I would really appreciate an answer to this question, as this is preventing me using this software for a particular project.
I have examined the masking in the refinement. The mask_fsc file appears to be excluding portions of my protein, therefore setting the contour threshold for the mask incorrectly.
I have tried fiddling with the masking options available in the refinement job, however I think this only changes the refinement rather than the FSC mask.
Could you please confirm whether the masking as part of the FSC calculation is dependent on these parameters and whether there is a user intervention possible to change the mask used for the FSC?
I have attached an example FSC below as a demonstration of the problem.