[modeller_usage] loop refinement

[Laura Lopez <laura.lopez@upf.edu>]

Hello!

I'm trying to obtain refined models of a loop region from a existing pdb 
file (a model I built before with modeller). I only want to refine a 
loop, and I've followed the steps in 
http://www.salilab.org/modeller/manual/node34.html. But it always 
appears me this error message:
File "<string>", line 1, in ?

File 
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", 
line 36, in run
self._runlines(self.lines)

File 
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", 
line 153, in _runlines
subrout)

File 
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", 
line 384, in _run_top_cmd
eval('self.topcmds.' + lowcmd + '()')

File "<string>", line 0, in ?

File 
"/Library/modeller-9v2/modlib/modeller/top_interpreter/commands.py", 
line 230, in optimize
optimization_method=ometh)

File "/Library/modeller-9v2/modlib/modeller/top_interpreter/topcmds.py", 
line 412, in optimize
outs = _modeller.mod_top_optimize(mdl, edat, libs, *args)

ValueError: read_op_662E> Invalid choice LONG for variable OUTPUT: can 
choose one or more from the following: NO_REPORT REPORT


I've tried to change  some settings in the .top file but always appear 
this error.What can I do?
Another question: if in the model I've built and from which I've to 
refine a loop, I had to make a disulfide bridge in this loop, in the 
loop refinement I also have to make the disulfide restraint?
Thank you!!
Laura