[modeller_usage] Problems with cis proline

[Eva María Priego <>]

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