[modeller_usage] difference side chain dihedrals of identical residues in model and the template

Dear All,

I have built a homology model of my protein using a single template sharing 38%
sequence identity. Some of the functionally important residues of target protein
are conserved in the template. These residues are well aligned in the input
sequence alignment file. In the top most model so obtained, I found difference
in side chain dihedral angles of such identical residues. Since both target as
well as template contain a few identical residues, their secondary structure is
also same, then why these conserved residues in the model adopt rotamers
different from those of the template.

Following is comparison of side chain dihedrals of arginine conserved in both
target as well as template.

                     chi1  chi2  chi3  chi4  chi5
   template          169   -100  179   -80    0
   model              65    81   75    -96    0

Here, chi1, chi2 and chi3 are drastically different

Can anybody please explain why this is so?

Thanks

Ruchi