Enzyme Design Not Editing Structure

Hello,

I'm quite new to all of this, so please let me know if I've missed anything. I've been tasked with designing a more thermodynamically stable protein to catalyze a reaction. I made a resfile for the new amino acid, made a constraints file, and pointed to the constraints in the PDB header. It seems to run (It discards some atoms and tells me there's no appropriate entry found in a constraint). Despite running successfully, it doesn't seem to actually change the structure. The most it's done is removed the leading residue in the PDB and spat it back out. Have I overconstrained it or is one of the warnings causing this issue?

Thank you so much for your help!

Header (PDB was too big):

REMARK 666 MATCH TEMPLATE H SeN   22 MATCH MOTIF P CYS  410  1  1         
REMARK 666 MATCH TEMPLATE H SeN   22 MATCH MOTIF P TYR  351  2  1
REMARK 666 MATCH TEMPLATE H SeN   22 MATCH MOTIF P THR  412  3  1