I am refining a protein structure at 2.5 A. 

After running some refinements with water update option on, I manually added water to some positions and ran without water update option as it removes those water from the sites and show green density around.    Then after some refinements like this, I tried to use water update option to add water to some newly appeared density.                                                  

When I check the option to update water using dev 1418 version it stops with the following error.  Also  when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options.

R work-0.1988 compared to 0.1920 with 1.8.2-1309

Rfree-0.2623 compared to 0.2490 with 1.8.2-1309

Traceback:

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", line 236, in run

    return_value = self._target(self._args, self._kwargs, self._c)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 94, in __call__

    result = self.target()

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 73, in __call__

    result = self.run()

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 69, in run

    refine_object = self._run(args, callback)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 85, in _run

    call_back_handler=callback)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", line 161, in run

    call_back_handler=call_back_handler)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", line 1630, in run

    ncs_manager             = self.ncs_manager).result

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", line 155, in __init__

    neutron_refinement2 = self.neutron_refinement2)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 26, in __init__

    self.__call__()

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 36, in __call__

    self.__getattribute__(method_name)()

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 106, in run_sol

    mc   = self.macro_cycle)

  File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 79, in _need_to_run

    else: raise RuntimeError("Not a valid mode: %s"%mode)

Thanks in advance for any help

Subhani