[phenixbb] B-factors for some sidechains were not refined well

Pavel Afonine pafonine at lbl.gov
Sun Jun 8 20:58:33 PDT 2014


Hi Tongqing,

can be a number of reasons, including:

- refinement did not converge (need to run more macro-cycles);
- choice of TLS groups is not optimal;
- side-chains are partially occupied (need to use partial occupancy or 
model multiple occupancies);
- see recent discussion on ccp4b about disulfides showing lots of 
residual density.

To tell more I will need to see data and model, focusing on 
residues/ligands in question.

Pavel

On 6/8/14, 5:32 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:
>
> Dear colleagues,
>
> I am refining one structure at 1.94 A with phenix.refine with 
> individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 
> 19.8%. But when inspecting the maps, I noticed that the sidechain tip 
> of some residues showed positive density and the b-factor for those 
> atoms were very high while those for the other atoms of the same 
> residues were normal; The b-factors for newly added ligands were also 
> not refined well showing high b-value and positive density at the same 
> time; the disulfide bonds also show positive density and high B. The 
> occupancy were all set to 1.
>
> Please give suggestions. Thanks!
>
> Best regards,
>
> **
>
> *Tongqing*
>
> **
>
> *Tongqing Zhou, Ph.D.*
>
> Staff Scientist
>
> Structural Biology Section
>
> Vaccine Research Center, NIAID/NIH
>
> Building 40, Room 4609B
>
> 40 Convent Drive, MSC3027
>
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>
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>
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>
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>
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