Also, don't get too hung up on your R/Rfree values, not all datasets are equally good and for some Rs just stay higher, even when you've done all you can in building and adjustment (map quality is influenced a lot by the model phases at 3.2Å).
Refining a 3.2Å structure is difficult and needs a lot of effort, so also consider trying to get better crystals/data.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 11 Jul 2015, at 12:39, Antonio Ariza wrote:
> Hi Sudipta,
>
> Your R factors don't look horribly high for an initial build and refinement at 3.2A, assuming you still need to substantially improve your structure ... if your structure is basically complete that's obviously a different matter. First of all I would look at your scaling output to check for twinning (aimless and pointless give very good indications) ... or simply re-run your last refmac job with twin refinement "on" and check the log file to see if the programme finds any twinning.
>
> Regards,
>
> Tony
>
> ------------------------------------------------------
>
> Dr. Antonio Ariza
> University of Oxford
> Sir William Dunn School of Pathology
> South Parks Road
> Oxford
> OX1 3RE
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Sudipta Bhattacharyya [[log in to unmask]]
> Sent: 10 July 2015 19:59
> To: [log in to unmask]
> Subject: [ccp4bb] refmac5/phenix refinement strategies with 3.2A data with pseudotranslation.
>
> Dear All,
>
> I am struggling with a 3.2A structure refinement which also suffers from translational NCS issue. Although the maps look very good but R/Rfree is not going down as expected. Could someone please suggest me tricks/tips with Refmac5/Phenix refinement optimization in this regard. The model has 4 molecules/ASU, space group initially appeared P212121 but later was found to be P21212; current R/Rfree is 33/36. Please let me know if you need any further details. Any suggestion/help will be really appreciated.
>
> My best regards,
> Sudipta.
>
>
>
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