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Re: [ccp4bb] an over refined structure
 

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CCP4bb <-- 2008 <-- February 2008 <-- 04 February 2008
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Subject: Re: 3D Glasses - Vuzix HMD by eDimensional
From: "Pedro M {- dot -} Matias" matias {- at -} ITQB {- dot -} UNL {- dot -} PT
Date: 2008-02-04 		Next message:
Subject: Re: 3D Glasses - Vuzix HMD by eDimensional
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2008-02-04


Subject: Re: an over refined structure
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-02-04
Hi Boaz,

Thank you for your opinions. The resolution is 2.8A and I remembered some people may think the structure is over-refined when the difference between Rfree/Rwork is greater than 6.

What do you think the greatest acceptable difference between the two?

Best,

Sun

Boaz Shaanan wrote: Hi,

Why do you think this structure is over-refined ? The Rfree/Rwork difference of 6.2% seems fine, although you didn't mention resolution. If anything, an over-refined structure would show a smaller difference, as far as I know. If all the other criteria (Ramachandran outliers, etc., map) are OK you should just be happy with your structure.

Cheers,

Boaz

----- Original Message -----
From: Sun Tang
Date: Monday, February 4, 2008 18:41
Subject: [ccp4bb] an over refined structure
To: CCP4BB@JISCMAIL.AC.UK

> Hello All,
>
> I refined a structure with Refmac in CCP4i and the R/Rfree is
> 0.215/0.277. The difference between R and Rfree is too much even
> though I used 0.01 for weighting term in the refinement (the
> default value is 0.3). The RMSD for bond length and bond angle
> is 0.016 A and 1.7 degree.
>
> What may be wrong with the over-refined structure? What is the
> reason for leading to an over-refined structure? How to avoid it?
>
> Best wishes,
>
> Sun Tang
>
>
> ---------------------------------
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Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan

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