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 pdb2ojw.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 5.073
CA-only RMS fit for the two chains : 5.628

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and D

All-atom RMS fit for the two chains : 4.813
CA-only RMS fit for the two chains : 3.853

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and E

All-atom RMS fit for the two chains : 5.855
CA-only RMS fit for the two chains : 5.273

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: D and E

All-atom RMS fit for the two chains : 4.831
CA-only RMS fit for the two chains : 4.277

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: D and E

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.

1809 ADP   ( 501-)  A  -
1817 ADP   ( 501-)  B  -
1825 ADP   ( 501-)  C  -
1834 ADP   ( 501-)  D  -
1843 ADP   ( 501-)  E  -

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

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'.

 302 SER   ( 307-)  A      OG
 723 LEU   (  -1-)  C      CG
 723 LEU   (  -1-)  C      CD1
 723 LEU   (  -1-)  C      CD2
1388 THR   ( 301-)  D      OG1
1388 THR   ( 301-)  D      CG2

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: 15

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 406 ARG   (  45-)  B
 467 ARG   ( 106-)  B
 541 ARG   ( 181-)  B
 676 ARG   ( 319-)  B
1256 ARG   ( 169-)  D
1757 ARG   ( 319-)  E

Warning: Tyrosine convention problem

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

 105 TYR   ( 104-)  A
 138 TYR   ( 137-)  A
 180 TYR   ( 180-)  A
 283 TYR   ( 283-)  A
 331 TYR   ( 336-)  A
 465 TYR   ( 104-)  B
 498 TYR   ( 137-)  B
 540 TYR   ( 180-)  B
 693 TYR   ( 336-)  B
 741 TYR   (  17-)  C
 828 TYR   ( 104-)  C
 861 TYR   ( 137-)  C
 904 TYR   ( 180-)  C
1057 TYR   ( 336-)  C
1191 TYR   ( 104-)  D
1224 TYR   ( 137-)  D
1267 TYR   ( 180-)  D
1272 TYR   ( 185-)  D
1522 TYR   (  78-)  E
1581 TYR   ( 137-)  E
1624 TYR   ( 180-)  E
1629 TYR   ( 185-)  E
1774 TYR   ( 336-)  E

Warning: Phenylalanine convention problem

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

   2 PHE   (   1-)  A
  63 PHE   (  62-)  A
 103 PHE   ( 102-)  A
 332 PHE   ( 337-)  A
 423 PHE   (  62-)  B
 463 PHE   ( 102-)  B
 669 PHE   ( 312-)  B
 694 PHE   ( 337-)  B
 725 PHE   (   1-)  C
 786 PHE   (  62-)  C
 809 PHE   (  85-)  C
 826 PHE   ( 102-)  C
 855 PHE   ( 131-)  C
1058 PHE   ( 337-)  C
1149 PHE   (  62-)  D
1172 PHE   (  85-)  D
1189 PHE   ( 102-)  D
1291 PHE   ( 204-)  D
1395 PHE   ( 312-)  D
1420 PHE   ( 337-)  D
1506 PHE   (  62-)  E
1529 PHE   (  85-)  E
1750 PHE   ( 312-)  E
1775 PHE   ( 337-)  E

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.

  77 ASP   (  76-)  A
 143 ASP   ( 143-)  A
 453 ASP   (  92-)  B
 503 ASP   ( 143-)  B
1163 ASP   (  76-)  D
1376 ASP   ( 289-)  D
1520 ASP   (  76-)  E

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.

 196 GLU   ( 196-)  A
 358 GLU   ( 363-)  A
 495 GLU   ( 134-)  B
 556 GLU   ( 196-)  B
 570 GLU   ( 210-)  B
 720 GLU   ( 363-)  B
 824 GLU   ( 100-)  C
 920 GLU   ( 196-)  C
 927 GLU   ( 203-)  C
1290 GLU   ( 203-)  D
1515 GLU   (  71-)  E
1640 GLU   ( 196-)  E
1654 GLU   ( 210-)  E
1776 GLU   ( 338-)  E
1801 GLU   ( 363-)  E

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.

 237 THR   ( 237-)  A      CA   CB    1.62    4.6
 458 VAL   (  97-)  B      CA   CB    1.61    4.1
 594 VAL   ( 234-)  B      CA   CB    1.61    4.0
 865 GLY   ( 141-)  C      N    CA    1.38   -4.2
1027 THR   ( 306-)  C      CA   CB    1.63    4.9
1087 TYR   (   0-)  D      N    CA    1.54    4.1
1311 ILE   ( 224-)  D      CA   CB    1.63    5.1
1345 THR   ( 258-)  D      CB   CG2   1.37   -4.6
1632 VAL   ( 188-)  E      CA   CB    1.62    4.4

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.994423 -0.000411 -0.000682|
 | -0.000411  0.998204 -0.000112|
 | -0.000682 -0.000112  0.994984|
Proposed new scale matrix

 |  0.005666  0.000003  0.004854|
 |  0.000003  0.008172  0.000000|
 |  0.000007  0.000001  0.010455|
With corresponding cell

    A    = 176.598  B   = 122.374  C    = 126.019
    Alpha=  89.975  Beta= 130.627  Gamma=  90.047

The CRYST1 cell dimensions

    A    = 177.600  B   = 122.600  C    = 126.600
    Alpha=  90.000  Beta= 130.600  Gamma=  90.000

Variance: 1127.756
(Under-)estimated Z-score: 24.750

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.

 227 ARG   ( 227-)  A      CA   CB   CG  122.69    4.3
 227 ARG   ( 227-)  A      CG   CD   NE  102.17   -4.9
 353 THR   ( 358-)  A      N    CA   CB  118.72    4.8
 504 GLY   ( 144-)  B      N    CA   C   127.89    5.3
 622 ARG   ( 262-)  B      CG   CD   NE  117.37    4.0
 816 ASP   (  92-)  C      C    CA   CB  101.26   -4.7
 866 THR   ( 142-)  C     -CA  -C    N   106.76   -4.6
 866 THR   ( 142-)  C      C    CA   CB  118.60    4.5
 866 THR   ( 142-)  C      CA   CB   CG2 119.31    5.2
 866 THR   ( 142-)  C      CA   CB   OG1 116.58    4.7
 866 THR   ( 142-)  C      CG2  CB   OG1 123.80    7.3
 941 HIS   ( 217-)  C      CG   ND1  CE1 109.93    4.3
 986 ARG   ( 262-)  C      CG   CD   NE  101.33   -5.4
 986 ARG   ( 262-)  C      CD   NE   CZ  129.24    4.2
1304 HIS   ( 217-)  D      CG   ND1  CE1 110.05    4.4
1314 ARG   ( 227-)  D      CA   CB   CG  122.93    4.4
1314 ARG   ( 227-)  D      CG   CD   NE  102.73   -4.6
1371 HIS   ( 284-)  D      CG   ND1  CE1 109.63    4.0
1386 ARG   ( 299-)  D      CD   NE   CZ  129.31    4.2
1402 ARG   ( 319-)  D      CG   CD   NE  103.69   -4.0
1521 MET   (  77-)  E      CG   SD   CE  110.73    4.5
1697 HIS   ( 253-)  E      CG   ND1  CE1 109.73    4.1
1724 ARG   ( 280-)  E      CG   CD   NE  119.43    5.3
1728 HIS   ( 284-)  E      CG   ND1  CE1 109.67    4.1

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.

  77 ASP   (  76-)  A
 143 ASP   ( 143-)  A
 196 GLU   ( 196-)  A
 358 GLU   ( 363-)  A
 406 ARG   (  45-)  B
 453 ASP   (  92-)  B
 467 ARG   ( 106-)  B
 495 GLU   ( 134-)  B
 503 ASP   ( 143-)  B
 541 ARG   ( 181-)  B
 556 GLU   ( 196-)  B
 570 GLU   ( 210-)  B
 676 ARG   ( 319-)  B
 720 GLU   ( 363-)  B
 824 GLU   ( 100-)  C
 920 GLU   ( 196-)  C
 927 GLU   ( 203-)  C
1163 ASP   (  76-)  D
1256 ARG   ( 169-)  D
1290 GLU   ( 203-)  D
1376 ASP   ( 289-)  D
1515 GLU   (  71-)  E
1520 ASP   (  76-)  E
1640 GLU   ( 196-)  E
1654 GLU   ( 210-)  E
1757 ARG   ( 319-)  E
1776 GLU   ( 338-)  E
1801 GLU   ( 363-)  E

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.

  93 ASP   (  92-)  A      C     -9.7   -14.89    -0.01
 207 GLY   ( 207-)  A      C     11.0    14.53     0.06
 567 GLY   ( 207-)  B      C     10.4    13.84     0.06
 816 ASP   (  92-)  C      C     -7.0   -10.86    -0.01
 866 THR   ( 142-)  C      CB   -13.6     3.56    34.09
 931 GLY   ( 207-)  C      C     11.0    14.62     0.06
1179 ASP   (  92-)  D      C     -7.9   -12.20    -0.01
1294 GLY   ( 207-)  D      C     10.8    14.37     0.06
1536 ASP   (  92-)  E      C     -6.8   -10.47    -0.01
1651 GLY   ( 207-)  E      C     10.8    14.27     0.06
The average deviation= 1.211

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.

 504 GLY   ( 144-)  B    5.13

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.

 925 GLN   ( 201-)  C    5.03
1326 ASP   ( 239-)  D    4.81
 963 ASP   ( 239-)  C    4.23

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.

  94 PRO   (  93-)  A    -3.0
1180 PRO   (  93-)  D    -3.0
 817 PRO   (  93-)  C    -3.0
1537 PRO   (  93-)  E    -3.0
1512 LEU   (  68-)  E    -2.8
 792 LEU   (  68-)  C    -2.6
  69 LEU   (  68-)  A    -2.5
 452 LYS   (  91-)  B    -2.5
1247 PRO   ( 160-)  D    -2.4
 504 GLY   ( 144-)  B    -2.4
 784 TRP   (  60-)  C    -2.4
 467 ARG   ( 106-)  B    -2.4
1147 TRP   (  60-)  D    -2.4
1550 ARG   ( 106-)  E    -2.3
 421 TRP   (  60-)  B    -2.3
 454 PRO   (  93-)  B    -2.3
  61 TRP   (  60-)  A    -2.3
1504 TRP   (  60-)  E    -2.3
 520 PRO   ( 160-)  B    -2.3
 661 THR   ( 301-)  B    -2.3
1679 ILE   ( 235-)  E    -2.2
 330 GLY   ( 335-)  A    -2.2
 640 ARG   ( 280-)  B    -2.2
1603 GLY   ( 159-)  E    -2.2
1246 GLY   ( 159-)  D    -2.1
 159 GLY   ( 159-)  A    -2.1
1418 GLY   ( 335-)  D    -2.1
 692 GLY   ( 335-)  B    -2.1
1056 GLY   ( 335-)  C    -2.1
 160 PRO   ( 160-)  A    -2.1
  62 ASN   (  61-)  A    -2.1
1604 PRO   ( 160-)  E    -2.1
 936 ILE   ( 212-)  C    -2.1
1613 ARG   ( 169-)  E    -2.1
1375 TYR   ( 288-)  D    -2.1
1219 GLY   ( 132-)  D    -2.1
 493 GLY   ( 132-)  B    -2.1
 519 GLY   ( 159-)  B    -2.1
 883 GLY   ( 159-)  C    -2.1
 133 GLY   ( 132-)  A    -2.1
1576 GLY   ( 132-)  E    -2.0
 429 LEU   (  68-)  B    -2.0
 856 GLY   ( 132-)  C    -2.0
 211 GLY   ( 211-)  A    -2.0
 108 ARG   ( 107-)  A    -2.0
 288 TYR   ( 288-)  A    -2.0
1013 ASP   ( 289-)  C    -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.

  35 ASP   (  34-)  A  Poor phi/psi
  61 TRP   (  60-)  A  Poor phi/psi
  69 LEU   (  68-)  A  Poor phi/psi
  75 ASN   (  74-)  A  omega poor
  92 LYS   (  91-)  A  Poor phi/psi
  93 ASP   (  92-)  A  PRO omega poor
  96 LYS   (  95-)  A  omega poor
 100 CYS   (  99-)  A  omega poor
 107 ARG   ( 106-)  A  Poor phi/psi
 194 ASN   ( 194-)  A  omega poor
 200 ALA   ( 200-)  A  Poor phi/psi
 207 GLY   ( 207-)  A  PRO omega poor
 246 ASN   ( 246-)  A  Poor phi/psi
 265 ASN   ( 265-)  A  Poor phi/psi
 300 LEU   ( 300-)  A  omega poor
 312 ALA   ( 317-)  A  Poor phi/psi
 328 LYS   ( 333-)  A  Poor phi/psi
 365 MET   (   4-)  B  omega poor
 429 LEU   (  68-)  B  Poor phi/psi
 435 ASN   (  74-)  B  omega poor
 452 LYS   (  91-)  B  Poor phi/psi, omega poor
 453 ASP   (  92-)  B  PRO omega poor
 460 CYS   (  99-)  B  omega poor
 467 ARG   ( 106-)  B  Poor phi/psi
 472 THR   ( 111-)  B  omega poor
And so on for a total of 109 lines.

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!

   5 MET   (   4-)  A      0
  11 ASN   (  10-)  A      0
  12 LYS   (  11-)  A      0
  25 GLU   (  24-)  A      0
  43 CYS   (  42-)  A      0
  54 CYS   (  53-)  A      0
  61 TRP   (  60-)  A      0
  62 ASN   (  61-)  A      0
  68 THR   (  67-)  A      0
  69 LEU   (  68-)  A      0
  70 GLN   (  69-)  A      0
  75 ASN   (  74-)  A      0
  76 SER   (  75-)  A      0
  77 ASP   (  76-)  A      0
  82 PRO   (  81-)  A      0
  83 ALA   (  82-)  A      0
  84 ALA   (  83-)  A      0
  91 ARG   (  90-)  A      0
  92 LYS   (  91-)  A      0
  93 ASP   (  92-)  A      0
  94 PRO   (  93-)  A      0
 107 ARG   ( 106-)  A      0
 114 LEU   ( 113-)  A      0
 129 HIS   ( 128-)  A      0
 130 PRO   ( 129-)  A      0
And so on for a total of 695 lines.

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!

1056 GLY   ( 335-)  C   1.65   25
 211 GLY   ( 211-)  A   1.57   16
 330 GLY   ( 335-)  A   1.57   20
 692 GLY   ( 335-)  B   1.57   23
 571 GLY   ( 211-)  B   1.57   18
1655 GLY   ( 211-)  E   1.53   19

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]

 244 PRO   ( 244-)  A    0.10 LOW
 412 PRO   (  51-)  B    0.17 LOW
 604 PRO   ( 244-)  B    0.12 LOW
 832 PRO   ( 108-)  C    0.14 LOW
1242 PRO   ( 155-)  D    0.19 LOW
1331 PRO   ( 244-)  D    0.06 LOW
1601 PRO   ( 157-)  E    0.12 LOW
1688 PRO   ( 244-)  E    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].

  22 PRO   (  21-)  A  -114.6 envelop C-gamma (-108 degrees)
 208 PRO   ( 208-)  A    51.6 half-chair C-delta/C-gamma (54 degrees)
 520 PRO   ( 160-)  B   -54.6 half-chair C-beta/C-alpha (-54 degrees)
 568 PRO   ( 208-)  B    46.1 half-chair C-delta/C-gamma (54 degrees)
 705 PRO   ( 348-)  B  -112.3 envelop C-gamma (-108 degrees)
 812 PRO   (  88-)  C   -64.7 envelop C-beta (-72 degrees)
1247 PRO   ( 160-)  D   -59.5 half-chair C-beta/C-alpha (-54 degrees)
1295 PRO   ( 208-)  D    49.8 half-chair C-delta/C-gamma (54 degrees)
1734 PRO   ( 290-)  E    52.9 half-chair C-delta/C-gamma (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.

1570 ASN   ( 126-)  E      ND2 <-> 1848 HOH   (1660 )  E      O      0.60    2.10  INTRA
 418 LEU   (  57-)  B      CD1 <->  445 MET   (  84-)  B      CE     0.58    2.62  INTRA BL
 663 THR   ( 306-)  B      N   <-> 1845 HOH   (1717 )  B      O      0.54    2.16  INTRA
1225 THR   ( 138-)  D      CG2 <-> 1227 MET   ( 140-)  D      CE     0.53    2.67  INTRA BL
 728 MET   (   4-)  C      SD  <->  866 THR   ( 142-)  C      CG2    0.50    2.90  INTRA
 843 ARG   ( 119-)  C      NE  <-> 1846 HOH   (1623 )  C      O      0.50    2.20  INTRA
 284 HIS   ( 284-)  A      NE2 <->  353 THR   ( 358-)  A      CG2    0.44    2.66  INTRA BL
1505 ASN   (  61-)  E      ND2 <-> 1848 HOH   (1591 )  E      O      0.42    2.28  INTRA BL
 834 GLU   ( 110-)  C      OE1 <-> 1846 HOH   (1729 )  C      O      0.41    1.99  INTRA
 201 GLN   ( 201-)  A      NE2 <-> 1844 HOH   (1594 )  A      O      0.39    2.31  INTRA
1844 HOH   (1515 )  A      O   <-> 1844 HOH   (1771 )  A      O      0.39    1.81  INTRA
  24 GLY   (  23-)  A      O   <-> 1844 HOH   (1659 )  A      O      0.36    2.04  INTRA
 561 GLN   ( 201-)  B      NE2 <-> 1845 HOH   (1635 )  B      O      0.34    2.36  INTRA
1146 GLU   (  59-)  D      OE2 <-> 1847 HOH   (1732 )  D      O      0.34    2.06  INTRA
1562 LYS   ( 118-)  E      NZ  <-> 1848 HOH   (1713 )  E      O      0.34    2.36  INTRA
 972 ASN   ( 248-)  C      ND2 <-> 1846 HOH   (1732 )  C      O      0.33    2.37  INTRA BL
1844 HOH   (1671 )  A      O   <-> 1848 HOH   (1752 )  E      O      0.32    2.08  INTRA
 134 MET   ( 133-)  A    A CE  <->  347 THR   ( 352-)  A      CG2    0.31    2.89  INTRA BL
1363 LYS   ( 276-)  D      NZ  <-> 1445 ASN   ( 362-)  D      OD1    0.31    2.39  INTRA
 487 ASN   ( 126-)  B      OD1 <-> 1845 HOH   (1771 )  B      O      0.30    2.10  INTRA
1389 THR   ( 306-)  D      CG2 <-> 1847 HOH   (1679 )  D      O      0.30    2.50  INTRA
 128 GLN   ( 127-)  A      NE2 <-> 1844 HOH   (1606 )  A      O      0.29    2.41  INTRA
1571 GLN   ( 127-)  E      OE1 <-> 1848 HOH   (1583 )  E      O      0.24    2.16  INTRA
 640 ARG   ( 280-)  B      NH1 <->  722 GLY   ( 365-)  B      C      0.24    2.86  INTRA
1844 HOH   (1561 )  A      O   <-> 1844 HOH   (1791 )  A      O      0.23    1.97  INTRA
And so on for a total of 163 lines.

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

 514 PHE   ( 154-)  B      -7.20
1598 PHE   ( 154-)  E      -7.16
 154 PHE   ( 154-)  A      -7.12
1241 PHE   ( 154-)  D      -7.12
 878 PHE   ( 154-)  C      -7.01
 724 TYR   (   0-)  C      -6.94
1548 TYR   ( 104-)  E      -6.46
1095 HIS   (   8-)  D      -6.19
 465 TYR   ( 104-)  B      -6.13
1452 HIS   (   8-)  E      -6.06
   9 HIS   (   8-)  A      -6.03
 105 TYR   ( 104-)  A      -5.99
 369 HIS   (   8-)  B      -5.99
1596 ASN   ( 152-)  E      -5.97
 732 HIS   (   8-)  C      -5.94
1139 LYS   (  52-)  D      -5.92
1239 ASN   ( 152-)  D      -5.91
 512 ASN   ( 152-)  B      -5.89
1191 TYR   ( 104-)  D      -5.88
 152 ASN   ( 152-)  A      -5.86
 828 TYR   ( 104-)  C      -5.84
 776 LYS   (  52-)  C      -5.84
 413 LYS   (  52-)  B      -5.83
 830 ARG   ( 106-)  C      -5.80
 876 ASN   ( 152-)  C      -5.77
And so on for a total of 53 lines.

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: 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: 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: C

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: D

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: E

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.

 529 ARG   ( 169-)  B   -2.70
 893 ARG   ( 169-)  C   -2.69
1256 ARG   ( 169-)  D   -2.69
1549 ASN   ( 105-)  E   -2.61
1500 GLU   (  56-)  E   -2.60
 106 ASN   ( 105-)  A   -2.55
 466 ASN   ( 105-)  B   -2.54
1192 ASN   ( 105-)  D   -2.54
 829 ASN   ( 105-)  C   -2.51

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

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

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.

1847 HOH   (1680 )  D      O     21.53   16.55  -13.15
1847 HOH   (1685 )  D      O     25.94   14.84  -12.33

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.

1844 HOH   (1791 )  A      O
1845 HOH   (1678 )  B      O
1845 HOH   (1715 )  B      O
1845 HOH   (1787 )  B      O
1846 HOH   (1656 )  C      O
1846 HOH   (1714 )  C      O
1846 HOH   (1775 )  C      O
1846 HOH   (1777 )  C      O
1847 HOH   (1774 )  D      O
1848 HOH   (1712 )  E      O
1848 HOH   (1768 )  E      O
1848 HOH   (1769 )  E      O
Marked this atom as acceptor 1807  CL  (1403-) E     CL
Marked this atom as acceptor 1808  CL  (1405-) A     CL
Marked this atom as acceptor 1816  CL  (1401-) B     CL
Marked this atom as acceptor 1824  CL  (1402-) C     CL
Marked this atom as acceptor 1833  CL  (1404-) D     CL
Metal-coordinating Histidine residue 253 fixed to   1
Metal-coordinating Histidine residue 613 fixed to   1
Metal-coordinating Histidine residue 977 fixed to   1
Metal-coordinating Histidine residue1340 fixed to   1
Metal-coordinating Histidine residue1697 fixed to   1

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.

  62 ASN   (  61-)  A
  70 GLN   (  69-)  A
 422 ASN   (  61-)  B
 785 ASN   (  61-)  C
 793 GLN   (  69-)  C
 972 ASN   ( 248-)  C
1095 HIS   (   8-)  D
1102 GLN   (  15-)  D
1148 ASN   (  61-)  D
1428 ASN   ( 345-)  D
1454 ASN   (  10-)  E
1505 ASN   (  61-)  E

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.

  33 TRP   (  32-)  A      NE1
  50 SER   (  49-)  A      N
  54 CYS   (  53-)  A      N
  62 ASN   (  61-)  A      N
  69 LEU   (  68-)  A      N
  77 ASP   (  76-)  A      N
 106 ASN   ( 105-)  A      N
 169 ARG   ( 169-)  A      NE
 247 TRP   ( 247-)  A      N
 257 SER   ( 257-)  A      OG
 280 ARG   ( 280-)  A      NE
 280 ARG   ( 280-)  A      NH2
 289 ASP   ( 289-)  A      N
 295 ASP   ( 295-)  A      N
 331 TYR   ( 336-)  A      N
 335 ARG   ( 340-)  A      NH2
 353 THR   ( 358-)  A      OG1
 357 ASN   ( 362-)  A      N
 393 TRP   (  32-)  B      NE1
 406 ARG   (  45-)  B      NH1
 414 CYS   (  53-)  B      N
 422 ASN   (  61-)  B      N
 430 GLN   (  69-)  B      NE2
 466 ASN   ( 105-)  B      N
 561 GLN   ( 201-)  B      NE2
And so on for a total of 78 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 284 HIS   ( 284-)  A      NE2
1288 GLN   ( 201-)  D      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1844 HOH   (1660 )  A      O  0.88  K  5 Ion-B
1844 HOH   (1770 )  A      O  0.99  K  4
1844 HOH   (1786 )  A      O  0.88  K  5
1845 HOH   (1760 )  B      O  0.80 NA  4 *2
1846 HOH   (1650 )  C      O  1.01  K  4 Ion-B
1847 HOH   (1598 )  D      O  1.05  K  5
1848 HOH   (1605 )  E      O  0.99  K  5 Ion-B
1848 HOH   (1616 )  E      O  0.92  K  4 Ion-B
1848 HOH   (1699 )  E      O  0.98  K  4

Warning: Possible wrong residue type

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

  60 GLU   (  59-)  A   H-bonding suggests Gln; but Alt-Rotamer
1121 ASP   (  34-)  D   H-bonding suggests Asn; but Alt-Rotamer
1394 ASP   ( 311-)  D   H-bonding suggests Asn
1587 ASP   ( 143-)  E   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 :  -0.798
  2nd generation packing quality :  -1.330
  Ramachandran plot appearance   :  -1.110
  chi-1/chi-2 rotamer normality  :  -0.868
  Backbone conformation          :  -0.074

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.861
  Bond angles                    :   0.878
  Omega angle restraints         :   1.245
  Side chain planarity           :   1.060
  Improper dihedral distribution :   1.076
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   1.042

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 :  -0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.861
  Bond angles                    :   0.878
  Omega angle restraints         :   1.245
  Side chain planarity           :   1.060
  Improper dihedral distribution :   1.076
  B-factor distribution          :   0.660
  Inside/Outside distribution    :   1.042
==============

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.