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Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?
 

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CCP4bb <-- 2007 <-- April 2007 <-- 04 April 2007
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Subject: Re: Summary - Valid to stop Refmac after TLS refinement?
From: "NM Burton, Biochemistry" Nick {- dot -} Burton {- at -} BRISTOL {- dot -} AC {- dot -} UK
Date: 2007-04-04
Hello,

Thanks very much to all who replied with thoughts and suggestions.

The consensus was that my interpretation was not correct, and it is not
valid to stop Refmac after TLS refinement. People also felt that the RMSD
bond/angle of 0.016/1.6 was still a little high. Phenix.refine was
suggested as a complete solution, with SA and TLS in the same package.

All the best,

Nick

--On 28 March 2007 16:34 +0100 "NM Burton, Biochemistry"
wrote:

> Hello,
>
> I've refined a structure with CNS to Rwork/free=0.226/0.273. I switched
> to Refmac5.2 to take advantage of TLS refinement and set up a run with 10
> cycles of TLS refinement (groups as suggested by the TLSMD server)
> followed by 10 cycles of restrained co-ordinate refinement. After the
> TLS cycles the model was improved (Rwork/free=0.222/0.241), however
> during co-ordinate refinement Rfree refined up (final
> Rwork/free=0.197/0.264). My understanding would be that the TLS
> refinement is modelling the ADPs most accurately, but that Refmac's
> co-ordinate refinement is over-fitting slightly. Would this seem
> correct? And if so, is it valid to run Refmac with no cycles of
> co-ordinate refinement and take the resulting model as the final
> structure?
>
> Thanks very much,
>
> Nick
>
> ----------------------
> NM Burton, Biochemistry
> Nick.Burton@bristol.ac.uk



----------------------
NM Burton, Biochemistry
Nick.Burton@bristol.ac.uk
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