[phenixbb] number of cycles

[Pavel Afonine]

  Hi Maia,

see page 78 and 130 here:
http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf

Essentially, this is the list flipped residues.

**PLEASE CHECK MANUALLY**  means that none of flip possibilities 
resolves the steric clashes, so it is recommended to check this manually.

Jeff Headd who implemented this in phenix.refine may be able to comment 
some more.

Pavel.

On 3/1/11 5:45 PM, Maia Cherney 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