Caveat: I don’t use ab initio, so I’m guessing.
A) I’m not sure what happens when you use both out::file::silent and out::pdb at the same time. Are you getting both PDBs and a silent file? and a score file too?
Are the columns not labeled in the score.fsc file…? What do the first few lines look like? I’m not familiar with .fsc, is that .fasc?
C) It’s perfectly possible you have a cloud with no funnel, it happens. What’s the spread in values? If the range is 1.2-2.3, then it’s probably not rosetta total score in that column. If it’s 1.7-500, then it probably is.
D) It’s possible to get all positive scores. It means Rosetta hates all the models it made.