Are you referring to the mutate tool? You shouldn't have been able to use the mutate tool in this puzzle. The protein segments in this puzzle should have a fixed identity, and the ligand in the middle of the protein should be adjustable with the Small-Mcl Design mode (hotkey 5) and popup, not the mutate tool.
Under what conditions were you able to get the M tool to run?
log.txt only shows:
...
internal_coords_atom:
autodeterimine_chi:
FinalE finalize:
replacing residue
setting game pose
marking chemical change
core.conformation.Residue: DANGER: almost got stuck in infinite loop! Atom 15 is apparently a parent AND child of atom 13.
delta_score: 0
Playing sound: 4
ending minimization: 7364.47
starting minimization: 7364.47
UNHANDLED EXCEPTION
1: no symbol (no line)
2: no symbol (no line)
3: no symbol (no line)
4: no symbol (no line)
5: no symbol (no line)
6: no symbol (no line)
7: no symbol (no line)
8: no symbol (no line)
9: no symbol (no line)
10: no symbol (no line)
11: no symbol (no line)
12: no symbol (no line)
13: no symbol (no line)
14: no symbol (no line)
Why the M tool lowers the score went run?