Dear all, I need to build models of a protien with a disulphide bond beetween monomers, four cis Proline and an aditional helix. I am using Modller 7v7. This is the top file I have used:

INCLUDE SET ATOM_FILES_DIRECTORY ='/home/evamaria/CTLA-4/Dimer/Model9/' SET PDB_EXT = '.pdb' SET SEQUENCE = 'CTLA4-D' SET STARTING_MODEL = 1 SET ENDING_MODEL = 40 SET DEVIATION = 4.0 SET KNOWNS = '1i8lc' '1i8ld' '1i85cd' '1ah1a' '1ah1b' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET ALIGNMENT_FORMAT = 'PIR' SET ALNFILE ='CTLA4-D.ali' CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = 'on' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '127:' '149:' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '284:' '306:' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '122:' '279:' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:101' 'C:101' 'N:102' 'CA:102', ; ATOM_IDS2 = 'CA:101' 'C:101' 'N:102' 'CA:102'

RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:103' 'C:103' 'N:104' 'CA:104', ; ATOM_IDS2 = 'CA:103' 'C:103' 'N:104' 'CA:104' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:258' 'C:258' 'N:259' 'CA:259', ; ATOM_IDS2 = 'CA:258' 'C:258' 'N:259' 'CA:259' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_restraints' CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:260' 'C:260' 'N:261' 'CA:261', ; ATOM_IDS2 = 'CA:260' 'C:260' 'N:261' 'CA:261' RETURN END_SUBROUTINE

The problem is the models obtained don't fit this script, I mean, none of them have the alpha helix and none have the four correct cis proline( or have more residues in cis) but they have the disulphide bond.What am I doing wrong?. Thank you in advance