WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb3dtu.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 : 0.382
CA-only RMS fit for the two chains : 0.304

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: B and D

All-atom RMS fit for the two chains : 0.504
CA-only RMS fit for the two chains : 0.318

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: Topology could not be determined for some ligands

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

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

1593 DMU   ( 567-)  D  -         OK
1594 A10   (1002-)  A  -         Fragmented
1595 DMU   (1005-)  A  -         OK
1600 HEA   (1502-)  A  -         Atom types
1601 HEA   (1503-)  A  -         Atom types
1602 TRD   (1504-)  A  -         OK
1603 TRD   (1506-)  A  -         OK
1609 DMU   ( 567-)  C  -         OK
1610 DMU   ( 568-)  C  -         OK
1616 HEA   ( 574-)  C  -         Atom types
1617 HEA   ( 575-)  C  -         Atom types
1618 TRD   ( 577-)  C  -         OK
1624 A32   (  23-)  D  -         OK
1625 A31   (  12-)  D  -         OK
1626 A30   ( 288-)  D  -         OK
1627 TRD   (   7-)  C  -         OK
1628 DMU   (  11-)  D  -         OK
1629 A29   ( 584-)  C  -         OK
1630 A28   ( 583-)  C  -         OK
1631 A27   ( 582-)  D  -         OK
1632 A26   ( 581-)  C  -         OK
1633 A25   ( 580-)  C  -         OK
1634 A24   ( 579-)  C  -         OK
1635 A23   ( 578-)  C  -         OK
1636 DXC   ( 576-)  C  -         OK
1637 HTO   (   1-)  D  -         OK
1638 A22   (1031-)  B  -         OK
1639 A21   (1012-)  B  -         OK
1640 A20   (1023-)  B  -         OK
1641 A19   (1011-)  B  -         OK
1642 A18   (1003-)  B  -         OK
1643 A17   (1015-)  A  -         OK
1644 A16   (1014-)  A  -         OK
1645 A15   (1013-)  A  -         OK
1646 A14   (1010-)  A  -         OK
1647 A13   (1009-)  A  -         OK
1648 A12   (1505-)  A  -         OK
1649 A11   (1004-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 ARG   (  13-)  A  -   CG
   1 ARG   (  13-)  A  -   CD
   1 ARG   (  13-)  A  -   NE
   1 ARG   (  13-)  A  -   CZ
   1 ARG   (  13-)  A  -   NH1
   1 ARG   (  13-)  A  -   NH2
  62 LYS   (  74-)  A  -   CG
  62 LYS   (  74-)  A  -   CD
  62 LYS   (  74-)  A  -   CE
  62 LYS   (  74-)  A  -   NZ
  65 PHE   (  77-)  A  -   CD1
  65 PHE   (  77-)  A  -   CD2
  65 PHE   (  77-)  A  -   CE1
  65 PHE   (  77-)  A  -   CE2
  65 PHE   (  77-)  A  -   CZ
 125 ARG   ( 137-)  A  -   CG
 125 ARG   ( 137-)  A  -   CD
 125 ARG   ( 137-)  A  -   NE
 125 ARG   ( 137-)  A  -   CZ
 125 ARG   ( 137-)  A  -   NH1
 125 ARG   ( 137-)  A  -   NH2
 212 LYS   ( 224-)  A  -   CG
 212 LYS   ( 224-)  A  -   CD
 212 LYS   ( 224-)  A  -   CE
 212 LYS   ( 224-)  A  -   NZ
And so on for a total of 101 lines.

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.

1597  MG   (1006-)  B  -
1622  CD   (   9-)  C  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

   2 ARG   (  14-)  A
  40 ARG   (  52-)  A
 509 ARG   ( 521-)  A
 512 ARG   ( 524-)  A
 546 ARG   (  35-)  B
 834 ARG   (  52-)  C
1306 ARG   ( 524-)  C
1342 ARG   (  35-)  D
1400 ARG   (  93-)  D

Warning: Tyrosine convention problem

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

  21 TYR   (  33-)  A
 173 TYR   ( 185-)  A
 436 TYR   ( 448-)  A
 474 TYR   ( 486-)  A
 518 TYR   ( 530-)  A
 589 TYR   (  78-)  B
 815 TYR   (  33-)  C
 967 TYR   ( 185-)  C
1095 TYR   ( 313-)  C
1230 TYR   ( 448-)  C
1268 TYR   ( 486-)  C
1299 TYR   ( 517-)  C
1312 TYR   ( 530-)  C
1385 TYR   (  78-)  D
1466 TYR   ( 159-)  D

Warning: Phenylalanine convention problem

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

   5 PHE   (  17-)  A
   9 PHE   (  21-)  A
 269 PHE   ( 281-)  A
 270 PHE   ( 282-)  A
 449 PHE   ( 461-)  A
 571 PHE   (  60-)  B
 582 PHE   (  71-)  B
 629 PHE   ( 118-)  B
 667 PHE   ( 156-)  B
 751 PHE   ( 240-)  B
 759 PHE   ( 248-)  B
 799 PHE   (  17-)  C
 844 PHE   (  62-)  C
 858 PHE   (  76-)  C
1063 PHE   ( 281-)  C
1064 PHE   ( 282-)  C
1243 PHE   ( 461-)  C
1367 PHE   (  60-)  D
1378 PHE   (  71-)  D
1425 PHE   ( 118-)  D

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 176 ASP   ( 188-)  A
 569 ASP   (  58-)  B
 662 ASP   ( 151-)  B
 680 ASP   ( 169-)  B
 740 ASP   ( 229-)  B
 970 ASP   ( 188-)  C
1365 ASP   (  58-)  D
1458 ASP   ( 151-)  D
1476 ASP   ( 169-)  D
1536 ASP   ( 229-)  D

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.

  42 GLU   (  54-)  A
  74 GLU   (  86-)  A
 521 GLU   ( 533-)  A
 612 GLU   ( 101-)  B
 668 GLU   ( 157-)  B
 688 GLU   ( 177-)  B
 783 GLU   ( 272-)  B
 784 GLU   ( 273-)  B
 791 GLU   ( 280-)  B
 836 GLU   (  54-)  C
 868 GLU   (  86-)  C
1408 GLU   ( 101-)  D
1455 GLU   ( 148-)  D
1464 GLU   ( 157-)  D
1484 GLU   ( 177-)  D
1579 GLU   ( 272-)  D
1587 GLU   ( 280-)  D

Geometric checks

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

 |  0.996003 -0.000095 -0.000505|
 | -0.000095  0.996481  0.000381|
 | -0.000505  0.000381  0.996950|
Proposed new scale matrix

 |  0.008147  0.000000  0.000004|
 |  0.000000  0.007600 -0.000003|
 |  0.000003 -0.000002  0.005972|
With corresponding cell

    A    = 122.751  B   = 131.583  C    = 167.442
    Alpha=  89.956  Beta=  90.058  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 123.243  B   = 132.052  C    = 167.966
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 682.560
(Under-)estimated Z-score: 19.255

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.

  40 ARG   (  52-)  A      CG   CD   NE  119.14    5.1
 272 HIS   ( 284-)  A      N    CA   CB  118.50    4.7
 272 HIS   ( 284-)  A      CA   CB   CG  109.07   -4.7
 272 HIS   ( 284-)  A      CG   ND1  CE1 109.93    4.3
 321 HIS   ( 333-)  A      CG   ND1  CE1 109.63    4.0
 834 ARG   (  52-)  C      CG   CD   NE  118.34    4.6
1066 HIS   ( 284-)  C      N    CA   CB  118.79    4.9
1066 HIS   ( 284-)  C      CA   CB   CG  108.62   -5.2
1066 HIS   ( 284-)  C      CG   ND1  CE1 109.96    4.4
1082 HIS   ( 300-)  C      CG   ND1  CE1 109.61    4.0
1403 HIS   (  96-)  D      CG   ND1  CE1 109.71    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.

   2 ARG   (  14-)  A
  40 ARG   (  52-)  A
  42 GLU   (  54-)  A
  74 GLU   (  86-)  A
 176 ASP   ( 188-)  A
 509 ARG   ( 521-)  A
 512 ARG   ( 524-)  A
 521 GLU   ( 533-)  A
 546 ARG   (  35-)  B
 569 ASP   (  58-)  B
 612 GLU   ( 101-)  B
 662 ASP   ( 151-)  B
 668 GLU   ( 157-)  B
 680 ASP   ( 169-)  B
 688 GLU   ( 177-)  B
 740 ASP   ( 229-)  B
 783 GLU   ( 272-)  B
 784 GLU   ( 273-)  B
 791 GLU   ( 280-)  B
 834 ARG   (  52-)  C
 836 GLU   (  54-)  C
 868 GLU   (  86-)  C
 970 ASP   ( 188-)  C
1306 ARG   ( 524-)  C
1342 ARG   (  35-)  D
1365 ASP   (  58-)  D
1400 ARG   (  93-)  D
1408 GLU   ( 101-)  D
1455 GLU   ( 148-)  D
1458 ASP   ( 151-)  D
1464 GLU   ( 157-)  D
1476 ASP   ( 169-)  D
1484 GLU   ( 177-)  D
1536 ASP   ( 229-)  D
1579 GLU   ( 272-)  D
1587 GLU   ( 280-)  D

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

1320 LEU   ( 538-)  C    4.42
 526 LEU   ( 538-)  A    4.14

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.

 749 LEU   ( 238-)  B    -2.6
1545 LEU   ( 238-)  D    -2.5
 162 LEU   ( 174-)  A    -2.4
 800 THR   (  18-)  C    -2.3
1006 LYS   ( 224-)  C    -2.3
1527 THR   ( 220-)  D    -2.3
 725 ASP   ( 214-)  B    -2.2
1521 ASP   ( 214-)  D    -2.1
 407 HIS   ( 419-)  A    -2.1
 206 PRO   ( 218-)  A    -2.1
1194 ASP   ( 412-)  C    -2.1
1209 GLY   ( 427-)  C    -2.1
 415 GLY   ( 427-)  A    -2.1
 279 VAL   ( 291-)  A    -2.1
 400 ASP   ( 412-)  A    -2.1
1046 PHE   ( 264-)  C    -2.1
 958 PRO   ( 176-)  C    -2.0
 731 THR   ( 220-)  B    -2.0
1518 THR   ( 211-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

 151 ASN   ( 163-)  A  Poor phi/psi
 162 LEU   ( 174-)  A  Poor phi/psi
 164 PRO   ( 176-)  A  PRO omega poor
 278 ILE   ( 290-)  A  omega poor
 295 LYS   ( 307-)  A  Poor phi/psi
 362 SER   ( 374-)  A  omega poor
 400 ASP   ( 412-)  A  Poor phi/psi
 470 ARG   ( 482-)  A  Poor phi/psi
 519 TRP   ( 531-)  A  Poor phi/psi
 522 HIS   ( 534-)  A  omega poor
 523 ALA   ( 535-)  A  omega poor
 532 SER   ( 544-)  A  PRO omega poor
 637 GLN   ( 126-)  B  omega poor
 643 ALA   ( 132-)  B  omega poor
 653 GLN   ( 142-)  B  omega poor
 681 ASN   ( 170-)  B  Poor phi/psi
 696 TYR   ( 185-)  B  Poor phi/psi
 702 LEU   ( 191-)  B  Poor phi/psi
 714 ASN   ( 203-)  B  Poor phi/psi
 800 THR   (  18-)  C  omega poor
 823 GLY   (  41-)  C  Poor phi/psi
 890 PHE   ( 108-)  C  omega poor
 892 VAL   ( 110-)  C  omega poor
 945 ASN   ( 163-)  C  Poor phi/psi
 956 LEU   ( 174-)  C  Poor phi/psi
 958 PRO   ( 176-)  C  PRO omega poor
 995 LEU   ( 213-)  C  omega poor
1039 ARG   ( 257-)  C  omega poor
1064 PHE   ( 282-)  C  omega poor
1072 ILE   ( 290-)  C  omega poor
1089 LYS   ( 307-)  C  Poor phi/psi
1112 VAL   ( 330-)  C  omega poor
1121 GLY   ( 339-)  C  Poor phi/psi
1156 SER   ( 374-)  C  omega poor
1194 ASP   ( 412-)  C  Poor phi/psi
1264 ARG   ( 482-)  C  Poor phi/psi
1313 TRP   ( 531-)  C  Poor phi/psi
1316 HIS   ( 534-)  C  omega poor
1317 ALA   ( 535-)  C  omega poor
1319 THR   ( 537-)  C  omega poor
1326 SER   ( 544-)  C  PRO omega poor
1333 PHE   ( 551-)  C  omega poor
1350 PHE   (  43-)  D  omega poor
1439 ALA   ( 132-)  D  omega poor
1449 GLN   ( 142-)  D  omega poor
1477 ASN   ( 170-)  D  Poor phi/psi
1492 TYR   ( 185-)  D  Poor phi/psi
1498 LEU   ( 191-)  D  Poor phi/psi
1510 ASN   ( 203-)  D  Poor phi/psi
1560 SER   ( 253-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -0.803

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.

 219 SER   ( 231-)  A    0.35
1286 SER   ( 504-)  C    0.36
1081 SER   ( 299-)  C    0.36
 188 SER   ( 200-)  A    0.36
 492 SER   ( 504-)  A    0.36
 495 SER   ( 507-)  A    0.37
 933 SER   ( 151-)  C    0.37
 982 SER   ( 200-)  C    0.38
 485 SER   ( 497-)  A    0.39
1279 SER   ( 497-)  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!

   8 TRP   (  20-)  A      0
   9 PHE   (  21-)  A      0
  12 THR   (  24-)  A      0
  13 ASN   (  25-)  A      0
  14 HIS   (  26-)  A      0
  44 MET   (  56-)  A      0
  46 PRO   (  58-)  A      0
  49 GLN   (  61-)  A      0
  51 MET   (  63-)  A      0
  52 CYS   (  64-)  A      0
  55 HIS   (  67-)  A      0
  58 SER   (  70-)  A      0
  69 TRP   (  81-)  A      0
  78 PRO   (  90-)  A      0
  95 MET   ( 107-)  A      0
  96 PHE   ( 108-)  A      0
  97 PHE   ( 109-)  A      0
  98 VAL   ( 110-)  A      0
  99 VAL   ( 111-)  A      0
 104 PHE   ( 116-)  A      0
 107 PHE   ( 119-)  A      0
 119 PRO   ( 131-)  A      0
 148 PRO   ( 160-)  A      0
 154 LEU   ( 166-)  A      0
 158 ILE   ( 170-)  A      0
And so on for a total of 440 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!

 150 GLY   ( 162-)  A   2.97   11

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].

 206 PRO   ( 218-)  A   109.4 envelop C-beta (108 degrees)
 641 PRO   ( 130-)  B    19.6 half-chair N/C-delta (18 degrees)
1231 PRO   ( 449-)  C    50.2 half-chair C-delta/C-gamma (54 degrees)
1269 PRO   ( 487-)  C   101.5 envelop C-beta (108 degrees)
1437 PRO   ( 130-)  D    42.5 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

 272 HIS   ( 284-)  A      NE2  <->   276 TYR   ( 288-)  A      CE2  1.72    1.38  INTRA BL
1066 HIS   ( 284-)  C      NE2  <->  1070 TYR   ( 288-)  C      CE2  1.72    1.38  INTRA BL
 272 HIS   ( 284-)  A      CD2  <->   276 TYR   ( 288-)  A      CE2  0.88    2.32  INTRA BL
1066 HIS   ( 284-)  C      CD2  <->  1070 TYR   ( 288-)  C      CE2  0.84    2.36  INTRA BL
1066 HIS   ( 284-)  C      NE2  <->  1070 TYR   ( 288-)  C      CD2  0.72    2.38  INTRA BL
 272 HIS   ( 284-)  A      NE2  <->   276 TYR   ( 288-)  A      CZ   0.70    2.40  INTRA BL
1066 HIS   ( 284-)  C      CE1  <->  1070 TYR   ( 288-)  C      CE2  0.69    2.51  INTRA BL
 272 HIS   ( 284-)  A      NE2  <->   276 TYR   ( 288-)  A      CD2  0.68    2.42  INTRA BL
 272 HIS   ( 284-)  A      CE1  <->   276 TYR   ( 288-)  A      CE2  0.66    2.54  INTRA BL
1066 HIS   ( 284-)  C      NE2  <->  1070 TYR   ( 288-)  C      CZ   0.66    2.44  INTRA BL
1614  OH   ( 572-)  C      O    <->  1652 HOH   ( 589 )  C      O    0.51    1.89  INTRA BL
1082 HIS   ( 300-)  C      ND1  <->  1629 A29   ( 584-)  C      C7   0.48    2.62  INTRA BL
 272 HIS   ( 284-)  A      CD2  <->   276 TYR   ( 288-)  A      CD2  0.48    2.72  INTRA BL
1066 HIS   ( 284-)  C      CD2  <->  1070 TYR   ( 288-)  C      CD2  0.47    2.73  INTRA BL
1604  CU   (1022-)  B     CU    <->  1605  CU   (1004-)  B     CU    0.44    2.56  INTRA BL
1316 HIS   ( 534-)  C      ND1  <->  1652 HOH   ( 747 )  C      O    0.43    2.27  INTRA BF
 739 GLN   ( 228-)  B      NE2  <->  1651 HOH   (1130 )  B      O    0.42    2.28  INTRA
1599  OH   (1501-)  A      O    <->  1650 HOH   (1511 )  A      O    0.40    2.00  INTRA BL
1619  CU   (   3-)  D     CU    <->  1620  CU   (   4-)  D     CU    0.40    2.60  INTRA BL
 884 HIS   ( 102-)  C      NE2  <->  1616 HEA   ( 574-)  C      ND   0.36    2.64  INTRA BL
 884 HIS   ( 102-)  C      NE2  <->  1616 HEA   ( 574-)  C      NC   0.30    2.70  INTRA BL
1548 ARG   ( 241-)  D      NH1  <->  1653 HOH   ( 432 )  D      O    0.25    2.45  INTRA BF
1617 HEA   ( 575-)  C      ND   <->  1652 HOH   ( 589 )  C      O    0.24    2.46  INTRA BL
 884 HIS   ( 102-)  C      CE1  <->  1616 HEA   ( 574-)  C      NC   0.24    2.86  INTRA BL
1535 GLN   ( 228-)  D      NE2  <->  1653 HOH   ( 387 )  D      O    0.23    2.47  INTRA BL
And so on for a total of 114 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.181

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 548 GLN   (  37-)  B      -6.61
1344 GLN   (  37-)  D      -6.45
1591 HIS   ( 284-)  D      -6.28
 797 HIS   ( 286-)  B      -6.14
 604 ARG   (  93-)  B      -5.83
 947 GLN   ( 165-)  C      -5.80
 115 HIS   ( 127-)  A      -5.74
1303 ARG   ( 521-)  C      -5.74
 153 GLN   ( 165-)  A      -5.73
1589 HIS   ( 282-)  D      -5.71
 909 HIS   ( 127-)  C      -5.69
 509 ARG   ( 521-)  A      -5.68
   2 ARG   (  14-)  A      -5.68
 537 HIS   ( 549-)  A      -5.64
 254 PRO   ( 266-)  A      -5.51
1048 PRO   ( 266-)  C      -5.51
1400 ARG   (  93-)  D      -5.46
 322 HIS   ( 334-)  A      -5.43
1333 PHE   ( 551-)  C      -5.39
1116 HIS   ( 334-)  C      -5.38
1396 LYS   (  89-)  D      -5.34
 246 ASN   ( 258-)  A      -5.31
1040 ASN   ( 258-)  C      -5.30
 945 ASN   ( 163-)  C      -5.29
 151 ASN   ( 163-)  A      -5.28
 755 ARG   ( 244-)  B      -5.14
 464 ARG   ( 476-)  A      -5.10
   7 ARG   (  19-)  A      -5.09
 851 GLU   (  69-)  C      -5.09
1039 ARG   ( 257-)  C      -5.08
1258 ARG   ( 476-)  C      -5.07
 245 ARG   ( 257-)  A      -5.05
 869 ASN   (  87-)  C      -5.05

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.

 150 GLY   ( 162-)  A       153 - GLN    165- ( A)         -4.83
 245 ARG   ( 257-)  A       247 - PHE    259- ( A)         -4.97
 254 PRO   ( 266-)  A       256 - GLY    268- ( A)         -4.76
 944 GLY   ( 162-)  C       947 - GLN    165- ( C)         -4.85
1039 ARG   ( 257-)  C      1041 - PHE    259- ( C)         -5.03
1048 PRO   ( 266-)  C      1050 - GLY    268- ( C)         -4.77

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1120 ALA   ( 338-)  C   -2.73
 326 ALA   ( 338-)  A   -2.63

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

  53 ALA   (  65-)  A     -   56 LEU   (  68-)  A        -1.69

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

1652 HOH   ( 695 )  C      O    -78.52  -19.42  -98.12

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.

1650 HOH   (1631 )  A      O
1652 HOH   ( 707 )  C      O
1652 HOH   ( 711 )  C      O
1652 HOH   ( 740 )  C      O
1652 HOH   ( 752 )  C      O
Metal-coordinating Histidine residue 272 fixed to   1
Metal-coordinating Histidine residue 321 fixed to   1
Metal-coordinating Histidine residue 322 fixed to   1
Metal-coordinating Histidine residue 399 fixed to   1
Metal-coordinating Histidine residue  90 fixed to   1
Metal-coordinating Histidine residue 409 fixed to   1
Metal-coordinating Histidine residue 407 fixed to   1
Metal-coordinating Histidine residue 771 fixed to   1
Metal-coordinating Histidine residue 728 fixed to   1
Metal-coordinating Histidine residue 794 fixed to   1
Metal-coordinating Histidine residue 796 fixed to   1
Metal-coordinating Histidine residue 607 fixed to   1
Metal-coordinating Histidine residue 795 fixed to   1
Metal-coordinating Histidine residue 797 fixed to   1
Metal-coordinating Histidine residue1066 fixed to   1
Metal-coordinating Histidine residue1115 fixed to   1
Metal-coordinating Histidine residue1116 fixed to   1
Metal-coordinating Histidine residue1193 fixed to   1
Metal-coordinating Histidine residue 884 fixed to   1
Metal-coordinating Histidine residue1203 fixed to   1
Metal-coordinating Histidine residue1201 fixed to   1
Metal-coordinating Histidine residue1567 fixed to   1
Metal-coordinating Histidine residue1524 fixed to   1
Metal-coordinating Histidine residue1590 fixed to   1
Metal-coordinating Histidine residue1592 fixed to   1
Metal-coordinating Histidine residue1403 fixed to   1

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  49 GLN   (  61-)  A
 128 ASN   ( 140-)  A
 762 GLN   ( 251-)  B
 843 GLN   (  61-)  C
 922 ASN   ( 140-)  C
1331 HIS   ( 549-)  C
1485 GLN   ( 178-)  D
1486 GLN   ( 179-)  D
1558 GLN   ( 251-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   7 ARG   (  19-)  A      NE
  40 ARG   (  52-)  A      NH1
  49 GLN   (  61-)  A      NE2
  83 TRP   (  95-)  A      NE1
 114 LEU   ( 126-)  A      N
 160 TRP   ( 172-)  A      N
 160 TRP   ( 172-)  A      NE1
 161 VAL   ( 173-)  A      N
 272 HIS   ( 284-)  A      NE2
 276 TYR   ( 288-)  A      OH
 282 ALA   ( 294-)  A      N
 320 ALA   ( 332-)  A      N
 360 GLY   ( 372-)  A      N
 366 LYS   ( 378-)  A      N
 371 TRP   ( 383-)  A      NE1
 391 GLN   ( 403-)  A      NE2
 402 TYR   ( 414-)  A      OH
 415 GLY   ( 427-)  A      N
 439 TRP   ( 451-)  A      NE1
 459 GLN   ( 471-)  A      NE2
 469 ARG   ( 481-)  A      NH2
 470 ARG   ( 482-)  A      N
 470 ARG   ( 482-)  A      NE
 473 ASP   ( 485-)  A      N
 518 TYR   ( 530-)  A      N
And so on for a total of 83 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.

 115 HIS   ( 127-)  A      ND1
 274 GLU   ( 286-)  A      OE2
 395 ASP   ( 407-)  A      OD1
 459 GLN   ( 471-)  A      OE1
 909 HIS   ( 127-)  C      ND1
1068 GLU   ( 286-)  C      OE2
1189 ASP   ( 407-)  C      OD1
1253 GLN   ( 471-)  C      OE1

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+.

1613  CA   ( 571-)  C     0.92   1.16 Scores about as good as NA

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.

1650 HOH   (1508 )  A      O  1.07  K  4
1650 HOH   (1605 )  A      O  0.91  K  4 Ion-B
1651 HOH   (1111 )  B      O  1.05  K  5
1652 HOH   ( 683 )  C      O  1.12  K  6 Ion-B
1652 HOH   ( 697 )  C      O  0.85  K  5 Ion-B NCS 1/1
1653 HOH   ( 368 )  D      O  1.00  K  4 NCS 1/1
1653 HOH   ( 375 )  D      O  1.03  K  4 NCS 1/1
1653 HOH   ( 384 )  D      O  0.93  K  4 Ion-B

Warning: Possible wrong residue type

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

 244 ASP   ( 256-)  A   H-bonding suggests Asn; but Alt-Rotamer
 274 GLU   ( 286-)  A   H-bonding suggests Gln
1038 ASP   ( 256-)  C   H-bonding suggests Asn; but Alt-Rotamer
1068 GLU   ( 286-)  C   H-bonding suggests Gln
1318 ASP   ( 536-)  C   H-bonding suggests Asn; Ligand-contact
1502 ASP   ( 195-)  D   H-bonding suggests Asn

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 :  -0.527
  2nd generation packing quality :  -0.588
  Ramachandran plot appearance   :  -0.500
  chi-1/chi-2 rotamer normality  :  -0.803
  Backbone conformation          :   0.330

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.631 (tight)
  Omega angle restraints         :   1.011
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.677
  B-factor distribution          :   0.574
  Inside/Outside distribution    :   1.181 (unusual)

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 : 2.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.631 (tight)
  Omega angle restraints         :   1.011
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.677
  B-factor distribution          :   0.574
  Inside/Outside distribution    :   1.181 (unusual)
==============

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.