++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:36:21 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: P43212_visc-standard P43212_visc-standard_fa -i -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P43212_visc-standard_fa.res FA and alpha from P43212_visc-standard_fa.hkl Native data from P43212_visc-standard.hkl Listing output to P43212_visc-standard_i.lst Phases output to P43212_visc-standard_i.phs Revised heavy atom sites output to P43212_visc-standard_i.hat Revised heavy atom phases output to P43212_visc-standard_i.pha Poly-Ala trace output to P43212_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 21 2 Allowed origin shift code: 9 21 atoms read from file P43212_visc-standard_fa.res Trimmed to 17 atoms with occupancy > 0.2 7603 Reflections read from file P43212_visc-standard_fa.hkl 11844 Reflections read from file P43212_visc-standard.hkl 11805 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000242h^2 +0.000242k^2 -0.000707l^2 +0.000000kl +0.000000hl +0.000000hk 4 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 11 0.000 <= z <= 0.125 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.770 ** Space group converted to enantiomorph ** ** Atom coordinates inverted ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 17.47% = 0.129 for phases from phiT = phiA + alpha = 0.281 after including heavy atoms = 0.170, Contrast = 0.026, Connect. = 0.516 for dens.mod. cycle 1 = 0.183, Contrast = 0.087, Connect. = 0.560 for dens.mod. cycle 2 = 0.195, Contrast = 0.104, Connect. = 0.570 for dens.mod. cycle 3 = 0.207, Contrast = 0.111, Connect. = 0.570 for dens.mod. cycle 4 = 0.218, Contrast = 0.121, Connect. = 0.572 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 891 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 50 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 10 4.003 1.312 0.698 0.288 0.778 0.222 CB 0.977 B: 10 2.208 1.294 0.225 0.166 0.778 0.444 CB 0.896 C: 11 3.368 1.315 0.367 0.203 0.900 0.400 CB 0.937 D: 16 3.773 1.282 0.375 0.328 0.733 0.267 CB 0.911 36 residues left after pruning, divided into chains as follows: A: 10 B: 10 C: 16 CC for partial structure against native data = 2.61 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.288, Contrast = 0.118, Connect. = 0.516 for dens.mod. cycle 1 = 0.288, Contrast = 0.128, Connect. = 0.461 for dens.mod. cycle 2 = 0.288, Contrast = 0.150, Connect. = 0.487 for dens.mod. cycle 3 = 0.288, Contrast = 0.170, Connect. = 0.511 for dens.mod. cycle 4 = 0.288, Contrast = 0.190, Connect. = 0.530 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 1088 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 67 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 18 7.121 1.970 0.218 0.260 0.706 0.294 CB 1.341 B: 8 4.158 1.583 0.323 0.440 1.000 0.286 CB 0.798 C: 6 3.025 1.289 0.353 0.394 0.800 0.600 CB 1.084 D: 6 3.580 1.697 -0.124 0.401 1.000 0.600 CA 1.196 E: 6 2.461 1.356 0.306 0.293 0.800 0.600 CB 0.980 Using tripeptides from previous cycle as seeds 28 residues left after pruning, divided into chains as follows: A: 18 B: 4 C: 6 CC for partial structure against native data = 5.84 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.288, Contrast = 0.181, Connect. = 0.508 for dens.mod. cycle 1 = 0.288, Contrast = 0.188, Connect. = 0.480 for dens.mod. cycle 2 = 0.288, Contrast = 0.206, Connect. = 0.505 for dens.mod. cycle 3 = 0.288, Contrast = 0.221, Connect. = 0.524 for dens.mod. cycle 4 = 0.288, Contrast = 0.239, Connect. = 0.542 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 1058 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 72 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 3.931 1.912 -0.015 0.339 0.667 0.500 CA 1.523 B: 6 3.194 1.648 0.136 0.488 0.600 0.600 N 1.287 C: 7 2.908 2.014 -0.332 0.304 0.833 0.500 CB 1.316 D: 6 2.040 1.102 0.588 0.704 0.800 0.400 C 0.541 E: 6 4.528 1.482 0.285 0.736 1.000 0.400 CB 0.860 F: 23 10.115 1.713 0.523 0.361 0.818 0.364 CB 1.173 Using tripeptides from previous cycle as seeds 27 residues left after pruning, divided into chains as follows: A: 4 B: 23 CC for partial structure against native data = 3.50 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.288, Contrast = 0.163, Connect. = 0.501 for dens.mod. cycle 1 = 0.288, Contrast = 0.181, Connect. = 0.472 for dens.mod. cycle 2 = 0.288, Contrast = 0.197, Connect. = 0.494 for dens.mod. cycle 3 = 0.288, Contrast = 0.213, Connect. = 0.514 for dens.mod. cycle 4 = 0.288, Contrast = 0.236, Connect. = 0.538 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 1069 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 62 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 8 5.984 1.886 0.291 0.418 1.000 0.429 CB 1.012 B: 6 2.938 1.429 0.143 0.374 1.000 0.600 N 0.920 C: 8 4.038 1.514 0.616 0.334 0.714 0.429 CB 1.047 8 1.574 1.411 0.315 0.248 0.571 0.286 CB 0.749 ? D: 9 4.957 1.732 0.770 0.283 0.875 0.500 CB 0.834 E: 8 2.985 1.688 0.162 0.389 0.571 0.286 CB 1.133 Using tripeptides from previous cycle as seeds F: 6 2.339 1.408 -0.256 0.347 1.000 0.600 C 1.179 20 residues left after pruning, divided into chains as follows: A: 8 B: 6 C: 6 CC for partial structure against native data = 3.77 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.288, Contrast = 0.184, Connect. = 0.508 for dens.mod. cycle 1 = 0.288, Contrast = 0.199, Connect. = 0.473 for dens.mod. cycle 2 = 0.288, Contrast = 0.226, Connect. = 0.502 for dens.mod. cycle 3 = 0.288, Contrast = 0.247, Connect. = 0.527 for dens.mod. cycle 4 = 0.288, Contrast = 0.266, Connect. = 0.544 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 12 heavy atoms with Occ*Z > 4.80 added to NOGO map 1085 peaks > 0.5 sigma used to seed fragment search Space for about 101 unique residues taking solvent into account 52 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 11 11.719 2.198 0.250 0.451 0.900 0.400 CB 1.575 B: 8 7.329 2.240 -0.072 0.315 0.857 0.571 CB 1.909 C: 9 8.629 1.613 0.425 0.572 1.000 0.500 CB 1.238 D: 11 2.734 1.270 0.443 0.343 0.800 0.500 CB 0.699 Using tripeptides from previous cycle as seeds 30 residues left after pruning, divided into chains as follows: A: 11 B: 9 C: 10 CC for partial structure against native data = 5.55 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 2 used as input for final density modification = 0.288, Contrast = 0.205, Connect. = 0.515 for dens.mod. cycle 1 = 0.288, Contrast = 0.223, Connect. = 0.485 for dens.mod. cycle 2 = 0.289, Contrast = 0.252, Connect. = 0.515 for dens.mod. cycle 3 = 0.289, Contrast = 0.275, Connect. = 0.541 for dens.mod. cycle 4 = 0.289, Contrast = 0.295, Connect. = 0.558 for dens.mod. cycle 5 Estimated mean FOM and mapCC as a function of resolution d inf - 3.80 - 2.97 - 2.58 - 2.34 - 2.17 - 2.03 - 1.93 - 1.84 - 1.77 - 1.71 0.288 0.446 0.403 0.268 0.227 0.306 0.323 0.257 0.219 0.189 0.429 0.610 0.541 0.337 0.296 0.420 0.475 0.403 0.355 0.313 N 1183 1196 1195 1173 1166 1263 1139 1251 1144 1095 Estimated mean FOM = 0.294 Pseudo-free CC = 32.50 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.2680 0.1171 0.8896 16.0000 26.63 2 0.3286 0.0443 0.7540 11.5360 19.64 3 0.4293 0.1648 1.1719 10.9440 19.37 4 0.3414 0.0641 0.7987 10.8384 17.94 5 0.3603 0.2243 1.0519 10.5072 16.99 6 0.5688 0.1722 1.2043 10.2736 14.83 7 0.5638 0.1987 1.1720 9.8752 15.69 8 0.3192 -0.0929 0.7667 9.4688 17.46 9 0.3501 0.1951 1.0186 9.2272 13.68 10 0.3447 -0.0970 0.7267 8.0240 13.55 11 0.3165 0.1107 0.6817 6.7472 9.05 12 0.4891 0.2887 0.8663 6.6352 9.62 13 0.4315 0.2734 0.7232 4.6944 7.09 14 0.3772 0.0955 1.2078 4.4000 6.11 15 0.2984 0.1182 0.8308 4.3088 7.36 16 0.3917 0.3237 0.8957 3.5680 5.81 17 0.3840 0.4753 0.8729 3.4592 5.42 Site x y z h(sig) near old near new 1 0.2676 0.1174 0.8892 26.7 1/0.03 15/2.05 13/3.47 4/7.36 2/8.88 2 0.3282 0.0449 0.7546 19.7 2/0.05 18/2.11 4/2.59 12/5.56 13/6.22 3 0.4295 0.1648 1.1715 19.4 3/0.02 16/6.07 6/8.24 7/9.03 9/9.06 4 0.3415 0.0636 0.7992 18.0 4/0.04 2/2.59 18/4.20 13/4.72 15/6.32 5 0.3185 -0.0925 0.7661 17.5 8/0.06 10/2.58 18/7.16 2/9.07 8/9.57 6 0.3600 0.2243 1.0523 17.0 5/0.03 9/2.50 3/8.24 17/10.06 16/11.31 7 0.5628 0.1981 1.1712 15.8 7/0.08 8/2.33 3/9.03 10/9.39 16/11.28 8 0.5681 0.1725 1.2045 14.9 6/0.05 7/2.33 10/7.67 3/9.25 5/9.57 9 0.3495 0.1954 1.0210 14.1 9/0.12 6/2.50 3/9.06 1/9.69 17/10.64 10 0.3447 -0.0965 0.7259 13.6 10/0.05 5/2.58 8/7.67 18/7.76 7/9.39 11 0.4883 0.2884 0.8655 9.5 12/0.07 17/6.89 14/7.76 6/12.91 15/13.18 12 0.3182 0.1101 0.6808 9.1 11/0.13 2/5.56 4/6.55 18/7.08 13/7.14 13 0.2984 0.1168 0.8294 7.4 15/0.11 1/3.47 15/3.77 4/4.72 2/6.22 14 0.4306 0.2738 0.7234 7.1 13/0.07 11/7.76 17/9.09 15/11.45 5/11.61 15 0.2730 0.0867 0.8875 -6.6 1/2.03 1/2.05 13/3.77 4/6.32 2/7.75 16 0.3751 0.0953 1.2096 6.2 14/0.16 3/6.07 9/11.19 7/11.28 6/11.31 17 0.3917 0.3230 0.8953 5.8 16/0.05 11/6.89 14/9.09 6/10.06 9/10.64 18 0.3143 0.0159 0.7537 -4.9 2/2.09 2/2.11 4/4.20 12/7.08 5/7.16 Best trace (cycle 2 with CC 5.84%) was saved as P43212_visc-standard_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 0.7 - FFTs and peak-searches 1.5 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 61.9 - Tripeptide search 18.5 - Chain tracing 0.0 - NCS analysis 1.1 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:37:45 Total time: 83.98 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++