I-TASSER - secondary structure specification

Dear I-TASSERS developers and users,
we are using I-TASSER for the modelling of a difficult membrane protein for which we have found some indication about the secondary structure in the literature.
We tried a first modelling using I-TASSER and we found that the secondary structure prediction done by the server is not in complete agreement with the experimental results found in literature.
We then tried to specify the secondary structure by using the "Specify secondary structure for specific residues." option, but the results are very similar to the previous run.
Are we doing something wrong?

Thanks in advance for you help.