CB 0.917 Using tripeptides from previous cycle as seeds N: 11 4.941 1.624 0.666 0.268 0.700 0.200 CB 1.074 7 residues pruned to eliminate duplicates 86 residues left after pruning, divided into chains as follows: A: 14 B: 6 C: 14 D: 13 E: 7 F: 7 G: 8 H: 6 I: 11 CC for partial structure against native data = 9.87 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 2 used as input for final density modification = 0.281, Contrast = 0.364, Connect. = 0.627 for dens.mod. cycle 1 = 0.282, Contrast = 0.412, Connect. = 0.630 for dens.mod. cycle 2 = 0.282, Contrast = 0.465, Connect. = 0.673 for dens.mod. cycle 3 = 0.282, Contrast = 0.479, Connect. = 0.688 for dens.mod. cycle 4 = 0.282, Contrast = 0.491, Connect. = 0.701 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 0.508 0.532 0.592 0.577 0.506 0.467 0.431 0.380 0.305 0.260 0.687 0.709 0.798 0.799 0.731 0.698 0.667 0.639 0.527 0.452 N 2111 2109 2124 2076 2180 2056 2102 2202 2180 1903 Estimated mean FOM = 0.457 Pseudo-free CC = 50.51 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.5000 0.5000 0.5000 1.0000 87.58 2 0.2545 0.3859 0.4829 0.8880 15.87 3 0.8483 0.7465 0.9826 0.8203 14.91 4 0.3501 0.1156 0.4765 0.7101 14.01 5 0.8442 0.8051 0.8812 0.7020 10.70 Site x y z h(sig) near old near new 1 0.5000 0.5000 0.5000 87.6 1/0.00 7/2.34 7/2.34 7/2.34 7/2.34 2 0.2530 0.3855 0.4841 16.1 2/0.14 11/9.91 11/9.91 10/11.08 10/11.08 3 0.8500 0.7466 0.9836 15.0 3/0.13 5/10.91 5/22.39 14/31.76 14/31.76 4 0.3502 0.1163 0.4767 14.0 4/0.06 4/17.83 4/19.79 2/23.04 9/27.88 5 0.8439 0.8046 0.8807 10.7 5/0.07 3/10.91 3/22.39 14/32.34 14/32.34 6 0.5000 0.5000 0.4728 -10.2 1/2.58 7/2.37 7/2.37 1/2.58 1/2.58 7 0.4943 0.4766 0.4866 -8.8 1/2.34 8/1.43 8/1.43 1/2.34 1/2.34 8 0.5000 0.5302 0.5000 -8.5 1/2.51 7/1.43 7/1.43 1/2.51 1/2.51 9 0.5000 0.5654 0.5000 -7.9 1/5.42 8/2.91 8/2.91 7/3.72 7/3.72 10 0.3484 0.5000 0.5000 -7.3 1/8.74 11/7.91 11/7.91 7/8.73 7/8.73 11 0.2112 0.5000 0.5000 -6.8 2/9.92 15/4.28 15/4.28 13/7.00 13/7.00 12 0.0000 0.5000 0.5000 -6.8 2/17.54 13/5.18 13/5.18 13/5.18 13/5.18 13 0.0899 0.5000 0.5000 -6.2 2/13.50 15/2.72 15/2.72 12/5.18 12/5.18 14 0.5000 0.5000 0.8412 -5.1 3/31.66 16/10.27 16/10.27 6/29.86 6/29.86 15 0.1370 0.5000 0.5000 -5.0 2/11.75 13/2.72 13/2.72 11/4.28 11/4.28 16 0.5000 0.5000 0.2668 -4.7 1/22.17 14/10.27 14/10.27 6/19.58 6/19.58 Best trace (cycle 2 with CC 10.52%) was saved as P222_pse14_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 3.5 - Setup, data input and phasing 2.4 - FFTs and peak-searches 5.2 - Sphere of influence 3.9 - Rest of density modification 0.0 - Alpha-helix search 49.8 - Tripeptide search 55.5 - Chain tracing 0.0 - NCS analysis 3.9 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:03:12 Total time: 124.43 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++