[phenixbb] High B-factors after Phenix restrained refinement

Dialing Pretty hdc123hdc123 at yahoo.com
Fri Dec 16 00:04:19 PST 2011

Hi Nat,

I have a protein-peptide complex crystal, and I got the 3-D structure of the protein part in the complex by rigid body refinement with isomophous crystal crystal structure as the search model, and I got the peptide structure by Coot peptide building, then I refine the whole protein-peptide complex.

Will you please tell me which Phenix program can be used to build the peptide as I mentioned in the situation above? I want to get  a Coot alternative for the peptide building.

I am looking forward to getting your reply.



 From: Nathaniel Echols <nechols at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org> 
Sent: Friday, 16 December 2011 3:31 PM
Subject: Re: [phenixbb] High B-factors after Phenix restrained refinement
On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca> wrote:
> I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of
> rigidbody refinement with Phenix Refine I proceeded to restrained
> refinement. The R/Rfree from the refinement decreased nicely as expected but
> the B average is at ~100 (using Group B factor refinement option). I took
> the same model and mtz through Refmac and the B average is about ~40. Has
> anyone experienced this before? I am almost positive it maybe a setting
> issue in Phenix Refine that i should be looking at to get the B factors to
> refine correctly.

How are you calculating the average B?  Refmac prints "residual"
B-factors in the B column of ATOM records - these do not include the
contribution from TLS and Ucryst (an overall B-factor for the entire
crystal).  In Phenix, the ATOM records always have the total isotropic
B-factor, and this will always be higher than the equivalent in
Refmac.  So it's quite likely that both programs are correct, they're
just reporting very different things.  (And for what it's worth, a
mean B-factor of 100 is totally normal at 3.3A resolution.)

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