No comment on the Auto debate, but the RMSD of bonds is a crude measure
unless you check the outliers..
You can make REFMAC list these - I think it should do so by default
actually..
Bad metal distances for instance can distort the number enormously.
Eleanor
Mark Mayer wrote:
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
