I've been working on a structure using NCS. When I run the phenix.apply_ncs to generate the whole structure using the original one chain PDB, it gave me a PDB with same atom number on the other chain. 

For example, I start with chain A and end in chain A and B (B is generated by NCS), while the atom number on chain B is just a duplicate of chain A, starting from 1. This cause error in the subsequent refinement trials. 

I'm wondering what program can correct this issue. 

Thanks,

Bingfa