++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:23:26 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: P4_visc-standard P4_visc-standard_fa -i -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P4_visc-standard_fa.res FA and alpha from P4_visc-standard_fa.hkl Native data from P4_visc-standard.hkl Listing output to P4_visc-standard_i.lst Phases output to P4_visc-standard_i.phs Revised heavy atom sites output to P4_visc-standard_i.hat Revised heavy atom phases output to P4_visc-standard_i.pha Poly-Ala trace output to P4_visc-standard_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 0.500 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: P 4 Allowed origin shift code: 7 21 atoms read from file P4_visc-standard_fa.res Trimmed to 19 atoms with occupancy > 0.2 14490 Reflections read from file P4_visc-standard_fa.hkl 22220 Reflections read from file P4_visc-standard.hkl 22220 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000220h^2 +0.000220k^2 -0.000674l^2 +0.000000kl +0.000000hl +0.000000hk 9 Reflections with d > 1.902 and 0 in range 1.902 > d > 1.702 added Density sharpening factor set to 1.20 Fourier grid = 128 x 128 x 82 0.000 <= z <= 1.000 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.760 ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 9.72% = 0.088 for phases from phiT = phiA + alpha = 0.142 after including heavy atoms = 0.132, Contrast = 0.020, Connect. = 0.514 for dens.mod. cycle 1 = 0.154, Contrast = 0.082, Connect. = 0.588 for dens.mod. cycle 2 = 0.173, Contrast = 0.115, Connect. = 0.614 for dens.mod. cycle 3 = 0.190, Contrast = 0.122, Connect. = 0.610 for dens.mod. cycle 4 = 0.203, Contrast = 0.126, Connect. = 0.602 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 1726 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 129 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 3.081 1.427 0.244 0.351 0.800 0.600 CB 1.141 B: 8 4.528 1.364 0.553 0.274 1.000 0.429 N 1.044 C: 10 3.751 1.228 0.201 0.476 0.889 0.556 CA 0.977 D: 6 3.257 1.264 0.413 0.427 0.800 0.600 N 1.099 E: 6 2.006 1.263 0.518 0.298 0.600 0.400 CA 0.977 8 1.507 1.234 0.539 0.071 0.571 0.143 CB 0.918 ? 6 1.757 1.203 0.486 0.584 0.800 0.600 CB 0.507 ? 6 1.356 1.054 0.525 0.433 1.000 0.600 CB 0.404 ? F: 8 3.797 1.300 0.216 0.437 1.000 0.429 CA 0.969 9 1.277 0.975 0.108 0.275 1.000 0.375 N 0.539 ? 38 residues left after pruning, divided into chains as follows: A: 8 B: 10 C: 6 D: 6 E: 8 CC for partial structure against native data = 0.89 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.266, Contrast = 0.165, Connect. = 0.548 for dens.mod. cycle 1 = 0.269, Contrast = 0.172, Connect. = 0.498 for dens.mod. cycle 2 = 0.275, Contrast = 0.179, Connect. = 0.510 for dens.mod. cycle 3 = 0.279, Contrast = 0.185, Connect. = 0.522 for dens.mod. cycle 4 = 0.281, Contrast = 0.193, Connect. = 0.533 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2197 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 157 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 5.641 2.312 0.004 0.212 0.714 0.429 CB 1.805 B: 9 6.498 2.218 0.259 0.255 0.750 0.500 CB 1.453 C: 13 12.560 2.378 0.035 0.411 0.833 0.583 CB 1.939 D: 10 13.840 2.432 0.182 0.431 0.889 0.444 CA 1.938 E: 12 13.293 2.235 0.254 0.295 1.000 0.455 CB 1.799 6 1.504 0.998 0.231 0.662 1.000 0.800 CA 0.471 ? Using tripeptides from previous cycle as seeds 48 residues left after pruning, divided into chains as follows: A: 7 B: 9 C: 13 D: 7 E: 12 CC for partial structure against native data = 3.71 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.236, Connect. = 0.522 for dens.mod. cycle 1 = 0.287, Contrast = 0.239, Connect. = 0.505 for dens.mod. cycle 2 = 0.287, Contrast = 0.243, Connect. = 0.517 for dens.mod. cycle 3 = 0.287, Contrast = 0.244, Connect. = 0.528 for dens.mod. cycle 4 = 0.287, Contrast = 0.251, Connect. = 0.540 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2116 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 161 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 5.736 2.235 0.053 0.169 0.667 0.333 CB 1.821 B: 18 10.561 2.207 0.268 0.188 0.824 0.353 CB 1.615 C: 10 8.461 2.545 -0.031 0.311 0.667 0.222 C 2.116 D: 12 8.974 2.510 0.239 0.321 0.545 0.455 CA 1.944 E: 10 10.309 1.803 0.261 0.717 1.000 0.667 CB 1.242 F: 14 16.897 2.649 0.112 0.399 0.846 0.538 CB 2.090 6 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 53 residues left after pruning, divided into chains as follows: A: 9 B: 8 C: 8 D: 10 E: 18 CC for partial structure against native data = 5.74 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.258, Connect. = 0.521 for dens.mod. cycle 1 = 0.287, Contrast = 0.261, Connect. = 0.512 for dens.mod. cycle 2 = 0.287, Contrast = 0.266, Connect. = 0.523 for dens.mod. cycle 3 = 0.287, Contrast = 0.266, Connect. = 0.532 for dens.mod. cycle 4 = 0.287, Contrast = 0.265, Connect. = 0.541 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2102 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 157 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 20 16.291 2.452 0.154 0.208 0.895 0.316 C 2.086 B: 15 16.977 2.619 0.207 0.421 0.714 0.500 CA 2.184 C: 12 6.521 2.362 -0.078 0.227 0.636 0.273 CB 1.950 D: 12 6.962 2.645 -0.012 0.234 0.545 0.364 CB 2.006 E: 12 14.118 2.014 0.316 0.690 0.909 0.455 CB 1.485 7 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 55 residues left after pruning, divided into chains as follows: A: 9 B: 9 C: 10 D: 12 E: 15 CC for partial structure against native data = 4.64 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.257, Connect. = 0.522 for dens.mod. cycle 1 = 0.287, Contrast = 0.261, Connect. = 0.509 for dens.mod. cycle 2 = 0.287, Contrast = 0.265, Connect. = 0.521 for dens.mod. cycle 3 = 0.287, Contrast = 0.265, Connect. = 0.531 for dens.mod. cycle 4 = 0.287, Contrast = 0.265, Connect. = 0.539 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 17 heavy atoms with Occ*Z > 4.80 added to NOGO map 2147 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 150 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 7.772 2.686 0.106 0.171 0.556 0.222 CA 2.338 B: 18 19.311 2.707 0.111 0.276 0.882 0.588 C 2.272 C: 34 19.168 2.271 0.322 0.318 0.727 0.333 CB 1.869 18 residues pruned to eliminate duplicates D: 13 8.050 2.847 0.120 0.219 0.417 0.333 CA 2.432 E: 9 9.494 2.108 0.443 0.367 0.750 0.375 CB 1.696 F: 7 4.968 1.612 0.388 0.550 0.833 0.500 CA 1.036 Using tripeptides from previous cycle as seeds 48 residues left after pruning, divided into chains as follows: A: 10 B: 27 C: 11 CC for partial structure against native data = 4.69 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 3 used as input for final density modification = 0.287, Contrast = 0.263, Connect. = 0.521 for dens.mod. cycle 1 = 0.287, Contrast = 0.266, Connect. = 0.510 for dens.mod. cycle 2 = 0.287, Contrast = 0.270, Connect. = 0.522 for dens.mod. cycle 3 = 0.287, Contrast = 0.269, Connect. = 0.530 for dens.mod. cycle 4 = 0.287, Contrast = 0.268, Connect. = 0.537 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 3.71 - 2.94 - 2.56 - 2.32 - 2.16 - 2.03 - 1.92 - 1.84 - 1.77 - 1.71 0.371 0.321 0.259 0.273 0.272 0.290 0.299 0.268 0.234 0.217 0.498 0.424 0.337 0.354 0.364 0.414 0.438 0.410 0.368 0.362 N 2232 2224 2250 2277 2141 2250 2426 2134 2190 2096 Estimated mean FOM = 0.281 Pseudo-free CC = 32.49 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.6137 0.1416 0.3621 16.0000 31.00 2 0.5222 0.1557 0.1658 14.0000 26.53 3 0.8331 0.3268 0.6817 13.7952 25.64 4 0.3793 0.1659 0.1619 12.3808 21.47 5 0.3140 0.1854 0.3368 11.2240 20.34 6 0.6485 0.1586 0.7668 11.1744 21.66 7 0.5000 0.5000 0.3486 2.6160 19.56 8 0.6526 0.1445 0.5862 9.7888 16.26 9 1.0000 0.0000 0.5692 2.2272 18.53 10 0.4582 0.1340 0.0911 8.5568 15.81 11 0.2281 0.2528 0.1509 8.0848 15.86 12 0.6176 0.0467 0.5632 8.0288 16.90 13 0.5573 0.1636 0.8705 7.1888 14.50 14 0.9612 0.1511 0.9043 7.1840 11.65 15 0.6000 0.1146 0.3001 6.9600 13.15 16 0.6012 0.0878 0.7465 6.4736 11.69 17 0.4902 0.3540 0.6752 5.5072 10.31 18 0.5387 0.3438 0.1808 5.4336 9.03 19 0.5857 0.3112 0.0873 5.1968 9.00 Site x y z h(sig) near old near new 1 0.6139 0.1418 0.3623 31.0 1/0.02 20/3.23 14/3.51 10/10.88 2/11.07 2 0.5224 0.1550 0.1660 26.6 2/0.05 12/5.67 14/8.63 5/9.45 21/10.40 3 0.8331 0.3271 0.6814 25.6 3/0.02 9/15.53 17/16.31 6/16.32 4/16.93 4 0.6482 0.1586 0.7667 21.7 6/0.02 15/5.65 13/7.78 10/8.57 9/12.24 5 0.3791 0.1655 0.1609 21.5 4/0.05 12/6.47 6/9.41 2/9.45 11/11.54 6 0.3143 0.1853 0.3368 20.3 5/0.02 5/9.41 11/11.39 12/15.31 20/15.33 7 0.5000 0.5000 0.3470 19.6 7/0.08 18/13.22 18/13.22 18/13.22 18/13.22 8 1.0000 0.0000 0.5671 18.6 9/0.10 16/18.97 16/18.97 16/18.97 16/18.97 9 0.6178 0.0468 0.5636 16.9 12/0.03 10/6.85 15/9.14 1/11.37 20/12.21 10 0.6532 0.1435 0.5863 16.3 8/0.08 9/6.85 4/8.57 15/9.10 1/10.88 11 0.2274 0.2535 0.1508 15.9 11/0.07 21/9.57 6/11.39 5/11.54 20/12.28 12 0.4580 0.1341 0.0916 15.8 10/0.03 2/5.67 5/6.47 13/12.39 21/12.99 13 0.5574 0.1638 0.8722 14.6 13/0.08 4/7.78 15/8.27 21/9.92 12/12.39 14 0.6019 0.1147 0.3003 13.3 15/0.13 1/3.51 20/4.76 2/8.63 21/13.09 15 0.6020 0.0874 0.7477 11.7 16/0.08 4/5.65 13/8.27 10/9.10 9/9.14 16 0.9616 0.1504 0.9062 11.7 14/0.10 16/14.43 3/17.85 11/18.94 8/18.97 17 0.4898 0.3542 0.6733 10.4 17/0.09 17/13.59 13/16.26 3/16.31 4/17.12 18 0.5380 0.3439 0.1784 9.1 18/0.12 19/5.63 2/12.47 7/13.22 7/13.22 19 0.5844 0.3119 0.0886 9.1 19/0.11 18/5.63 21/11.50 2/11.67 11/12.37 20 0.6615 0.1385 0.3468 -4.8 1/3.23 1/3.23 14/4.76 10/11.31 9/12.21 21 0.1542 0.3493 0.0370 -4.6 11/9.63 11/9.57 13/9.92 2/10.40 19/11.50 Best trace (cycle 3 with CC 5.74%) was saved as P4_visc-standard_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.5 - Setup, data input and phasing 3.3 - FFTs and peak-searches 4.0 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 123.4 - Tripeptide search 21.0 - Chain tracing 0.0 - NCS analysis 2.5 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:26:01 Total time: 154.91 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++