Flexible docking

I am using HADDOCK to dock a protein-peptide complex.
To test how well haddock is good for my system I have done a practice test, using restraints from the original PDB structure and in the binding site made the amino acids fully flexible.
However, the results show that the amino acids at the N and C terminus are not in the right position (probably due to the change in orientation because of the fully flexible segment). Is there a way to overcome this issue? So the docking will still be flexible for some amino acids but on the other amino acids will stay in place?
Attached is a Pymol image of the original on the docked structure.
The original PDB is yellow-green (green are the amino acids that are fully flexible) and the docked is colored orange (flexible) and wheat.
And as seen in the figure the N and C terminus are not in the right place. how can I keep them in the right orientation?
Thank you!