Thank you very much for the information!  After I use PDB editor to set atloc, give chain I atloc to "P" and give chain K atloc to "Q" both Phenix Refine and Refmac goes normally. To my surprise, even I force chain K to be chain I with the same residue number and name, as long as I set atloc to P for Chain I, Ala7th--13th 0.5 occupancy and atloc to Q for Chain I, Ala7th--13th 0.5 occupancy, the Phenix Refine and Refmac goes normally. So the key here is to set atloc with PDB editor. Is there any difference between using the same chain ID (Chain I, atloc P and Q, half occupancy) or using the different chain ID (Chain I, atloc P, half occupancy and then Chain K, atloc Q, half occupancy)?