Have you got enough data for your parameters?
Health of your structure at a glanceOlex2 provides a lot of visual feedback, informing you about the status and 'health' of your structure. There is the visual display of the molecule itself, and especially the appearance of the atoms. Various other diagnostics are prominently displayed on the GUI. It is well worth looking at these things -- sometimes it will be very obvious that there may be big problems with a structure just by looking at the diffraction data statistics, for example.