Hydrogen bond related checks

Error: HIS, ASN, GLN side chain flips

 Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favorable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. 

  50 ASN  (  53 )
 137 ASN  ( 140 )

Note: Histidine type assignments

 For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber histidine geometries fits best to the structure.

In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters.

As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement.

Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the Z-scores are much higher than 1.0.

If the two assignments differ, or the ``geometry'' Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it. 

  31 HIS  (  31 )   HIS-E   0.69 HIS-H   1.28

Warning: Buried unsatisfied hydrogen bond donors

 The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero. 

   2 ASN  (   2 )      N
  14 ARG  (  14 )      NH1
  21 THR  (  21 )      N
  21 THR  (  21 )      OG1
  25 TYR  (  25 )      N
  89 ASP  (  92 )      N
  93 ARG  (  96 )      NH1
 138 GLN  ( 141 )      NE2

Note: Buried hydrogen bond acceptors OK

 All buried polar side-chain hydrogen bond acceptors are involved in a hydrogen bond in the optimized hydrogen bond network.