WHAT IF Check report

This file was created 2011-12-16 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 pdb3ml5.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.

 265 AZM   ( 264-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 8.83

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

   7 TYR   (   7-)  A
  40 TYR   (  40-)  A
  51 TYR   (  51-)  A
  88 TYR   (  88-)  A
 128 TYR   ( 128-)  A
 194 TYR   ( 194-)  A

Warning: Phenylalanine convention problem

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

 169 PHE   ( 169-)  A
 226 PHE   ( 226-)  A
 231 PHE   ( 231-)  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.

  72 ASP   (  72-)  A
 110 ASP   ( 110-)  A
 139 ASP   ( 139-)  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.

  72 ASP   (  72-)  A
 110 ASP   ( 110-)  A
 139 ASP   ( 139-)  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.

 207 VAL   ( 207-)  A    4.18

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

   3 HIS   (   3-)  A      CB   6.01
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.180

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 THR   (  80-)  A    -2.7
 176 PHE   ( 176-)  A    -2.4
   3 HIS   (   3-)  A    -2.2
  92 GLN   (  92-)  A    -2.1
 193 THR   ( 193-)  A    -2.1
  83 PRO   (  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.

   3 HIS   (   3-)  A  Poor phi/psi
  29 SER   (  29-)  A  PRO omega poor
 201 PRO   ( 201-)  A  PRO omega poor
 203 LEU   ( 203-)  A  Poor phi/psi
 243 ASN   ( 243-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.525

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 HIS   (   3-)  A      0
   5 TRP   (   5-)  A      0
   7 TYR   (   7-)  A      0
  19 LEU   (  19-)  A      0
  24 GLN   (  24-)  A      0
  27 ARG   (  27-)  A      0
  28 GLN   (  28-)  A      0
  29 SER   (  29-)  A      0
  54 CYS   (  54-)  A      0
  55 MET   (  55-)  A      0
  56 SER   (  56-)  A      0
  58 SER   (  58-)  A      0
  62 ASN   (  62-)  A      0
  64 HIS   (  64-)  A      0
  65 SER   (  65-)  A      0
  66 VAL   (  66-)  A      0
  72 ASP   (  72-)  A      0
  77 THR   (  77-)  A      0
  80 THR   (  80-)  A      0
  83 PRO   (  83-)  A      0
  85 GLU   (  85-)  A      0
  91 LYS   (  91-)  A      0
  92 GLN   (  92-)  A      0
 101 HIS   ( 101-)  A      0
 103 VAL   ( 103-)  A      0
And so on for a total of 123 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.600

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]

  46 PRO   (  46-)  A    0.13 LOW
 247 PRO   ( 247-)  A    0.14 LOW

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].

  87 PRO   (  87-)  A    41.9 envelop C-delta (36 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.

   2 HIS   (   2-)  A      NE2 <->   64 HIS   (  64-)  A      NE2    0.48    2.52  INTRA
   3 HIS   (   3-)  A      CG  <->    4 GLY   (   4-)  A      N      0.48    2.52  INTRA BF
   3 HIS   (   3-)  A      ND1 <->    4 GLY   (   4-)  A      N      0.37    2.53  INTRA BF
   3 HIS   (   3-)  A      NE2 <->   19 LEU   (  19-)  A      CD1    0.36    2.74  INTRA
   3 HIS   (   3-)  A      CE1 <->   20 TYR   (  20-)  A      CE1    0.23    2.97  INTRA
 168 ARG   ( 168-)  A      NE  <->  266 HOH   ( 434 )  A      O      0.23    2.47  INTRA
 238 ARG   ( 238-)  A      NH2 <->  266 HOH   ( 491 )  A      O      0.18    2.52  INTRA
 137 ALA   ( 137-)  A      O   <->  206 SER   ( 206-)  A      CB     0.16    2.64  INTRA BL
 182 LYS   ( 182-)  A      NZ  <->  266 HOH   ( 479 )  A      O      0.15    2.55  INTRA
 189 ARG   ( 189-)  A      NH2 <->  266 HOH   ( 464 )  A      O      0.13    2.57  INTRA
   2 HIS   (   2-)  A      CE1 <->   64 HIS   (  64-)  A      NE2    0.12    2.98  INTRA
  74 ASP   (  74-)  A      OD2 <->   76 ARG   (  76-)  A      NE     0.11    2.59  INTRA BF
   3 HIS   (   3-)  A      CB  <->    4 GLY   (   4-)  A      N      0.10    2.60  INTRA BF
 107 HIS   ( 107-)  A      NE2 <->  194 TYR   ( 194-)  A      OH     0.09    2.61  INTRA BL
  60 THR   (  60-)  A      N   <->   67 GLN   (  67-)  A      O      0.09    2.61  INTRA BL
 117 GLU   ( 117-)  A      OE2 <->  119 HIS   ( 119-)  A      NE2    0.07    2.63  INTRA BL
   3 HIS   (   3-)  A      CE1 <->    5 TRP   (   5-)  A      CB     0.07    3.13  INTRA
 101 HIS   ( 101-)  A      ND1 <->  266 HOH   ( 510 )  A      O      0.07    2.63  INTRA
  62 ASN   (  62-)  A      ND2 <->   64 HIS   (  64-)  A      N      0.07    2.78  INTRA BL
  72 ASP   (  72-)  A      C   <->   74 ASP   (  74-)  A      N      0.06    2.84  INTRA
 229 LEU   ( 229-)  A      O   <->  241 MET   ( 241-)  A      N      0.06    2.64  INTRA BL
   3 HIS   (   3-)  A      CD2 <->   19 LEU   (  19-)  A      CD1    0.04    3.16  INTRA
  25 GLY   (  25-)  A      O   <->  252 LYS   ( 252-)  A      NZ     0.04    2.66  INTRA BL
  60 THR   (  60-)  A      O   <->   67 GLN   (  67-)  A      N      0.03    2.67  INTRA BL
   9 GLN   (   9-)  A      N   <->  266 HOH   ( 419 )  A      O      0.03    2.67  INTRA
  97 TRP   (  97-)  A      NE1 <->  241 MET   ( 241-)  A      O      0.03    2.67  INTRA BL
  55 MET   (  55-)  A      N   <->   56 SER   (  56-)  A      N      0.02    2.58  INTRA BL
  72 ASP   (  72-)  A      N   <->   73 SER   (  73-)  A      N      0.01    2.59  INTRA BL
 231 PHE   ( 231-)  A      N   <->  232 THR   ( 232-)  A      N      0.01    2.59  INTRA BL
 159 ARG   ( 159-)  A      NH2 <->  177 SER   ( 177-)  A    A O      0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 261 ARG   ( 261-)  A      -7.15
  85 GLU   (  85-)  A      -6.17
   9 GLN   (   9-)  A      -6.02
   2 HIS   (   2-)  A      -5.78
  24 GLN   (  24-)  A      -5.68
  37 GLN   (  37-)  A      -5.44
 213 ARG   ( 213-)  A      -5.23
  44 LEU   (  44-)  A      -5.06

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.

  18 LYS   (  18-)  A   -2.58

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.

 266 HOH   ( 473 )  A      O    -22.03  -10.44   15.81
 266 HOH   ( 481 )  A      O     10.59  -13.30   -5.72
 266 HOH   ( 502 )  A      O     -0.01  -13.18   -5.33
 266 HOH   ( 557 )  A      O     12.69   22.74   13.25

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.

  24 GLN   (  24-)  A
  32 ASN   (  32-)  A
  62 ASN   (  62-)  A
  67 GLN   (  67-)  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.

   4 GLY   (   4-)  A      N
   5 TRP   (   5-)  A      NE1
  20 TYR   (  20-)  A      OH
  31 ILE   (  31-)  A      N
  75 ASP   (  75-)  A      N
  76 ARG   (  76-)  A      N
  77 THR   (  77-)  A      OG1
 100 LYS   ( 100-)  A      N
 130 THR   ( 130-)  A      N
 188 SER   ( 188-)  A      N
 200 THR   ( 200-)  A      N
 219 SER   ( 219-)  A      OG
 238 ARG   ( 238-)  A      NH2
 245 PHE   ( 245-)  A      N
 260 PHE   ( 260-)  A      N
Only metal coordination for   96 HIS  (  96-) A      NE2
Only metal coordination for  119 HIS  ( 119-) A      ND1

Warning: Possible wrong residue type

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

  69 ASP   (  69-)  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 :  -0.404
  2nd generation packing quality :  -1.198
  Ramachandran plot appearance   :  -1.180
  chi-1/chi-2 rotamer normality  :  -1.525
  Backbone conformation          :  -1.311

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.289 (tight)
  Bond angles                    :   0.716
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.289 (tight)
  Improper dihedral distribution :   0.636
  Inside/Outside distribution    :   0.983

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -1.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.289 (tight)
  Bond angles                    :   0.716
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.289 (tight)
  Improper dihedral distribution :   0.636
  Inside/Outside distribution    :   0.983
==============

WHAT IF
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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Ion Checks
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      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
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Checking checks
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      Who checks the checkers
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