Ramachandran outliers aside, amount of other outliers seem a bit worrying to me, especially given that it may not be all that trivial to justify them against 3.5A resolution map:
all-atom clashscore : 29.19 ramachandran plot: outliers : 0.51 % allowed : 5.44 % favored : 94.05 % rotamer outliers : 8.23 % cbeta deviations : 5 (Command used to get the numbers above: phenix.pdbtools model_stat=true 4x4m.pdb ) Pavel On Mon, Apr 27, 2015 at 7:54 AM, Todd Jason Green <tgr...@uab.edu> wrote: > 7 out of 1361 Ramachandran outliers (all prolines) doesn't seem high to > me. > > ------------------------------ > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of > Oganesyan, Vaheh [oganesy...@medimmune.com] > *Sent:* Monday, April 27, 2015 9:04 AM > > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! > > Hi Robbie and Co, > > > > These things are happening now too. Look at the entry 4x4m. The paper got > published in January, PDB released coordinates in April. That means > reviewers did not have a chance to look even at validation report. In my > opinion, whatever it is worth, every journal dealing with crystal > structures should, at the very least, request the validation report from > PDB including Nature, Science and PNAS. > > What is also interesting that at the end PDB released the coordinates with > large number of outliers. I don’t think those can be justified with low > resolution of the data. >
