Hi all, In phenix.real_space_refine, I'm using a reference model for torsion restraints for a RNA/protein complex. I noticed in the log file under the section "Adding Reference Model Restraints (torsion)" that only the amino acid residues and some modified nucleotides are listed in the "Reference Model Matching Summary" but not the standard nucleotides. Does this mean that they are not restrained? I checked the _initial.geo file and there are no torsion restraints for the standard nucleotides in the "Reference torsion angle restraints" section. Are they not supported by default? My workflow was this: run ready_set on the initial model and then supply real_space_refine with a reference model and the ready_set cif file with the ligands. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy