[phenixbb] close contact and torsion angle

Edward A. Berry BerryE at upstate.edu
Fri Oct 12 06:54:31 PDT 2012

Nathaniel Echols wrote:
> On Thu, Oct 11, 2012 at 8:09 PM,<hchxia at ujs.edu.cn>  wrote:
>> There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what?  I added hydrogen for refinement since the resolution is 1.47 A.  Should I remove all these added hydrogens and refine again?
>> Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause?  And should I re-refine to correct them? Or just go ahead to deposit it?
> 2) Phenix is using very new Ramachandran distributions from the
> Richardson lab based on a larger set of reference structures, which
> changed the boundary between "allowed" and "outlier" slightly.  Right
> now it may still disagree with the Molprobity web server (hopefully
> this will change very soon); I have no idea what the PDB uses.

 From a recent PDB validation:
==> The following table contains a list of torsion angles outside the expected
     Ramachandran regions [GJ. Kleywegt and TA. Jones, PHI/PSI-chology:
     Ramachandran Revisited, Structure  1996, 4, 1395 - 1400].

       Residue  Chain  Sequence              PSI       PHI
         ASN      A       35             -101.76    -94.29
         LYS      A       45             -111.15     60.76
         LEU      B       12               84.56    -68.33
         ASN      B       35             -102.05    -94.34
         LYS      B       45             -127.20     70.13

Looking at Kleywegt's paper, their allowed region contains 98% of residues in hi-res structures.
So if your protein has, say 1000 residues, you would expect about 20 true "outliers".
At Chuan's resolution, if the region is well ordered, it should be very obvious whether
the geometry is right or wrong.

> Additionally, slight differences in the way values are stored and/or
> interpolated can determine whether a residue is flagged - this is why
> Phenix often disagrees with Coot on corner cases.  Regardless, I would
> trust the output of Phenix over most other sources, as it is based on
> the best statistics the Richardson lab has been able to obtain so far,
> sampled very finely.
> As always, if you are able to show us the model and data (OFF-LIST -
> just email Pavel and/or me), we may have a more detailed answer.
> -Nat
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