Hi i am using phenix version 1.4 release tag 70 hari@charlie:~$ phenix.refine --version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 70 Platform: intel-linux-2.6-x86_64 linux User: hari ------------------------------------------------------------------------------- I am seeing a strange shifting of my coordinates "out of my experimental phases map" before and after refinement without simulated annelaing I am at the final stages of my refinement. When I refine without simulated annealing the resulting model is shifted relative to my experimental phases map into which I build my model The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference. I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 . Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST record . I am using coot version 0.61 for my building and map display using fft inside of coot . hari