WHAT IF Check report

This file was created 2011-12-28 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 pdb1hcs.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.

 115 PTR   ( 101-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

   1 GLU   ( 102-)  A  -   N   bound to  115 PTR   ( 101-)  A  -   C

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: 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Warning: Temperature factors given as "U", not as "B"

The average temperature factor found is very low. Probably they are given as "U" values, and not as "B" values. Values will be multiplied by 8-pi-squared for the analysis of B-factors.

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 : 3.224 over 579 bonds
Average difference in B over a bond : 9.44
RMS difference in B over a bond : 15.65

Note: B-factor plot

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

Chain identifier: B

Geometric checks

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

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.

  15 PHE   ( 150-)  B      CA   CB   CG  109.53   -4.3
  37 PHE   ( 172-)  B      CA   CB   CG  109.53   -4.3
  56 PHE   ( 191-)  B      CA   CB   CG  109.45   -4.3
  66 HIS   ( 201-)  B      CA   CB   CG  109.54   -4.3
  77 PHE   ( 212-)  B      CA   CB   CG  109.69   -4.1
  85 PHE   ( 220-)  B      CA   CB   CG  109.51   -4.3
  98 HIS   ( 233-)  B      CA   CB   CG  109.57   -4.2
 104 HIS   ( 239-)  B      CA   CB   CG  109.59   -4.2

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  70 ARG   ( 205-)  B    8.52
  34 ARG   ( 169-)  B    8.11
  40 ARG   ( 175-)  B    7.99
  20 ARG   ( 155-)  B    7.40
  82 ARG   ( 217-)  B    7.15
  25 ARG   ( 160-)  B    6.16
 105 ARG   ( 240-)  B    4.68

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 : -4.858

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.

  45 THR   ( 180-)  B    -2.6
  38 LEU   ( 173-)  B    -2.4
  98 HIS   ( 233-)  B    -2.4
  15 PHE   ( 150-)  B    -2.3
 102 LEU   ( 237-)  B    -2.2
  75 GLY   ( 210-)  B    -2.2
 100 ASP   ( 235-)  B    -2.1
  40 ARG   ( 175-)  B    -2.0
  57 ASP   ( 192-)  B    -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.

  45 THR   ( 180-)  B  Poor phi/psi
  78 TYR   ( 213-)  B  Poor phi/psi
 100 ASP   ( 235-)  B  Poor phi/psi
 104 HIS   ( 239-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -6.749

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 : -6.749

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.

  23 SER   ( 158-)  B    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!

   3 ILE   ( 104-)  A      0
   4 GLU   ( 105-)  A      0
   5 MET   ( 140-)  B      0
   6 ASP   ( 141-)  B      0
  10 ALA   ( 145-)  B      0
  13 TRP   ( 148-)  B      0
  15 PHE   ( 150-)  B      0
  17 LYS   ( 152-)  B      0
  28 LEU   ( 163-)  B      0
  29 ASN   ( 164-)  B      0
  34 ARG   ( 169-)  B      0
  36 THR   ( 171-)  B      0
  42 SER   ( 177-)  B      0
  43 GLU   ( 178-)  B      0
  46 LYS   ( 181-)  B      0
  48 ALA   ( 183-)  B      0
  58 ASN   ( 193-)  B      0
  59 ALA   ( 194-)  B      0
  60 LYS   ( 195-)  B      0
  62 LEU   ( 197-)  B      0
  74 SER   ( 209-)  B      0
  79 ILE   ( 214-)  B      0
  81 SER   ( 216-)  B      0
  82 ARG   ( 217-)  B      0
  83 THR   ( 218-)  B      0
And so on for a total of 53 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 : 0.193

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  75 GLY   ( 210-)  B   1.59   80

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].

  33 PRO   ( 168-)  B   -61.8 half-chair C-beta/C-alpha (-54 degrees)
 111 PRO   ( 246-)  B   -63.0 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.

   1 GLU   ( 102-)  A      N   <->  115 PTR   ( 101-)  A      C      1.40    1.30  INTRA BF
 112 ACE   ( 100-)  A      C   <->  115 PTR   ( 101-)  A      N      1.39    1.31  INTRA BF
   1 GLU   ( 102-)  A      CA  <->  115 PTR   ( 101-)  A      C      0.78    2.42  INTRA BF
 112 ACE   ( 100-)  A      CH3 <->  115 PTR   ( 101-)  A      N      0.67    2.43  INTRA BF
 112 ACE   ( 100-)  A      O   <->  115 PTR   ( 101-)  A      N      0.50    2.20  INTRA BF
  28 LEU   ( 163-)  B      CD2 <->   64 VAL   ( 199-)  B      CG2    0.35    2.85  INTRA BL
  76 GLY   ( 211-)  B      C   <->   77 PHE   ( 212-)  B      CD1    0.25    2.85  INTRA BF
  38 LEU   ( 173-)  B      CD2 <->  110 CYS   ( 245-)  B      SG     0.21    3.19  INTRA BF
  26 LEU   ( 161-)  B      O   <->   32 ASN   ( 167-)  B      ND2    0.21    2.49  INTRA BL
  11 GLU   ( 146-)  B      OE2 <->   13 TRP   ( 148-)  B      CZ2    0.19    2.61  INTRA BF
  28 LEU   ( 163-)  B      CG  <->   64 VAL   ( 199-)  B      CG2    0.19    3.01  INTRA BL
  76 GLY   ( 211-)  B      C   <->   77 PHE   ( 212-)  B      CG     0.18    2.92  INTRA BL
  37 PHE   ( 172-)  B      CD1 <->  108 THR   ( 243-)  B      O      0.18    2.62  INTRA BF
  56 PHE   ( 191-)  B      CD1 <->   57 ASP   ( 192-)  B      N      0.16    2.84  INTRA BF
   5 MET   ( 140-)  B      CG  <->    6 ASP   ( 141-)  B      N      0.16    2.84  INTRA BF
   3 ILE   ( 104-)  A      CD1 <->   67 TYR   ( 202-)  B      CE2    0.14    3.06  INTRA BF
  92 VAL   ( 227-)  B      O   <->   96 SER   ( 231-)  B      CB     0.14    2.66  INTRA BL
  52 SER   ( 187-)  B      C   <->   53 VAL   ( 188-)  B      CG2    0.11    2.99  INTRA BL
   1 GLU   ( 102-)  A      CA  <->  115 PTR   ( 101-)  A      O      0.11    2.69  INTRA BF
 112 ACE   ( 100-)  A      O   <->  115 PTR   ( 101-)  A      CA     0.11    2.69  INTRA BF
  87 SER   ( 222-)  B      C   <->   89 GLN   ( 224-)  B      N      0.10    2.80  INTRA BL
  27 LEU   ( 162-)  B      CD1 <->   64 VAL   ( 199-)  B      CG1    0.10    3.10  INTRA BL
  72 LEU   ( 207-)  B      C   <->   74 SER   ( 209-)  B      N      0.06    2.84  INTRA BL
   5 MET   ( 140-)  B      O   <->    7 SER   ( 142-)  B      N      0.06    2.64  INTRA BF
  68 LYS   ( 203-)  B      N   <->  115 PTR   ( 101-)  A      CD1    0.06    3.04  INTRA BF
  87 SER   ( 222-)  B      O   <->   89 GLN   ( 224-)  B      N      0.05    2.65  INTRA BL
  13 TRP   ( 148-)  B      CE3 <->   39 VAL   ( 174-)  B      CG2    0.05    3.15  INTRA BL
  37 PHE   ( 172-)  B      CE1 <->  108 THR   ( 243-)  B      O      0.04    2.76  INTRA BF
  92 VAL   ( 227-)  B      O   <->   96 SER   ( 231-)  B      OG     0.04    2.36  INTRA BL
  42 SER   ( 177-)  B      OG  <->   48 ALA   ( 183-)  B      O      0.03    2.37  INTRA BF
  48 ALA   ( 183-)  B      C   <->   49 TYR   ( 184-)  B      CD1    0.03    3.07  INTRA BF
  49 TYR   ( 184-)  B      C   <->   50 CYS   ( 185-)  B      SG     0.02    3.28  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: 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.

  60 LYS   ( 195-)  B      -6.62
  34 ARG   ( 169-)  B      -5.81
  82 ARG   ( 217-)  B      -5.41
  17 LYS   ( 152-)  B      -5.22

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 - 111 : -1.594

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   ( 146-)  B      N
  13 TRP   ( 148-)  B      N
  16 GLY   ( 151-)  B      N
  18 ILE   ( 153-)  B      N
  23 SER   ( 158-)  B      OG
  31 GLU   ( 166-)  B      N
  40 ARG   ( 175-)  B      NH1
  40 ARG   ( 175-)  B      NH2
  45 THR   ( 180-)  B      N
  60 LYS   ( 195-)  B      N
  68 LYS   ( 203-)  B      N
  79 ILE   ( 214-)  B      N
  80 THR   ( 215-)  B      N
  83 THR   ( 218-)  B      N
  87 SER   ( 222-)  B      N
  95 TYR   ( 230-)  B      OH

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  43 GLU   ( 178-)  B   H-bonding suggests Gln
  55 ASP   ( 190-)  B   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 :  -2.735
  2nd generation packing quality :  -2.216
  Ramachandran plot appearance   :  -4.858 (bad)
  chi-1/chi-2 rotamer normality  :  -6.749 (bad)
  Backbone conformation          :  -1.109

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.007
  Omega angle restraints         :   0.035 (tight)
  Side chain planarity           :   2.805 (loose)
  Improper dihedral distribution :   0.734
  B-factor distribution          :   3.224 (loose)
  Inside/Outside distribution    :   0.919
==============

WHAT IF
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DSSP
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Matthews' Coefficient
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Protein side chain planarity
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Quality Control
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
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Checking checks
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      Who checks the checkers
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