WHAT IF Check report

This file was created 2012-01-13 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 pdb1twa.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: I 2 2 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 8

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 395861.063
Volume of the Unit Cell V= 10258465.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.479
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.730 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 8
which would result in the much more normal Vm= 3.239
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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.

3500 ATP   (3011-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 517 LYS   ( 567-)  A  -   NZ  3089 TYR   (  95-)  H  -   CE2

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

1307 THR   (1405-)  A  -
2313 GLY   (1078-)  B  -

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.

 517 LYS   ( 567-)  A  -   NZ  bound to 3087 TYR   (  95-)  H  -   CE2

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: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

Warning: B-factors outside the range 0.0 - 100.0

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

   1 GLY   (   3-)  A    High
   2 GLN   (   4-)  A    High
   3 GLN   (   5-)  A    High
   4 TYR   (   6-)  A    High
  34 ARG   (  36-)  A    High
  35 PHE   (  37-)  A    High
  36 PRO   (  38-)  A    High
  37 GLU   (  39-)  A    High
  38 THR   (  40-)  A    High
  39 MET   (  41-)  A    High
  40 ASP   (  42-)  A    High
  41 GLU   (  43-)  A    High
  42 THR   (  44-)  A    High
  43 GLN   (  45-)  A    High
  44 THR   (  46-)  A    High
  45 ARG   (  47-)  A    High
  46 ALA   (  48-)  A    High
  47 LYS   (  49-)  A    High
  48 ILE   (  50-)  A    High
  49 GLY   (  51-)  A    High
  50 GLY   (  52-)  A    High
  51 LEU   (  53-)  A    High
  52 ASN   (  54-)  A    High
  53 ASP   (  55-)  A    High
  54 PRO   (  56-)  A    High
And so on for a total of 264 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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.

 973 ARG   (1023-)  A
1263 ARG   (1345-)  A
2907 ARG   ( 200-)  E

Warning: Tyrosine convention problem

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

 333 TYR   ( 383-)  A
 354 TYR   ( 404-)  A
 367 TYR   ( 417-)  A
 378 TYR   ( 428-)  A
 428 TYR   ( 478-)  A
 754 TYR   ( 804-)  A
 847 TYR   ( 897-)  A
 985 TYR   (1035-)  A
1205 TYR   (1287-)  A
1271 TYR   (1353-)  A
1280 TYR   (1362-)  A
1471 TYR   ( 180-)  B
1481 TYR   ( 190-)  B
1566 TYR   ( 275-)  B
1594 TYR   ( 303-)  B
1722 TYR   ( 431-)  B
1760 TYR   ( 486-)  B
1934 TYR   ( 666-)  B
1951 TYR   ( 692-)  B
2019 TYR   ( 769-)  B
2035 TYR   ( 785-)  B
2048 TYR   ( 798-)  B
2061 TYR   ( 811-)  B
2116 TYR   ( 866-)  B
2228 TYR   ( 994-)  B
2298 TYR   (1064-)  B
2409 TYR   (1192-)  B
2434 TYR   (1217-)  B
2521 TYR   (  82-)  C
2630 TYR   ( 191-)  C
2660 TYR   ( 221-)  C
2668 TYR   ( 229-)  C
2735 TYR   (  28-)  E
2753 TYR   (  46-)  E
2875 TYR   ( 168-)  E
2894 TYR   ( 187-)  E
2918 TYR   ( 211-)  E
2939 TYR   (  88-)  F
3024 TYR   (  20-)  H
3087 TYR   (  95-)  H
3108 TYR   ( 116-)  H
3121 TYR   ( 129-)  H
3153 TYR   (  15-)  I
3172 TYR   (  34-)  I
3182 TYR   (  44-)  I
3322 TYR   (  63-)  J
3384 TYR   (  61-)  K
3404 TYR   (  81-)  K

Warning: Phenylalanine convention problem

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

  17 PHE   (  19-)  A
  20 PHE   (  22-)  A
  79 PHE   (  81-)  A
  93 PHE   (  95-)  A
 222 PHE   ( 224-)  A
 226 PHE   ( 228-)  A
 250 PHE   ( 264-)  A
 297 PHE   ( 347-)  A
 418 PHE   ( 468-)  A
 432 PHE   ( 482-)  A
 490 PHE   ( 540-)  A
 671 PHE   ( 721-)  A
 727 PHE   ( 777-)  A
 729 PHE   ( 779-)  A
 737 PHE   ( 787-)  A
 763 PHE   ( 813-)  A
 765 PHE   ( 815-)  A
 843 PHE   ( 893-)  A
 897 PHE   ( 947-)  A
 921 PHE   ( 971-)  A
1003 PHE   (1053-)  A
1148 PHE   (1220-)  A
1153 PHE   (1225-)  A
1311 PHE   (1410-)  A
1352 PHE   (  18-)  B
And so on for a total of 67 lines.

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.

  40 ASP   (  42-)  A
 114 ASP   ( 116-)  A
 154 ASP   ( 156-)  A
 312 ASP   ( 362-)  A
 358 ASP   ( 408-)  A
 433 ASP   ( 483-)  A
 435 ASP   ( 485-)  A
 559 ASP   ( 609-)  A
 666 ASP   ( 716-)  A
 740 ASP   ( 790-)  A
 776 ASP   ( 826-)  A
 899 ASP   ( 949-)  A
1126 ASP   (1198-)  A
1132 ASP   (1204-)  A
1175 ASP   (1257-)  A
1354 ASP   (  20-)  B
1422 ASP   ( 106-)  B
1489 ASP   ( 198-)  B
1585 ASP   ( 294-)  B
1617 ASP   ( 326-)  B
1623 ASP   ( 332-)  B
1682 ASP   ( 391-)  B
1972 ASP   ( 722-)  B
2040 ASP   ( 790-)  B
2141 ASP   ( 891-)  B
2170 ASP   ( 936-)  B
2436 ASP   (1219-)  B
2665 ASP   ( 226-)  C
2688 ASP   ( 249-)  C
2707 ASP   ( 268-)  C
2791 ASP   (  84-)  E
2967 ASP   ( 116-)  F
3012 ASP   (   8-)  H
3078 ASP   (  86-)  H
3157 ASP   (  19-)  I
3199 ASP   (  61-)  I
3232 ASP   (  94-)  I
3347 ASP   (  24-)  K

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.

  37 GLU   (  39-)  A
 204 GLU   ( 206-)  A
 263 GLU   ( 277-)  A
 266 GLU   ( 280-)  A
 279 GLU   ( 293-)  A
 348 GLU   ( 398-)  A
 543 GLU   ( 593-)  A
 568 GLU   ( 618-)  A
 586 GLU   ( 636-)  A
 628 GLU   ( 678-)  A
 674 GLU   ( 724-)  A
 751 GLU   ( 801-)  A
 772 GLU   ( 822-)  A
 829 GLU   ( 879-)  A
 881 GLU   ( 931-)  A
 882 GLU   ( 932-)  A
1043 GLU   (1103-)  A
1174 GLU   (1256-)  A
1195 GLU   (1277-)  A
1198 GLU   (1280-)  A
1269 GLU   (1351-)  A
1305 GLU   (1403-)  A
1308 GLU   (1407-)  A
1327 GLU   (1426-)  A
1348 GLU   (1447-)  A
And so on for a total of 60 lines.

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.

   1 GLY   (   3-)  A      N    CA    1.53    4.8
   2 GLN   (   4-)  A      CA   C     1.63    5.0
   2 GLN   (   4-)  A      CB   CG    1.73    6.9
   3 GLN   (   5-)  A      N    CA    1.54    4.4
   3 GLN   (   5-)  A      CA   CB    1.64    5.7
   3 GLN   (   5-)  A      CB   CG    1.76    7.9
   3 GLN   (   5-)  A      CG   CD    1.62    4.1
   3 GLN   (   5-)  A      N   -C     1.41    4.2
   6 SER   (   8-)  A      CA   CB    1.63    4.9
   7 ALA   (   9-)  A      N    CA    1.54    4.1
   7 ALA   (   9-)  A      CA   C     1.42   -5.2
   9 LEU   (  11-)  A      C    O     1.13   -4.9
  10 ARG   (  12-)  A      C    O     1.12   -5.3
  10 ARG   (  12-)  A      CZ   NH1   1.42    5.4
  12 VAL   (  14-)  A      C    O     1.04   -9.4
  13 LYS   (  15-)  A      C    O     1.07   -8.1
  13 LYS   (  15-)  A      CB   CG    1.64    4.1
  13 LYS   (  15-)  A      CD   CE    1.66    4.6
  13 LYS   (  15-)  A      CE   NZ    1.62    4.5
  14 GLU   (  16-)  A      C    O     1.32    4.5
  14 GLU   (  16-)  A      CG   CD    1.64    4.9
  14 GLU   (  16-)  A      CD   OE1   1.42    8.8
  14 GLU   (  16-)  A      CD   OE2   1.40    8.0
  15 VAL   (  17-)  A      CA   CB    1.41   -6.0
  17 PHE   (  19-)  A      C    O     1.15   -4.1
And so on for a total of 5390 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken 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 higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 3.051
RMS-deviation in bond distances: 0.073

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

 |  0.999603  0.000064  0.000626|
 |  0.000064  1.001334 -0.000316|
 |  0.000626 -0.000316  1.001390|
Proposed new scale matrix

 |  0.008133  0.000000 -0.000005|
 |  0.000000  0.004478  0.000001|
 | -0.000002  0.000000  0.002670|
With corresponding cell

    A    = 122.952  B   = 223.313  C    = 374.491
    Alpha=  90.020  Beta=  89.928  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 123.000  B   = 223.000  C    = 374.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 93.027
(Under-)estimated Z-score: 7.108

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.

   2 GLN   (   4-)  A      C    CA   CB  119.41    4.9
   3 GLN   (   5-)  A     -C    N    CA  130.84    5.1
   3 GLN   (   5-)  A      N    CA   CB  119.36    5.2
   9 LEU   (  11-)  A     -CA  -C    N   126.49    5.1
   9 LEU   (  11-)  A      CD1  CG   CD2  96.64   -6.4
  10 ARG   (  12-)  A      CG   CD   NE   99.70   -6.4
  12 VAL   (  14-)  A      CA   C    O   112.93   -4.6
  13 LYS   (  15-)  A     -CA  -C    N   126.31    5.1
  13 LYS   (  15-)  A      N    CA   CB  102.91   -4.5
  14 GLU   (  16-)  A     -O   -C    N   115.34   -4.8
  14 GLU   (  16-)  A      CG   CD   OE2 108.75   -4.2
  15 VAL   (  17-)  A      CG1  CB   CG2 101.82   -4.1
  19 LEU   (  21-)  A      N    CA   CB  102.69   -4.6
  20 PHE   (  22-)  A      N    CA   C    99.37   -4.2
  23 GLU   (  25-)  A      CB   CG   CD  121.80    5.4
  25 VAL   (  27-)  A     -C    N    CA  114.49   -4.0
  26 ARG   (  28-)  A      CA   CB   CG  105.94   -4.1
  27 ALA   (  29-)  A      N    CA   C   122.73    4.1
  29 SER   (  31-)  A      CA   CB   OG  101.64   -4.7
  30 VAL   (  32-)  A     -CA  -C    N   107.91   -4.1
  30 VAL   (  32-)  A      N    CA   CB  101.27   -5.4
  30 VAL   (  32-)  A      C    CA   CB  119.54    5.0
  30 VAL   (  32-)  A      CG1  CB   CG2  99.04   -5.3
  33 ILE   (  35-)  A     -CA  -C    N   126.22    5.0
  33 ILE   (  35-)  A      C    CA   CB  118.24    4.3
And so on for a total of 3153 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean 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, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.312
RMS-deviation in bond angles: 4.618

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.

  37 GLU   (  39-)  A
  40 ASP   (  42-)  A
 114 ASP   ( 116-)  A
 154 ASP   ( 156-)  A
 204 GLU   ( 206-)  A
 263 GLU   ( 277-)  A
 266 GLU   ( 280-)  A
 279 GLU   ( 293-)  A
 312 ASP   ( 362-)  A
 348 GLU   ( 398-)  A
 358 ASP   ( 408-)  A
 433 ASP   ( 483-)  A
 435 ASP   ( 485-)  A
 543 GLU   ( 593-)  A
 559 ASP   ( 609-)  A
 568 GLU   ( 618-)  A
 586 GLU   ( 636-)  A
 628 GLU   ( 678-)  A
 666 ASP   ( 716-)  A
 674 GLU   ( 724-)  A
 740 ASP   ( 790-)  A
 751 GLU   ( 801-)  A
 772 GLU   ( 822-)  A
 776 ASP   ( 826-)  A
 829 GLU   ( 879-)  A
And so on for a total of 101 lines.

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.

  27 ALA   (  29-)  A      CA    -7.0    25.14    34.09
  91 VAL   (  93-)  A      C     -6.1    -8.21     0.15
  94 ILE   (  96-)  A      CB    14.2    50.74    32.31
  97 ILE   (  99-)  A      CB     6.2    40.40    32.31
 163 GLY   ( 165-)  A      C     -6.4    -8.43     0.06
 172 ILE   ( 174-)  A      CB     9.1    44.20    32.31
 208 ILE   ( 210-)  A      CB     7.4    41.92    32.31
 218 THR   ( 220-)  A      C      6.0     9.37     0.30
 293 ILE   ( 325-)  A      CB     6.4    40.65    32.31
 302 VAL   ( 352-)  A      CB   -14.7   -52.28   -32.96
 320 ILE   ( 370-)  A      CB     6.9    41.29    32.31
 329 VAL   ( 379-)  A      CB    -6.3   -41.15   -32.96
 339 THR   ( 389-)  A      CB     7.4    50.59    34.09
 349 HIS   ( 399-)  A      C      7.4    11.26     0.15
 350 PRO   ( 400-)  A      N      9.2    27.54    -2.48
 374 ILE   ( 424-)  A      CB     7.8    42.49    32.31
 410 VAL   ( 460-)  A      CB    -6.1   -41.00   -32.96
 411 LYS   ( 461-)  A      CA     6.1    44.08    33.92
 412 VAL   ( 462-)  A      C     -6.6    -8.89     0.15
 412 VAL   ( 462-)  A      CB    -6.7   -41.70   -32.96
 414 PRO   ( 464-)  A      C     -7.2   -10.89     0.42
 419 ARG   ( 469-)  A      C      6.6    10.22     0.13
 422 LEU   ( 472-)  A      CG     7.4   -20.00   -33.01
 424 VAL   ( 474-)  A      CB     7.9   -22.59   -32.96
 434 GLY   ( 484-)  A      C     -7.1    -9.30     0.06
And so on for a total of 247 lines.

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals 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 2.5 worries us. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.723

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.

2679 VAL   ( 240-)  C   10.98
1177 MET   (1259-)  A   10.70
2478 ALA   (  39-)  C    9.39
2695 ALA   ( 256-)  C    9.08
3297 ARG   (  38-)  J    9.07
 637 LYS   ( 687-)  A    8.57
1014 VAL   (1064-)  A    8.56
1390 ASP   (  56-)  B    8.51
 135 ALA   ( 137-)  A    8.41
1910 ASP   ( 642-)  B    8.38
2516 ILE   (  77-)  C    8.37
 833 LEU   ( 883-)  A    8.33
 674 GLU   ( 724-)  A    8.25
1705 ALA   ( 414-)  B    8.24
 919 GLN   ( 969-)  A    8.12
 914 ILE   ( 964-)  A    8.04
1114 LEU   (1176-)  A    8.00
1276 SER   (1358-)  A    7.96
 269 GLY   ( 283-)  A    7.95
 675 ALA   ( 725-)  A    7.94
  27 ALA   (  29-)  A    7.84
 694 LYS   ( 744-)  A    7.83
1380 GLN   (  46-)  B    7.83
2923 LYS   (  72-)  F    7.78
2467 ALA   (  28-)  C    7.75
And so on for a total of 410 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 : 2.612

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 609 HIS   ( 659-)  A   32.90
2218 HIS   ( 984-)  B   22.71
1786 HIS   ( 518-)  B   22.48
 581 HIS   ( 631-)  A   20.78
2259 HIS   (1025-)  B   18.59
1285 HIS   (1367-)  A   13.92
1768 HIS   ( 494-)  B   13.60
2854 HIS   ( 147-)  E   13.16
2358 HIS   (1141-)  B   12.00
2412 HIS   (1195-)  B   11.72
1990 HIS   ( 740-)  B   11.02
 361 ASP   ( 411-)  A   10.95
2840 GLU   ( 133-)  E   10.74
2249 HIS   (1015-)  B   10.64
2855 GLU   ( 148-)  E   10.46
2330 HIS   (1097-)  B   10.16
2084 ASN   ( 834-)  B   10.14
1880 GLU   ( 612-)  B    9.87
 207 ASN   ( 209-)  A    9.79
1196 ASN   (1278-)  A    9.24
 467 ASN   ( 517-)  A    9.21
1590 GLU   ( 299-)  B    9.02
3312 HIS   (  53-)  J    8.92
3161 ASN   (  23-)  I    8.74
 745 GLU   ( 795-)  A    8.74
And so on for a total of 167 lines.

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

3217 HIS   (  79-)  I      CB   6.32
2296 HIS   (1062-)  B      CB   6.14
1783 HIS   ( 515-)  B      CB   5.96
2394 HIS   (1177-)  B      CB   5.36
2875 TYR   ( 168-)  E      OH   5.36
3172 TYR   (  34-)  I      OH   5.33
1984 HIS   ( 734-)  B      CB   4.58
2083 TYR   ( 833-)  B      OH   4.57
1925 HIS   ( 657-)  B      CB   4.56
3153 TYR   (  15-)  I      OH   4.47
1481 TYR   ( 190-)  B      OH   4.34
3094 TYR   ( 102-)  H      OH   4.28
2736 PHE   (  29-)  E      CB   4.06
2530 HIS   (  91-)  C      CB   4.06
3280 TYR   (  21-)  J      CB   4.01
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.410

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.410

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.

3096 PHE   ( 104-)  H    -3.5
2189 THR   ( 955-)  B    -3.5
2330 HIS   (1097-)  B    -3.3
3456 THR   (  43-)  L    -3.3
1983 HIS   ( 733-)  B    -3.3
2281 PHE   (1047-)  B    -3.2
2482 THR   (  43-)  C    -3.1
 350 PRO   ( 400-)  A    -3.1
2439 ARG   (1222-)  B    -3.1
  36 PRO   (  38-)  A    -3.0
2431 PRO   (1214-)  B    -3.0
3021 PRO   (  17-)  H    -2.9
1062 PRO   (1122-)  A    -2.9
 835 THR   ( 885-)  A    -2.9
2133 LEU   ( 883-)  B    -2.8
1749 TRP   ( 466-)  B    -2.8
2568 ILE   ( 129-)  C    -2.8
  42 THR   (  44-)  A    -2.8
1913 SER   ( 645-)  B    -2.8
3179 PRO   (  41-)  I    -2.8
  82 ILE   (  84-)  A    -2.7
2744 LEU   (  37-)  E    -2.7
 549 SER   ( 599-)  A    -2.7
1725 ARG   ( 434-)  B    -2.7
3459 VAL   (  46-)  L    -2.7
And so on for a total of 270 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.

   3 GLN   (   5-)  A  omega poor
   8 PRO   (  10-)  A  omega poor
  20 PHE   (  22-)  A  omega poor
  29 SER   (  31-)  A  omega poor
  30 VAL   (  32-)  A  Poor phi/psi
  33 ILE   (  35-)  A  Poor phi/psi
  38 THR   (  40-)  A  omega poor
  39 MET   (  41-)  A  Poor phi/psi
  40 ASP   (  42-)  A  Poor phi/psi, omega poor
  41 GLU   (  43-)  A  omega poor
  42 THR   (  44-)  A  Poor phi/psi, omega poor
  43 GLN   (  45-)  A  Poor phi/psi
  45 ARG   (  47-)  A  Poor phi/psi
  46 ALA   (  48-)  A  Poor phi/psi
  49 GLY   (  51-)  A  Poor phi/psi, omega poor
  50 GLY   (  52-)  A  omega poor
  52 ASN   (  54-)  A  Poor phi/psi
  54 PRO   (  56-)  A  Poor phi/psi
  55 ARG   (  57-)  A  Poor phi/psi
  57 GLY   (  59-)  A  Poor phi/psi
  58 SER   (  60-)  A  Poor phi/psi, omega poor
  60 ASP   (  62-)  A  Poor phi/psi, omega poor
  61 ARG   (  63-)  A  Poor phi/psi
  62 ASN   (  64-)  A  omega poor
  63 LEU   (  65-)  A  Poor phi/psi, omega poor
And so on for a total of 652 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 : -4.758

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.

1232 SER   (1314-)  A    0.36
1478 SER   ( 187-)  B    0.37
1767 SER   ( 493-)  B    0.37
3279 SER   (  20-)  J    0.37
1369 SER   (  35-)  B    0.38
1326 SER   (1425-)  A    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!

   3 GLN   (   5-)  A      0
   4 TYR   (   6-)  A      0
  17 PHE   (  19-)  A      0
  28 ILE   (  30-)  A      0
  30 VAL   (  32-)  A      0
  31 ALA   (  33-)  A      0
  32 LYS   (  34-)  A      0
  33 ILE   (  35-)  A      0
  34 ARG   (  36-)  A      0
  36 PRO   (  38-)  A      0
  38 THR   (  40-)  A      0
  39 MET   (  41-)  A      0
  40 ASP   (  42-)  A      0
  41 GLU   (  43-)  A      0
  42 THR   (  44-)  A      0
  43 GLN   (  45-)  A      0
  45 ARG   (  47-)  A      0
  46 ALA   (  48-)  A      0
  47 LYS   (  49-)  A      0
  51 LEU   (  53-)  A      0
  52 ASN   (  54-)  A      0
  53 ASP   (  55-)  A      0
  54 PRO   (  56-)  A      0
  55 ARG   (  57-)  A      0
  56 LEU   (  58-)  A      0
And so on for a total of 1502 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 11.481

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!

3022 GLY   (  18-)  H   3.15   21
 269 GLY   ( 283-)  A   2.84   16
3119 GLY   ( 127-)  H   2.61   18
1554 GLY   ( 263-)  B   1.95   67
 657 GLY   ( 707-)  A   1.88   78
 744 PRO   ( 794-)  A   1.79   12
2544 GLY   ( 105-)  C   1.76   19
2655 GLY   ( 216-)  C   1.67   50
2276 GLY   (1042-)  B   1.64   16
2783 GLY   (  76-)  E   1.55   14

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...

 282 LEU   ( 296-)  A   1.60
 898 VAL   ( 948-)  A   1.76
1116 GLN   (1188-)  A   1.51
1979 ILE   ( 729-)  B   1.70
2129 ARG   ( 879-)  B   1.90
2178 THR   ( 944-)  B   2.12
2428 ASN   (1211-)  B   1.51
2799 THR   (  92-)  E   1.72
3232 ASP   (  94-)  I   1.82
3244 CYS   ( 106-)  I   1.74
3359 GLU   (  36-)  K   2.34
3360 LYS   (  37-)  K   1.58
3439 THR   (  26-)  L   2.52
3445 ALA   (  32-)  L   1.76
3461 CYS   (  48-)  L   1.83

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]

  76 PRO   (  78-)  A    0.12 LOW
 241 PRO   ( 243-)  A    0.62 HIGH
 242 PRO   ( 244-)  A    0.50 HIGH
 271 PRO   ( 285-)  A    0.10 LOW
 307 PRO   ( 357-)  A    0.06 LOW
 332 PRO   ( 382-)  A    0.07 LOW
 346 PRO   ( 396-)  A    0.18 LOW
 350 PRO   ( 400-)  A    0.07 LOW
 427 PRO   ( 477-)  A    0.19 LOW
 513 PRO   ( 563-)  A    0.19 LOW
 589 PRO   ( 639-)  A    0.11 LOW
 744 PRO   ( 794-)  A    0.55 HIGH
 760 PRO   ( 810-)  A    0.56 HIGH
 905 PRO   ( 955-)  A    0.15 LOW
 928 PRO   ( 978-)  A    0.70 HIGH
1025 PRO   (1075-)  A    0.50 HIGH
1054 PRO   (1114-)  A    0.13 LOW
1104 PRO   (1164-)  A    0.07 LOW
1210 PRO   (1292-)  A    0.16 LOW
1242 PRO   (1324-)  A    0.17 LOW
1358 PRO   (  24-)  B    0.53 HIGH
1416 PRO   ( 100-)  B    0.53 HIGH
1487 PRO   ( 196-)  B    0.15 LOW
1522 PRO   ( 231-)  B    0.46 HIGH
1572 PRO   ( 281-)  B    0.19 LOW
And so on for a total of 56 lines.

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].

   8 PRO   (  10-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
  36 PRO   (  38-)  A   -55.5 half-chair C-beta/C-alpha (-54 degrees)
  54 PRO   (  56-)  A  -116.8 envelop C-gamma (-108 degrees)
  87 PRO   (  89-)  A  -114.8 envelop C-gamma (-108 degrees)
 242 PRO   ( 244-)  A  -120.8 half-chair C-delta/C-gamma (-126 degrees)
 246 PRO   ( 248-)  A   -31.7 envelop C-alpha (-36 degrees)
 327 PRO   ( 377-)  A    39.0 envelop C-delta (36 degrees)
 414 PRO   ( 464-)  A  -112.7 envelop C-gamma (-108 degrees)
 469 PRO   ( 519-)  A   100.6 envelop C-beta (108 degrees)
 533 PRO   ( 583-)  A   -46.5 half-chair C-beta/C-alpha (-54 degrees)
 550 PRO   ( 600-)  A  -130.2 half-chair C-delta/C-gamma (-126 degrees)
 624 PRO   ( 674-)  A  -118.3 half-chair C-delta/C-gamma (-126 degrees)
1039 PRO   (1099-)  A   109.4 envelop C-beta (108 degrees)
1062 PRO   (1122-)  A   137.9 envelop C-alpha (144 degrees)
1098 PRO   (1158-)  A   -44.6 envelop C-alpha (-36 degrees)
1118 PRO   (1190-)  A   -64.1 envelop C-beta (-72 degrees)
1212 PRO   (1294-)  A  -125.1 half-chair C-delta/C-gamma (-126 degrees)
1220 PRO   (1302-)  A   -23.3 half-chair C-alpha/N (-18 degrees)
1358 PRO   (  24-)  B    49.9 half-chair C-delta/C-gamma (54 degrees)
1416 PRO   ( 100-)  B    47.8 half-chair C-delta/C-gamma (54 degrees)
1430 PRO   ( 114-)  B  -133.7 half-chair C-delta/C-gamma (-126 degrees)
1524 PRO   ( 233-)  B   -13.9 half-chair C-alpha/N (-18 degrees)
1904 PRO   ( 636-)  B   -57.8 half-chair C-beta/C-alpha (-54 degrees)
1971 PRO   ( 712-)  B    26.8 half-chair N/C-delta (18 degrees)
2068 PRO   ( 818-)  B    40.0 envelop C-delta (36 degrees)
2174 PRO   ( 940-)  B    13.0 half-chair N/C-delta (18 degrees)
2248 PRO   (1014-)  B  -119.4 half-chair C-delta/C-gamma (-126 degrees)
2280 PRO   (1046-)  B   -55.8 half-chair C-beta/C-alpha (-54 degrees)
2431 PRO   (1214-)  B   -32.4 envelop C-alpha (-36 degrees)
2621 PRO   ( 182-)  C  -117.5 half-chair C-delta/C-gamma (-126 degrees)
2652 PRO   ( 213-)  C   -21.6 half-chair C-alpha/N (-18 degrees)
2760 PRO   (  53-)  E    33.8 envelop C-delta (36 degrees)
2771 PRO   (  64-)  E   109.5 envelop C-beta (108 degrees)
2780 PRO   (  73-)  E    37.9 envelop C-delta (36 degrees)
2825 PRO   ( 118-)  E   122.8 half-chair C-beta/C-alpha (126 degrees)
2832 PRO   ( 125-)  E   -51.3 half-chair C-beta/C-alpha (-54 degrees)
2836 PRO   ( 129-)  E   -54.1 half-chair C-beta/C-alpha (-54 degrees)
2858 PRO   ( 151-)  E   -65.3 envelop C-beta (-72 degrees)
2926 PRO   (  75-)  F  -117.6 half-chair C-delta/C-gamma (-126 degrees)
3021 PRO   (  17-)  H   -34.6 envelop C-alpha (-36 degrees)
3052 PRO   (  48-)  H    52.3 half-chair C-delta/C-gamma (54 degrees)
3073 PRO   (  81-)  H    50.5 half-chair C-delta/C-gamma (54 degrees)
3074 PRO   (  82-)  H   -59.5 half-chair C-beta/C-alpha (-54 degrees)
3154 PRO   (  16-)  I    42.5 envelop C-delta (36 degrees)
3179 PRO   (  41-)  I   -27.3 envelop C-alpha (-36 degrees)
3204 PRO   (  66-)  I  -128.8 half-chair C-delta/C-gamma (-126 degrees)
3327 PRO   (   4-)  K   -47.7 half-chair C-beta/C-alpha (-54 degrees)
3346 PRO   (  23-)  K    33.9 envelop C-delta (36 degrees)
3351 PRO   (  28-)  K   -39.0 envelop C-alpha (-36 degrees)
3406 PRO   (  83-)  K  -121.6 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

  68 CYS   (  70-)  A      SG   <->    78 HIS   (  80-)  A      NE2  1.18    2.12  INTRA BF
  54 PRO   (  56-)  A      O    <->    55 ARG   (  57-)  A      CD   1.10    1.60  INTRA BF
 319 SER   ( 369-)  A      OG   <->  3325 ASN   (   2-)  K      ND2  1.09    1.61  INTRA BF
3096 PHE   ( 104-)  H      O    <->  3098 GLU   ( 106-)  H      N    1.08    1.62  INTRA BF
2380 CYS   (1163-)  B      SG   <->  2402 CYS   (1185-)  B      SG   1.05    2.55  INTRA BF
 108 CYS   ( 110-)  A      SG   <->   146 CYS   ( 148-)  A      SG   0.94    2.66  INTRA BF
  40 ASP   (  42-)  A      OD1  <->    45 ARG   (  47-)  A      N    0.84    1.86  INTRA BF
2383 CYS   (1166-)  B      SG   <->  2402 CYS   (1185-)  B      SG   0.81    2.79  INTRA BF
3120 ASN   ( 128-)  H      O    <->  3123 ASN   ( 131-)  H      ND2  0.78    1.92  INTRA BF
 108 CYS   ( 110-)  A      SG   <->   165 CYS   ( 167-)  A      SG   0.78    2.82  INTRA BF
3098 GLU   ( 106-)  H      O    <->  3099 VAL   ( 107-)  H      C    0.78    1.82  INTRA BF
1029 MET   (1079-)  A      SD   <->  1277 ASP   (1359-)  A      OD2  0.75    2.25  INTRA BF
3067 LEU   (  63-)  H      C    <->  3082 ALA   (  90-)  H      CB   0.74    2.46  INTRA BF
3444 CYS   (  31-)  L      SG   <->  3461 CYS   (  48-)  L      SG   0.74    2.71  INTRA BF
3167 CYS   (  29-)  I      SG   <->  3170 CYS   (  32-)  I      SG   0.72    2.73  INTRA BL
3433 ASN   ( 110-)  K      O    <->  3435 GLN   ( 112-)  K      N    0.72    1.98  INTRA BF
 517 LYS   ( 567-)  A      CG   <->   518 PRO   ( 568-)  A      CD   0.72    2.48  INTRA BF
2129 ARG   ( 879-)  B      NH2  <->  2135 MET   ( 885-)  B      CE   0.69    2.41  INTRA BF
3130 GLU   ( 138-)  H      O    <->  3131 ASN   ( 139-)  H      C    0.67    1.93  INTRA BF
2525 CYS   (  86-)  C      SG   <->  2534 CYS   (  95-)  C      SG   0.66    2.79  INTRA BL
 105 CYS   ( 107-)  A      SG   <->   146 CYS   ( 148-)  A      SG   0.66    2.79  INTRA BF
3142 PHE   (   4-)  I      CE1  <->  3151 MET   (  13-)  I      CE   0.64    2.56  INTRA BF
 319 SER   ( 369-)  A      CB   <->  3325 ASN   (   2-)  K      ND2  0.64    2.46  INTRA BF
3266 CYS   (   7-)  J      SG   <->  3304 CYS   (  45-)  J      SG   0.62    2.83  INTRA BL
2962 LEU   ( 111-)  F      O    <->  2964 GLY   ( 113-)  F      N    0.62    2.08  INTRA BF
And so on for a total of 1373 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

2341 ARG   (1108-)  B      -8.29
 187 ARG   ( 189-)  A      -8.01
2346 ARG   (1129-)  B      -7.73
2118 MET   ( 868-)  B      -7.68
 245 ARG   ( 247-)  A      -7.60
1859 ARG   ( 591-)  B      -7.59
2116 TYR   ( 866-)  B      -7.41
3455 ARG   (  42-)  L      -7.22
1453 TYR   ( 137-)  B      -7.20
2706 GLN   ( 267-)  C      -7.17
1099 ARG   (1159-)  A      -7.05
3072 ARG   (  80-)  H      -6.97
  34 ARG   (  36-)  A      -6.95
2128 GLN   ( 878-)  B      -6.94
3121 TYR   ( 129-)  H      -6.77
2137 HIS   ( 887-)  B      -6.70
2439 ARG   (1222-)  B      -6.64
   4 TYR   (   6-)  A      -6.60
2329 ARG   (1096-)  B      -6.56
3069 ARG   (  77-)  H      -6.49
   2 GLN   (   4-)  A      -6.45
2443 GLU   (   4-)  C      -6.35
1632 LEU   ( 341-)  B      -6.33
3124 LEU   ( 132-)  H      -6.27
  72 MET   (  74-)  A      -6.23
And so on for a total of 115 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.

   2 GLN   (   4-)  A         4 - TYR      6- ( A)         -6.02
  72 MET   (  74-)  A        75 - CYS     77- ( A)         -4.78
 244 VAL   ( 246-)  A       246 - PRO    248- ( A)         -5.44
 347 ASN   ( 397-)  A       349 - HIS    399- ( A)         -4.88
 655 LYS   ( 705-)  A       657 - GLY    707- ( A)         -4.77
1160 ASN   (1232-)  A      1162 - GLU   1234- ( A)         -4.51
1450 LYS   ( 134-)  B      1453 - TYR    137- ( B)         -5.55
1535 LEU   ( 244-)  B      1538 - GLY    247- ( B)         -4.84
2114 LYS   ( 864-)  B      2116 - TYR    866- ( B)         -5.94
2134 ARG   ( 884-)  B      2137 - HIS    887- ( B)         -5.88
2344 GLY   (1127-)  B      2347 - PHE   1130- ( B)         -5.28

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: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: F

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: H

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: I

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: J

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: K

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: L

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.

1699 LEU   ( 408-)  B   -2.98
 454 LEU   ( 504-)  A   -2.77
  74 GLU   (  76-)  A   -2.76
 402 LYS   ( 452-)  A   -2.71
2677 ILE   ( 238-)  C   -2.71
3308 MET   (  49-)  J   -2.63
 422 LEU   ( 472-)  A   -2.56
2564 MET   ( 125-)  C   -2.54
3095 LYS   ( 103-)  H   -2.54
1887 ILE   ( 619-)  B   -2.53
 540 ARG   ( 590-)  A   -2.51

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.

3330 PHE   (   7-)  K     - 3333 PHE   (  10-)  K        -1.56

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

  66 GLN   (  68-)  A
  90 HIS   (  92-)  A
 169 GLN   ( 171-)  A
 211 HIS   ( 213-)  A
 285 HIS   ( 299-)  A
 349 HIS   ( 399-)  A
 453 GLN   ( 503-)  A
 467 ASN   ( 517-)  A
 686 ASN   ( 736-)  A
 691 ASN   ( 741-)  A
 695 GLN   ( 745-)  A
 707 ASN   ( 757-)  A
 718 GLN   ( 768-)  A
 736 HIS   ( 786-)  A
 808 ASN   ( 858-)  A
 853 ASN   ( 903-)  A
 876 GLN   ( 926-)  A
 944 GLN   ( 994-)  A
1080 HIS   (1140-)  A
1113 HIS   (1173-)  A
1282 ASN   (1364-)  A
1333 GLN   (1432-)  A
1506 GLN   ( 215-)  B
1527 HIS   ( 236-)  B
1591 HIS   ( 300-)  B
And so on for a total of 53 lines.

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.

   4 TYR   (   6-)  A      N
   5 SER   (   7-)  A      OG
  31 ALA   (  33-)  A      N
  35 PHE   (  37-)  A      N
  37 GLU   (  39-)  A      N
  44 THR   (  46-)  A      N
  51 LEU   (  53-)  A      N
  56 LEU   (  58-)  A      N
  57 GLY   (  59-)  A      N
  60 ASP   (  62-)  A      N
  66 GLN   (  68-)  A      N
  68 CYS   (  70-)  A      N
  69 GLN   (  71-)  A      N
  77 GLY   (  79-)  A      N
  78 HIS   (  80-)  A      N
  86 LYS   (  88-)  A      N
  91 VAL   (  93-)  A      N
 110 LYS   ( 112-)  A      N
 113 LEU   ( 115-)  A      N
 115 GLU   ( 117-)  A      N
 118 GLU   ( 120-)  A      N
 126 ILE   ( 128-)  A      N
 145 VAL   ( 147-)  A      N
 154 ASP   ( 156-)  A      N
 162 ARG   ( 164-)  A      NH1
And so on for a total of 402 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.

  40 ASP   (  42-)  A      OD1
  66 GLN   (  68-)  A      OE1
  81 HIS   (  83-)  A      ND1
 266 GLU   ( 280-)  A      OE1
 395 ASN   ( 445-)  A      OD1
 436 GLU   ( 486-)  A      OE2
 440 HIS   ( 490-)  A      ND1
 598 ASN   ( 648-)  A      OD1
 717 GLN   ( 767-)  A      OE1
1070 GLN   (1130-)  A      OE1
1347 ASP   (1446-)  A      OD1
1347 ASP   (1446-)  A      OD2
1485 GLU   ( 194-)  B      OE1
1955 GLU   ( 696-)  B      OE1
1957 GLU   ( 698-)  B      OE1
2044 ASN   ( 794-)  B      OD1
2122 GLU   ( 872-)  B      OE1
2249 HIS   (1015-)  B      NE2
2259 HIS   (1025-)  B      ND1
2310 HIS   (1076-)  B      ND1
2378 HIS   (1161-)  B      ND1
2712 ASN   (   5-)  E      OD1
2860 HIS   ( 153-)  E      NE2
2955 ASN   ( 104-)  F      OD1
3083 ASP   (  91-)  H      OD1
3126 ASN   ( 134-)  H      OD1
3275 ASP   (  16-)  J      OD1
3361 GLU   (  38-)  K      OE1
3466 HIS   (  53-)  L      ND1

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.

  40 ASP   (  42-)  A   H-bonding suggests Asn; but Alt-Rotamer
  41 GLU   (  43-)  A   H-bonding suggests Gln
  53 ASP   (  55-)  A   H-bonding suggests Asn; but Alt-Rotamer
  70 GLU   (  72-)  A   H-bonding suggests Gln; but Alt-Rotamer
 186 ASP   ( 188-)  A   H-bonding suggests Asn; but Alt-Rotamer
 266 GLU   ( 280-)  A   H-bonding suggests Gln
 436 GLU   ( 486-)  A   H-bonding suggests Gln
 631 GLU   ( 681-)  A   H-bonding suggests Gln
 776 ASP   ( 826-)  A   H-bonding suggests Asn
 963 ASP   (1013-)  A   H-bonding suggests Asn; but Alt-Rotamer
1291 ASP   (1373-)  A   H-bonding suggests Asn
1305 GLU   (1403-)  A   H-bonding suggests Gln
1399 GLU   (  65-)  B   H-bonding suggests Gln
1645 ASP   ( 354-)  B   H-bonding suggests Asn
1662 GLU   ( 371-)  B   H-bonding suggests Gln
1911 ASP   ( 643-)  B   H-bonding suggests Asn
1936 ASP   ( 668-)  B   H-bonding suggests Asn
2122 GLU   ( 872-)  B   H-bonding suggests Gln; but Alt-Rotamer
2353 ASP   (1136-)  B   H-bonding suggests Asn; but Alt-Rotamer
2373 ASP   (1156-)  B   H-bonding suggests Asn
2423 GLU   (1206-)  B   H-bonding suggests Gln
2489 GLU   (  50-)  C   H-bonding suggests Gln
2532 ASP   (  93-)  C   H-bonding suggests Asn
2620 ASP   ( 181-)  C   H-bonding suggests Asn; but Alt-Rotamer
2656 ASP   ( 217-)  C   H-bonding suggests Asn
2709 ASP   (   2-)  E   H-bonding suggests Asn
2732 ASP   (  25-)  E   H-bonding suggests Asn; but Alt-Rotamer
3012 ASP   (   8-)  H   H-bonding suggests Asn; but Alt-Rotamer
3078 ASP   (  86-)  H   H-bonding suggests Asn
3083 ASP   (  91-)  H   H-bonding suggests Asn
3102 ASP   ( 110-)  H   H-bonding suggests Asn
3345 ASP   (  22-)  K   H-bonding suggests Asn
3429 GLU   ( 106-)  K   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.597
  2nd generation packing quality :  -1.792
  Ramachandran plot appearance   :  -3.410 (poor)
  chi-1/chi-2 rotamer normality  :  -4.758 (bad)
  Backbone conformation          :  -0.734

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.051 (loose)
  Bond angles                    :   2.312 (loose)
  Omega angle restraints         :   2.087 (loose)
  Side chain planarity           :   3.218 (loose)
  Improper dihedral distribution :   2.723 (loose)
  B-factor distribution          :   0.486
  Inside/Outside distribution    :   1.035

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 : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.051 (loose)
  Bond angles                    :   2.312 (loose)
  Omega angle restraints         :   2.087 (loose)
  Side chain planarity           :   3.218 (loose)
  Improper dihedral distribution :   2.723 (loose)
  B-factor distribution          :   0.486
  Inside/Outside distribution    :   1.035
==============

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.