I submitted 2 PDB structures via Haddock 2.4 web server.
I obtained several clusters and I considered the first one with HS (49) and z-score (-1,1) lower than the other clusters. Then I selected the first model structure (interaction complex) of the cluster and I submitted it via refinement tool (haddock 2.4 website). Then I selected the final model on the basis of FNAT, L-RMSD and I-RMSD values.
Is this method correct? Or can I consider only the first cluster that I obtained, without making any refinement?