WHAT IF Check report

This file was created 2013-12-09 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 pdb3v3i.ent

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  39 PRO   (  42-)  B  -
  66 GLU   (  69-)  B  -
 213 SER   ( 217-)  B  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  39 PRO   (  42-)  B  -
  40 SER   (  43-)  B  -
  66 GLU   (  69-)  B  -
 213 SER   ( 217-)  B  -

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: B

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  50 GLN   (  53-)  B    High
 217 GLU   ( 221-)  B    High
 231 GLY   ( 235-)  B    High

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: 0

Crystal temperature (K) :100.000

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 : 1.622 over 1848 bonds
Average difference in B over a bond : 4.04
RMS difference in B over a bond : 5.64

Note: B-factor plot

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

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 187 TYR   ( 191-)  B

Warning: Phenylalanine convention problem

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

   4 PHE   (   7-)  B
  63 PHE   (  66-)  B
 127 PHE   ( 131-)  B
 256 PHE   ( 260-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  31 ASP   (  34-)  B
  69 ASP   (  72-)  B
  72 ASP   (  75-)  B

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.

  66 GLU   (  69-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.513
RMS-deviation in bond distances: 0.012

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.

  93 HIS   (  96-)  B      CG   ND1  CE1 109.66    4.1

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.

  31 ASP   (  34-)  B
  66 GLU   (  69-)  B
  69 ASP   (  72-)  B
  72 ASP   (  75-)  B

Torsion-related checks

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.

  80 PRO   (  83-)  B    -2.5
 198 PRO   ( 202-)  B    -2.4
 172 PHE   ( 176-)  B    -2.3
 159 VAL   ( 163-)  B    -2.2
  89 GLN   (  92-)  B    -2.1

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.

  26 SER   (  29-)  B  PRO omega poor
  28 VAL   (  31-)  B  omega poor
  57 LEU   (  60-)  B  omega poor
  61 HIS   (  64-)  B  Poor phi/psi
  74 ALA   (  77-)  B  omega poor
 108 LYS   ( 111-)  B  Poor phi/psi
 153 LEU   ( 157-)  B  omega poor
 174 ASN   ( 178-)  B  Poor phi/psi
 193 SER   ( 197-)  B  omega poor
 195 THR   ( 199-)  B  omega poor
 197 PRO   ( 201-)  B  PRO omega poor
 199 LEU   ( 203-)  B  Poor phi/psi
 203 VAL   ( 207-)  B  omega poor
 239 ASP   ( 243-)  B  Poor phi/psi
 248 LYS   ( 252-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.852

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!

   4 PHE   (   7-)  B      0
  12 HIS   (  15-)  B      0
  13 TRP   (  16-)  B      0
  16 ASP   (  19-)  B      0
  17 PHE   (  20-)  B      0
  21 LYS   (  24-)  B      0
  23 GLU   (  26-)  B      0
  24 ARG   (  27-)  B      0
  25 GLN   (  28-)  B      0
  26 SER   (  29-)  B      0
  47 SER   (  50-)  B      0
  59 ASN   (  62-)  B      0
  61 HIS   (  64-)  B      0
  69 ASP   (  72-)  B      0
  71 GLN   (  74-)  B      0
  72 ASP   (  75-)  B      0
  74 ALA   (  77-)  B      0
  77 LYS   (  80-)  B      0
  80 PRO   (  83-)  B      0
  82 ASP   (  85-)  B      0
  88 ILE   (  91-)  B      0
  89 GLN   (  92-)  B      0
  96 SER   (  99-)  B      0
  97 HIS   ( 100-)  B      0
  98 ASP   ( 101-)  B      0
And so on for a total of 122 lines.

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].

  10 PRO   (  13-)  B   101.2 envelop C-beta (108 degrees)
  18 PRO   (  21-)  B  -114.3 envelop C-gamma (-108 degrees)
 211 PRO   ( 215-)  B    45.4 half-chair C-delta/C-gamma (54 degrees)
 233 PRO   ( 237-)  B    26.6 half-chair N/C-delta (18 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.

 157 VAL   ( 161-)  B    A CG1 <->  221 LYS   ( 225-)  B      CD     0.46    2.74  INTRA
  24 ARG   (  27-)  B      NE  <->  260 HOH   ( 466 )  B      O      0.31    2.39  INTRA
 155 LYS   ( 159-)  B      NZ  <->  173 THR   ( 177-)  B      O      0.24    2.46  INTRA
  37 TYR   (  40-)  B      CD1 <->  256 PHE   ( 260-)  B      C      0.17    3.03  INTRA
  12 HIS   (  15-)  B      ND1 <->   15 LYS   (  18-)  B      NZ     0.13    2.87  INTRA
 228 ASN   ( 232-)  B      OD1 <->  235 GLU   ( 239-)  B      N      0.11    2.59  INTRA
 209 LYS   ( 213-)  B      CD  <->  256 PHE   ( 260-)  B      CE2    0.09    3.11  INTRA
 232 GLU   ( 236-)  B      CB  <->  233 PRO   ( 237-)  B      CD     0.08    3.02  INTRA BF
  69 ASP   (  72-)  B      OD2 <->  120 TRP   ( 123-)  B      NE1    0.06    2.64  INTRA BL
 164 LYS   ( 168-)  B      NZ  <->  260 HOH   ( 468 )  B      O      0.05    2.65  INTRA
 176 ASP   ( 180-)  B      OD2 <->  178 ARG   ( 182-)  B      NH2    0.04    2.66  INTRA
  49 ASP   (  52-)  B      OD2 <->   50 GLN   (  53-)  B      NE2    0.04    2.66  INTRA BF
  96 SER   (  99-)  B      N   <->   97 HIS   ( 100-)  B      N      0.02    2.58  INTRA BL
  29 ASP   (  32-)  B      OD1 <->  108 LYS   ( 111-)  B      N      0.01    2.69  INTRA BL
  97 HIS   ( 100-)  B      C   <->  223 ARG   ( 227-)  B      NH2    0.01    3.09  INTRA BL
 104 HIS   ( 107-)  B      NE2 <->  190 TYR   ( 194-)  B      OH     0.01    2.69  INTRA BL
 103 GLU   ( 106-)  B      OE2 <->  242 ARG   ( 246-)  B      N      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: B

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.

   7 HIS   (  10-)  B      -6.26
 234 GLU   ( 238-)  B      -5.07

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: B

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: B

Water, ion, and hydrogenbond related checks

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 GLU   (  14-)  B      N
  28 VAL   (  31-)  B      N
  97 HIS   ( 100-)  B      N
 126 ASP   ( 130-)  B      N
 176 ASP   ( 180-)  B      N
 200 LEU   ( 204-)  B      N
 228 ASN   ( 232-)  B      N
 240 ASN   ( 244-)  B      ND2
 241 TRP   ( 245-)  B      N
 256 PHE   ( 260-)  B      N
Only metal coordination for   93 HIS  (  96-) B      NE2

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.

 232 GLU   ( 236-)  B   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 :  -0.047
  2nd generation packing quality :   0.364
  Ramachandran plot appearance   :  -1.564
  chi-1/chi-2 rotamer normality  :  -0.852
  Backbone conformation          :  -1.026

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.513 (tight)
  Bond angles                    :   0.730
  Omega angle restraints         :   1.243
  Side chain planarity           :   0.621 (tight)
  Improper dihedral distribution :   0.765
  B-factor distribution          :   1.622 (loose)
  Inside/Outside distribution    :   0.915

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 : 1.73


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.513 (tight)
  Bond angles                    :   0.730
  Omega angle restraints         :   1.243
  Side chain planarity           :   0.621 (tight)
  Improper dihedral distribution :   0.765
  B-factor distribution          :   1.622 (loose)
  Inside/Outside distribution    :   0.915
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      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.