Dear taylortamu,
Let me first point you to both the manual and the paper related to the usage of HADDOCK with only PCS restraints:
C. Schmitz and A.M.J.J. Bonvin Protein-Protein HADDocking using exclusively Pseudocontact Shift. J. Biomol. NMR, 50, 263-266 (2011).
Averaged PCS data over a population of conformations can be tricky. A recent paper shows that unrestrained molecular dynamics (MD) simulations starting from the HADDOCK models can help refining the prediction. Maybe the way to go …
Brewer KD, Bacaj T, Cavalli A, et al. Dynamic Binding Mode of a Synaptotagmin-1-SNARE Complex in Solution. Nature structural & molecular biology. 2015;22(7):555-564.
Best regards
Adrien