++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2019/1 + + Copyright (c) George M. Sheldrick and Isabel Uson 2001-19 + + Started at 12:29:50 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: P42_visc-standard P42_visc-standard_fa -a5 -h -s0.5 -m5 Cell, symmetry and heavy atoms from: P42_visc-standard_fa.res FA and alpha from P42_visc-standard_fa.hkl Native data from P42_visc-standard.hkl Listing output to P42_visc-standard.lst Phases output to P42_visc-standard.phs Revised heavy atom sites output to P42_visc-standard.hat Revised heavy atom phases output to P42_visc-standard.pha Poly-Ala trace output to P42_visc-standard.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 0.500 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 42 Allowed origin shift code: 7 21 atoms read from file P42_visc-standard_fa.res 14490 Reflections read from file P42_visc-standard_fa.hkl 22220 Reflections read from file P42_visc-standard.hkl 22206 Unique data, highest resolution = 1.702 Angstroms Anisotropic scaling: intensities multiplied by 0.000221h^2 +0.000221k^2 -0.000677l^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 42 0.000 <= z <= 0.500 92 Point spherical net set up with radius 2.42A 32 Extra Fourier layers will be generated <|E^2-1|> = 0.759 Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 10.75% = 0.094 for phases from phiT = phiA + alpha = 0.144 after including heavy atoms = 0.145, Contrast = 0.019, Connect. = 0.501 for dens.mod. cycle 1 = 0.167, Contrast = 0.086, Connect. = 0.577 for dens.mod. cycle 2 = 0.187, Contrast = 0.122, Connect. = 0.608 for dens.mod. cycle 3 = 0.202, Contrast = 0.127, Connect. = 0.603 for dens.mod. cycle 4 = 0.213, Contrast = 0.129, Connect. = 0.595 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 20 heavy atoms with Occ*Z > 4.80 added to NOGO map 1752 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 134 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 6 2.042 1.286 0.128 0.434 0.800 0.600 C 0.843 B: 7 4.522 1.298 0.343 0.721 1.000 0.833 CB 0.867 6 1.749 1.252 0.091 0.537 0.800 0.600 CB 0.691 ? C: 7 3.977 1.244 0.718 0.785 0.833 0.500 CB 0.709 D: 6 2.982 1.459 0.401 0.399 0.600 0.400 CA 1.210 7 1.795 1.283 0.573 0.208 0.500 0.333 CB 1.027 ? E: 6 3.217 1.229 0.224 0.665 0.800 0.800 O 1.026 6 1.058 1.170 0.651 0.298 0.600 0.600 N 0.511 ? F: 6 2.188 1.261 0.253 0.299 0.800 0.400 N 0.968 G: 6 2.630 1.124 0.671 0.379 0.800 0.600 CA 0.891 H: 11 4.183 1.265 0.317 0.401 0.900 0.600 CB 0.979 I: 6 3.155 1.336 -0.027 0.526 1.000 0.600 CB 1.057 7 1.722 1.260 0.176 0.245 0.667 0.500 CB 0.956 ? J: 7 2.073 1.003 0.663 0.381 0.833 0.833 CA 0.691 K: 8 2.652 1.399 0.381 0.247 0.857 0.571 CB 0.810 L: 7 2.367 1.219 0.711 0.438 0.833 0.500 CB 0.592 31 residues left after pruning, divided into chains as follows: A: 7 B: 7 C: 11 D: 6 CC for partial structure against native data = 2.95 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.287, Contrast = 0.194, Connect. = 0.526 for dens.mod. cycle 1 = 0.287, Contrast = 0.202, Connect. = 0.487 for dens.mod. cycle 2 = 0.287, Contrast = 0.207, Connect. = 0.501 for dens.mod. cycle 3 = 0.287, Contrast = 0.209, Connect. = 0.512 for dens.mod. cycle 4 = 0.287, Contrast = 0.214, Connect. = 0.523 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 20 heavy atoms with Occ*Z > 4.80 added to NOGO map 2196 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 134 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 14 7.582 2.236 -0.057 0.278 0.846 0.462 CB 1.515 B: 11 11.346 1.895 0.241 0.659 0.800 0.500 CA 1.645 C: 9 15.048 2.397 0.278 0.374 1.000 0.500 C 1.987 4 residues pruned to eliminate duplicates D: 12 6.943 1.898 0.012 0.487 0.818 0.545 CB 1.349 E: 12 7.025 1.667 0.295 0.372 0.909 0.636 CB 1.238 11 residues pruned to eliminate duplicates Using tripeptides from previous cycle as seeds 35 residues left after pruning, divided into chains as follows: A: 14 B: 16 C: 5 CC for partial structure against native data = 2.35 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.235, Connect. = 0.516 for dens.mod. cycle 1 = 0.287, Contrast = 0.239, Connect. = 0.494 for dens.mod. cycle 2 = 0.287, Contrast = 0.242, Connect. = 0.505 for dens.mod. cycle 3 = 0.287, Contrast = 0.243, Connect. = 0.517 for dens.mod. cycle 4 = 0.287, Contrast = 0.243, Connect. = 0.526 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 20 heavy atoms with Occ*Z > 4.80 added to NOGO map 2181 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 152 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 17 12.829 2.689 -0.076 0.250 0.750 0.375 CB 2.296 B: 11 20.767 2.501 0.081 0.802 1.000 0.500 CA 1.865 C: 18 33.156 2.784 0.494 0.477 0.882 0.588 CB 2.244 12 residues pruned to eliminate duplicates D: 7 4.167 2.237 -0.445 0.446 0.833 0.667 CA 1.739 Using tripeptides from previous cycle as seeds 40 residues left after pruning, divided into chains as follows: A: 17 B: 17 C: 6 CC for partial structure against native data = 4.27 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.280, Connect. = 0.518 for dens.mod. cycle 1 = 0.287, Contrast = 0.283, Connect. = 0.503 for dens.mod. cycle 2 = 0.287, Contrast = 0.284, Connect. = 0.515 for dens.mod. cycle 3 = 0.287, Contrast = 0.282, Connect. = 0.525 for dens.mod. cycle 4 = 0.287, Contrast = 0.278, Connect. = 0.533 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 20 heavy atoms with Occ*Z > 4.80 added to NOGO map 2168 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 141 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 19 29.893 2.895 0.177 0.480 0.889 0.444 CB 2.374 B: 6 2.935 1.802 -0.121 0.585 0.600 0.600 CB 1.272 C: 12 9.351 2.421 -0.017 0.339 0.727 0.455 C 1.941 D: 6 8.846 2.175 0.015 0.472 1.000 0.800 CA 1.843 E: 9 2.275 1.130 0.363 0.244 0.750 0.750 CB 0.936 F: 9 2.321 1.220 0.002 0.319 0.875 0.375 CB 0.937 G: 7 2.281 1.289 0.312 0.471 0.833 0.333 N 0.681 Using tripeptides from previous cycle as seeds 59 residues left after pruning, divided into chains as follows: A: 19 B: 6 C: 12 D: 6 E: 9 F: 7 CC for partial structure against native data = 7.05 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.282, Connect. = 0.524 for dens.mod. cycle 1 = 0.287, Contrast = 0.285, Connect. = 0.513 for dens.mod. cycle 2 = 0.287, Contrast = 0.289, Connect. = 0.524 for dens.mod. cycle 3 = 0.287, Contrast = 0.286, Connect. = 0.532 for dens.mod. cycle 4 = 0.287, Contrast = 0.283, Connect. = 0.539 for dens.mod. cycle 5 NOGO map generated for regions about rotation axes (if any) 20 heavy atoms with Occ*Z > 4.80 added to NOGO map 2135 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: 14 10.328 2.567 0.124 0.239 0.692 0.462 CA 1.941 B: 6 3.989 2.321 -0.507 0.477 0.800 0.600 CA 1.995 C: 14 22.186 2.407 0.236 0.696 0.846 0.538 C 2.043 D: 12 5.809 2.045 0.170 0.416 0.545 0.455 CB 1.466 E: 9 6.668 1.990 -0.008 0.354 0.875 0.500 CB 1.597 F: 14 10.766 2.299 0.183 0.326 0.692 0.538 CB 1.921 G: 6 3.066 1.593 0.150 0.603 0.800 0.600 CB 0.848 Using tripeptides from previous cycle as seeds 57 residues left after pruning, divided into chains as follows: A: 10 B: 6 C: 14 D: 7 E: 14 F: 6 CC for partial structure against native data = 6.04 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.287, Contrast = 0.271, Connect. = 0.525 for dens.mod. cycle 1 = 0.287, Contrast = 0.276, Connect. = 0.512 for dens.mod. cycle 2 = 0.287, Contrast = 0.279, Connect. = 0.523 for dens.mod. cycle 3 = 0.287, Contrast = 0.278, Connect. = 0.532 for dens.mod. cycle 4 = 0.287, Contrast = 0.276, Connect. = 0.539 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 0.295 0.249 0.167 0.242 0.264 0.322 0.332 0.282 0.234 0.225 0.400 0.341 0.217 0.309 0.343 0.462 0.490 0.434 0.368 0.362 N 2226 2222 2249 2276 2140 2249 2426 2133 2190 2095 Estimated mean FOM = 0.262 Pseudo-free CC = 30.93 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.4721 0.8021 0.3260 16.0000 36.90 2 0.5301 0.8133 0.1177 13.6432 30.95 3 0.5969 0.7384 0.4831 9.8192 19.18 4 0.4691 0.5815 0.2802 7.9280 16.81 5 0.3460 0.9213 0.1369 7.4288 15.08 6 0.6632 0.7966 0.6143 7.1024 16.09 7 0.4737 0.7686 0.5456 7.0400 16.53 8 0.4880 0.7291 0.2667 6.8432 15.08 9 0.5232 0.7512 -0.1180 6.7904 15.63 10 0.5163 0.8450 -0.2198 6.4928 15.58 11 0.3044 0.9940 0.0561 6.4752 14.36 12 0.4461 0.9719 0.0754 6.4400 14.01 13 0.2867 1.0490 0.3857 6.3184 13.85 14 0.7291 0.7566 0.6065 6.2576 14.53 15 0.2489 0.8087 0.5005 6.1936 13.10 16 0.2473 0.8800 0.4059 5.5040 11.19 17 0.2877 1.1656 0.3722 5.2640 12.60 18 0.5218 0.9635 0.4606 5.1344 12.19 19 0.3161 0.7408 0.6116 5.0608 11.78 20 0.4078 0.8613 0.2164 4.9392 11.31 21 0.6462 0.9456 0.6170 4.6832 9.84 Site x y z h(sig) near old near new 1 0.4723 0.8023 0.3264 36.9 1/0.03 9/5.65 19/7.77 2/10.54 5/10.57 2 0.5302 0.8133 0.1185 31.0 2/0.04 9/9.33 19/9.88 1/10.54 7/11.92 3 0.5965 0.7388 0.4838 19.2 3/0.05 6/8.45 5/8.78 12/10.55 16/11.21 4 0.4690 0.5814 0.2805 16.8 4/0.02 9/9.84 4/11.45 1/14.68 7/15.70 5 0.4741 0.7687 0.5455 16.5 7/0.02 3/8.78 1/10.57 18/10.99 8/12.49 6 0.6632 0.7970 0.6137 16.1 6/0.04 12/5.11 3/8.45 21/9.77 16/12.05 7 0.5237 0.7513 -0.1188 15.7 9/0.05 8/7.84 2/11.92 4/15.70 6/15.88 8 0.5157 0.8459 -0.2195 15.6 10/0.08 7/7.84 5/12.49 6/12.90 21/13.24 9 0.4885 0.7295 0.2671 15.1 8/0.05 1/5.65 2/9.33 4/9.84 19/10.46 10 0.3461 0.9210 0.1369 15.1 5/0.02 11/6.66 19/6.75 13/7.86 2/14.05 11 0.3043 0.9934 0.0572 15.1 11/0.06 10/6.66 13/9.39 19/13.32 14/15.96 12 0.7292 0.7562 0.6071 14.6 14/0.04 6/5.11 3/10.55 16/12.25 21/13.53 13 0.4450 0.9718 0.0754 14.1 12/0.07 10/7.86 13/8.13 11/9.39 19/10.21 14 0.2864 1.0487 0.3857 13.9 13/0.03 16/7.61 20/11.44 21/11.79 17/13.10 15 0.2482 0.8088 0.4993 13.2 15/0.08 20/6.39 18/8.20 5/15.24 1/16.84 16 0.2879 1.1640 0.3735 12.7 17/0.12 14/7.61 3/11.21 6/12.05 12/12.25 17 0.5220 0.9647 0.4598 12.3 18/0.09 17/5.47 21/11.13 1/12.81 14/13.10 18 0.3159 0.7415 0.6111 11.8 19/0.05 15/8.20 5/10.99 20/14.00 16/16.02 19 0.4063 0.8608 0.2168 11.4 20/0.11 10/6.75 1/7.77 2/9.88 13/10.21 20 0.2474 0.8797 0.4065 11.2 16/0.04 15/6.39 14/11.44 19/13.81 18/14.00 21 0.6465 0.9446 0.6173 9.9 21/0.07 6/9.77 17/11.13 14/11.79 8/13.24 Best trace (cycle 4 with CC 7.05%) was saved as P42_visc-standard.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.3 - Setup, data input and phasing 2.0 - FFTs and peak-searches 3.4 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 125.9 - Tripeptide search 20.0 - Chain tracing 0.0 - NCS analysis 2.4 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:32:24 Total time: 154.06 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++