WHAT IF Check report

This file was created 2012-01-31 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 pdb2oau.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 C

All-atom RMS fit for the two chains : 2.329
CA-only RMS fit for the two chains : 2.316

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 D

All-atom RMS fit for the two chains : 1.329
CA-only RMS fit for the two chains : 1.313

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 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: A and E

All-atom RMS fit for the two chains : 0.602
CA-only RMS fit for the two chains : 0.573

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 F

All-atom RMS fit for the two chains : 1.966
CA-only RMS fit for the two chains : 1.939

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 F

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 : 1.725
CA-only RMS fit for the two chains : 1.712

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

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 192663.828
Volume of the Unit Cell V= 8844274.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.738
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.770

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

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

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

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 TYR   (  27-)  A    High
   2 ALA   (  28-)  A    High
   3 VAL   (  29-)  A    High
   4 ASN   (  30-)  A    High
   5 ILE   (  31-)  A    High
   6 VAL   (  32-)  A    High
   7 ALA   (  33-)  A    High
   8 ALA   (  34-)  A    High
   9 LEU   (  35-)  A    High
  10 ALA   (  36-)  A    High
  11 ILE   (  37-)  A    High
  12 ILE   (  38-)  A    High
  13 ILE   (  39-)  A    High
  14 VAL   (  40-)  A    High
  15 GLY   (  41-)  A    High
  16 LEU   (  42-)  A    High
  17 ILE   (  43-)  A    High
  18 ILE   (  44-)  A    High
  19 ALA   (  45-)  A    High
  20 ARG   (  46-)  A    High
  21 MET   (  47-)  A    High
  22 ILE   (  48-)  A    High
  23 SER   (  49-)  A    High
  24 ASN   (  50-)  A    High
  25 ALA   (  51-)  A    High
And so on for a total of 886 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Nomenclature related problems

Warning: Tyrosine convention problem

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

  49 TYR   (  75-)  A
 168 TYR   ( 194-)  A
 303 TYR   (  75-)  B
 422 TYR   ( 194-)  B
 557 TYR   (  75-)  C
 676 TYR   ( 194-)  C
 811 TYR   (  75-)  D
 930 TYR   ( 194-)  D
1065 TYR   (  75-)  E
1184 TYR   ( 194-)  E
1319 TYR   (  75-)  F
1438 TYR   ( 194-)  F
1573 TYR   (  75-)  G
1692 TYR   ( 194-)  G

Warning: Phenylalanine convention problem

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

 104 PHE   ( 130-)  A
 125 PHE   ( 151-)  A
 242 PHE   ( 268-)  A
 251 PHE   ( 277-)  A
 358 PHE   ( 130-)  B
 379 PHE   ( 151-)  B
 463 PHE   ( 235-)  B
 496 PHE   ( 268-)  B
 505 PHE   ( 277-)  B
 612 PHE   ( 130-)  C
 633 PHE   ( 151-)  C
 717 PHE   ( 235-)  C
 750 PHE   ( 268-)  C
 759 PHE   ( 277-)  C
 887 PHE   ( 151-)  D
1004 PHE   ( 268-)  D
1013 PHE   ( 277-)  D
1120 PHE   ( 130-)  E
1141 PHE   ( 151-)  E
1225 PHE   ( 235-)  E
1258 PHE   ( 268-)  E
1267 PHE   ( 277-)  E
1395 PHE   ( 151-)  F
1479 PHE   ( 235-)  F
1512 PHE   ( 268-)  F
1521 PHE   ( 277-)  F
1628 PHE   ( 130-)  G
1649 PHE   ( 151-)  G
1733 PHE   ( 235-)  G
1766 PHE   ( 268-)  G
1775 PHE   ( 277-)  G

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.

  41 ASP   (  67-)  A
 295 ASP   (  67-)  B
 549 ASP   (  67-)  C
 803 ASP   (  67-)  D
1057 ASP   (  67-)  E
1311 ASP   (  67-)  F
1565 ASP   (  67-)  G

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.

 201 GLU   ( 227-)  A
 234 GLU   ( 260-)  A
 409 GLU   ( 181-)  B
 455 GLU   ( 227-)  B
 488 GLU   ( 260-)  B
 663 GLU   ( 181-)  C
 709 GLU   ( 227-)  C
 742 GLU   ( 260-)  C
 963 GLU   ( 227-)  D
 996 GLU   ( 260-)  D
1171 GLU   ( 181-)  E
1217 GLU   ( 227-)  E
1250 GLU   ( 260-)  E
1425 GLU   ( 181-)  F
1471 GLU   ( 227-)  F
1504 GLU   ( 260-)  F
1679 GLU   ( 181-)  G
1725 GLU   ( 227-)  G
1758 GLU   ( 260-)  G

Geometric checks

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.

 101 PHE   ( 127-)  A      N    CA   C   122.74    4.1
 102 ARG   ( 128-)  A      N    CA   C   128.80    6.3
 199 LEU   ( 225-)  A      N    CA   C    99.40   -4.2
 203 GLY   ( 229-)  A      N    CA   C   124.15    4.0
 207 ILE   ( 233-)  A      N    CA   C    96.33   -5.3
 242 PHE   ( 268-)  A      N    CA   C    98.30   -4.6
 356 ARG   ( 128-)  B      N    CA   C   127.68    5.9
 356 ARG   ( 128-)  B      C    CA   CB  102.29   -4.1
 453 LEU   ( 225-)  B      N    CA   C    99.82   -4.1
 461 ILE   ( 233-)  B      N    CA   C    99.54   -4.2
 496 PHE   ( 268-)  B      N    CA   C    96.50   -5.2
 498 TYR   ( 270-)  B      N    CA   C    99.67   -4.1
 610 ARG   ( 128-)  C      N    CA   C   130.29    6.8
 622 GLY   ( 140-)  C      N    CA   C   100.27   -4.2
 715 ILE   ( 233-)  C      N    CA   C    98.03   -4.7
 750 PHE   ( 268-)  C      N    CA   C    98.90   -4.4
 863 PHE   ( 127-)  D      N    CA   C   123.95    4.6
 864 ARG   ( 128-)  D      N    CA   C   133.65    8.0
 876 GLY   ( 140-)  D      N    CA   C   100.01   -4.3
 969 ILE   ( 233-)  D      N    CA   C    99.20   -4.3
1004 PHE   ( 268-)  D      N    CA   C    98.44   -4.6
1005 PRO   ( 269-)  D      N    CA   C   121.84    4.0
1118 ARG   ( 128-)  E      N    CA   C   131.21    7.1
1130 GLY   ( 140-)  E      N    CA   C   100.00   -4.3
1215 LEU   ( 225-)  E      N    CA   C    99.52   -4.2
1223 ILE   ( 233-)  E      N    CA   C    99.56   -4.2
1260 TYR   ( 270-)  E      N    CA   C    99.68   -4.1
1372 ARG   ( 128-)  F      N    CA   C   129.37    6.5
1372 ARG   ( 128-)  F      C    CA   CB  102.46   -4.0
1384 GLY   ( 140-)  F      N    CA   C   100.54   -4.1
1477 ILE   ( 233-)  F      N    CA   C    97.39   -4.9
1626 ARG   ( 128-)  G      N    CA   C   133.86    8.1
1626 ARG   ( 128-)  G      C    CA   CB  101.10   -4.7
1638 GLY   ( 140-)  G      N    CA   C    98.82   -4.7
1723 LEU   ( 225-)  G      N    CA   C    99.56   -4.2
1731 ILE   ( 233-)  G      N    CA   C    99.75   -4.1
1766 PHE   ( 268-)  G      N    CA   C    96.43   -5.3

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.

  41 ASP   (  67-)  A
 201 GLU   ( 227-)  A
 234 GLU   ( 260-)  A
 295 ASP   (  67-)  B
 409 GLU   ( 181-)  B
 455 GLU   ( 227-)  B
 488 GLU   ( 260-)  B
 549 ASP   (  67-)  C
 663 GLU   ( 181-)  C
 709 GLU   ( 227-)  C
 742 GLU   ( 260-)  C
 803 ASP   (  67-)  D
 963 GLU   ( 227-)  D
 996 GLU   ( 260-)  D
1057 ASP   (  67-)  E
1171 GLU   ( 181-)  E
1217 GLU   ( 227-)  E
1250 GLU   ( 260-)  E
1311 ASP   (  67-)  F
1425 GLU   ( 181-)  F
1471 GLU   ( 227-)  F
1504 GLU   ( 260-)  F
1565 ASP   (  67-)  G
1679 GLU   ( 181-)  G
1725 GLU   ( 227-)  G
1758 GLU   ( 260-)  G

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.

 918 PRO   ( 182-)  D      N     -7.6   -27.29    -2.48
The average deviation= 0.855

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.

1626 ARG   ( 128-)  G    8.44
 864 ARG   ( 128-)  D    8.36
1118 ARG   ( 128-)  E    7.45
 610 ARG   ( 128-)  C    7.11
 863 PHE   ( 127-)  D    6.76
1372 ARG   ( 128-)  F    6.76
 102 ARG   ( 128-)  A    6.55
 356 ARG   ( 128-)  B    6.13
 101 PHE   ( 127-)  A    6.10
 220 LEU   ( 246-)  A    5.90
 355 PHE   ( 127-)  B    5.86
1744 LEU   ( 246-)  G    5.83
1236 LEU   ( 246-)  E    5.74
  60 LEU   (  86-)  A    5.72
1766 PHE   ( 268-)  G    5.70
 496 PHE   ( 268-)  B    5.68
 474 LEU   ( 246-)  B    5.67
1117 PHE   ( 127-)  E    5.58
 728 LEU   ( 246-)  C    5.55
 207 ILE   ( 233-)  A    5.49
1623 VAL   ( 125-)  G    5.30
1115 VAL   ( 125-)  E    5.30
1638 GLY   ( 140-)  G    5.29
 982 LEU   ( 246-)  D    5.27
1477 ILE   ( 233-)  F    5.01
And so on for a total of 66 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.748

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.

 918 PRO   ( 182-)  D    -2.7
 357 PRO   ( 129-)  B    -2.6
 664 PRO   ( 182-)  C    -2.5
 877 VAL   ( 141-)  D    -2.5
1172 PRO   ( 182-)  E    -2.4
1260 TYR   ( 270-)  E    -2.4
 247 MET   ( 273-)  A    -2.4
 156 PRO   ( 182-)  A    -2.4
1627 PRO   ( 129-)  G    -2.4
 671 ILE   ( 189-)  C    -2.4
1639 VAL   ( 141-)  G    -2.4
 369 VAL   ( 141-)  B    -2.4
 115 VAL   ( 141-)  A    -2.4
 105 ARG   ( 131-)  A    -2.4
1375 ARG   ( 131-)  F    -2.4
1472 LEU   ( 228-)  F    -2.3
1218 LEU   ( 228-)  E    -2.3
1223 ILE   ( 233-)  E    -2.3
 456 LEU   ( 228-)  B    -2.3
1263 MET   ( 273-)  E    -2.3
 359 ARG   ( 131-)  B    -2.3
 501 MET   ( 273-)  B    -2.3
1433 ILE   ( 189-)  F    -2.3
 710 LEU   ( 228-)  C    -2.3
 715 ILE   ( 233-)  C    -2.3
And so on for a total of 68 lines.

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.

  33 ARG   (  59-)  A  Poor phi/psi
 101 PHE   ( 127-)  A  omega poor
 115 VAL   ( 141-)  A  Poor phi/psi
 121 SER   ( 147-)  A  Poor phi/psi
 203 GLY   ( 229-)  A  Poor phi/psi
 217 SER   ( 243-)  A  Poor phi/psi
 218 GLY   ( 244-)  A  Poor phi/psi
 247 MET   ( 273-)  A  Poor phi/psi
 287 ARG   (  59-)  B  Poor phi/psi
 355 PHE   ( 127-)  B  omega poor
 361 GLY   ( 133-)  B  Poor phi/psi
 369 VAL   ( 141-)  B  Poor phi/psi
 375 SER   ( 147-)  B  Poor phi/psi
 442 ARG   ( 214-)  B  Poor phi/psi
 472 GLY   ( 244-)  B  Poor phi/psi
 541 ARG   (  59-)  C  Poor phi/psi
 609 PHE   ( 127-)  C  omega poor
 623 VAL   ( 141-)  C  Poor phi/psi
 711 GLY   ( 229-)  C  Poor phi/psi
 726 GLY   ( 244-)  C  Poor phi/psi
 795 ARG   (  59-)  D  Poor phi/psi
 826 GLY   (  90-)  D  Poor phi/psi
 863 PHE   ( 127-)  D  omega poor
 877 VAL   ( 141-)  D  Poor phi/psi
 883 SER   ( 147-)  D  Poor phi/psi
 918 PRO   ( 182-)  D  Poor phi/psi
 965 GLY   ( 229-)  D  Poor phi/psi
 979 SER   ( 243-)  D  Poor phi/psi
 980 GLY   ( 244-)  D  Poor phi/psi
1049 ARG   (  59-)  E  Poor phi/psi
1080 GLY   (  90-)  E  Poor phi/psi
1117 PHE   ( 127-)  E  omega poor
1131 VAL   ( 141-)  E  Poor phi/psi
1233 SER   ( 243-)  E  Poor phi/psi
1234 GLY   ( 244-)  E  Poor phi/psi
1263 MET   ( 273-)  E  Poor phi/psi
1303 ARG   (  59-)  F  Poor phi/psi
1371 PHE   ( 127-)  F  omega poor
1377 GLY   ( 133-)  F  Poor phi/psi
1385 VAL   ( 141-)  F  Poor phi/psi
1487 SER   ( 243-)  F  Poor phi/psi
1557 ARG   (  59-)  G  Poor phi/psi
1625 PHE   ( 127-)  G  omega poor
1639 VAL   ( 141-)  G  Poor phi/psi
1727 GLY   ( 229-)  G  Poor phi/psi
1742 GLY   ( 244-)  G  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.191

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.191

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.

 598 SER   ( 116-)  C    0.36
 298 SER   (  70-)  B    0.36
1060 SER   (  70-)  E    0.36
1106 SER   ( 116-)  E    0.37

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!

  33 ARG   (  59-)  A      0
  34 LYS   (  60-)  A      0
  63 VAL   (  89-)  A      0
  67 THR   (  93-)  A      0
 102 ARG   ( 128-)  A      0
 105 ARG   ( 131-)  A      0
 106 ALA   ( 132-)  A      0
 112 LEU   ( 138-)  A      0
 115 VAL   ( 141-)  A      0
 116 ALA   ( 142-)  A      0
 123 GLN   ( 149-)  A      0
 124 ILE   ( 150-)  A      0
 125 PHE   ( 151-)  A      0
 146 ALA   ( 172-)  A      0
 152 PHE   ( 178-)  A      0
 154 ARG   ( 180-)  A      0
 155 GLU   ( 181-)  A      0
 166 VAL   ( 192-)  A      0
 172 ILE   ( 198-)  A      0
 193 ARG   ( 219-)  A      0
 198 ARG   ( 224-)  A      0
 200 ASN   ( 226-)  A      0
 201 GLU   ( 227-)  A      0
 202 LEU   ( 228-)  A      0
 205 SER   ( 231-)  A      0
And so on for a total of 453 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.933

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!

1638 GLY   ( 140-)  G   3.00   13
 876 GLY   ( 140-)  D   2.88   16
1130 GLY   ( 140-)  E   2.88   17

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]

 140 PRO   ( 166-)  A    0.48 HIGH
 394 PRO   ( 166-)  B    0.46 HIGH
 611 PRO   ( 129-)  C    0.45 HIGH
 648 PRO   ( 166-)  C    0.46 HIGH
 902 PRO   ( 166-)  D    0.47 HIGH
1119 PRO   ( 129-)  E    0.46 HIGH
1627 PRO   ( 129-)  G    0.45 HIGH
1664 PRO   ( 166-)  G    0.47 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].

 156 PRO   ( 182-)  A   -64.0 envelop C-beta (-72 degrees)
 918 PRO   ( 182-)  D   -45.0 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 606 LEU   ( 124-)  C      O   <->  610 ARG   ( 128-)  C      CB     0.45    2.35  INTRA BF
 325 ILE   (  97-)  B      CD1 <->  577 SER   (  95-)  C      CA     0.35    2.85  INTRA BF
1368 LEU   ( 124-)  F      O   <-> 1372 ARG   ( 128-)  F      CB     0.35    2.45  INTRA BL
1622 LEU   ( 124-)  G      O   <-> 1626 ARG   ( 128-)  G      CB     0.34    2.46  INTRA BL
  69 SER   (  95-)  A      CA  <-> 1595 ILE   (  97-)  G      CD1    0.34    2.86  INTRA BF
1375 ARG   ( 131-)  F      N   <-> 1378 GLU   ( 134-)  F      OE1    0.32    2.38  INTRA BL
1626 ARG   ( 128-)  G      CA  <-> 1627 PRO   ( 129-)  G      CD     0.31    2.49  INTRA BL
1655 THR   ( 157-)  G      OG1 <-> 1656 ALA   ( 158-)  G      N      0.30    2.30  INTRA BL
 248 ASP   ( 274-)  A      OD1 <-> 1774 ASN   ( 276-)  G      ND2    0.29    2.41  INTRA BL
  98 LEU   ( 124-)  A      O   <->  102 ARG   ( 128-)  A      CB     0.29    2.51  INTRA BF
 579 ILE   (  97-)  C      CD1 <->  831 SER   (  95-)  D      CA     0.29    2.91  INTRA BF
 610 ARG   ( 128-)  C      CA  <->  611 PRO   ( 129-)  C      CD     0.29    2.51  INTRA BL
1372 ARG   ( 128-)  F      CA  <-> 1373 PRO   ( 129-)  F      CD     0.28    2.52  INTRA BL
 356 ARG   ( 128-)  B      CA  <->  357 PRO   ( 129-)  B      CD     0.27    2.53  INTRA BL
 221 GLN   ( 247-)  A      NE2 <->  225 TRP   ( 251-)  A      CD2    0.27    2.83  INTRA BL
 352 LEU   ( 124-)  B      O   <->  356 ARG   ( 128-)  B      CB     0.27    2.53  INTRA BL
1401 THR   ( 157-)  F      CG2 <-> 1405 LYS   ( 161-)  F      CB     0.27    2.93  INTRA BL
 357 PRO   ( 129-)  B      CG  <->  358 PHE   ( 130-)  B      N      0.27    2.73  INTRA BL
1114 LEU   ( 124-)  E      O   <-> 1118 ARG   ( 128-)  E      CB     0.25    2.55  INTRA BF
1222 SER   ( 232-)  E      OG  <-> 1223 ILE   ( 233-)  E      N      0.25    2.35  INTRA BL
 385 THR   ( 157-)  B      CG2 <->  389 LYS   ( 161-)  B      CB     0.25    2.95  INTRA BL
 359 ARG   ( 131-)  B      N   <->  362 GLU   ( 134-)  B      OE1    0.24    2.46  INTRA BL
1118 ARG   ( 128-)  E      CA  <-> 1119 PRO   ( 129-)  E      CD     0.24    2.56  INTRA BF
 841 LEU   ( 105-)  D      CD1 <-> 1095 LEU   ( 105-)  E      CD2    0.24    2.96  INTRA BL
 385 THR   ( 157-)  B      CG2 <->  389 LYS   ( 161-)  B      N      0.24    2.86  INTRA BL
And so on for a total of 342 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

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.

1777 ARG   ( 279-)  G      -8.32
1015 ARG   ( 279-)  D      -8.29
1523 ARG   ( 279-)  F      -8.28
1269 ARG   ( 279-)  E      -8.22
 761 ARG   ( 279-)  C      -8.17
 253 ARG   ( 279-)  A      -8.05
 507 ARG   ( 279-)  B      -7.98
 154 ARG   ( 180-)  A      -6.21
1678 ARG   ( 180-)  G      -6.13
 916 ARG   ( 180-)  D      -5.97
1170 ARG   ( 180-)  E      -5.91
 662 ARG   ( 180-)  C      -5.78
  33 ARG   (  59-)  A      -5.65
 287 ARG   (  59-)  B      -5.63
1424 ARG   ( 180-)  F      -5.59
1586 ARG   (  88-)  G      -5.56
 316 ARG   (  88-)  B      -5.50
1078 ARG   (  88-)  E      -5.43
 356 ARG   ( 128-)  B      -5.43
1332 ARG   (  88-)  F      -5.38
 408 ARG   ( 180-)  B      -5.37
 570 ARG   (  88-)  C      -5.35
  62 ARG   (  88-)  A      -5.33
 824 ARG   (  88-)  D      -5.23
1629 ARG   ( 131-)  G      -5.19
 867 ARG   ( 131-)  D      -5.12
  66 GLN   (  92-)  A      -5.11
 359 ARG   ( 131-)  B      -5.09
 613 ARG   ( 131-)  C      -5.06
 105 ARG   ( 131-)  A      -5.05
1121 ARG   ( 131-)  E      -5.04
1626 ARG   ( 128-)  G      -5.03
 863 PHE   ( 127-)  D      -5.03
1375 ARG   ( 131-)  F      -5.01
1118 ARG   ( 128-)  E      -5.00

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  32 SER   (  58-)  A        34 - LYS     60- ( A)         -4.61
 540 SER   (  58-)  C       542 - LYS     60- ( C)         -4.29
 794 SER   (  58-)  D       796 - LYS     60- ( D)         -4.37
1048 SER   (  58-)  E      1050 - LYS     60- ( E)         -4.35
1302 SER   (  58-)  F      1304 - LYS     60- ( F)         -4.33
1556 SER   (  58-)  G      1558 - LYS     60- ( G)         -4.23

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

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: F

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

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.

 762 VAL   ( 280-)  C   -2.68
1778 VAL   ( 280-)  G   -2.65
1524 VAL   ( 280-)  F   -2.59
1016 VAL   ( 280-)  D   -2.59
1270 VAL   ( 280-)  E   -2.57
 254 VAL   ( 280-)  A   -2.56

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

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Water, ion, and hydrogenbond related checks

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.

 123 GLN   ( 149-)  A
 141 ASN   ( 167-)  A
 148 ASN   ( 174-)  A
 208 ASN   ( 234-)  A
 395 ASN   ( 167-)  B
 414 ASN   ( 186-)  B
 649 ASN   ( 167-)  C
 903 ASN   ( 167-)  D
 922 ASN   ( 186-)  D
 978 ASN   ( 242-)  D
1157 ASN   ( 167-)  E
1176 ASN   ( 186-)  E
1224 ASN   ( 234-)  E
1411 ASN   ( 167-)  F
1665 ASN   ( 167-)  G
1684 ASN   ( 186-)  G

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.

   3 VAL   (  29-)  A      N
   4 ASN   (  30-)  A      N
  48 ARG   (  74-)  A      NE
  62 ARG   (  88-)  A      NE
 104 PHE   ( 130-)  A      N
 126 SER   ( 152-)  A      N
 128 THR   ( 154-)  A      OG1
 132 ALA   ( 158-)  A      N
 141 ASN   ( 167-)  A      ND2
 148 ASN   ( 174-)  A      ND2
 155 GLU   ( 181-)  A      N
 157 VAL   ( 183-)  A      N
 159 ARG   ( 185-)  A      NE
 206 SER   ( 232-)  A      N
 214 TRP   ( 240-)  A      N
 215 SER   ( 241-)  A      OG
 258 ASN   (  30-)  B      N
 302 ARG   (  74-)  B      NE
 323 SER   (  95-)  B      N
 358 PHE   ( 130-)  B      N
 405 ASN   ( 177-)  B      ND2
 409 GLU   ( 181-)  B      N
 411 VAL   ( 183-)  B      N
 413 ARG   ( 185-)  B      NE
 422 TYR   ( 194-)  B      N
And so on for a total of 92 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.

 402 ASN   ( 174-)  B      OD1
 716 ASN   ( 234-)  C      OD1
1418 ASN   ( 174-)  F      OD1
1732 ASN   ( 234-)  G      OD1

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.

 108 GLU   ( 134-)  A   H-bonding suggests Gln; but Alt-Rotamer
 111 ASP   ( 137-)  A   H-bonding suggests Asn; but Alt-Rotamer
 362 GLU   ( 134-)  B   H-bonding suggests Gln
 365 ASP   ( 137-)  B   H-bonding suggests Asn; but Alt-Rotamer
 616 GLU   ( 134-)  C   H-bonding suggests Gln
 619 ASP   ( 137-)  C   H-bonding suggests Asn; but Alt-Rotamer
 870 GLU   ( 134-)  D   H-bonding suggests Gln
 873 ASP   ( 137-)  D   H-bonding suggests Asn; but Alt-Rotamer
 949 ASP   ( 213-)  D   H-bonding suggests Asn
1057 ASP   (  67-)  E   H-bonding suggests Asn; but Alt-Rotamer
1124 GLU   ( 134-)  E   H-bonding suggests Gln; but Alt-Rotamer
1127 ASP   ( 137-)  E   H-bonding suggests Asn; but Alt-Rotamer
1378 GLU   ( 134-)  F   H-bonding suggests Gln
1381 ASP   ( 137-)  F   H-bonding suggests Asn; but Alt-Rotamer
1632 GLU   ( 134-)  G   H-bonding suggests Gln
1635 ASP   ( 137-)  G   H-bonding suggests Asn; but Alt-Rotamer
1679 GLU   ( 181-)  G   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.957
  2nd generation packing quality :   0.753
  Ramachandran plot appearance   :  -0.136
  chi-1/chi-2 rotamer normality  :  -4.191 (bad)
  Backbone conformation          :   0.829

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.431 (tight)
  Bond angles                    :   0.728
  Omega angle restraints         :   0.351 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.773
  B-factor distribution          :   0.528
  Inside/Outside distribution    :   1.127

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 : 3.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   2.3
  2nd generation packing quality :   2.5
  Ramachandran plot appearance   :   2.6
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   1.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.431 (tight)
  Bond angles                    :   0.728
  Omega angle restraints         :   0.351 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.773
  B-factor distribution          :   0.528
  Inside/Outside distribution    :   1.127
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      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.