Hello Smith,

Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers?

For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order?

I wonder why phenix.refine does not eliminate them as part of default run? Technically, it is supposed to do this. Would you be willing to send me data and model files so that I can investigate? Pavel