Electron density maps real space refinement

This methodology has also been used to carry out a potential energy-constrained real-space refinement of the structure of BPTI, using limited diffraction data [39]. Figure 6 illustrates how the energy-refined map on the right identifies more of the electron density of Arg-42 than the map on the left. 

Refinement also may be accomplished in real space by calculating difference Fourier syntheses using as coefficients A F = F i,s — Fcaic and phases caic derived from the trial structure. In general, if an atom has been incorrectly placed near its true location, a negative peak will appear at its assigned position and a positive peak will appear at its proper location. That is, in the difference Fourier we have subtracted electron density from where the atom isn t, and not subtracted density from where it is. The atom is then shifted by altering x, y, z, improved atomic parameters are included in a new round of structure factor calculations, and another difference Fourier computed. The process is repeated until the map is devoid of significant features. 

---