Hi @emil,
Did you ever manage to refine your glycoprotein? You probably finished a long time a go but I just wanted to mention what worked for me in the end to help anyone facing a similar problem with glycans.
I first tried dilating the mask by 6 or 8 with padding of 12 during NU Refine. This seemed to work at first but then I noticed strong streaks of density near N-glycan sites. It seemed like the mask near the glycans caused overfitting there and a decrease in protein resolution. It was even worse after local refinement even when using a static mask. Dilating more (up to 20+) and way past the point of any observable glycan density, different lowpass filters, etc didn’t help. I then tried to vary all the settings in both NUR and local refine again and the *only thing that worked was to use a mask that extended just beyond the protein density (using dilation of 6 thus cutting through the N-glycans) but then padding by 20 or 30 to have a very, very soft edge. This gave me really nice refinement of the protein and good enough glycan density to allow building of the core fucosylated pentasaccharide. I’m not sure why dilating to cover the glycans caused overfitting streaks while dilating for the protein only and wide padding for the glycans worked. Maybe someone else can offer an explanation?