Hi,
Got some questions in using phenix.refine.
1) Can phenix.refine use the ligand library generated by refmac5?
2) How do I use elbow to generate the ligand library when I have more
than one kind of ligands? When I used --residue=xxx more than once,
elbow will only generated library for the last ligand. If I use
elbow multiple times to generate multiple libraries, how do I read
the libraries in? Should I combine them to one file?
3) When I ran phenix.refine, I found the following message in the log.
Number of residues, atoms: 32, 418
Unusual residues: {'NAG': 22, 'MAN': 10}
Classifications: {'undetermined': 32}
Link IDs: {None: 31}
Unresolved non-hydrogen bonds: 32
Unresolved non-hydrogen angles: 64
Unresolved non-hydrogen dihedrals: 22
Unresolved non-hydrogen chiralities: 32
Number of residues, atoms: 18, 28
Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14}
Classifications: {'undetermined': 18}
Link IDs: {None: 17}
I already gave the cif library for NAG. Looks like nothing
happened. How come phenix.refine doesn't recognize Glycerol, Mg, and
Ca?
4) The refinement (TLS + ML + B individual) went through, I got
reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are
pretty low. The B factor of the backbone is much lower than the side
chain, some have numbers like 4. Some metal atoms also have B
factors around 4. What did I do wrong?
Thanks.
Jianghai
