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Dear Gerard,
I use one monomer (6 monomers per asu) to run whatcheck again, and got a report:
Structure Z-scores, positive is better than average:
2nd generation packing quality : -0.126
Ramachandran plot appearance : 0.197
chi-1/chi-2 rotamer normality : 2.482
Backbone conformation : -7.432 (bad)
RMS Z-scores, should be close to 1.0:
Bond lengths : 0.424 (tight)
Bond angles : 0.548 (tight)
Omega angle restraints : 0.895
Side chain planarity : 0.333 (tight)
Improper dihedral distribution : 0.530
B-factor distribution : 0.364
Inside/Outside distribution : 0.957
In your mail:
>From: Gerard DVD Kleywegt <[EMAIL PROTECTED]>
>Reply-To:
>To: ZhiYi Wei <[EMAIL PROTECTED]>
>Subject: Re: [ccp4bb]: whatcheck report an error
>Date:Mon, 5 Dec 2005 15:50:27 +0100 (CET)
>
>
> mmmm, sounds strange - an all-helical protein should have a very common
> backbone structure. the only time i've ever had a low score myself was with a
> protein that had an unusually high loop content. however, if rfree and
> ramachandran are reasonable it would seem unlikely that the model is
> particularly poor (unless it is one small protein in a humongous complex)
>
> at the bottom of the whatif/whatcheck output there is a final summary
> ('Summary report for users of a structure') - what are the values of the
> other
> 'Structure Z-scores' listed there (packing quality, ramachandran, rotamer
> normality) ?
>
> --dvd
>
> ******************************************************************
> Gerard J. Kleywegt
> [Research Fellow of the Royal Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology University of Uppsala
> Biomedical Centre Box 596
> SE-751 24 Uppsala SWEDEN
>
> http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
>
------------------------------
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
