The first issue is that you have centroid poses, not fullatom poses. It is expected that centroid poses have positive scores. I thought you had fullatom poses. So, at least the only-positive scores aren’t a worry.
You might be able to try running abrelax with a pre-supplied secondary structure prediction, that might improve Rosetta’s results. You could also try running the post-abinitio relax phase (that’s what it’s abrelax) and/or getting fullatom results, but I don’t know if that will help any.