My usual targets are 0.010 for the bonds and 1.50 for the angles. Bernie Santarsiero
On Tue, September 11, 2007 3:22 pm, Lari Lehtio wrote: > Hello! > > Jaskolski & other experts say in "Stereochemical restraints revisited: how > accurate are > refinement targets and > how much should protein structures be allowed to deviate from them?" > (2007) Acta Cryst. > D63:611-620 > > that > > quote: "A correctly set balance will be reflected in root-mean-square > deviations from ideal > bond lengths in the > range 0.015-0.020 A for structures refined to R factors of 0.15-0.20." > > I would set the weigth manually. > > ~L~ > > _______________________________________ > > Lari Lehtiö > Structural Genomics Consortium > Medical Biochemistry & Biophysics Dept. > Karolinska Institute > Stockholm, Sweden > _______________________________________ > > ----- Original Message ----- > From: Mark Mayer <[EMAIL PROTECTED]> > Date: Tuesday, September 11, 2007 10:08 pm > Subject: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds > To: [email protected] > >> Hello all, >> >> I believer the suggested matrix weight for running refmac is >> 'auto'. I'm at the end of refinment for >> a data set that I've cut at 1.59 A, so maps are pretty. Here's the >> logfile with auto weighting ... >> >> NOTE bond rmsds !!!!!!! >> >> REMARK 3 R VALUE (WORKING SET) : .15481 >> REMARK 3 FREE R VALUE : .18739 >> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .033 ; >> .022 >> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ; 2.776 ; >> 1.990 >> Am I correct that at this resolution one should aim for bond rmsds >> of < 0.02. e.g for a weight of >> 1.0 the rmsd is 0.017, which seems more reasonable. >> >> REMARK 3 R VALUE (WORKING SET) : .16228 >> REMARK 3 FREE R VALUE : .19032 >> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .017 ; >> .022 >> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ; 1.689 ; >> 1.990 >> I know this has been discussed many times before, but expert >> opinion always appreciated. >> >> Thanks - Mark >> >
