I wasn't suggesting the space group was wrong - just a lower symmetry equivalent of the true SG. e.g. all structures can be solved in P1 but several of the molecules in the cell will be related by crystal symmetry operators. The same is true for the associated P1 intensities. So IF you had assigned FreeR flags as for P1 it is more than likely that say h k l and -h k -l will have different FreeR status..

And then the FreeR is not really free and it is very likely they will refine to much the same value. 

However if you had been careful to assign the FreeRs to the highest possible Laue symmetry then expand them to cover P1 you usually find that the freeR and R differ as expected


On 1 July 2015 at 12:33, <[log in to unmask]> wrote:

Dear Boaz,

 

One can equally well describe a R32 crystal with one molecule in the asymmetric unit as P1 and 6 molecules in the asymmetric unit. In this case, the NCS in P1 is identical to the crystallographic symmetry in R32.

 

Best,

Herman

 

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Boaz Shaanan
Gesendet: Mittwoch, 1. Juli 2015 12:10
An: [log in to unmask]
Betreff: Re: [ccp4bb] Rfree below Rwork

 

Just wondering about Eleanor's interesting remark: would the Rf & Rw go as low as reported by Wolfram (0.22) in case of a wrong space group?

 

 Boaz

 

 

Boaz Shaanan, Ph.D.                                        
Dept. of Life Sciences                                     
Ben-Gurion University of the Negev                         
Beer-Sheva 84105                                           
Israel                                                     
                                                           
E-mail: [log in to unmask]
Phone: 972-8-647-2220  Skype: boaz.shaanan                 
Fax:   972-8-647-2992 or 972-8-646-1710    

 

 

                

From: CCP4 bulletin board [[log in to unmask]] on behalf of Eleanor Dodson [[log in to unmask]]
Sent: Tuesday, June 30, 2015 8:55 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Rfree below Rwork

I suppose if I was the referee for this structure and your FreeR is so close to the Rfactor I would ask you to ensure you had the right space group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3 fold..

Cases occur where R32 is indexed as C2.. 

 

Certainly if the Rfree set is assigned randomly to reflections which are symmetry equivalents then you see this phenomena of Rfree = Rfactor

 

Eleanor

 

On 30 June 2015 at 18:26, Gerard Bricogne <[log in to unmask]> wrote:

Dear Wolfram,

     I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a "problem". People
have agonised to extreme degrees over the "difficulty" of choosing a
free set of reflections that would produce the expected gap between
Rwork and Rfree, and some of the conclusions were that you would need
to hide almost half of your data in some cases!

     I think it is best to remember that the idea of cross-validation
by Rfree is to prevent overfitting, i.e. ending up with a model that
fits the amplitudes too well compared to how well it determines the
phases. In the case of high-order NCS (in your case, the U/V ratio
that the old papers on NCS identified as the key quantity to measure
the phasing power of NCS would be less than 0.1!) the phases and the
amplitudes are so tightly coupled that it is simply impossible to fit
the amplitudes without delivering phases of an equally good quality.
In other words there is no overfitting problem (provided you do have
good and complete data) and the difference between Rfree and Rwork is
simply within the bounds of the statistical spread of Rfree depending
on the free set chosen.

     You are lucky to have 6-fold NCS, so don't let any reviewer
convince you that it is a curse, and make you suffer for it :-) .


     With best wishes,

          Gerard.

--

On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote:
> Hello,
> my question concerns refinement of a structure with 6-fold NCS (local
> automatic restraints in REFMAC) against 2.8 A data. The size of my free set
> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
> 4.3 % of reflections.
> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at
> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes,
> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
> I understand that NCS stresses the independence assumption of the free set.
> Am I correct in believing that Rfree *may* be smaller than Rcryst even in
> the absence of a major mistake? My hope is that the combined wisdom of
> ccp4bb followers can point out my possible mistake,  suggest tests that I
> may perform to avoid them and, possibly, arguments in defense of a
> crystallographic model with Rfree < Rcryst.
> Many thanks,
> Wolfram Tempel

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