++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + 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 -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.lst Phases output to P222_pse14.phs Revised heavy atom sites output to P222_pse14.hat Revised heavy atom phases output to P222_pse14.pha Poly-Ala trace output to P222_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 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 5 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 5 12.58% 0.706 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 12.46% = 0.098 for phases from phiT = phiA + alpha = 0.195 after including heavy atoms = 0.160, Contrast = 0.045, Connect. = 0.525 for dens.mod. cycle 1 = 0.189, Contrast = 0.154, Connect. = 0.629 for dens.mod. cycle 2 = 0.206, Contrast = 0.203, Connect. = 0.647 for dens.mod. cycle 3 = 0.219, Contrast = 0.233, Connect. = 0.659 for dens.mod. cycle 4 = 0.229, Contrast = 0.257, Connect. = 0.669 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 1757 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 253 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 2.322 1.335 0.295 0.499 0.833 0.333 N 0.659 6 1.866 1.381 0.685 0.149 0.600 0.200 O 0.921 ? B: 7 2.734 1.592 0.582 0.243 0.500 0.333 CB 1.194 C: 14 3.383 1.402 0.283 0.287 0.692 0.385 CB 0.957 D: 7 5.108 1.471 0.700 0.584 0.833 0.500 CB 0.923 E: 7 2.604 1.240 0.185 0.341 0.833 0.500 CB 1.033 F: 10 2.724 1.334 0.448 0.242 0.778 0.333 N 0.815 G: 8 2.128 1.245 0.416 0.240 0.571 0.429 CB 1.079 H: 6 4.611 1.644 0.129 0.574 0.800 0.400 CB 1.293 I: 6 4.223 1.398 0.492 0.318 1.000 0.600 CB 1.106 J: 11 6.352 1.497 0.712 0.290 0.900 0.500 CB 1.102 K: 9 5.146 1.291 0.373 0.424 1.000 0.500 CB 1.110 L: 8 3.759 1.477 0.211 0.369 0.857 0.429 N 1.066 8 1.407 1.125 0.394 0.279 0.571 0.286 N 0.762 ? M: 9 4.023 1.338 0.621 0.362 0.750 0.500 CB 1.014 N: 7 2.445 1.385 -0.206 0.520 0.833 0.500 CB 1.067 O: 9 3.081 1.259 0.677 0.317 0.625 0.250 CB 1.011 P: 9 2.675 1.101 0.600 0.290 0.750 0.375 N 0.906 Q: 7 3.431 1.518 0.625 0.248 0.667 0.500 CA 1.139 93 residues left after pruning, divided into chains as follows: A: 14 B: 7 C: 6 D: 6 E: 11 F: 9 G: 8 H: 9 I: 7 J: 9 K: 7 CC for partial structure against native data = 7.98 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.258, Connect. = 0.607 for dens.mod. cycle 1 = 0.281, Contrast = 0.280, Connect. = 0.595 for dens.mod. cycle 2 = 0.281, Contrast = 0.322, Connect. = 0.632 for dens.mod. cycle 3 = 0.281, Contrast = 0.339, Connect. = 0.649 for dens.mod. cycle 4 = 0.281, Contrast = 0.355, Connect. = 0.663 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 2220 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 248 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 6.251 1.854 0.356 0.369 0.750 0.583 CB 1.101 B: 6 10.212 1.992 0.847 0.579 0.800 0.400 CB 1.437 C: 14 14.465 2.225 0.453 0.363 0.846 0.538 CB 1.700 D: 6 4.069 1.685 0.660 0.567 1.000 0.400 CB 0.610 E: 9 5.360 1.861 0.293 0.348 0.625 0.375 CB 1.486 F: 9 8.444 1.990 0.369 0.492 0.750 0.375 CB 1.474 G: 7 8.620 2.202 0.223 0.474 0.833 0.500 CA 1.609 H: 9 5.152 1.769 0.302 0.351 0.625 0.500 CA 1.487 I: 11 6.483 1.971 0.073 0.317 0.800 0.400 CB 1.482 J: 9 4.233 2.050 0.237 0.191 0.625 0.375 CA 1.366 K: 17 9.287 1.834 0.391 0.344 0.812 0.312 CB 1.327 L: 8 2.716 1.165 0.168 0.478 1.000 0.714 CB 0.771 M: 8 3.432 1.500 0.460 0.229 0.714 0.429 CB 1.137 N: 23 11.777 2.107 0.470 0.262 0.727 0.409 CB 1.462 26 residues pruned to eliminate duplicates O: 7 2.650 1.549 0.599 0.245 0.667 0.333 CB 0.880 P: 6 2.303 1.194 0.565 0.486 0.800 0.600 CB 0.699 Q: 14 7.303 1.636 0.683 0.390 0.615 0.308 CB 1.343 Using tripeptides from previous cycle as seeds 107 residues left after pruning, divided into chains as follows: A: 13 B: 6 C: 9 D: 9 E: 7 F: 9 G: 11 H: 9 I: 28 J: 6 CC for partial structure against native data = 9.68 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.320, Connect. = 0.616 for dens.mod. cycle 1 = 0.281, Contrast = 0.356, Connect. = 0.619 for dens.mod. cycle 2 = 0.281, Contrast = 0.400, Connect. = 0.658 for dens.mod. cycle 3 = 0.281, Contrast = 0.413, Connect. = 0.675 for dens.mod. cycle 4 = 0.281, Contrast = 0.423, Connect. = 0.686 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 2091 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 236 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 7.618 2.289 0.237 0.377 0.714 0.429 CB 1.622 B: 10 8.147 2.054 0.146 0.308 0.889 0.333 CB 1.607 C: 11 6.611 1.834 0.304 0.235 0.800 0.500 CB 1.487 D: 6 8.670 2.031 0.413 0.690 0.800 0.400 CB 1.419 E: 8 4.486 2.221 -0.072 0.373 0.571 0.286 CA 1.650 F: 27 12.889 1.978 0.445 0.320 0.769 0.500 CB 1.402 G: 20 8.999 1.869 0.289 0.345 0.737 0.474 CB 1.376 20 residues pruned to eliminate duplicates H: 6 4.357 1.657 -0.031 0.663 0.800 0.600 O 1.304 I: 8 5.758 1.591 0.223 0.321 1.000 0.571 N 1.363 J: 6 3.068 1.606 0.367 0.389 1.000 0.200 CB 0.703 K: 10 7.582 1.906 0.105 0.376 1.000 0.556 N 1.370 L: 9 3.942 1.508 0.585 0.264 0.625 0.250 CB 1.221 M: 8 5.665 1.181 0.592 0.811 1.000 0.714 CB 0.868 N: 12 3.147 1.472 0.662 0.184 0.545 0.364 CB 1.040 O: 6 4.427 1.488 0.572 0.644 0.800 0.600 CB 0.925 6 1.483 1.145 0.156 0.255 1.000 0.400 CB 0.664 ? 6 1.830 1.127 0.662 0.273 0.600 0.200 N 0.942 ? P: 6 3.507 1.307 0.038 0.642 1.000 0.600 C 1.013 7 1.725 1.552 -0.214 0.558 0.667 0.333 CB 0.819 ? Using tripeptides from previous cycle as seeds 110 residues left after pruning, divided into chains as follows: A: 8 B: 10 C: 10 D: 6 E: 8 F: 27 G: 8 H: 10 I: 8 J: 9 K: 6 CC for partial structure against native data = 11.79 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.333, Connect. = 0.619 for dens.mod. cycle 1 = 0.281, Contrast = 0.373, Connect. = 0.627 for dens.mod. cycle 2 = 0.281, Contrast = 0.416, Connect. = 0.664 for dens.mod. cycle 3 = 0.281, Contrast = 0.428, Connect. = 0.679 for dens.mod. cycle 4 = 0.281, Contrast = 0.438, Connect. = 0.690 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 2042 peaks > 0.5 sigma used to seed fragment search Space for about 497 unique residues taking solvent into account 237 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 9.982 2.010 0.217 0.476 1.000 0.667 N 1.393 B: 14 11.221 2.169 0.226 0.332 0.846 0.308 CB 1.662 C: 10 8.555 2.081 0.115 0.446 1.000 0.556 CB 1.299 D: 7 7.127 1.842 0.457 0.580 0.833 0.333 CB 1.204 E: 7 3.834 1.815 0.147 0.526 0.667 0.500 CB 1.099 F: 7 8.099 1.748 0.294 0.668 0.833 0.833 CB 1.501 G: 9 5.083 2.201 0.165 0.233 0.625 0.375 CB 1.531 H: 10 5.778 1.903 0.432 0.337 0.667 0.667 CB 1.267 I: 6 4.075 1.767 0.130 0.788 0.800 0.600 CB 0.886 J: 7 7.807 1.731 0.519 0.607 0.833 0.833 CB 1.314 K: 6 3.769 1.249 0.696 0.711 1.000 0.600 N 0.657 L: 9 5.819 1.686 0.177 0.353 0.875 0.375 CB 1.390 M: 7 4.637 1.335 0.752 0.389 0.833 0.500 CB 1.093 N: 14 5.134 1.696 0.384 0.220 0.692 0.231 CB 1.217 Using tripeptides from previous cycle as seeds O: 7 5.119 2.160 0.186 0.413 0.667 0.333 CB 1.340 90 residues left after pruning, divided into chains as follows: A: 10 B: 14 C: 10 D: 7 E: 7 F: 9 G: 10 H: 7 I: 9 J: 7 CC for partial structure against native data = 9.14 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.340, Connect. = 0.619 for dens.mod. cycle 1 = 0.281, Contrast = 0.382, Connect. = 0.625 for dens.mod. cycle 2 = 0.281, Contrast = 0.428, Connect. = 0.666 for dens.mod. cycle 3 = 0.281, Contrast = 0.442, Connect. = 0.682 for dens.mod. cycle 4 = 0.281, Contrast = 0.449, Connect. = 0.694 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 2047 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: 21 10.258 2.328 0.019 0.283 0.700 0.300 CB 1.763 B: 8 3.822 1.796 0.314 0.214 0.714 0.286 CB 1.201 C: 10 7.266 2.136 0.376 0.389 0.667 0.222 CB 1.390 D: 9 7.696 1.862 0.091 0.493 0.875 0.500 CB 1.541 E: 10 4.521 1.908 0.101 0.226 0.667 0.444 CB 1.482 F: 7 6.749 1.978 0.161 0.457 0.833 0.500 CB 1.505 G: 8 6.614 1.882 0.255 0.477 0.857 0.429 CB 1.264 H: 7 4.682 1.717 0.167 0.414 0.833 0.500 CB 1.252 I: 8 5.102 1.130 0.827 0.661 0.857 0.429 O 0.938 J: 7 5.762 1.423 0.372 0.471 1.000 0.333 N 1.241 K: 8 6.910 1.382 0.795 0.775 1.000 0.714 CB 0.826 6 1.400 1.402 0.171 0.298 0.800 0.400 CB 0.598 ? L: 6 3.257 1.680 0.769 0.204 0.600 0.200 N 1.161 M: 10 3.165 1.412 0.571 0.393 0.778 0.444 CB 0.685 N: 12 5.551 1.883 0.184 0.408 0.727 0.636 CB 1.137 Using tripeptides from previous cycle as seeds O: 7 4.927 1.961 0.320 0.410 0.667 0.333 CB 1.280 95 residues left after pruning, divided into chains as follows: A: 21 B: 7 C: 10 D: 9 E: 10 F: 7 G: 8 H: 8 I: 8 J: 7 CC for partial structure against native data = 10.58 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 3 used as input for final density modification = 0.281, Contrast = 0.362, Connect. = 0.628 for dens.mod. cycle 1 = 0.282, Contrast = 0.404, Connect. = 0.629 for dens.mod. cycle 2 = 0.282, Contrast = 0.455, Connect. = 0.669 for dens.mod. cycle 3 = 0.282, Contrast = 0.467, Connect. = 0.685 for dens.mod. cycle 4 = 0.282, Contrast = 0.476, Connect. = 0.696 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 0.540 0.561 0.546 0.522 0.516 0.445 0.419 0.399 0.294 0.231 0.730 0.745 0.756 0.721 0.735 0.673 0.649 0.662 0.511 0.402 N 2111 2109 2124 2076 2180 2056 2102 2202 2180 1903 Estimated mean FOM = 0.449 Pseudo-free CC = 49.28 % 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 89.67 2 0.7455 0.6140 0.5171 0.8848 16.48 3 0.1517 0.2534 0.0172 0.8122 14.17 4 0.6499 0.8846 0.5235 0.7068 11.72 5 0.1559 0.1949 0.1188 0.7059 11.45 Site x y z h(sig) near old near new 1 0.5000 0.5000 0.5000 89.7 1/0.00 6/2.50 6/2.50 6/2.50 6/2.50 2 0.7455 0.6137 0.5166 16.5 2/0.06 11/11.13 11/11.13 7/11.18 7/11.18 3 0.1504 0.2533 0.0177 14.2 3/0.09 5/10.67 15/12.35 3/17.67 5/22.46 4 0.6445 0.8840 0.5236 12.1 4/0.31 14/12.92 14/12.92 14/12.92 14/12.92 5 0.1575 0.1960 0.1181 11.6 5/0.15 15/10.43 3/10.67 3/22.46 5/28.89 6 0.5011 0.5236 0.5163 -9.8 1/2.50 9/1.67 9/1.67 1/2.50 1/2.50 7 0.3551 0.5000 0.5000 -7.7 1/8.36 1/8.36 1/8.36 1/8.36 1/8.36 8 0.5000 0.5640 0.5000 -7.3 1/5.31 9/2.75 9/2.75 6/3.70 6/3.70 9 0.5000 0.5309 0.5000 -7.1 1/2.56 6/1.67 6/1.67 1/2.56 1/2.56 10 0.9651 0.5000 0.5000 -6.6 2/15.89 12/3.16 12/3.16 10/4.02 10/4.02 11 0.8444 0.5000 0.5000 -6.0 2/11.17 12/3.81 12/3.81 10/6.96 10/6.96 12 0.9104 0.5000 0.5000 -5.6 2/13.51 10/3.16 10/3.16 11/3.81 11/3.81 13 0.5000 0.5000 0.1617 -5.5 3/31.79 16/19.73 16/19.73 15/22.27 15/22.2 14 0.5000 1.0000 0.5000 -5.3 4/13.09 4/12.92 4/12.92 4/12.92 4/12.92 15 0.2339 0.3096 0.1268 4.7 5/10.55 5/10.43 3/12.35 13/22.27 13/22.27 16 0.5000 0.5000 0.3692 -4.7 1/12.43 17/3.19 17/3.19 6/11.05 6/11.05 17 0.5000 0.5000 0.4028 -4.6 1/9.24 16/3.19 16/3.19 6/7.93 6/7.93 Best trace (cycle 3 with CC 11.79%) was saved as P222_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 3.7 - Setup, data input and phasing 2.3 - FFTs and peak-searches 5.1 - Sphere of influence 4.0 - Rest of density modification 0.0 - Alpha-helix search 48.3 - Tripeptide search 53.7 - Chain tracing 0.0 - NCS analysis 4.4 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:03:09 Total time: 121.63 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++