4. Justify choice of template(s)
For homology modelling, the choice of the template(s) is crucial. Sequence similarity is an important factor, but there are also other issues. If several different types of structures are available, then a choice of e.g. apo vs holo form or active vs inactive conformation has be be described. Many proteins have several conformations, functional relevance of which varies. If you are interested on a specific part or domain within a large protein, it obviously should be included to the template. In case of drugs and other ligands, it may be more relevant to have a template with similar or related compound in relevant protein conformation than to take a structure with best resolution, R factor or other crystallographic or NMR quality measures. Mention PDB ids of the templates.
Example: The structure was modelled by using 9xyz as a template. The template protein shares the highest sequence identity with the protein (49%) among existing structures. There is a minimal number of gaps and they are short (2 gaps of two and three residues, respectively) and the sequences match along the entire chain length. Further, the investigated protein and the template have close substrate specificity.