A WHAT IF check report: what does it mean?

http://swift.cmbi.kun.nl/gv/pdbreport/checkhelp/explain.html

Some of the 20 amino acid types in proteins have atoms that "look" the same. So, for instance, the C-delta-1 and C-delta-2 atoms in phenylalanine look the same, and thus all PHE residues would have two ways of naming the atoms:
Naming in Phenylalanine

This would result in infinite confusion. So, a committee designed a standard: the torsion angle Chi-2 (defined by C-alpha, C-beta, C-gamma, C-delta-1) should always be between -90 and 90 degrees.

Similar considerations hold for ASP, GLU, PHE and TYR.