Recent advances in low resolution refinement tools in REFMAC5

Abstract

This contribution deals with some aspects of low resolution refinement and map calculation, as implemented in the crystallographic refinement program - REFMAC5. Refinement at low resolution is considered as a regularisation problem. Regularisers for application in both real space and reciprocal space have been implemented. In real space, regularisers are applied as interatomic distance restraints. There are two types of real space regularisers: those with a target, and those without a target. External restraints to reference structures belong to the class with a target, where targets are calculated using corresponding interatomic distances in the reference structure(s). Such reference structures may arise from homologous structures, secondary structural elements, generic or specific structural fragments (including self-restraints), and other sources of generically derived information, e.g. hydrogen bonds. Such interatomic distance restraints are generated using the conformation-independent protein structure comparison and analysis program - ProSMART. Jelly-body restraints belong to the real space targetless class of regularisers, where interatomic distance self-restraints are recalculated at every cycle. This regulariser has the power to stabilise refinement without imposing externally-derived information. Importantly, it is not dependent on initial values, and does not change the extrema of the target function. Regularisers in reciprocal space are designed to sharpen (deblur) the electron density map, whilst inhibiting the amplification of noise. These regularisers do not affect refinement. Rather, they are applied at the end of a refinement session, with the intention of aiding subsequent map interpretation. © 2013 Springer Science+Business Media Dordrecht.