WHAT IF Check report

This file was created 2013-12-10 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 pdb4m5o.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.

 205 X48   ( 306-)  A  -
 206 X48   ( 307-)  A  -
 208 X48   ( 308-)  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: 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.

  17 MET   (  12-)  A    High
  61 GLU   (  56-)  A    High
  62 ARG   (  57-)  A    High
  69 GLU   (  64-)  A    High
  70 SER   (  65-)  A    High
  71 GLY   (  66-)  A    High
  72 ASP   (  67-)  A    High
  73 PRO   (  68-)  A    High
  74 ASN   (  69-)  A    High
 101 ASN   (  96-)  A    High
 106 GLU   ( 101-)  A    High
 109 LYS   ( 104-)  A    High
 131 GLU   ( 126-)  A    High
 133 HIS   ( 128-)  A    High
 142 LYS   ( 137-)  A    High
 143 ILE   ( 138-)  A    High
 144 LYS   ( 139-)  A    High
 145 SER   ( 140-)  A    High
 146 GLU   ( 141-)  A    High
 171 GLU   ( 166-)  A    High
 194 ASP   ( 189-)  A    High
 197 ARG   ( 192-)  A    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: 3

Crystal temperature (K) :100.000

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: Tyrosine convention problem

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

  53 TYR   (  48-)  A
 136 TYR   ( 131-)  A
 166 TYR   ( 161-)  A

Warning: Phenylalanine convention problem

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

  58 PHE   (  53-)  A
 153 PHE   ( 148-)  A
 155 PHE   ( 150-)  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.

  85 GLU   (  80-)  A
 159 GLU   ( 154-)  A
 171 GLU   ( 166-)  A

Geometric checks

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.

  85 GLU   (  80-)  A
 159 GLU   ( 154-)  A
 171 GLU   ( 166-)  A

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.

  56 PHE   (  51-)  A    -2.5
 144 LYS   ( 139-)  A    -2.2
 112 PRO   ( 107-)  A    -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.

  56 PHE   (  51-)  A  Poor phi/psi
  81 PHE   (  76-)  A  omega poor
 114 LEU   ( 109-)  A  omega poor
 120 ASN   ( 115-)  A  Poor phi/psi
 146 GLU   ( 141-)  A  Poor phi/psi
 163 LYS   ( 158-)  A  Poor phi/psi
 164 ALA   ( 159-)  A  Poor phi/psi
 167 THR   ( 162-)  A  Poor phi/psi
 191 SER   ( 186-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.783

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!

  13 CYS   (   8-)  A      0
  15 ASN   (  10-)  A      0
  29 TYR   (  24-)  A      0
  36 GLU   (  31-)  A      0
  37 THR   (  32-)  A      0
  55 ASP   (  50-)  A      0
  56 PHE   (  51-)  A      0
  57 HIS   (  52-)  A      0
  74 ASN   (  69-)  A      0
  85 GLU   (  80-)  A      0
 110 PHE   ( 105-)  A      0
 113 ASP   ( 108-)  A      0
 120 ASN   ( 115-)  A      0
 129 ARG   ( 124-)  A      0
 130 ARG   ( 125-)  A      0
 143 ILE   ( 138-)  A      0
 145 SER   ( 140-)  A      0
 146 GLU   ( 141-)  A      0
 156 THR   ( 151-)  A      0
 161 ALA   ( 156-)  A      0
 162 THR   ( 157-)  A      0
 163 LYS   ( 158-)  A      0
 164 ALA   ( 159-)  A      0
 166 TYR   ( 161-)  A      0
 167 THR   ( 162-)  A      0
And so on for a total of 53 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].

 112 PRO   ( 107-)  A   -57.3 half-chair C-beta/C-alpha (-54 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.

  13 CYS   (   8-)  A      SG  <->  209 HOH   ( 536 )  A      O      0.48    2.52  INTRA BF
 101 ASN   (  96-)  A      ND2 <->  209 HOH   ( 486 )  A      O      0.29    2.41  INTRA BF
  28 GLU   (  23-)  A      OE2 <->  209 HOH   ( 533 )  A      O      0.28    2.12  INTRA BF
 204 SO4   ( 304-)  A      O3  <->  209 HOH   ( 502 )  A      O      0.25    2.15  INTRA BF
  11 ARG   (   6-)  A      NH2 <->   23 GLU   (  18-)  A      OE2    0.23    2.47  INTRA BF
 120 ASN   ( 115-)  A      ND2 <->  209 HOH   ( 452 )  A      O      0.20    2.50  INTRA BL
 195 SER   ( 190-)  A      N   <->  209 HOH   ( 453 )  A      O      0.19    2.51  INTRA BF
  60 ASP   (  55-)  A      OD1 <->   63 GLY   (  58-)  A      N      0.13    2.57  INTRA BF
  88 ASP   (  83-)  A      OD2 <->  209 HOH   ( 459 )  A      O      0.13    2.27  INTRA BF
 195 SER   ( 190-)  A      OG  <->  209 HOH   ( 476 )  A      O      0.12    2.28  INTRA BF
 177 LYS   ( 172-)  A      NZ  <->  209 HOH   ( 406 )  A      O      0.12    2.58  INTRA BL
  60 ASP   (  55-)  A      OD1 <->   64 GLU   (  59-)  A      N      0.11    2.59  INTRA BF
 166 TYR   ( 161-)  A      O   <->  168 LEU   ( 163-)  A      N      0.11    2.59  INTRA BL
  78 LYS   (  73-)  A      NZ  <->  209 HOH   ( 509 )  A      O      0.10    2.60  INTRA BF
 129 ARG   ( 124-)  A      N   <->  200 GLU   ( 195-)  A      OE1    0.10    2.60  INTRA BF
 133 HIS   ( 128-)  A      ND1 <->  160 MET   ( 155-)  A      SD     0.09    3.21  INTRA BF
 156 THR   ( 151-)  A      OG1 <->  158 GLU   ( 153-)  A      OE1    0.08    2.32  INTRA BF
  59 ILE   (  54-)  A      N   <->   78 LYS   (  73-)  A      O      0.06    2.64  INTRA BL
  46 HIS   (  41-)  A      CE1 <->  205 X48   ( 306-)  A      C1     0.05    3.15  INTRA BL
 175 ARG   ( 170-)  A      NH1 <->  209 HOH   ( 440 )  A      O      0.04    2.66  INTRA BF
 209 HOH   ( 517 )  A      O   <->  209 HOH   ( 520 )  A      O      0.01    2.19  INTRA BF

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.

  62 ARG   (  57-)  A      -6.12
 110 PHE   ( 105-)  A      -5.60

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

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 143 ILE   ( 138-)  A   -2.68

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.

 209 HOH   ( 493 )  A      O      5.76    3.89  -18.34
 209 HOH   ( 498 )  A      O      7.59   -2.36   17.91
 209 HOH   ( 511 )  A      O      1.45   16.84  -17.76

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.

 106 GLU   ( 101-)  A      N
 109 LYS   ( 104-)  A      N
 119 GLU   ( 114-)  A      N
 121 ARG   ( 116-)  A      NH2
 133 HIS   ( 128-)  A      N
 147 LYS   ( 142-)  A      N
 148 THR   ( 143-)  A      N
 207 EDO   ( 305-)  A      O2
Only metal coordination for   46 HIS  (  41-) A      NE2
Only metal coordination for   85 GLU  (  80-) A      OE1
Only metal coordination for  113 ASP  ( 108-) A      OD1

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.

   7 GLU   (   2-)  A      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 201  MN   ( 301-)  A   -.-  -.-  Part of ionic cluster
 202  MN   ( 302-)  A   -.-  -.-  Low probability ion. Occ=0.69
 203  MN   ( 303-)  A   -.-  -.-  Low probability ion. Occ=0.77

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.

  60 ASP   (  55-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :   0.770
  2nd generation packing quality :  -0.307
  Ramachandran plot appearance   :   1.093
  chi-1/chi-2 rotamer normality  :   0.783
  Backbone conformation          :   0.492

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.596 (tight)
  Omega angle restraints         :   0.883
  Side chain planarity           :   0.811
  Improper dihedral distribution :   0.679
  B-factor distribution          :   1.317
  Inside/Outside distribution    :   1.038

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :   1.3
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.596 (tight)
  Omega angle restraints         :   0.883
  Side chain planarity           :   0.811
  Improper dihedral distribution :   0.679
  B-factor distribution          :   1.317
  Inside/Outside distribution    :   1.038
==============

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.