Section 18.3.3.1. Confidence in restraints versus information from diffraction

Primarily in cases of new structures, such as small-ligand- or metal-binding proteins, the refinement may indicate that the expected geometries and applied restraints seem incompatible with evidence from the electron density. Several sources for such discrepancies must be considered for an evaluation of the true geometries or the confidence level of such an evaluation. The quality of the experimental information, such as data resolution and reduction parameters, must be considered. Physical phenomena possibly ignored by the refinement model might include anisotropies of motion and/or electron distribution, or disorder in the crystal. These might lead to systematic deviations in the refined structure that mimic alternate parameterizations. Finally, newly derived parameters should be examined to decide whether the fragments and chemical environments were inappropriate for the refinement problem, or whether errors in fragment structures artifactually distorted the parameterization.