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Figure 2
Ramachandran plots for general residues at key stages of rebuilding/refinement. (a) PDB entry 3ja8 was originally refined from a largely hand-built model with the aid of Ramachandran and rotamer restraints, achieving a MolProbity score of 2.51. Such restraints can be problematic when the nearest allowed region of the plot is not the true conformation for a given residue. (b) After energy minimization and 3000 MD steps in ISOLDE the number of outliers had increased substantially, suggesting that portions of the original model were indeed overfitted into energetically unfavourable conformations. (c) Extensive remodelling and restrained refinement yielded a final model with no Ramachandran outliers and an overall MolProbity score of 1.44.

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ISSN: 2059-7983
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