If you actually need to place the model you might as well just run the full Phaser MR_AUTO mode; otherwise you can use the MR_RNP mode.  I had expected to be able to do it like this:

phenix.phaser model.pdb data.mtz seq.fa model_rmsd=1.0 phaser.mode=MR_RNP

although that crashes, which I guess may be a bug.