WHAT IF Check report

This file was created 2011-12-17 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 pdb2nsb.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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 109 PRO   ( 109-)  A      CG
 109 PRO   ( 109-)  A      CD

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.

   1 MET   (   1-)  A    High
   2 GLU   (   2-)  A    High
   3 VAL   (   3-)  A    High
   4 LYS   (   4-)  A    High
   8 ARG   (   8-)  A    High
   9 ASP   (   9-)  A    High
  10 LYS   (  10-)  A    High
  11 ASN   (  11-)  A    High
  12 ARG   (  12-)  A    High
  22 GLU   (  22-)  A    High
  23 GLU   (  23-)  A    High
  26 GLN   (  26-)  A    High
  30 LYS   (  30-)  A    High
  33 ARG   (  33-)  A    High
  36 ASN   (  36-)  A    High
  37 GLN   (  37-)  A    High
  38 ARG   (  38-)  A    High
  39 VAL   (  39-)  A    High
  40 GLU   (  40-)  A    High
  41 ILE   (  41-)  A    High
  42 PRO   (  42-)  A    High
  43 GLY   (  43-)  A    High
  44 PHE   (  44-)  A    High
  45 ARG   (  45-)  A    High
  46 LYS   (  46-)  A    High
And so on for a total of 59 lines.

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: 4

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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

  17 TYR   (  17-)  A
  34 TYR   (  34-)  A
  65 TYR   (  65-)  A

Warning: Phenylalanine convention problem

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

  19 PHE   (  19-)  A

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.

   9 ASP   (   9-)  A
  29 ASP   (  29-)  A
  72 ASP   (  72-)  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.

   2 GLU   (   2-)  A
   5 GLU   (   5-)  A
  23 GLU   (  23-)  A
  40 GLU   (  40-)  A
  60 GLU   (  60-)  A
  93 GLU   (  93-)  A
 107 GLU   ( 107-)  A
 108 GLU   ( 108-)  A

Geometric checks

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.

 109 PRO   ( 109-)  A      N    CA   CB  109.57    6.0

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.

   2 GLU   (   2-)  A
   5 GLU   (   5-)  A
   9 ASP   (   9-)  A
  23 GLU   (  23-)  A
  29 ASP   (  29-)  A
  40 GLU   (  40-)  A
  60 GLU   (  60-)  A
  72 ASP   (  72-)  A
  93 GLU   (  93-)  A
 107 GLU   ( 107-)  A
 108 GLU   ( 108-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

  22 GLU   (  22-)  A    4.11

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.694

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.

  58 LEU   (  58-)  A    -2.3
  75 PRO   (  75-)  A    -2.3
  98 THR   (  98-)  A    -2.3
  91 GLU   (  91-)  A    -2.2
  88 ILE   (  88-)  A    -2.1
  83 LEU   (  83-)  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.

   6 LEU   (   6-)  A  Poor phi/psi
  10 LYS   (  10-)  A  Poor phi/psi
  38 ARG   (  38-)  A  Poor phi/psi
  58 LEU   (  58-)  A  Poor phi/psi
  76 ASP   (  76-)  A  Poor phi/psi
  92 ARG   (  92-)  A  Poor phi/psi
 108 GLU   ( 108-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.866

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.866

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

  61 GLU   (  61-)  A    0.36

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!

   7 GLU   (   7-)  A      0
   9 ASP   (   9-)  A      0
  10 LYS   (  10-)  A      0
  11 ASN   (  11-)  A      0
  12 ARG   (  12-)  A      0
  38 ARG   (  38-)  A      0
  39 VAL   (  39-)  A      0
  42 PRO   (  42-)  A      0
  46 LYS   (  46-)  A      0
  48 ARG   (  48-)  A      0
  58 LEU   (  58-)  A      0
  60 GLU   (  60-)  A      0
  84 ILE   (  84-)  A      0
  85 LEU   (  85-)  A      0
  90 THR   (  90-)  A      0
  91 GLU   (  91-)  A      0
  92 ARG   (  92-)  A      0
  93 GLU   (  93-)  A      0
  97 VAL   (  97-)  A      0
  49 ILE   (  49-)  A      1
   6 LEU   (   6-)  A      2
  44 PHE   (  44-)  A      2
  57 LYS   (  57-)  A      2
  86 SER   (  86-)  A      2
 100 ARG   ( 100-)  A      2
 107 GLU   ( 107-)  A      2

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 : 1.095

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

 109 PRO   ( 109-)  A    0.00 LOW

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.

  35 LEU   (  35-)  A      O   <->   38 ARG   (  38-)  A      N      0.29    2.41  INTRA BF
  53 VAL   (  53-)  A      O   <->   57 LYS   (  57-)  A      N      0.16    2.54  INTRA BF
  71 MET   (  71-)  A      O   <->   74 ILE   (  74-)  A      N      0.14    2.56  INTRA BL
  31 ALA   (  31-)  A      CA  <->   69 PHE   (  69-)  A      CE2    0.14    3.06  INTRA BL
  24 ILE   (  24-)  A      O   <->   28 GLU   (  28-)  A      N      0.12    2.58  INTRA BL
  54 LEU   (  54-)  A      O   <->   58 LEU   (  58-)  A      N      0.11    2.59  INTRA BF
  78 LEU   (  78-)  A      CD1 <->   87 PRO   (  87-)  A      CG     0.10    3.10  INTRA BL
  25 ALA   (  25-)  A      O   <->   29 ASP   (  29-)  A      N      0.06    2.64  INTRA BL
  74 ILE   (  74-)  A      N   <->   75 PRO   (  75-)  A      CD     0.06    2.94  INTRA BL
  75 PRO   (  75-)  A      C   <->   77 THR   (  77-)  A      N      0.05    2.85  INTRA BL
  28 GLU   (  28-)  A      O   <->   31 ALA   (  31-)  A      CB     0.05    2.75  INTRA BL
  26 GLN   (  26-)  A      O   <->   30 LYS   (  30-)  A      N      0.02    2.68  INTRA BL
  22 GLU   (  22-)  A      O   <->   25 ALA   (  25-)  A      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: 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.

  48 ARG   (  48-)  A      -6.73
 100 ARG   ( 100-)  A      -6.54
 108 GLU   ( 108-)  A      -6.42
  92 ARG   (  92-)  A      -6.39
  85 LEU   (  85-)  A      -6.34
 107 GLU   ( 107-)  A      -5.80
 106 HIS   ( 106-)  A      -5.61
  45 ARG   (  45-)  A      -5.56
  82 LYS   (  82-)  A      -5.39
  91 GLU   (  91-)  A      -5.25
  97 VAL   (  97-)  A      -5.13

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  82 LYS   (  82-)  A        85 - LEU     85- ( A)         -5.26
  90 THR   (  90-)  A        92 - ARG     92- ( A)         -5.24
 106 HIS   ( 106-)  A       108 - GLU    108- ( A)         -5.94

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 109 : -1.924

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.

  63 GLN   (  63-)  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.

   7 GLU   (   7-)  A      N
  79 LYS   (  79-)  A      N
  85 LEU   (  85-)  A      N
  89 VAL   (  89-)  A      N
 106 HIS   ( 106-)  A      N

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.

  68 ASP   (  68-)  A   H-bonding suggests Asn

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 :  -3.559
  2nd generation packing quality :  -0.623
  Ramachandran plot appearance   :  -4.694 (bad)
  chi-1/chi-2 rotamer normality  :  -4.866 (bad)
  Backbone conformation          :   1.158

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.459 (tight)
  Bond angles                    :   0.636 (tight)
  Omega angle restraints         :   0.199 (tight)
  Side chain planarity           :   0.304 (tight)
  Improper dihedral distribution :   0.644
  B-factor distribution          :   0.516
  Inside/Outside distribution    :   1.104

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 : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.2
  2nd generation packing quality :   1.3
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.4
  Backbone conformation          :   2.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.459 (tight)
  Bond angles                    :   0.636 (tight)
  Omega angle restraints         :   0.199 (tight)
  Side chain planarity           :   0.304 (tight)
  Improper dihedral distribution :   0.644
  B-factor distribution          :   0.516
  Inside/Outside distribution    :   1.104
==============

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

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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
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DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.