This chapter begins by emphasizing that the initial electron density for a protein will be significantly affected by errors in the experimental phases and, subsequently, additional errors of interpretation will arise when a model of the structure is built. It describes methods for fitting a protein molecule to its electron density map (both manual and automated) and demonstrates the importance of interactive computer graphics in these processes. It then covers the underlying theory of methods by which the model is adjusted to maximise its agreement with the experimental structure factor or intensity data. The chapter describes the role of stereochemical restraints in macromolecular refinement; recently developed methods of improving the efficiency of refinement which exploit molecular dynamics at high temperature and/or maximum likelihood statistics; the exploitation of non-crystallographic symmetry in refinement; and the process of treating the protein, or parts of it, as rigid groups to improve the radius of convergence or analyse the dynamics of the molecule. Methods for calculating electron density maps which minimise the problem of model bias are described in detail along with criteria by which the success or otherwise of refinement may be judged.
Keywords: trial structure, molecular graphics, least squares, normal equations, displacement parameter, stereochemical restraints, non-crystallographic symmetry, rigid-group displacement, simulated annealing, molecular dynamics
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