++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:09:07 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: P2122_pse14 P2122_pse14_fa -i -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P2122_pse14_fa.res FA and alpha from P2122_pse14_fa.hkl Native data from P2122_pse14.hkl Listing output to P2122_pse14_i.lst Phases output to P2122_pse14_i.phs Revised heavy atom sites output to P2122_pse14_i.hat Revised heavy atom phases output to P2122_pse14_i.pha Poly-Ala trace output to P2122_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 21 2 2 Allowed origin shift code: 4 14 atoms read from file P2122_pse14_fa.res Trimmed to 12 atoms with occupancy > 0.2 11695 Reflections read from file P2122_pse14_fa.hkl 21043 Reflections read from file P2122_pse14.hkl 21033 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003986h^2 -0.000437k^2 -0.000492l^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 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 ** Atom coordinates inverted ** 12 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 12 19.02% 0.261 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 18.64% = 0.122 for phases from phiT = phiA + alpha = 0.197 after including heavy atoms = 0.172, Contrast = 0.034, Connect. = 0.522 for dens.mod. cycle 1 = 0.191, Contrast = 0.104, Connect. = 0.581 for dens.mod. cycle 2 = 0.205, Contrast = 0.145, Connect. = 0.606 for dens.mod. cycle 3 = 0.218, Contrast = 0.184, Connect. = 0.629 for dens.mod. cycle 4 = 0.228, Contrast = 0.212, Connect. = 0.643 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 1787 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 229 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 6 1.881 1.541 -0.458 0.546 1.000 0.600 CB 0.962 ? A: 6 3.140 1.409 0.625 0.462 0.800 0.800 CB 0.797 B: 6 3.929 1.388 0.673 0.388 0.800 0.400 CB 1.065 6 1.520 1.274 0.194 0.299 0.600 0.600 CB 0.933 ? C: 6 2.115 1.235 0.269 0.769 0.600 0.600 CB 0.792 D: 6 5.601 1.524 0.833 0.309 0.800 0.600 CB 1.386 6 1.480 1.312 0.207 0.111 0.800 0.400 CB 0.856 ? E: 7 3.156 1.395 0.454 0.357 0.667 0.500 CB 1.112 F: 8 4.686 1.313 0.384 0.487 1.000 0.571 CB 0.988 G: 10 4.813 1.459 0.421 0.479 0.778 0.778 CB 1.016 H: 6 4.969 1.337 0.339 0.577 1.000 0.800 CB 1.152 I: 6 2.042 1.318 0.016 0.324 0.800 0.400 O 1.034 J: 10 2.130 1.334 0.370 0.157 0.556 0.444 O 1.064 K: 9 4.191 1.519 0.661 0.303 0.625 0.375 CB 1.171 L: 6 3.206 1.364 0.157 0.687 1.000 0.600 CB 0.765 M: 6 3.203 1.295 0.036 0.540 1.000 0.800 CB 1.027 N: 9 3.666 1.296 0.521 0.308 0.750 0.375 N 1.085 O: 6 2.577 1.419 0.247 0.497 0.600 0.400 CB 1.088 P: 6 2.323 1.339 0.311 0.537 0.600 0.400 N 0.951 Q: 6 3.923 1.492 0.665 0.387 0.600 0.600 O 1.328 6 1.967 1.226 0.186 0.396 0.800 0.400 N 0.844 ? R: 8 3.382 1.259 0.470 0.487 0.857 0.571 CB 0.816 S: 6 3.921 1.258 0.363 0.640 0.800 0.800 C 1.122 T: 10 3.140 1.399 0.243 0.281 0.778 0.556 CB 0.991 7 1.342 1.252 0.534 0.425 0.333 0.167 N 0.925 ? 7 1.608 1.357 0.130 0.235 0.500 0.167 N 1.165 ? 96 residues left after pruning, divided into chains as follows: A: 6 B: 6 C: 6 D: 7 E: 8 F: 6 G: 10 H: 6 I: 6 J: 8 K: 6 L: 6 M: 8 N: 7 CC for partial structure against native data = 8.15 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.237, Connect. = 0.591 for dens.mod. cycle 1 = 0.281, Contrast = 0.263, Connect. = 0.576 for dens.mod. cycle 2 = 0.281, Contrast = 0.311, Connect. = 0.621 for dens.mod. cycle 3 = 0.281, Contrast = 0.336, Connect. = 0.643 for dens.mod. cycle 4 = 0.281, Contrast = 0.360, Connect. = 0.661 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 2225 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 228 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 7.601 2.229 0.574 0.247 0.571 0.429 N 1.919 B: 6 2.605 1.937 0.293 0.687 0.800 0.600 CB 0.490 C: 6 5.124 2.185 0.738 0.449 0.600 0.200 CB 1.060 D: 11 13.922 1.966 0.394 0.601 1.000 0.400 CB 1.459 E: 13 6.882 1.759 0.527 0.272 0.750 0.417 CB 1.278 F: 6 2.652 1.512 0.314 0.299 0.600 0.400 CA 1.245 G: 6 2.313 1.382 0.091 0.523 0.600 0.400 O 1.117 H: 14 2.882 1.495 0.070 0.122 0.692 0.385 CB 1.159 I: 6 4.869 1.509 1.151 0.396 0.600 0.400 C 1.248 7 1.532 1.660 0.070 0.103 0.500 0.167 CA 1.168 ? J: 8 4.126 1.385 0.815 0.359 0.714 0.429 O 1.011 K: 8 3.726 1.367 0.338 0.268 0.857 0.571 N 1.171 L: 10 2.368 1.299 0.343 0.250 0.667 0.333 CB 0.905 M: 8 7.264 1.902 0.991 0.257 0.714 0.429 CB 1.341 Using tripeptides from previous cycle as seeds N: 12 2.852 1.819 0.219 0.093 0.545 0.364 CB 1.199 O: 6 2.066 1.408 0.406 0.128 0.800 0.200 N 0.930 90 residues left after pruning, divided into chains as follows: A: 6 B: 11 C: 13 D: 7 E: 6 F: 7 G: 10 H: 8 I: 10 J: 12 CC for partial structure against native data = 5.98 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.276, Connect. = 0.607 for dens.mod. cycle 1 = 0.281, Contrast = 0.319, Connect. = 0.607 for dens.mod. cycle 2 = 0.281, Contrast = 0.375, Connect. = 0.651 for dens.mod. cycle 3 = 0.281, Contrast = 0.402, Connect. = 0.673 for dens.mod. cycle 4 = 0.281, Contrast = 0.421, Connect. = 0.686 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 2035 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 230 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 6.640 2.138 0.511 0.224 0.667 0.556 CB 1.419 B: 13 15.688 2.194 0.385 0.507 0.833 0.500 CB 1.776 C: 14 9.388 2.111 0.219 0.309 0.846 0.308 CB 1.479 D: 8 5.680 1.656 0.530 0.306 0.714 0.286 CA 1.473 E: 13 5.686 1.700 0.426 0.297 0.750 0.333 CB 1.132 F: 8 6.291 1.787 0.343 0.384 0.714 0.571 CA 1.569 G: 6 5.457 1.979 0.295 0.299 0.800 0.400 CB 1.490 H: 9 4.015 1.559 0.417 0.437 0.750 0.375 CB 0.915 I: 9 5.509 1.744 0.327 0.285 0.875 0.250 CB 1.225 J: 7 2.135 1.242 0.414 0.247 0.667 0.500 C 0.998 K: 7 4.880 1.805 -0.079 0.444 0.833 0.333 N 1.524 L: 6 3.459 1.273 0.566 0.504 0.800 0.600 CB 0.966 M: 6 2.945 1.664 -0.001 0.318 0.800 0.400 CA 1.211 N: 14 4.771 1.359 0.406 0.382 0.692 0.462 CB 1.134 O: 11 4.407 1.655 0.326 0.375 0.700 0.400 CB 1.037 P: 7 4.362 1.388 0.437 0.474 0.833 0.667 CB 1.100 Using tripeptides from previous cycle as seeds Q: 8 3.813 1.419 0.582 0.465 0.857 0.571 N 0.776 81 residues left after pruning, divided into chains as follows: A: 10 B: 13 C: 14 D: 10 E: 8 F: 6 G: 6 H: 7 I: 7 CC for partial structure against native data = 8.26 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.326, Connect. = 0.608 for dens.mod. cycle 1 = 0.281, Contrast = 0.379, Connect. = 0.615 for dens.mod. cycle 2 = 0.281, Contrast = 0.440, Connect. = 0.662 for dens.mod. cycle 3 = 0.281, Contrast = 0.465, Connect. = 0.684 for dens.mod. cycle 4 = 0.281, Contrast = 0.479, Connect. = 0.696 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 1963 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 245 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 6.433 2.347 0.262 0.278 0.600 0.500 CB 1.472 B: 15 8.496 1.915 -0.015 0.372 0.929 0.357 CB 1.488 C: 14 10.313 2.022 0.465 0.284 0.846 0.385 CB 1.456 D: 10 6.306 1.985 0.434 0.256 0.778 0.444 CB 1.256 E: 29 6.665 1.614 0.422 0.210 0.714 0.250 CB 1.081 29 residues pruned to eliminate duplicates F: 12 4.323 1.646 -0.034 0.508 0.727 0.545 CB 1.118 G: 10 4.507 1.871 0.482 0.356 0.667 0.333 CB 0.950 H: 8 9.249 2.004 0.249 0.477 0.857 0.571 CA 1.668 6 1.144 1.757 -0.233 0.288 0.600 0.400 CB 0.802 ? I: 10 3.223 1.405 0.608 0.200 0.556 0.444 O 1.222 J: 6 3.423 1.510 0.341 0.296 0.800 0.600 CB 1.186 K: 6 4.137 1.280 0.242 0.546 1.000 1.000 CB 1.112 L: 12 3.910 1.492 0.383 0.135 0.727 0.182 CB 1.236 M: 6 2.898 1.436 0.583 0.447 0.800 0.400 CB 0.753 7 1.817 1.422 0.047 0.386 0.667 0.333 O 0.844 ? Using tripeptides from previous cycle as seeds 89 residues left after pruning, divided into chains as follows: A: 14 B: 14 C: 10 D: 7 E: 7 F: 8 G: 9 H: 6 I: 14 CC for partial structure against native data = 10.13 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.338, Connect. = 0.616 for dens.mod. cycle 1 = 0.281, Contrast = 0.402, Connect. = 0.632 for dens.mod. cycle 2 = 0.281, Contrast = 0.471, Connect. = 0.678 for dens.mod. cycle 3 = 0.281, Contrast = 0.487, Connect. = 0.695 for dens.mod. cycle 4 = 0.281, Contrast = 0.495, Connect. = 0.704 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 1885 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 218 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 2.758 2.136 -0.025 0.232 0.500 0.500 CB 1.476 B: 21 11.468 2.108 0.324 0.266 0.700 0.300 CB 1.714 C: 15 11.475 2.152 0.369 0.285 0.929 0.286 CB 1.428 D: 6 9.497 2.632 0.284 0.290 0.800 0.800 CB 1.989 E: 6 3.606 1.819 0.345 0.293 0.600 0.600 N 1.387 7 1.681 1.674 0.128 0.303 0.500 0.333 CB 0.905 ? F: 8 2.342 1.717 0.202 0.214 0.571 0.286 CB 1.051 G: 7 5.261 1.770 0.199 0.573 0.833 0.667 CB 1.131 7 1.714 1.574 0.196 0.241 0.500 0.500 CB 1.004 ? H: 9 3.117 1.719 0.087 0.287 0.625 0.250 CA 1.199 6 1.712 1.773 0.552 0.328 0.600 0.400 CB 0.560 ? I: 12 6.132 1.426 0.332 0.472 0.818 0.364 CB 1.224 J: 6 2.417 1.427 0.301 0.390 0.800 0.400 N 0.818 K: 9 2.724 1.919 0.355 0.262 0.500 0.375 CB 0.972 L: 9 2.403 1.266 0.368 0.244 0.750 0.375 N 0.878 Using tripeptides from previous cycle as seeds 85 residues left after pruning, divided into chains as follows: A: 21 B: 15 C: 6 D: 6 E: 7 F: 12 G: 9 H: 9 CC for partial structure against native data = 8.86 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.281, Contrast = 0.343, Connect. = 0.614 for dens.mod. cycle 1 = 0.282, Contrast = 0.410, Connect. = 0.629 for dens.mod. cycle 2 = 0.282, Contrast = 0.480, Connect. = 0.677 for dens.mod. cycle 3 = 0.282, Contrast = 0.496, Connect. = 0.695 for dens.mod. cycle 4 = 0.282, Contrast = 0.505, Connect. = 0.705 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 0.558 0.631 0.607 0.544 0.488 0.463 0.448 0.423 0.406 0.339 0.740 0.824 0.821 0.752 0.697 0.691 0.683 0.696 0.684 0.586 N 2106 2109 2123 2075 2180 2055 2102 2201 2180 1902 Estimated mean FOM = 0.492 Pseudo-free CC = 54.65 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.9094 0.5658 0.7686 1.0000 26.33 2 0.9072 0.5156 0.8743 0.9621 23.90 3 1.0636 0.1834 0.7453 0.8499 20.58 4 0.8354 0.3177 0.7505 0.8115 22.14 5 0.7640 0.5794 0.7927 0.6159 16.43 6 0.8634 0.0023 0.5940 0.5624 14.36 7 0.8094 0.0735 0.7302 0.5457 14.72 8 0.8357 0.6494 0.7049 0.4882 14.28 9 0.9728 0.0741 0.7008 0.4242 10.26 10 0.8979 0.8208 0.7693 0.3996 9.92 11 0.8594 0.7036 0.7893 0.3285 8.48 12 1.0086 0.3442 0.8274 0.2606 7.26 Site x y z h(sig) near old near new 1 0.9095 0.5661 0.7680 26.4 1/0.06 15/2.44 16/6.30 5/8.74 8/10.14 2 0.9078 0.5157 0.8736 23.9 2/0.07 13/2.60 15/9.10 1/10.88 16/12.42 3 0.8360 0.3183 0.7496 22.3 4/0.11 5/11.06 8/11.15 11/12.10 12/12.59 4 1.0627 0.1839 0.7447 20.7 3/0.09 9/11.25 12/15.87 3/17.19 6/17.44 5 0.7645 0.5791 0.7921 16.5 5/0.07 16/3.36 1/8.74 15/9.08 8/11.00 6 0.8065 0.0735 0.7304 14.9 7/0.17 9/10.06 14/10.69 6/13.82 7/14.64 7 0.8642 0.0032 0.5936 14.4 6/0.09 14/5.03 14/11.04 7/13.18 9/13.42 8 0.8356 0.6491 0.7037 14.4 8/0.11 11/9.56 16/9.64 1/10.14 5/11.00 9 0.9744 0.0735 0.7017 10.3 9/0.14 6/10.06 4/11.25 14/12.40 7/13.42 10 0.8986 0.8217 0.7707 9.9 10/0.16 11/10.14 6/15.17 8/16.09 3/17.94 11 0.8599 0.7047 0.7905 8.6 11/0.15 8/9.56 10/10.14 5/11.78 1/12.04 12 1.0067 0.3444 0.8289 7.4 12/0.19 3/12.59 13/13.52 4/15.87 2/15.89 13 0.9127 0.4846 0.8739 -5.4 2/2.59 2/2.60 15/10.02 1/12.13 12/13.52 14 0.8114 0.0386 0.6222 5.0 6/5.02 7/5.03 14/9.55 6/10.69 7/11.04 15 0.9104 0.5402 0.7803 -4.6 1/2.40 1/2.44 16/6.72 5/9.08 2/9.10 16 0.8003 0.5627 0.7681 -4.6 5/3.43 5/3.36 1/6.30 15/6.72 8/9.64 Best trace (cycle 4 with CC 10.13%) was saved as P2122_pse14_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 9.3 - Setup, data input and phasing 2.3 - FFTs and peak-searches 5.2 - Sphere of influence 1.4 - Rest of density modification 0.0 - Alpha-helix search 48.1 - Tripeptide search 54.7 - Chain tracing 0.0 - NCS analysis 4.0 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:11:12 Total time: 125.11 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++