It is a little hard to tell what is happening. It could be that your model is already refined, and so morph_model cannot see anything to do.  Or it could be that something is not right.  

I would first try this test:

   phenix_regression.wizards.test_command_line test_morph_model

and make sure it runs. You can see all the output in the directory 

  test_morph_model/

after you run it.

Also have a close look at your output model. Is it exactly the same as the input, or only very slightly changed?  These are pretty different situations.

Then you can substitute your model and data for the test model and data and make sure it still runs.

You might want to take just a small piece of your model and run it.  That will be quicker and it should be the same (more or less) as if that piece was still in the middle of the whole structure.

Let me know if that doesn't help!

All the best,

Tom T