I was using Rosetta 2016.02 "local refinement" to calculate the interface scores of known protein complexes (in a bound form).
Now, I tried docking the same protein complexes, with exactly the same flags with Rosetta 2018.21. I realized that the content of the score file has changed and it gives totally different I_sc and total_score. Almost any protein complex that I tried gives favorable results now (i.e. I_sc < -5). Why is this the case?
I couldn't find what has changed since 2016.02 version.
As an example, I tried local refinement for B and J chains of the attached pdb file (after prepacking). Rosetta 2016.02 (local refinment) gave me total_score of -150 and I_sc of -4.73. However, Rosetta 2018.21 gave me total_score -96 and I_sc -19.5.
I would be very glad if you could help me.