Just to add to the outliers in Refmac - careful when some of your atoms
have zero
occupancy. The bond restraints are not applied any more to these atoms
(my feeling) and
CERTAINLY are NOT CHECKED FOR OUTLIERS by Refmac at the end of the
refinement.
Jan Dohnalek
Eleanor Dodson wrote:
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
