WHAT IF Check report

This file was created 2012-01-30 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 pdb3crt.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.

 216 GSH   ( 215-)  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) :150.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.518 over 1592 bonds
Average difference in B over a bond : 3.12
RMS difference in B over a bond : 4.14

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: Phenylalanine convention problem

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

 179 PHE   ( 179-)  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.

  25 GLU   (  25-)  A
  51 GLU   (  51-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 109 ILE   ( 109-)  A      CB   CG1   1.27   -8.5
 110 ALA   ( 110-)  A      N    CA    1.55    5.0
 111 TYR   ( 111-)  A      CA   C     1.43   -4.6
 111 TYR   ( 111-)  A      CA   CB    1.86   16.5
 112 SER   ( 112-)  A      N   -C     1.45    6.1
 113 LYS   ( 113-)  A      CB   CG    1.84   10.5
 114 ASP   ( 114-)  A      CB   CG    1.64    5.1

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.496
RMS-deviation in bond distances: 0.012

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 109 ILE   ( 109-)  A      CA   CB   CG2  91.36  -11.3
 110 ALA   ( 110-)  A      C    CA   CB  100.21   -6.9
 111 TYR   ( 111-)  A      CA   C    O   111.81   -5.3
 111 TYR   ( 111-)  A      N    CA   CB  103.26   -4.3
 111 TYR   ( 111-)  A      C    CA   CB   93.65   -8.7
 113 LYS   ( 113-)  A      CA   CB   CG  103.65   -5.2
 114 ASP   ( 114-)  A      CA   CB   CG  107.52   -5.1
 171 ASP   ( 171-)  A      N    CA   C    98.60   -4.5

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.

  25 GLU   (  25-)  A
  51 GLU   (  51-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 109 ILE   ( 109-)  A      CB     8.6    43.50    32.31
 111 TYR   ( 111-)  A      CA    12.3    53.42    34.03
The average deviation= 0.784

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.

  14 VAL   (  14-)  A    5.98
 171 ASP   ( 171-)  A    4.29

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.

 187 PRO   ( 187-)  A    -2.4
   7 TYR   (   7-)  A    -2.3
  54 ASN   (  54-)  A    -2.3
  14 VAL   (  14-)  A    -2.2
  63 VAL   (  63-)  A    -2.1
   5 LEU   (   5-)  A    -2.1
  53 PRO   (  53-)  A    -2.1
  32 LEU   (  32-)  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.

   2 SER   (   2-)  A  Poor phi/psi
  12 GLY   (  12-)  A  Poor phi/psi
  25 GLU   (  25-)  A  Poor phi/psi
  54 ASN   (  54-)  A  Poor phi/psi
  55 LEU   (  55-)  A  PRO omega poor
  80 ASN   (  80-)  A  Poor phi/psi
  84 GLY   (  84-)  A  Poor phi/psi
 111 TYR   ( 111-)  A  Poor phi/psi
 172 ALA   ( 172-)  A  Poor phi/psi
 201 TRP   ( 201-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.484

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 TYR   (   7-)  A      0
   8 TRP   (   8-)  A      0
   9 LYS   (   9-)  A      0
  10 ILE   (  10-)  A      0
  11 LYS   (  11-)  A      0
  13 LEU   (  13-)  A      0
  37 GLU   (  37-)  A      0
  53 PRO   (  53-)  A      0
  54 ASN   (  54-)  A      0
  55 LEU   (  55-)  A      0
  62 ASP   (  62-)  A      0
  63 VAL   (  63-)  A      0
  66 THR   (  66-)  A      0
  81 MET   (  81-)  A      0
  82 LEU   (  82-)  A      0
  85 CYS   (  85-)  A      0
 110 ALA   ( 110-)  A      0
 111 TYR   ( 111-)  A      0
 139 HIS   ( 139-)  A      0
 142 TYR   ( 142-)  A      0
 144 ASN   ( 144-)  A      0
 146 ASP   ( 146-)  A      0
 150 HIS   ( 150-)  A      0
 151 PRO   ( 151-)  A      0
 165 MET   ( 165-)  A      0
And so on for a total of 63 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 : 1.685

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!

  83 GLY   (  83-)  A   1.92   14

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.

 110 ALA   ( 110-)  A      O   <->  111 TYR   ( 111-)  A      CD2    0.75    1.95  INTRA
 110 ALA   ( 110-)  A      O   <->  111 TYR   ( 111-)  A      CB     0.59    2.01  INTRA
 110 ALA   ( 110-)  A      O   <->  111 TYR   ( 111-)  A      CG     0.59    2.11  INTRA
  10 ILE   (  10-)  A      O   <->   18 ARG   (  18-)  A      NH2    0.33    2.37  INTRA BL
  96 GLU   (  96-)  A      OE2 <->  150 HIS   ( 150-)  A      NE2    0.27    2.43  INTRA
  42 ARG   (  42-)  A      NH1 <->   46 PHE   (  46-)  A      CE2    0.21    2.89  INTRA BF
  67 GLN   (  67-)  A      NE2 <->  216 GSH   ( 215-)  A      N1     0.21    2.79  INTRA
 126 LEU   ( 126-)  A      N   <->  127 PRO   ( 127-)  A      CD     0.19    2.81  INTRA BL
 110 ALA   ( 110-)  A      C   <->  111 TYR   ( 111-)  A      CG     0.19    2.91  INTRA
 144 ASN   ( 144-)  A      N   <->  217 HOH   ( 229 )  A      O      0.18    2.52  INTRA BF
 110 ALA   ( 110-)  A      C   <->  111 TYR   ( 111-)  A      CB     0.18    2.62  INTRA B3
 159 LEU   ( 159-)  A      O   <->  163 LEU   ( 163-)  A      CD2    0.17    2.63  INTRA
  91 GLU   (  91-)  A      OE2 <->  136 ARG   ( 136-)  A      NH1    0.15    2.55  INTRA
 150 HIS   ( 150-)  A      N   <->  151 PRO   ( 151-)  A      CD     0.14    2.86  INTRA BL
  91 GLU   (  91-)  A      OE2 <->  136 ARG   ( 136-)  A      NH2    0.13    2.57  INTRA
 122 PHE   ( 122-)  A      CD2 <->  165 MET   ( 165-)  A      CE     0.13    3.07  INTRA
  31 HIS   (  31-)  A      ND1 <->   57 TYR   (  57-)  A      OH     0.13    2.57  INTRA BL
 110 ALA   ( 110-)  A      C   <->  111 TYR   ( 111-)  A      CD2    0.12    2.98  INTRA
  21 LEU   (  21-)  A      CD1 <->   75 ILE   (  75-)  A      CD1    0.12    3.08  INTRA
  61 GLY   (  61-)  A      N   <->   62 ASP   (  62-)  A      N      0.12    2.48  INTRA B3
  23 TYR   (  23-)  A      CD2 <->   24 LEU   (  24-)  A      CD1    0.11    3.09  INTRA
  55 LEU   (  55-)  A      O   <->  216 GSH   ( 215-)  A      N2     0.11    2.59  INTRA
  60 ASP   (  60-)  A      C   <->   62 ASP   (  62-)  A      N      0.11    2.79  INTRA
  39 ASP   (  39-)  A      CG  <->   40 LYS   (  40-)  A      N      0.10    2.90  INTRA
 119 LYS   ( 119-)  A      CG  <->  165 MET   ( 165-)  A      CE     0.10    3.10  INTRA
 171 ASP   ( 171-)  A      O   <->  172 ALA   ( 172-)  A      CB     0.10    2.50  INTRA
  63 VAL   (  63-)  A      CG2 <->   64 LYS   (  64-)  A      N      0.10    2.90  INTRA
   4 ILE   (   4-)  A      CD1 <->   29 GLU   (  29-)  A      CB     0.10    3.10  INTRA
  35 ARG   (  35-)  A      NH1 <->  214 ASP   ( 214-)  A      CG     0.09    3.01  INTRA
 117 THR   ( 117-)  A      O   <->  120 VAL   ( 120-)  A      CG1    0.09    2.71  INTRA
  17 THR   (  17-)  A      O   <->   21 LEU   (  21-)  A      CD1    0.09    2.71  INTRA
  54 ASN   (  54-)  A      ND2 <->  216 GSH   ( 215-)  A      N3     0.08    2.92  INTRA
  41 TRP   (  41-)  A      O   <->   45 LYS   (  45-)  A      N      0.08    2.62  INTRA
 111 TYR   ( 111-)  A      CE1 <->  207 GLN   ( 207-)  A      NE2    0.08    3.02  INTRA
 123 LEU   ( 123-)  A      CD1 <->  165 MET   ( 165-)  A      CE     0.08    3.12  INTRA
  96 GLU   (  96-)  A      O   <->   99 VAL   (  99-)  A      CG2    0.07    2.73  INTRA
  20 LEU   (  20-)  A      CD2 <->   24 LEU   (  24-)  A      CD1    0.06    3.14  INTRA
  99 VAL   (  99-)  A      CG2 <->  100 LEU   ( 100-)  A      N      0.06    2.94  INTRA
  99 VAL   (  99-)  A      CG2 <->  154 MET   ( 154-)  A      CE     0.06    3.14  INTRA
 149 THR   ( 149-)  A      C   <->  151 PRO   ( 151-)  A      CD     0.05    3.15  INTRA BL
 114 ASP   ( 114-)  A      CB  <->  118 LEU   ( 118-)  A      CD1    0.05    3.15  INTRA
   7 TYR   (   7-)  A      CG  <->    8 TRP   (   8-)  A      N      0.05    2.95  INTRA BL
  72 ILE   (  72-)  A      CG2 <->   73 ARG   (  73-)  A      N      0.05    2.95  INTRA BL
  73 ARG   (  73-)  A      O   <->   77 ASP   (  77-)  A      N      0.03    2.67  INTRA BL
 186 ILE   ( 186-)  A      O   <->  190 ASP   ( 190-)  A      N      0.02    2.68  INTRA BL
  15 GLN   (  15-)  A      N   <->   16 PRO   (  16-)  A      CD     0.02    2.98  INTRA BL
 170 LEU   ( 170-)  A      C   <->  171 ASP   ( 171-)  A      C      0.01    2.79  INTRA B3

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.

  27 LYS   (  27-)  A      -5.99
  52 PHE   (  52-)  A      -5.59
 139 HIS   ( 139-)  A      -5.31

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: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 217 HOH   ( 330 )  A      O
 217 HOH   ( 332 )  A      O
 217 HOH   ( 367 )  A      O

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.

  15 GLN   (  15-)  A
  54 ASN   (  54-)  A
  67 GLN   (  67-)  A
 147 HIS   ( 147-)  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.

   8 TRP   (   8-)  A      N
  28 TYR   (  28-)  A      N
  36 ASP   (  36-)  A      N
  40 LYS   (  40-)  A      N
  41 TRP   (  41-)  A      NE1
  62 ASP   (  62-)  A      N
  68 SER   (  68-)  A      N
  85 CYS   (  85-)  A      N
 111 TYR   ( 111-)  A      N
 140 LYS   ( 140-)  A      N
 149 THR   ( 149-)  A      OG1
 206 TRP   ( 206-)  A      N
 210 PHE   ( 210-)  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.

  29 GLU   (  29-)  A   H-bonding suggests Gln
  47 GLU   (  47-)  A   H-bonding suggests Gln; but Alt-Rotamer
 121 ASP   ( 121-)  A   H-bonding suggests Asn
 152 ASP   ( 152-)  A   H-bonding suggests Asn; but Alt-Rotamer
 184 GLU   ( 184-)  A   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.554
  2nd generation packing quality :  -1.863
  Ramachandran plot appearance   :  -0.586
  chi-1/chi-2 rotamer normality  :  -2.484
  Backbone conformation          :  -0.056

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.496 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.306 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.908
  B-factor distribution          :   1.518 (loose)
  Inside/Outside distribution    :   1.048

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.496 (tight)
  Bond angles                    :   0.722
  Omega angle restraints         :   0.306 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.908
  B-factor distribution          :   1.518 (loose)
  Inside/Outside distribution    :   1.048
==============

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.