====================== Modifying start model if requested =====================

Size before: 505 size after: 491
Traceback (most recent call last):
  File "/home/user1/phenix-1.16-3549/build/../modules/phenix/phenix/command_line/refine.py", line 11, in 
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/command_line.py", line 106, in run
    log=log)
  File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/driver.py", line 271, in __init__
    self.model.set_xray_structure(modify_model_obj.xray_structure)
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 693, in set_xray_structure
    self.set_sites_cart_from_xrs()
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 1722, in set_sites_cart_from_xrs
    self._pdb_hierarchy.adopt_xray_structure(self._xray_structure)
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 688, in adopt_xray_structure
    raise RuntimeError("Incompatible size of hierarchy and scatterers array.")
RuntimeError: Incompatible size of hierarchy and scatterers array.