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 pdb1twg.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: 395424.625
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= 6.486
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= 3.243
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.

3497 CTP   (3008-)  B  -

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  3086 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.

 939 GLY   ( 989-)  A  -
2307 GLY   (1075-)  B  -
2310 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 3083 TYR   (  95-)  H  -   CE2

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

3485  MN   (3010-)  B  -

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: Artificial side chains detected

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

2157 VAL   ( 910-)  B
2923 LYS   (  76-)  F

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
   6 SER   (   8-)  A    High
  10 ARG   (  12-)  A    High
  30 VAL   (  32-)  A    High
  32 LYS   (  34-)  A    High
  35 PHE   (  37-)  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
  52 ASN   (  54-)  A    High
  53 ASP   (  55-)  A    High
  55 ARG   (  57-)  A    High
  56 LEU   (  58-)  A    High
And so on for a total of 441 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

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 21.62

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.

 972 ARG   (1023-)  A
1262 ARG   (1345-)  A
2903 ARG   ( 200-)  E
2915 ARG   ( 212-)  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
 742 TYR   ( 792-)  A
 754 TYR   ( 804-)  A
 847 TYR   ( 897-)  A
 984 TYR   (1035-)  A
1204 TYR   (1287-)  A
1270 TYR   (1353-)  A
1279 TYR   (1362-)  A
1468 TYR   ( 180-)  B
1478 TYR   ( 190-)  B
1563 TYR   ( 275-)  B
1591 TYR   ( 303-)  B
1757 TYR   ( 486-)  B
1931 TYR   ( 666-)  B
1948 TYR   ( 692-)  B
2016 TYR   ( 769-)  B
2032 TYR   ( 785-)  B
2045 TYR   ( 798-)  B
2058 TYR   ( 811-)  B
2113 TYR   ( 866-)  B
2225 TYR   ( 994-)  B
2295 TYR   (1064-)  B
2405 TYR   (1192-)  B
2430 TYR   (1217-)  B
2517 TYR   (  82-)  C
2626 TYR   ( 191-)  C
2664 TYR   ( 229-)  C
2731 TYR   (  28-)  E
2749 TYR   (  46-)  E
2871 TYR   ( 168-)  E
2890 TYR   ( 187-)  E
2914 TYR   ( 211-)  E
2935 TYR   (  88-)  F
3020 TYR   (  20-)  H
3083 TYR   (  95-)  H
3103 TYR   ( 115-)  H
3104 TYR   ( 116-)  H
3117 TYR   ( 129-)  H
3149 TYR   (  15-)  I
3178 TYR   (  44-)  I
3318 TYR   (  63-)  J
3380 TYR   (  61-)  K
3400 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
  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
 737 PHE   ( 787-)  A
 763 PHE   ( 813-)  A
 765 PHE   ( 815-)  A
 816 PHE   ( 866-)  A
 843 PHE   ( 893-)  A
 897 PHE   ( 947-)  A
 921 PHE   ( 971-)  A
1002 PHE   (1053-)  A
1147 PHE   (1220-)  A
1152 PHE   (1225-)  A
1308 PHE   (1410-)  A
1349 PHE   (  18-)  B
1368 PHE   (  37-)  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
1125 ASP   (1198-)  A
1131 ASP   (1204-)  A
1174 ASP   (1257-)  A
1351 ASP   (  20-)  B
1419 ASP   ( 106-)  B
1486 ASP   ( 198-)  B
1582 ASP   ( 294-)  B
1614 ASP   ( 326-)  B
1620 ASP   ( 332-)  B
1679 ASP   ( 391-)  B
1969 ASP   ( 722-)  B
2037 ASP   ( 790-)  B
2138 ASP   ( 891-)  B
2167 ASP   ( 936-)  B
2432 ASP   (1219-)  B
2661 ASP   ( 226-)  C
2684 ASP   ( 249-)  C
2703 ASP   ( 268-)  C
2787 ASP   (  84-)  E
3008 ASP   (   8-)  H
3053 ASP   (  53-)  H
3074 ASP   (  86-)  H
3153 ASP   (  19-)  I
3195 ASP   (  61-)  I
3228 ASP   (  94-)  I
3343 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
1042 GLU   (1103-)  A
1194 GLU   (1277-)  A
1197 GLU   (1280-)  A
1268 GLU   (1351-)  A
1305 GLU   (1407-)  A
1324 GLU   (1426-)  A
1417 GLU   ( 104-)  B
1482 GLU   ( 194-)  B
1497 GLU   ( 209-)  B
And so on for a total of 56 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    1.60    9.6
   2 GLN   (   4-)  A      CA   C     1.69    7.7
   2 GLN   (   4-)  A      CB   CG    1.80    9.5
   3 GLN   (   5-)  A      CA   C     1.39   -6.5
   3 GLN   (   5-)  A      C    O     1.10   -6.6
   3 GLN   (   5-)  A      CA   CB    1.67    7.2
   3 GLN   (   5-)  A      CB   CG    1.89   12.4
   4 TYR   (   6-)  A      N    CA    1.37   -4.8
   4 TYR   (   6-)  A      C    O     1.36    6.4
   4 TYR   (   6-)  A      CG   CD1   1.50    5.3
   4 TYR   (   6-)  A      CZ   OH    1.28   -4.8
   5 SER   (   7-)  A      N    CA    1.64    9.7
   5 SER   (   7-)  A      CB   OG    1.33   -4.2
   5 SER   (   7-)  A      N   -C     1.44    5.6
   6 SER   (   8-)  A      CA   CB    1.62    4.3
   7 ALA   (   9-)  A      CA   CB    1.81    8.6
   8 PRO   (  10-)  A      CA   CB    1.62    4.7
   8 PRO   (  10-)  A      CB   CG    1.29   -4.1
   8 PRO   (  10-)  A      CG   CD    1.71    6.0
   9 LEU   (  11-)  A      CA   C     1.42   -5.2
   9 LEU   (  11-)  A      C    O     1.13   -5.2
  10 ARG   (  12-)  A      CA   C     1.40   -6.2
  10 ARG   (  12-)  A      C    O     1.06   -8.6
  10 ARG   (  12-)  A      CZ   NH1   1.44    6.3
  13 LYS   (  15-)  A      CB   CG    1.79    9.1
And so on for a total of 8840 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: 3.781
RMS-deviation in bond distances: 0.088

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

 |  0.996728  0.000099  0.001301|
 |  0.000099  1.001513 -0.000312|
 |  0.001301 -0.000312  1.000665|
Proposed new scale matrix

 |  0.008157  0.000000 -0.000011|
 |  0.000000  0.004477  0.000001|
 | -0.000003  0.000000  0.002672|
With corresponding cell

    A    = 122.599  B   = 223.353  C    = 374.220
    Alpha=  90.020  Beta=  89.851  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: 176.819
(Under-)estimated Z-score: 9.800

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      N    CA   CB  101.11   -5.5
   2 GLN   (   4-)  A      C    CA   CB  123.64    7.1
   3 GLN   (   5-)  A      N    CA   CB  121.96    6.7
   5 SER   (   7-)  A     -C    N    CA  129.16    4.1
   6 SER   (   8-)  A      CA   CB   OG  119.32    4.1
   8 PRO   (  10-)  A     -CA  -C    N   110.40   -4.3
   9 LEU   (  11-)  A     -CA  -C    N   125.27    4.5
   9 LEU   (  11-)  A     -C    N    CA  114.27   -4.1
   9 LEU   (  11-)  A      CB   CG   CD2 124.88    4.7
   9 LEU   (  11-)  A      CD1  CG   CD2 101.33   -4.3
  10 ARG   (  12-)  A      CG   CD   NE   94.44   -9.4
  11 THR   (  13-)  A     -O   -C    N   113.61   -5.9
  11 THR   (  13-)  A     -C    N    CA  129.17    4.1
  13 LYS   (  15-)  A      N    CA   CB  100.10   -6.1
  14 GLU   (  16-)  A      CG   CD   OE2 108.85   -4.2
  15 VAL   (  17-)  A      CG1  CB   CG2  97.64   -6.0
  16 GLN   (  18-)  A      N    CA   CB  119.18    5.1
  16 GLN   (  18-)  A      CB   CG   CD  121.48    5.2
  17 PHE   (  19-)  A     -O   -C    N   131.78    5.5
  19 LEU   (  21-)  A      CA   C    O   129.16    4.9
  19 LEU   (  21-)  A      N    CA   CB  101.79   -5.1
  20 PHE   (  22-)  A      N    CA   C    93.61   -6.3
  21 SER   (  23-)  A      N    CA   CB  103.58   -4.1
  22 PRO   (  24-)  A      CG   CD   N   114.33    7.4
  22 PRO   (  24-)  A      CD   N    CA  117.83    4.2
And so on for a total of 5714 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: 2.780
RMS-deviation in bond angles: 5.524

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 98 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.

  30 VAL   (  32-)  A      CB    -6.7   -41.74   -32.96
  67 THR   (  69-)  A      CA    -7.2    21.78    33.84
  70 GLU   (  72-)  A      CA    -6.8    22.88    33.96
  76 PRO   (  78-)  A      C      7.7    12.54     0.42
  81 HIS   (  83-)  A      C     -6.0    -8.90     0.15
  82 ILE   (  84-)  A      C     -6.5    -8.49     0.03
  88 VAL   (  90-)  A      CA     8.5    45.54    33.23
  91 VAL   (  93-)  A      CA     6.4    42.49    33.23
  91 VAL   (  93-)  A      C     -7.5   -10.06     0.15
  93 PHE   (  95-)  A      CA     6.1    43.73    33.98
  94 ILE   (  96-)  A      CB    15.7    52.75    32.31
  97 ILE   (  99-)  A      C      6.3     8.24     0.03
  97 ILE   (  99-)  A      CB    12.3    48.26    32.31
 136 ILE   ( 138-)  A      CA    -6.1    24.08    33.24
 156 PRO   ( 158-)  A      C      7.6    12.49     0.42
 157 THR   ( 159-)  A      C     -8.0   -11.77     0.30
 163 GLY   ( 165-)  A      C     -8.7   -11.42     0.06
 168 THR   ( 170-)  A      CB     9.3    54.88    34.09
 172 ILE   ( 174-)  A      CB    11.1    46.69    32.31
 205 ILE   ( 207-)  A      CB     6.8    41.12    32.31
 208 ILE   ( 210-)  A      CB     6.5    40.77    32.31
 258 ALA   ( 272-)  A      CA    -7.1    25.08    34.09
 271 PRO   ( 285-)  A      C     -6.3    -9.55     0.42
 278 ALA   ( 292-)  A      C     -6.1    -9.25     0.08
 293 ILE   ( 325-)  A      CB     6.7    41.08    32.31
And so on for a total of 497 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 : 3.190

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.

1113 LEU   (1176-)  A   14.14
1022 GLY   (1073-)  A   12.14
1702 ALA   ( 414-)  B   11.75
2769 GLU   (  66-)  E   11.34
2000 ALA   ( 753-)  B   11.34
3276 TYR   (  21-)  J   11.01
1907 ASP   ( 642-)  B   10.81
 776 ASP   ( 826-)  A   10.58
2474 ALA   (  39-)  C   10.57
1965 ASP   ( 709-)  B   10.49
  25 VAL   (  27-)  A   10.01
3293 ARG   (  38-)  J    9.99
1700 LEU   ( 412-)  B    9.95
1176 MET   (1259-)  A    9.87
3407 LYS   (  88-)  K    9.84
3306 LEU   (  51-)  J    9.84
1733 ILE   ( 453-)  B    9.83
2603 ALA   ( 168-)  C    9.68
 287 ALA   ( 301-)  A    9.59
 866 GLY   ( 916-)  A    9.52
 826 ALA   ( 876-)  A    9.50
2019 ALA   ( 772-)  B    9.31
 675 ALA   ( 725-)  A    9.12
 344 ASN   ( 394-)  A    9.12
1169 VAL   (1242-)  A    9.08
And so on for a total of 629 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 : 3.108

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   29.23
2256 HIS   (1025-)  B   24.39
2215 HIS   ( 984-)  B   22.26
2354 HIS   (1141-)  B   18.74
1524 HIS   ( 236-)  B   16.46
2850 HIS   ( 147-)  E   15.58
1195 ASN   (1278-)  A   13.97
1783 HIS   ( 518-)  B   13.33
1284 HIS   (1367-)  A   12.81
2635 GLU   ( 200-)  C   12.60
 600 GLN   ( 650-)  A   12.41
2246 HIS   (1015-)  B   11.83
 581 HIS   ( 631-)  A   11.44
2081 ASN   ( 834-)  B   11.05
1587 GLU   ( 299-)  B   10.86
 207 ASN   ( 209-)  A   10.74
1688 HIS   ( 400-)  B   10.67
2009 ASN   ( 762-)  B   10.65
3308 HIS   (  53-)  J   10.57
2033 ASN   ( 786-)  B   10.56
 361 ASP   ( 411-)  A   10.50
 408 HIS   ( 458-)  A   10.49
1987 HIS   ( 740-)  B   10.15
3079 ASP   (  91-)  H   10.01
2326 HIS   (1097-)  B    9.93
And so on for a total of 300 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.

1245 TYR   (1328-)  A      OH   8.95
1490 TYR   ( 202-)  B      OH   7.76
2032 TYR   ( 785-)  B      OH   6.56
2430 TYR   (1217-)  B      OH   6.21
 802 TYR   ( 852-)  A      OH   5.90
1547 TYR   ( 259-)  B      OH   5.73
3213 HIS   (  79-)  I      CB   5.69
1215 TYR   (1298-)  A      OH   5.69
2526 HIS   (  91-)  C      CB   5.47
1491 PHE   ( 203-)  B      CB   5.22
1437 TYR   ( 124-)  B      CB   5.18
1922 HIS   ( 657-)  B      CB   5.13
2455 PHE   (  20-)  C      CB   5.07
2417 PHE   (1204-)  B      CB   5.05
2911 TYR   ( 208-)  E      OH   4.98
1437 TYR   ( 124-)  B      OH   4.95
2137 TYR   ( 890-)  B      OH   4.87
3299 TYR   (  44-)  J      OH   4.86
2935 TYR   (  88-)  F      OH   4.71
2134 HIS   ( 887-)  B      CB   4.57
 742 TYR   ( 792-)  A      OH   4.50
 749 PHE   ( 799-)  A      CB   4.45
1426 TYR   ( 113-)  B      OH   4.38
  89 PHE   (  91-)  A      CB   4.38
2613 PHE   ( 178-)  C      CB   4.27
 211 HIS   ( 213-)  A      CB   4.24
1739 TYR   ( 459-)  B      OH   4.11
 843 PHE   ( 893-)  A      CB   4.11
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.985

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 : -3.985

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.

3092 PHE   ( 104-)  H    -3.8
2186 THR   ( 955-)  B    -3.5
2326 HIS   (1097-)  B    -3.4
1980 HIS   ( 733-)  B    -3.3
2278 PHE   (1047-)  B    -3.2
2478 THR   (  43-)  C    -3.2
2126 ARG   ( 879-)  B    -3.1
 350 PRO   ( 400-)  A    -3.1
2435 ARG   (1222-)  B    -3.1
3452 THR   (  43-)  L    -3.0
3017 PRO   (  17-)  H    -3.0
2427 PRO   (1214-)  B    -3.0
  36 PRO   (  38-)  A    -2.9
3070 PRO   (  82-)  H    -2.9
 835 THR   ( 885-)  A    -2.9
3175 PRO   (  41-)  I    -2.8
2130 LEU   ( 883-)  B    -2.8
  76 PRO   (  78-)  A    -2.8
  54 PRO   (  56-)  A    -2.8
1100 THR   (1161-)  A    -2.8
1746 TRP   ( 466-)  B    -2.7
 549 SER   ( 599-)  A    -2.7
3455 VAL   (  46-)  L    -2.7
1722 ARG   ( 434-)  B    -2.7
  82 ILE   (  84-)  A    -2.7
And so on for a total of 328 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
  11 THR   (  13-)  A  omega poor
  19 LEU   (  21-)  A  omega poor
  20 PHE   (  22-)  A  omega poor
  24 GLU   (  26-)  A  omega poor
  29 SER   (  31-)  A  omega poor
  30 VAL   (  32-)  A  Poor phi/psi
  33 ILE   (  35-)  A  Poor phi/psi
  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
  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
  56 LEU   (  58-)  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
And so on for a total of 845 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 : -5.225

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.

1359 GLU   (  28-)  B    0.36
1475 SER   ( 187-)  B    0.37
1084 SER   (1145-)  A    0.37
1366 SER   (  35-)  B    0.38
1764 SER   ( 493-)  B    0.38
2228 GLU   ( 997-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

  14 GLU   (  16-)  A      0
  17 PHE   (  19-)  A      0
  28 ILE   (  30-)  A      0
  30 VAL   (  32-)  A      0
  31 ALA   (  33-)  A      0
  33 ILE   (  35-)  A      0
  34 ARG   (  36-)  A      0
  35 PHE   (  37-)  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
  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
  58 SER   (  60-)  A      0
  59 ILE   (  61-)  A      0
And so on for a total of 1579 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 : 12.468

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!

3018 GLY   (  18-)  H   3.17   17
 269 GLY   ( 283-)  A   2.94   18
3115 GLY   ( 127-)  H   2.64   13
1912 GLY   ( 647-)  B   2.12   12
 657 GLY   ( 707-)  A   1.98   50
1551 GLY   ( 263-)  B   1.94   37
2651 GLY   ( 216-)  C   1.94   64
2540 GLY   ( 105-)  C   1.84   17
 744 PRO   ( 794-)  A   1.60   11
1701 LEU   ( 413-)  B   1.58   30

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...

 487 ARG   ( 537-)  A   1.51
1134 LEU   (1207-)  A   1.54
1742 ALA   ( 462-)  B   1.56
2127 THR   ( 880-)  B   2.30
2175 THR   ( 944-)  B   1.68
2199 VAL   ( 968-)  B   2.57
2701 ASP   ( 266-)  C   1.94
2795 THR   (  92-)  E   2.58
3028 ALA   (  28-)  H   1.97
3147 MET   (  13-)  I   1.70
3164 ARG   (  30-)  I   2.62
3228 ASP   (  94-)  I   3.11
3253 THR   ( 119-)  I   2.77
3435 THR   (  26-)  L   2.24
3457 CYS   (  48-)  L   1.80

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]

 238 PRO   ( 240-)  A    0.47 HIGH
 241 PRO   ( 243-)  A    0.53 HIGH
 242 PRO   ( 244-)  A    0.47 HIGH
 271 PRO   ( 285-)  A    0.14 LOW
 307 PRO   ( 357-)  A    0.12 LOW
 332 PRO   ( 382-)  A    0.19 LOW
 350 PRO   ( 400-)  A    0.05 LOW
 398 PRO   ( 448-)  A    0.18 LOW
 427 PRO   ( 477-)  A    0.17 LOW
 458 PRO   ( 508-)  A    0.47 HIGH
 511 PRO   ( 561-)  A    0.50 HIGH
 744 PRO   ( 794-)  A    0.53 HIGH
 760 PRO   ( 810-)  A    0.45 HIGH
 928 PRO   ( 978-)  A    0.71 HIGH
1024 PRO   (1075-)  A    0.51 HIGH
1038 PRO   (1099-)  A    0.17 LOW
1053 PRO   (1114-)  A    0.15 LOW
1103 PRO   (1164-)  A    0.08 LOW
1209 PRO   (1292-)  A    0.17 LOW
1211 PRO   (1294-)  A    0.60 HIGH
1355 PRO   (  24-)  B    0.57 HIGH
1413 PRO   ( 100-)  B    0.56 HIGH
1484 PRO   ( 196-)  B    0.15 LOW
1519 PRO   ( 231-)  B    0.47 HIGH
1521 PRO   ( 233-)  B    0.19 LOW
And so on for a total of 60 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].

  36 PRO   (  38-)  A   -56.8 half-chair C-beta/C-alpha (-54 degrees)
  54 PRO   (  56-)  A  -128.9 half-chair C-delta/C-gamma (-126 degrees)
  76 PRO   (  78-)  A   123.8 half-chair C-beta/C-alpha (126 degrees)
  87 PRO   (  89-)  A  -113.9 envelop C-gamma (-108 degrees)
 195 PRO   ( 197-)  A    36.1 envelop C-delta (36 degrees)
 240 PRO   ( 242-)  A  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 242 PRO   ( 244-)  A  -116.7 envelop C-gamma (-108 degrees)
 246 PRO   ( 248-)  A   -27.6 envelop C-alpha (-36 degrees)
 327 PRO   ( 377-)  A    38.6 envelop C-delta (36 degrees)
 414 PRO   ( 464-)  A  -115.9 envelop C-gamma (-108 degrees)
 533 PRO   ( 583-)  A   -49.5 half-chair C-beta/C-alpha (-54 degrees)
 550 PRO   ( 600-)  A  -137.1 envelop C-delta (-144 degrees)
 589 PRO   ( 639-)  A  -143.3 envelop C-delta (-144 degrees)
 624 PRO   ( 674-)  A  -115.4 envelop C-gamma (-108 degrees)
 860 PRO   ( 910-)  A   -63.3 envelop C-beta (-72 degrees)
 907 PRO   ( 957-)  A   -60.1 half-chair C-beta/C-alpha (-54 degrees)
1061 PRO   (1122-)  A   110.6 envelop C-beta (108 degrees)
1097 PRO   (1158-)  A   -42.2 envelop C-alpha (-36 degrees)
1211 PRO   (1294-)  A  -116.5 envelop C-gamma (-108 degrees)
1219 PRO   (1302-)  A   -16.4 half-chair C-alpha/N (-18 degrees)
1241 PRO   (1324-)  A   -33.3 envelop C-alpha (-36 degrees)
1427 PRO   ( 114-)  B  -132.3 half-chair C-delta/C-gamma (-126 degrees)
1776 PRO   ( 511-)  B  -116.4 envelop C-gamma (-108 degrees)
1816 PRO   ( 551-)  B   -57.7 half-chair C-beta/C-alpha (-54 degrees)
1901 PRO   ( 636-)  B   -59.6 half-chair C-beta/C-alpha (-54 degrees)
And so on for a total of 52 lines.

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  1.36    1.94  INTRA BF
3092 PHE   ( 104-)  H      O    <->  3094 GLU   ( 106-)  H      N    1.20    1.50  INTRA BF
3494 CTP   (3008-)  B      C2'  <->  3496 HOH   (3010 )  B      O    1.15    1.65  INTRA
 319 SER   ( 369-)  A      OG   <->  3321 ASN   (   2-)  K      ND2  1.10    1.60  INTRA BF
2521 CYS   (  86-)  C      SG   <->  2530 CYS   (  95-)  C      SG   1.07    2.53  INTRA BL
3494 CTP   (3008-)  B      C3'  <->  3496 HOH   (3010 )  B      O    1.06    1.74  INTRA
  54 PRO   (  56-)  A      O    <->    55 ARG   (  57-)  A      CD   1.05    1.65  INTRA BF
 108 CYS   ( 110-)  A      SG   <->   165 CYS   ( 167-)  A      SG   1.01    2.59  INTRA BF
 108 CYS   ( 110-)  A      SG   <->   146 CYS   ( 148-)  A      SG   1.00    2.60  INTRA BF
3209 CYS   (  75-)  I      SG   <->  3212 CYS   (  78-)  I      SG   0.91    2.54  INTRA BF
3440 CYS   (  31-)  L      SG   <->  3443 CYS   (  34-)  L      SG   0.90    2.55  INTRA BF
3116 ASN   ( 128-)  H      O    <->  3119 ASN   ( 131-)  H      ND2  0.88    1.82  INTRA BF
  40 ASP   (  42-)  A      OD1  <->    45 ARG   (  47-)  A      N    0.86    1.84  INTRA BF
2379 CYS   (1166-)  B      SG   <->  2398 CYS   (1185-)  B      SG   0.85    2.60  INTRA BF
 505 ASP   ( 555-)  A      OD1  <->  3345 LYS   (  26-)  K      NZ   0.81    1.89  INTRA BF
3138 PHE   (   4-)  I      CE1  <->  3147 MET   (  13-)  I      CE   0.75    2.45  INTRA BF
2013 ARG   ( 766-)  B      NH2  <->  3494 CTP   (3008-)  B      C5'  0.75    2.35  INTRA BL
3262 CYS   (   7-)  J      SG   <->  3265 CYS   (  10-)  J      SG   0.74    2.71  INTRA BL
3126 GLU   ( 138-)  H      O    <->  3127 ASN   ( 139-)  H      C    0.73    1.87  INTRA BF
1028 MET   (1079-)  A      SD   <->  1276 ASP   (1359-)  A      OD2  0.71    2.29  INTRA BF
  53 ASP   (  55-)  A      O    <->    55 ARG   (  57-)  A      N    0.71    1.99  INTRA BF
3262 CYS   (   7-)  J      SG   <->  3300 CYS   (  45-)  J      SG   0.70    2.75  INTRA BF
3429 ASN   ( 110-)  K      O    <->  3431 GLN   ( 112-)  K      N    0.69    2.01  INTRA BF
2379 CYS   (1166-)  B      O    <->  2381 LEU   (1168-)  B      N    0.69    2.01  INTRA BL
3077 LEU   (  89-)  H      O    <->  3079 ASP   (  91-)  H      N    0.68    2.02  INTRA BF
And so on for a total of 2460 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.

2337 ARG   (1108-)  B      -8.24
 187 ARG   ( 189-)  A      -8.16
1856 ARG   ( 591-)  B      -7.98
 245 ARG   ( 247-)  A      -7.75
2342 ARG   (1129-)  B      -7.65
3451 ARG   (  42-)  L      -7.37
2115 MET   ( 868-)  B      -7.35
1450 TYR   ( 137-)  B      -7.28
2113 TYR   ( 866-)  B      -7.10
2435 ARG   (1222-)  B      -7.06
2702 GLN   ( 267-)  C      -7.04
3068 ARG   (  80-)  H      -7.04
2125 GLN   ( 878-)  B      -6.98
1098 ARG   (1159-)  A      -6.90
  34 ARG   (  36-)  A      -6.87
   4 TYR   (   6-)  A      -6.83
2134 HIS   ( 887-)  B      -6.78
3065 ARG   (  77-)  H      -6.63
2325 ARG   (1096-)  B      -6.61
  72 MET   (  74-)  A      -6.54
3120 LEU   ( 132-)  H      -6.53
2126 ARG   ( 879-)  B      -6.44
2439 GLU   (   4-)  C      -6.36
1447 LYS   ( 134-)  B      -6.33
2753 MET   (  50-)  E      -6.27
And so on for a total of 121 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)         -5.89
  72 MET   (  74-)  A        75 - CYS     77- ( A)         -4.96
 244 VAL   ( 246-)  A       246 - PRO    248- ( A)         -5.44
 347 ASN   ( 397-)  A       349 - HIS    399- ( A)         -4.74
 655 LYS   ( 705-)  A       657 - GLY    707- ( A)         -4.85
1159 ASN   (1232-)  A      1161 - GLU   1234- ( A)         -4.44
1447 LYS   ( 134-)  B      1450 - TYR    137- ( B)         -5.48
1532 LEU   ( 244-)  B      1535 - GLY    247- ( B)         -4.88
2111 LYS   ( 864-)  B      2113 - TYR    866- ( B)         -5.85
2131 ARG   ( 884-)  B      2134 - HIS    887- ( B)         -5.87
2337 ARG   (1108-)  B      2339 - PRO   1110- ( B)         -5.60
2340 GLY   (1127-)  B      2343 - PHE   1130- ( B)         -5.24
2568 ILE   ( 133-)  C      2570 - GLN    135- ( C)         -4.65
3251 LYS   ( 117-)  I      3254 - GLN    120- ( I)         -5.04

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.

3304 MET   (  49-)  J   -2.99
1696 LEU   ( 408-)  B   -2.96
  74 GLU   (  76-)  A   -2.78
 454 LEU   ( 504-)  A   -2.77
2673 ILE   ( 238-)  C   -2.73
 402 LYS   ( 452-)  A   -2.71
1957 ILE   ( 701-)  B   -2.70
2733 ILE   (  30-)  E   -2.66
 422 LEU   ( 472-)  A   -2.64
3091 LYS   ( 103-)  H   -2.58
1884 ILE   ( 619-)  B   -2.53
1995 ILE   ( 748-)  B   -2.53
2826 LEU   ( 123-)  E   -2.51
2603 ALA   ( 168-)  C   -2.50
2560 MET   ( 125-)  C   -2.50
 540 ARG   ( 590-)  A   -2.50

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.

1992 PRO   ( 745-)  B     - 1995 ILE   ( 748-)  B        -1.95
3222 SER   (  88-)  I     - 3226 ARG   (  92-)  I        -1.78
3326 PHE   (   7-)  K     - 3329 PHE   (  10-)  K        -1.65

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: 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.

3496 HOH   (3010 )  B      O
Metal-coordinating Histidine residue  78 fixed to   1

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.

  90 HIS   (  92-)  A
 169 GLN   ( 171-)  A
 211 HIS   ( 213-)  A
 349 HIS   ( 399-)  A
 401 HIS   ( 451-)  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
 812 ASN   ( 862-)  A
 853 ASN   ( 903-)  A
 876 GLN   ( 926-)  A
 943 GLN   ( 994-)  A
1045 ASN   (1106-)  A
1069 GLN   (1130-)  A
1079 HIS   (1140-)  A
1112 HIS   (1173-)  A
1281 ASN   (1364-)  A
1330 GLN   (1432-)  A
1503 GLN   ( 215-)  B
And so on for a total of 56 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
  23 GLU   (  25-)  A      N
  31 ALA   (  33-)  A      N
  35 PHE   (  37-)  A      N
  37 GLU   (  39-)  A      N
  43 GLN   (  45-)  A      N
  44 THR   (  46-)  A      N
  52 ASN   (  54-)  A      N
  56 LEU   (  58-)  A      N
  57 GLY   (  59-)  A      N
  60 ASP   (  62-)  A      N
  66 GLN   (  68-)  A      N
  66 GLN   (  68-)  A      NE2
  68 CYS   (  70-)  A      N
  69 GLN   (  71-)  A      N
  75 CYS   (  77-)  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
And so on for a total of 415 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 ASN   (  64-)  A      OD1
  81 HIS   (  83-)  A      ND1
 266 GLU   ( 280-)  A      OE1
 395 ASN   ( 445-)  A      OD1
 436 GLU   ( 486-)  A      OE2
 505 ASP   ( 555-)  A      OD1
 598 ASN   ( 648-)  A      OD1
 674 GLU   ( 724-)  A      OE1
 717 GLN   ( 767-)  A      OE1
 804 ASN   ( 854-)  A      OD1
1181 GLU   (1264-)  A      OE1
1344 ASP   (1446-)  A      OD1
1344 ASP   (1446-)  A      OD2
1378 GLN   (  47-)  B      OE1
1482 GLU   ( 194-)  B      OE2
1837 HIS   ( 572-)  B      ND1
1952 GLU   ( 696-)  B      OE1
1954 GLU   ( 698-)  B      OE1
2031 ASN   ( 784-)  B      OD1
2041 ASN   ( 794-)  B      OD1
2246 HIS   (1015-)  B      NE2
2256 HIS   (1025-)  B      ND1
2306 HIS   (1076-)  B      ND1
2374 HIS   (1161-)  B      ND1
2454 ASP   (  19-)  C      OD1
2500 HIS   (  65-)  C      ND1
2708 ASN   (   5-)  E      OD1
2856 HIS   ( 153-)  E      NE2
2951 ASN   ( 104-)  F      OD1
3122 ASN   ( 134-)  H      OD1
3271 ASP   (  16-)  J      OD1
3357 GLU   (  38-)  K      OE1

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
 149 ASP   ( 151-)  A   H-bonding suggests Asn; but Alt-Rotamer
 186 ASP   ( 188-)  A   H-bonding suggests Asn; but Alt-Rotamer
 230 GLU   ( 232-)  A   H-bonding suggests Gln; but Alt-Rotamer
 266 GLU   ( 280-)  A   H-bonding suggests Gln
 436 GLU   ( 486-)  A   H-bonding suggests Gln; but Alt-Rotamer
 450 GLU   ( 500-)  A   H-bonding suggests Gln; but Alt-Rotamer
 631 GLU   ( 681-)  A   H-bonding suggests Gln
 772 GLU   ( 822-)  A   H-bonding suggests Gln
 776 ASP   ( 826-)  A   H-bonding suggests Asn
1161 GLU   (1234-)  A   H-bonding suggests Gln
1290 ASP   (1373-)  A   H-bonding suggests Asn
1396 GLU   (  65-)  B   H-bonding suggests Gln
1642 ASP   ( 354-)  B   H-bonding suggests Asn; but Alt-Rotamer
1659 GLU   ( 371-)  B   H-bonding suggests Gln
1906 GLU   ( 641-)  B   H-bonding suggests Gln
1908 ASP   ( 643-)  B   H-bonding suggests Asn; but Alt-Rotamer
1933 ASP   ( 668-)  B   H-bonding suggests Asn
2349 ASP   (1136-)  B   H-bonding suggests Asn; but Alt-Rotamer
2419 GLU   (1206-)  B   H-bonding suggests Gln
2528 ASP   (  93-)  C   H-bonding suggests Asn; but Alt-Rotamer
2616 ASP   ( 181-)  C   H-bonding suggests Asn; but Alt-Rotamer
2652 ASP   ( 217-)  C   H-bonding suggests Asn
2728 ASP   (  25-)  E   H-bonding suggests Asn
3008 ASP   (   8-)  H   H-bonding suggests Asn; but Alt-Rotamer
3074 ASP   (  86-)  H   H-bonding suggests Asn
3079 ASP   (  91-)  H   H-bonding suggests Asn
3098 ASP   ( 110-)  H   H-bonding suggests Asn
3341 ASP   (  22-)  K   H-bonding suggests Asn; but Alt-Rotamer
3425 GLU   ( 106-)  K   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 :  -1.880
  2nd generation packing quality :  -2.120
  Ramachandran plot appearance   :  -3.985 (poor)
  chi-1/chi-2 rotamer normality  :  -5.225 (bad)
  Backbone conformation          :  -1.130

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.781 (loose)
  Bond angles                    :   2.780 (loose)
  Omega angle restraints         :   2.267 (loose)
  Side chain planarity           :   3.732 (loose)
  Improper dihedral distribution :   3.190 (loose)
  Inside/Outside distribution    :   1.034

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 : 3.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.781 (loose)
  Bond angles                    :   2.780 (loose)
  Omega angle restraints         :   2.267 (loose)
  Side chain planarity           :   3.732 (loose)
  Improper dihedral distribution :   3.190 (loose)
  Inside/Outside distribution    :   1.034
==============

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.