++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:32:58 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: P43_visc-standard P43_visc-standard_fa -i -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P43_visc-standard_fa.res FA and alpha from P43_visc-standard_fa.hkl Native data from P43_visc-standard.hkl Listing output to P43_visc-standard_i.lst Phases output to P43_visc-standard_i.phs Revised heavy atom sites output to P43_visc-standard_i.hat Revised heavy atom phases output to P43_visc-standard_i.pha Poly-Ala trace output to P43_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 43 Allowed origin shift code: 7 21 atoms read from file P43_visc-standard_fa.res 14490 Reflections read from file P43_visc-standard_fa.hkl 22220 Reflections read from file P43_visc-standard.hkl 22199 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000221h^2 +0.000221k^2 -0.000681l^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 21 0.000 <= z <= 0.250 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.759 ** Space group converted to enantiomorph ** ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 13.96% = 0.107 for phases from phiT = phiA + alpha = 0.195 after including heavy atoms = 0.158, Contrast = 0.023, Connect. = 0.530 for dens.mod. cycle 1 = 0.176, Contrast = 0.081, Connect. = 0.578 for dens.mod. cycle 2 = 0.194, Contrast = 0.093, Connect. = 0.585 for dens.mod. cycle 3 = 0.208, Contrast = 0.100, Connect. = 0.580 for dens.mod. cycle 4 = 0.219, Contrast = 0.112, Connect. = 0.581 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 1791 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 107 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 9 1.248 1.411 0.058 0.062 0.625 0.250 CB 0.841 ? A: 6 2.492 1.290 0.828 0.294 0.600 0.400 CB 0.993 7 1.570 1.385 0.298 0.313 0.667 0.167 CB 0.658 ? 6 1.169 1.380 0.407 0.213 0.800 0.400 CB 0.472 ? B: 8 2.170 1.300 0.474 0.307 0.571 0.571 CB 0.928 C: 6 2.852 1.394 0.344 0.293 0.800 0.600 C 1.073 D: 8 2.332 1.452 0.519 0.071 0.714 0.429 CB 0.979 7 1.997 1.334 0.351 0.251 0.833 0.500 CB 0.722 ? 6 0.829 1.187 0.411 0.100 0.400 0.200 CB 0.922 ? E: 10 2.398 1.334 0.599 0.313 0.556 0.333 CB 0.829 F: 9 2.426 1.287 0.351 0.294 0.625 0.375 C 0.995 31 residues left after pruning, divided into chains as follows: A: 8 B: 6 C: 7 D: 10 CC for partial structure against native data = 3.21 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.287, Contrast = 0.170, Connect. = 0.523 for dens.mod. cycle 1 = 0.287, Contrast = 0.180, Connect. = 0.469 for dens.mod. cycle 2 = 0.287, Contrast = 0.185, Connect. = 0.486 for dens.mod. cycle 3 = 0.287, Contrast = 0.187, Connect. = 0.500 for dens.mod. cycle 4 = 0.287, Contrast = 0.198, Connect. = 0.515 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2160 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 114 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 8.002 2.289 0.239 0.292 0.600 0.500 CB 1.878 B: 10 6.817 2.044 0.175 0.354 0.778 0.444 CB 1.425 C: 11 4.415 1.765 0.123 0.227 0.700 0.400 CB 1.384 D: 7 2.582 1.307 0.244 0.306 1.000 0.500 N 0.804 8 1.828 1.141 0.161 0.271 0.857 0.429 CA 0.789 ? Using tripeptides from previous cycle as seeds E: 9 2.075 2.060 0.642 0.176 0.250 0.125 CB 1.283 36 residues left after pruning, divided into chains as follows: A: 11 B: 10 C: 8 D: 7 CC for partial structure against native data = 1.80 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.196, Connect. = 0.516 for dens.mod. cycle 1 = 0.287, Contrast = 0.204, Connect. = 0.475 for dens.mod. cycle 2 = 0.287, Contrast = 0.208, Connect. = 0.489 for dens.mod. cycle 3 = 0.287, Contrast = 0.209, Connect. = 0.502 for dens.mod. cycle 4 = 0.287, Contrast = 0.221, Connect. = 0.518 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2192 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 111 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 12 12.518 2.848 0.127 0.273 0.636 0.545 CB 2.389 B: 9 6.347 2.529 -0.177 0.268 0.750 0.500 CB 1.871 C: 17 9.994 2.445 0.045 0.310 0.688 0.375 CB 1.755 9 residues pruned to eliminate duplicates D: 9 5.256 1.764 0.043 0.316 1.000 0.625 CB 1.239 E: 7 9.908 2.219 0.090 0.511 1.000 0.833 CA 1.654 F: 6 2.995 1.282 0.435 0.469 0.800 0.400 CA 0.939 7 1.745 1.129 -0.270 0.347 1.000 0.667 CB 1.021 ? Using tripeptides from previous cycle as seeds 44 residues left after pruning, divided into chains as follows: A: 12 B: 17 C: 9 D: 6 CC for partial structure against native data = 3.56 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.225, Connect. = 0.518 for dens.mod. cycle 1 = 0.287, Contrast = 0.229, Connect. = 0.483 for dens.mod. cycle 2 = 0.287, Contrast = 0.231, Connect. = 0.496 for dens.mod. cycle 3 = 0.287, Contrast = 0.230, Connect. = 0.507 for dens.mod. cycle 4 = 0.287, Contrast = 0.237, Connect. = 0.520 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2194 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 124 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 13 14.241 2.805 0.263 0.242 0.667 0.417 CB 2.345 B: 9 4.666 2.437 -0.186 0.198 0.625 0.625 CB 1.905 C: 12 12.720 2.304 0.234 0.282 0.909 0.545 CB 1.896 D: 8 6.845 2.164 0.234 0.336 0.714 0.286 CB 1.623 E: 11 5.155 1.580 0.135 0.384 0.800 0.400 CA 1.285 F: 6 6.855 2.366 0.106 0.476 0.600 0.400 C 2.000 8 1.259 1.190 0.140 0.278 0.571 0.286 CA 0.789 ? Using tripeptides from previous cycle as seeds 48 residues left after pruning, divided into chains as follows: A: 13 B: 9 C: 12 D: 8 E: 6 CC for partial structure against native data = 3.54 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.227, Connect. = 0.519 for dens.mod. cycle 1 = 0.287, Contrast = 0.229, Connect. = 0.484 for dens.mod. cycle 2 = 0.287, Contrast = 0.231, Connect. = 0.497 for dens.mod. cycle 3 = 0.287, Contrast = 0.236, Connect. = 0.511 for dens.mod. cycle 4 = 0.287, Contrast = 0.239, Connect. = 0.521 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 16 heavy atoms with Occ*Z > 4.80 added to NOGO map 2157 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 132 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 13.616 2.724 0.217 0.280 0.643 0.429 CB 2.189 B: 14 14.412 2.563 0.106 0.336 0.846 0.615 CB 1.994 C: 13 7.793 2.067 0.383 0.284 0.667 0.167 CB 1.507 D: 15 7.614 2.246 0.096 0.218 0.643 0.429 CB 1.791 15 residues pruned to eliminate duplicates E: 9 4.445 2.471 -0.229 0.386 0.625 0.375 CB 1.490 F: 16 8.873 2.229 0.170 0.426 0.600 0.267 CB 1.581 9 residues pruned to eliminate duplicates 6 1.570 1.386 0.273 0.411 0.600 0.400 CB 0.729 ? Using tripeptides from previous cycle as seeds 58 residues left after pruning, divided into chains as follows: A: 15 B: 14 C: 13 D: 16 CC for partial structure against native data = 6.46 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 5 used as input for final density modification = 0.287, Contrast = 0.236, Connect. = 0.516 for dens.mod. cycle 1 = 0.287, Contrast = 0.239, Connect. = 0.492 for dens.mod. cycle 2 = 0.287, Contrast = 0.240, Connect. = 0.506 for dens.mod. cycle 3 = 0.287, Contrast = 0.242, Connect. = 0.518 for dens.mod. cycle 4 = 0.287, Contrast = 0.242, Connect. = 0.526 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 0.235 0.286 0.246 0.301 0.308 0.298 0.304 0.288 0.248 0.252 0.310 0.351 0.310 0.386 0.403 0.420 0.442 0.445 0.397 0.426 N 2223 2221 2248 2276 2140 2248 2426 2133 2189 2095 Estimated mean FOM = 0.277 Pseudo-free CC = 33.04 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.4238 0.6591 0.8176 16.0000 33.93 2 0.5550 0.6662 1.1903 14.1584 28.82 3 0.3442 0.6969 0.6938 13.9968 28.06 4 0.0500 0.8268 0.8801 12.9648 26.22 5 0.6253 0.7251 1.3026 12.1072 24.10 6 0.4080 0.6806 1.1647 11.8768 24.34 7 0.1149 0.7562 0.7864 10.3536 21.69 8 0.1584 0.9269 0.4850 9.5328 21.07 9 0.1907 1.0693 0.4811 8.9392 18.09 10 0.5696 0.6940 0.8297 8.6464 16.67 11 0.3987 0.6573 1.1181 7.6592 16.37 12 0.2091 0.8525 0.6161 7.6112 14.38 13 0.4455 0.7767 1.3716 6.5536 12.68 14 0.0993 1.1577 0.4254 5.7856 12.66 15 0.5542 0.5697 1.1011 5.7760 12.97 16 0.0470 0.6842 0.6106 5.2032 11.08 17 0.5652 0.8724 1.0583 4.1696 8.10 18 0.5096 0.9452 0.8237 4.0064 8.74 19 0.4900 0.8874 1.1093 3.9152 7.76 20 0.2730 1.0073 0.3958 3.7920 9.00 21 0.5287 0.9353 0.9082 3.3888 6.68 Site x y z h(sig) near old near new 1 0.4232 0.6583 0.8169 34.1 1/0.07 3/8.17 10/9.88 11/14.40 10/15.74 2 0.5549 0.6657 1.1901 28.8 2/0.04 14/7.61 6/8.02 5/9.78 11/10.84 3 0.3443 0.6970 0.6944 28.1 3/0.03 1/8.17 6/9.40 13/14.04 2/15.21 4 0.0494 0.8266 0.8788 26.3 4/0.07 7/7.67 16/10.09 19/14.38 17/15.70 5 0.4080 0.6804 1.1651 24.3 6/0.02 11/2.72 2/9.78 10/10.76 15/11.93 6 0.6251 0.7251 1.3019 24.1 5/0.04 2/8.02 3/9.40 15/12.71 14/14.71 7 0.1154 0.7567 0.7866 21.7 7/0.05 4/7.67 17/10.53 13/11.98 3/16.14 8 0.1584 0.9267 0.4856 21.1 8/0.03 12/0.75 13/8.52 9/9.58 18/9.64 9 0.1897 1.0690 0.4806 18.2 9/0.08 18/0.97 19/7.94 16/8.77 8/9.58 10 0.5688 0.6947 0.8293 16.7 10/0.08 11/8.61 1/9.88 5/10.76 14/15.29 11 0.3981 0.6564 1.1201 16.7 11/0.11 5/2.72 10/8.61 2/10.84 14/11.80 12 0.1579 0.9262 0.5014 14.6 8/0.77 8/0.75 13/7.99 18/9.66 9/9.67 13 0.2098 0.8530 0.6157 14.4 12/0.06 12/7.99 8/8.52 7/11.98 3/14.04 14 0.5543 0.5690 1.1013 13.0 15/0.05 2/7.61 11/11.80 5/12.17 5/12.46 15 0.4457 0.7755 1.3740 12.9 13/0.14 5/11.93 6/12.71 2/13.37 14/14.61 16 0.0998 1.1590 0.4246 12.8 14/0.10 9/8.77 18/9.09 4/10.09 19/14.61 17 0.0475 0.6851 0.6107 11.1 16/0.06 7/10.53 20/14.50 13/15.35 4/15.70 18 0.1899 1.0696 0.5011 9.1 9/0.94 9/0.97 19/8.48 16/9.09 8/9.64 19 0.2732 1.0079 0.3940 9.0 20/0.09 9/7.94 18/8.48 8/10.20 12/10.58 20 0.5091 0.9463 0.8251 8.8 18/0.10 23/4.14 21/12.67 22/14.04 17/14.50 21 0.5646 0.8721 1.0607 8.2 17/0.12 22/5.52 23/8.69 20/12.67 2/14.89 22 0.4896 0.8862 1.1094 8.0 19/0.09 21/5.52 23/10.37 20/14.04 15/14.73 23 0.5279 0.9356 0.9075 6.7 21/0.07 20/4.14 21/8.69 22/10.37 19/13.61 Best trace (cycle 5 with CC 6.46%) was saved as P43_visc-standard_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 1.1 - FFTs and peak-searches 3.0 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 126.4 - Tripeptide search 26.8 - Chain tracing 0.0 - NCS analysis 2.3 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:35:38 Total time: 160.02 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++