WHAT IF Check report

This file was created 2011-12-22 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 pdb1evu.ent

Checks that need to be done early-on in validation

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.

1418 PGO   (1203-)  B  -
1419 SAC   (   1-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 539 PHE   ( 559-)  A  - A CD2  708 PHE   (   8-)  B  -   CZ
 539 PHE   ( 559-)  A  - A CE2  708 PHE   (   8-)  B  -   CE2
 539 PHE   ( 559-)  A  - A CE2  708 PHE   (   8-)  B  -   CZ
 539 PHE   ( 559-)  A  - A CZ   708 PHE   (   8-)  B  -   CD2
 539 PHE   ( 559-)  A  - A CZ   708 PHE   (   8-)  B  -   CE2

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 539 PHE   ( 559-)  A  -

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

   1 GLU   (   2-)  A  -   N   bound to 1418 SAC   (   1-)  A  -   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

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

Warning: Missing atoms

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

   4 ARG   (   5-)  A      CG
   4 ARG   (   5-)  A      CD
   4 ARG   (   5-)  A      NE
   4 ARG   (   5-)  A      CZ
   4 ARG   (   5-)  A      NH1
   4 ARG   (   5-)  A      NH2
1202 ARG   ( 515-)  B      CG
1202 ARG   ( 515-)  B      CD
1202 ARG   ( 515-)  B      NE
1202 ARG   ( 515-)  B      CZ
1202 ARG   ( 515-)  B      NH1
1202 ARG   ( 515-)  B      NH2

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.

   2 THR   (   3-)  A    0.50
   3 SER   (   4-)  A    0.40
   4 ARG   (   5-)  A    0.40
   5 THR   (   6-)  A    0.70

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

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

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 118 GLY   ( 131-)  A      N    CA    1.52    4.1

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

 |  0.996002 -0.000821  0.000934|
 | -0.000821  0.999600  0.000481|
 |  0.000934  0.000481  0.998639|
Proposed new scale matrix

 |  0.010020  0.000007  0.002878|
 |  0.000012  0.014137 -0.000007|
 | -0.000007 -0.000004  0.007789|
With corresponding cell

    A    =  99.770  B   =  70.738  C    = 133.546
    Alpha=  89.921  Beta= 105.969  Gamma=  90.094

The CRYST1 cell dimensions

    A    = 100.172  B   =  70.764  C    = 133.822
    Alpha=  90.000  Beta= 106.110  Gamma=  90.000

Variance: 240.068
(Under-)estimated Z-score: 11.419

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.

  33 ASN   (  46-)  A      N    CA   CB  102.05   -5.0
  33 ASN   (  46-)  A      ND2  CG   OD1 128.96    6.4
  38 HIS   (  51-)  A     -O   -C    N   116.27   -4.2
  52 HIS   (  65-)  A      CG   ND1  CE1 112.74    7.1
  52 HIS   (  65-)  A      ND1  CE1  NE2 105.17   -5.0
  63 VAL   (  76-)  A      N    CA   CB  117.71    4.2
  71 VAL   (  84-)  A      CA   C    O   113.62   -4.2
  72 GLN   (  85-)  A     -O   -C    N   129.61    4.1
  72 GLN   (  85-)  A      N    CA   CB  102.93   -4.5
  73 ILE   (  86-)  A      C    CA   CB  102.34   -4.1
  87 ARG   ( 100-)  A      C    CA   CB  118.91    4.6
  87 ARG   ( 100-)  A      CG   CD   NE  118.92    4.9
  87 ARG   ( 100-)  A      CD   NE   CZ  142.61   11.6
  91 VAL   ( 104-)  A      C    CA   CB  119.91    5.2
  91 VAL   ( 104-)  A      CA   CB   CG2 121.08    6.2
  94 ARG   ( 107-)  A      CD   NE   CZ  130.78    5.0
 117 TRP   ( 130-)  A     -C    N    CA  114.31   -4.1
 118 GLY   ( 131-)  A     -C    N    CA  112.40   -4.8
 130 ARG   ( 143-)  A      CD   NE   CZ  132.49    6.0
 134 GLN   ( 147-)  A      NE2  CD   OE1 133.58   11.0
 145 ARG   ( 158-)  A      CG   CD   NE  118.54    4.7
 145 ARG   ( 158-)  A      CD   NE   CZ  132.62    6.1
 147 TYR   ( 160-)  A      N    CA   CB  117.34    4.0
 171 PHE   ( 184-)  A      CA   CB   CG  109.75   -4.0
 180 VAL   ( 193-)  A      N    CA   CB  102.42   -4.8
And so on for a total of 236 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

  37 VAL   (  50-)  A      C     -6.5    -8.76     0.15
  91 VAL   ( 104-)  A      CA    -6.5    23.83    33.23
  92 ILE   ( 105-)  A      C    -10.3   -13.51     0.03
 105 PRO   ( 118-)  A      N      6.3    18.04    -2.48
 161 ARG   ( 174-)  A      C      6.2     9.53     0.13
 180 VAL   ( 193-)  A      CB     7.0   -23.73   -32.96
 196 ILE   ( 209-)  A      C     -6.8    -8.85     0.03
 236 LEU   ( 249-)  A      C      6.3    10.12     0.20
 264 GLY   ( 277-)  A      C     -6.6    -8.60     0.06
 276 PRO   ( 289-)  A      N     -6.3   -23.21    -2.48
 276 PRO   ( 289-)  A      C     -6.0    -9.11     0.42
 405 LYS   ( 418-)  A      C      6.5     9.89     0.11
 486 MET   ( 499-)  A      C     -6.4    -9.40     0.17
 636 LEU   ( 656-)  A      CG    -6.5   -44.38   -33.01
 715 PRO   (  16-)  B      N      7.2    21.06    -2.48
 728 VAL   (  29-)  B      C     -7.4    -9.93     0.15
 731 GLN   (  32-)  B      C      7.3    11.49     0.15
 768 ILE   (  75-)  B      C     -9.1   -11.93     0.03
 797 VAL   ( 104-)  B      CB     8.8   -21.41   -32.96
 847 VAL   ( 154-)  B      C     -6.7    -9.01     0.15
 852 MET   ( 159-)  B      C     -6.3    -9.18     0.17
 886 VAL   ( 193-)  B      CB    10.9   -18.63   -32.96
 908 GLY   ( 215-)  B      C      6.6     8.75     0.06
1158 VAL   ( 465-)  B      CB     9.3   -20.84   -32.96
1164 GLY   ( 471-)  B      C      6.5     8.69     0.06
1244 ILE   ( 557-)  B      C     -7.5    -9.76     0.03
1291 LEU   ( 604-)  B      C      7.3    11.74     0.20
1319 ILE   ( 632-)  B      C     -9.1   -11.89     0.03
The average deviation= 2.075

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.

1071 ALA   ( 378-)  B    4.33
 834 SER   ( 141-)  B    4.16
 774 SER   (  81-)  B    4.13
 731 GLN   (  32-)  B    4.05

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 446 HIS   ( 459-)  A    4.63
 241 ASN   ( 254-)  A    4.30
1152 HIS   ( 459-)  B    4.11
 360 HIS   ( 373-)  A    4.03

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.

 635 PRO   ( 655-)  A    -3.0
   5 THR   (   6-)  A    -2.7
 665 PRO   ( 685-)  A    -2.7
  83 ARG   (  96-)  A    -2.6
 209 THR   ( 222-)  A    -2.5
1310 LYS   ( 623-)  B    -2.5
 609 ILE   ( 629-)  A    -2.5
 976 TYR   ( 283-)  B    -2.4
 605 THR   ( 625-)  A    -2.4
 514 LYS   ( 534-)  A    -2.4
1360 THR   ( 673-)  B    -2.3
1156 LEU   ( 463-)  B    -2.3
 596 ARG   ( 616-)  A    -2.3
1403 HIS   ( 716-)  B    -2.3
 180 VAL   ( 193-)  A    -2.3
  32 LEU   (  45-)  A    -2.3
1348 ARG   ( 661-)  B    -2.2
 886 VAL   ( 193-)  B    -2.2
1197 LYS   ( 504-)  B    -2.2
  11 ARG   (  12-)  A    -2.2
 182 LEU   ( 195-)  A    -2.2
1391 LYS   ( 704-)  B    -2.2
1356 GLY   ( 669-)  B    -2.2
1408 LEU   ( 721-)  B    -2.2
 270 TYR   ( 283-)  A    -2.2
 696 HIS   ( 716-)  A    -2.2
1159 THR   ( 466-)  B    -2.2
 789 ARG   (  96-)  B    -2.1
 738 LEU   (  45-)  B    -2.1
 649 GLY   ( 669-)  A    -2.1
 474 GLN   ( 487-)  A    -2.1
1365 LYS   ( 678-)  B    -2.1
1155 LYS   ( 462-)  B    -2.1
1291 LEU   ( 604-)  B    -2.1
 916 ARG   ( 223-)  B    -2.1
 641 ARG   ( 661-)  A    -2.1
 581 GLN   ( 601-)  A    -2.1
 653 THR   ( 673-)  A    -2.1
 736 GLU   (  43-)  B    -2.1
1043 MET   ( 350-)  B    -2.0
  33 ASN   (  46-)  A    -2.0
 511 LYS   ( 531-)  A    -2.0
1233 ARG   ( 546-)  B    -2.0
 570 GLN   ( 590-)  A    -2.0
 563 LYS   ( 583-)  A    -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.

   2 THR   (   3-)  A  omega poor
   3 SER   (   4-)  A  omega poor
   5 THR   (   6-)  A  Poor phi/psi
  16 ASN   (  17-)  A  omega poor
  33 ASN   (  46-)  A  omega poor
  52 HIS   (  65-)  A  Poor phi/psi
  64 ARG   (  77-)  A  omega poor
  71 VAL   (  84-)  A  omega poor
 102 THR   ( 115-)  A  omega poor
 126 ASP   ( 139-)  A  Poor phi/psi
 131 LEU   ( 144-)  A  omega poor
 147 TYR   ( 160-)  A  omega poor
 201 TYR   ( 214-)  A  Poor phi/psi
 208 LYS   ( 221-)  A  omega poor
 213 SER   ( 226-)  A  omega poor
 257 ASP   ( 270-)  A  Poor phi/psi
 260 GLY   ( 273-)  A  omega poor
 268 ASN   ( 281-)  A  Poor phi/psi
 270 TYR   ( 283-)  A  Poor phi/psi
 271 ALA   ( 284-)  A  omega poor
 279 TRP   ( 292-)  A  Poor phi/psi
 293 GLU   ( 306-)  A  Poor phi/psi
 297 ARG   ( 310-)  A  omega poor
 326 PHE   ( 339-)  A  Poor phi/psi
 333 ALA   ( 346-)  A  Poor phi/psi
And so on for a total of 118 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.233

Warning: Unusual backbone conformations

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

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

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

   3 SER   (   4-)  A      0
   4 ARG   (   5-)  A      0
   5 THR   (   6-)  A      0
   6 ALA   (   7-)  A      0
  10 ARG   (  11-)  A      0
  11 ARG   (  12-)  A      0
  12 ALA   (  13-)  A      0
  16 ASN   (  17-)  A      0
  17 ASN   (  18-)  A      0
  21 ALA   (  22-)  A      0
  26 PRO   (  27-)  A      0
  28 VAL   (  29-)  A      0
  29 GLU   (  30-)  A      0
  30 GLU   (  43-)  A      0
  31 PHE   (  44-)  A      0
  32 LEU   (  45-)  A      0
  35 THR   (  48-)  A      0
  36 SER   (  49-)  A      0
  39 LEU   (  52-)  A      0
  41 LYS   (  54-)  A      0
  44 TRP   (  57-)  A      0
  52 HIS   (  65-)  A      0
  53 THR   (  66-)  A      0
  54 ASP   (  67-)  A      0
  56 TYR   (  69-)  A      0
And so on for a total of 629 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.866

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!

 649 GLY   ( 669-)  A   1.93   15
1179 GLY   ( 486-)  B   1.64   64

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  15 PRO   (  16-)  A    0.48 HIGH
  81 PRO   (  94-)  A    0.13 LOW
 163 PRO   ( 176-)  A    0.20 LOW
 370 PRO   ( 383-)  A    0.19 LOW
 492 PRO   ( 505-)  A    0.19 LOW
 655 PRO   ( 675-)  A    0.54 HIGH
 677 PRO   ( 697-)  A    0.15 LOW
 843 PRO   ( 150-)  B    0.49 HIGH
1317 PRO   ( 630-)  B    0.09 LOW
1384 PRO   ( 697-)  B    0.11 LOW

Warning: Unusual PRO puckering phases

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

  26 PRO   (  27-)  A  -137.8 envelop C-delta (-144 degrees)
 105 PRO   ( 118-)  A   -27.5 envelop C-alpha (-36 degrees)
 107 PRO   ( 120-)  A   -44.1 envelop C-alpha (-36 degrees)
 153 PRO   ( 166-)  A   114.2 envelop C-beta (108 degrees)
 276 PRO   ( 289-)  A   138.9 envelop C-alpha (144 degrees)
 318 PRO   ( 331-)  A    49.4 half-chair C-delta/C-gamma (54 degrees)
 398 PRO   ( 411-)  A  -116.8 envelop C-gamma (-108 degrees)
 610 PRO   ( 630-)  A  -147.4 envelop C-delta (-144 degrees)
 635 PRO   ( 655-)  A   -41.1 envelop C-alpha (-36 degrees)
 650 PRO   ( 670-)  A  -114.7 envelop C-gamma (-108 degrees)
 665 PRO   ( 685-)  A   135.8 envelop C-alpha (144 degrees)
 715 PRO   (  16-)  B    39.7 envelop C-delta (36 degrees)
 811 PRO   ( 118-)  B   -44.8 envelop C-alpha (-36 degrees)
 813 PRO   ( 120-)  B   -42.6 envelop C-alpha (-36 degrees)
 869 PRO   ( 176-)  B   100.2 envelop C-beta (108 degrees)
 982 PRO   ( 289-)  B   105.6 envelop C-beta (108 degrees)
1198 PRO   ( 505-)  B    39.9 envelop C-delta (36 degrees)
1266 PRO   ( 579-)  B   116.2 envelop C-beta (108 degrees)
1342 PRO   ( 655-)  B   -57.7 half-chair C-beta/C-alpha (-54 degrees)
1372 PRO   ( 685-)  B   113.0 envelop C-beta (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.

   1 GLU   (   2-)  A      N   <-> 1418 SAC   (   1-)  A      C      1.38    1.32  INTRA BF
   1 GLU   (   2-)  A      CA  <-> 1418 SAC   (   1-)  A      C      0.72    2.48  INTRA BF
 277 SER   ( 290-)  A      OG  <->  696 HIS   ( 716-)  A      ND1    0.61    2.09  INTRA BF
  82 ARG   (  95-)  A      NH1 <->   83 ARG   (  96-)  A      NH1    0.54    2.31  INTRA BF
 890 ASN   ( 197-)  B      ND2 <->  893 GLU   ( 200-)  B      OE1    0.45    2.25  INTRA BL
1165 ASP   ( 472-)  B      OD2 <-> 1391 LYS   ( 704-)  B      NZ     0.37    2.33  INTRA BF
 525 ASN   ( 545-)  A      ND2 <->  527 TYR   ( 547-)  A      CZ     0.34    2.76  INTRA BF
 645 VAL   ( 665-)  A      N   <->  658 LYS   ( 678-)  A      O      0.31    2.39  INTRA BF
1181 GLU   ( 488-)  B      OE1 <-> 1184 ARG   ( 491-)  B      NH1    0.30    2.40  INTRA BF
 712 ALA   (  13-)  B      N   <-> 1420 HOH   (1499 )  B      O      0.29    2.41  INTRA BF
 523 SER   ( 543-)  A      OG  <->  525 ASN   ( 545-)  A      ND2    0.29    2.41  INTRA BF
1111 LYS   ( 418-)  B      NZ  <-> 1172 ASP   ( 479-)  B      O      0.29    2.41  INTRA BL
 983 SER   ( 290-)  B      OG  <-> 1403 HIS   ( 716-)  B      ND1    0.29    2.41  INTRA BL
1361 ARG   ( 674-)  B      NH1 <-> 1420 HOH   (1516 )  B      O      0.29    2.41  INTRA BF
 360 HIS   ( 373-)  A      NE2 <->  383 ASP   ( 396-)  A      OD2    0.26    2.44  INTRA BL
 363 ASN   ( 376-)  A      ND2 <-> 1419 HOH   (1515 )  A      O      0.26    2.44  INTRA BF
 259 GLU   ( 272-)  A      O   <-> 1419 HOH   (1507 )  A      O      0.26    2.14  INTRA BF
 819 GLN   ( 126-)  B      O   <->  840 GLN   ( 147-)  B      NE2    0.25    2.45  INTRA BF
 184 ASN   ( 197-)  A      OD1 <->  187 GLU   ( 200-)  A      N      0.25    2.45  INTRA BF
 343 GLU   ( 356-)  A      O   <->  591 ARG   ( 611-)  A      NE     0.24    2.46  INTRA BF
1239 TYR   ( 552-)  B      N   <-> 1296 THR   ( 609-)  B      O      0.23    2.47  INTRA BL
 229 MET   ( 242-)  A      CE  <->  245 VAL   ( 258-)  A      CG2    0.23    2.97  INTRA BL
 662 GLU   ( 682-)  A      CD  <->  664 ARG   ( 684-)  A      NE     0.23    2.87  INTRA BF
 474 GLN   ( 487-)  A      NE2 <->  476 GLU   ( 489-)  A      OE1    0.23    2.47  INTRA BF
 652 VAL   ( 672-)  A      O   <-> 1419 HOH   (1332 )  A      O      0.23    2.17  INTRA BF
And so on for a total of 275 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

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.

 978 TYR   ( 285-)  B      -8.15
 154 TYR   ( 167-)  A      -8.09
 272 TYR   ( 285-)  A      -7.53
 867 ARG   ( 174-)  B      -7.33
 161 ARG   ( 174-)  A      -6.95
 710 ARG   (  11-)  B      -6.43
  82 ARG   (  95-)  A      -6.40
  10 ARG   (  11-)  A      -6.25
  83 ARG   (  96-)  A      -6.23
1368 ARG   ( 681-)  B      -6.19
 788 ARG   (  95-)  B      -6.18
  95 TYR   ( 108-)  A      -6.00
 801 TYR   ( 108-)  B      -5.87
 819 GLN   ( 126-)  B      -5.80
1139 LYS   ( 446-)  B      -5.79
1161 GLN   ( 468-)  B      -5.78
 731 GLN   (  32-)  B      -5.78
 455 GLN   ( 468-)  A      -5.71
 113 GLN   ( 126-)  A      -5.69
 789 ARG   (  96-)  B      -5.67
 471 GLN   ( 484-)  A      -5.67
1177 GLN   ( 484-)  B      -5.63
 661 ARG   ( 681-)  A      -5.62
 617 ARG   ( 637-)  A      -5.62
  94 ARG   ( 107-)  A      -5.60
 433 LYS   ( 446-)  A      -5.59
 654 ARG   ( 674-)  A      -5.56
1200 ASN   ( 507-)  B      -5.53
 757 HIS   (  64-)  B      -5.47
 393 MET   ( 406-)  A      -5.46
  51 HIS   (  64-)  A      -5.40
1099 MET   ( 406-)  B      -5.37
 800 ARG   ( 107-)  B      -5.37
 494 ASN   ( 507-)  A      -5.28
 805 ASN   ( 112-)  B      -5.26
 785 TYR   (  92-)  B      -5.26
  99 ASN   ( 112-)  A      -5.25
 733 VAL   (  34-)  B      -5.24
  79 TYR   (  92-)  A      -5.20
 374 VAL   ( 387-)  A      -5.13
1129 ASN   ( 436-)  B      -5.13
1080 VAL   ( 387-)  B      -5.11
 423 ASN   ( 436-)  A      -5.02

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.

 393 MET   ( 406-)  A       395 - ARG    408- ( A)         -5.05
1099 MET   ( 406-)  B      1101 - ARG    408- ( B)         -4.83

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

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.

 394 TYR   ( 407-)  A   -2.52
 278 ALA   ( 291-)  A   -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

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.

1419 HOH   (1655 )  A      O     53.39    1.06   13.80
1420 HOH   (1670 )  B      O    -21.76   11.73   36.05

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.

1419 HOH   (1442 )  A      O
1419 HOH   (1461 )  A      O
1419 HOH   (1481 )  A      O
1419 HOH   (1497 )  A      O
1419 HOH   (1517 )  A      O
1419 HOH   (1532 )  A      O
1419 HOH   (1587 )  A      O
1419 HOH   (1595 )  A      O
1419 HOH   (1715 )  A      O
1420 HOH   (1616 )  B      O
1420 HOH   (1676 )  B      O
1420 HOH   (1682 )  B      O
1420 HOH   (1701 )  B      O
1420 HOH   (1751 )  B      O
1420 HOH   (1818 )  B      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.

  97 GLN   ( 110-)  A
 911 ASN   ( 218-)  B
1064 ASN   ( 371-)  B
1143 HIS   ( 450-)  B
1292 HIS   ( 605-)  B
1338 GLN   ( 651-)  B
1377 GLN   ( 690-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   3 SER   (   4-)  A      N
  28 VAL   (  29-)  A      N
  62 ILE   (  75-)  A      N
  87 ARG   ( 100-)  A      NH1
  88 VAL   ( 101-)  A      N
 127 ARG   ( 140-)  A      NE
 130 ARG   ( 143-)  A      NE
 136 SER   ( 149-)  A      N
 158 ARG   ( 171-)  A      NH1
 184 ASN   ( 197-)  A      N
 188 ARG   ( 201-)  A      NH1
 237 SER   ( 250-)  A      N
 256 LYS   ( 269-)  A      N
 277 SER   ( 290-)  A      N
 279 TRP   ( 292-)  A      N
 280 THR   ( 293-)  A      N
 281 GLY   ( 294-)  A      N
 285 ILE   ( 298-)  A      N
 300 GLN   ( 313-)  A      N
 302 TRP   ( 315-)  A      N
 309 ASN   ( 322-)  A      ND2
 336 GLN   ( 349-)  A      N
 359 TYR   ( 372-)  A      N
 450 LEU   ( 463-)  A      N
 472 GLU   ( 485-)  A      N
And so on for a total of 67 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.

   1 GLU   (   2-)  A      OE1
 324 ASN   ( 337-)  A      OD1
 329 HIS   ( 342-)  A      ND1
 360 HIS   ( 373-)  A      ND1
 441 ASN   ( 454-)  A      OD1
 702 ASP   ( 722-)  A      OD1
 805 ASN   ( 112-)  B      OD1
1030 ASN   ( 337-)  B      OD1
1066 HIS   ( 373-)  B      ND1

Warning: Unusual ion packing

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

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

1415  CA   (1201-)  A     0.48   1.38 Scores about as good as  K
1416  CA   (1202-)  B     0.48   0.68 Scores about as good as NA *2

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.

1419 HOH   (1300 )  A      O  0.87  K  4 NCS 1/1
1419 HOH   (1415 )  A      O  0.89  K  5 Ion-B
1419 HOH   (1535 )  A      O  0.87  K  4 ION-B NCS 1/1
1420 HOH   (1244 )  B      O  1.06  K  4
1420 HOH   (1249 )  B      O  1.03  K  4 NCS 1/1
1420 HOH   (1340 )  B      O  0.97  K  4 NCS 1/1
1420 HOH   (1377 )  B      O  0.88  K  4 NCS 1/1
1420 HOH   (1433 )  B      O  0.93  K  4 H2O-B
1420 HOH   (1453 )  B      O  0.96  K  4 NCS 1/1
1420 HOH   (1562 )  B      O  0.91  K  4 Ion-B
1420 HOH   (1576 )  B      O  0.97  K  5 Ion-B
1420 HOH   (1787 )  B      O  1.07  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.

  24 ASP   (  25-)  A   H-bonding suggests Asn; but Alt-Rotamer
 111 GLU   ( 124-)  A   H-bonding suggests Gln
 203 GLU   ( 216-)  A   H-bonding suggests Gln
 259 GLU   ( 272-)  A   H-bonding suggests Gln; but Alt-Rotamer
 554 ASP   ( 574-)  A   H-bonding suggests Asn; but Alt-Rotamer
 736 GLU   (  43-)  B   H-bonding suggests Gln
 817 GLU   ( 124-)  B   H-bonding suggests Gln
 909 GLU   ( 216-)  B   H-bonding suggests Gln
1318 GLU   ( 631-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.628
  2nd generation packing quality :  -1.975
  Ramachandran plot appearance   :  -1.186
  chi-1/chi-2 rotamer normality  :  -3.233 (poor)
  Backbone conformation          :  -0.512

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.657 (tight)
  Bond angles                    :   1.480
  Omega angle restraints         :   1.430 (loose)
  Side chain planarity           :   1.075
  Improper dihedral distribution :   1.802 (loose)
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   1.039

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 : 2.01


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.657 (tight)
  Bond angles                    :   1.480
  Omega angle restraints         :   1.430 (loose)
  Side chain planarity           :   1.075
  Improper dihedral distribution :   1.802 (loose)
  B-factor distribution          :   0.668
  Inside/Outside distribution    :   1.039
==============

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.