++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 13:38:09 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: I41_p9 I41_p9_fa -i -h -a5 -s0.6 -e1.2 Cell, symmetry and heavy atoms from: I41_p9_fa.res FA and alpha from I41_p9_fa.hkl Native data from I41_p9.hkl Listing output to I41_p9_i.lst Phases output to I41_p9_i.phs Revised heavy atom sites output to I41_p9_i.hat Revised heavy atom phases output to I41_p9_i.pha Poly-Ala trace output to I41_p9_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 1.200 high resolution limit for data extrapolation -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 10 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 0.600 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 unset do not optimize heavy atoms -z 0 read heavy atoms from .res Space group: I 41 Allowed origin shift code:108 7 atoms read from file I41_p9_fa.res 16206 Reflections read from file I41_p9_fa.hkl 21557 Reflections read from file I41_p9.hkl 21557 Unique data, highest resolution = 1.744 Angstroms Anisotropic scaling: intensities multiplied by -0.000103h^2 -0.000103k^2 +0.003717l^2 +0.000000kl +0.000000hl +0.000000hk 7 Reflections with d > 1.944 and 44090 in range 1.944 > d > 1.200 added Density sharpening factor set to 1.13 Fourier grid = 256 x 256 x 15 0.000 <= z <= 0.250 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.746 ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 30.95% = 0.230 for phases from phiT = phiA + alpha = 0.316 after including heavy atoms = 0.269, Contrast = 0.042, Connect. = 0.493 for dens.mod. cycle 1 = 0.280, Contrast = 0.221, Connect. = 0.608 for dens.mod. cycle 2 = 0.285, Contrast = 0.275, Connect. = 0.626 for dens.mod. cycle 3 = 0.291, Contrast = 0.319, Connect. = 0.640 for dens.mod. cycle 4 = 0.293, Contrast = 0.357, Connect. = 0.656 for dens.mod. cycle 5 = 0.294, Contrast = 0.401, Connect. = 0.675 for dens.mod. cycle 6 = 0.295, Contrast = 0.436, Connect. = 0.691 for dens.mod. cycle 7 = 0.295, Contrast = 0.468, Connect. = 0.704 for dens.mod. cycle 8 = 0.295, Contrast = 0.497, Connect. = 0.718 for dens.mod. cycle 9 = 0.295, Contrast = 0.522, Connect. = 0.728 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1886 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 177 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 14 14.227 2.042 0.426 0.447 1.000 0.692 CA 1.431 B: 19 13.142 1.695 0.820 0.485 0.833 0.611 CB 1.223 C: 10 4.818 1.731 0.739 0.235 0.778 0.333 CB 0.933 D: 11 10.557 1.918 0.657 0.573 0.800 0.600 CB 1.223 E: 7 5.022 1.542 0.567 0.524 0.667 0.667 CB 1.242 F: 9 11.840 1.724 0.926 0.668 0.875 0.750 CB 1.233 G: 10 5.749 1.659 0.611 0.294 0.889 0.333 CA 1.016 H: 9 7.666 1.630 0.670 0.487 0.875 0.625 CB 1.153 I: 18 9.120 1.590 0.610 0.358 0.765 0.471 CB 1.317 J: 7 7.294 1.727 0.683 0.703 0.833 0.833 CA 1.022 K: 12 8.528 1.770 0.570 0.391 0.727 0.636 CA 1.427 L: 12 5.990 1.494 0.480 0.529 1.000 0.636 CB 0.793 M: 9 5.800 1.803 0.518 0.282 0.875 0.500 CB 1.095 4 residues pruned to eliminate duplicates N: 11 7.245 1.607 1.092 0.347 1.000 0.500 CB 0.804 97 residues left after pruning, divided into chains as follows: A: 14 B: 8 C: 11 D: 8 E: 6 F: 18 G: 7 H: 6 I: 19 CC for partial structure against native data = 15.23 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.295, Contrast = 0.321, Connect. = 0.619 for dens.mod. cycle 1 = 0.295, Contrast = 0.381, Connect. = 0.639 for dens.mod. cycle 2 = 0.295, Contrast = 0.491, Connect. = 0.700 for dens.mod. cycle 3 = 0.295, Contrast = 0.536, Connect. = 0.723 for dens.mod. cycle 4 = 0.295, Contrast = 0.567, Connect. = 0.737 for dens.mod. cycle 5 = 0.295, Contrast = 0.589, Connect. = 0.748 for dens.mod. cycle 6 = 0.295, Contrast = 0.605, Connect. = 0.754 for dens.mod. cycle 7 = 0.295, Contrast = 0.616, Connect. = 0.759 for dens.mod. cycle 8 = 0.295, Contrast = 0.625, Connect. = 0.763 for dens.mod. cycle 9 = 0.295, Contrast = 0.629, Connect. = 0.765 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1680 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 156 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 18 12.456 2.208 0.322 0.357 0.765 0.706 CA 1.580 B: 11 7.595 1.911 0.409 0.347 0.800 0.500 CB 1.317 C: 11 14.400 2.018 0.629 0.497 0.800 0.500 CB 1.736 D: 10 6.387 1.785 0.397 0.486 1.000 0.667 CB 0.866 E: 24 11.986 1.840 0.464 0.470 0.739 0.565 CB 1.294 F: 9 8.646 1.730 0.736 0.505 0.875 0.625 CB 1.158 G: 9 7.225 1.910 0.627 0.334 0.625 0.500 CB 1.576 H: 7 4.688 1.564 0.473 0.463 1.000 1.000 CA 0.863 I: 19 13.058 1.899 0.863 0.495 0.833 0.667 CB 1.048 7 residues pruned to eliminate duplicates J: 7 7.826 1.817 0.590 0.507 0.833 0.500 CA 1.318 K: 10 9.909 1.786 0.953 0.388 0.889 0.556 CB 1.200 L: 11 14.594 1.930 0.749 0.485 1.000 0.600 CB 1.388 5 residues pruned to eliminate duplicates M: 6 2.573 1.156 0.541 0.796 0.800 0.600 CB 0.623 N: 7 5.889 1.450 0.535 0.674 1.000 0.833 CB 0.920 Using tripeptides from previous cycle as seeds 95 residues left after pruning, divided into chains as follows: A: 7 B: 8 C: 11 D: 7 E: 15 F: 7 G: 10 H: 30 CC for partial structure against native data = 14.79 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.295, Contrast = 0.336, Connect. = 0.631 for dens.mod. cycle 1 = 0.295, Contrast = 0.400, Connect. = 0.648 for dens.mod. cycle 2 = 0.295, Contrast = 0.521, Connect. = 0.713 for dens.mod. cycle 3 = 0.295, Contrast = 0.559, Connect. = 0.734 for dens.mod. cycle 4 = 0.295, Contrast = 0.587, Connect. = 0.746 for dens.mod. cycle 5 = 0.295, Contrast = 0.603, Connect. = 0.754 for dens.mod. cycle 6 = 0.295, Contrast = 0.618, Connect. = 0.760 for dens.mod. cycle 7 = 0.295, Contrast = 0.624, Connect. = 0.764 for dens.mod. cycle 8 = 0.295, Contrast = 0.633, Connect. = 0.766 for dens.mod. cycle 9 = 0.295, Contrast = 0.636, Connect. = 0.769 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1676 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 161 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 22 12.788 2.053 0.453 0.327 0.810 0.429 CB 1.397 B: 27 21.848 2.014 0.809 0.381 0.846 0.500 CA 1.578 C: 14 6.501 1.865 0.406 0.337 0.769 0.462 CB 1.067 D: 13 13.648 1.923 0.795 0.509 0.833 0.500 CB 1.358 E: 10 5.828 1.883 0.612 0.379 0.667 0.444 CB 1.092 F: 6 4.480 1.692 0.531 0.489 0.800 0.600 CA 0.977 G: 34 33.734 2.116 0.936 0.460 0.939 0.515 CA 1.588 27 residues pruned to eliminate duplicates H: 22 14.421 1.925 0.638 0.411 0.905 0.810 CB 1.211 I: 7 6.273 1.520 0.618 0.590 0.833 0.833 CB 1.146 Using tripeptides from previous cycle as seeds 100 residues left after pruning, divided into chains as follows: A: 8 B: 12 C: 13 D: 7 E: 34 F: 9 G: 10 H: 7 CC for partial structure against native data = 16.52 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.295, Contrast = 0.344, Connect. = 0.628 for dens.mod. cycle 1 = 0.295, Contrast = 0.408, Connect. = 0.648 for dens.mod. cycle 2 = 0.295, Contrast = 0.532, Connect. = 0.712 for dens.mod. cycle 3 = 0.295, Contrast = 0.574, Connect. = 0.736 for dens.mod. cycle 4 = 0.295, Contrast = 0.599, Connect. = 0.749 for dens.mod. cycle 5 = 0.295, Contrast = 0.612, Connect. = 0.756 for dens.mod. cycle 6 = 0.295, Contrast = 0.625, Connect. = 0.761 for dens.mod. cycle 7 = 0.295, Contrast = 0.630, Connect. = 0.765 for dens.mod. cycle 8 = 0.295, Contrast = 0.638, Connect. = 0.767 for dens.mod. cycle 9 = 0.295, Contrast = 0.638, Connect. = 0.769 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1672 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 162 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 13.093 1.999 0.995 0.557 0.857 0.857 CB 1.369 B: 28 17.116 1.957 0.534 0.374 0.889 0.444 CB 1.413 5 residues pruned to eliminate duplicates C: 34 35.208 2.130 0.948 0.452 0.939 0.545 CB 1.651 D: 11 9.366 1.824 0.539 0.560 0.800 0.500 CB 1.244 E: 11 12.160 2.243 0.694 0.367 0.800 0.400 CB 1.459 F: 6 5.776 1.643 0.307 0.759 1.000 0.600 CB 0.956 G: 16 10.757 1.868 0.627 0.451 0.867 0.533 CB 1.109 16 residues pruned to eliminate duplicates H: 10 6.613 1.656 0.677 0.392 0.778 0.444 C 1.144 I: 7 2.943 1.615 0.084 0.400 0.833 0.833 CB 0.914 J: 6 5.711 1.641 0.551 0.398 1.000 0.600 CB 1.116 K: 8 12.771 1.813 1.201 0.436 1.000 0.857 CB 1.293 L: 6 3.338 1.710 0.151 0.368 0.800 0.600 CB 1.092 7 1.585 1.342 0.883 0.393 0.667 0.333 CB 0.430 ? M: 6 2.577 1.198 0.997 0.448 0.800 0.400 N 0.635 N: 7 7.171 1.747 0.414 0.635 1.000 1.000 CB 1.044 Using tripeptides from previous cycle as seeds O: 6 4.199 1.580 1.557 0.464 0.400 0.400 CB 1.205 83 residues left after pruning, divided into chains as follows: A: 8 B: 34 C: 8 D: 11 E: 6 F: 10 G: 6 CC for partial structure against native data = 13.52 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.295, Contrast = 0.333, Connect. = 0.625 for dens.mod. cycle 1 = 0.295, Contrast = 0.393, Connect. = 0.643 for dens.mod. cycle 2 = 0.295, Contrast = 0.518, Connect. = 0.710 for dens.mod. cycle 3 = 0.295, Contrast = 0.562, Connect. = 0.734 for dens.mod. cycle 4 = 0.295, Contrast = 0.590, Connect. = 0.746 for dens.mod. cycle 5 = 0.295, Contrast = 0.607, Connect. = 0.754 for dens.mod. cycle 6 = 0.295, Contrast = 0.621, Connect. = 0.760 for dens.mod. cycle 7 = 0.295, Contrast = 0.628, Connect. = 0.765 for dens.mod. cycle 8 = 0.295, Contrast = 0.635, Connect. = 0.767 for dens.mod. cycle 9 = 0.295, Contrast = 0.639, Connect. = 0.769 for dens.mod. cycle 10 NOGO map generated for regions about rotation axes (if any) 6 heavy atoms with Occ*Z > 10.20 added to NOGO map 1672 peaks > 0.5 sigma used to seed fragment search Space for about 168 unique residues taking solvent into account 157 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 19.538 2.051 0.796 0.529 0.929 0.714 CB 1.483 B: 19 16.948 2.033 0.578 0.449 0.889 0.500 CA 1.476 C: 32 33.645 2.184 0.820 0.445 0.903 0.613 CA 1.782 19 residues pruned to eliminate duplicates D: 9 12.605 2.157 0.440 0.612 0.750 0.500 CB 1.721 E: 9 6.394 1.874 0.729 0.484 0.875 0.500 CB 0.810 F: 14 14.523 2.096 1.019 0.431 0.923 0.462 CB 1.107 9 residues pruned to eliminate duplicates G: 7 7.701 1.643 0.304 0.770 1.000 1.000 CB 1.156 H: 14 6.711 1.832 0.292 0.355 0.846 0.538 CB 1.087 I: 19 12.740 1.758 1.152 0.431 0.778 0.556 CB 1.096 J: 9 9.329 1.730 0.916 0.392 1.000 0.875 CB 1.116 K: 11 5.520 1.520 0.395 0.332 0.900 0.700 CB 1.100 L: 9 10.341 1.687 1.049 0.644 0.875 0.625 CB 1.057 M: 6 5.659 1.485 1.212 0.345 0.800 0.600 CA 1.140 N: 10 6.177 1.567 0.979 0.308 0.778 0.778 CB 1.056 Using tripeptides from previous cycle as seeds 116 residues left after pruning, divided into chains as follows: A: 12 B: 32 C: 8 D: 13 E: 7 F: 14 G: 11 H: 9 I: 10 CC for partial structure against native data = 19.17 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.295, Contrast = 0.326, Connect. = 0.635 for dens.mod. cycle 1 = 0.297, Contrast = 0.396, Connect. = 0.660 for dens.mod. cycle 2 = 0.309, Contrast = 0.564, Connect. = 0.753 for dens.mod. cycle 3 = 0.309, Contrast = 0.600, Connect. = 0.767 for dens.mod. cycle 4 = 0.312, Contrast = 0.620, Connect. = 0.779 for dens.mod. cycle 5 = 0.313, Contrast = 0.598, Connect. = 0.773 for dens.mod. cycle 6 = 0.314, Contrast = 0.603, Connect. = 0.778 for dens.mod. cycle 7 = 0.315, Contrast = 0.578, Connect. = 0.768 for dens.mod. cycle 8 = 0.316, Contrast = 0.579, Connect. = 0.771 for dens.mod. cycle 9 = 0.316, Contrast = 0.555, Connect. = 0.759 for dens.mod. cycle 10 Estimated mean FOM and mapCC as a function of resolution d inf - 3.82 - 3.02 - 2.63 - 2.39 - 2.21 - 2.08 - 1.98 - 1.89 - 1.81 - 1.75 0.519 0.603 0.626 0.587 0.606 0.588 0.596 0.596 0.640 0.717 0.717 0.788 0.813 0.790 0.806 0.792 0.819 0.825 0.865 0.909 N 2172 2153 2174 2129 2262 2141 2064 2233 2385 1844 Estimated mean FOM = 0.607 Pseudo-free CC = 63.19 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.1125 -0.3208 0.9989 34.0000 43.97 2 -0.1862 -0.2610 1.2236 33.1840 41.41 3 -0.1809 -0.3866 0.9979 29.5188 39.35 4 -0.1648 -0.2934 1.1538 29.1958 38.53 5 0.2372 -0.3137 0.7152 22.8990 32.47 6 0.2050 -0.3348 0.6512 18.4756 25.53 7 0.2493 -0.4673 0.7196 8.5918 5.99 Site x y z h(sig) near old near new 1 0.1124 -0.3206 0.9989 44.0 1/0.03 23/1.90 24/3.97 7/12.02 8/12.41 2 -0.1859 -0.2616 1.2208 41.5 2/0.11 22/1.80 19/1.89 17/2.30 16/3.75 3 -0.1806 -0.3871 0.9981 39.5 3/0.07 4/12.00 14/12.74 16/13.24 18/13.27 4 -0.1649 -0.2931 1.1557 38.7 4/0.07 16/2.20 22/3.76 2/4.81 17/6.25 5 0.2371 -0.3137 0.7134 32.6 5/0.06 20/1.70 13/1.99 6/4.73 13/12.28 6 0.2058 -0.3353 0.6550 25.6 6/0.16 5/4.73 20/5.03 13/5.74 11/11.89 7 0.2069 -0.3349 1.1560 -11.2 1/12.01 8/4.92 23/10.45 1/12.02 8/12.58 8 0.1850 -0.2396 0.9760 -10.7 1/12.43 7/4.92 23/11.62 13/11.71 1/12.41 9 -0.1125 -0.1774 1.2537 -9.1 2/12.74 10/11.80 22/12.49 2/12.77 17/12.83 10 -0.2049 -0.1661 1.4130 -7.0 2/12.63 14/4.36 18/4.92 17/11.71 19/11.80 11 0.1133 -0.3183 0.4966 -6.4 6/11.75 20/10.92 6/11.89 12/12.07 24/12.37 12 0.2481 -0.4658 0.7193 6.3 7/0.23 21/4.65 15/8.21 11/12.07 6/15.77 13 0.2332 -0.3090 0.7707 -5.9 5/1.93 5/1.99 20/3.28 6/5.74 8/11.71 14 -0.2647 -0.3144 0.9569 -5.8 3/12.67 18/3.74 10/4.36 18/11.32 17/11.54 15 0.2574 -0.5289 0.8368 5.7 7/8.04 12/8.21 21/10.62 3/13.99 10/16.39 16 -0.1697 -0.2903 1.2204 -5.4 4/2.27 4/2.20 22/2.45 2/3.75 17/4.50 17 -0.1871 -0.2612 1.2915 -5.3 2/2.21 2/2.30 22/2.75 19/2.93 16/4.50 18 -0.2386 -0.1840 1.3423 -5.0 2/11.29 14/3.74 10/4.92 17/9.77 19/9.88 19 -0.2004 -0.2535 1.2191 -4.9 2/1.83 2/1.89 17/2.93 22/3.68 16/5.45 20 0.2466 -0.3245 0.6998 -4.9 5/1.71 5/1.70 13/3.28 6/5.03 11/10.92 21 0.2380 -0.4733 0.5833 4.8 7/4.66 12/4.65 15/10.62 11/14.46 6/16.32 22 -0.1723 -0.2691 1.2305 -4.8 2/1.85 2/1.80 16/2.45 17/2.75 19/3.68 23 0.1286 -0.3244 0.9928 -4.8 1/1.89 1/1.90 24/4.15 7/10.45 8/11.62 24 0.1133 -0.3230 0.8771 -4.6 1/3.96 1/3.97 23/4.15 11/12.37 6/12.84 Best trace (cycle 5 with CC 19.17%) was saved as I41_p9_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.6 - Setup, data input and phasing 4.1 - FFTs and peak-searches 9.1 - Sphere of influence 0.3 - Rest of density modification 0.0 - Alpha-helix search 76.6 - Tripeptide search 45.6 - Chain tracing 0.0 - NCS analysis 4.5 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 13:40:30 Total time: 141.04 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++