Re: [ccp4bb] high z-scores, negative LLG in Phaser

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: I compressed my images by ~ a factor of two, and they load and process in mosflm faster
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-09-17

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Subject: Re: I compressed my images by ~ a factor of two, and they load and process in mosflm faster
From: "Waterman, David (DLSLtd,RAL,DIA)" david {- dot -} waterman {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2009-09-18

Subject: Re: high z-scores, negative LLG in Phaser
From: Randy Read rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2009-09-18

Dear Sean,

What a negative LLG combined with a large Z-score usually means is
that the answer is correct, but that the model doesn't predict the
data as well as expected. One possible reason is that you told Phaser
that the model is better than it really is (e.g. provided identity
values higher than they really are -- for instance, it's a common
mistake to assign the sequence identity to 1 for a homology model,
when it should be set to the sequence identity with the template used
to build the model -- alternatively, the RMS error of the model is
higher than one would expect from the sequence identity, perhaps
because of domain movements). Another possibility is that you told
Phaser the model is more complete than it really is -- the defined
COMPOSITION has to describe what is in the asymmetric unit of the
crystal, not what is in the model (another common mistake!).
Something else that could play a role is that, under some
circumstances, Phaser overestimates the accuracy of the structure
factors derived from an ensemble; you could try scoring the individual
models, and you should make sure that the individual structures in the
ensemble are really well superimposed.

If none of this explains your LLG values, then you could send me the
logfile (preferably offline to avoid filling up too many mailboxes)
and I could see if there's anything obvious in the output.

Best wishes,

Randy Read

On 17 Sep 2009, at 19:06, Sean Gay wrote:

> I have a 2.0A data set that I solved using an ensemble of 5 related
> structures in Phaser. My Z-scores for the solution are fantastic
> (RFZ= 28.7, TFZ=24.6), but my LLG is very negative (-698.2). The LLG
> increases by almost 800 (started at -1488.6) during the course of
> the run. The density for the solution is great and the solution
> model fits it very well. I'm wondering why the Z-scores and LLG
> contradict each other. Should I be happy with the large increase in
> LLG or should I be concerned about the final value still being
> negative?
>
> Sean C. Gay, PhD
> Postdoctoral Scholar
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> University of California, San Diego
> 9500 Gilman Dr.
> La Jolla, CA 92093

------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: rjr27@cam.ac.uk
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999