You should not worry. A Ramchandran outlier does not mean a residue must never be in such a configuration, but that it is energetically unfavourable. Since you describe that the chemical environment supports the respective conformation it tells you that these residues have a different net energy (different from what one might expect from an "undisturbed" residue).
This applies for your 12-14 outliers, too: when their conformation energetically makes sense, do not worry. (Somebody firmer in statistics might be able to tell you how many "outliers" you SHOULD expect, and I suppose with as many as 1200 residues you are not only chemically safe (for the above reasons), but also statistically on "the safe side". I would say that 2.1A is good enough to believe in your observations. Tim On Fri, Apr 30, 2010 at 08:27:27AM -0700, xaravich ivan wrote: > Hi everyone, > I have a few residues sharing hydrogen bonding and salt bridges and they > tend to be fitting the density perfectly, but are Ramchandran outliers, > irrespective of the cycles of refinement. > It seems to me that it might be expected as these residues have some kind of > strained geometry because of the H-bond/ salt bridges. > > Am I correct or should I worry. > > Also I have around 1200 residues in my structure and there are about 12-14 > outliers (including those mentioned above) which would not buzz from their > spot. > Should I really worry to get the number of ouliers much below 1% to get the > reviewers nod. What is a good acceptable percentage of outliers in a > structure that is otherwise reasonable? > The Rfactor/Rfree is 23/29 at 2.1 Angs resolution. > > Thanks, > Ivan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
signature.asc
Description: Digital signature
