Dear Stanislav, Depending on the program you are using to perform the refinement and the particular space group of your structure, it could happen that the coordinates you got from the database refer to a different origin of the coordinate system than the coordinates you got from the structure determination. In many censtrosymmetric space groups the highest symmetry point in the cell have no -1 (center of symmetry), the convention used to place the origin of the cell in this highest symmetry point, however most of the refinement and solution programs will assume the origin is on the highest symmetry point of the cell containing a center of symmetry (no matter if there is a higher symmetry point) because it simplifies computations, etc. This discrepancy in origin choice could account for your problem. This happens very frequently with quartz where two sets of coordinates are stored in databases referring to two possible origins of the unit cells not always given with the coordinates, producing confussion. Check if your space group got two alternative origins (for most centrosymmetric space groups with the highest symmetry point not containing a center of symmetry both descriptions are given in the International Tables with alternative choices)
I hope this helps, Good luck Leo Prof. Dr. Leopoldo Suescun Cryssmat-Lab/DETEMA/Facultad de Quimica Universidad de la Republica Montevideo, Uruguay
