I am using Rosetta local refinement to calculate the interface scores of known protein complexes (in a bound form).
In the docking protocol, it says "Typical values for I_sc of godd decoys are in the range of -5 to -10.". However, for some complexes, rosetta local refinement gives me I_sc as low as -5988.1. This number doesn't seem realistic to me. Could you please explain why we see such small numbers? How can we interpret this result, if the good binding score is in the range of -5 and -10?
As an example, I tried local refinement for D and F chains of 1n86.pdb (after prepacking) and it gave me I_sc of -5988.1. You can find the pdb file (with only D and F chains) attached.
I would be very glad if you could help me.