The initial model built into the electron density map must be examined and further adjusted to better fit the experimental data. This process is called refinement. An improved model provides better phases and allows calculation of a better map that may reveal new details (e.g., missing loop density, missing density for parts of a ligand, or new solvent molecules). The crystallographic R-factor and R-free monitor refinement progress and assess the overall agreement between the model and the experimental data. However, we should keep in mind that the resolution of the X-ray data ultimately determines both the quality and level of detail in the interpretation of the structure. Crystallographic software such as REFMAC (CCP4) and BUSTER (Global Phasing), along with the graphics program Coot (CCP4), are used for model building and refinement. Generally, a higher resolution allows more reliable model interpretation, whereas for lower-resolution models (e.g., under 2.5 Å), the interpretation of the electron density map may be more subjective. However, higher resolution does not automatically guarantee good model quality. Many high-resolution structures may have poor overall quality. For this reason, in addition to the R-factor and resolution, the PDB provides other factors for quality assessment. They include the Ramachandran plot and deviations of bond lengths and bond angles from their ideal values, collectively referred to as overall geometry (stereochemistry) criteria.
