"4.5% and 6% for Qualcomm

0.0004% or 0.0006% for MMP Portfolio"

As we've discussed before, I think this may be an apples to lug nuts type of comparison.  PTSC's royalty percentages you are posting here are based on the OVERALL revenue of a licensee, while the Qualcomm percentages are based on the cost of a particular INFRINGING UNIT.  It's like trying to get the rate tied to the overall cost of the car, instead of tying it to the cost of the radio in that car, if you're the radio patent holder.