Hi Meranda,
Those plane wave artefacts in the volume are sometimes observed after the sharpening of the maps (see this post for some discussion). In the streamlog, refinements always plot the sharpened versions of the maps but the artefacts might not be present in the full unsharpened map, or the half-maps. For an iteration that has these artefacts, if you download the full unsharpened map, and one of the half maps, do you also see these plane-wave artefacts when you open either map in UCSF Chimera?
You can download these maps by going to the “Outputs” tab in the job panel, scrolling down to the “JXX.volume.map” (and “JXX.volume.map_half_A”) sections, clicking the “versions” drop down menu, and clicking the download icon at the right side of the iteration bar, for any of the iterations that show this problem. Below is a screenshot of the expanded drop down menus with the download buttons for an example job output.
Best,
Michael