WHAT IF Check report

This file was created 2011-12-13 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 pdb2c6n.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1231 LPR   ( 705-)  A  -
1236 ACT   ( 710-)  A  -
1237 LPR   ( 705-)  B  -
1238 NDG   ( 693-)  B  -

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.

1222 NAG   ( 691-)  A  -   O4  bound to 1223 NAG   ( 696-)  A  -   C1
1226 NAG   ( 691-)  B  -   O4  bound to 1227 NAG   ( 696-)  B  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  46 ILE   (  46-)  A  -   CD1
  92 ILE   (  92-)  A  -   CD1
 126 LYS   ( 126-)  A  -   CE
 126 LYS   ( 126-)  A  -   NZ
 274 LYS   ( 274-)  A  -   CD
 274 LYS   ( 274-)  A  -   CE
 274 LYS   ( 274-)  A  -   NZ
 677 GLU   (  66-)  B  -   CD
 677 GLU   (  66-)  B  -   OE1
 677 GLU   (  66-)  B  -   OE2
 709 LEU   (  98-)  B  -   CD1
 709 LEU   (  98-)  B  -   CD2
1018 ILE   ( 408-)  B  -   CD1
1037 LYS   ( 427-)  B  -   CD
1037 LYS   ( 427-)  B  -   CE
1037 LYS   ( 427-)  B  -   NZ

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 LEU   (   1-)  A      CG
   1 LEU   (   1-)  A      CD1
   1 LEU   (   1-)  A      CD2
  18 GLN   (  18-)  A      CG
  18 GLN   (  18-)  A      CD
  18 GLN   (  18-)  A      OE1
  18 GLN   (  18-)  A      NE2
  22 GLN   (  22-)  A      CG
  22 GLN   (  22-)  A      CD
  22 GLN   (  22-)  A      OE1
  22 GLN   (  22-)  A      NE2
  23 SER   (  23-)  A      OG
  24 TYR   (  24-)  A      CG
  24 TYR   (  24-)  A      CD1
  24 TYR   (  24-)  A      CD2
  24 TYR   (  24-)  A      CE1
  24 TYR   (  24-)  A      CE2
  24 TYR   (  24-)  A      CZ
  24 TYR   (  24-)  A      OH
  26 SER   (  26-)  A      OG
  30 GLN   (  30-)  A      CG
  30 GLN   (  30-)  A      CD
  30 GLN   (  30-)  A      OE1
  30 GLN   (  30-)  A      NE2
  49 GLU   (  49-)  A      CG
And so on for a total of 538 lines.

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.

1223 NAG   ( 696-)  A    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:

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

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  96 ARG   (  96-)  A
 151 ARG   ( 151-)  A
 199 ARG   ( 199-)  A
 231 ARG   ( 231-)  A
 467 ARG   ( 467-)  A
 707 ARG   (  96-)  B
 762 ARG   ( 151-)  B
 810 ARG   ( 199-)  B
 842 ARG   ( 231-)  B
 950 ARG   ( 340-)  B
1077 ARG   ( 467-)  B
1151 ARG   ( 541-)  B

Warning: Tyrosine convention problem

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

  76 TYR   (  76-)  A
 122 TYR   ( 122-)  A
 186 TYR   ( 186-)  A
 237 TYR   ( 237-)  A
 241 TYR   ( 241-)  A
 368 TYR   ( 368-)  A
 369 TYR   ( 369-)  A
 459 TYR   ( 459-)  A
 501 TYR   ( 501-)  A
 573 TYR   ( 573-)  A
 687 TYR   (  76-)  B
 797 TYR   ( 186-)  B
 813 TYR   ( 202-)  B
 848 TYR   ( 237-)  B
 852 TYR   ( 241-)  B
 876 TYR   ( 265-)  B
 978 TYR   ( 368-)  B
 979 TYR   ( 369-)  B
 982 TYR   ( 372-)  B
1069 TYR   ( 459-)  B
1183 TYR   ( 573-)  B
1217 TYR   ( 607-)  B

Warning: Phenylalanine convention problem

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

  10 PHE   (  10-)  A
  20 PHE   (  20-)  A
  33 PHE   (  33-)  A
  64 PHE   (  64-)  A
 178 PHE   ( 178-)  A
 191 PHE   ( 191-)  A
 271 PHE   ( 271-)  A
 300 PHE   ( 300-)  A
 301 PHE   ( 301-)  A
 343 PHE   ( 343-)  A
 450 PHE   ( 450-)  A
 461 PHE   ( 461-)  A
 490 PHE   ( 490-)  A
 509 PHE   ( 509-)  A
 574 PHE   ( 574-)  A
 631 PHE   (  20-)  B
 882 PHE   ( 271-)  B
 910 PHE   ( 300-)  B
 911 PHE   ( 301-)  B
 923 PHE   ( 313-)  B
1045 PHE   ( 435-)  B
1060 PHE   ( 450-)  B
1094 PHE   ( 484-)  B
1100 PHE   ( 490-)  B
1184 PHE   ( 574-)  B

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.

  43 ASP   (  43-)  A
  85 ASP   (  85-)  A
 140 ASP   ( 140-)  A
 354 ASP   ( 354-)  A
 417 ASP   ( 417-)  A
 654 ASP   (  43-)  B
 820 ASP   ( 209-)  B
 888 ASP   ( 278-)  B
1031 ASP   ( 421-)  B

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.

  29 GLU   (  29-)  A
  77 GLU   (  77-)  A
 161 GLU   ( 161-)  A
 212 GLU   ( 212-)  A
 219 GLU   ( 219-)  A
 299 GLU   ( 299-)  A
 320 GLU   ( 320-)  A
 481 GLU   ( 481-)  A
 518 GLU   ( 518-)  A
 590 GLU   ( 590-)  A
 674 GLU   (  63-)  B
 772 GLU   ( 161-)  B
 819 GLU   ( 208-)  B
 915 GLU   ( 305-)  B
1200 GLU   ( 590-)  B

Geometric checks

Warning: Unusual bond lengths

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

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

 140 ASP   ( 140-)  A      CG   OD1   1.33    4.3
 350 ARG   ( 350-)  A      CB   CG    1.66    4.7
 351 VAL   ( 351-)  A      N    CA    1.38   -4.3
 351 VAL   ( 351-)  A      CA   CB    1.45   -4.2
 381 ARG   ( 381-)  A      N    CA    1.36   -5.1
 381 ARG   ( 381-)  A      CB   CG    1.74    7.4
 381 ARG   ( 381-)  A      CG   CD    1.67    4.9
 614 PRO   (   3-)  B      CD   N     1.53    4.0
 636 ASN   (  25-)  B      CB   CG    1.36   -6.3
 728 ASN   ( 117-)  B      CB   CG    1.41   -4.4
 960 ARG   ( 350-)  B      CA   C     1.63    4.9
 960 ARG   ( 350-)  B      CA   CB    1.65    6.0
1150 LEU   ( 540-)  B      C    O     1.14   -4.3
1151 ARG   ( 541-)  B      CB   CG    1.69    5.6
1222 NAG   ( 691-)  A      C8   C7    1.32   -4.2
1227 NAG   ( 696-)  B      C8   C7    1.32   -4.2
 739 CYS   ( 128-)  B      SG  -SG*   1.81   -5.9
 747 CYS   ( 136-)  B      SG  -SG*   1.81   -5.9

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

 |  1.000780  0.000282  0.000188|
 |  0.000282  1.000908 -0.000236|
 |  0.000188 -0.000236  1.001314|
Proposed new scale matrix

 |  0.009864 -0.000003 -0.000002|
 | -0.000001  0.004738  0.000001|
 | -0.000001  0.000001  0.005840|
With corresponding cell

    A    = 101.376  B   = 211.073  C    = 171.223
    Alpha=  90.027  Beta=  89.979  Gamma=  89.968

The CRYST1 cell dimensions

    A    = 101.300  B   = 210.900  C    = 171.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 42.199
(Under-)estimated Z-score: 4.788

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.

   6 GLN   (   6-)  A      CG   CD   NE2 127.01    7.1
   6 GLN   (   6-)  A      NE2  CD   OE1 112.75   -9.8
   8 GLY   (   8-)  A     -C    N    CA  128.81    4.8
  19 LEU   (  19-)  A     -C    N    CA  109.82   -6.6
  63 GLU   (  63-)  A     -C    N    CA  104.78   -9.4
  63 GLU   (  63-)  A      CB   CG   CD  102.83   -5.7
  64 PHE   (  64-)  A      N    CA   C    95.87   -5.5
  91 ILE   (  91-)  A      N    CA   C    96.51   -5.2
 206 THR   ( 206-)  A      N    CA   CB  101.51   -5.3
 206 THR   ( 206-)  A      C    CA   CB  118.60    4.5
 250 ALA   ( 250-)  A      N    CA   C   122.55    4.1
 279 VAL   ( 279-)  A      N    CA   C    97.04   -5.1
 280 THR   ( 280-)  A      N    CA   C    92.64   -6.6
 288 TRP   ( 288-)  A      N    CA   C   125.47    5.1
 303 SER   ( 303-)  A     -C    N    CA  128.95    4.0
 349 THR   ( 349-)  A      N    CA   C   127.83    5.9
 349 THR   ( 349-)  A      C    CA   CB   99.65   -5.5
 350 ARG   ( 350-)  A     -C    N    CA  111.22   -5.8
 350 ARG   ( 350-)  A      N    CA   C   123.19    4.3
 350 ARG   ( 350-)  A      N    CA   CB  120.10    5.6
 350 ARG   ( 350-)  A      CB   CG   CD  123.05    4.5
 351 VAL   ( 351-)  A     -CA  -C    N   105.85   -5.2
 351 VAL   ( 351-)  A     -C    N    CA  130.14    4.7
 351 VAL   ( 351-)  A      N    CA   CB   94.41   -9.5
 351 VAL   ( 351-)  A      C    CA   CB  118.12    4.2
And so on for a total of 76 lines.

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.

  29 GLU   (  29-)  A
  43 ASP   (  43-)  A
  77 GLU   (  77-)  A
  85 ASP   (  85-)  A
  96 ARG   (  96-)  A
 140 ASP   ( 140-)  A
 151 ARG   ( 151-)  A
 161 GLU   ( 161-)  A
 199 ARG   ( 199-)  A
 212 GLU   ( 212-)  A
 219 GLU   ( 219-)  A
 231 ARG   ( 231-)  A
 299 GLU   ( 299-)  A
 320 GLU   ( 320-)  A
 354 ASP   ( 354-)  A
 417 ASP   ( 417-)  A
 467 ARG   ( 467-)  A
 481 GLU   ( 481-)  A
 518 GLU   ( 518-)  A
 590 GLU   ( 590-)  A
 654 ASP   (  43-)  B
 674 GLU   (  63-)  B
 707 ARG   (  96-)  B
 762 ARG   ( 151-)  B
 772 GLU   ( 161-)  B
 810 ARG   ( 199-)  B
 819 GLU   ( 208-)  B
 820 ASP   ( 209-)  B
 842 ARG   ( 231-)  B
 888 ASP   ( 278-)  B
 915 GLU   ( 305-)  B
 950 ARG   ( 340-)  B
1031 ASP   ( 421-)  B
1077 ARG   ( 467-)  B
1151 ARG   ( 541-)  B
1200 GLU   ( 590-)  B

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.

 350 ARG   ( 350-)  A      CA    -6.5    23.18    33.91
 380 ARG   ( 380-)  A      C      9.8    15.05     0.13
 550 ARG   ( 550-)  A      C      6.6    10.14     0.13
 608 PRO   ( 608-)  A      N     -6.6   -24.16    -2.48
 689 PRO   (  78-)  B      N    -11.7   -40.70    -2.48
 752 PRO   ( 141-)  B      N     -7.7   -27.73    -2.48
 918 PRO   ( 308-)  B      N    -12.3   -42.69    -2.48
 960 ARG   ( 350-)  B      C      7.5    11.49     0.13
1140 ILE   ( 530-)  B      CB   -50.2   -33.01    32.31 Wrong hand
1151 ARG   ( 541-)  B      C     -8.2   -12.36     0.13
1218 PRO   ( 608-)  B      N     -8.1   -29.21    -2.48
The average deviation= 0.951

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.

 687 TYR   (  76-)  B   12.21
 686 LEU   (  75-)  B    9.81
  91 ILE   (  91-)  A    9.53
 915 GLU   ( 305-)  B    8.89
  64 PHE   (  64-)  A    8.69
 614 PRO   (   3-)  B    7.90
 523 GLY   ( 523-)  A    7.68
 922 GLU   ( 312-)  B    7.59
  21 ALA   (  21-)  A    7.43
 380 ARG   ( 380-)  A    6.98
 616 LEU   (   5-)  B    6.90
 945 TRP   ( 335-)  B    6.52
 685 GLU   (  74-)  B    6.44
 283 MET   ( 283-)  A    6.43
1185 GLN   ( 575-)  B    6.29
 280 THR   ( 280-)  A    6.23
  30 GLN   (  30-)  A    6.17
 778 ALA   ( 167-)  B    5.96
 286 GLN   ( 286-)  A    5.83
  18 GLN   (  18-)  A    5.82
 575 GLN   ( 575-)  A    5.80
 689 PRO   (  78-)  B    5.74
 936 ARG   ( 326-)  B    5.71
1029 GLU   ( 419-)  B    5.66
 349 THR   ( 349-)  A    5.66
And so on for a total of 83 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 : 2.123

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -5.029

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.

 614 PRO   (   3-)  B    -3.1
 608 PRO   ( 608-)  A    -3.1
 918 PRO   ( 308-)  B    -3.1
1218 PRO   ( 608-)  B    -3.1
 689 PRO   (  78-)  B    -3.0
 618 PRO   (   7-)  B    -2.9
1021 LEU   ( 411-)  B    -2.8
   7 PRO   (   7-)  A    -2.8
 379 LEU   ( 379-)  A    -2.8
 755 THR   ( 144-)  B    -2.7
 144 THR   ( 144-)  A    -2.7
 484 PHE   ( 484-)  A    -2.7
 875 ILE   ( 264-)  B    -2.7
1018 ILE   ( 408-)  B    -2.7
 245 ARG   ( 245-)  A    -2.6
 950 ARG   ( 340-)  B    -2.6
 890 THR   ( 280-)  B    -2.6
 207 PHE   ( 207-)  A    -2.6
1025 THR   ( 415-)  B    -2.6
 741 PRO   ( 130-)  B    -2.5
 982 TYR   ( 372-)  B    -2.5
  46 ILE   (  46-)  A    -2.5
 708 THR   (  97-)  B    -2.5
1109 ILE   ( 499-)  B    -2.5
 499 ILE   ( 499-)  A    -2.5
And so on for a total of 70 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.

   4 GLY   (   4-)  A  Poor phi/psi
   5 LEU   (   5-)  A  Poor phi/psi
   7 PRO   (   7-)  A  Poor phi/psi
  79 ILE   (  79-)  A  Poor phi/psi
  81 GLN   (  81-)  A  Poor phi/psi
 101 ALA   ( 101-)  A  Poor phi/psi
 129 LEU   ( 129-)  A  PRO omega poor
 131 ASN   ( 131-)  A  omega poor
 132 LYS   ( 132-)  A  omega poor
 133 THR   ( 133-)  A  Poor phi/psi
 134 ALA   ( 134-)  A  omega poor
 140 ASP   ( 140-)  A  PRO omega poor
 258 ALA   ( 258-)  A  Poor phi/psi
 272 PRO   ( 272-)  A  Poor phi/psi
 273 ASP   ( 273-)  A  Poor phi/psi
 304 LEU   ( 304-)  A  Poor phi/psi, omega poor
 316 GLY   ( 316-)  A  Poor phi/psi
 322 PRO   ( 322-)  A  Poor phi/psi
 340 ARG   ( 340-)  A  Poor phi/psi
 341 LYS   ( 341-)  A  Poor phi/psi
 376 PRO   ( 376-)  A  Poor phi/psi
 380 ARG   ( 380-)  A  Poor phi/psi, omega poor
 381 ARG   ( 381-)  A  omega poor
 412 ASP   ( 412-)  A  omega poor
 413 ARG   ( 413-)  A  Poor phi/psi, omega poor
And so on for a total of 70 lines.

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 : -4.624

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.

 727 SER   ( 116-)  B    0.35
 672 SER   (  61-)  B    0.36
 504 SER   ( 504-)  A    0.36
  35 SER   (  35-)  A    0.36
 793 SER   ( 182-)  B    0.39
 634 SER   (  23-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

   5 LEU   (   5-)  A      0
   7 PRO   (   7-)  A      0
   9 ASN   (   9-)  A      0
  44 THR   (  44-)  A      0
  63 GLU   (  63-)  A      0
  75 LEU   (  75-)  A      0
  79 ILE   (  79-)  A      0
  80 TRP   (  80-)  A      0
  81 GLN   (  81-)  A      0
  82 ASN   (  82-)  A      0
  86 PRO   (  86-)  A      0
  87 GLN   (  87-)  A      0
  97 THR   (  97-)  A      0
  98 LEU   (  98-)  A      0
 130 PRO   ( 130-)  A      0
 131 ASN   ( 131-)  A      0
 132 LYS   ( 132-)  A      0
 133 THR   ( 133-)  A      0
 134 ALA   ( 134-)  A      0
 136 CYS   ( 136-)  A      0
 139 LEU   ( 139-)  A      0
 140 ASP   ( 140-)  A      0
 149 SER   ( 149-)  A      0
 150 SER   ( 150-)  A      0
 186 TYR   ( 186-)  A      0
And so on for a total of 406 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

   4 GLY   (   4-)  A   1.83   63

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 350 ARG   ( 350-)  A   2.89

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]

 551 PRO   ( 551-)  A    0.47 HIGH
 689 PRO   (  78-)  B    0.51 HIGH
 781 PRO   ( 170-)  B    0.45 HIGH
 932 PRO   ( 322-)  B    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].

  86 PRO   (  86-)  A    22.7 half-chair N/C-delta (18 degrees)
 104 PRO   ( 104-)  A  -112.8 envelop C-gamma (-108 degrees)
 604 PRO   ( 604-)  A   120.2 half-chair C-beta/C-alpha (126 degrees)
 608 PRO   ( 608-)  A   -62.8 half-chair C-beta/C-alpha (-54 degrees)
 614 PRO   (   3-)  B   108.7 envelop C-beta (108 degrees)
 618 PRO   (   7-)  B    41.1 envelop C-delta (36 degrees)
 689 PRO   (  78-)  B    99.1 envelop C-beta (108 degrees)
 741 PRO   ( 130-)  B   113.5 envelop C-beta (108 degrees)
 918 PRO   ( 308-)  B   -44.4 envelop C-alpha (-36 degrees)
1047 PRO   ( 437-)  B  -116.7 envelop C-gamma (-108 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.

 636 ASN   (  25-)  B      ND2 <-> 1238 NDG   ( 693-)  B      C1     1.25    1.45  INTRA B3
 128 CYS   ( 128-)  A      SG  <->  136 CYS   ( 136-)  A      SG     0.87    2.58  INTRA BF
 636 ASN   (  25-)  B      CG  <-> 1238 NDG   ( 693-)  B      C1     0.77    2.43  INTRA
 847 ARG   ( 236-)  B      NE  <->  878 MET   ( 267-)  B      CE     0.76    2.34  INTRA BL
1092 THR   ( 482-)  B      CG2 <-> 1226 NAG   ( 691-)  B      C8     0.73    2.47  INTRA BL
 615 GLY   (   4-)  B      O   <->  617 GLN   (   6-)  B      N      0.67    2.03  INTRA BF
 300 PHE   ( 300-)  A      CE1 <->  304 LEU   ( 304-)  A      CD1    0.65    2.55  INTRA BF
1162 TRP   ( 552-)  B      CD1 <-> 1163 GLN   ( 553-)  B      N      0.63    2.37  INTRA BF
 994 ASN   ( 384-)  B      ND2 <-> 1162 TRP   ( 552-)  B      CE3    0.62    2.48  INTRA BF
 740 LEU   ( 129-)  B      O   <->  742 ASN   ( 131-)  B      N      0.62    2.08  INTRA BF
 380 ARG   ( 380-)  A      N   <->  381 ARG   ( 381-)  A      N      0.60    2.00  INTRA BF
 846 ARG   ( 235-)  B      NH1 <-> 1240 HOH   (2004 )  B      O      0.60    2.10  INTRA BL
 813 TYR   ( 202-)  B      O   <-> 1162 TRP   ( 552-)  B      CZ2    0.59    2.21  INTRA BF
 352 THR   ( 352-)  A      CG2 <->  354 ASP   ( 354-)  A      OD1    0.57    2.23  INTRA BF
 280 THR   ( 280-)  A      N   <->  281 SER   ( 281-)  A      N      0.55    2.05  INTRA BF
  86 PRO   (  86-)  A      C   <->   88 LEU   (  88-)  A      N      0.55    2.35  INTRA BF
 191 PHE   ( 191-)  A      CE2 <->  197 TYR   ( 197-)  A      CD1    0.54    2.66  INTRA
 369 TYR   ( 369-)  A      CD1 <->  372 TYR   ( 372-)  A      OH     0.53    2.27  INTRA BF
 890 THR   ( 280-)  B      O   <->  893 MET   ( 283-)  B      N      0.52    2.18  INTRA BF
 279 VAL   ( 279-)  A      CG1 <->  282 THR   ( 282-)  A      CG2    0.52    2.68  INTRA BF
 147 LEU   ( 147-)  A      CD2 <->  256 MET   ( 256-)  A      N      0.51    2.59  INTRA BL
 550 ARG   ( 550-)  A      CB  <->  551 PRO   ( 551-)  A      CD     0.51    2.59  INTRA BF
 615 GLY   (   4-)  B      C   <->  617 GLN   (   6-)  B      N      0.50    2.40  INTRA BF
 709 LEU   (  98-)  B      CB  <->  713 ASN   ( 102-)  B      ND2    0.50    2.60  INTRA BF
   6 GLN   (   6-)  A      CG  <->    7 PRO   (   7-)  A      CD     0.50    2.70  INTRA BF
And so on for a total of 583 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: 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

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.

 885 LYS   ( 274-)  B   -3.96
1160 ARG   ( 550-)  B   -3.70
 340 ARG   ( 340-)  A   -3.51
 341 LYS   ( 341-)  A   -3.45
 380 ARG   ( 380-)  A   -3.34
1020 LEU   ( 410-)  B   -3.14
 694 PHE   (  83-)  B   -3.07
 737 LYS   ( 126-)  B   -3.00
1023 ARG   ( 413-)  B   -2.99
1221 ILE   ( 611-)  B   -2.92
 413 ARG   ( 413-)  A   -2.91
 617 GLN   (   6-)  B   -2.88
 410 LEU   ( 410-)  A   -2.86
1172 LEU   ( 562-)  B   -2.81
 375 LEU   ( 375-)  A   -2.81
 922 GLU   ( 312-)  B   -2.76
 240 ARG   ( 240-)  A   -2.70
 692 GLN   (  81-)  B   -2.70
 951 LYS   ( 341-)  B   -2.69
 985 LEU   ( 375-)  B   -2.65
 925 GLU   ( 315-)  B   -2.64
1098 ALA   ( 488-)  B   -2.60
 873 GLU   ( 262-)  B   -2.52

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  78 PRO   (  78-)  A     -   81 GLN   (  81-)  A        -1.88
 811 SER   ( 200-)  B     -  814 ASN   ( 203-)  B        -1.54

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

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.

  42 HIS   (  42-)  A
 286 GLN   ( 286-)  A
 656 ASN   (  45-)  B
1026 ASN   ( 416-)  B

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 LEU   (   5-)  A      N
  13 ASP   (  13-)  A      N
  19 LEU   (  19-)  A      N
  21 ALA   (  21-)  A      N
  61 SER   (  61-)  A      OG
  77 GLU   (  77-)  A      N
  79 ILE   (  79-)  A      N
  80 TRP   (  80-)  A      N
  97 THR   (  97-)  A      N
 129 LEU   ( 129-)  A      N
 142 ASP   ( 142-)  A      N
 153 TYR   ( 153-)  A      OH
 174 LEU   ( 174-)  A      N
 175 TYR   ( 175-)  A      OH
 189 ASP   ( 189-)  A      N
 191 PHE   ( 191-)  A      N
 193 ASP   ( 193-)  A      N
 202 TYR   ( 202-)  A      N
 230 ARG   ( 230-)  A      NH2
 241 TYR   ( 241-)  A      N
 243 ASN   ( 243-)  A      N
 251 HIS   ( 251-)  A      NE2
 253 LEU   ( 253-)  A      N
 255 ASP   ( 255-)  A      N
 260 SER   ( 260-)  A      N
And so on for a total of 155 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.

 184 GLU   ( 184-)  A      OE1
 213 HIS   ( 213-)  A      ND1
 226 HIS   ( 226-)  A      ND1
 347 GLN   ( 347-)  A      OE1
 362 GLU   ( 362-)  A      OE1
 362 GLU   ( 362-)  A      OE2
 471 GLN   ( 471-)  A      OE1
 794 ASN   ( 183-)  B      OD1
 837 HIS   ( 226-)  B      ND1
 941 HIS   ( 331-)  B      ND1
 957 GLN   ( 347-)  B      OE1
 972 GLU   ( 362-)  B      OE1
 972 GLU   ( 362-)  B      OE2
1193 GLU   ( 583-)  B      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1234  ZN   ( 701-)  B   -.-  -.-  Too few ligands (3)

Warning: Possible wrong residue type

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

  29 GLU   (  29-)  A   H-bonding suggests Gln
 210 ASP   ( 210-)  A   H-bonding suggests Asn
 312 GLU   ( 312-)  A   H-bonding suggests Gln
 558 ASP   ( 558-)  A   H-bonding suggests Asn
 583 GLU   ( 583-)  A   H-bonding suggests Gln
 787 GLU   ( 176-)  B   H-bonding suggests Gln; but Alt-Rotamer
 972 GLU   ( 362-)  B   H-bonding suggests Gln; Ligand-contact
1139 ASP   ( 529-)  B   H-bonding suggests Asn
1168 ASP   ( 558-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -3.457 (poor)
  Ramachandran plot appearance   :  -5.029 (bad)
  chi-1/chi-2 rotamer normality  :  -4.624 (bad)
  Backbone conformation          :  -0.854

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.555 (tight)
  Bond angles                    :   0.930
  Omega angle restraints         :   0.791
  Side chain planarity           :   0.363 (tight)
  Improper dihedral distribution :   0.933
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   1.048

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.555 (tight)
  Bond angles                    :   0.930
  Omega angle restraints         :   0.791
  Side chain planarity           :   0.363 (tight)
  Improper dihedral distribution :   0.933
  B-factor distribution          :   0.613
  Inside/Outside distribution    :   1.048
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.