[phenixbb] missing/extra atoms in phenix.refine

[Pavel Afonine]

Hi Michael,

can you send me the PDB file (please send it off-list)? It's hard to 
tell anything without looking at the file.

Pavel.

On 5/13/11 5:23 AM, R.M. Garavito wrote:
> We are trying to finish up the refinement on two structures, but we 
> have run into a strange problem that I have never seen before.  So we 
> need to ask the Phenix experts.  As background, we recently solved the 
> structure of an 808 residue enzyme, which crystallizes as a tetramer. 
>  In the asymmetric unit there are two tetramers (>6400 residues, 
> ~52,000 atoms, but 67% solvent).  After SAD phasing and autobuild 
> (many kudos to the Phenix team), we were able to trace easily the 
> chain in two different ligand complexes, one at 2.85 Å and the other 
> at 2.8 Å.  Although the C-terminal domains are quite well resolved 
> (and obey 222 NCS), the first domain (~110 residues out of 808) is a 
> bit disordered and shows some conformational differences between each 
> monomer.  While the main chain in this domain can be traced, side 
> chain densities are mediocre to missing in spots.  In order to ensure 
> a consistent tracing and sequence assignment between all 8 N-terminal 
> domain, we built in the "correct" sequence, but truncated the side 
> chains to CB if the side chain density was poor to non-existent. 
>  After several rounds of refinement and model building, the finished 
> structures look quite good, have a consistent sequence assignment, and 
> have Rwork in the high teens and Rfree in the low 20s.
>
> THE PROBLEM: It is the 2.8 Å complex that has the problem.  We used 
> Moleman2 to evaluate the B-factors for the 4 domains in the 8 monomers 
> in the ASU.  When we compiled the numbers, we noticed that Moleman2 
> and phenix.refine gave different numbers for the protein atoms for 
> chain B in the 2.8 Å complex (6152 versus 6289).  We checked the PDB 
> and confirmed that there are 6152 protein atoms in chain B; the other 
> 7 chains show no differences between the programs.  So where did 
> phenix.refine get 6289 protein atoms when only 6152 protein atoms are 
> input for chain B?  The number of residues are correct (780).
>
> Adding to the confusion, there are truncated residues in each of the 8 
> chains.  In the phenix.refine output attached below, the PDB file is 
> being read in. For chain A, the number of atoms and the number of 
> residues are correct, as well as the number of incomplete residues 
> ({'truncation_to_alanine': 14}).  However, for chain B, the number of 
> incomplete residues ({'truncation_to_alanine': 21}) should be 37.
>
> Any ideas?
>
> Thanks,
>
> Michael
>
> /****************************************************************/
>
> /R. Michael Garavito, Ph.D./
>
> /Professor of Biochemistry & Molecular Biology/
>
> /513 Biochemistry Bldg. /
>
> /Michigan State University/
>
> /East Lansing, MI 48824-1319/
>
> /Office:////(517) 355-9724Lab:(517) 353-9125/
>
> /FAX:(517) 353-9334Email:garavito at msu.edu <mailto:garavito at msu.edu>/
>
> /****************************************************************/
>
> phenix.refine output:
>
>   Monomer Library directory:
>     "/usr/local/phenix-1.7-650/chem_data/mon_lib"
>   Total number of atoms: 51463
>   Number of models: 1
>   Model: ""
>     Number of chains: 57
>     Chain: "A"
>       Number of atoms: 6289
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 781, 6289 <==== matches PDB file
>           Classifications: {'peptide': 781}
>           Incomplete info: {'truncation_to_alanine': 14} <==== MATCHES 
> PDB file
>           Link IDs: {'PTRANS': 34, 'TRANS': 746}
>           Unresolved non-hydrogen bonds: 47
>           Unresolved non-hydrogen angles: 60
>           Unresolved non-hydrogen dihedrals: 36
>           Unresolved non-hydrogen chiralities: 7
>           Planarities with less than four sites: {'PHE:plan': 1, 
> 'GLU:plan': 3, 'ASN:plan2': 1, 'ASN:plan1': 1}
>           Unresolved non-hydrogen planarities: 23
>                   .
>                   .
>                   .
>                   .
>     Chain: "B"
>       Number of atoms: 6236
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 780, 6236 <==== DOES NOT MATCH PDB 
> file 780 residues with 6152 atoms
>           Classifications: {'peptide': 780}
>           Incomplete info: {'truncation_to_alanine': 21} <====  37 
> truncation_to_alanine
>           Link IDs: {'PTRANS': 34, 'TRANS': 745}
>           Unresolved chain links: 1
>           Chain breaks: 1
>           Unresolved chain link angles: 3
>           Unresolved chain link dihedrals: 4
>           Unresolved chain link planarities: 2
>           Unresolved non-hydrogen bonds: 80
>           Unresolved non-hydrogen angles: 101
>           Unresolved non-hydrogen dihedrals: 62
>           Unresolved non-hydrogen chiralities: 9
>           Planarities with less than four sites: {'GLN:plan1': 1, 
> 'GLN:plan2': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 
> 'ARG:plan': 2}
>           Unresolved non-hydrogen planarities: 49
>
>
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