Hi Sun Tang Unfortunately there's no such thing as a fixed value for the maximum acceptable Rfree-Rwork difference that applies in all circumstances, because the 'normal' difference depends on a number of factors, mainly the observation/parameter ratio, which depends in turn on the resolution and the solvent content (a greater solvent content means a bigger cell volume which means more reflections for a given number of ordered atoms in the a.u. and hence a bigger obs/param ratio). The Rfree-Rwork difference also depends on Rwork itself (i.e. you tend to get higher values of Rfree-Rwork for higher values of Rwork), so it's better to think in terms of the Rfree/Rwork ratio (which is independent of Rwork).
So for example at very high resolution a 'normal' value for Rfree-Rwork might be only 0.02 (so 0.05 which is what many people consider acceptable would actually be unacceptably high), whereas at low resolution it might be 0.1 (so 0.05 would be unacceptably low). Also you need to bear in mind that Rfree tends to have a quite high uncertainty, particularly at low resolution (because it's usually based on a relatively small number of observations), so the deviation has to be quite big (e.g. > 3 SU) before it can be considered to be statistically significant. So Rfree needs to be compared not with Rwork at all but with the value of the optimal Rfree/Rwork expected on the basis that the model parameterisation and weighting of X-ray terms and restraints are optimal and the errors in the model have the same effect as the random experimental errors in the data (i.e. a statistical 'null hypothesis'). As Tim just pointed out we tried to do this in our Acta D (1998) papers: there you can compare your observed Rfree/Rwork ratio either with the theoretical value or with the value found for 'typical' structures in the PDB at the same resolution. An abnormal Rfree/Rwork ratio could arise from a number of causes, not just over-fitting (I assume that's what you mean by 'over-refinement' - it's not clear to me how a structure can be 'over-refined' since a fundamental requirement of the maximum likelihood method is that the structure is always refined to convergence, and refining beyond that will by definition produce no further statistically significant changes in the parameters). For example the number of parameters being refined may be either too low, or too high (over-fitting), or the values of the weighting parameters may not be appropriate, or there may be something badly wrong with the atomic model (e.g. mistraced chain). Given the values you are reporting I think the latter is very unlikely, possibly you just need to tweak the X-ray and/or restraint weights. HTH Cheers -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Sun Tang > Sent: 04 February 2008 16:56 > To: Boaz Shaanan > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] an over refined structure > > Hi Boaz, > > Thank you for your opinions. The resolution is 2.8A and I > remembered some people may think the structure is > over-refined when the difference between Rfree/Rwork is > greater than 6. > > What do you think the greatest acceptable difference between the two? > > Best, > > Sun > > Boaz Shaanan <[EMAIL PROTECTED]> wrote: > > Hi, > > Why do you think this structure is over-refined ? The > Rfree/Rwork difference of 6.2% seems fine, although you > didn't mention resolution. If anything, an over-refined > structure would show a smaller difference, as far as I know. > If all the other criteria (Ramachandran outliers, etc., map) > are OK you should just be happy with your structure. > > Cheers, > > Boaz > > ----- Original Message ----- > From: Sun Tang <[EMAIL PROTECTED]> > Date: Monday, February 4, 2008 18:41 > Subject: [ccp4bb] an over refined structure > To: CCP4BB@JISCMAIL.AC.UK > > > Hello All, > > > > I refined a structure with Refmac in CCP4i and the R/Rfree is > > 0.215/0.277. The difference between R and Rfree is > too much even > > though I used 0.01 for weighting term in the refinement (the > > default value is 0.3). The RMSD for bond length and > bond angle > > is 0.016 A and 1.7 degree. > > > > What may be wrong with the over-refined structure? > What is the > > reason for leading to an over-refined structure? How > to avoid it? > > > > Best wishes, > > > > Sun Tang > > > > > > --------------------------------- > > Be a better friend, newshound, and know-it-all with Yahoo! > > Mobile. Try it now. > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > Phone: 972-8-647-2220 ; Fax: 646-1710 > Skype: boaz.shaanan > > ââ'¬Å½ > > > ________________________________ > > Never miss a thing. Make Yahoo your homepage. > <http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
