So I have a solution that covers some of target and I ran it through phenix.mr_rosetta and I am actually kinda happy with the output from there. However, while I can place both (NCS=2) with the original model I only seem to be able to place one of the rosetta models, even with 'packing function' set to 'all' or 'allow'.

Original model - 

Refinement after placing component 1: LLG 175

Refinement after placing component 2: LLG 620

Rosetta model (packing 'all') - 

More notably there is little to no increase in TFZ with the placement of the second component...

There are more residues in the Rosetta model and I would expect more clashes but this looks weird.

Cheers,

Morten
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Morten K Grøftehauge, PhD