Not sure what you mean by "complete reference protein" - presumably you mean that a corresponding sequence record (e.g. in UniProt) is annotated as "complete"?
However: to expand on the comment by dpryan79. It is not uncommon for residues to be missing from protein structures. This happens when regions of protein molecules in the protein crystal are disordered, mobile or "floppy" and so do not generate an interpretable X-ray diffraction pattern.
Here is an introduction to protein crystallography which explains this and other issues; there are many others on the Web.