Structure D, E and F shows secondary structures we found using the 1b2s and 1b3s models. Structure D is a 1.7 resides-per-turn helix, structure E is a folded sheet-like structure and structure F is a 5.5 residues-per-turn helix. The longer side chains in the 1b2s and 1b3s models adds more conformational flexibility compared to the 1b1s model, making models folding difficult due to many competing partially folded metastable states. To address this conformational flexibility we added model parameters that aim to reduce the conformational flexibility of these models. For example, in structure D steric clashes between large side chains reduced conformational flexibility. In model F rigid torsion constraints of the side chains also helped reduce conformational flexibility.