WHAT IF Check report

This file was created 2011-12-16 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 pdb1m6v.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.359
CA-only RMS fit for the two chains : 0.196

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.405
CA-only RMS fit for the two chains : 0.256

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 0.402
CA-only RMS fit for the two chains : 0.275

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and G

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.488
CA-only RMS fit for the two chains : 0.381

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and F

All-atom RMS fit for the two chains : 0.365
CA-only RMS fit for the two chains : 0.226

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and F

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.

5754 ADP   (4001-)  A  -
5755 ADP   (4007-)  A  -
5756 ORN   (4011-)  A  -
5757 NET   (4012-)  A  -
5776 ADP   (4021-)  C  -
5778 ADP   (4027-)  C  -
5779 ORN   (4031-)  C  -
5780 NET   (4032-)  C  -
5798 ADP   (4044-)  E  -
5800 ADP   (4050-)  E  -
5801 ORN   (4054-)  E  -
5802 NET   (4055-)  E  -
5820 ADP   (4066-)  G  -
5824 NET   (4077-)  G  -
5825 ORN   (4076-)  G  -
5826 ADP   (4072-)  G  -

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.

5803   K   (4058-)  E  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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.

3919 VAL   (1065-)  E
4925 LEU   ( 623-)  G

Warning: Missing atoms

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

 716 PRO   ( 716-)  A      CG
 716 PRO   ( 716-)  A      CD
 717 SER   ( 717-)  A      OG
2150 PRO   ( 716-)  C      CG
2150 PRO   ( 716-)  C      CD
2151 SER   ( 717-)  C      OG
3584 PRO   ( 716-)  E      CG
3584 PRO   ( 716-)  E      CD
3585 SER   ( 717-)  E      OG
5018 PRO   ( 716-)  G      CG
5018 PRO   ( 716-)  G      CD
5019 SER   ( 717-)  G      OG

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

1439 THR   (   5-)  C    0.66
2437 THR   (1017-)  C    0.66
4455 GLU   ( 153-)  G    0.66

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) :110.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 3.161 over 36300 bonds
Average difference in B over a bond : 9.10
RMS difference in B over a bond : 12.51

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

1178 ARG   ( 120-)  B
2911 ARG   (  43-)  E
3377 ARG   ( 509-)  E
3427 ARG   ( 559-)  E
3858 ARG   (1004-)  E

Warning: Tyrosine convention problem

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

  42 TYR   (  42-)  A
  65 TYR   (  65-)  A
 216 TYR   ( 216-)  A
 330 TYR   ( 330-)  A
 354 TYR   ( 354-)  A
 438 TYR   ( 438-)  A
 544 TYR   ( 544-)  A
 547 TYR   ( 547-)  A
 617 TYR   ( 617-)  A
 731 TYR   ( 737-)  A
 785 TYR   ( 799-)  A
 824 TYR   ( 838-)  A
 873 TYR   ( 887-)  A
1022 TYR   (1036-)  A
1026 TYR   (1040-)  A
1097 TYR   (  39-)  B
1308 TYR   ( 250-)  B
1431 TYR   ( 377-)  B
1764 TYR   ( 330-)  C
1788 TYR   ( 354-)  C
1872 TYR   ( 438-)  C
1978 TYR   ( 544-)  C
1981 TYR   ( 547-)  C
2165 TYR   ( 737-)  C
2219 TYR   ( 799-)  C
And so on for a total of 61 lines.

Warning: Phenylalanine convention problem

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

 111 PHE   ( 111-)  A
 164 PHE   ( 164-)  A
 172 PHE   ( 172-)  A
 237 PHE   ( 237-)  A
 286 PHE   ( 286-)  A
 348 PHE   ( 348-)  A
 362 PHE   ( 362-)  A
 409 PHE   ( 409-)  A
 453 PHE   ( 453-)  A
 816 PHE   ( 830-)  A
 838 PHE   ( 852-)  A
 914 PHE   ( 928-)  A
 955 PHE   ( 969-)  A
1073 PHE   (  15-)  B
1150 PHE   (  92-)  B
1208 PHE   ( 150-)  B
1250 PHE   ( 192-)  B
1372 PHE   ( 314-)  B
1406 PHE   ( 348-)  B
1421 PHE   ( 367-)  B
1460 PHE   (  26-)  C
1598 PHE   ( 164-)  C
1671 PHE   ( 237-)  C
1720 PHE   ( 286-)  C
1782 PHE   ( 348-)  C
And so on for a total of 73 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.

   6 ASP   (   6-)  A
  27 ASP   (  27-)  A
  57 ASP   (  57-)  A
  84 ASP   (  84-)  A
 121 ASP   ( 121-)  A
 161 ASP   ( 161-)  A
 207 ASP   ( 207-)  A
 226 ASP   ( 226-)  A
 246 ASP   ( 246-)  A
 353 ASP   ( 353-)  A
 416 ASP   ( 416-)  A
 417 ASP   ( 417-)  A
 430 ASP   ( 430-)  A
 441 ASP   ( 441-)  A
 450 ASP   ( 450-)  A
 459 ASP   ( 459-)  A
 499 ASP   ( 499-)  A
 518 ASP   ( 518-)  A
 521 ASP   ( 521-)  A
 579 ASP   ( 579-)  A
 592 ASP   ( 592-)  A
 611 ASP   ( 611-)  A
 614 ASP   ( 614-)  A
 625 ASP   ( 625-)  A
 667 ASP   ( 667-)  A
And so on for a total of 220 lines.

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.

  25 GLU   (  25-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  59 GLU   (  59-)  A
  67 GLU   (  67-)  A
  81 GLU   (  81-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 127 GLU   ( 127-)  A
 189 GLU   ( 189-)  A
 190 GLU   ( 190-)  A
 203 GLU   ( 203-)  A
 208 GLU   ( 208-)  A
 215 GLU   ( 215-)  A
 219 GLU   ( 219-)  A
 235 GLU   ( 235-)  A
 274 GLU   ( 274-)  A
 365 GLU   ( 365-)  A
 393 GLU   ( 393-)  A
 467 GLU   ( 467-)  A
 468 GLU   ( 468-)  A
 473 GLU   ( 473-)  A
 510 GLU   ( 510-)  A
And so on for a total of 234 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.

 109 GLU   ( 109-)  A      CD   OE1   1.33    4.4
 121 ASP   ( 121-)  A      CG   OD1   1.33    4.4
 186 GLU   ( 186-)  A      CD   OE2   1.33    4.1
 207 ASP   ( 207-)  A      CG   OD1   1.34    4.7
 217 GLU   ( 217-)  A      CD   OE2   1.33    4.4
 299 GLU   ( 299-)  A      CD   OE2   1.33    4.2
 365 GLU   ( 365-)  A      CD   OE1   1.33    4.2
 372 ASP   ( 372-)  A      CG   OD2   1.33    4.1
 383 GLU   ( 383-)  A      CD   OE2   1.33    4.0
 427 GLU   ( 427-)  A      CD   OE2   1.33    4.1
 473 GLU   ( 473-)  A      CD   OE1   1.33    4.4
 539 ASP   ( 539-)  A      CG   OD2   1.33    4.1
 683 GLU   ( 683-)  A      CD   OE2   1.35    5.5
 699 GLU   ( 699-)  A      CD   OE1   1.33    4.3
 707 GLU   ( 707-)  A      CD   OE1   1.33    4.4
 725 GLU   ( 731-)  A      CD   OE1   1.33    4.3
 769 GLU   ( 783-)  A      CD   OE1   1.33    4.2
 793 ASP   ( 807-)  A      CG   OD1   1.33    4.1
 862 GLU   ( 876-)  A      CD   OE2   1.34    4.8
 896 GLU   ( 910-)  A      CD   OE2   1.33    4.2
 939 ASP   ( 953-)  A      CG   OD1   1.33    4.2
 941 GLU   ( 955-)  A      CD   OE1   1.34    4.8
 945 ASP   ( 959-)  A      CG   OD2   1.33    4.0
1046 GLU   (1060-)  A      CD   OE2   1.33    4.1
1125 ASP   (  67-)  B      CG   OD1   1.33    4.1
And so on for a total of 134 lines.

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000677  0.000164  0.000203|
 |  0.000164  1.001622 -0.000207|
 |  0.000203 -0.000207  1.001366|
Proposed new scale matrix

 |  0.006597 -0.000001 -0.000001|
 | -0.000001  0.006080  0.000001|
 |  0.000000  0.000000  0.003013|
With corresponding cell

    A    = 151.595  B   = 164.470  C    = 331.908
    Alpha=  90.014  Beta=  89.990  Gamma=  89.981

The CRYST1 cell dimensions

    A    = 151.500  B   = 164.200  C    = 331.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 290.555
(Under-)estimated Z-score: 12.563

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 PRO   (   2-)  A      N    CA   CB  107.91    4.5
  26 PHE   (  26-)  A      CA   CB   CG  106.81   -7.0
  27 ASP   (  27-)  A     -C    N    CA  114.21   -4.2
  39 GLU   (  39-)  A      C    CA   CB  100.67   -5.0
  62 ASP   (  62-)  A      CA   CB   CG  107.94   -4.7
  88 PRO   (  88-)  A      C    CA   CB  101.31   -4.6
 132 PHE   ( 132-)  A      CA   CB   CG  108.80   -5.0
 139 ILE   ( 139-)  A      N    CA   CB  119.03    5.0
 142 GLU   ( 142-)  A      C    CA   CB  118.47    4.4
 145 ARG   ( 145-)  A      N    CA   CB  102.90   -4.5
 150 HIS   ( 150-)  A      CA   CB   CG  108.39   -5.4
 151 THR   ( 151-)  A      C    CA   CB  102.13   -4.2
 164 PHE   ( 164-)  A      CA   CB   CG  109.10   -4.7
 173 THR   ( 173-)  A      N    CA   CB  118.03    4.4
 205 LEU   ( 205-)  A      N    CA   CB  118.26    4.6
 210 LEU   ( 210-)  A      N    CA   CB  118.72    4.8
 225 ASN   ( 225-)  A      CA   CB   CG  106.93   -5.7
 238 ASP   ( 238-)  A      CA   CB   CG  108.19   -4.4
 246 ASP   ( 246-)  A      CA   CB   CG  119.63    7.0
 248 ILE   ( 248-)  A      N    CA   C    98.42   -4.6
 258 ASP   ( 258-)  A      CA   CB   CG  108.34   -4.3
 283 ASN   ( 283-)  A      CA   CB   CG  118.31    5.7
 285 GLN   ( 285-)  A      CA   CB   CG  122.26    4.1
 289 ASN   ( 289-)  A      CA   CB   CG  107.57   -5.0
 290 PRO   ( 290-)  A      N    CA   CB  107.62    4.2
And so on for a total of 439 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   6 ASP   (   6-)  A
  25 GLU   (  25-)  A
  27 ASP   (  27-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  57 ASP   (  57-)  A
  59 GLU   (  59-)  A
  67 GLU   (  67-)  A
  81 GLU   (  81-)  A
  84 ASP   (  84-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 121 ASP   ( 121-)  A
 127 GLU   ( 127-)  A
 161 ASP   ( 161-)  A
 189 GLU   ( 189-)  A
 190 GLU   ( 190-)  A
 203 GLU   ( 203-)  A
 207 ASP   ( 207-)  A
 208 GLU   ( 208-)  A
 215 GLU   ( 215-)  A
 219 GLU   ( 219-)  A
 226 ASP   ( 226-)  A
And so on for a total of 459 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.

  58 PRO   (  58-)  A      N      7.8    23.09    -2.48
 142 GLU   ( 142-)  A      CA    -6.4    23.41    33.96
 651 ALA   ( 651-)  A      CA    -7.6    24.47    34.09
 720 GLU   ( 726-)  A      CA    -6.6    23.19    33.96
 871 PRO   ( 885-)  A      N      7.1    20.68    -2.48
 940 LYS   ( 954-)  A      CA    -6.7    22.74    33.92
 961 HIS   ( 975-)  A      CA    -6.8    21.54    34.11
 985 PRO   ( 999-)  A      N    -10.3   -36.16    -2.48
1056 ALA   (1070-)  A      CA    -7.2    24.88    34.09
1185 ALA   ( 127-)  B      CA   -13.7    16.74    34.09
1242 ALA   ( 184-)  B      CA    -8.5    23.32    34.09
1245 GLU   ( 187-)  B      CA    -6.7    22.97    33.96
1291 PRO   ( 233-)  B      N     -6.2   -22.92    -2.48
1380 PRO   ( 322-)  B      N     -7.6   -27.39    -2.48
1394 THR   ( 336-)  B      CA    -7.2    21.90    33.84
1773 ILE   ( 339-)  C      CA   -10.7    17.02    33.24
1854 ALA   ( 420-)  C      CA    -6.4    26.02    34.09
1883 VAL   ( 449-)  C      CB    -7.0   -42.13   -32.96
2085 ALA   ( 651-)  C      CA    -7.3    24.77    34.09
2154 GLU   ( 726-)  C      CA    -6.0    24.07    33.96
2374 LYS   ( 954-)  C      CA    -7.3    21.86    33.92
2456 TYR   (1036-)  C      CA    -7.0    22.95    34.03
2630 PRO   ( 138-)  D      N      6.3    18.33    -2.48
2658 GLU   ( 166-)  D      CA    -8.9    19.44    33.96
2696 ASN   ( 204-)  D      CA    -6.1    22.02    33.59
And so on for a total of 51 lines.

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.

5720 ALA   ( 364-)  H    5.78
1773 ILE   ( 339-)  C    5.77
5413 VAL   (  53-)  H    5.76
3647 ALA   ( 793-)  E    5.73
1869 ARG   ( 435-)  C    5.72
3206 ASP   ( 338-)  E    5.43
2440 ARG   (1020-)  C    5.40
4641 ILE   ( 339-)  G    5.34
3207 ILE   ( 339-)  E    5.33
5138 VAL   ( 850-)  G    5.28
5576 LEU   ( 216-)  H    5.25
 961 HIS   ( 975-)  A    5.14
2581 ALA   (  89-)  D    5.11
 612 THR   ( 612-)  A    5.09
 543 MET   ( 543-)  A    4.95
2085 ALA   ( 651-)  C    4.88
2895 ASP   (  27-)  E    4.80
5429 ASP   (  69-)  H    4.78
 651 ALA   ( 651-)  A    4.73
1147 ALA   (  89-)  B    4.57
5081 ALA   ( 793-)  G    4.54
4292 PHE   ( 370-)  F    4.52
2213 ALA   ( 793-)  C    4.51
 486 ALA   ( 486-)  A    4.50
 456 THR   ( 456-)  A    4.49
And so on for a total of 53 lines.

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.

2489 HIS   (1069-)  C   10.13
1891 ASN   ( 457-)  C    5.31
1164 ASN   ( 106-)  B    4.15

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

4677 THR   ( 375-)  G    -3.1
1809 THR   ( 375-)  C    -3.1
  88 PRO   (  88-)  A    -3.0
2956 PRO   (  88-)  E    -3.0
1522 PRO   (  88-)  C    -3.0
 252 PRO   ( 252-)  A    -2.9
5583 THR   ( 223-)  H    -2.9
 375 THR   ( 375-)  A    -2.9
5132 PRO   ( 844-)  G    -2.9
2265 ARG   ( 845-)  C    -2.9
1713 THR   ( 279-)  C    -2.9
4390 PRO   (  88-)  G    -2.9
3070 LYS   ( 202-)  E    -2.8
4272 PRO   ( 346-)  F    -2.8
2005 ARG   ( 571-)  C    -2.7
4014 ILE   (  88-)  F    -2.7
5726 PHE   ( 370-)  H    -2.7
5174 PRO   ( 886-)  G    -2.7
 696 THR   ( 696-)  A    -2.7
 882 PRO   ( 896-)  A    -2.7
 961 HIS   ( 975-)  A    -2.6
1686 PRO   ( 252-)  C    -2.6
 559 ARG   ( 559-)  A    -2.6
 202 LYS   ( 202-)  A    -2.6
2395 HIS   ( 975-)  C    -2.6
And so on for a total of 219 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.

  23 ALA   (  23-)  A  Poor phi/psi
 164 PHE   ( 164-)  A  PRO omega poor
 172 PHE   ( 172-)  A  Poor phi/psi
 226 ASP   ( 226-)  A  Poor phi/psi
 251 ALA   ( 251-)  A  PRO omega poor
 276 GLY   ( 276-)  A  Poor phi/psi
 302 PRO   ( 302-)  A  Poor phi/psi
 303 ARG   ( 303-)  A  Poor phi/psi
 342 GLY   ( 342-)  A  Poor phi/psi
 375 THR   ( 375-)  A  Poor phi/psi
 403 GLU   ( 403-)  A  Poor phi/psi
 409 PHE   ( 409-)  A  Poor phi/psi
 457 ASN   ( 457-)  A  Poor phi/psi
 484 LEU   ( 484-)  A  Poor phi/psi
 521 ASP   ( 521-)  A  Poor phi/psi
 530 ASP   ( 530-)  A  Poor phi/psi
 531 THR   ( 531-)  A  Poor phi/psi
 534 ALA   ( 534-)  A  Poor phi/psi
 548 GLU   ( 548-)  A  Poor phi/psi
 686 LYS   ( 686-)  A  Poor phi/psi
 710 TYR   ( 710-)  A  PRO omega poor
 716 PRO   ( 716-)  A  Poor phi/psi
 782 LEU   ( 796-)  A  PRO omega poor
 786 THR   ( 800-)  A  Poor phi/psi
 807 GLN   ( 821-)  A  Poor phi/psi
And so on for a total of 169 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 : -4.044

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.

2776 VAL   ( 284-)  D    0.33
3708 SER   ( 854-)  E    0.35
5142 SER   ( 854-)  G    0.35
 268 SER   ( 268-)  A    0.35
1702 SER   ( 268-)  C    0.36
4026 SER   ( 100-)  F    0.36
 394 SER   ( 394-)  A    0.36
2592 SER   ( 100-)  D    0.36
4610 SER   ( 308-)  G    0.36
4614 SER   ( 312-)  G    0.36
1746 SER   ( 312-)  C    0.37
2591 SER   (  99-)  D    0.38
2020 SER   ( 586-)  C    0.38
3136 SER   ( 268-)  E    0.38
4210 VAL   ( 284-)  F    0.38
5459 SER   (  99-)  H    0.39
1158 SER   ( 100-)  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!

   3 LYS   (   3-)  A      0
   5 THR   (   5-)  A      0
   7 ILE   (   7-)  A      0
   9 SER   (   9-)  A      0
  17 PRO   (  17-)  A      0
  20 ILE   (  20-)  A      0
  22 GLN   (  22-)  A      0
  23 ALA   (  23-)  A      0
  24 CYS   (  24-)  A      0
  40 GLU   (  40-)  A      0
  42 TYR   (  42-)  A      0
  49 SER   (  49-)  A      0
  52 ALA   (  52-)  A      0
  60 MET   (  60-)  A      0
  62 ASP   (  62-)  A      0
  69 ILE   (  69-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 105 GLN   ( 105-)  A      0
 107 VAL   ( 107-)  A      0
 116 ILE   ( 116-)  A      0
 146 SER   ( 146-)  A      0
 151 THR   ( 151-)  A      0
 152 MET   ( 152-)  A      0
And so on for a total of 2010 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.204

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!

 567 GLY   ( 567-)  A   3.18   21
2001 GLY   ( 567-)  C   3.18   30
4869 GLY   ( 567-)  G   3.16   32
3435 GLY   ( 567-)  E   3.11   36

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...

1457 ALA   (  23-)  C   1.93
4325 ALA   (  23-)  G   1.61
5715 GLU   ( 355-)  H   1.54

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]

   2 PRO   (   2-)  A    0.10 LOW
  17 PRO   (  17-)  A    0.16 LOW
  58 PRO   (  58-)  A    0.19 LOW
  68 PRO   (  68-)  A    0.13 LOW
  83 PRO   (  83-)  A    0.08 LOW
 170 PRO   ( 170-)  A    0.13 LOW
 200 PRO   ( 200-)  A    0.17 LOW
 290 PRO   ( 290-)  A    0.13 LOW
 360 PRO   ( 360-)  A    0.13 LOW
 418 PRO   ( 418-)  A    0.16 LOW
 555 PRO   ( 555-)  A    0.06 LOW
 603 PRO   ( 603-)  A    0.19 LOW
 647 PRO   ( 647-)  A    0.18 LOW
 666 PRO   ( 666-)  A    0.14 LOW
 690 PRO   ( 690-)  A    0.09 LOW
 711 PRO   ( 711-)  A    0.17 LOW
 716 PRO   ( 716-)  A    0.00 LOW
 783 PRO   ( 797-)  A    0.12 LOW
 846 PRO   ( 860-)  A    0.19 LOW
 882 PRO   ( 896-)  A    0.13 LOW
 887 PRO   ( 901-)  A    0.10 LOW
 985 PRO   ( 999-)  A    0.20 LOW
1116 PRO   (  58-)  B    0.11 LOW
1144 PRO   (  86-)  B    0.19 LOW
1196 PRO   ( 138-)  B    0.20 LOW
And so on for a total of 142 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].

  51 PRO   (  51-)  A   -57.5 half-chair C-beta/C-alpha (-54 degrees)
  88 PRO   (  88-)  A   -63.2 envelop C-beta (-72 degrees)
 302 PRO   ( 302-)  A   -54.8 half-chair C-beta/C-alpha (-54 degrees)
 318 PRO   ( 318-)  A   -61.1 half-chair C-beta/C-alpha (-54 degrees)
 345 PRO   ( 345-)  A   -44.5 envelop C-alpha (-36 degrees)
 524 PRO   ( 524-)  A   -41.7 envelop C-alpha (-36 degrees)
 569 PRO   ( 569-)  A   -59.3 half-chair C-beta/C-alpha (-54 degrees)
 830 PRO   ( 844-)  A   -14.5 half-chair C-alpha/N (-18 degrees)
 871 PRO   ( 885-)  A     4.4 envelop N (0 degrees)
 891 PRO   ( 905-)  A   -12.9 half-chair C-alpha/N (-18 degrees)
 895 PRO   ( 909-)  A   -55.5 half-chair C-beta/C-alpha (-54 degrees)
1104 PRO   (  46-)  B   111.1 envelop C-beta (108 degrees)
1305 PRO   ( 247-)  B   -23.5 half-chair C-alpha/N (-18 degrees)
1354 PRO   ( 296-)  B   -65.2 envelop C-beta (-72 degrees)
1380 PRO   ( 322-)  B  -145.9 envelop C-delta (-144 degrees)
1404 PRO   ( 346-)  B   -54.3 half-chair C-beta/C-alpha (-54 degrees)
1416 PRO   ( 358-)  B   -50.6 half-chair C-beta/C-alpha (-54 degrees)
1451 PRO   (  17-)  C   -52.8 half-chair C-beta/C-alpha (-54 degrees)
1502 PRO   (  68-)  C  -169.8 half-chair N/C-delta (-162 degrees)
1522 PRO   (  88-)  C   -57.4 half-chair C-beta/C-alpha (-54 degrees)
1736 PRO   ( 302-)  C   -55.7 half-chair C-beta/C-alpha (-54 degrees)
1752 PRO   ( 318-)  C   -63.2 envelop C-beta (-72 degrees)
1779 PRO   ( 345-)  C   -61.0 half-chair C-beta/C-alpha (-54 degrees)
1784 PRO   ( 350-)  C   104.9 envelop C-beta (108 degrees)
2100 PRO   ( 666-)  C   133.4 half-chair C-beta/C-alpha (126 degrees)
And so on for a total of 58 lines.

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 961 HIS   ( 975-)  A      ND1 <-> 5263 HIS   ( 975-)  G      ND1    0.55    2.45  INTRA BL
 930 ARG   ( 944-)  A      N   <-> 5827 HOH   (4490 )  A      O      0.50    2.20  INTRA BF
3795 LYS   ( 941-)  E      NZ  <-> 5831 HOH   (2769 )  E      O      0.49    2.21  INTRA BF
4797 LYS   ( 495-)  G      NZ  <-> 5833 HOH   (4624 )  G      O      0.45    2.25  INTRA BF
 684 ARG   ( 684-)  A      NE  <-> 5827 HOH   (4618 )  A      O      0.43    2.27  INTRA BF
4345 ARG   (  43-)  G      NH2 <-> 4383 GLU   (  81-)  G      OE1    0.42    2.28  INTRA BF
4129 ARG   ( 203-)  F      NH2 <-> 5832 HOH   (3236 )  F      O      0.42    2.28  INTRA BF
2322 GLY   ( 902-)  C      O   <-> 2447 ARG   (1027-)  C      NH2    0.41    2.29  INTRA BF
3285 ASP   ( 417-)  E      OD2 <-> 3291 LYS   ( 423-)  E      NZ     0.41    2.29  INTRA BF
1755 LYS   ( 321-)  C      NZ  <-> 2045 ASP   ( 611-)  C      OD2    0.41    2.29  INTRA BF
3588 GLU   ( 726-)  E      OE2 <-> 3874 ARG   (1020-)  E      NE     0.41    2.29  INTRA BF
5537 LEU   ( 177-)  H      N   <-> 5834 HOH   (1943 )  H      O      0.41    2.29  INTRA
1226 TYR   ( 168-)  B      O   <-> 1276 ILE   ( 218-)  B      N      0.41    2.29  INTRA BF
5011 GLY   ( 709-)  G      O   <-> 5042 HIS   ( 754-)  G      ND1    0.41    2.29  INTRA BF
5160 LYS   ( 872-)  G      O   <-> 5165 GLN   ( 877-)  G      NE2    0.41    2.29  INTRA BF
2149 ARG   ( 715-)  C      NH2 <-> 5778 ADP   (4027-)  C      O1A    0.41    2.29  INTRA BF
4642 THR   ( 340-)  G      O   <-> 4645 ARG   ( 343-)  G      NE     0.41    2.29  INTRA BF
 709 GLY   ( 709-)  A      O   <->  740 HIS   ( 754-)  A      ND1    0.41    2.29  INTRA BF
2130 THR   ( 696-)  C      N   <-> 2134 MET   ( 700-)  C      SD     0.41    2.89  INTRA BF
 729 ARG   ( 735-)  A      O   <->  732 PHE   ( 738-)  A      N      0.40    2.30  INTRA BF
4286 ALA   ( 364-)  F      O   <-> 4290 ASP   ( 368-)  F      N      0.40    2.30  INTRA BF
5720 ALA   ( 364-)  H      O   <-> 5724 ASP   ( 368-)  H      N      0.40    2.30  INTRA BF
 150 HIS   ( 150-)  A      N   <->  154 GLU   ( 154-)  A      OE1    0.40    2.30  INTRA BF
  43 ARG   (  43-)  A      NH2 <->   81 GLU   (  81-)  A      OE1    0.40    2.30  INTRA BF
4119 HIS   ( 193-)  F      N   <-> 4160 ASP   ( 234-)  F      OD2    0.40    2.30  INTRA BF
And so on for a total of 2054 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

2418 ARG   ( 998-)  C      -7.77
5286 ARG   ( 998-)  G      -7.45
3211 ARG   ( 343-)  E      -7.18
 984 ARG   ( 998-)  A      -6.94
3852 ARG   ( 998-)  E      -6.82
4645 ARG   ( 343-)  G      -6.79
1777 ARG   ( 343-)  C      -6.69
 343 ARG   ( 343-)  A      -6.67
3051 TYR   ( 183-)  E      -6.45
3776 ARG   ( 922-)  E      -6.32
1617 TYR   ( 183-)  C      -6.30
 908 ARG   ( 922-)  A      -6.29
 183 TYR   ( 183-)  A      -6.27
5283 HIS   ( 995-)  G      -6.26
4476 MET   ( 174-)  G      -6.22
2342 ARG   ( 922-)  C      -6.22
4485 TYR   ( 183-)  G      -6.21
3042 MET   ( 174-)  E      -6.11
 174 MET   ( 174-)  A      -6.07
1608 MET   ( 174-)  C      -6.06
2304 ILE   ( 884-)  C      -5.93
5172 ILE   ( 884-)  G      -5.91
1094 MET   (  36-)  B      -5.88
2528 MET   (  36-)  D      -5.84
3738 ILE   ( 884-)  E      -5.80
And so on for a total of 71 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.

1413 GLU   ( 355-)  B      1416 - PRO    358- ( B)         -4.39
2847 GLU   ( 355-)  D      2850 - PRO    358- ( D)         -4.44
4281 GLU   ( 355-)  F      4283 - SER    357- ( F)         -4.43
5715 GLU   ( 355-)  H      5717 - SER    357- ( H)         -4.55

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

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

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.

1434 THR   ( 380-)  B   -3.68
 174 MET   ( 174-)  A   -3.31
1457 ALA   (  23-)  C   -2.85
 239 ALA   ( 239-)  A   -2.84
2891 ALA   (  23-)  E   -2.83
4325 ALA   (  23-)  G   -2.83
3273 GLY   ( 405-)  E   -2.82
1673 ALA   ( 239-)  C   -2.81
 405 GLY   ( 405-)  A   -2.79
 879 VAL   ( 893-)  A   -2.79
  23 ALA   (  23-)  A   -2.78
3747 VAL   ( 893-)  E   -2.74
2313 VAL   ( 893-)  C   -2.73
1839 GLY   ( 405-)  C   -2.72
1210 GLY   ( 152-)  B   -2.71
1289 MET   ( 231-)  B   -2.65
5181 VAL   ( 893-)  G   -2.65
2319 LYS   ( 899-)  C   -2.57
 632 ILE   ( 632-)  A   -2.55
5512 GLY   ( 152-)  H   -2.50
2644 GLY   ( 152-)  D   -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.

 575 GLY   ( 575-)  A     -  578 PHE   ( 578-)  A        -1.78
 878 GLU   ( 892-)  A     -  881 LEU   ( 895-)  A        -1.89
2009 GLY   ( 575-)  C     - 2012 PHE   ( 578-)  C        -1.79
4011 LEU   (  85-)  F     - 4014 ILE   (  88-)  F        -1.83
4877 GLY   ( 575-)  G     - 4880 PHE   ( 578-)  G        -1.79
5180 GLU   ( 892-)  G     - 5183 LEU   ( 895-)  G        -1.89

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

5827 HOH   (4705 )  A      O      1.87  104.07   90.68
5827 HOH   (4708 )  A      O      1.34  105.01   87.82
5827 HOH   (4712 )  A      O     -0.77  103.67   84.72
5827 HOH   (4716 )  A      O      2.40  105.92   82.68
5829 HOH   (4704 )  C      O    -33.05   69.00   28.86
5832 HOH   (3304 )  F      O    -11.66   47.16  105.98

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.

5827 HOH   (4085 )  A      O
5827 HOH   (4133 )  A      O
5827 HOH   (4285 )  A      O
5827 HOH   (4361 )  A      O
5827 HOH   (4508 )  A      O
5827 HOH   (4517 )  A      O
5827 HOH   (4550 )  A      O
5827 HOH   (4555 )  A      O
5827 HOH   (4561 )  A      O
5827 HOH   (4593 )  A      O
5827 HOH   (4599 )  A      O
5827 HOH   (4627 )  A      O
5827 HOH   (4666 )  A      O
5827 HOH   (4676 )  A      O
5827 HOH   (4698 )  A      O
5827 HOH   (4700 )  A      O
5827 HOH   (4757 )  A      O
5827 HOH   (4770 )  A      O
5827 HOH   (4789 )  A      O
5827 HOH   (4811 )  A      O
5828 HOH   (4123 )  B      O
5828 HOH   (4140 )  B      O
5829 HOH   (4108 )  C      O
5829 HOH   (4285 )  C      O
5829 HOH   (4510 )  C      O
And so on for a total of 68 lines.

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.

 105 GLN   ( 105-)  A
 457 ASN   ( 457-)  A
 554 ASN   ( 554-)  A
 740 HIS   ( 754-)  A
 770 GLN   ( 784-)  A
 821 ASN   ( 835-)  A
 918 GLN   ( 932-)  A
 928 HIS   ( 942-)  A
 973 ASN   ( 987-)  A
 986 HIS   (1000-)  A
1074 HIS   (  16-)  B
1280 GLN   ( 222-)  B
1314 GLN   ( 256-)  B
1369 ASN   ( 311-)  B
1382 ASN   ( 324-)  B
1409 GLN   ( 351-)  B
1888 ASN   ( 454-)  C
2204 GLN   ( 784-)  C
2208 HIS   ( 788-)  C
2255 ASN   ( 835-)  C
2356 ASN   ( 936-)  C
2362 HIS   ( 942-)  C
2407 ASN   ( 987-)  C
2415 HIS   ( 995-)  C
2422 GLN   (1002-)  C
And so on for a total of 52 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.

   3 LYS   (   3-)  A      N
   7 ILE   (   7-)  A      N
  46 ASN   (  46-)  A      ND2
  53 THR   (  53-)  A      N
  67 GLU   (  67-)  A      N
 106 GLY   ( 106-)  A      N
 169 ARG   ( 169-)  A      NH1
 173 THR   ( 173-)  A      N
 176 GLY   ( 176-)  A      N
 184 ASN   ( 184-)  A      N
 210 LEU   ( 210-)  A      N
 236 ASN   ( 236-)  A      ND2
 241 GLY   ( 241-)  A      N
 244 THR   ( 244-)  A      N
 341 GLY   ( 341-)  A      N
 344 THR   ( 344-)  A      N
 354 TYR   ( 354-)  A      N
 377 GLN   ( 377-)  A      N
 389 ARG   ( 389-)  A      NH2
 390 THR   ( 390-)  A      N
 396 GLN   ( 396-)  A      NE2
 465 GLN   ( 465-)  A      NE2
 558 ASP   ( 558-)  A      N
 559 ARG   ( 559-)  A      N
 602 ASN   ( 602-)  A      N
And so on for a total of 273 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.

  46 ASN   (  46-)  A      OD1
 215 GLU   ( 215-)  A      OE1
 236 ASN   ( 236-)  A      OD1
 391 GLN   ( 391-)  A      OE1
 747 GLU   ( 761-)  A      OE1
 747 GLU   ( 761-)  A      OE2
1025 HIS   (1039-)  A      NE2
1480 ASN   (  46-)  C      OD1
1649 GLU   ( 215-)  C      OE2
1670 ASN   ( 236-)  C      OD1
1825 GLN   ( 391-)  C      OE1
2107 GLU   ( 673-)  C      OE2
2181 GLU   ( 761-)  C      OE2
2914 ASN   (  46-)  E      OD1
3259 GLN   ( 391-)  E      OE1
3615 GLU   ( 761-)  E      OE2
4517 GLU   ( 215-)  G      OE2
4538 ASN   ( 236-)  G      OD1
4693 GLN   ( 391-)  G      OE1
4906 GLU   ( 604-)  G      OE1
5041 ASP   ( 753-)  G      OD1
5049 GLU   ( 761-)  G      OE2
5288 HIS   (1000-)  G      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

5741  MN   (4002-)  A   -.-  -.-  Part of ionic cluster
5742  MN   (4003-)  A   -.-  -.-  Part of ionic cluster
5744   K   (4005-)  A   -.-  -.-  Part of ionic cluster
5745  MN   (4008-)  A   -.-  -.-  Part of ionic cluster
5746   K   (4009-)  A   -.-  -.-  Low probability ion. B= 80.8
5760  MN   (4022-)  C   -.-  -.-  Part of ionic cluster
5761  MN   (4023-)  C   -.-  -.-  Part of ionic cluster
5763   K   (4025-)  C   -.-  -.-  Part of ionic cluster
5764  MN   (4028-)  C   -.-  -.-  Part of ionic cluster
5765   K   (4029-)  C   -.-  -.-  Part of ionic cluster
5765   K   (4029-)  C   -.-  -.-  Too few ligands (3)
5766   K   (4030-)  C     2.05   0.82 Is perhaps NA (Few ligands (4) )
5767   K   (4033-)  C   -.-  -.-  Too few ligands (2)
5768   K   (4034-)  C    1.62  -.-   Poor packing (Few ligands (4) )
5783  MN   (4045-)  E   -.-  -.-  Part of ionic cluster
5784  MN   (4046-)  E   -.-  -.-  Part of ionic cluster
5785   K   (4047-)  E     1.69   0.75 Scores about as good as NA
5786   K   (4048-)  E   -.-  -.-  Part of ionic cluster
5787  MN   (4051-)  E   -.-  -.-  Part of ionic cluster
5788   K   (4052-)  E   -.-  -.-  Part of ionic cluster
5788   K   (4052-)  E    17.32   1.14 Should be MN (Few ligands (4) ) *1 and *2
5789   K   (4053-)  E    1.55  -.-   Poor packing
5790   K   (4056-)  E   -.-  -.-  Too few ligands (3)
5805  MN   (4067-)  G   -.-  -.-  Part of ionic cluster
5806  MN   (4068-)  G   -.-  -.-  Part of ionic cluster
5807   K   (4069-)  G     1.91   0.78 Scores about as good as NA
5808   K   (4070-)  G   -.-  -.-  Part of ionic cluster
5808   K   (4070-)  G   -.-  -.-  Too few ligands (2)
5810   K   (4074-)  G   -.-  -.-  Low probability ion. B= 86.8
5811   K   (4075-)  G     2.26   0.84 Is perhaps NA (Few ligands (4) )
5812   K   (4078-)  G   -.-  -.-  Too few ligands (3)
5813   K   (4079-)  G   -.-  -.-  Too few ligands (3)

Warning: Unusual water packing

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

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

5827 HOH   (4214 )  A      O  0.87  K  4 *1
5827 HOH   (4344 )  A      O  0.91  K  4 *1
5827 HOH   (4393 )  A      O  0.92  K  4 *1
5827 HOH   (4712 )  A      O  0.99  K  4 *1
5829 HOH   (4231 )  C      O  0.98  K  5 *1 NCS 1/1
5830 HOH   (2857 )  D      O  1.06  K  4 *1 NCS 1/1
5831 HOH   (1206 )  E      O  1.13  K  4 *1 NCS 2/2
5831 HOH   (1371 )  E      O  1.10  K  4 *1 NCS 2/2
5831 HOH   (1376 )  E      O  1.01  K  4 *1 NCS 2/2
5831 HOH   (1388 )  E      O  0.98  K  4 *1 NCS 2/2
5832 HOH   (1517 )  F      O  0.97  K  6 *1
5833 HOH   (4380 )  G      O  1.13  K  4 *1 NCS 2/2
5833 HOH   (4430 )  G      O  1.02  K  4 *1 NCS 3/3

Warning: Possible wrong residue type

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

 334 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   ( 410-)  A   H-bonding suggests Asn
 518 ASP   ( 518-)  A   H-bonding suggests Asn; but Alt-Rotamer
 739 ASP   ( 753-)  A   H-bonding suggests Asn
 755 ASP   ( 769-)  A   H-bonding suggests Asn; but Alt-Rotamer
 777 ASP   ( 791-)  A   H-bonding suggests Asn
1011 ASP   (1025-)  A   H-bonding suggests Asn
1099 GLU   (  41-)  B   H-bonding suggests Gln
1768 GLU   ( 334-)  C   H-bonding suggests Gln; but Alt-Rotamer
1844 ASP   ( 410-)  C   H-bonding suggests Asn; but Alt-Rotamer
1864 ASP   ( 430-)  C   H-bonding suggests Asn; but Alt-Rotamer
2173 ASP   ( 753-)  C   H-bonding suggests Asn
2189 ASP   ( 769-)  C   H-bonding suggests Asn; but Alt-Rotamer
2211 ASP   ( 791-)  C   H-bonding suggests Asn; but Alt-Rotamer
2445 ASP   (1025-)  C   H-bonding suggests Asn
2703 ASP   ( 211-)  D   H-bonding suggests Asn; but Alt-Rotamer
2856 ASP   ( 368-)  D   H-bonding suggests Asn
3202 GLU   ( 334-)  E   H-bonding suggests Gln; but Alt-Rotamer
3278 ASP   ( 410-)  E   H-bonding suggests Asn; but Alt-Rotamer
3298 ASP   ( 430-)  E   H-bonding suggests Asn
3386 ASP   ( 518-)  E   H-bonding suggests Asn; but Alt-Rotamer
3623 ASP   ( 769-)  E   H-bonding suggests Asn; but Alt-Rotamer
3645 ASP   ( 791-)  E   H-bonding suggests Asn; but Alt-Rotamer
3879 ASP   (1025-)  E   H-bonding suggests Asn
3895 ASP   (1041-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
3967 GLU   (  41-)  F   H-bonding suggests Gln
4038 ASP   ( 112-)  F   H-bonding suggests Asn
4290 ASP   ( 368-)  F   H-bonding suggests Asn
4521 GLU   ( 219-)  G   H-bonding suggests Gln
4636 GLU   ( 334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4712 ASP   ( 410-)  G   H-bonding suggests Asn
4732 ASP   ( 430-)  G   H-bonding suggests Asn
4820 ASP   ( 518-)  G   H-bonding suggests Asn; but Alt-Rotamer
5041 ASP   ( 753-)  G   H-bonding suggests Asn
5053 ASP   ( 765-)  G   H-bonding suggests Asn; but Alt-Rotamer
5057 ASP   ( 769-)  G   H-bonding suggests Asn; but Alt-Rotamer
5079 ASP   ( 791-)  G   H-bonding suggests Asn
5095 ASP   ( 807-)  G   H-bonding suggests Asn
5312 GLU   (1024-)  G   H-bonding suggests Gln; but Alt-Rotamer
5329 ASP   (1041-)  G   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
5472 ASP   ( 112-)  H   H-bonding suggests Asn
5571 ASP   ( 211-)  H   H-bonding suggests Asn
5594 ASP   ( 234-)  H   H-bonding suggests Asn
5620 GLU   ( 260-)  H   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.111
  2nd generation packing quality :  -1.261
  Ramachandran plot appearance   :  -1.866
  chi-1/chi-2 rotamer normality  :  -4.044 (bad)
  Backbone conformation          :   0.381

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.875
  Bond angles                    :   1.303
  Omega angle restraints         :   0.401 (tight)
  Side chain planarity           :   0.927
  Improper dihedral distribution :   1.439
  B-factor distribution          :   3.161 (loose)
  Inside/Outside distribution    :   1.007

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.875
  Bond angles                    :   1.303
  Omega angle restraints         :   0.401 (tight)
  Side chain planarity           :   0.927
  Improper dihedral distribution :   1.439
  B-factor distribution          :   3.161 (loose)
  Inside/Outside distribution    :   1.007
==============

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.