++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:06:17 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: P2212_pse14 P2212_pse14_fa -h -a5 -s0.45 -z -e -m5 Cell, symmetry and heavy atoms from: P2212_pse14_fa.res FA and alpha from P2212_pse14_fa.hkl Native data from P2212_pse14.hkl Listing output to P2212_pse14.lst Phases output to P2212_pse14.phs Revised heavy atom sites output to P2212_pse14.hat Revised heavy atom phases output to P2212_pse14.pha Poly-Ala trace output to P2212_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 21 2 Allowed origin shift code: 4 14 atoms read from file P2212_pse14_fa.res Trimmed to 7 atoms with occupancy > 0.2 11695 Reflections read from file P2212_pse14_fa.hkl 21043 Reflections read from file P2212_pse14.hkl 21026 Unique data, highest resolution = 2.289 Angstroms Anisotropic scaling: intensities multiplied by 0.003964h^2 -0.000439k^2 -0.000491l^2 +0.000000kl +0.000000hl +0.000000hk 27 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 7 potential heavy atoms found Substructure optimization LOR = lowest occupancy retained, HOR = highest occupancy rejected Nats CC(HA) LOR HOR 7 17.14% 0.383 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 16.76% = 0.115 for phases from phiT = phiA + alpha = 0.185 after including heavy atoms = 0.170, Contrast = 0.040, Connect. = 0.531 for dens.mod. cycle 1 = 0.190, Contrast = 0.130, Connect. = 0.607 for dens.mod. cycle 2 = 0.204, Contrast = 0.178, Connect. = 0.631 for dens.mod. cycle 3 = 0.217, Contrast = 0.216, Connect. = 0.650 for dens.mod. cycle 4 = 0.227, Contrast = 0.248, Connect. = 0.663 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 1749 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 233 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 9 2.989 1.493 0.276 0.318 0.625 0.375 CB 1.085 B: 7 3.189 1.389 0.176 0.406 0.833 0.667 CB 1.055 C: 10 2.568 1.332 -0.047 0.338 0.889 0.556 CB 0.905 6 1.634 1.526 0.451 0.284 0.600 0.600 CB 0.702 ? D: 13 4.628 1.383 0.332 0.331 0.833 0.250 CB 1.047 6 0.815 1.219 0.356 0.436 0.800 0.400 CB 0.294 ? E: 7 2.656 1.421 0.105 0.349 0.833 0.667 CA 0.976 6 1.262 1.117 0.197 0.300 0.800 0.400 N 0.660 ? F: 12 5.923 1.247 0.388 0.735 0.818 0.636 N 1.021 G: 6 3.007 1.228 0.506 0.446 0.800 0.600 N 0.961 H: 6 2.219 1.169 0.512 0.481 0.800 0.600 N 0.716 I: 10 2.731 1.331 0.397 0.248 0.667 0.556 N 0.981 J: 13 4.644 1.463 0.223 0.424 0.833 0.417 CB 0.973 K: 7 2.620 1.302 0.476 0.326 0.667 0.333 N 1.011 L: 14 2.639 1.319 0.351 0.190 0.769 0.462 CB 0.774 M: 8 4.515 1.408 0.220 0.485 0.857 0.429 N 1.177 N: 6 2.248 1.187 0.301 0.420 0.800 0.800 CB 0.885 6 0.802 1.295 0.226 0.309 0.600 0.200 N 0.465 ? O: 6 2.205 1.164 0.417 0.452 0.800 0.400 CB 0.785 105 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 13 D: 7 E: 12 F: 6 G: 10 H: 12 I: 14 J: 8 K: 6 CC for partial structure against native data = 7.63 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.281, Contrast = 0.263, Connect. = 0.602 for dens.mod. cycle 1 = 0.281, Contrast = 0.290, Connect. = 0.584 for dens.mod. cycle 2 = 0.281, Contrast = 0.335, Connect. = 0.627 for dens.mod. cycle 3 = 0.281, Contrast = 0.357, Connect. = 0.649 for dens.mod. cycle 4 = 0.281, Contrast = 0.375, Connect. = 0.665 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 2231 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 217 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 5.523 1.823 0.292 0.439 0.800 0.600 CA 1.396 B: 9 3.687 1.798 0.661 0.193 0.750 0.625 CB 0.840 C: 7 4.312 1.232 0.555 0.758 1.000 0.833 CB 0.730 D: 11 8.511 1.884 0.559 0.392 0.900 0.500 CB 1.142 E: 10 15.130 1.856 0.578 0.827 0.889 0.667 CB 1.460 6 1.309 1.532 0.302 0.293 0.600 0.400 CB 0.617 ? 6 1.654 1.078 0.400 0.675 0.800 0.800 N 0.521 ? F: 11 3.918 1.416 0.738 0.285 0.700 0.400 N 0.916 G: 20 7.639 1.712 0.501 0.134 0.789 0.474 CB 1.362 6 residues pruned to eliminate duplicates H: 7 3.064 1.281 0.225 0.808 1.000 0.833 CB 0.609 I: 7 4.204 1.470 0.496 0.570 0.833 0.667 N 0.875 J: 8 2.942 1.456 0.309 0.520 1.000 0.286 CB 0.572 K: 6 3.843 1.222 0.440 0.476 1.000 0.600 CA 1.001 L: 7 2.093 1.415 0.112 0.412 0.667 0.500 O 0.893 M: 8 2.794 1.300 0.235 0.362 0.714 0.714 N 1.068 6 1.299 1.295 0.383 0.121 0.600 0.200 N 0.870 ? Using tripeptides from previous cycle as seeds N: 6 4.098 1.557 0.478 0.650 0.800 0.400 CA 0.866 O: 6 4.248 1.753 0.268 0.296 0.800 0.400 CA 1.341 81 residues left after pruning, divided into chains as follows: A: 8 B: 7 C: 11 D: 10 E: 11 F: 8 G: 6 H: 8 I: 6 J: 6 CC for partial structure against native data = 9.29 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.281, Contrast = 0.307, Connect. = 0.613 for dens.mod. cycle 1 = 0.281, Contrast = 0.345, Connect. = 0.608 for dens.mod. cycle 2 = 0.281, Contrast = 0.392, Connect. = 0.650 for dens.mod. cycle 3 = 0.281, Contrast = 0.411, Connect. = 0.669 for dens.mod. cycle 4 = 0.281, Contrast = 0.429, Connect. = 0.685 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 2108 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 227 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 13.659 2.240 0.262 0.691 0.778 0.556 N 1.738 B: 11 12.967 1.896 0.374 0.816 0.800 0.800 CB 1.495 C: 11 7.532 2.144 0.193 0.376 0.800 0.400 CB 1.328 D: 6 3.596 2.009 0.133 0.449 0.800 0.600 CB 0.930 E: 6 4.630 1.656 0.994 0.291 0.800 0.400 CB 0.990 F: 8 3.251 1.719 0.506 0.322 0.571 0.286 CB 1.011 G: 6 3.148 1.699 0.716 0.551 0.800 0.600 CB 0.574 6 1.809 1.357 0.577 0.285 0.600 0.600 N 0.802 ? H: 9 9.359 1.969 0.182 0.486 0.875 0.500 N 1.647 I: 7 10.798 1.693 0.594 0.724 1.000 0.333 CA 1.334 J: 13 7.356 1.731 0.308 0.410 0.750 0.500 CB 1.374 13 residues pruned to eliminate duplicates K: 7 4.316 1.615 0.646 0.447 0.667 0.500 CB 1.051 L: 7 2.495 1.678 0.523 0.342 0.667 0.500 CB 0.710 M: 12 4.760 1.381 0.574 0.232 0.818 0.636 N 1.101 12 residues pruned to eliminate duplicates N: 7 3.178 1.440 0.002 0.585 0.833 0.333 N 0.995 6 0.480 1.003 0.404 0.348 0.600 0.400 CB 0.299 ? Using tripeptides from previous cycle as seeds 82 residues left after pruning, divided into chains as follows: A: 10 B: 11 C: 11 D: 6 E: 8 F: 6 G: 9 H: 7 I: 7 J: 7 CC for partial structure against native data = 9.04 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.281, Contrast = 0.340, Connect. = 0.615 for dens.mod. cycle 1 = 0.281, Contrast = 0.383, Connect. = 0.615 for dens.mod. cycle 2 = 0.281, Contrast = 0.432, Connect. = 0.658 for dens.mod. cycle 3 = 0.281, Contrast = 0.450, Connect. = 0.678 for dens.mod. cycle 4 = 0.281, Contrast = 0.462, Connect. = 0.692 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 2093 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 234 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 18.323 2.046 0.404 0.804 0.917 0.833 CB 1.540 B: 11 11.633 2.264 0.517 0.401 0.700 0.500 CA 1.698 C: 12 13.017 1.953 0.204 0.826 0.909 0.636 N 1.385 D: 6 2.921 1.950 -0.042 0.296 0.800 0.600 CB 1.098 E: 7 4.841 1.987 0.199 0.573 0.833 0.667 CB 0.928 F: 7 4.336 1.790 0.635 0.234 0.667 0.500 CB 1.236 G: 9 6.420 1.484 0.767 0.617 0.625 0.500 O 1.240 H: 6 2.428 1.767 -0.141 0.387 1.000 0.400 CB 0.806 I: 6 4.067 1.514 0.311 0.371 1.000 0.400 CA 1.052 J: 6 2.130 1.607 0.389 0.485 0.400 0.400 N 1.082 K: 6 3.032 1.645 0.139 0.491 0.800 0.600 CA 0.912 L: 13 13.253 1.848 0.582 0.529 0.833 0.667 C 1.526 13 residues pruned to eliminate duplicates 6 1.326 1.183 0.031 0.276 0.800 0.400 O 0.783 ? M: 11 6.487 1.820 0.287 0.336 0.700 0.500 CB 1.497 11 residues pruned to eliminate duplicates N: 9 3.645 1.098 0.796 0.373 0.875 0.375 CB 0.856 6 1.184 1.009 0.119 0.534 0.800 0.600 CB 0.567 ? O: 13 7.742 1.906 0.165 0.453 0.750 0.417 CB 1.408 12 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 91 residues left after pruning, divided into chains as follows: A: 13 B: 11 C: 7 D: 9 E: 6 F: 6 G: 6 H: 9 I: 13 J: 11 CC for partial structure against native data = 10.98 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.281, Contrast = 0.347, Connect. = 0.621 for dens.mod. cycle 1 = 0.281, Contrast = 0.397, Connect. = 0.626 for dens.mod. cycle 2 = 0.281, Contrast = 0.453, Connect. = 0.673 for dens.mod. cycle 3 = 0.281, Contrast = 0.467, Connect. = 0.688 for dens.mod. cycle 4 = 0.281, Contrast = 0.477, Connect. = 0.700 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 7 heavy atoms with Occ*Z > 0.30 added to NOGO map 2104 peaks > 0.5 sigma used to seed fragment search Space for about 498 unique residues taking solvent into account 218 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 18.575 2.141 0.567 0.771 0.857 0.571 CB 1.358 B: 9 11.318 2.615 0.271 0.412 0.750 0.500 CB 1.760 C: 13 12.896 2.070 0.263 0.711 0.833 0.667 CB 1.411 D: 9 6.571 1.841 0.161 0.554 0.875 0.625 CB 1.179 E: 7 4.229 1.854 0.096 0.421 0.833 0.667 CB 1.108 F: 9 2.310 1.846 0.128 0.312 0.500 0.250 CB 0.966 G: 6 3.568 1.832 0.055 0.487 0.600 0.400 CB 1.393 H: 12 5.602 1.705 0.501 0.208 0.727 0.364 CB 1.282 I: 7 7.851 1.768 0.515 0.498 0.833 0.500 N 1.439 J: 6 3.341 1.672 0.068 0.279 1.000 0.600 N 1.074 K: 14 6.953 1.813 0.098 0.447 0.769 0.385 CB 1.330 14 residues pruned to eliminate duplicates L: 7 2.250 1.258 0.278 0.344 0.833 0.500 CA 0.812 M: 15 9.469 1.837 0.224 0.482 0.857 0.286 CB 1.336 12 residues pruned to eliminate duplicates N: 7 2.866 1.215 0.435 0.361 0.833 0.500 CB 0.936 O: 10 2.043 1.416 0.346 0.289 0.667 0.333 CB 0.679 Using tripeptides from previous cycle as seeds P: 9 6.710 1.774 0.458 0.347 0.750 0.375 CB 1.445 99 residues left after pruning, divided into chains as follows: A: 15 B: 13 C: 9 D: 6 E: 9 F: 6 G: 6 H: 7 I: 12 J: 7 K: 9 CC for partial structure against native data = 12.18 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.281, Contrast = 0.347, Connect. = 0.622 for dens.mod. cycle 1 = 0.282, Contrast = 0.401, Connect. = 0.630 for dens.mod. cycle 2 = 0.282, Contrast = 0.462, Connect. = 0.679 for dens.mod. cycle 3 = 0.282, Contrast = 0.477, Connect. = 0.694 for dens.mod. cycle 4 = 0.282, Contrast = 0.486, 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 - 3.14 - 2.91 - 2.74 - 2.60 - 2.48 - 2.38 - 2.29 0.506 0.618 0.600 0.537 0.443 0.389 0.389 0.389 0.302 0.236 0.658 0.812 0.816 0.753 0.643 0.582 0.597 0.635 0.518 0.412 N 2104 2107 2122 2159 2095 2055 2101 2201 2180 1902 Estimated mean FOM = 0.443 Pseudo-free CC = 48.30 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.3024 0.2500 0.5000 1.0000 52.28 2 0.5496 0.3623 0.4810 0.8763 23.41 3 0.0499 0.4966 0.0181 0.8597 18.96 4 0.1047 0.4946 0.0459 0.7182 19.61 5 0.0448 0.4482 0.1249 0.6591 14.24 6 0.5506 0.4145 0.3777 0.4637 10.76 7 0.3098 0.2705 0.6128 0.3831 8.81 Site x y z h(sig) near old near new 1 0.3018 0.2500 0.5000 52.3 1/0.04 8/2.75 8/2.75 9/5.55 9/5.55 2 0.5491 0.3622 0.4815 23.4 2/0.06 13/2.48 14/4.78 10/6.16 6/10.76 3 0.1032 0.4942 0.0464 19.7 4/0.10 11/2.82 4/4.05 5/9.04 4/9.28 4 0.0503 0.4962 0.0184 19.0 3/0.05 11/3.51 3/4.05 11/9.21 3/9.28 5 0.0443 0.4476 0.1246 14.3 5/0.06 3/9.04 5/10.08 4/10.88 11/11.78 6 0.5540 0.4127 0.3772 11.0 6/0.25 2/10.76 13/10.87 14/11.89 10/12.47 7 0.3114 0.2702 0.6125 8.8 7/0.10 8/9.71 1/10.84 1/10.84 9/11.92 8 0.3045 0.2754 0.4814 -7.7 1/2.75 1/2.75 1/2.75 9/6.05 9/6.05 9 0.3980 0.2500 0.5000 -6.4 1/5.51 1/5.55 1/5.55 8/6.05 8/6.05 10 0.4422 0.3621 0.4805 -5.5 2/6.19 14/1.45 2/6.16 13/7.13 9/9.82 11 0.1094 0.5062 0.0189 -5.5 4/2.76 3/2.82 4/3.51 4/9.21 5/11.78 12 0.1206 0.2500 0.5000 -5.4 1/10.48 1/10.45 1/10.45 8/10.95 8/10.95 13 0.5582 0.3898 0.4898 -5.2 2/2.47 2/2.48 14/5.69 10/7.13 6/10.87 14 0.4664 0.3661 0.4829 -5.0 2/4.82 10/1.45 2/4.78 13/5.69 9/10.53 Best trace (cycle 5 with CC 12.18%) was saved as P2212_pse14.pdb ============================================================================== CPU times required in seconds ----------------------------- 5.3 - Setup, data input and phasing 2.4 - FFTs and peak-searches 5.2 - Sphere of influence 2.9 - Rest of density modification 0.0 - Alpha-helix search 50.1 - Tripeptide search 51.1 - Chain tracing 0.0 - NCS analysis 4.2 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:08:19 Total time: 121.15 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++