Dear Pavel, I have recently encountered a similar situation, where I took a CIF file for a ligand from the CCP4 monomer library and found planarity restraints are silently ignored in PHENIX. This is very confusing and dangerous.
with this logic you interpret the number and not use it. Follow this road you may end up with odd things, like let's treat 0 as "constraints", 0.1 as "strong restraints", 1.5 as "weak restraints", etc and in each case do something very different - I hope you get the idea.
The "zero sigma" limit of a Gaussian is an infinitely sharp probability distribution (= delta function). So I think the transition from restraints to constraints is not "odd" but quite natural both mathematically and semantically. Anyway, if PHENIX does not want to treat 0 as constraints, I would prefer an error stop, not just a warning, because most people don't mean "ignore this record" by zero sigma. Takanori Nakane