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Dear Robbie, Thank you for your suggestions. The structure is an all alpha-helix structure. I checked an older version with low z-score also but a little better: -5.8. This older structure has R and R-free of 0.28 and 0.31 respectively and the final structure has R and R-free of 0.17 and 0.20 respectively. I think the structure is refined well because procheck give a reasonable G factor of 0.2 and ramachadran plot is ok (99.9% residues in core and additional allowed regions). In your mail: >From: "R.P. Joosten" <[EMAIL PROTECTED]> >Reply-To: >To: ZhiYi Wei <[EMAIL PROTECTED]> >Subject: Re: [ccp4bb]: whatcheck report an error >Date:Mon, 05 Dec 2005 09:48:49 +0100 > >Dear ZhiYi, > > The backbone conformation check is a reasonably good quality indicator. > We see that it has improved over time. I.e. newer structures have on > average a better backbone quality. We have recently seen that rerefining > old structures (decreasing both R and R-free) from the PDB can also give > a better backbone score. > I do not know what kind of structure you are working on, nor do I know > what you R and R-free stats are. If they indicate overrefinement, you > may want to take a few steps back in your refinement process. Check a > few older versions of you structure to see the evolution of the backbone > score. > > Best wishes, > Robbie Joosten > CMBI, Nijmegen > The Netherlands > > > ZhiYi Wei wrote: > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Hi, all > > > > I met a problem during check my structure (160aa, 1.5A resolution) by whatcheck, > > which gave out an error: > > > > # 73 # Error: Backbone conformation Z-score very low > > A comparison of the backbone conformation with database proteins > > shows that the backbone fold in this structure is very unusual. > > > > Backbone conformation Z-score : -6.877 > > > > I wondered if it should be worried about. > > > > Any suggestion? > > > > Thank you in advance. > > > > I am sorry if you received this mail twice. > > > ------------------------------ Zhiyi Wei --------------------------------------------- Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing, P.R.China, 100101 --------------------------------------------- School of Life Sciences, University of Science & Technology of China, Hefei, Anhui, P.R.China, 230026 Tel:86-551-3607334 Fax:86-551-3607154
