The formal refinement methods of least-squares adjustment or difference-map analysis give atomic positions in protein structures with standard deviations which are large compared with the standard deviations of accepted molecular dimensions. This paper describes a method of adjusting the Cartesian coordinates to obtain a properly weighted fit to both the positions from the refinement and the molecular parameters. The equations which have to be solved have many unknowns but few coefficients, and an effective iterative method can be used. The results of applications of the method to insulin are summarized.

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