Hi, I entirely agree with Phoebe. This is 2008 structure (publish date, so refinement was probably done in 2007) - that is before all the new methods and tools for low-res refinement became available.
Now, let's have a closer look... Given rather large amount of various geometry outliers (in model taken straight from PDB): Ramachandran plot, number of: outliers : 76 (16.52 %) allowed : 120 (26.09 %) favored : 264 (57.39 %) Rotamer outliers : 60 (15.27 %) Cbeta deviations >0.25A : 6 All-atom clashscore : 53.54 it is unlikely for conventional gradient-driven refinement tools to correct them (since correcting some of them requires jumping over energy barriers). Now, if I idealize the model geometry using 2mFo-DFc map as restraint: phenix.real_space_refine 3bd.pdb map.ccp4 run=minimization_global+morphing morphing=every_macro_cycle I get the model that still fits the map as well as staring model (starting map CC vs final map CC: 0.737/0.782) but has outliers virtually gone: Ramachandran plot: outliers : 1.52 % allowed : 19.35 % favored : 79.13 % Rotamer outliers : 0.00 % Cbeta deviations : 0 All-atom clashscore : 17.09 Now if I run this model through reciprocal space refinement so that it fits the Fobs data under restraints to preserve good input geometry (phenix.refine with rotamer and secondary-structure restraints, weights optimization), I get the model that still has reasonable geometry: Ramachandran plot: outliers : 1.74 % allowed : 20.22 % favored : 78.04 % Rotamer outliers : 0.00 % Cbeta deviations : 0 All-atom clashscore : 18.16 with R-factors R-work = 0.3012, R-free = 0.3518 that are slightly better than published (0.292/0.374, taken from PDB). Bottom line in my opinion is: we can't really blame rather old(ish) models for not using modern improved methods, but there is no excuse for not using these methods today! All the best, Pavel On Thu, Apr 23, 2015 at 9:03 AM, Misbah ud Din Ahmad <misba.ah...@gmail.com> wrote: > Dear crystallographers, > > The PDB entry > http://www.rcsb.org/pdb/explore.do?structureId=3BDN > has 16.5% Ramachandran outliers. When I opened this PDB file in coot and > checked for Ramachandran outliers, the results are: > In preffered region: 58.04% > In allowed regions: 19.78% > > *Outliers: 22.17% !!!!!!!!!* > > With an R-free of 37.4% at 3.9 A resolution, could you please tell me how > reliable this structure of Lambda repressor bound to DNA is? >
