WHAT IF Check report

This file was created 2012-01-31 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 pdb3znc.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 252 BZ1   ( 500-)  A  -

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :295.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.959 over 1816 bonds
Average difference in B over a bond : 2.29
RMS difference in B over a bond : 5.55

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 251  ZN   (   1-)  A      SG  -SG*   2.46   10.4
 251  ZN   (   1-)  A      SG  -SG*   2.46   10.4
  24 CYS   (  23-)  A      SG  -SG*   2.42    9.6
 193 CYS   ( 203-)  A      SG  -SG*   2.42    9.6

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

 |  0.995017  0.000747 -0.000823|
 |  0.000747  0.996988  0.000690|
 | -0.000823  0.000690  0.992979|
Proposed new scale matrix

 |  0.018786 -0.000014  0.000016|
 | -0.000009  0.011772 -0.000008|
 |  0.000007 -0.000006  0.008261|
With corresponding cell

    A    =  53.232  B   =  84.944  C    = 121.051
    Alpha=  89.921  Beta=  90.095  Gamma=  89.914

The CRYST1 cell dimensions

    A    =  53.500  B   =  85.200  C    = 121.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 226.458
(Under-)estimated Z-score: 11.091

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.263

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

  67 THR   (  65-)  A    -3.0
   5 ILE   (   9-)  A    -2.4
  73 GLY   (  71-)  A    -2.4
 162 THR   ( 175-)  A    -2.3
 102 ASN   ( 103-)  A    -2.2
 228 LEU   ( 239-)  A    -2.2
 144 PHE   ( 157-)  A    -2.1
 161 SER   ( 174-)  A    -2.1
  97 SER   (  98-)  A    -2.0

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.

  12 SER   (  11-)  A  Poor phi/psi
  22 GLY   (  21-)  A  Poor phi/psi
  23 ALA   (  22-)  A  Poor phi/psi
  30 SER   (  29-)  A  PRO omega poor
  45 LEU   (  44-)  A  Poor phi/psi
  65 GLN   (  63-)  A  Poor phi/psi
  66 HIS   (  64-)  A  Poor phi/psi
  73 GLY   (  71-)  A  Poor phi/psi
  97 SER   (  98-)  A  Poor phi/psi
 109 ASP   ( 110-)  A  Poor phi/psi
 126 LYS   ( 140-)  A  Poor phi/psi
 158 HIS   ( 171-)  A  Poor phi/psi
 184 TYR   ( 194-)  A  Poor phi/psi
 191 PRO   ( 201-)  A  omega poor
 193 CYS   ( 203-)  A  Poor phi/psi
 195 GLU   ( 205-)  A  Poor phi/psi
 232 ASP   ( 243-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.184

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!

   3 TYR   (   7-)  A      0
   8 GLU   (  11-)  A      0
  11 ARG   (  11-)  A      0
  12 SER   (  11-)  A      0
  19 LYS   (  15-)  A      0
  20 TRP   (  16-)  A      0
  23 ALA   (  22-)  A      0
  24 CYS   (  23-)  A      0
  28 GLN   (  27-)  A      0
  29 GLN   (  28-)  A      0
  30 SER   (  29-)  A      0
  38 ARG   (  37-)  A      0
  45 LEU   (  44-)  A      0
  46 THR   (  45-)  A      0
  51 VAL   (  50-)  A      0
  57 GLN   (  55-)  A      0
  64 ASN   (  62-)  A      0
  65 GLN   (  63-)  A      0
  66 HIS   (  64-)  A      0
  67 THR   (  65-)  A      0
  79 ILE   (  80-)  A      0
  82 ASP   (  83-)  A      0
  84 PRO   (  85-)  A      0
  85 ALA   (  86-)  A      0
  86 ARG   (  87-)  A      0
And so on for a total of 119 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.173

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  26 GLU   (  25-)  A   2.20

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  21 PRO   (  20-)  A  -127.4 half-chair C-delta/C-gamma (-126 degrees)
  47 PRO   (  46-)  A  -113.0 envelop C-gamma (-108 degrees)
 157 PRO   ( 170-)  A  -113.8 envelop C-gamma (-108 degrees)

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.

 209 HIS   ( 219-)  A      ND1 <->  210 LYS   ( 220-)  A      N      0.14    2.76  INTRA
  55 GLN   (  53-)  A      NE2 <->   57 GLN   (  55-)  A      OE1    0.10    2.60  INTRA BF
 106 HIS   ( 107-)  A      NE2 <->  184 TYR   ( 194-)  A      OH     0.08    2.62  INTRA BL
  44 ARG   (  43-)  A      O   <->   46 THR   (  45-)  A      N      0.07    2.63  INTRA
 116 GLU   ( 117-)  A      OE2 <->  118 HIS   ( 119-)  A      NE2    0.07    2.63  INTRA BL
  91 GLN   (  92-)  A      OE1 <->   93 HIS   (  94-)  A      ND1    0.07    2.63  INTRA BL
 101 ASP   ( 102-)  A      O   <->  102 ASN   ( 103-)  A      ND2    0.05    2.55  INTRA BF
 123 LYS   ( 124-)  A      N   <->  126 LYS   ( 140-)  A      O      0.03    2.67  INTRA
  63 ASN   (  61-)  A      O   <->  158 HIS   ( 171-)  A      N      0.02    2.68  INTRA
 145 GLN   ( 158-)  A      N   <->  146 PRO   ( 159-)  A      CD     0.02    2.98  INTRA
 220 LEU   ( 229-)  A      O   <->  230 MET   ( 241-)  A      N      0.01    2.69  INTRA BL
 104 SER   ( 105-)  A      OG  <->  113 PHE   ( 114-)  A      N      0.01    2.69  INTRA
 182 PHE   ( 192-)  A      N   <->  201 VAL   ( 211-)  A      O      0.01    2.69  INTRA BL

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.

  11 ARG   (  11-)  A      -7.50
 164 ARG   ( 177-)  A      -5.98
  38 ARG   (  37-)  A      -5.65
 204 GLN   ( 214-)  A      -5.32
  65 GLN   (  63-)  A      -5.28
 203 LYS   ( 213-)  A      -5.08

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

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.

   6 GLN   (  10-)  A
 121 HIS   ( 122-)  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.

  11 ARG   (  11-)  A      N
  11 ARG   (  11-)  A      NH1
  14 CYS   (  11-)  A      N
  15 LEU   (  11-)  A      N
  25 LYS   (  24-)  A      N
  29 GLN   (  28-)  A      NE2
  32 ILE   (  31-)  A      N
  53 TYR   (  51-)  A      N
  55 GLN   (  53-)  A      N
  76 ALA   (  77-)  A      N
  81 GLY   (  82-)  A      N
  85 ALA   (  86-)  A      N
  87 TYR   (  88-)  A      OH
  97 SER   (  98-)  A      N
 101 ASP   ( 102-)  A      N
 111 ARG   ( 112-)  A      N
 126 LYS   ( 140-)  A      N
 133 MET   ( 147-)  A      N
 156 LYS   ( 169-)  A      N
 168 LEU   ( 181-)  A      N
 179 TYR   ( 189-)  A      N
 190 THR   ( 200-)  A      N
 204 GLN   ( 214-)  A      N
 211 ASN   ( 221-)  A      N
 231 LYS   ( 242-)  A      N
 234 VAL   ( 245-)  A      N
 249 HIS   ( 260-)  A      N
Only metal coordination for   93 HIS  (  94-) A      NE2
Only metal coordination for   95 HIS  (  96-) A      NE2
Only metal coordination for  118 HIS  ( 119-) A      ND1

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  66 HIS   (  64-)  A      ND1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 195 GLU   ( 205-)  A   H-bonding suggests Gln

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 :  -1.054
  2nd generation packing quality :  -1.476
  Ramachandran plot appearance   :  -3.263 (poor)
  chi-1/chi-2 rotamer normality  :  -2.184
  Backbone conformation          :  -1.680

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.795
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.213 (tight)
  Side chain planarity           :   0.406 (tight)
  Improper dihedral distribution :   0.748
  B-factor distribution          :   1.959 (loose)
  Inside/Outside distribution    :   0.973

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 : 2.80

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.795
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   0.213 (tight)
  Side chain planarity           :   0.406 (tight)
  Improper dihedral distribution :   0.748
  B-factor distribution          :   1.959 (loose)
  Inside/Outside distribution    :   0.973

      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
    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).

    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
      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
    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.