[phenixbb] link restraints for modified nucleotides in RNA

[Gerwald Jogl]

Hi All,

I am refining several modified nucleotides in ribosomal RNA 
(N2-methyl-guanosine and similar). While the restraints generation with 
phenix.reel work quite well, I am unable to get the phosphate oxygen 
restraints applied properly. Phenix.refine recognizes the links but for 
some reason the phosphate groups come out quite distorted...

For example, angles after refinement:
O3 (1) - P (2, modified) - OP2 (2) = 80 deg and
O3 (1) - P (2, modified) - OP1 (2) = 127 deg


Here is part of the phenix.refine log on reading the coordinates:

     Chain: "A"
       Number of atoms: 32526
       Number of conformers: 1
       Conformer: ""
         Number of residues, atoms: 1513, 32526
           Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, 
'5MC%rna2p': 1, '7M
G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1}
           Classifications: {'undetermined': 11, 'RNA': 1502}
           Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195}
           Link IDs: {'rna3p': 1318, 'rna2p': 194}
           Chain breaks: 1

I am at a loss about how to fix this as all links and restraints seem to 
be in place.

Many thanks for advice,
Gerwald