++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:14:46 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: P21221_pse14 P21221_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P21221_pse14_fa.res FA and alpha from P21221_pse14_fa.hkl Native data from P21221_pse14.hkl Listing output to P21221_pse14.lst Phases output to P21221_pse14.phs Revised heavy atom sites output to P21221_pse14.hat Revised heavy atom phases output to P21221_pse14.pha Poly-Ala trace output to P21221_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 21 Allowed origin shift code: 4 14 atoms read from file P21221_pse14_fa.res Trimmed to 11 atoms with occupancy > 0.2 11695 Reflections read from file P21221_pse14_fa.hkl 21043 Reflections read from file P21221_pse14.hkl 21014 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003997h^2 -0.000434k^2 -0.000495l^2 +0.000000kl +0.000000hl +0.000000hk 23 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 11 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 11 20.07% 0.293 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 20.02% = 0.126 for phases from phiT = phiA + alpha = 0.209 after including heavy atoms = 0.175, Contrast = 0.040, Connect. = 0.537 for dens.mod. cycle 1 = 0.194, Contrast = 0.108, Connect. = 0.594 for dens.mod. cycle 2 = 0.211, Contrast = 0.136, Connect. = 0.604 for dens.mod. cycle 3 = 0.224, Contrast = 0.165, Connect. = 0.617 for dens.mod. cycle 4 = 0.234, Contrast = 0.197, Connect. = 0.631 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 10 heavy atoms with Occ*Z > 0.30 added to NOGO map 1985 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 280 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 2.472 1.365 0.305 0.463 0.600 0.400 CB 1.074 B: 6 4.920 1.441 0.490 0.462 0.800 0.600 N 1.332 C: 10 2.319 1.453 0.652 0.115 0.444 0.222 CB 1.178 6 0.784 1.161 0.418 0.462 0.800 0.600 CB 0.277 ? D: 7 3.751 1.340 0.056 0.543 1.000 1.000 CB 1.037 E: 6 2.232 1.256 0.156 0.246 0.800 0.400 CA 1.152 F: 6 2.834 1.495 0.207 0.294 0.800 0.600 CB 1.106 G: 8 3.346 1.277 0.280 0.407 0.857 0.286 N 0.995 H: 10 2.501 1.284 0.369 0.305 0.556 0.444 C 1.060 I: 10 3.012 1.421 0.359 0.299 0.889 0.556 CB 0.732 J: 6 2.254 1.424 0.002 0.306 0.800 0.600 CB 1.096 K: 7 4.726 1.489 0.515 0.600 0.833 0.500 CB 0.934 L: 8 2.149 1.276 0.687 0.348 0.714 0.429 CB 0.622 M: 7 3.567 1.091 0.267 0.750 1.000 0.833 O 0.843 N: 6 4.547 1.137 0.553 0.863 1.000 1.000 N 0.845 6 0.974 0.912 0.293 0.310 0.600 0.200 N 0.760 ? O: 6 2.436 1.234 0.714 0.356 0.600 0.600 N 1.003 P: 6 3.002 1.242 0.385 0.753 0.800 0.800 CB 0.779 Q: 7 2.776 1.274 0.203 0.522 1.000 0.833 CB 0.723 R: 6 2.284 1.286 0.254 0.575 0.800 0.600 CB 0.736 S: 6 2.434 1.393 0.065 0.493 0.800 0.800 CB 0.924 T: 7 3.888 1.405 0.666 0.269 0.833 0.333 CB 1.058 U: 9 2.536 1.248 0.306 0.319 0.750 0.500 CB 0.896 V: 10 3.009 1.256 0.207 0.347 0.889 0.222 CB 0.878 W: 6 3.069 1.281 0.243 0.571 0.800 0.400 N 1.006 X: 11 2.875 1.392 0.461 0.158 0.700 0.400 CB 0.970 6 1.559 1.403 0.230 0.299 0.600 0.400 CB 0.842 ? Y: 7 2.054 1.373 -0.185 0.486 0.833 0.667 CB 0.912 105 residues left after pruning, divided into chains as follows: A: 6 B: 7 C: 6 D: 8 E: 10 F: 6 G: 7 H: 7 I: 6 J: 6 K: 9 L: 10 M: 6 N: 11 CC for partial structure against native data = 9.56 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.219, Connect. = 0.594 for dens.mod. cycle 1 = 0.281, Contrast = 0.241, Connect. = 0.578 for dens.mod. cycle 2 = 0.281, Contrast = 0.280, Connect. = 0.619 for dens.mod. cycle 3 = 0.281, Contrast = 0.303, Connect. = 0.638 for dens.mod. cycle 4 = 0.281, Contrast = 0.320, Connect. = 0.650 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 10 heavy atoms with Occ*Z > 0.30 added to NOGO map 2265 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 8.629 1.856 -0.042 0.784 1.000 0.571 CB 1.428 B: 14 6.875 1.808 0.566 0.380 0.692 0.308 CB 1.105 C: 9 7.264 1.835 0.504 0.231 0.875 0.500 CB 1.454 D: 7 4.900 1.724 -0.047 0.680 0.833 0.333 N 1.238 E: 11 3.713 1.681 0.434 0.242 0.600 0.300 CB 1.094 F: 7 6.525 1.626 0.063 0.774 1.000 0.833 CB 1.209 G: 10 5.139 1.979 0.216 0.284 0.778 0.556 CB 1.167 H: 12 3.823 1.828 0.276 0.174 0.727 0.364 CB 1.007 I: 10 7.463 1.719 0.236 0.547 0.889 0.556 CB 1.258 J: 7 2.946 1.339 0.303 0.551 0.833 0.667 CB 0.787 K: 6 3.362 1.545 0.303 0.286 0.800 0.600 CB 1.187 L: 7 2.508 1.442 0.288 0.231 0.667 0.333 CB 1.130 M: 15 5.706 1.468 0.486 0.241 0.929 0.429 CB 1.016 N: 9 3.267 1.227 0.240 0.327 0.875 0.125 O 1.050 O: 6 2.306 1.225 0.265 0.297 0.800 0.400 CB 1.043 P: 7 2.641 1.518 0.327 0.228 0.833 0.167 N 0.883 7 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds Q: 6 2.481 1.521 0.400 0.392 0.600 0.600 N 0.973 114 residues left after pruning, divided into chains as follows: A: 8 B: 14 C: 9 D: 11 E: 10 F: 12 G: 10 H: 7 I: 6 J: 6 K: 9 L: 6 M: 6 CC for partial structure against native data = 10.56 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.279, Connect. = 0.608 for dens.mod. cycle 1 = 0.281, Contrast = 0.305, Connect. = 0.598 for dens.mod. cycle 2 = 0.281, Contrast = 0.346, Connect. = 0.637 for dens.mod. cycle 3 = 0.281, Contrast = 0.367, Connect. = 0.655 for dens.mod. cycle 4 = 0.281, Contrast = 0.385, Connect. = 0.670 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 10 heavy atoms with Occ*Z > 0.30 added to NOGO map 2186 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 254 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 5.066 2.100 0.102 0.271 0.714 0.429 CB 1.503 B: 7 9.730 1.819 0.361 0.749 1.000 0.667 CB 1.285 C: 10 10.384 1.975 0.139 0.525 1.000 0.556 CB 1.500 6 1.751 1.400 0.243 0.467 0.600 0.400 CB 0.776 ? D: 10 5.103 1.604 0.671 0.235 0.889 0.556 CB 0.971 9 1.952 1.716 0.039 0.185 0.750 0.500 CB 0.753 ? E: 9 5.172 1.887 0.053 0.276 0.875 0.625 CB 1.355 F: 9 2.763 1.644 0.181 0.277 0.750 0.375 CB 0.864 G: 6 9.015 1.739 0.537 0.727 0.800 0.800 CA 1.536 H: 9 3.678 1.476 0.610 0.320 0.625 0.250 CB 1.068 I: 7 2.275 1.492 0.184 0.310 0.667 0.500 CB 0.973 6 1.995 1.608 0.081 0.154 0.800 0.400 CB 0.981 ? J: 6 4.669 1.717 0.507 0.287 0.800 0.600 CA 1.282 K: 8 4.327 1.529 0.520 0.522 0.714 0.286 CB 0.964 L: 9 3.474 1.589 0.186 0.292 0.750 0.250 CB 1.097 M: 6 2.672 1.435 0.628 0.587 0.800 0.600 CB 0.588 N: 6 2.858 1.272 0.761 0.834 0.800 0.800 CB 0.535 O: 11 4.410 1.535 0.542 0.292 0.600 0.400 CB 1.240 P: 6 3.716 1.570 0.255 0.622 0.800 0.400 CB 0.939 Q: 6 4.030 2.077 0.247 0.352 0.600 0.400 CB 1.361 R: 13 5.816 1.940 0.160 0.292 0.750 0.333 CB 1.256 6 1.590 1.333 -0.212 0.406 0.800 0.400 N 0.935 ? 7 1.599 1.136 0.046 0.353 0.833 0.333 CA 0.772 ? Using tripeptides from previous cycle as seeds S: 16 5.029 1.721 0.453 0.206 0.667 0.600 CB 1.104 97 residues left after pruning, divided into chains as follows: A: 8 B: 7 C: 10 D: 8 E: 9 F: 6 G: 9 H: 6 I: 9 J: 6 K: 6 L: 13 CC for partial structure against native data = 9.45 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.289, Connect. = 0.609 for dens.mod. cycle 1 = 0.281, Contrast = 0.327, Connect. = 0.605 for dens.mod. cycle 2 = 0.281, Contrast = 0.377, Connect. = 0.651 for dens.mod. cycle 3 = 0.281, Contrast = 0.397, Connect. = 0.670 for dens.mod. cycle 4 = 0.281, Contrast = 0.414, Connect. = 0.685 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 10 heavy atoms with Occ*Z > 0.30 added to NOGO map 2084 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 251 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 8.662 2.476 0.123 0.175 0.778 0.444 CB 1.976 B: 7 5.384 1.831 0.007 0.678 0.833 0.667 CB 1.213 C: 8 5.737 1.793 0.151 0.398 0.857 0.571 CB 1.366 D: 8 3.459 1.986 0.191 0.316 0.714 0.429 CB 0.948 E: 8 9.758 2.008 0.415 0.608 0.857 0.571 CA 1.367 F: 12 4.607 1.769 0.065 0.513 0.636 0.273 CB 1.144 G: 8 3.859 1.870 0.283 0.211 0.571 0.429 CB 1.497 H: 8 3.493 1.539 0.745 0.287 0.571 0.286 CB 1.093 I: 15 5.554 1.826 0.028 0.227 0.786 0.429 CB 1.383 J: 6 2.872 1.571 0.296 0.374 0.600 0.400 O 1.202 K: 6 5.719 1.723 0.507 0.537 0.800 0.400 CB 1.187 L: 8 2.804 1.568 0.328 0.213 0.714 0.143 CB 1.000 M: 6 2.157 1.389 0.505 0.375 0.600 0.400 N 0.879 6 1.236 1.403 0.057 0.279 0.600 0.400 CB 0.798 ? N: 6 2.039 1.382 -0.227 0.367 0.800 0.400 CA 1.230 O: 7 3.115 1.519 0.423 0.363 0.667 0.500 CB 1.022 P: 7 2.240 1.149 0.495 0.274 0.833 0.500 N 0.826 Using tripeptides from previous cycle as seeds 112 residues left after pruning, divided into chains as follows: A: 10 B: 7 C: 8 D: 8 E: 8 F: 12 G: 8 H: 7 I: 11 J: 6 K: 8 L: 6 M: 6 N: 7 CC for partial structure against native data = 12.39 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.313, Connect. = 0.619 for dens.mod. cycle 1 = 0.281, Contrast = 0.358, Connect. = 0.623 for dens.mod. cycle 2 = 0.281, Contrast = 0.412, Connect. = 0.668 for dens.mod. cycle 3 = 0.281, Contrast = 0.428, Connect. = 0.683 for dens.mod. cycle 4 = 0.281, Contrast = 0.440, Connect. = 0.694 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 10 heavy atoms with Occ*Z > 0.30 added to NOGO map 1987 peaks > 0.5 sigma used to seed fragment search Space for about 499 unique residues taking solvent into account 254 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 10.021 2.531 0.232 0.172 0.700 0.500 CB 2.161 B: 8 9.315 1.986 0.120 0.721 0.857 0.571 N 1.512 C: 13 5.282 1.912 0.253 0.207 0.750 0.417 CB 1.201 D: 6 7.330 2.289 -0.121 0.621 0.800 0.600 CB 1.817 E: 8 8.631 2.050 0.298 0.454 0.857 0.429 CB 1.499 F: 7 4.373 1.960 -0.078 0.572 0.833 0.333 CB 1.106 G: 6 4.801 1.893 0.358 0.420 0.600 0.400 N 1.512 H: 11 4.803 1.805 0.146 0.338 0.700 0.500 CB 1.252 I: 13 7.433 1.681 0.534 0.223 0.833 0.417 N 1.382 J: 6 2.238 1.621 0.125 0.290 0.600 0.400 N 1.157 K: 11 5.610 1.608 0.313 0.296 0.800 0.400 CB 1.319 L: 8 2.997 1.607 0.342 0.386 0.571 0.429 CA 1.037 M: 8 3.212 1.344 0.664 0.433 0.714 0.429 N 0.814 N: 6 2.978 1.381 0.275 0.376 1.000 0.800 CB 0.863 O: 7 2.935 1.179 0.731 0.341 0.833 0.833 CB 0.838 P: 10 2.795 1.334 0.179 0.217 0.889 0.556 N 0.929 6 1.999 1.621 0.093 0.264 0.600 0.200 CB 1.101 ? Q: 10 6.063 1.551 0.534 0.448 0.889 0.556 CB 1.008 R: 7 5.083 1.465 0.611 0.502 0.833 0.667 CB 1.053 Using tripeptides from previous cycle as seeds S: 6 2.729 1.653 0.577 0.100 0.600 0.200 CA 1.300 111 residues left after pruning, divided into chains as follows: A: 11 B: 8 C: 6 D: 8 E: 7 F: 6 G: 11 H: 13 I: 11 J: 7 K: 10 L: 7 M: 6 CC for partial structure against native data = 12.06 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.281, Contrast = 0.318, Connect. = 0.621 for dens.mod. cycle 1 = 0.282, Contrast = 0.363, Connect. = 0.625 for dens.mod. cycle 2 = 0.282, Contrast = 0.419, Connect. = 0.671 for dens.mod. cycle 3 = 0.282, Contrast = 0.436, Connect. = 0.686 for dens.mod. cycle 4 = 0.282, Contrast = 0.448, Connect. = 0.697 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 0.564 0.622 0.565 0.569 0.485 0.425 0.404 0.383 0.310 0.261 0.739 0.813 0.776 0.787 0.697 0.642 0.623 0.636 0.531 0.445 N 2112 2093 2121 2158 2095 2054 2101 2200 2179 1901 Estimated mean FOM = 0.460 Pseudo-free CC = 51.06 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.0000 0.1808 0.0000 1.0000 50.14 2 -0.2463 0.0676 -0.0185 0.9480 21.04 3 0.1516 0.5685 -0.0219 0.9274 22.32 4 0.3966 0.6854 -0.0078 0.7542 14.86 5 0.1506 0.5188 -0.1269 0.7484 18.36 6 -0.2498 0.0402 -0.1338 0.6894 13.99 7 -0.0907 0.0776 -0.0467 0.6834 17.25 8 0.0239 0.5538 0.0618 0.4929 12.03 9 -0.1643 0.1557 0.0475 0.4454 9.79 10 0.0112 0.3418 0.0598 0.3028 7.54 11 0.3990 0.6836 0.1752 0.2926 5.03 Site x y z h(sig) near old near new 1 0.0000 0.1808 0.0000 50.1 1/0.00 11/2.65 11/2.65 13/2.66 13/2.66 2 0.1519 0.5694 -0.0221 22.4 3/0.08 4/10.82 8/10.91 8/10.97 6/17.07 3 -0.2449 0.0677 -0.0187 21.2 2/0.09 5/9.36 12/10.33 9/10.74 7/11.22 4 0.1487 0.5176 -0.1266 18.5 5/0.15 2/10.82 8/12.06 10/18.59 8/19.55 5 -0.0900 0.0774 -0.0471 17.3 7/0.05 11/9.06 11/9.06 15/9.28 3/9.36 6 0.3951 0.6856 -0.0081 14.9 4/0.09 2/17.07 14/17.62 14/19.88 4/22.87 7 -0.2486 0.0396 -0.1341 14.0 6/0.09 3/11.22 5/12.72 12/17.71 15/18.50 8 0.0238 0.5531 0.0620 12.0 8/0.06 2/10.91 2/10.97 4/12.06 8/12.11 9 -0.1629 0.1552 0.0482 9.8 9/0.11 12/5.33 15/5.60 11/10.46 11/10.46 10 0.0117 0.3405 0.0567 7.9 10/0.32 10/10.86 13/11.88 13/13.36 1/14.32 11 0.0000 0.1488 0.0000 -7.1 1/2.66 1/2.65 1/2.65 13/4.96 13/4.96 12 -0.1791 0.1820 -0.0018 -5.6 9/5.24 15/3.63 9/5.33 13/9.96 3/10.33 13 0.0115 0.2045 0.0174 -5.6 1/2.66 1/2.66 1/2.66 13/3.57 11/4.96 14 0.4023 0.6877 0.1772 5.5 11/0.44 6/17.62 6/19.88 4/25.43 2/25.76 15 -0.1172 0.1743 -0.0011 -4.7 9/5.57 12/3.63 9/5.60 13/6.77 1/6.78 16 -0.5000 0.1787 0.0000 -4.6 2/17.38 3/17.45 3/17.45 12/18.51 12/18.51 Best trace (cycle 4 with CC 12.39%) was saved as P21221_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 8.1 - 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 50.8 - Tripeptide search 61.2 - Chain tracing 0.0 - NCS analysis 4.8 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:16:57 Total time: 131.10 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++