I have a similar problem to this. In my case, refinement stops after a few steps, and nothing is really refined. I have multiple values that should be refined, so it doesn't make sense that nothing changes. My input file contains rigid bodies and free atoms. Previously, I had a similar problem where I received a warning message like "site A has a recurring decimal coordinate, change the format to =1/3;." This site A was part of a rigid body, and I could only avoid this error by rotating the coordinates to @ 0, @ 0, @ 0. But in the current case, no error message is displayed. What could be the cause, and how can I avoid this problem?
A screenshot of my topas window: