Re: [ccp4bb] How to reduce free-R factor

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: How to reduce free-R factor
From: Pankaj Chauhan pankajimtech {- at -} GMAIL {- dot -} COM
Date: 2009-12-03

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From: Ming Zhou ming_zhou30 {- at -} HOTMAIL {- dot -} COM
Date: 2009-12-04

Subject: Re: How to reduce free-R factor
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-12-04

Hi Pankaj,

if you are refining in phenix.refine:

- is automatic ordered solvent (water) update is turned on;
- you can try weight optimization: "optimize_wxc=true optimize_wxu=true";
- is NCS available. Use it if so.

In fact, the Rworks seems fine, but the gap Rfree-Rwork seems large.

Insignificant remark: TLS is a more adequate model for ADPs, and not the
tool to reduce R-factors.

Good luck!
Pavel.

On 12/3/09 9:07 PM, Pankaj Chauhan wrote:
> Hi all,
>
> In one of my 2.52 A structure, which is dimeric, the R-factor is 21.4
> and free-R is 29.3. I have tried all ways to reduce the free-R
> including TLS (even by defining the number of TLS group per chain),
> but still factors are not getting reduced. Even i have tried some
> other space group, but no use. Even i have the same structure with
> some complex at 1.86 A in the same space group , but everything is
> fine in that.
> Any suggestion,
> Regards,
>
>
> --
> Pankaj Chauhan
> Senior Research Fellow, Graduate student
> Crystallography Laboratory
> Division of Protein Science & Engg.
> IMTECH , Chandigarh, INDIA

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: How to reduce free-R factor
From: Pankaj Chauhan pankajimtech {- at -} GMAIL {- dot -} COM
Date: 2009-12-03

Next message:
Subject: PLEASE I NEED YOUR HELP.
From: Ming Zhou ming_zhou30 {- at -} HOTMAIL {- dot -} COM
Date: 2009-12-04