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 >
