[ccp4bb] Should I be worried about negative electron density?

Hello Everyone, I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because my model is still not good enough or it’s natural to most model fit

[ccp4bb] Cut ligand or keep in whole piece when only part of it can be resolved

Hi everyone, I have two types of ligands cocrystallized with my protein, ligand 1 and ligand 2. I am only interested in resolving ligand 2. In my electron density map, only part of ligand 1 can be identified. Is it ok for me to cut ligand 1 so only the identifiable part is left or should I keep

[ccp4bb] updated mtz file or original one in refmac5

Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay