The second step is to convert the roughly folded decoys to realistic proteins with correct hydrogen bonding patterns. This is done by the macro 'nmr_refinevacuo', which runs molecular dynamics simulations in vacuo using the NOVA force field. It performs several refinement cycles, some of which are done without non-bonded interactions, so that atoms can pass through each other and kinetic traps like knots in the peptide chain can be resolved. For each ensemble member, the structure with the lowest restraint violation energy is kept and passed on to the next step.