Disulfide bonds

Hello,

I'm working on a crystal structure with 255 AA and a total of 56 Cys. In the crystal structure all the cysteins are in disulfide bond.
When I submitted the FASTA format of the protein to the I-TASSER server, I'm getting a model with most of the cys residues unbound.
I was wondering how the server takes disufide bond in account? Are energy calculations determine if a disulfide bond is formed or not?

Thank you in advance,
Lihie