Hi Daniel,

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?

Yes.

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?

They are supported. Most likely there is a large discrepancy between model and reference and Phenix was not able to match them. What is sequence similarity between them? Currently the threshold is 0.85. You can change it: reference_model.search_options.chain_similarity_threshold If you send me (off-list) the files (model, reference, ligands, no map needed) I can take a closer look. Files will be kept confidential. Best regards, Oleg Sobolev.

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

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