[phenixbb] A few questions

[Pavel Afonine]

Hi Christopher,

thanks for your questions!

> We are working on a refinement at 1.14A which was suffering from lots of NPD atoms when refined anisotropically with refmac5 and/or shelx. 

The implementation of anisotropic B-factors refinement in phenix.refine 
should never lead to non-positive definite ADP matrices or any 
"instability" in refinement.

> 1. In our model we have a few solvent ligands, and these show up in the log file as:
>           Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1}
>           Classifications: {'undetermined': 13, 'water': 437}
> We've used a cif file for EDO with H's when needed, but still see this message. Is this normal? What is unusual?
>   

Yes, it is normal. In this context "unusual" means that this is not 
"usual amino acid, water, dna/rna fragment".

> 2. When choosing "indivdual_occupancies" for the refinement, all the atoms within an alt-conf are refined to different occupancies- is this expected? It seems that all atoms in the A conf should have the same value, and the occ of all atoms in the B conf should also be the same. Instead, we see this:
> ATOM    232  CA AGLU A  28      26.163   7.163   4.422  0.77  6.73           C
> ATOM    233  CB AGLU A  28      24.851   7.269   3.672  0.80  9.27           C
> ATOM    234  CG AGLU A  28      24.978   6.767   2.259  0.66 12.91           C
> ATOM    235  CD AGLU A  28      23.662   6.717   1.554  1.00 16.51           C
> ATOM    236  OE1AGLU A  28      22.874   7.667   1.757  0.71 18.78           O
> ATOM    237  OE2AGLU A  28      23.429   5.733   0.803  0.60 16.77           O
> ATOM    240  CA BGLU A  28      26.140   7.156   4.424  0.23  6.33           C
> ATOM    241  CB BGLU A  28      24.794   7.230   3.713  0.20  6.48           C
> ATOM    242  CG BGLU A  28      24.877   6.766   2.280  0.34  6.55           C
> ATOM    243  CD BGLU A  28      23.536   6.702   1.598  0.00  7.53           C
> ATOM    244  OE1BGLU A  28      23.497   7.014   0.381  0.29  7.85           O
> ATOM    245  OE2BGLU A  28      22.543   6.341   2.280  0.40  8.40           O
>   

This is correct behavior and this is exactly what you should expect 
refining occupancies of atoms in alternative conformations: the sum of 
occupancies of conformation A and B must be one. So, in your example above:

ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C
...
ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C

the total occupancy is: 0.77+0.23=1
Same for other atoms.

> 3. Adding hydrogens during anisotropic refinement results in the Parvati server giving "Illegal Biso" errors for many of the hydrogens. 

The H atoms at normal resolutions (not subatomic resolution) are treated 
as a special case. For example (default behavior), they ride on bonded 
atoms during coordinates refinement (riding model, distances X-H do not 
change), we refine one occupancy and isotropic B-factor per all H atoms 
in your molecule, etc. I don't know what exactly "Illegal Biso" means in 
Parvati server, but most likely you want to exclude H atoms for this 
analysis.

Just a suggestion: at resolution 1.4A you can try to change the default 
behavior for H refinement to this:

  hydrogens {
    refine_adp = *one_b_per_residue one_b_per_molecule individual
    refine_occupancies = *one_q_per_residue one_q_per_molecule individual
  }

Please let us know if you have any questions or problems!
Pavel.