Hi all, I am running the enzyme_design application with one input Resfile and no cstfile. I know for the fact that the Resfie is being read based on the output, part of which is shown here: **** protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: mutations.resfile protocols.enzdes.EnzdesTaskOperations: Design Interface: detected 0 design-shell residues and 68 repack-shell residues, shell sizes cut1-4 used were 0 0 10 12 **** The relevant part of options file (the indentation is correct in the original file): **** -resfile mutations.resfile -enzdes -detect_design_interface -cut1 6.0 -cut2 8.0 -cut3 10.0 -cut4 12.0 **** A portion of Resfile: **** 74 A NOTAA A EX 1 EX 2 328 A NOTAA A EX 1 EX 2 437 A NOTAA L EX 1 EX 2 **** I am expecting the output files to not have residue A at position 74 based on the above inputs. However, all of output PDBs have the native residues A, A, and L at 74, 328 and 437 respectively. Note that these are native residues so the input PDB file has them. Am I missing something? Any possible explanation? Also, what is the difference between the options, NATAA ("allow only the natural amino acid") and ALLAA ("allow all 20 amino acids INCLUDING the cystein amino acid")? Thanks in advance!