[phenixbb] rotamer outlier and clash socre

Hello everyone I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? Another question is the value of clash score are also too high. When I set the nonbonded_weight to 10000, the clash score get better, but the value of rotamer outlier get worse. The high clash score maybe due to including hydrogens for refinement? Can I exclude hydrogen for refinement and how to do? Thanks ! Pan [email protected]