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![[Figure 7]](dz5393fig7mag.jpg)
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Figure 7
The results of Fitmunk refinement can be used for different types of validation. In the left panel, `conformation change' gives the fraction of all side chains (by residue type) that had their conformation changed by Fitmunk and had an improved fit to electron density as evaluated by EDSTATS after REFMAC refinement; `missing side chain' gives the fraction of missing side chains that were rebuilt by Fitmunk and were fitted to significant electron density as evaluated by EDSTATS. Right panel, examples of corrections introduced into models and problems spotted resulting from Fitmunk refinement. Original models are represented as white sticks and Fitmunk-corrected models as blue sticks. Original 2mFo − DFc density at the 1 r.m.s.d. level is displayed as a gray mesh. In selected cases 2mFo −DFc electron density resulting from the refinement of a Fitmunk-corrected model is displayed at the 1 r.m.s.d. level as a blue mesh. Top row, conformational changes introduced by Fitmunk. A.1, correction of wrong conformation selection: several alternative conformations and a water were replaced by better fitting conformations. A.2, selection of a rotamer that forms better interactions. A.3, selection of a conformation that has a better density fit. Middle row, missing side chains that were rebuilt by Fitmunk. B.1, small residues such as Ser can be rebuilt most of the time. B.2, missing side chains were improperly compensated for by the introduction of water. B.3, rebuilding of missing residues allowed better packing and better main-chain placement after refinement. Bottom row, problems spotted after Fitmunk was unable to fit any conformation or resolve steric clashes for a given residue. C.1, possible wrong sequence or register shift; Fitmunk was unable to fit Asp in the space available. C.2, main-chain break and wrong main-chain orientation; Fitmunk was unable to fit any conformation of Ile with the given backbone orientation. C.3, wrong loop conformation; Fitmunk was unable to resolve collisions in the tight loop because of the incorrect backbone conformation. |
![[Figure 7]](dz5393fig7.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
