3DVA only shows shell of density for some flexible region

Dear community,
I have a big complex and I want to see how each component moves relative to the other. So I run 3DVA at a resolution of 8A. I noticed that for the first several frames, it only shows the density of a flexible region as a shell, instead of a rigid body. Is this normal? If not, what’s the best way to correct this?
Thank you so much.

Best wishes,