WHAT IF Check report

This file was created 2011-12-15 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 pdb3fz8.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.430
CA-only RMS fit for the two chains : 0.245

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.457
CA-only RMS fit for the two chains : 0.270

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.419
CA-only RMS fit for the two chains : 0.259

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.572
CA-only RMS fit for the two chains : 0.407

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 F

All-atom RMS fit for the two chains : 0.377
CA-only RMS fit for the two chains : 0.247

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 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.

2754 PLR   ( 500-)  A  -
2755 PLR   ( 500-)  B  -
2756 PLR   ( 500-)  C  -
2757 PLR   ( 500-)  D  -
2758 PLR   ( 500-)  E  -
2759 PLR   ( 500-)  F  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 265 LYS   ( 276-)  A  -   NZ  bound to 2754 PLR   ( 500-)  A  -   C4A
 728 LYS   ( 276-)  B  -   NZ  bound to 2755 PLR   ( 500-)  B  -   C4A
1183 LYS   ( 276-)  C  -   NZ  bound to 2756 PLR   ( 500-)  C  -   C4A
1638 LYS   ( 276-)  D  -   NZ  bound to 2757 PLR   ( 500-)  D  -   C4A
2102 LYS   ( 276-)  E  -   NZ  bound to 2758 PLR   ( 500-)  E  -   C4A
2557 LYS   ( 276-)  F  -   NZ  bound to 2759 PLR   ( 500-)  F  -   C4A

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 6

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 : 33.31

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

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.

 359 ARG   ( 370-)  A
 596 ARG   ( 144-)  B
 822 ARG   ( 370-)  B
 874 ARG   ( 422-)  B
1051 ARG   ( 144-)  C
1277 ARG   ( 370-)  C
1393 ARG   (  31-)  D
1545 ARG   ( 183-)  D
1732 ARG   ( 370-)  D
1789 ARG   ( 427-)  D
1864 ARG   (  38-)  E
2651 ARG   ( 370-)  F

Warning: Tyrosine convention problem

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

  40 TYR   (  51-)  A
 379 TYR   ( 390-)  A
 899 TYR   ( 447-)  B
1354 TYR   ( 447-)  C
2216 TYR   ( 390-)  E
2273 TYR   ( 447-)  E
2728 TYR   ( 447-)  F

Warning: Phenylalanine convention problem

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

 266 PHE   ( 277-)  A
 354 PHE   ( 365-)  A
 422 PHE   ( 433-)  A
 753 PHE   ( 301-)  B
 817 PHE   ( 365-)  B
1126 PHE   ( 219-)  C
1208 PHE   ( 301-)  C
1394 PHE   (  32-)  D
1639 PHE   ( 277-)  D
1663 PHE   ( 301-)  D
1727 PHE   ( 365-)  D
1858 PHE   (  32-)  E
2103 PHE   ( 277-)  E
2127 PHE   ( 301-)  E
2259 PHE   ( 433-)  E
2313 PHE   (  32-)  F
2500 PHE   ( 219-)  F
2558 PHE   ( 277-)  F
2582 PHE   ( 301-)  F

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.

 246 ASP   ( 257-)  A
 709 ASP   ( 257-)  B
1164 ASP   ( 257-)  C
1430 ASP   (  68-)  D
1619 ASP   ( 257-)  D
1834 ASP   (   8-)  E
2083 ASP   ( 257-)  E
2349 ASP   (  68-)  F
2538 ASP   ( 257-)  F

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.

   1 GLU   (  12-)  A
  17 GLU   (  28-)  A
 345 GLU   ( 356-)  A
 424 GLU   ( 435-)  A
 808 GLU   ( 356-)  B
 887 GLU   ( 435-)  B
1263 GLU   ( 356-)  C
1304 GLU   ( 397-)  C
1342 GLU   ( 435-)  C
1390 GLU   (  28-)  D
1718 GLU   ( 356-)  D
1797 GLU   ( 435-)  D
1838 GLU   (  12-)  E
2182 GLU   ( 356-)  E
2261 GLU   ( 435-)  E
2309 GLU   (  28-)  F
2637 GLU   ( 356-)  F
2716 GLU   ( 435-)  F

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.

 594 ARG   ( 142-)  B      N    CA    1.56    5.2
 594 ARG   ( 142-)  B      N   -C     1.24   -4.2
1183 LYS   ( 276-)  C      CE   NZ    1.31   -5.9

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.999307 -0.000003  0.000105|
 | -0.000003  0.998981 -0.000031|
 |  0.000105 -0.000031  0.998540|
Proposed new scale matrix

 |  0.008561  0.004944  0.000000|
 |  0.000000  0.009888  0.000000|
 |  0.000000  0.000000  0.004801|
With corresponding cell

    A    = 116.810  B   = 116.786  C    = 208.289
    Alpha=  90.001  Beta=  90.002  Gamma= 120.008

The CRYST1 cell dimensions

    A    = 116.896  B   = 116.894  C    = 208.586
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 105.416
(Under-)estimated Z-score: 7.567

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.

  38 GLU   (  49-)  A     -C    N    CA  114.42   -4.0
 460 ASP   (   8-)  B      N    CA   C    98.83   -4.4
1182 HIS   ( 275-)  C      CG   ND1  CE1 109.60    4.0
1183 LYS   ( 276-)  C      CD   CE   NZ  131.63    6.2
1307 ARG   ( 400-)  C      CG   CD   NE  117.33    4.0
1411 GLU   (  49-)  D     -C    N    CA  113.78   -4.4
1935 HIS   ( 109-)  E      CG   ND1  CE1 109.65    4.1
1983 LEU   ( 157-)  E      CA   CB   CG  134.25    5.1
2102 LYS   ( 276-)  E      CG   CD   CE  121.18    4.3
2262 LEU   ( 436-)  E      CA   CB   CG  130.62    4.1

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.

   1 GLU   (  12-)  A
  17 GLU   (  28-)  A
 246 ASP   ( 257-)  A
 345 GLU   ( 356-)  A
 359 ARG   ( 370-)  A
 424 GLU   ( 435-)  A
 596 ARG   ( 144-)  B
 709 ASP   ( 257-)  B
 808 GLU   ( 356-)  B
 822 ARG   ( 370-)  B
 874 ARG   ( 422-)  B
 887 GLU   ( 435-)  B
1051 ARG   ( 144-)  C
1164 ASP   ( 257-)  C
1263 GLU   ( 356-)  C
1277 ARG   ( 370-)  C
1304 GLU   ( 397-)  C
1342 GLU   ( 435-)  C
1390 GLU   (  28-)  D
1393 ARG   (  31-)  D
1430 ASP   (  68-)  D
1545 ARG   ( 183-)  D
1619 ASP   ( 257-)  D
1718 GLU   ( 356-)  D
1732 ARG   ( 370-)  D
1789 ARG   ( 427-)  D
1797 GLU   ( 435-)  D
1834 ASP   (   8-)  E
1838 GLU   (  12-)  E
1864 ARG   (  38-)  E
2083 ASP   ( 257-)  E
2182 GLU   ( 356-)  E
2261 GLU   ( 435-)  E
2309 GLU   (  28-)  F
2349 ASP   (  68-)  F
2538 ASP   ( 257-)  F
2637 GLU   ( 356-)  F
2651 ARG   ( 370-)  F
2716 GLU   ( 435-)  F

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.

  38 GLU   (  49-)  A      CA    -6.4    23.42    33.96
 956 GLU   (  49-)  C      CA    -6.5    23.37    33.96
The average deviation= 0.910

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.

1694 LEU   ( 332-)  D    4.47
 460 ASP   (   8-)  B    4.21

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.

 594 ARG   ( 142-)  B    -3.1
2669 PRO   ( 388-)  F    -2.9
 868 THR   ( 416-)  B    -2.7
2242 THR   ( 416-)  E    -2.7
 351 PRO   ( 362-)  A    -2.6
2490 PHE   ( 209-)  F    -2.6
1833 THR   (   7-)  E    -2.6
1553 PRO   ( 191-)  D    -2.6
1839 LEU   (  13-)  E    -2.6
2366 ILE   (  85-)  F    -2.6
 661 PHE   ( 209-)  B    -2.6
1906 ILE   (  80-)  E    -2.5
  20 ARG   (  31-)  A    -2.5
 426 LEU   ( 437-)  A    -2.5
 992 ILE   (  85-)  C    -2.5
1049 ARG   ( 142-)  C    -2.5
1393 ARG   (  31-)  D    -2.5
1116 PHE   ( 209-)  C    -2.5
2102 LYS   ( 276-)  E    -2.5
  74 ILE   (  85-)  A    -2.5
 480 GLU   (  28-)  B    -2.5
2312 ARG   (  31-)  F    -2.5
 537 ILE   (  85-)  B    -2.5
1911 ILE   (  85-)  E    -2.5
 483 ARG   (  31-)  B    -2.4
And so on for a total of 113 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.

   8 GLY   (  19-)  A  Poor phi/psi
  11 SER   (  22-)  A  omega poor
  16 ALA   (  27-)  A  Poor phi/psi
  17 GLU   (  28-)  A  Poor phi/psi
  24 HIS   (  35-)  A  omega poor
  45 ALA   (  56-)  A  Poor phi/psi
  52 PHE   (  63-)  A  omega poor
  98 HIS   ( 109-)  A  Poor phi/psi
 123 GLY   ( 134-)  A  Poor phi/psi
 176 LEU   ( 187-)  A  omega poor
 203 THR   ( 214-)  A  Poor phi/psi
 206 TYR   ( 217-)  A  omega poor
 246 ASP   ( 257-)  A  omega poor
 250 ASP   ( 261-)  A  Poor phi/psi
 265 LYS   ( 276-)  A  Poor phi/psi
 267 GLY   ( 278-)  A  omega poor
 268 LEU   ( 279-)  A  Poor phi/psi
 306 PHE   ( 317-)  A  Poor phi/psi
 311 GLY   ( 322-)  A  Poor phi/psi
 378 GLY   ( 389-)  A  Poor phi/psi
 396 PRO   ( 407-)  A  omega poor
 409 VAL   ( 420-)  A  omega poor
 453 LYS   ( 464-)  A  omega poor
 479 ALA   (  27-)  B  omega poor
 480 GLU   (  28-)  B  Poor phi/psi, omega poor
And so on for a total of 136 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.544

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.

1253 SER   ( 346-)  C    0.35
  82 SER   (  93-)  A    0.36
 116 SER   ( 127-)  A    0.37
 901 SER   ( 449-)  B    0.38
1034 SER   ( 127-)  C    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!

   9 ALA   (  20-)  A      0
  17 GLU   (  28-)  A      0
  18 SER   (  29-)  A      0
  20 ARG   (  31-)  A      0
  21 PHE   (  32-)  A      0
  22 PRO   (  33-)  A      0
  23 LEU   (  34-)  A      0
  24 HIS   (  35-)  A      0
  38 GLU   (  49-)  A      0
  40 TYR   (  51-)  A      0
  42 ASP   (  53-)  A      0
  47 GLN   (  58-)  A      0
  49 LEU   (  60-)  A      0
  52 PHE   (  63-)  A      0
  55 THR   (  66-)  A      0
  73 TRP   (  84-)  A      0
  74 ILE   (  85-)  A      0
  97 TRP   ( 108-)  A      0
  98 HIS   ( 109-)  A      0
  99 ALA   ( 110-)  A      0
 103 LYS   ( 114-)  A      0
 113 ILE   ( 124-)  A      0
 140 PRO   ( 151-)  A      0
 141 THR   ( 152-)  A      0
 142 ASP   ( 153-)  A      0
And so on for a total of 1073 lines.

Warning: Backbone oxygen evaluation

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

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

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

2017 PRO   ( 191-)  E   2.20   10
 643 PRO   ( 191-)  B   1.62   15
1098 PRO   ( 191-)  C   1.51   11

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]

 708 PRO   ( 256-)  B    0.16 LOW
 940 PRO   (  33-)  C    0.14 LOW
 998 PRO   (  91-)  C    0.18 LOW
1018 PRO   ( 111-)  C    0.14 LOW
1475 PRO   ( 113-)  D    0.15 LOW
1569 PRO   ( 207-)  D    0.10 LOW
2503 PRO   ( 222-)  F    0.15 LOW

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].

 100 PRO   ( 111-)  A  -130.0 half-chair C-delta/C-gamma (-126 degrees)
 173 PRO   ( 184-)  A   116.3 envelop C-beta (108 degrees)
 196 PRO   ( 207-)  A    -2.8 envelop N (0 degrees)
 245 PRO   ( 256-)  A   -38.8 envelop C-alpha (-36 degrees)
 270 PRO   ( 281-)  A  -118.5 half-chair C-delta/C-gamma (-126 degrees)
 285 PRO   ( 296-)  A   104.2 envelop C-beta (108 degrees)
 351 PRO   ( 362-)  A   -31.9 envelop C-alpha (-36 degrees)
 563 PRO   ( 111-)  B   100.1 envelop C-beta (108 degrees)
 565 PRO   ( 113-)  B    40.6 envelop C-delta (36 degrees)
 643 PRO   ( 191-)  B   112.1 envelop C-beta (108 degrees)
 659 PRO   ( 207-)  B    -3.3 envelop N (0 degrees)
 717 PRO   ( 265-)  B  -116.9 envelop C-gamma (-108 degrees)
 828 PRO   ( 376-)  B    15.5 half-chair N/C-delta (18 degrees)
 840 PRO   ( 388-)  B   -50.8 half-chair C-beta/C-alpha (-54 degrees)
1020 PRO   ( 113-)  C   -36.8 envelop C-alpha (-36 degrees)
1062 PRO   ( 155-)  C  -115.3 envelop C-gamma (-108 degrees)
1114 PRO   ( 207-)  C    31.7 envelop C-delta (36 degrees)
1227 PRO   ( 320-)  C  -114.8 envelop C-gamma (-108 degrees)
1283 PRO   ( 376-)  C     5.2 envelop N (0 degrees)
1473 PRO   ( 111-)  D  -157.5 half-chair N/C-delta (-162 degrees)
1517 PRO   ( 155-)  D   -57.2 half-chair C-beta/C-alpha (-54 degrees)
1543 PRO   ( 181-)  D   -61.5 half-chair C-beta/C-alpha (-54 degrees)
1553 PRO   ( 191-)  D   111.6 envelop C-beta (108 degrees)
1614 PRO   ( 252-)  D   104.2 envelop C-beta (108 degrees)
1643 PRO   ( 281-)  D  -114.8 envelop C-gamma (-108 degrees)
1658 PRO   ( 296-)  D    99.8 envelop C-beta (108 degrees)
1724 PRO   ( 362-)  D   -56.3 half-chair C-beta/C-alpha (-54 degrees)
1917 PRO   (  91-)  E    28.6 envelop C-delta (36 degrees)
1937 PRO   ( 111-)  E   102.1 envelop C-beta (108 degrees)
2007 PRO   ( 181-)  E   -34.8 envelop C-alpha (-36 degrees)
2010 PRO   ( 184-)  E    48.9 half-chair C-delta/C-gamma (54 degrees)
2033 PRO   ( 207-)  E    45.0 half-chair C-delta/C-gamma (54 degrees)
2048 PRO   ( 222-)  E    99.4 envelop C-beta (108 degrees)
2091 PRO   ( 265-)  E  -121.3 half-chair C-delta/C-gamma (-126 degrees)
2202 PRO   ( 376-)  E    50.7 half-chair C-delta/C-gamma (54 degrees)
2392 PRO   ( 111-)  F  -171.1 envelop N (180 degrees)
2432 PRO   ( 151-)  F    35.5 envelop C-delta (36 degrees)
2472 PRO   ( 191-)  F   105.7 envelop C-beta (108 degrees)
2488 PRO   ( 207-)  F   -41.3 envelop C-alpha (-36 degrees)
2601 PRO   ( 320-)  F  -112.9 envelop C-gamma (-108 degrees)
2669 PRO   ( 388-)  F     6.0 envelop N (0 degrees)
2733 PRO   ( 452-)  F    34.0 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

2557 LYS   ( 276-)  F      NZ  <-> 2759 PLR   ( 500-)  F      C4A    1.16    1.54  INTRA B3
2557 LYS   ( 276-)  F      CE  <-> 2759 PLR   ( 500-)  F      C4A    0.58    2.62  INTRA
2014 PHE   ( 188-)  E      CZ  <-> 2042 ASN   ( 216-)  E      ND2    0.56    2.54  INTRA BL
  16 ALA   (  27-)  A      O   <->   18 SER   (  29-)  A      N      0.52    2.18  INTRA BF
1550 PHE   ( 188-)  D      CZ  <-> 1578 ASN   ( 216-)  D      ND2    0.51    2.59  INTRA
 571 VAL   ( 119-)  B      N   <-> 2760 HOH   ( 518 )  E      O      0.45    2.25  INTRA BL
 943 GLU   (  36-)  C      OE2 <-> 1703 LYS   ( 341-)  D      NZ     0.45    2.25  INTRA
2469 PHE   ( 188-)  F      CZ  <-> 2497 ASN   ( 216-)  F      ND2    0.44    2.66  INTRA
1839 LEU   (  13-)  E      O   <-> 1848 SER   (  22-)  E      N      0.43    2.27  INTRA
1095 PHE   ( 188-)  C      CZ  <-> 1123 ASN   ( 216-)  C      ND2    0.41    2.69  INTRA
1088 PRO   ( 181-)  C      O   <-> 1100 ARG   ( 193-)  C      NH2    0.41    2.29  INTRA BL
 170 PRO   ( 181-)  A      O   <->  182 ARG   ( 193-)  A      NH2    0.34    2.36  INTRA BL
2471 ASP   ( 190-)  F      OD1 <-> 2474 ARG   ( 193-)  F      CD     0.34    2.46  INTRA BL
2007 PRO   ( 181-)  E      O   <-> 2019 ARG   ( 193-)  E      NH2    0.34    2.36  INTRA BL
1389 ALA   (  27-)  D      O   <-> 1391 SER   (  29-)  D      N      0.34    2.36  INTRA BF
 287 GLU   ( 298-)  A      O   <->  623 ARG   ( 171-)  B      NH1    0.31    2.39  INTRA
1839 LEU   (  13-)  E      O   <-> 1848 SER   (  22-)  E      CB     0.31    2.49  INTRA
  81 GLN   (  92-)  A      CG  <->  501 GLU   (  49-)  B      O      0.29    2.51  INTRA BL
 966 ASN   (  59-)  C      OD1 <->  968 ALA   (  61-)  C      N      0.29    2.41  INTRA BL
  25 GLU   (  36-)  A      OE2 <->  793 LYS   ( 341-)  B      NZ     0.28    2.42  INTRA
 633 PRO   ( 181-)  B      O   <->  645 ARG   ( 193-)  B      NH2    0.27    2.43  INTRA BL
1183 LYS   ( 276-)  C      NZ  <-> 1373 THR   ( 466-)  C      OG1    0.26    2.44  INTRA
 230 HIS   ( 241-)  A      ND1 <->  258 SER   ( 269-)  A      OG     0.26    2.44  INTRA BL
1714 TYR   ( 352-)  D      OH  <-> 1797 GLU   ( 435-)  D      OE2    0.26    2.14  INTRA
1949 THR   ( 123-)  E      O   <-> 2111 GLY   ( 285-)  E      N      0.25    2.45  INTRA BL
And so on for a total of 312 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

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.

 457 GLN   (   5-)  B      -6.49
 566 LYS   ( 114-)  B      -6.21
 103 LYS   ( 114-)  A      -6.20
1476 LYS   ( 114-)  D      -6.19
1021 LYS   ( 114-)  C      -6.17
2395 LYS   ( 114-)  F      -5.96
1940 LYS   ( 114-)  E      -5.92
1575 TYR   ( 213-)  D      -5.62
1213 LEU   ( 306-)  C      -5.46
1392 LYS   (  30-)  D      -5.36
  23 LEU   (  34-)  A      -5.17
 758 LEU   ( 306-)  B      -5.17
1789 ARG   ( 427-)  D      -5.17
1197 ARG   ( 290-)  C      -5.16
 938 ARG   (  31-)  C      -5.13
  20 ARG   (  31-)  A      -5.12
2132 LEU   ( 306-)  E      -5.09
 295 LEU   ( 306-)  A      -5.09
2571 ARG   ( 290-)  F      -5.06
1836 ARG   (  10-)  E      -5.04
1120 TYR   ( 213-)  C      -5.04
  19 LYS   (  30-)  A      -5.02
2039 TYR   ( 213-)  E      -5.01

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

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.

1414 LEU   (  52-)  D   -2.77
1906 ILE   (  80-)  E   -2.76
2252 ARG   ( 426-)  E   -2.68
1819 ILE   ( 457-)  D   -2.64
2361 ILE   (  80-)  F   -2.63
1788 ARG   ( 426-)  D   -2.62
1087 ILE   ( 180-)  C   -2.62
 632 ILE   ( 180-)  B   -2.60
2283 ILE   ( 457-)  E   -2.60
 169 ILE   ( 180-)  A   -2.59
2738 ILE   ( 457-)  F   -2.59
2461 ILE   ( 180-)  F   -2.59
1542 ILE   ( 180-)  D   -2.58
2006 ILE   ( 180-)  E   -2.58
 446 ILE   ( 457-)  A   -2.56
 909 ILE   ( 457-)  B   -2.53

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

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.

2760 HOH   ( 486 )  E      O
2760 HOH   ( 495 )  E      O
2760 HOH   ( 506 )  E      O
2760 HOH   ( 519 )  E      O
2760 HOH   ( 525 )  E      O
2760 HOH   ( 526 )  E      O
2760 HOH   ( 527 )  E      O

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.

 156 HIS   ( 167-)  A
 619 HIS   ( 167-)  B
1366 GLN   ( 459-)  C
1529 HIS   ( 167-)  D
1993 HIS   ( 167-)  E
2448 HIS   ( 167-)  F

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.

  19 LYS   (  30-)  A      N
  20 ARG   (  31-)  A      N
  57 ASP   (  68-)  A      N
  69 ILE   (  80-)  A      N
  72 ASN   (  83-)  A      N
 114 GLY   ( 125-)  A      N
 115 SER   ( 126-)  A      N
 115 SER   ( 126-)  A      OG
 116 SER   ( 127-)  A      N
 129 ARG   ( 140-)  A      NH2
 149 GLY   ( 160-)  A      N
 152 GLN   ( 163-)  A      N
 152 GLN   ( 163-)  A      NE2
 153 ILE   ( 164-)  A      N
 162 TRP   ( 173-)  A      NE1
 177 PHE   ( 188-)  A      N
 189 GLU   ( 200-)  A      N
 193 GLY   ( 204-)  A      N
 197 THR   ( 208-)  A      OG1
 201 THR   ( 212-)  A      OG1
 202 TYR   ( 213-)  A      N
 203 THR   ( 214-)  A      OG1
 205 ASN   ( 216-)  A      ND2
 210 GLN   ( 221-)  A      N
 235 SER   ( 246-)  A      OG
And so on for a total of 335 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.

 287 GLU   ( 298-)  A      OE1
 454 HIS   ( 465-)  A      ND1
 549 ASP   (  97-)  B      OD1
 750 GLU   ( 298-)  B      OE1
 917 HIS   ( 465-)  B      ND1
1164 ASP   ( 257-)  C      OD2
1459 ASP   (  97-)  D      OD1
1660 GLU   ( 298-)  D      OE1
1827 HIS   ( 465-)  D      ND1
1831 GLN   (   5-)  E      OE1
1923 ASP   (  97-)  E      OD1
2124 GLU   ( 298-)  E      OE1
2291 HIS   ( 465-)  E      ND1

Warning: Possible wrong residue type

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

 222 ASP   ( 233-)  A   H-bonding suggests Asn
 344 ASP   ( 355-)  A   H-bonding suggests Asn
 685 ASP   ( 233-)  B   H-bonding suggests Asn
 846 ASP   ( 394-)  B   H-bonding suggests Asn; but Alt-Rotamer
1164 ASP   ( 257-)  C   H-bonding suggests Asn
1357 ASP   ( 450-)  C   H-bonding suggests Asn
1756 ASP   ( 394-)  D   H-bonding suggests Asn; but Alt-Rotamer
1812 ASP   ( 450-)  D   H-bonding suggests Asn
2181 ASP   ( 355-)  E   H-bonding suggests Asn
2220 ASP   ( 394-)  E   H-bonding suggests Asn; but Alt-Rotamer
2309 GLU   (  28-)  F   H-bonding suggests Gln
2514 ASP   ( 233-)  F   H-bonding suggests Asn
2675 ASP   ( 394-)  F   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.740
  2nd generation packing quality :  -1.556
  Ramachandran plot appearance   :  -2.642
  chi-1/chi-2 rotamer normality  :  -3.544 (poor)
  Backbone conformation          :  -0.142

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.567 (tight)
  Bond angles                    :   0.740
  Omega angle restraints         :   1.135
  Side chain planarity           :   0.437 (tight)
  Improper dihedral distribution :   0.764
  Inside/Outside distribution    :   0.995

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.567 (tight)
  Bond angles                    :   0.740
  Omega angle restraints         :   1.135
  Side chain planarity           :   0.437 (tight)
  Improper dihedral distribution :   0.764
  Inside/Outside distribution    :   0.995
==============

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.