WHAT IF Check report

This file was created 2014-10-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3rgp.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.524
CA-only RMS fit for the two chains : 0.175

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.573
CA-only RMS fit for the two chains : 0.207

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 : 0.508
CA-only RMS fit for the two chains : 0.158

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: B and C

All-atom RMS fit for the two chains : 0.592
CA-only RMS fit for the two chains : 0.201

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: B 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: B and D

All-atom RMS fit for the two chains : 0.557
CA-only RMS fit for the two chains : 0.224

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: B and D

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1997  NO   ( 502-)  A  -         Size
1998 HEM   (   1-)  A  -         OK
1999  NO   ( 502-)  B  -         Size
2000 HEM   (   1-)  B  -         OK
2001  NO   ( 502-)  C  -         Size
2002 HEM   (   1-)  C  -         OK
2003  NO   ( 502-)  D  -         Size
2004 HEM   (   1-)  D  -         OK

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

1372 CYS   ( 376-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 374 CYS   ( 376-)  A    0.66
 873 CYS   ( 376-)  B    0.75
1372 CYS   ( 376-)  C    0.50
1871 CYS   ( 376-)  D    0.75

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

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.

 103 ARG   ( 105-)  A
 153 ARG   ( 155-)  A
 543 ARG   (  46-)  B
 927 ARG   ( 430-)  B
1042 ARG   (  46-)  C
1088 ARG   (  92-)  C
1151 ARG   ( 155-)  C
1184 ARG   ( 188-)  C

Warning: Tyrosine convention problem

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

 212 TYR   ( 214-)  A
 257 TYR   ( 259-)  A
 322 TYR   ( 324-)  A
 367 TYR   ( 369-)  A
 444 TYR   ( 446-)  A
 866 TYR   ( 369-)  B
1210 TYR   ( 214-)  C
1374 TYR   ( 378-)  C
1631 TYR   ( 136-)  D
1819 TYR   ( 324-)  D

Warning: Phenylalanine convention problem

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

 422 PHE   ( 424-)  A
 730 PHE   ( 233-)  B
 762 PHE   ( 265-)  B
 921 PHE   ( 424-)  B
1059 PHE   (  63-)  C
1289 PHE   ( 293-)  C
1351 PHE   ( 355-)  C
1477 PHE   ( 481-)  C
1760 PHE   ( 265-)  D
1786 PHE   ( 291-)  D

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.

1493 ASP   ( 497-)  C

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.

1134 GLU   ( 138-)  C
1580 GLU   (  85-)  D
1782 GLU   ( 287-)  D
1955 GLU   ( 460-)  D

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.279
RMS-deviation in bond distances: 0.007

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998987 -0.000175 -0.000095|
 | -0.000175  0.999086 -0.000113|
 | -0.000095 -0.000113  0.998464|
Proposed new scale matrix

 |  0.011625  0.000002  0.000001|
 |  0.000001  0.007153  0.000000|
 |  0.000000  0.000000  0.004393|
With corresponding cell

    A    =  86.023  B   = 139.811  C    = 227.648
    Alpha=  90.002  Beta=  90.007  Gamma=  90.020

The CRYST1 cell dimensions

    A    =  86.110  B   = 139.940  C    = 228.020
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 94.760
(Under-)estimated Z-score: 7.174

Warning: Unusual bond angles

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

1776 GLN   ( 281-)  D      N    CA   C    99.35   -4.2

Warning: Low bond angle variability

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

RMS Z-score for bond angles: 0.653
RMS-deviation in bond angles: 1.402

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.

 103 ARG   ( 105-)  A
 153 ARG   ( 155-)  A
 543 ARG   (  46-)  B
 927 ARG   ( 430-)  B
1042 ARG   (  46-)  C
1088 ARG   (  92-)  C
1134 GLU   ( 138-)  C
1151 ARG   ( 155-)  C
1184 ARG   ( 188-)  C
1493 ASP   ( 497-)  C
1580 GLU   (  85-)  D
1782 GLU   ( 287-)  D
1955 GLU   ( 460-)  D

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.

 853 ALA   ( 356-)  B    6.69
 354 ALA   ( 356-)  A    6.60
1352 ALA   ( 356-)  C    6.43
1851 ALA   ( 356-)  D    6.41
1822 GLU   ( 327-)  D    4.46
 181 ASP   ( 183-)  A    4.43
 824 GLU   ( 327-)  B    4.37
1678 ASP   ( 183-)  D    4.36
  53 VAL   (  55-)  A    4.30
 936 VAL   ( 439-)  B    4.25
1942 LEU   ( 447-)  D    4.21
1323 GLU   ( 327-)  C    4.08
1776 GLN   ( 281-)  D    4.08
1623 PRO   ( 128-)  D    4.06

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.

1369 PRO   ( 373-)  C    -2.8
 870 PRO   ( 373-)  B    -2.8
1868 PRO   ( 373-)  D    -2.8
 371 PRO   ( 373-)  A    -2.7
1626 PHE   ( 131-)  D    -2.7
 628 PHE   ( 131-)  B    -2.6
 129 PHE   ( 131-)  A    -2.5
1127 PHE   ( 131-)  C    -2.5
 166 LYS   ( 168-)  A    -2.4
 172 HIS   ( 174-)  A    -2.4
1000 ARG   (   4-)  C    -2.4
   2 ARG   (   4-)  A    -2.4
1669 HIS   ( 174-)  D    -2.4
1170 HIS   ( 174-)  C    -2.4
 787 ILE   ( 290-)  B    -2.3
1231 TYR   ( 235-)  C    -2.3
 732 TYR   ( 235-)  B    -2.3
 671 HIS   ( 174-)  B    -2.3
 233 TYR   ( 235-)  A    -2.3
1125 ARG   ( 129-)  C    -2.3
 379 ARG   ( 381-)  A    -2.3
1730 TYR   ( 235-)  D    -2.3
1148 PHE   ( 152-)  C    -2.2
1647 PHE   ( 152-)  D    -2.2
 649 PHE   ( 152-)  B    -2.2
 874 PRO   ( 377-)  B    -2.2
1904 SER   ( 409-)  D    -2.2
1405 SER   ( 409-)  C    -2.2
 540 VAL   (  43-)  B    -2.2
 150 PHE   ( 152-)  A    -2.2
  41 VAL   (  43-)  A    -2.1
 589 ARG   (  92-)  B    -2.1
 382 ASN   ( 384-)  A    -2.1
 906 SER   ( 409-)  B    -2.1
1532 LYS   (  37-)  D    -2.1
 288 ILE   ( 290-)  A    -2.1
1879 ASN   ( 384-)  D    -2.1
1791 PHE   ( 296-)  D    -2.1
 836 PRO   ( 339-)  B    -2.1
 890 MET   ( 393-)  B    -2.1
  35 LYS   (  37-)  A    -2.1
1538 VAL   (  43-)  D    -2.1
1033 LYS   (  37-)  C    -2.1
 793 PHE   ( 296-)  B    -2.1
 626 ARG   ( 129-)  B    -2.0
 816 ARG   ( 319-)  B    -2.0
1123 ASP   ( 127-)  C    -2.0
 143 VAL   ( 145-)  A    -2.0
 294 PHE   ( 296-)  A    -2.0
1380 ASN   ( 384-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 ARG   (   4-)  A  Poor phi/psi
  17 ALA   (  19-)  A  Poor phi/psi
  72 HIS   (  74-)  A  Poor phi/psi
 125 ASP   ( 127-)  A  Poor phi/psi
 166 LYS   ( 168-)  A  Poor phi/psi
 172 HIS   ( 174-)  A  Poor phi/psi
 214 SER   ( 216-)  A  Poor phi/psi
 382 ASN   ( 384-)  A  Poor phi/psi
 386 ASP   ( 388-)  A  Poor phi/psi
 392 MET   ( 394-)  A  Poor phi/psi
 394 ASN   ( 396-)  A  Poor phi/psi
 395 GLN   ( 397-)  A  Poor phi/psi
 402 TYR   ( 404-)  A  PRO omega poor
 407 SER   ( 409-)  A  Poor phi/psi
 435 ASP   ( 437-)  A  Poor phi/psi
 437 VAL   ( 439-)  A  Poor phi/psi
 501 ARG   (   4-)  B  Poor phi/psi
 516 ALA   (  19-)  B  Poor phi/psi
 571 HIS   (  74-)  B  Poor phi/psi
 610 SER   ( 113-)  B  Poor phi/psi
 624 ASP   ( 127-)  B  Poor phi/psi
 665 LYS   ( 168-)  B  Poor phi/psi
 671 HIS   ( 174-)  B  Poor phi/psi
 713 SER   ( 216-)  B  Poor phi/psi
 881 ASN   ( 384-)  B  Poor phi/psi
And so on for a total of 62 lines.

Warning: Unusual backbone conformations

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

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

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

  17 ALA   (  19-)  A      0
  30 ASN   (  32-)  A      0
  35 LYS   (  37-)  A      0
  37 ASN   (  39-)  A      0
  41 VAL   (  43-)  A      0
  44 ARG   (  46-)  A      0
  48 LEU   (  50-)  A      0
  64 GLU   (  66-)  A      0
  70 VAL   (  72-)  A      0
  71 VAL   (  73-)  A      0
  72 HIS   (  74-)  A      0
  73 ALA   (  75-)  A      0
  74 LYS   (  76-)  A      0
  88 ILE   (  90-)  A      0
  89 THR   (  91-)  A      0
  91 TYR   (  93-)  A      0
  93 LYS   (  95-)  A      0
  99 HIS   ( 101-)  A      0
 100 ILE   ( 102-)  A      0
 102 LYS   ( 104-)  A      0
 113 VAL   ( 115-)  A      0
 122 THR   ( 124-)  A      0
 124 ARG   ( 126-)  A      0
 125 ASP   ( 127-)  A      0
 137 ASP   ( 139-)  A      0
And so on for a total of 772 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 : 1.325

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].

 272 PRO   ( 274-)  A    52.0 half-chair C-delta/C-gamma (54 degrees)
 912 PRO   ( 415-)  B  -113.4 envelop C-gamma (-108 degrees)
1157 PRO   ( 161-)  C  -115.4 envelop C-gamma (-108 degrees)
1174 PRO   ( 178-)  C  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1482 PRO   ( 486-)  C  -119.9 half-chair C-delta/C-gamma (-126 degrees)
1673 PRO   ( 178-)  D  -117.6 half-chair C-delta/C-gamma (-126 degrees)
1834 PRO   ( 339-)  D    43.5 envelop C-delta (36 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.

 534 LYS   (  37-)  B      NZ  <-> 2006 HOH   ( 511 )  B      O      0.79    1.91  INTRA
1615 GLY   ( 120-)  D      N   <-> 2008 HOH   ( 638 )  D      O      0.62    2.08  INTRA
1258 ARG   ( 262-)  C      NH1 <-> 2007 HOH   ( 986 )  C      O      0.52    2.18  INTRA
 118 GLY   ( 120-)  A      N   <-> 2008 HOH   ( 638 )  D      O      0.51    2.19  INTRA
2001  NO   ( 502-)  C      N   <-> 2002 HEM   (   1-)  C      NC     0.49    2.41  INTRA
 673 LYS   ( 176-)  B      NZ  <-> 2006 HOH   (2022 )  B      O      0.49    2.21  INTRA
1999  NO   ( 502-)  B      N   <-> 2000 HEM   (   1-)  B      NC     0.47    2.43  INTRA
 759 ARG   ( 262-)  B      NH2 <-> 2006 HOH   (1356 )  B      O      0.46    2.24  INTRA
1433 ASP   ( 437-)  C      N   <-> 2007 HOH   ( 842 )  C      O      0.46    2.24  INTRA
1814 ARG   ( 319-)  D      NH1 <-> 2008 HOH   ( 626 )  D      O      0.46    2.24  INTRA
  16 ARG   (  18-)  A      NE  <-> 2005 HOH   ( 649 )  A      O      0.45    2.25  INTRA BF
1421 SER   ( 425-)  C      N   <-> 2007 HOH   (1937 )  C      O      0.45    2.25  INTRA BF
1014 ARG   (  18-)  C      NE  <-> 2007 HOH   ( 592 )  C      O      0.45    2.25  INTRA
2005 HOH   ( 644 )  A      O   <-> 2006 HOH   (2025 )  B      O      0.44    1.96  INTRA BF
1997  NO   ( 502-)  A      N   <-> 1998 HEM   (   1-)  A      NC     0.44    2.46  INTRA
 374 CYS   ( 376-)  A    A SG  <-> 2005 HOH   (1508 )  A      O      0.44    2.56  INTRA
2005 HOH   (1744 )  A      O   <-> 2006 HOH   (1604 )  B      O      0.43    1.97  INTRA BF
2003  NO   ( 502-)  D      N   <-> 2004 HEM   (   1-)  D      NC     0.43    2.47  INTRA
 717 LYS   ( 220-)  B      NZ  <-> 2006 HOH   ( 544 )  B      O      0.40    2.30  INTRA
1677 TRP   ( 182-)  D      NE1 <-> 1960 HIS   ( 465-)  D      ND1    0.39    2.61  INTRA
2003  NO   ( 502-)  D      N   <-> 2004 HEM   (   1-)  D      ND     0.39    2.51  INTRA
 427 GLN   ( 429-)  A      NE2 <-> 2005 HOH   (1605 )  A      O      0.39    2.31  INTRA
 419 ARG   ( 421-)  A      NH2 <-> 2005 HOH   (1747 )  A      O      0.39    2.31  INTRA BF
1178 TRP   ( 182-)  C      NE1 <-> 1461 HIS   ( 465-)  C      ND1    0.38    2.62  INTRA
 967 GLN   ( 470-)  B      NE2 <-> 2006 HOH   (1574 )  B      O      0.38    2.32  INTRA
And so on for a total of 447 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

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.

1042 ARG   (  46-)  C      -8.09
1541 ARG   (  46-)  D      -7.95
  44 ARG   (  46-)  A      -7.87
 543 ARG   (  46-)  B      -7.76
  65 ARG   (  67-)  A      -6.43
 564 ARG   (  67-)  B      -6.41
1562 ARG   (  67-)  D      -6.41
 501 ARG   (   4-)  B      -6.37
1063 ARG   (  67-)  C      -6.29
1916 ARG   ( 421-)  D      -6.25
1417 ARG   ( 421-)  C      -6.07
1516 GLN   (  21-)  D      -6.05
  19 GLN   (  21-)  A      -5.93
1873 TYR   ( 378-)  D      -5.90
 875 TYR   ( 378-)  B      -5.88
1390 MET   ( 394-)  C      -5.85
1017 GLN   (  21-)  C      -5.82
1671 LYS   ( 176-)  D      -5.81
 376 TYR   ( 378-)  A      -5.77
 518 GLN   (  21-)  B      -5.72
 918 ARG   ( 421-)  B      -5.64
 876 ARG   ( 379-)  B      -5.64
1664 ARG   ( 169-)  D      -5.60
 891 MET   ( 394-)  B      -5.59
1375 ARG   ( 379-)  C      -5.59
And so on for a total of 60 lines.

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.

1419 HIS   ( 423-)  C      1421 - SER    425- ( C)         -4.41

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

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.

1912 ALA   ( 417-)  D   -3.05
 415 ALA   ( 417-)  A   -3.02
 914 ALA   ( 417-)  B   -2.96
1390 MET   ( 394-)  C   -2.89
 890 MET   ( 393-)  B   -2.77
1888 MET   ( 393-)  D   -2.73
 174 LYS   ( 176-)  A   -2.69
1389 MET   ( 393-)  C   -2.66
 673 LYS   ( 176-)  B   -2.65
 391 MET   ( 393-)  A   -2.63

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.

1373 PRO   ( 377-)  C     - 1376 ALA   ( 380-)  C        -1.48

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2005 HOH   (1774 )  A      O     28.19   21.37  126.61
2005 HOH   (1778 )  A      O     67.22   25.59   80.48
2006 HOH   (1023 )  B      O     13.68  -21.32   62.61
2008 HOH   (1599 )  D      O      2.38   52.48  116.77

Error: Water molecules without hydrogen bonds

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

2005 HOH   (1146 )  A      O
2005 HOH   (1445 )  A      O
2005 HOH   (1598 )  A      O
2005 HOH   (1792 )  A      O
2005 HOH   (1881 )  A      O
2006 HOH   (1200 )  B      O
2006 HOH   (1306 )  B      O
2006 HOH   (1675 )  B      O
2006 HOH   (1762 )  B      O
2006 HOH   (1918 )  B      O
2006 HOH   (1947 )  B      O
2006 HOH   (1958 )  B      O
2006 HOH   (1969 )  B      O
2007 HOH   ( 609 )  C      O
2007 HOH   (1244 )  C      O
2007 HOH   (1289 )  C      O
2007 HOH   (1349 )  C      O
2007 HOH   (1539 )  C      O
2007 HOH   (1589 )  C      O
2007 HOH   (1671 )  C      O
2007 HOH   (1839 )  C      O
2007 HOH   (1909 )  C      O
2007 HOH   (1967 )  C      O
2008 HOH   (1088 )  D      O
2008 HOH   (1479 )  D      O
2008 HOH   (1659 )  D      O
2008 HOH   (1719 )  D      O
2008 HOH   (1849 )  D      O
2008 HOH   (1921 )  D      O
2008 HOH   (1925 )  D      O
2008 HOH   (1940 )  D      O
2008 HOH   (1945 )  D      O
2008 HOH   (1999 )  D      O
ERROR. No convergence in HB2STD
Old,New value: 3372.359 3372.378
ERROR. No convergence in HB2STD
Old,New value: 3375.009 3375.025

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.

 146 ASN   ( 148-)  A
 241 ASN   ( 243-)  A
 411 HIS   ( 413-)  A
 452 GLN   ( 454-)  A
 500 ASN   (   3-)  B
 510 HIS   (  13-)  B
 690 HIS   ( 193-)  B
 893 ASN   ( 396-)  B
 958 ASN   ( 461-)  B
 967 GLN   ( 470-)  B
1168 GLN   ( 172-)  C
1239 ASN   ( 243-)  C
1333 ASN   ( 337-)  C
1410 GLN   ( 414-)  C
1431 ASN   ( 435-)  C
1434 ASN   ( 438-)  C
1457 ASN   ( 461-)  C
1470 GLN   ( 474-)  C
1476 ASN   ( 480-)  C
1481 HIS   ( 485-)  C
1489 GLN   ( 493-)  C
1496 ASN   ( 500-)  C
1516 GLN   (  21-)  D
1547 GLN   (  52-)  D
1643 ASN   ( 148-)  D
1665 ASN   ( 170-)  D
1688 HIS   ( 193-)  D
1799 HIS   ( 304-)  D
1832 ASN   ( 337-)  D
1858 HIS   ( 363-)  D
1863 ASN   ( 368-)  D
1995 ASN   ( 500-)  D

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.

  69 ARG   (  71-)  A      NE
  71 VAL   (  73-)  A      N
  86 HIS   (  88-)  A      ND1
  99 HIS   ( 101-)  A      N
 109 ARG   ( 111-)  A      NH1
 147 THR   ( 149-)  A      N
 151 PHE   ( 153-)  A      N
 152 ILE   ( 154-)  A      N
 167 ARG   ( 169-)  A      NH1
 180 TRP   ( 182-)  A      NE1
 209 MET   ( 211-)  A      N
 243 SER   ( 245-)  A      OG
 291 PHE   ( 293-)  A      N
 343 SER   ( 345-)  A      N
 351 ARG   ( 353-)  A      NE
 351 ARG   ( 353-)  A      NH2
 355 TYR   ( 357-)  A      OH
 362 ARG   ( 364-)  A      NE
 362 ARG   ( 364-)  A      NH2
 377 ARG   ( 379-)  A      NH2
 400 ASN   ( 402-)  A      ND2
 401 TYR   ( 403-)  A      N
 420 THR   ( 422-)  A      N
 453 ARG   ( 455-)  A      NH1
 501 ARG   (   4-)  B      NH1
And so on for a total of 108 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.

  62 ASP   (  64-)  A      OD1
  62 ASP   (  64-)  A      OD2
 145 ASN   ( 147-)  A      OD1
 561 ASP   (  64-)  B      OD1
 561 ASP   (  64-)  B      OD2
 635 GLU   ( 138-)  B      OE1
 644 ASN   ( 147-)  B      OD1
 664 GLN   ( 167-)  B      OE1
 834 ASN   ( 337-)  B      OD1
1060 ASP   (  64-)  C      OD1
1060 ASP   (  64-)  C      OD2
1143 ASN   ( 147-)  C      OD1
1433 ASP   ( 437-)  C      OD2
1559 ASP   (  64-)  D      OD1
1559 ASP   (  64-)  D      OD2
1642 ASN   ( 147-)  D      OD1
1662 GLN   ( 167-)  D      OE1
1897 ASN   ( 402-)  D      OD1
1908 HIS   ( 413-)  D      ND1

Warning: Unusual water packing

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

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

2005 HOH   ( 572 )  A      O  0.85  K  4
2005 HOH   ( 575 )  A      O  0.90  K  4
2005 HOH   ( 589 )  A      O  1.08  K  5
2005 HOH   ( 942 )  A      O  0.86  K  4 Ion-B
2005 HOH   (1180 )  A      O  1.08  K  6 Ion-B
2005 HOH   (1603 )  A      O  1.00  K  5 ION-B
2006 HOH   ( 768 )  B      O  1.08  K  4
2006 HOH   (1731 )  B      O  0.97  K  4 Ion-B
2007 HOH   ( 600 )  C      O  0.95  K  4
2007 HOH   (1314 )  C      O  0.92  K  5 Ion-B
2007 HOH   (1411 )  C      O  0.96  K  5
2008 HOH   ( 534 )  D      O  0.98  K  5
2008 HOH   ( 543 )  D      O  0.98  K  4
2008 HOH   ( 560 )  D      O  0.89  K  4
2008 HOH   ( 608 )  D      O  0.90  K  4
2008 HOH   ( 633 )  D      O  0.89  K  4
2008 HOH   ( 802 )  D      O  0.92  K  4
2008 HOH   (1554 )  D      O  0.86  K  4 Ion-B

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.

   7 ASP   (   9-)  A   H-bonding suggests Asn
  62 ASP   (  64-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 495 ASP   ( 497-)  A   H-bonding suggests Asn
 499 GLU   ( 501-)  A   H-bonding suggests Gln
 506 ASP   (   9-)  B   H-bonding suggests Asn
 561 ASP   (  64-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 994 ASP   ( 497-)  B   H-bonding suggests Asn
1060 ASP   (  64-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1432 ASP   ( 436-)  C   H-bonding suggests Asn
1493 ASP   ( 497-)  C   H-bonding suggests Asn
1559 ASP   (  64-)  D   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1842 ASP   ( 347-)  D   H-bonding suggests Asn
1931 ASP   ( 436-)  D   H-bonding suggests Asn
1992 ASP   ( 497-)  D   H-bonding suggests Asn
1996 GLU   ( 501-)  D   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 :  -0.741
  2nd generation packing quality :  -1.703
  Ramachandran plot appearance   :  -1.067
  chi-1/chi-2 rotamer normality  :  -0.687
  Backbone conformation          :  -0.500

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.653 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.579
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   1.101

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.88


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.279 (tight)
  Bond angles                    :   0.653 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.579
  B-factor distribution          :   0.532
  Inside/Outside distribution    :   1.101
==============

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.