[phenixbb] number of cycles

Jeff Headd jjheadd at lbl.gov
Tue Mar 1 18:35:42 PST 2011

Hi Maia,

Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle
and determines which orientation is likely correct given the local
environment of the sidechain. The best orientation will have no steric
clashes and satisfy local H-bond donors/acceptors. In cases where
there are other model errors in the region of the sidechain and both
orientations clash significantly, you'll see the **PLEASE CHECK
MANUALLY** warning which indicates that there are likely multiple
misfit sidechains that need to be corrected, and refinement alone is
not powerful enough to escape the false minimum.

If you want to turn this feature off, you can add main.nqh_flips=False
to your refinement call or

main {

to your param file. However, we highly recommend leaving this option
on as it is an excellent diagnostic of model errors.

If you have any further questions please let me know.


On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney <chern at ualberta.ca> wrote:
> Hi,
> I am using now the latest phenix version and I am curious how to understand
> these lines:
> Flipped N/Q/H residues before refinement:
> A  28 HIS
> A  72 HIS
> A 141 GLN
> A 202 GLN
> A 296 ASN
> ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
> ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
> A 353 ASN
> A 388 HIS
> Maia
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