If you set infill to 100%, you'd expect all structures to be completely compact but that is not the case.
Inspecting the print preview below, you can see that most tubes of this protein structure are fill while the middle one isn't.
That's because those tiny areas of infill are smaller than your "minimum infill length" setting (on the Infill tab). That setting tells the software not to print any infill areas that are shorter than the min length, which can be really useful since frequently these tiny areas don't add much value and only slow down the print.
If you want to include the infill for EVERYTHING, even these tiny tiny sections, then just set the "minimum infill length" to zero.