Hi Phenix gurus, I have done a refinement with an sodium ion. I had generated a phil file for the distance restraints to the surrounding water. Now i am not sure if it is really there. I removed it and removed the phil from the list in the gui. Now phenix complains about no Atom selected and stops. In the .eff file all restraints are incorporated and in I deleted therefore the geometric restraints manually from the . eff file. As a consequence an unused parameter warning appears about unused parameters or spelling errors in the input file. I guess the .eff file. My default parameter folder is empty. Does phenix load the .eff file from the previous run and would it help to remove this? I dont wanne start a new project just to be in the default configuration mode without additional information in the .eff file. I did this using the gui so I am not sure how to incorporate the --unused_ok command to which may help to convince phenix to process the job. I hope it is clear what I mean and thanks for any suggestion. Christian