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Andrew The ratio Rfree/R = 24/20.5 = 1.17 is indeed a little on the low side compared with values found for typical structures refined at 2.4 Ang. However there may be some feature of the structure (a high solvent content in particular) which would lead one to expect a somewhat lower ratio than average. A high solvent content of course increases the volume of the unit cell and thus the number of diffraction observations without increasing the number of variable parameters, and this in turn increases the observation/parameter ratio upon which the expected value of the Rfree/R ratio (i.e. expected assuming only random experimental errors are present) mainly depends. Without knowing more details of this particular case it's obviously impossible to say, and as you point out our calculations described in the Acta D series of papers were done assuming a LS target, whereas the Adams et al paper in PNAS makes a cogent argument that the Rfree/R ratio for an ML target would be expected to be even lower (how much lower they don't say of course). -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Andrew Torelli > Sent: Thursday, September 28, 2006 9:41 PM > To: [email protected] > Subject: [ccp4bb]: Rfree and R value differences in maximum > likelihood refinement > > Professor Dodson (and the ccp4 community), > > I apologize for dragging up old messages, but I'm > interested in a response you gave to a previous post and I > needed time to research it myself. On September 11th, in the > "question about refinement" thread, you commented that Rfree > and R values of 24% and 20.5%, respectively for a 2.4angstrom > structure are "unreasonably close". > > I understand that there are theoretical values for the > Rfree/Rfactor ratio that are expected for refined structures > (at a given resolution) using a least-squares target (thanks > to Jack Tanner's July 5th post with references from Ian > Tickle's group). However, for maximum likelihood (which I > assume was being used to refine the structure in question), I > would expect the difference between the Rfree and Rfactor to > be the same or smaller compared to a least-squares > refinement. I reference: > Adams P.D., Pannu N.S., Read R.J. & Brunger A.T. (1997) > Cross-validated maximum likelihood enhances crystallographic > simulated annealing refinement. Proc Natl Acad Sci U S A, 94, 5018. > > Assuming a properly chosen test set (i.e. sufficient > size, NCS is accounted for properly, etc.), what > considerations lead you to expect (and desire)a much larger > difference in the Rfree/Rfactor values? Under what > circumstances should one interpret large differences as > overfitting? I look forward to learning more about useful > studies, criteria and guidelines you and other members of the > ccp4bb community rely upon during (maximum likelihood) refinement. > > Thank you in advance for your time, > Best Regards, > -Andy Torelli > > Andrew Torelli, M.S. > Ph.D. Candidate, Dept. of Biochemistry & Biophysics > University of Rochester School of Medicine & Dentistry > Box 712, 601 Elmwood Ave, Rochester, NY 14642 > 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.
