Can we have a moratorium on plugs for books please? James
-- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 ________________________________________ From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp [...@ruppweb.org] Sent: Tuesday, December 15, 2009 8:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] When can I say the refinement is done? page 682 :-) BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine Sent: Monday, December 14, 2009 9:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] When can I say the refinement is done? This is pointed out (in absolutely unobvious way - I wish I can add voice to that PDF) at the slide #19 -:) (except loosening weights). P. On 12/14/09 8:35 AM, Anastassis Perrakis wrote: A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polygon ideas, is: "very well done, but have another look at this couple of Ramachandran outliers and also consider loosening up the geometry a bit". ;-) A. On Dec 14, 2009, at 17:04, Pavel Afonine wrote: Hi, the exact answer to your question is here: http://cci.lbl.gov/~afonine/for_ak/validation.pdf<http://cci.lbl.gov/%7Eafonine/for_ak/validation.pdf> In particular, your question below is spelled out is discussed staring from slide #2. Pavel. On 12/14/09 7:50 AM, rui wrote: Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap > 0.4 A. Ramachandran outliers: 0.2% (Goal: < 0.2%) Ramachandran favored: 97.7% (Goal: > 98%) Rotamer outliers: 1.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 14.16 Generally speaking, should I remove all those bad contact or is there any miminum requirement that ok, the structure is acceptable? I know the refinement can be endless, but I just want to get an idea how far away I'm . Thanks. R P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
