Hi all - is it possible to specify custom planar restraints in phenix.refine?

Nope, sorry. It may be possible to do this with a cif link but I haven't actually tried it out. A link without the bonds (because you cannot specify the slack from the cif file) but only the extra plane you want. If you try it and you get stuck, send me a sample from your pdb, your best try at making the link file and the apply_cif_link params and I'll try to help out. Ralf