++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2014/4 + + Copyright (c) George M. Sheldrick 2001-14 + + Started at 18:30:40 on 09 Feb 2015 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please cite: G.M. Sheldrick (2010), "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification", Acta Cryst. D66, 479-485 (Open Access) if SHELXE proves useful. Command line parameters: shelxe-input.pda -a15 -q -s0.231 -o -n -t4 -e1.0 -l5 -x Cell and symmetry from shelxe-input.pda Phases calculated using atoms from shelxe-input.pda Native data from shelxe-input.hkl Pruned PDB fragment output to shelxe-input.pdo Listing output to shelxe-input.lst Phases output to shelxe-input.phs Poly-Ala trace output to shelxe-input.pdb Summary of parameters to be employed: -a 15 global autotracing cycles -b 5.0 extra B for revised heavy atom sites -c 0.400 fraction of pixels in crossover region -d 0.000 high resolution limit to be applied to input data -e 1.000 high resolution limit for data extrapolation -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 -i unset no structure inversion -k 4.5 minimum height/sigma for revised heavy atom sites -l 5 space for 5000000 reflections -L 6 minimum number of residues per chain (if more than 3 chains) -m 20 cycles of density modification -G 0.700 FOM threshold for initial tripeptides and chain extension -n unset do not apply NCS in autotracing -o omit residues from fragment to optimize CC -q alpha-helix search -r 3.00 map resolution (multiplies maximum indices) -s 0.231 solvent fraction -t 4.00 time factor for peptide searches (increase if difficult) -u 500 MB allocatable memory for fragment optimization -U 0.00 abort if less than this % of fragment CA retained within 0.7A -v 0.000 density sharpening factor -w 0.200 weight for experimental phases after cycle 1 -x 2 read name.ent, generate phase and trace diagnostics -y 1.80 highest resolution in Ang. for starting phases from model -z unset do not optimize heavy atoms Space group: P 1 21 1 Allowed origin shift code: 2 22113 Reflections read from file shelxe-input.hkl 22113 Unique data, highest resolution = 0.809 Angstroms Anisotropic scaling: intensities multiplied by 0.000779h^2 +0.000045k^2 -0.000247l^2 +0.000000kl -0.000136hl +0.000000hk 765 Reflections with d > 1.009 and 66 in range 1.009 > d > 1.000 added 531 Atoms read from PDB format file shelxe-input.ent Fourier grid = 128 x 64 x 55 0.000 <= z <= 0.500 92 Point spherical net set up with radius 2.42A 72 Extra Fourier layers will be generated <|E^2-1|> = 0.739 116 Atoms read from PDB format file shelxe-input.pda 0 NCS groups defined in .pda input file 5 Residue blocks eliminated out of 17, increasing CC from 12.03 to 13.98% 12 residues written to shelxe-input.pdo Overall CC between native Eobs and Ecalc (from fragment) = 14.01% Statistics for fragment phases: 0.040 / 0.000 0.403 / 0.607 MPE 87.2 / 90.0 wMPE 86.4 / 86.7 Starting from fragment phases truncated to 1.800A 0.040 / 0.000 0.403 / 0.607 MPE 87.2 / 90.0 wMPE 86.4 / 86.7 = 0.045 for fragment phases 0.014 / 0.005 0.089 / 0.187 MPE 89.0 / 89.5 wMPE 87.0 / 84.1 = 0.089, Contrast = 0.152, Connect. = 0.717 for dens.mod. cycle 1 0.009 / 0.020 0.165 / 0.315 MPE 89.4 / 88.2 wMPE 88.4 / 86.1 = 0.165, Contrast = 0.155, Connect. = 0.686 for dens.mod. cycle 2 0.014 / 0.012 0.280 / 0.458 MPE 88.9 / 89.0 wMPE 88.5 / 87.3 = 0.280, Contrast = 0.112, Connect. = 0.640 for dens.mod. cycle 3 0.009 /-0.013 0.300 / 0.406 MPE 89.4 / 91.2 wMPE 88.9 / 88.5 = 0.300, Contrast = 0.082, Connect. = 0.564 for dens.mod. cycle 4 0.011 /-0.001 0.300 / 0.375 MPE 89.2 / 90.1 wMPE 88.8 / 88.9 = 0.300, Contrast = 0.092, Connect. = 0.570 for dens.mod. cycle 5 0.014 / 0.009 0.300 / 0.360 MPE 89.0 / 89.2 wMPE 88.8 / 89.0 = 0.300, Contrast = 0.103, Connect. = 0.587 for dens.mod. cycle 6 0.014 / 0.004 0.300 / 0.348 MPE 89.0 / 89.7 wMPE 88.8 / 89.1 = 0.300, Contrast = 0.112, Connect. = 0.600 for dens.mod. cycle 7 0.015 / 0.015 0.300 / 0.341 MPE 88.9 / 88.7 wMPE 88.8 / 89.3 = 0.300, Contrast = 0.118, Connect. = 0.610 for dens.mod. cycle 8 0.014 / 0.002 0.300 / 0.338 MPE 89.0 / 89.8 wMPE 88.8 / 89.5 = 0.300, Contrast = 0.124, Connect. = 0.616 for dens.mod. cycle 9 0.016 / 0.007 0.300 / 0.336 MPE 88.8 / 89.4 wMPE 88.7 / 89.5 = 0.300, Contrast = 0.128, Connect. = 0.622 for dens.mod. cycle 10 0.016 / 0.009 0.300 / 0.335 MPE 88.8 / 89.2 wMPE 88.7 / 89.4 = 0.300, Contrast = 0.132, Connect. = 0.627 for dens.mod. cycle 11 0.017 / 0.002 0.300 / 0.333 MPE 88.8 / 89.8 wMPE 88.7 / 89.3 = 0.300, Contrast = 0.135, Connect. = 0.631 for dens.mod. cycle 12 0.017 / 0.002 0.300 / 0.332 MPE 88.7 / 89.8 wMPE 88.6 / 89.2 = 0.300, Contrast = 0.137, Connect. = 0.634 for dens.mod. cycle 13 0.017 / 0.001 0.300 / 0.331 MPE 88.7 / 89.9 wMPE 88.6 / 89.1 = 0.300, Contrast = 0.139, Connect. = 0.637 for dens.mod. cycle 14 0.017 / 0.005 0.300 / 0.330 MPE 88.7 / 89.5 wMPE 88.6 / 88.9 = 0.300, Contrast = 0.141, Connect. = 0.640 for dens.mod. cycle 15 0.018 / 0.007 0.300 / 0.330 MPE 88.7 / 89.4 wMPE 88.6 / 88.7 = 0.300, Contrast = 0.142, Connect. = 0.642 for dens.mod. cycle 16 0.017 / 0.004 0.300 / 0.330 MPE 88.7 / 89.7 wMPE 88.6 / 88.5 = 0.300, Contrast = 0.144, Connect. = 0.643 for dens.mod. cycle 17 0.017 / 0.005 0.300 / 0.331 MPE 88.7 / 89.5 wMPE 88.6 / 88.5 = 0.300, Contrast = 0.145, Connect. = 0.645 for dens.mod. cycle 18 0.017 /-0.001 0.300 / 0.330 MPE 88.7 / 90.1 wMPE 88.6 / 88.6 = 0.300, Contrast = 0.146, Connect. = 0.647 for dens.mod. cycle 19 0.016 /-0.012 0.300 / 0.330 MPE 88.8 / 91.0 wMPE 88.6 / 88.6 = 0.300, Contrast = 0.148, Connect. = 0.648 for dens.mod. cycle 20 Shift from model in .ent: dx=-0.500 dy= 0.439 dz= 0.000 NOGO map generated for regions about rotation axes (if any) 433 peaks > 0.5 sigma used to seed fragment search 0 potential (overlapping) alpha-helix fragments found #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) 36 potential tripeptides employed #(CA) CFOM DenFit NH...O SecStr Rama98 Rama80 DenMin (?=rej.) 6 1.552 1.890 -0.688 0.499 1.000 0.400 CA 1.180 ? 0.00 0.00 0.00 0.00 0.00 8.00 0.00 0.00 0.00 92.000 15.244 2.275 6 1.502 1.308 -0.283 0.330 1.000 0.800 CA 0.862 ? 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.000 15.244 2.391 A: 6 2.866 1.233 0.398 0.553 1.000 0.600 C 0.706 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.000 15.244 2.419 Global chain diagnostics: 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.000 15.244 2.419 0.0% of CA within 1.0A, 0.0% within 0.5A and 14.6% incorrect CA 6 residues left after pruning, divided into chains as follows: A: 6 16.7% starting CA preserved within 1.0A, 8.3% / 0.7A and 8.3% / 0.5A CC for partial structure against native data = -0.12 % ** CC is less than zero - giving up ** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 18:40:10 Total time: 569.32 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++