Sorry your message was stuck waiting for approval because of the attachment size.  I've now increased the limit to 1000 kB.

I think I have solved about 80% of your problem.  Since several residues were represented only by their "P" atoms, MMB was probably not able to match structure.  I have deleted these incomplete residues.  I also added a model of chain "X" as an extended chain (I can do this by doing a stage 1 MMB run).  I then used "loadSequencesFromPdb," which reads sequences and residue numbers directly from last.1.pdb, and tolerates missing residues (as long as the remaining residues have all their backbone atoms).  

I adjusted the "threading" command to not thread the missing residues.  I fixed chain A to the Ground frame (rootMobilizer A Weld). Lastly, I turned on the Amber99 potential for chain X only (with setDefaultMDParameters and "includeAllNonBondAtomsInResidues X 57 91").  

So now, the only part not threaded is the span from residue 71 to 81.  If you want to thread to the "P" atoms from those residues in chain A, I suggest creating eleven "springToGround" commands, connecting the  P atoms on chain X to the locations of the P atoms on chain X.  Look at the reference guide for the springToGround syntax.  You may want a nice strong spring constant, e.g. 300 or more.

Let me know how you do with the last part.  I have attached my commands.dat and last.1.pdb.

Sam