Clustering only generates a single cluster?

I did a docking run using the ab initio protein ligand docking settings for the sampling, temperatures, and clustering settings but I only got one cluster back, with 200 structures lumped into it. When I look at the scatter plots at the bottom, it seems like there should be more clusters than just one? I think part of the issue may be that I’m docking a protein onto the surface of a nanodisc (given as a ligand, with some AIRs defined), and so the energy could be largely driven by the 100+ lipids/the MSP rather than the interaction between the protein of interest and the lipids? Someone else has done a similar docking run before but they got 10 clusters back, so I think it’s an issue with my settings and not the concept (Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis | Nature Structural & Molecular Biology). I ran the same docking run again, but with the RMSD cutoff set lower (2-> 1), which I thought would encourage the creation of more clusters, but I got back pretty much the exact same results as far as I can tell. How can I separate out the clusters more?