Table 1. Model-quality metrics.

Metric	Description
R	The standard R factor, R = , where h, k and l are the Miller indices of the reflections and m is a scale factor. Used with the subscripts head†, calc‡, TLS§, co¶, complex†† and simple††.
Rfree	Like R, but calculated over a subset of the reflection data (Brünger, 1992 ▶). Subscripts: head†, calc‡, TLS§, co¶, complex††, simple†† and final‡‡.
Rratio	The expected ratio of Rfree/R for a converged refinement (Tickle et al., 1998 ▶).
Rw	The weighted R factor, Rw = (Hamilton, 1965 ▶), where whkl is the the weight for an individual reflection. Subscripts: complex, simple.
Rfree,w	The weighted free R factor. Subscripts: complex, simple.
σ(Rfree)	The estimated standard deviation of Rfree: Rfree/[2(No. of test-set reflections)]1/2. Subscripts: calc (Tickle et al., 2000 ▶).
Rfree,unb	The expected Rfree for a converged unbiased refinement (Tickle et al., 1998 ▶): Rfree,unb = R × Rratio. Subscripts: calc.
Z score	Z = (xmodel − xtarget)/σ(x), where x is a metric such as bond length and σ(x) is its standard deviation.
Z(Rfree)	The RfreeZ score§§: Z(Rfree) = (Rfree,unb − Rfree)/σ(Rfree). Subscripts: calc, complex.
Rfree,max	The maximal allowed Rfree value calculated by picker.
fit(ρ)	The weighted mean fit of a group of atoms a with mean displacement U to the map at grid points xg: WM = ; t(x) = , where ratom is the radius of the atom and xa is the position of the atom (Joosten, Joosten et al., 2011 ▶).
BWilson	The Wilson B factor.
r.m.s.Z(bond)	The root-mean-square Z score for n bonds with Z score Zi: r.m.s.Z(bond) = . Subscripts: calc, co, wcori¶¶, wcfin†††.
r.m.s.Z(angle)	Like r.m.s.Z(bond), but calculated for bond-angle deviations. Subscripts: calc, co, wcori, wcfin.

^†Extracted from the header of the input PDB file.

^‡Calculated by REFMAC before refinement.

^§Calculated during TLS refinement in REFMAC directly after resetting the B factors.

^¶Used as a cutoff value for picker.

^††Complex refers to the model with the most (B-factor-related) parameters and simple to the model with fewest.

^‡‡Calculated by REFMAC after the final refinement.

^§§The terms are swapped to compensate for the ‘lower-is-better’ nature of R _free.

^¶¶Calculated by WHAT_CHECK for the input PDB file.

^†††Calculated by WHAT_CHECK for the final model.