Hi Noelia, it sounds like that molecule (the 5th) may be disordered and the fact that its occupancy refines to 0.8 is a good indication of this.. I suggest you do your best fixing outliers manually, then run refinement with - Ramachandran plot restraints enabled (you can apply them to all model or to just that 5th molecule only); - weights optimization (it runs much slower but if you can use multiple CPUs that will speed it up); - may be secondary structure restraints (that will rely on SS annotation provided in HELIX/SHEET records, so make sure it is correct if you choose to use it). If this does not help please feel free to send me files and I will have a look to see what else can be done! Good luck (and I guess I'll see you at Crystallography School in Madrid in May?), Pavel
Dear colleagues,
I am dealing with the refinement of a protein with 5 monomers in the asymmetric unit at 2.2 Å resolution. Four of them have correct geometry and good density map, however, the fifth molecule has poor density and bad geometry. Ramachandran plot is presents 91.05% (favored), 3.23 % (outliers). I have modified the occupancy of the molecule, the refinement results in 0.8 occupancy for this chain. I also tried to refined the structure without this chain, but the R values increased and the density map indicated that it should be there. I would like to refine this chain fixing the geometry of the others which are correct. Do you have any ideas about how to proceed?
Some info: Protein residues 305 5 monomers in the a.u Space group C121 a=151.390, b= 67.81, c=155.420Å, 94.53º R value 0.23 / Rfree 0.28
Many thanks,
Noelia