++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + 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 -i -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_i.lst Phases output to P42_visc-standard_i.phs Revised heavy atom sites output to P42_visc-standard_i.hat Revised heavy atom phases output to P42_visc-standard_i.pha Poly-Ala trace output to P42_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 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 ** Atom coordinates inverted ** 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 = 0.147, Contrast = 0.019, Connect. = 0.502 for dens.mod. cycle 1 = 0.169, Contrast = 0.082, Connect. = 0.574 for dens.mod. cycle 2 = 0.190, Contrast = 0.120, Connect. = 0.605 for dens.mod. cycle 3 = 0.205, Contrast = 0.126, Connect. = 0.601 for dens.mod. cycle 4 = 0.216, Contrast = 0.133, Connect. = 0.596 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 1796 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 144 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 7 3.629 1.528 0.396 0.348 0.667 0.333 CB 1.229 7 1.481 1.359 0.063 0.367 0.833 0.500 CB 0.579 ? B: 6 2.779 1.383 0.340 0.423 0.800 0.400 CB 0.908 C: 6 5.396 1.436 0.517 0.605 1.000 0.800 N 1.003 D: 6 3.275 1.308 0.229 0.493 1.000 1.000 CB 0.918 E: 7 2.801 1.266 0.117 0.357 0.833 0.500 N 1.132 F: 12 4.967 1.416 0.444 0.235 0.909 0.455 N 1.096 G: 6 2.426 1.192 0.596 0.487 0.600 0.600 N 0.963 H: 6 3.780 1.286 0.175 0.557 1.000 0.600 CB 1.058 I: 7 2.233 1.259 0.102 0.394 0.833 0.667 CB 0.882 7 1.965 1.046 0.250 0.526 0.667 0.500 O 0.897 ? 6 1.661 1.283 0.338 0.222 0.600 0.200 C 0.998 ? J: 10 4.669 1.193 0.709 0.265 1.000 0.444 O 0.998 6 1.708 1.308 0.593 0.225 0.800 0.200 CB 0.631 ? K: 8 2.273 1.137 0.116 0.356 1.000 0.571 C 0.792 56 residues left after pruning, divided into chains as follows: A: 7 B: 6 C: 6 D: 7 E: 8 F: 6 G: 10 H: 6 CC for partial structure against native data = 3.68 % ------------------------------------------------------------------------------ Global autotracing cycle 2 = 0.287, Contrast = 0.171, Connect. = 0.529 for dens.mod. cycle 1 = 0.287, Contrast = 0.174, Connect. = 0.487 for dens.mod. cycle 2 = 0.287, Contrast = 0.182, Connect. = 0.500 for dens.mod. cycle 3 = 0.287, Contrast = 0.186, Connect. = 0.511 for dens.mod. cycle 4 = 0.287, Contrast = 0.189, Connect. = 0.518 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 2201 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: 12 8.264 2.178 0.157 0.364 0.636 0.364 CB 1.798 B: 19 7.468 1.796 0.556 0.191 0.722 0.556 CB 1.262 C: 8 9.092 1.919 0.040 0.580 1.000 0.857 C 1.594 D: 8 8.124 1.864 0.461 0.575 0.857 0.857 CB 1.224 E: 16 6.629 1.837 0.005 0.328 0.800 0.333 CB 1.400 F: 13 7.281 2.011 0.181 0.194 0.833 0.500 CB 1.531 G: 6 7.822 2.030 0.307 0.684 0.800 0.800 O 1.392 H: 6 2.472 2.152 -0.267 0.100 0.800 0.600 CB 1.461 I: 10 3.153 1.155 0.285 0.324 0.889 0.222 CB 0.967 Using tripeptides from previous cycle as seeds 62 residues left after pruning, divided into chains as follows: A: 12 B: 6 C: 11 D: 8 E: 6 F: 13 G: 6 CC for partial structure against native data = 4.66 % ------------------------------------------------------------------------------ Global autotracing cycle 3 = 0.287, Contrast = 0.205, Connect. = 0.510 for dens.mod. cycle 1 = 0.287, Contrast = 0.210, Connect. = 0.498 for dens.mod. cycle 2 = 0.287, Contrast = 0.217, Connect. = 0.510 for dens.mod. cycle 3 = 0.287, Contrast = 0.220, Connect. = 0.520 for dens.mod. cycle 4 = 0.287, Contrast = 0.221, Connect. = 0.527 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 2162 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 156 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 10.322 2.461 0.099 0.248 0.643 0.357 CB 2.121 B: 13 10.271 2.424 0.332 0.191 0.667 0.417 CB 1.991 C: 11 7.448 1.996 0.012 0.431 0.800 0.700 CB 1.567 D: 12 10.987 2.011 0.200 0.401 0.909 0.545 CA 1.677 E: 12 5.558 1.864 0.314 0.340 0.636 0.364 CB 1.280 F: 14 12.013 2.394 0.257 0.185 0.769 0.385 CB 2.101 6 1.568 1.443 0.023 0.579 0.600 0.600 CB 0.734 ? G: 6 3.306 1.553 0.705 0.428 0.600 0.600 CB 1.003 Using tripeptides from previous cycle as seeds 63 residues left after pruning, divided into chains as follows: A: 8 B: 11 C: 11 D: 12 E: 7 F: 14 CC for partial structure against native data = 4.47 % ------------------------------------------------------------------------------ Global autotracing cycle 4 = 0.287, Contrast = 0.228, Connect. = 0.522 for dens.mod. cycle 1 = 0.287, Contrast = 0.232, Connect. = 0.505 for dens.mod. cycle 2 = 0.287, Contrast = 0.238, Connect. = 0.515 for dens.mod. cycle 3 = 0.287, Contrast = 0.239, Connect. = 0.524 for dens.mod. cycle 4 = 0.287, Contrast = 0.239, Connect. = 0.531 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 2162 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 163 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 15 8.412 2.393 0.287 0.184 0.571 0.357 CB 1.867 B: 14 8.437 2.305 0.030 0.330 0.615 0.538 CB 1.929 C: 11 9.228 2.232 0.099 0.365 0.800 0.400 CB 1.718 D: 14 12.470 2.419 -0.007 0.371 0.846 0.462 CB 1.953 E: 12 10.109 2.571 0.259 0.291 0.545 0.364 CB 2.184 F: 16 10.606 2.413 0.225 0.164 0.667 0.333 C 2.094 Using tripeptides from previous cycle as seeds 66 residues left after pruning, divided into chains as follows: A: 11 B: 9 C: 9 D: 14 E: 7 F: 16 CC for partial structure against native data = 4.94 % ------------------------------------------------------------------------------ Global autotracing cycle 5 = 0.287, Contrast = 0.244, Connect. = 0.524 for dens.mod. cycle 1 = 0.287, Contrast = 0.247, Connect. = 0.510 for dens.mod. cycle 2 = 0.287, Contrast = 0.252, Connect. = 0.520 for dens.mod. cycle 3 = 0.287, Contrast = 0.252, Connect. = 0.527 for dens.mod. cycle 4 = 0.287, Contrast = 0.252, Connect. = 0.535 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 2191 peaks > 0.5 sigma used to seed fragment search Space for about 203 unique residues taking solvent into account 170 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 A: 24 15.965 2.470 0.018 0.334 0.783 0.348 CB 2.029 B: 11 6.573 2.309 0.226 0.245 0.600 0.400 CB 1.642 C: 15 14.494 2.642 0.323 0.173 0.714 0.357 CA 2.305 D: 7 5.464 1.686 0.115 0.476 0.833 0.500 C 1.458 E: 7 7.259 2.089 0.622 0.245 0.667 0.333 C 1.760 F: 16 9.992 2.271 0.205 0.241 0.733 0.533 CB 1.736 11 residues pruned to eliminate duplicates G: 10 2.867 1.445 0.208 0.238 0.778 0.556 CB 0.954 Using tripeptides from previous cycle as seeds 67 residues left after pruning, divided into chains as follows: A: 24 B: 15 C: 6 D: 6 E: 16 CC for partial structure against native data = 3.75 % ------------------------------------------------------------------------------ Global autotracing cycle 6 Phases from autotracing cycle 4 used as input for final density modification = 0.287, Contrast = 0.239, Connect. = 0.526 for dens.mod. cycle 1 = 0.287, Contrast = 0.243, Connect. = 0.506 for dens.mod. cycle 2 = 0.287, Contrast = 0.249, Connect. = 0.517 for dens.mod. cycle 3 = 0.287, Contrast = 0.249, Connect. = 0.526 for dens.mod. cycle 4 = 0.287, Contrast = 0.248, Connect. = 0.531 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 0.284 0.276 0.232 0.264 0.260 0.255 0.299 0.286 0.232 0.211 0.384 0.373 0.296 0.341 0.347 0.369 0.440 0.455 0.368 0.343 N 2226 2222 2249 2276 2140 2249 2426 2133 2190 2095 Estimated mean FOM = 0.260 Pseudo-free CC = 30.74 % Anomalous density (in sigma units) at initial heavy atom sites Site x y z occ*Z density 1 0.5279 0.1979 0.6740 16.0000 38.19 2 0.4699 0.1867 0.8823 13.6432 31.25 3 0.4031 0.2616 0.5169 9.8192 19.86 4 0.5309 0.4185 0.7198 7.9280 17.99 5 0.6540 0.0787 0.8631 7.4288 16.54 6 0.3368 0.2034 0.3857 7.1024 16.92 7 0.5263 0.2314 0.4544 7.0400 16.53 8 0.5120 0.2709 0.7333 6.8432 15.91 9 0.4768 0.2488 1.1180 6.7904 16.22 10 0.4837 0.1550 1.2198 6.4928 16.65 11 0.6956 0.0060 0.9439 6.4752 14.26 12 0.5539 0.0281 0.9246 6.4400 14.94 13 0.7133 -0.0490 0.6143 6.3184 13.97 14 0.2709 0.2434 0.3935 6.2576 14.48 15 0.7511 0.1913 0.4995 6.1936 13.54 16 0.7527 0.1200 0.5941 5.5040 12.24 17 0.7123 -0.1656 0.6278 5.2640 13.36 18 0.4782 0.0365 0.5394 5.1344 12.80 19 0.6839 0.2592 0.3884 5.0608 12.01 20 0.5922 0.1387 0.7836 4.9392 11.38 21 0.3538 0.0544 0.3830 4.6832 9.83 Site x y z h(sig) near old near new 1 0.5279 0.1980 0.6739 38.2 1/0.01 10/5.67 20/7.80 2/10.55 8/10.58 2 0.4700 0.1865 0.8819 31.3 2/0.02 10/9.34 20/9.91 1/10.55 9/11.85 3 0.4032 0.2622 0.5161 19.9 3/0.06 5/8.46 8/8.81 13/10.55 16/11.21 4 0.5307 0.4185 0.7195 18.0 4/0.02 10/9.79 4/11.45 1/14.66 9/15.76 5 0.3371 0.2031 0.3860 16.9 6/0.03 13/5.13 3/8.46 21/9.79 16/12.08 6 0.4844 0.1547 1.2190 16.7 10/0.06 9/7.81 8/12.50 5/12.88 21/13.27 7 0.6541 0.0783 0.8633 16.6 5/0.03 12/6.61 20/6.74 11/7.85 2/14.06 8 0.5260 0.2316 0.4544 16.5 7/0.02 3/8.81 1/10.58 19/10.95 6/12.50 9 0.4763 0.2484 1.1178 16.2 9/0.04 6/7.81 2/11.85 4/15.76 5/15.89 10 0.5117 0.2711 0.7337 15.8 8/0.03 1/5.67 2/9.34 4/9.79 20/10.51 11 0.5550 0.0281 0.9247 15.0 12/0.07 7/7.85 12/9.37 20/10.21 2/11.99 12 0.6952 0.0063 0.9426 14.6 11/0.07 7/6.61 11/9.37 20/13.28 14/15.90 13 0.2707 0.2440 0.3925 14.5 14/0.06 5/5.13 3/10.55 16/12.28 21/13.56 14 0.7126 -0.0485 0.6150 14.0 13/0.07 16/7.65 18/11.37 21/11.82 17/13.06 15 0.7518 0.1926 0.5008 13.7 15/0.11 18/6.54 19/8.20 8/15.22 1/16.84 16 0.7119 -0.1647 0.6270 13.4 17/0.08 14/7.65 3/11.21 5/12.08 13/12.28 17 0.4785 0.0362 0.5408 12.8 18/0.07 17/5.54 21/11.20 1/12.77 14/13.06 18 0.7534 0.1189 0.5939 12.3 16/0.08 15/6.54 14/11.37 20/13.82 19/14.13 19 0.6834 0.2592 0.3889 12.2 19/0.04 15/8.20 8/10.95 18/14.13 16/16.00 20 0.5945 0.1391 0.7836 11.6 20/0.15 7/6.74 1/7.80 2/9.91 11/10.21 21 0.3533 0.0551 0.3819 9.9 21/0.08 5/9.79 17/11.20 14/11.82 6/13.27 Best trace (cycle 4 with CC 4.94%) was saved as P42_visc-standard_i.pdb ============================================================================== CPU times required in seconds ----------------------------- 0.2 - Setup, data input and phasing 1.9 - FFTs and peak-searches 3.4 - Sphere of influence 0.1 - Rest of density modification 0.0 - Alpha-helix search 125.0 - Tripeptide search 26.6 - Chain tracing 0.0 - NCS analysis 3.1 - B-value refinement for trace 0.1 - Rest of tracing 0.0 - Comparison with known structure ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 12:32:31 Total time: 160.44 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++