[phenixbb] Structure with high clashscore

Hello all, I'm happy to join the forum! I have a problem with clashscores and would be grateful for support. I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30. I wondered if you could describe the best way to reduce these? Attached is my latest round of refinement should you wish to take a look! Best, Jerome