Hi Juliana,
After running phenix real space refine with different refinement strategies. My map-model FSC curve has some interesting features:
1. It does not starts at 1 as it does the map FSC curve, is that ok? What could be causing this?
which one is it? Is it FSC(half_map1, half_map2) or FSC(experimental_map, model_map) ?
1. It has a dip around 5-6Å, this deep can be a bit up or down depending the refinement strategy I use, therefore the FSC model at 0.5 can cut the resolution at 3.9 or 6 Å. What this deep mean? Am I doing something wrong in the refinement?
How different these models are?
1. The mask and unmask curves completely overlap, is that ok?
This suggests to me the map is probably already masked or somehow 'normalized'..
1. Also, my refinement shows a high clash score (15-20), if I change the nonbonded_weight parameter from 100 (default) to higher values the clash score decreases but the FSC curves gets lower them the FSC curve crosses the 0.5 cutoff at 6A.
When it comes to clashscore, generally the lower the better but zero is not the goal. Looking at one of screenshots I see you have 2.42% of atoms with occupancy less than 1. Do you really see partially occupied atoms in 4A resolution map? Unlikely! So.. please check those out! I can run more diagnostics for you if you share maps and models (off-list of course!). Pavel