I have developed a homology model with different templates. For checking the overall deviation from template structure, RMSD calculation was performed using Match Maker option in Chimera. It gives two values one value is for the target -template alignment after selection of the Needleman Wunsch and BLOSSUM 62 matrix. The other value is the overall value.
According to me, I need to consider the overall value and which should ideally be less than 2 Angstroms. This value gives a better representation of the deviation in the entire structure and not just the sequence level.
I would like some researchers to verify this.