This seems to be a duplicate of NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site). Please, don’t make multiple posts with the same topic. Be patient, it can take a long time before anyone has time to help you. If it has taken multiple weeks without a reply, you might make another post in the same thread to bring more attention to it, perhaps your post has not been seen. Another explanation might be that no-one knows.