WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2x6m.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 2

Crystal temperature (K) :173.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  39 ARG   (  40-)  A

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  31 TYR   (  32-)  A
  94 TYR   (  95-)  A

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  36 PHE   (  37-)  A
 100 PHE   ( 101-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  43 GLU   (  44-)  A

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.996293 -0.000870  0.000233|
 | -0.000870  0.995354 -0.000799|
 |  0.000233 -0.000799  0.996172|
Proposed new scale matrix

 |  0.016682  0.000015 -0.000004|
 |  0.000014  0.015917  0.000013|
 | -0.000004  0.000013  0.015967|
With corresponding cell

    A    =  59.945  B   =  62.826  C    =  62.629
    Alpha=  90.092  Beta=  89.973  Gamma=  90.100

The CRYST1 cell dimensions

    A    =  60.170  B   =  63.120  C    =  62.870
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 71.653
(Under-)estimated Z-score: 6.239

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  18 ARG   (  19-)  A      CB   CG   CD  104.68   -4.7

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  39 ARG   (  40-)  A
  43 GLU   (  44-)  A

Torsion-related checks

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  30 SER   (  31-)  A  omega poor
  51 ASN   (  52-)  A  omega poor
  66 ASP   (  67-)  A  Poor phi/psi
  92 ALA   (  93-)  A  Poor phi/psi, omega poor
  99 LYS   ( 100-)  A  omega poor
 111 ASN   ( 112-)  A  Poor phi/psi
 112 PHE   ( 113-)  A  omega poor
 113 GLY   ( 114-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.948

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   6 SER   (   7-)  A      0
  10 SER   (  11-)  A      0
  13 ALA   (  14-)  A      0
  16 SER   (  17-)  A      0
  24 SER   (  25-)  A      0
  31 TYR   (  32-)  A      0
  40 PRO   (  41-)  A      0
  44 ARG   (  45-)  A      0
  45 GLU   (  46-)  A      0
  48 ALA   (  49-)  A      0
  53 LEU   (  54-)  A      0
  56 VAL   (  57-)  A      0
  65 LYS   (  66-)  A      0
  66 ASP   (  67-)  A      0
  78 THR   (  79-)  A      0
  84 ASN   (  85-)  A      0
  85 SER   (  86-)  A      0
  91 THR   (  92-)  A      0
  92 ALA   (  93-)  A      0
 100 PHE   ( 101-)  A      0
 102 PRO   ( 103-)  A      0
 104 TYR   ( 105-)  A      0
 105 CYS   ( 106-)  A      0
 108 SER   ( 109-)  A      0
 112 PHE   ( 113-)  A      0
And so on for a total of 54 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.014

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 134 HOH   (2158 )  A      O   <->  134 HOH   (2161 )  A      O      0.73    1.47  INTRA
 134 HOH   (2185 )  A      O   <->  135 HOH   (2007 )  B      O      0.43    1.97  INTRA
 134 HOH   (2088 )  A      O   <->  134 HOH   (2089 )  A      O      0.40    1.80  INTRA
  18 ARG   (  19-)  A      NH1 <->  134 HOH   (2032 )  A      O      0.31    2.39  INTRA BF
  18 ARG   (  19-)  A      NE  <->  134 HOH   (2035 )  A      O      0.26    2.44  INTRA
 111 ASN   ( 112-)  A      ND2 <->  134 HOH   (2170 )  A      O      0.11    2.59  INTRA BL
 100 PHE   ( 101-)  A      CE1 <->  113 GLY   ( 114-)  A      CA     0.08    3.12  INTRA
  80 TYR   (  81-)  A      OH  <->  134 HOH   (2137 )  A      O      0.07    2.33  INTRA
 100 PHE   ( 101-)  A      CZ  <->  113 GLY   ( 114-)  A      CA     0.04    3.16  INTRA
  21 CYS   (  22-)  A      N   <->   79 VAL   (  80-)  A      O      0.03    2.67  INTRA BL
  44 ARG   (  45-)  A      NH1 <->  115 TRP   ( 116-)  A      CE3    0.03    3.07  INTRA
  65 LYS   (  66-)  A      NZ  <->  134 HOH   (2112 )  A      O      0.03    2.67  INTRA
  18 ARG   (  19-)  A      NH2 <->  134 HOH   (2034 )  A      O      0.02    2.68  INTRA
  39 ARG   (  40-)  A      NH1 <->   89 GLU   (  90-)  A      OE2    0.01    2.69  INTRA
 134 HOH   (2002 )  A      O   <->  134 HOH   (2003 )  A      O      0.01    2.19  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 128 TYR   ( 136-)  B      -8.30
 117 GLN   ( 118-)  A      -6.50
 131 GLU   ( 139-)  B      -5.52
 104 TYR   ( 105-)  A      -5.45
 100 PHE   ( 101-)  A      -5.32

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 134 HOH   (2085 )  A      O     -0.77    0.47   15.77

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 favourable 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. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  12 GLN   (  13-)  A
 111 ASN   ( 112-)  A

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.

Waters are not listed by this option.

  35 TRP   (  36-)  A      NE1
 101 SER   ( 102-)  A      N
 108 SER   ( 109-)  A      N

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.475
  2nd generation packing quality :  -0.148
  Ramachandran plot appearance   :  -0.404
  chi-1/chi-2 rotamer normality  :  -0.948
  Backbone conformation          :  -0.439

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.801
  Bond angles                    :   0.823
  Omega angle restraints         :   1.275 (loose)
  Side chain planarity           :   1.652
  Improper dihedral distribution :   1.383
  B-factor distribution          :   0.817
  Inside/Outside distribution    :   1.000

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.62


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -1.3
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.801
  Bond angles                    :   0.823
  Omega angle restraints         :   1.275 (loose)
  Side chain planarity           :   1.652
  Improper dihedral distribution :   1.383
  B-factor distribution          :   0.817
  Inside/Outside distribution    :   1.000
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.