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 pdb2rma.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  72.600  B   = 160.900  C    =  95.300
    Alpha=  90.000  Beta=  90.600  Gamma=  90.000

Dimensions of a reduced cell

    A    =  72.600  B   =  95.300  C    = 160.900
    Alpha=  90.000  Beta=  90.000  Gamma=  89.400

Dimensions of the conventional cell

    A    =  72.600  B   =  95.300  C    = 160.900
    Alpha=  90.000  Beta=  90.000  Gamma=  89.400

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  0.000000  0.000000 -1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: P

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 C

All-atom RMS fit for the two chains : 0.439
CA-only RMS fit for the two chains : 0.225

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 C

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 E

All-atom RMS fit for the two chains : 0.454
CA-only RMS fit for the two chains : 0.179

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 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: A and G

All-atom RMS fit for the two chains : 0.457
CA-only RMS fit for the two chains : 0.208

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 G

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 I

All-atom RMS fit for the two chains : 0.439
CA-only RMS fit for the two chains : 0.167

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 I

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 K

All-atom RMS fit for the two chains : 0.482
CA-only RMS fit for the two chains : 0.272

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 K

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

1712 DAL   (   1-)  B  -
1713 MVA   (   4-)  B  -
1714 BMT   (   5-)  B  -
1715 ABA   (   6-)  B  -
1716 SAR   (   7-)  B  -
1718 DAL   (   1-)  D  -
1719 MVA   (   4-)  D  -
1720 BMT   (   5-)  D  -
1721 ABA   (   6-)  D  -
1722 SAR   (   7-)  D  -
1724 DAL   (   1-)  F  -
1725 MVA   (   4-)  F  -
1726 BMT   (   5-)  F  -
1727 ABA   (   6-)  F  -
1728 SAR   (   7-)  F  -
1730 DAL   (   1-)  H  -
1731 MVA   (   4-)  H  -
1732 BMT   (   5-)  H  -
1733 ABA   (   6-)  H  -
1734 SAR   (   7-)  H  -
1736 DAL   (   1-)  J  -
1737 MVA   (   4-)  J  -
1738 BMT   (   5-)  J  -
1739 ABA   (   6-)  J  -
1740 SAR   (   7-)  J  -
1742 DAL   (   1-)  L  -
1743 MVA   (   4-)  L  -
1744 BMT   (   5-)  L  -
1745 ABA   (   6-)  L  -
1746 SAR   (   7-)  L  -
1748 DAL   (   1-)  N  -
1749 MVA   (   4-)  N  -
1750 BMT   (   5-)  N  -
1751 ABA   (   6-)  N  -
1752 SAR   (   7-)  N  -
1754 DAL   (   1-)  P  -
1755 MVA   (   4-)  P  -
1756 BMT   (   5-)  P  -
1757 ABA   (   6-)  P  -
1758 SAR   (   7-)  P  -
1760 DAL   (   1-)  R  -
1761 MVA   (   4-)  R  -
1762 BMT   (   5-)  R  -
1763 ABA   (   6-)  R  -
1764 SAR   (   7-)  R  -
1766 SAR   (   7-)  T  -
1767 ABA   (   6-)  T  -
1768 BMT   (   5-)  T  -
1769 MVA   (   4-)  T  -
1770 DAL   (   1-)  T  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

 166 MLE   (   2-)  B  -   N   bound to 1712 DAL   (   1-)  B  -   C
 337 MLE   (   2-)  D  -   N   bound to 1718 DAL   (   1-)  D  -   C
 508 MLE   (   2-)  F  -   N   bound to 1724 DAL   (   1-)  F  -   C
 679 MLE   (   2-)  H  -   N   bound to 1730 DAL   (   1-)  H  -   C
 850 MLE   (   2-)  J  -   N   bound to 1736 DAL   (   1-)  J  -   C
1021 MLE   (   2-)  L  -   N   bound to 1742 DAL   (   1-)  L  -   C
1192 MLE   (   2-)  N  -   N   bound to 1748 DAL   (   1-)  N  -   C
1363 MLE   (   2-)  P  -   N   bound to 1754 DAL   (   1-)  P  -   C
1534 MLE   (   2-)  R  -   N   bound to 1760 DAL   (   1-)  R  -   C
1705 MLE   (   2-)  T  -   N   bound to 1770 DAL   (   1-)  T  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: S

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 166 MLE   (   2-)  B
 167 MLE   (   3-)  B
 168 MLE   (   8-)  B
 169 VAL   (   9-)  B
 170 MLE   (  10-)  B
 337 MLE   (   2-)  D
 338 MLE   (   3-)  D
 339 MLE   (   8-)  D
 341 MLE   (  10-)  D
 508 MLE   (   2-)  F
 509 MLE   (   3-)  F
 510 MLE   (   8-)  F
 512 MLE   (  10-)  F
 679 MLE   (   2-)  H
 680 MLE   (   3-)  H
 681 MLE   (   8-)  H
 683 MLE   (  10-)  H
 850 MLE   (   2-)  J
 851 MLE   (   3-)  J
 852 MLE   (   8-)  J
 854 MLE   (  10-)  J
1021 MLE   (   2-)  L
1022 MLE   (   3-)  L
1023 MLE   (   8-)  L
1025 MLE   (  10-)  L
1192 MLE   (   2-)  N
1193 MLE   (   3-)  N
1194 MLE   (   8-)  N
1196 MLE   (  10-)  N
1363 MLE   (   2-)  P
1364 MLE   (   3-)  P
1365 MLE   (   8-)  P
1367 MLE   (  10-)  P
1534 MLE   (   2-)  R
1535 MLE   (   3-)  R
1536 MLE   (   8-)  R
1538 MLE   (  10-)  R
1705 MLE   (   2-)  T
1706 MLE   (   3-)  T
1707 MLE   (   8-)  T
1709 MLE   (  10-)  T

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 MET   (   1-)  A    High
 165 GLU   ( 165-)  A    High
 336 GLU   ( 165-)  C    High
 343 MET   (   1-)  E    High
 507 GLU   ( 165-)  E    High
 514 MET   (   1-)  G    High
 678 GLU   ( 165-)  G    High
 832 ARG   ( 148-)  I    High
 849 GLU   ( 165-)  I    High
1020 GLU   ( 165-)  K    High
1027 MET   (   1-)  M    High
1041 GLU   (  15-)  M    High
1174 ARG   ( 148-)  M    High
1198 MET   (   1-)  O    High
1362 GLU   ( 165-)  O    High
1369 MET   (   1-)  Q    High
1533 GLU   ( 165-)  Q    High
1540 MET   (   1-)  S    High
1704 GLU   ( 165-)  S    High

Warning: What type of B-factor?

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

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

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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: S

Geometric checks

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

 |  1.001422 -0.000302  0.000147|
 | -0.000302  1.000324 -0.000129|
 |  0.000147 -0.000129  1.000290|
Proposed new scale matrix

 |  0.013754  0.000004  0.000142|
 |  0.000002  0.006213  0.000000|
 | -0.000002  0.000001  0.010491|
With corresponding cell

    A    =  72.704  B   = 160.953  C    =  95.325
    Alpha=  90.008  Beta=  90.583  Gamma=  90.035

The CRYST1 cell dimensions

    A    =  72.600  B   = 160.900  C    =  95.300
    Alpha=  90.000  Beta=  90.600  Gamma=  90.000

Variance: 32.073
(Under-)estimated Z-score: 4.174

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.

   8 PHE   (   8-)  A      CA   CB   CG  118.37    4.6
  13 ASP   (  13-)  A      CA   CB   CG  116.86    4.3
  34 GLU   (  34-)  A      CB   CG   CD  120.11    4.4
  46 PHE   (  46-)  A      CA   CB   CG  118.97    5.2
  60 PHE   (  60-)  A      CA   CB   CG  119.08    5.3
  67 PHE   (  67-)  A      CA   CB   CG  118.86    5.1
  81 GLU   (  81-)  A      C    CA   CB  101.04   -4.8
  81 GLU   (  81-)  A      CA   CB   CG  125.90    5.9
  83 PHE   (  83-)  A      CA   CB   CG  120.23    6.4
  87 ASN   (  87-)  A      CA   CB   CG  118.13    5.5
  91 LYS   (  91-)  A      CG   CD   CE  122.22    4.7
  99 SER   (  99-)  A      N    CA   CB  103.70   -4.0
  99 SER   (  99-)  A      CA   CB   OG  119.34    4.1
 106 ASN   ( 106-)  A      ND2  CG   OD1 118.05   -4.5
 113 PHE   ( 113-)  A      CA   CB   CG  118.37    4.6
 118 LYS   ( 118-)  A      CG   CD   CE  100.40   -4.7
 120 GLU   ( 120-)  A      CA   CB   CG  122.58    4.2
 121 TRP   ( 121-)  A      CG   CD2  CE2 101.59   -4.7
 137 ASN   ( 137-)  A      ND2  CG   OD1 118.51   -4.1
 157 THR   ( 157-)  A      CA   CB   OG1 103.32   -4.2
 158 ILE   ( 158-)  A      N    CA   C    99.79   -4.1
 172 MET   (   1-)  C      N    CA   C    99.15   -4.3
 179 PHE   (   8-)  C      CA   CB   CG  120.75    7.0
 205 GLU   (  34-)  C      CB   CG   CD  119.56    4.1
 231 PHE   (  60-)  C      CA   CB   CG  117.81    4.0
And so on for a total of 198 lines.

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.

1028 VAL   (   2-)  M    4.47
 354 VAL   (  12-)  E    4.36
1488 GLU   ( 120-)  Q    4.33
 515 VAL   (   2-)  G    4.25
 729 GLY   (  45-)  I    4.07

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.

 355 ASP   (  13-)  E    5.15
1528 ASP   ( 160-)  Q    4.67
1186 ASP   ( 160-)  M    4.65
 673 ASP   ( 160-)  G    4.57
 184 ASP   (  13-)  C    4.48
 160 ASP   ( 160-)  A    4.28
 502 ASP   ( 160-)  E    4.26
 849 GLU   ( 165-)  I    4.21
 976 TRP   ( 121-)  K    4.09

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.

1438 HIS   (  70-)  Q      CB   6.69
1609 HIS   (  70-)  S      CB   5.52
1323 HIS   ( 126-)  O      CB   5.05
1267 HIS   (  70-)  O      CB   4.92
 981 HIS   ( 126-)  K      CB   4.63
1665 HIS   ( 126-)  S      CB   4.52
1096 HIS   (  70-)  M      CB   4.41
 297 HIS   ( 126-)  C      CB   4.36
 126 HIS   ( 126-)  A      CB   4.31
1494 HIS   ( 126-)  Q      CB   4.17
 967 PHE   ( 112-)  K      CB   4.11
 754 HIS   (  70-)  I      CB   4.06
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.986

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.

1499 LYS   ( 131-)  Q    -2.4
 916 MET   (  61-)  K    -2.3
1258 MET   (  61-)  O    -2.3
  61 MET   (  61-)  A    -2.3
  60 PHE   (  60-)  A    -2.3
1600 MET   (  61-)  S    -2.3
 574 MET   (  61-)  G    -2.3
 232 MET   (  61-)  C    -2.2
1039 ASP   (  13-)  M    -2.2
 697 ASP   (  13-)  I    -2.2
 745 MET   (  61-)  I    -2.2
1648 GLY   ( 109-)  S    -2.2
 403 MET   (  61-)  E    -2.2
1429 MET   (  61-)  Q    -2.2
1087 MET   (  61-)  M    -2.2
 280 GLY   ( 109-)  C    -2.2
1173 SER   ( 147-)  M    -2.2
1306 GLY   ( 109-)  O    -2.1
1477 GLY   ( 109-)  Q    -2.1
1381 ASP   (  13-)  Q    -2.1
 622 GLY   ( 109-)  G    -2.1
 451 GLY   ( 109-)  E    -2.1
 793 GLY   ( 109-)  I    -2.1
 109 GLY   ( 109-)  A    -2.1
 964 GLY   ( 109-)  K    -2.1
1257 PHE   (  60-)  O    -2.1
1135 GLY   ( 109-)  M    -2.1
 915 PHE   (  60-)  K    -2.1
 868 ASP   (  13-)  K    -2.1
1177 LYS   ( 151-)  M    -2.1
 402 PHE   (  60-)  E    -2.1
 835 LYS   ( 151-)  I    -2.1
1040 GLY   (  14-)  M    -2.1
 323 THR   ( 152-)  C    -2.1
 573 PHE   (  60-)  G    -2.1
 231 PHE   (  60-)  C    -2.1
 744 PHE   (  60-)  I    -2.0
 489 SER   ( 147-)  E    -2.0
1552 ASP   (  13-)  S    -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.

  70 HIS   (  70-)  A  Poor phi/psi
  71 ASN   (  71-)  A  Poor phi/psi
  87 ASN   (  87-)  A  Poor phi/psi
 106 ASN   ( 106-)  A  Poor phi/psi
 135 GLY   ( 135-)  A  Poor phi/psi
 184 ASP   (  13-)  C  Poor phi/psi
 185 GLY   (  14-)  C  Poor phi/psi
 241 HIS   (  70-)  C  Poor phi/psi
 355 ASP   (  13-)  E  Poor phi/psi
 356 GLY   (  14-)  E  Poor phi/psi
 412 HIS   (  70-)  E  Poor phi/psi
 429 ASN   (  87-)  E  Poor phi/psi
 475 LYS   ( 133-)  E  Poor phi/psi
 526 ASP   (  13-)  G  Poor phi/psi
 527 GLY   (  14-)  G  Poor phi/psi
 583 HIS   (  70-)  G  Poor phi/psi
 600 ASN   (  87-)  G  Poor phi/psi
 619 ASN   ( 106-)  G  Poor phi/psi
 677 LEU   ( 164-)  G  Poor phi/psi
 754 HIS   (  70-)  I  Poor phi/psi
 771 ASN   (  87-)  I  Poor phi/psi
 790 ASN   ( 106-)  I  Poor phi/psi
 925 HIS   (  70-)  K  Poor phi/psi
 961 ASN   ( 106-)  K  Poor phi/psi
1039 ASP   (  13-)  M  Poor phi/psi
1096 HIS   (  70-)  M  Poor phi/psi
1113 ASN   (  87-)  M  Poor phi/psi
1132 ASN   ( 106-)  M  Poor phi/psi
1267 HIS   (  70-)  O  Poor phi/psi
1284 ASN   (  87-)  O  Poor phi/psi
1303 ASN   ( 106-)  O  Poor phi/psi
1332 GLY   ( 135-)  O  Poor phi/psi
1438 HIS   (  70-)  Q  Poor phi/psi
1455 ASN   (  87-)  Q  Poor phi/psi
1474 ASN   ( 106-)  Q  Poor phi/psi
1609 HIS   (  70-)  S  Poor phi/psi
1626 ASN   (  87-)  S  Poor phi/psi
1645 ASN   ( 106-)  S  Poor phi/psi
1649 SER   ( 110-)  S  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.304

Warning: Unusual rotamers

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

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

 895 SER   (  40-)  K    0.33
 724 SER   (  40-)  I    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  12 VAL   (  12-)  A      0
  16 PRO   (  16-)  A      0
  25 PHE   (  25-)  A      0
  26 ALA   (  26-)  A      0
  28 LYS   (  28-)  A      0
  43 GLU   (  43-)  A      0
  44 LYS   (  44-)  A      0
  46 PHE   (  46-)  A      0
  48 TYR   (  48-)  A      0
  49 LYS   (  49-)  A      0
  51 SER   (  51-)  A      0
  53 PHE   (  53-)  A      0
  54 HIS   (  54-)  A      0
  55 ARG   (  55-)  A      0
  58 PRO   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  68 THR   (  68-)  A      0
  70 HIS   (  70-)  A      0
  71 ASN   (  71-)  A      0
  73 THR   (  73-)  A      0
  79 TYR   (  79-)  A      0
  81 GLU   (  81-)  A      0
  83 PHE   (  83-)  A      0
  86 GLU   (  86-)  A      0
And so on for a total of 863 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 : 3.811

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]

  58 PRO   (  58-)  A    0.45 HIGH
 266 PRO   (  95-)  C    0.45 HIGH

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].

 447 PRO   ( 105-)  E  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 529 PRO   (  16-)  G  -117.7 half-chair C-delta/C-gamma (-126 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.

1710 ALA   (  11-)  T      C   <-> 1770 DAL   (   1-)  T      N      1.37    1.33  INTRA BL
1767 ABA   (   6-)  T      N   <-> 1768 BMT   (   5-)  T      C      1.37    1.33  INTRA BL
1766 SAR   (   7-)  T      N   <-> 1767 ABA   (   6-)  T      C      1.36    1.34  INTRA BL
1705 MLE   (   2-)  T      N   <-> 1770 DAL   (   1-)  T      C      1.36    1.34  INTRA BL
1707 MLE   (   8-)  T      N   <-> 1766 SAR   (   7-)  T      C      1.35    1.35  INTRA BL
1706 MLE   (   3-)  T      C   <-> 1769 MVA   (   4-)  T      N      1.35    1.35  INTRA BL
1768 BMT   (   5-)  T      N   <-> 1769 MVA   (   4-)  T      C      1.35    1.35  INTRA BL
1768 BMT   (   5-)  T      CA  <-> 1769 MVA   (   4-)  T      C      0.80    2.40  INTRA BL
1707 MLE   (   8-)  T      CA  <-> 1766 SAR   (   7-)  T      C      0.79    2.41  INTRA BL
1705 MLE   (   2-)  T      CA  <-> 1770 DAL   (   1-)  T      C      0.77    2.43  INTRA BL
1705 MLE   (   2-)  T      CN  <-> 1770 DAL   (   1-)  T      C      0.74    2.46  INTRA BL
1707 MLE   (   8-)  T      CN  <-> 1766 SAR   (   7-)  T      C      0.72    2.48  INTRA BL
1768 BMT   (   5-)  T      CN  <-> 1769 MVA   (   4-)  T      C      0.71    2.49  INTRA BL
1710 ALA   (  11-)  T      CA  <-> 1770 DAL   (   1-)  T      N      0.69    2.41  INTRA BL
1767 ABA   (   6-)  T      CA  <-> 1768 BMT   (   5-)  T      C      0.66    2.44  INTRA BL
1706 MLE   (   3-)  T      CA  <-> 1769 MVA   (   4-)  T      N      0.60    2.50  INTRA BL
1766 SAR   (   7-)  T      CN  <-> 1767 ABA   (   6-)  T      C      0.58    2.52  INTRA BL
1766 SAR   (   7-)  T      CA  <-> 1767 ABA   (   6-)  T      C      0.56    2.44  INTRA BL
 736 CYS   (  52-)  I      SG  <->  839 LYS   ( 155-)  I      NZ     0.46    2.84  INTRA BF
1706 MLE   (   3-)  T      O   <-> 1769 MVA   (   4-)  T      N      0.46    2.24  INTRA BL
1710 ALA   (  11-)  T      O   <-> 1770 DAL   (   1-)  T      N      0.42    2.28  INTRA BL
1768 BMT   (   5-)  T      CN  <-> 1769 MVA   (   4-)  T      CA     0.30    2.90  INTRA BL
 355 ASP   (  13-)  E      CG  <->  496 LYS   ( 154-)  E      NZ     0.29    2.81  INTRA BF
1705 MLE   (   2-)  T      CN  <-> 1770 DAL   (   1-)  T      CA     0.26    2.94  INTRA BL
 184 ASP   (  13-)  C      CG  <->  325 LYS   ( 154-)  C      NZ     0.25    2.85  INTRA BF
And so on for a total of 266 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

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.

 319 ARG   ( 148-)  C      -7.91
 490 ARG   ( 148-)  E      -7.82
 148 ARG   ( 148-)  A      -7.71
 661 ARG   ( 148-)  G      -7.67
1687 ARG   ( 148-)  S      -7.65
1516 ARG   ( 148-)  Q      -7.62
1174 ARG   ( 148-)  M      -7.61
1345 ARG   ( 148-)  O      -7.48
1003 ARG   ( 148-)  K      -7.30
 832 ARG   ( 148-)  I      -7.28
 999 ARG   ( 144-)  K      -5.68
1341 ARG   ( 144-)  O      -5.63
 828 ARG   ( 144-)  I      -5.62
 315 ARG   ( 144-)  C      -5.57
 144 ARG   ( 144-)  A      -5.53
1170 ARG   ( 144-)  M      -5.53
1512 ARG   ( 144-)  Q      -5.52
 657 ARG   ( 144-)  G      -5.51
 857 VAL   (   2-)  K      -5.50
 515 VAL   (   2-)  G      -5.41
 686 VAL   (   2-)  I      -5.40
1541 VAL   (   2-)  S      -5.39
1199 VAL   (   2-)  O      -5.39
   2 VAL   (   2-)  A      -5.38
 344 VAL   (   2-)  E      -5.37
1028 VAL   (   2-)  M      -5.35
 486 ARG   ( 144-)  E      -5.33
 853 VAL   (   9-)  J      -5.30
1370 VAL   (   2-)  Q      -5.29
1024 VAL   (   9-)  L      -5.25
 169 VAL   (   9-)  B      -5.19
 682 VAL   (   9-)  H      -5.19
1683 ARG   ( 144-)  S      -5.18
 173 VAL   (   2-)  C      -5.17
1195 VAL   (   9-)  N      -5.16
1708 VAL   (   9-)  T      -5.15
 340 VAL   (   9-)  D      -5.14
 511 VAL   (   9-)  F      -5.11
1537 VAL   (   9-)  R      -5.10

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: 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: E

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: G

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: I

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: K

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: M

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: O

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: Q

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: S

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: C

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: S

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.

1779 HOH   (2001 )  J      O
1785 HOH   (2001 )  P      O
1789 HOH   (2001 )  T      O
Unrecognized bound group for 167
  Bound atom= 1713 MVA  (   4-) B      N

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.

   5 THR   (   5-)  A      OG1
  46 PHE   (  46-)  A      N
  65 GLY   (  65-)  A      N
  82 LYS   (  82-)  A      N
  87 ASN   (  87-)  A      N
 102 ASN   ( 102-)  A      N
 117 ALA   ( 117-)  A      N
 121 TRP   ( 121-)  A      N
 154 LYS   ( 154-)  A      N
 176 THR   (   5-)  C      OG1
 217 PHE   (  46-)  C      N
 236 GLY   (  65-)  C      N
 258 ASN   (  87-)  C      N
 273 ASN   ( 102-)  C      N
 288 ALA   ( 117-)  C      N
 292 TRP   ( 121-)  C      N
 325 LYS   ( 154-)  C      N
 328 THR   ( 157-)  C      OG1
 347 THR   (   5-)  E      OG1
 386 LYS   (  44-)  E      N
 429 ASN   (  87-)  E      N
 436 GLY   (  94-)  E      N
 444 ASN   ( 102-)  E      N
 459 ALA   ( 117-)  E      N
 463 TRP   ( 121-)  E      N
And so on for a total of 82 lines.

Warning: No crystallisation information

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

Warning: 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.

1776 HOH   (2053 )  G      O  0.90  K  4
1778 HOH   (2062 )  I      O  0.86  K  4
1786 HOH   (2024 )  Q      O  1.00  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.

 357 GLU   (  15-)  E   H-bonding suggests Gln
 599 GLU   (  86-)  G   H-bonding suggests Gln; but Alt-Rotamer
1283 GLU   (  86-)  O   H-bonding suggests Gln; 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 :  -1.013
  2nd generation packing quality :  -1.206
  Ramachandran plot appearance   :  -0.986
  chi-1/chi-2 rotamer normality  :  -1.304
  Backbone conformation          :  -0.340

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.614 (tight)
  Bond angles                    :   1.287
  Omega angle restraints         :   0.693 (tight)
  Side chain planarity           :   1.227
  Improper dihedral distribution :   1.138
  B-factor distribution          :   0.919
  Inside/Outside distribution    :   0.952

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.614 (tight)
  Bond angles                    :   1.287
  Omega angle restraints         :   0.693 (tight)
  Side chain planarity           :   1.227
  Improper dihedral distribution :   1.138
  B-factor distribution          :   0.919
  Inside/Outside distribution    :   0.952
==============

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.