Hello: I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1. here is some list, can you tell me why?

THX

-----------------------------Loop refinement---------------------------------------------- EXPDTA THEORETICAL MODEL, MODELLER 9v8 2011/02/18 21:54:47 REMARK 6 MODELLER OBJECTIVE FUNCTION: -11.8879 ATOM 1 N SER A 1 53.405 4.206 73.937 59.86 59.86 ATOM 2 CA SER A 1 54.091 5.156 73.036 59.86 59.86 ATOM 3 CB SER A 1 53.358 5.255 71.687 59.86 59.86 ATOM 4 OG SER A 1 53.443 4.020 70.992 59.86 59.86 ATOM 5 C SER A 1 54.148 6.519 73.639 59.86 59.86 ATOM 6 O SER A 1 54.469 6.679 74.816 59.86 59.86 ATOM 7 N ALA A 2 53.848 7.547 72.824 39.90 39.90 ATOM 8 CA ALA A 2 53.862 8.892 73.313 39.90 39.90