A 12σ planarity deviation means that a few atoms are 0.1 Ångström
away from where they should be. That is much less than the average
coordinate error in the average PDB file. However, if an experimentalist
can make such 12σ errors, he or she can also make other big errors...
A flipped His, Asn, or Gln means nothing to the crystallographic quality in terms of comparing the experimentally observed diffraction pattern with the one calculated back from the coordinates. But such a flip puts hydrogen bond donors and acceptors at the wrong spot in space! And that makes it hard to properly dock a ligand in a drug design project.