InternationalCrystallography of biological macromoleculesTables for Crystallography Volume F Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 21.1, p. 505
## Section 21.1.7.4.2. Real-space fits |

The fit of a model to the data can also be assessed in real space, which has the advantage that it can be performed for arbitrary sets of atoms (*e.g.* for every residue separately). Jones *et al.* (1991) introduced the real-space *R* value, which measures the similarity of a map calculated directly from the model (ρ_{ c}) and one which incorporates experimental data (ρ_{ o}) as where the sums extend over all grid points in the map that surround the selected set of atoms. The real-space fit can also be expressed as a correlation coefficient (Jones & Kjeldgaard, 1997), which has the advantage that no scaling of the two densities is necessary. Chapman (1995) described a modification in which the density calculated from the model is derived by Fourier transformation of resolution-truncated atomic scattering factors.

The program *SFCHECK* (Vaguine *et al.*, 1999) implements several variations on the real-space fit. The normalized average displacement measures the tendency of groups of atoms to move away from their current position. The density correlation is a modification of the real-space correlation coefficient. The residue-density index is calculated as the geometric mean of the density values of a set of atoms, divided by the average density of all atoms in the model. It therefore measures how high the electron-density level is for the set of atoms considered (*e.g.* all side-chain atoms of a residue). The connectivity index is identical to the residue-density index, but is calculated only for the N, C^{α} and C atoms. It thus provides an indication of the continuity of the main-chain electron density.

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