Dear @cryo-lg,
Glad to help! Looks like the mask was definitely the issue here. You can also check the subtraction by running a local refinement and checking for density in the subtracted region. Typically at this point, any residual density left over after subtraction would be due to suboptimal pose estimates, or heterogeneity/disorder (a recent discussion of this is here Particle subtraction of detergent belts still maintain low level signal of the belt).
Best,
Michael