WHAT IF Check report

This file was created 2011-12-17 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 pdb3q1k.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  85.153  B   =  85.813  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  85.153  B   =  85.813  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  85.813  B   =  85.153  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 21

Bravais type of conventional cell is: P

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 : 4.354
CA-only RMS fit for the two chains : 3.760

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

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 3 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

1404 ADP   ( 370-)  A  -
1407 ADP   ( 370-)  B  -
1414 ADP   ( 370-)  C  -
1420 ADP   ( 370-)  D  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 495 MSE   ( 139-)  B  -
1027 ILE   ( 343-)  C  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 495 MSE   ( 139-)  B  -
1027 ILE   ( 343-)  C  -

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

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

Warning: B-factors outside the range 0.0 - 100.0

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

  52 ASP   (  53-)  A    High
  54 GLU   (  55-)  A    High
  55 ASN   (  56-)  A    High
  58 GLN   (  59-)  A    High
  59 ASN   (  60-)  A    High
  61 ASP   (  62-)  A    High
  62 ASP   (  63-)  A    High
  63 PRO   (  64-)  A    High
  64 ALA   (  65-)  A    High
  65 HIS   (  66-)  A    High
  69 ARG   (  70-)  A    High
  73 ILE   (  74-)  A    High
 166 HIS   ( 167-)  A    High
 169 SER   ( 170-)  A    High
 172 GLU   ( 173-)  A    High
 174 GLU   ( 175-)  A    High
 176 ARG   ( 177-)  A    High
 200 GLU   ( 201-)  A    High
 253 LYS   ( 259-)  A    High
 254 TYR   ( 260-)  A    High
 258 ASN   ( 264-)  A    High
 271 GLU   ( 277-)  A    High
 411 GLU   (  55-)  B    High
 421 ALA   (  65-)  B    High
 422 HIS   (  66-)  B    High
And so on for a total of 69 lines.

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

 118 MSE   ( 119-)  A    0.81
 138 MSE   ( 139-)  A    0.80
 292 MSE   ( 298-)  A    0.80
 321 MSE   ( 327-)  A    0.78
 475 MSE   ( 119-)  B    0.79
 638 MSE   ( 298-)  B    0.80
 667 MSE   ( 327-)  B    0.77
 821 MSE   ( 119-)  C    0.74
 841 MSE   ( 139-)  C    0.77
1011 MSE   ( 327-)  C    0.75
1048 MSE   ( 364-)  C    0.74
1165 MSE   ( 119-)  D    0.77
1185 MSE   ( 139-)  D    0.76
1338 MSE   ( 298-)  D    0.79
1367 MSE   ( 327-)  D    0.78

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: 4

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.

 120 ARG   ( 121-)  A
 347 ARG   ( 353-)  A
 519 ARG   ( 163-)  B
1167 ARG   ( 121-)  D
1209 ARG   ( 163-)  D

Warning: Tyrosine convention problem

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

  56 TYR   (  57-)  A
 284 TYR   ( 290-)  A
 322 TYR   ( 328-)  A
 413 TYR   (  57-)  B
 668 TYR   ( 328-)  B
 759 TYR   (  57-)  C
 974 TYR   ( 290-)  C
1012 TYR   ( 328-)  C
1103 TYR   (  57-)  D
1368 TYR   ( 328-)  D

Warning: Phenylalanine convention problem

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

   9 PHE   (  10-)  A
 102 PHE   ( 103-)  A
 157 PHE   ( 158-)  A
 182 PHE   ( 183-)  A
 211 PHE   ( 212-)  A
 316 PHE   ( 322-)  A
 366 PHE   (  10-)  B
 459 PHE   ( 103-)  B
 514 PHE   ( 158-)  B
 525 PHE   ( 169-)  B
 539 PHE   ( 183-)  B
 568 PHE   ( 212-)  B
 712 PHE   (  10-)  C
 805 PHE   ( 103-)  C
 860 PHE   ( 158-)  C
 871 PHE   ( 169-)  C
 885 PHE   ( 183-)  C
 914 PHE   ( 212-)  C
1056 PHE   (  10-)  D
1149 PHE   ( 103-)  D
1204 PHE   ( 158-)  D
1229 PHE   ( 183-)  D
1258 PHE   ( 212-)  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.

  28 ASP   (  29-)  A
  61 ASP   (  62-)  A
 130 ASP   ( 131-)  A
 400 ASP   (  44-)  B
 487 ASP   ( 131-)  B
 746 ASP   (  44-)  C
 764 ASP   (  62-)  C
 833 ASP   ( 131-)  C
 852 ASP   ( 150-)  C
1090 ASP   (  44-)  D
1108 ASP   (  62-)  D
1177 ASP   ( 131-)  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.

  15 GLU   (  16-)  A
 172 GLU   ( 173-)  A
 200 GLU   ( 201-)  A
 220 GLU   ( 221-)  A
 227 GLU   ( 228-)  A
 229 GLU   ( 230-)  A
 251 GLU   ( 252-)  A
 271 GLU   ( 277-)  A
 309 GLU   ( 315-)  A
 529 GLU   ( 173-)  B
 557 GLU   ( 201-)  B
 584 GLU   ( 228-)  B
 655 GLU   ( 315-)  B
 688 GLU   ( 348-)  B
 692 GLU   ( 352-)  B
 875 GLU   ( 173-)  C
 877 GLU   ( 175-)  C
 915 GLU   ( 213-)  C
 930 GLU   ( 228-)  C
 932 GLU   ( 230-)  C
 961 GLU   ( 277-)  C
1101 GLU   (  55-)  D
1219 GLU   ( 173-)  D
1221 GLU   ( 175-)  D
1259 GLU   ( 213-)  D
1350 GLU   ( 310-)  D
1388 GLU   ( 348-)  D
1392 GLU   ( 352-)  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

 |  0.998785 -0.000014  0.000497|
 | -0.000014  0.999449  0.000063|
 |  0.000497  0.000063  0.999486|
Proposed new scale matrix

 |  0.011758  0.000000 -0.000006|
 |  0.000000  0.011659  0.000000|
 | -0.000002  0.000000  0.004333|
With corresponding cell

    A    =  85.046  B   =  85.768  C    = 230.775
    Alpha=  90.002  Beta=  89.943  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  85.153  B   =  85.813  C    = 230.893
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 30.155
(Under-)estimated Z-score: 4.047

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.

1147 VAL   ( 101-)  D      C    CA   CB  101.34   -4.6

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.

  15 GLU   (  16-)  A
  28 ASP   (  29-)  A
  61 ASP   (  62-)  A
 120 ARG   ( 121-)  A
 130 ASP   ( 131-)  A
 172 GLU   ( 173-)  A
 200 GLU   ( 201-)  A
 220 GLU   ( 221-)  A
 227 GLU   ( 228-)  A
 229 GLU   ( 230-)  A
 251 GLU   ( 252-)  A
 271 GLU   ( 277-)  A
 309 GLU   ( 315-)  A
 347 ARG   ( 353-)  A
 400 ASP   (  44-)  B
 487 ASP   ( 131-)  B
 519 ARG   ( 163-)  B
 529 GLU   ( 173-)  B
 557 GLU   ( 201-)  B
 584 GLU   ( 228-)  B
 655 GLU   ( 315-)  B
 688 GLU   ( 348-)  B
 692 GLU   ( 352-)  B
 746 ASP   (  44-)  C
 764 ASP   (  62-)  C
 833 ASP   ( 131-)  C
 852 ASP   ( 150-)  C
 875 GLU   ( 173-)  C
 877 GLU   ( 175-)  C
 915 GLU   ( 213-)  C
 930 GLU   ( 228-)  C
 932 GLU   ( 230-)  C
 961 GLU   ( 277-)  C
1090 ASP   (  44-)  D
1101 GLU   (  55-)  D
1108 ASP   (  62-)  D
1167 ARG   ( 121-)  D
1177 ASP   ( 131-)  D
1209 ARG   ( 163-)  D
1219 GLU   ( 173-)  D
1221 GLU   ( 175-)  D
1259 GLU   ( 213-)  D
1350 GLU   ( 310-)  D
1388 GLU   ( 348-)  D
1392 GLU   ( 352-)  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.

  29 ALA   (  30-)  A    4.43

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.

1151 ILE   ( 105-)  D    -2.8
1112 HIS   (  66-)  D    -2.8
 104 ILE   ( 105-)  A    -2.8
 461 ILE   ( 105-)  B    -2.7
 811 THR   ( 109-)  C    -2.7
 807 ILE   ( 105-)  C    -2.7
 190 SER   ( 191-)  A    -2.6
1359 LEU   ( 319-)  D    -2.6
 659 LEU   ( 319-)  B    -2.6
1156 LEU   ( 110-)  D    -2.5
 547 SER   ( 191-)  B    -2.5
 154 ILE   ( 155-)  A    -2.5
1237 SER   ( 191-)  D    -2.4
1365 ILE   ( 325-)  D    -2.4
1205 ILE   ( 159-)  D    -2.4
 158 ILE   ( 159-)  A    -2.4
1238 SER   ( 192-)  D    -2.4
 861 ILE   ( 159-)  C    -2.3
 191 SER   ( 192-)  A    -2.3
 548 SER   ( 192-)  B    -2.3
  40 LEU   (  41-)  A    -2.3
 894 SER   ( 192-)  C    -2.3
 188 GLN   ( 189-)  A    -2.3
1147 VAL   ( 101-)  D    -2.3
1009 ILE   ( 325-)  C    -2.2
1087 LEU   (  41-)  D    -2.2
 743 LEU   (  41-)  C    -2.2
1130 GLN   (  84-)  D    -2.2
 665 ILE   ( 325-)  B    -2.2
 287 LEU   ( 293-)  A    -2.2
 977 LEU   ( 293-)  C    -2.1
1333 LEU   ( 293-)  D    -2.1
 940 ASN   ( 238-)  C    -2.1
 803 VAL   ( 101-)  C    -2.1
1235 GLN   ( 189-)  D    -2.1
 614 ILE   ( 274-)  B    -2.1
 459 PHE   ( 103-)  B    -2.1
 457 VAL   ( 101-)  B    -2.1
 805 PHE   ( 103-)  C    -2.1
 893 SER   ( 191-)  C    -2.0
 100 VAL   ( 101-)  A    -2.0
 545 GLN   ( 189-)  B    -2.0
 613 GLN   ( 273-)  B    -2.0
1314 ILE   ( 274-)  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.

  35 PHE   (  36-)  A  omega poor
  59 ASN   (  60-)  A  Poor phi/psi
  84 HIS   (  85-)  A  Poor phi/psi
 107 GLY   ( 108-)  A  omega poor
 109 LEU   ( 110-)  A  Poor phi/psi
 176 ARG   ( 177-)  A  omega poor
 179 LEU   ( 180-)  A  PRO omega poor
 190 SER   ( 191-)  A  Poor phi/psi
 191 SER   ( 192-)  A  Poor phi/psi
 235 ASN   ( 236-)  A  Poor phi/psi
 257 ASP   ( 263-)  A  Poor phi/psi
 264 VAL   ( 270-)  A  PRO omega poor
 267 GLN   ( 273-)  A  Poor phi/psi
 303 ASN   ( 309-)  A  Poor phi/psi
 391 ARG   (  35-)  B  omega poor
 422 HIS   (  66-)  B  Poor phi/psi
 430 ILE   (  74-)  B  omega poor
 451 PRO   (  95-)  B  omega poor
 466 LEU   ( 110-)  B  Poor phi/psi
 480 ASN   ( 124-)  B  Poor phi/psi
 536 LEU   ( 180-)  B  PRO omega poor
 547 SER   ( 191-)  B  Poor phi/psi
 548 SER   ( 192-)  B  Poor phi/psi
 592 ASN   ( 236-)  B  Poor phi/psi
 610 VAL   ( 270-)  B  PRO omega poor
 649 ASN   ( 309-)  B  Poor phi/psi
 738 PHE   (  36-)  C  omega poor
 762 ASN   (  60-)  C  Poor phi/psi
 768 HIS   (  66-)  C  Poor phi/psi
 794 ASN   (  92-)  C  Poor phi/psi
 810 GLY   ( 108-)  C  omega poor
 860 PHE   ( 158-)  C  omega poor
 882 LEU   ( 180-)  C  PRO omega poor
 894 SER   ( 192-)  C  Poor phi/psi
 938 ASN   ( 236-)  C  Poor phi/psi
 954 VAL   ( 270-)  C  PRO omega poor
 993 ASN   ( 309-)  C  Poor phi/psi
1005 GLY   ( 321-)  C  Poor phi/psi
1106 ASN   (  60-)  D  Poor phi/psi
1112 HIS   (  66-)  D  Poor phi/psi
1156 LEU   ( 110-)  D  Poor phi/psi
1226 LEU   ( 180-)  D  PRO omega poor
1237 SER   ( 191-)  D  Poor phi/psi
1238 SER   ( 192-)  D  Poor phi/psi
1282 ASN   ( 236-)  D  Poor phi/psi
1288 SER   ( 242-)  D  omega poor
1303 ASP   ( 263-)  D  Poor phi/psi
1304 ASN   ( 264-)  D  Poor phi/psi
1310 VAL   ( 270-)  D  PRO omega poor
1349 ASN   ( 309-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.044

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 722 SER   (  20-)  C    0.35
1069 SER   (  23-)  D    0.35
  22 SER   (  23-)  A    0.35
1384 SER   ( 344-)  D    0.35
1180 SER   ( 134-)  D    0.36
1028 SER   ( 344-)  C    0.36
 175 SER   ( 176-)  A    0.36
 532 SER   ( 176-)  B    0.36
 837 SER   ( 135-)  C    0.37
 490 SER   ( 134-)  B    0.38
 134 SER   ( 135-)  A    0.39
 379 SER   (  23-)  B    0.40

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 PHE   (  10-)  A      0
  12 LYS   (  13-)  A      0
  30 ILE   (  31-)  A      0
  34 ARG   (  35-)  A      0
  48 TRP   (  49-)  A      0
  55 ASN   (  56-)  A      0
  56 TYR   (  57-)  A      0
  58 GLN   (  59-)  A      0
  59 ASN   (  60-)  A      0
  79 PRO   (  80-)  A      0
  81 LYS   (  82-)  A      0
  83 GLN   (  84-)  A      0
  84 HIS   (  85-)  A      0
  85 GLN   (  86-)  A      0
  88 ASN   (  89-)  A      0
  91 ASN   (  92-)  A      0
  97 THR   (  98-)  A      0
 103 PRO   ( 104-)  A      0
 104 ILE   ( 105-)  A      0
 106 HIS   ( 107-)  A      0
 108 THR   ( 109-)  A      0
 109 LEU   ( 110-)  A      0
 111 GLU   ( 112-)  A      0
 112 ASP   ( 113-)  A      0
 118 MSE   ( 119-)  A      0
And so on for a total of 470 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  70 PRO   (  71-)  A  -122.4 half-chair C-delta/C-gamma (-126 degrees)
 103 PRO   ( 104-)  A   -64.7 envelop C-beta (-72 degrees)
 542 PRO   ( 186-)  B    46.1 half-chair C-delta/C-gamma (54 degrees)
 595 PRO   ( 239-)  B   -63.9 envelop C-beta (-72 degrees)
 766 PRO   (  64-)  C   119.7 half-chair C-beta/C-alpha (126 degrees)
 782 PRO   (  80-)  C  -116.1 envelop C-gamma (-108 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.

  32 LYS   (  33-)  A      CE  <-> 1421 HOH   ( 435 )  A      O      0.66    2.14  INTRA BF
  58 GLN   (  59-)  A      NE2 <->   69 ARG   (  70-)  A      CD     0.42    2.68  INTRA BF
 815 ASP   ( 113-)  C      OD2 <-> 1167 ARG   ( 121-)  D      NH2    0.41    2.29  INTRA BF
 162 ARG   ( 163-)  A      NH1 <->  215 HIS   ( 216-)  A      CD2    0.38    2.72  INTRA BF
 833 ASP   ( 131-)  C      OD2 <-> 1037 ARG   ( 353-)  C      NH2    0.37    2.33  INTRA BF
 191 SER   ( 192-)  A      N   <-> 1404 ADP   ( 370-)  A      O2B    0.36    2.34  INTRA BF
1072 ASN   (  26-)  D      ND2 <-> 1364 ASN   ( 324-)  D      N      0.30    2.55  INTRA BL
 765 ASP   (  63-)  C      CG  <->  767 ALA   (  65-)  C      O      0.30    2.50  INTRA BF
1290 CYS   ( 244-)  D      SG  <-> 1319 ASN   ( 279-)  D      ND2    0.30    3.00  INTRA BL
1076 ALA   (  30-)  D      CB  <-> 1379 TYR   ( 339-)  D    A CD2    0.30    2.90  INTRA BL
 223 ILE   ( 224-)  A      N   <-> 1404 ADP   ( 370-)  A      N1     0.29    2.71  INTRA BL
1301 ILE   ( 261-)  D      CG2 <-> 1305 GLY   ( 265-)  D      N      0.28    2.82  INTRA BF
 301 ALA   ( 307-)  A      N   <-> 1421 HOH   ( 476 )  A      O      0.28    2.42  INTRA BF
1270 ILE   ( 224-)  D      N   <-> 1420 ADP   ( 370-)  D      N1     0.27    2.73  INTRA BL
 580 ILE   ( 224-)  B      N   <-> 1407 ADP   ( 370-)  B      N1     0.27    2.73  INTRA BL
 811 THR   ( 109-)  C      CG2 <->  812 LEU   ( 110-)  C      N      0.26    2.74  INTRA BF
1238 SER   ( 192-)  D      N   <-> 1420 ADP   ( 370-)  D      O2B    0.26    2.44  INTRA BF
1236 GLY   ( 190-)  D      O   <-> 1239 VAL   ( 193-)  D      CG1    0.26    2.54  INTRA BF
 926 ILE   ( 224-)  C      N   <-> 1414 ADP   ( 370-)  C      N1     0.25    2.75  INTRA BF
 519 ARG   ( 163-)  B      NH2 <-> 1422 HOH   ( 461 )  B      O      0.24    2.46  INTRA BF
  58 GLN   (  59-)  A      CG  <->   69 ARG   (  70-)  A      CD     0.23    2.97  INTRA BF
 762 ASN   (  60-)  C      ND2 <->  768 HIS   (  66-)  C      O      0.23    2.47  INTRA BF
1038 HIS   ( 354-)  C      ND1 <-> 1417 GOL   ( 372-)  C      O1     0.23    2.47  INTRA BF
 809 HIS   ( 107-)  C      NE2 <-> 1423 HOH   ( 440 )  C      O      0.22    2.48  INTRA BF
1038 HIS   ( 354-)  C      CB  <-> 1417 GOL   ( 372-)  C      C3     0.22    2.98  INTRA BF
And so on for a total of 167 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

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.

 267 GLN   ( 273-)  A      -6.63
1313 GLN   ( 273-)  D      -6.59
 957 GLN   ( 273-)  C      -6.58
 715 LYS   (  13-)  C      -6.04
 447 GLN   (  91-)  B      -5.88
 613 GLN   ( 273-)  B      -5.81
1137 GLN   (  91-)  D      -5.80
  90 GLN   (  91-)  A      -5.69
 785 HIS   (  83-)  C      -5.68
1271 LYS   ( 225-)  D      -5.67
1129 HIS   (  83-)  D      -5.67
  82 HIS   (  83-)  A      -5.64
1223 ARG   ( 177-)  D      -5.61
 581 LYS   ( 225-)  B      -5.61
 879 ARG   ( 177-)  C      -5.60
 176 ARG   ( 177-)  A      -5.59
 927 LYS   ( 225-)  C      -5.57
 533 ARG   ( 177-)  B      -5.55
 224 LYS   ( 225-)  A      -5.47
 369 LYS   (  13-)  B      -5.46
 439 HIS   (  83-)  B      -5.45
1003 LEU   ( 319-)  C      -5.44
 188 GLN   ( 189-)  A      -5.39
1235 GLN   ( 189-)  D      -5.14
1304 ASN   ( 264-)  D      -5.13
 545 GLN   ( 189-)  B      -5.04
 258 ASN   ( 264-)  A      -5.03
  12 LYS   (  13-)  A      -5.00

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.

 257 ASP   ( 263-)  A       259 - GLY    265- ( A)         -4.45
1303 ASP   ( 263-)  D      1305 - GLY    265- ( D)         -4.48

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.

1169 ALA   ( 123-)  D   -2.55
 122 ALA   ( 123-)  A   -2.54
 718 GLU   (  16-)  C   -2.53
1062 GLU   (  16-)  D   -2.51

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

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.

1421 HOH   ( 446 )  A      O
1422 HOH   ( 454 )  B      O
1422 HOH   ( 458 )  B      O
1423 HOH   ( 407 )  C      O
1423 HOH   ( 457 )  C      O
1423 HOH   ( 458 )  C      O
1423 HOH   ( 473 )  C      O
1424 HOH   ( 383 )  D      O
1424 HOH   ( 438 )  D      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.

  51 ASN   (  52-)  A
  58 GLN   (  59-)  A
 106 HIS   ( 107-)  A
 164 ASN   ( 165-)  A
 187 ASN   ( 188-)  A
 215 HIS   ( 216-)  A
 239 GLN   ( 240-)  A
 267 GLN   ( 273-)  A
 327 GLN   ( 333-)  A
 378 GLN   (  22-)  B
 434 GLN   (  78-)  B
 450 GLN   (  94-)  B
 463 HIS   ( 107-)  B
 480 ASN   ( 124-)  B
 572 HIS   ( 216-)  B
 619 ASN   ( 279-)  B
 728 ASN   (  26-)  C
 796 GLN   (  94-)  C
 826 ASN   ( 124-)  C
 856 ASN   ( 154-)  C
 867 ASN   ( 165-)  C
 890 ASN   ( 188-)  C
 908 GLN   ( 206-)  C
 918 HIS   ( 216-)  C
 993 ASN   ( 309-)  C
1124 GLN   (  78-)  D
1153 HIS   ( 107-)  D
1262 HIS   ( 216-)  D
1313 GLN   ( 273-)  D
1319 ASN   ( 279-)  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.

  13 SER   (  14-)  A      N
  50 VAL   (  51-)  A      N
  54 GLU   (  55-)  A      N
  77 GLN   (  78-)  A      NE2
 105 VAL   ( 106-)  A      N
 112 ASP   ( 113-)  A      N
 168 PHE   ( 169-)  A      N
 191 SER   ( 192-)  A      N
 216 LYS   ( 217-)  A      N
 252 PHE   ( 253-)  A      N
 254 TYR   ( 260-)  A      N
 255 ILE   ( 261-)  A      N
 261 GLN   ( 267-)  A      NE2
 302 ASP   ( 308-)  A      N
 356 THR   ( 362-)  A      N
 407 VAL   (  51-)  B      N
 426 ARG   (  70-)  B      NH1
 434 GLN   (  78-)  B      NE2
 440 GLN   (  84-)  B      N
 441 HIS   (  85-)  B      N
 462 VAL   ( 106-)  B      N
 463 HIS   ( 107-)  B      N
 469 ASP   ( 113-)  B      N
 497 LYS   ( 141-)  B      NZ
 525 PHE   ( 169-)  B      N
And so on for a total of 64 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.

  65 HIS   (  66-)  A      ND1
  77 GLN   (  78-)  A      OE1
 309 GLU   ( 315-)  A      OE1
 408 ASN   (  52-)  B      OD1
 780 GLN   (  78-)  C      OE1
1096 HIS   (  50-)  D      ND1
1098 ASN   (  52-)  D      OD1
1276 GLU   ( 230-)  D      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+.

1405  MG   ( 372-)  A     0.51   1.02 Is perhaps NA
1408  MG   ( 371-)  B   -.-  -.-  Low probability ion. B= 86.0
1418  MG   ( 372-)  D     0.58   0.93 Is perhaps CA

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.

1422 HOH   ( 441 )  B      O  0.91  K  4

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.

 112 ASP   ( 113-)  A   H-bonding suggests Asn; but Alt-Rotamer
 309 GLU   ( 315-)  A   H-bonding suggests Gln; Ligand-contact
 419 ASP   (  63-)  B   H-bonding suggests Asn
 655 GLU   ( 315-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 731 ASP   (  29-)  C   H-bonding suggests Asn
 765 ASP   (  63-)  C   H-bonding suggests Asn; but Alt-Rotamer
 814 GLU   ( 112-)  C   H-bonding suggests Gln
 815 ASP   ( 113-)  C   H-bonding suggests Asn; but Alt-Rotamer
1109 ASP   (  63-)  D   H-bonding suggests Asn
1159 ASP   ( 113-)  D   H-bonding suggests Asn; but Alt-Rotamer
1219 GLU   ( 173-)  D   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.909
  2nd generation packing quality :  -0.519
  Ramachandran plot appearance   :   0.346
  chi-1/chi-2 rotamer normality  :  -2.044
  Backbone conformation          :   1.306

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.428 (tight)
  Bond angles                    :   0.629 (tight)
  Omega angle restraints         :   0.951
  Side chain planarity           :   0.447 (tight)
  Improper dihedral distribution :   0.706
  B-factor distribution          :   1.185
  Inside/Outside distribution    :   0.970

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   1.4
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.428 (tight)
  Bond angles                    :   0.629 (tight)
  Omega angle restraints         :   0.951
  Side chain planarity           :   0.447 (tight)
  Improper dihedral distribution :   0.706
  B-factor distribution          :   1.185
  Inside/Outside distribution    :   0.970
==============

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.