Hi Haytham,

How to get rid of restraints_edite.params in the following run of phenix.refine, i mean after using it in previous run.
and

When you run phenix.refine it creates a number of files, and one of them is .def file that contains all the parameters for the next subsequent refinement run. This includes the information taken from restraints_edite.params file. So to do what you want just edit .def file to remove the lines that were in restraints_edite.params file.

what is .def files. and bond.slack

These two questions are answered in phenix.refine manual:
http://phenix-online.org/documentation/refinement.htm

Pavel.