WHAT IF Check report

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

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

Verification log for pdb3f7u.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.704
CA-only RMS fit for the two chains : 0.349

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.753
CA-only RMS fit for the two chains : 0.432

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.705
CA-only RMS fit for the two chains : 0.392

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.751
CA-only RMS fit for the two chains : 0.379

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.762
CA-only RMS fit for the two chains : 0.419

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: 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.

 994 AG4   ( 265-)  A  -
 996 AG4   ( 266-)  B  -
 998 AG4   ( 267-)  C  -
1000 AG4   ( 268-)  D  -

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: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) : 95.000

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.

  24 ARG   (  27-)  A
 271 ARG   (  27-)  B
 518 ARG   (  27-)  C
 765 ARG   (  27-)  D

Warning: Tyrosine convention problem

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

  97 TYR   ( 102-)  A
 344 TYR   ( 102-)  B

Warning: Phenylalanine convention problem

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

 201 PHE   ( 212-)  A
 291 PHE   (  47-)  B
 695 PHE   ( 212-)  C
 786 PHE   (  48-)  D
 942 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.

  50 ASP   (  52-)  A
 124 ASP   ( 139-)  A
 270 ASP   (  26-)  B
 371 ASP   ( 139-)  B
 618 ASP   ( 139-)  C
 865 ASP   ( 139-)  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.

   4 GLU   (   8-)  A
   8 GLU   (  11-)  A
 120 GLU   ( 125-)  A
 157 GLU   ( 171-)  A
 174 GLU   ( 187-)  A
 175 GLU   ( 187-)  A
 210 GLU   ( 221-)  A
 224 GLU   ( 236-)  A
 255 GLU   (  11-)  B
 354 GLU   ( 112-)  B
 388 GLU   ( 155-)  B
 404 GLU   ( 171-)  B
 411 GLU   ( 178-)  B
 421 GLU   ( 187-)  B
 422 GLU   ( 187-)  B
 450 GLU   ( 214-)  B
 471 GLU   ( 236-)  B
 498 GLU   (   8-)  C
 502 GLU   (  11-)  C
 617 GLU   ( 138-)  C
 619 GLU   ( 140-)  C
 651 GLU   ( 171-)  C
 658 GLU   ( 178-)  C
 668 GLU   ( 187-)  C
 669 GLU   ( 187-)  C
 697 GLU   ( 214-)  C
 704 GLU   ( 221-)  C
 718 GLU   ( 236-)  C
 745 GLU   (   8-)  D
 749 GLU   (  11-)  D
 810 GLU   (  71-)  D
 861 GLU   ( 125-)  D
 864 GLU   ( 138-)  D
 866 GLU   ( 140-)  D
 898 GLU   ( 171-)  D
 905 GLU   ( 178-)  D
 915 GLU   ( 187-)  D
 944 GLU   ( 214-)  D
 951 GLU   ( 221-)  D
 965 GLU   ( 236-)  D

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.

  58 GLN   (  60-)  A      CG   CD    1.62    4.0
  71 LYS   (  76-)  A      N   -C     1.43    5.2
  98 LYS   ( 103-)  A      CB   CG    1.64    4.1
  98 LYS   ( 103-)  A      CG   CD    1.66    4.7
  98 LYS   ( 103-)  A      CD   CE    1.66    4.7
  98 LYS   ( 103-)  A      CE   NZ    1.74    8.3
 264 GLY   (  20-)  B      N   -C     1.59   13.0
 297 ASP   (  52-)  B      CB   CG    1.64    4.8
 318 LYS   (  76-)  B      N   -C     1.43    5.1
 346 GLY   ( 104-)  B      N    CA    1.61    9.9
 346 GLY   ( 104-)  B      CA   C     1.59    5.2
 382 ALA   ( 150-)  B      N    CA    1.55    4.6
 384 THR   ( 151-)  B      CA   CB    1.64    5.6
 384 THR   ( 151-)  B      CB   CG2   1.71    5.7
 385 GLN   ( 152-)  B      CA   C     1.43   -4.4
 511 GLY   (  20-)  C      N   -C     1.49    7.9
 544 ASP   (  52-)  C      CA   CB    1.62    4.4
 544 ASP   (  52-)  C      CB   CG    1.65    5.5
 565 LYS   (  76-)  C      N   -C     1.52    9.7
 742 TRP   (   5-)  D      N    CA    1.54    4.1
 745 GLU   (   8-)  D      CD   OE1   1.35    5.1
 751 CYS   (  11-)  D      N    CA    1.54    4.1
 758 GLY   (  20-)  D      N   -C     1.50    8.7
 771 ILE   (  33-)  D      CG1  CD1   1.70    4.8
 812 LYS   (  76-)  D      N   -C     1.51    9.0
 839 LYS   ( 103-)  D      CE   NZ    1.64    4.9
 965 GLU   ( 236-)  D      N   -C     1.46    6.6
 986 ILE   ( 257-)  D      CA   CB    1.62    4.5

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

 |  0.998208 -0.000654 -0.001075|
 | -0.000654  0.992218 -0.000073|
 | -0.001075 -0.000073  0.994847|
Proposed new scale matrix

 |  0.015440  0.000010  0.000017|
 |  0.000005  0.008139  0.000000|
 |  0.000007  0.000000  0.006582|
With corresponding cell

    A    =  64.768  B   = 122.860  C    = 151.931
    Alpha=  90.001  Beta=  90.124  Gamma=  90.075

The CRYST1 cell dimensions

    A    =  64.886  B   = 123.830  C    = 152.723
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 915.698
(Under-)estimated Z-score: 22.302

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.

  17 GLY   (  20-)  A     -C    N    CA  138.45   10.5
  24 ARG   (  27-)  A      CG   CD   NE  118.17    4.5
  28 ILE   (  31-)  A      C    CA   CB  102.17   -4.2
  59 ASN   (  61-)  A      N    CA   C    99.77   -4.1
  71 LYS   (  76-)  A     -O   -C    N   115.13   -4.9
  89 HIS   (  94-)  A      CG   ND1  CE1 109.62    4.0
  91 HIS   (  96-)  A      CG   ND1  CE1 109.91    4.3
  98 LYS   ( 103-)  A      CD   CE   NZ  129.81    5.6
 108 HIS   ( 113-)  A      CG   ND1  CE1 109.93    4.3
 179 HIS   ( 190-)  A      CG   ND1  CE1 109.97    4.4
 224 GLU   ( 236-)  A     -O   -C    N   111.60   -7.1
 224 GLU   ( 236-)  A     -CA  -C    N   124.83    4.3
 224 GLU   ( 236-)  A     -C    N    CA  139.98   10.2
 258 LEU   (  11-)  B      CA   CB   CG  133.75    5.0
 261 VAL   (  14-)  B      N    CA   CB  117.50    4.1
 264 GLY   (  20-)  B     -C    N    CA  101.28  -11.4
 297 ASP   (  52-)  B     -C    N    CA  133.00    6.3
 318 LYS   (  76-)  B     -O   -C    N   112.01   -6.9
 318 LYS   (  76-)  B     -CA  -C    N   128.10    6.0
 318 LYS   (  76-)  B     -C    N    CA  131.23    5.3
 338 HIS   (  96-)  B      CG   ND1  CE1 109.76    4.2
 346 GLY   ( 104-)  B     -O   -C    N   111.98   -6.9
 346 GLY   ( 104-)  B     -CA  -C    N   128.11    6.0
 346 GLY   ( 104-)  B     -C    N    CA  102.69  -10.5
 346 GLY   ( 104-)  B      N    CA   C   131.58    6.6
 360 MET   ( 118-)  B      CG   SD   CE   85.63   -6.9
 382 ALA   ( 150-)  B      N    CA   C   124.39    4.7
 382 ALA   ( 150-)  B      C    CA   CB   97.65   -8.6
 385 GLN   ( 152-)  B     -C    N    CA  112.82   -4.9
 385 GLN   ( 152-)  B      N    CA   C   122.54    4.1
 456 ARG   ( 220-)  B      CG   CD   NE  101.46   -5.3
 511 GLY   (  20-)  C     -O   -C    N   115.95   -4.4
 517 ASP   (  26-)  C     -C    N    CA  130.78    5.0
 517 ASP   (  26-)  C      C    CA   CB  101.27   -4.6
 544 ASP   (  52-)  C     -C    N    CA  130.73    5.0
 565 LYS   (  76-)  C      N    CA   C   123.08    4.2
 592 LYS   ( 103-)  C      N    CA   C   126.55    5.5
 645 SER   ( 165-)  C     -C    N    CA  114.25   -4.1
 718 GLU   ( 236-)  C     -O   -C    N   102.12  -13.1
 718 GLU   ( 236-)  C     -CA  -C    N   129.88    6.8
 718 GLU   ( 236-)  C     -C    N    CA  144.52   12.7
 726 ASN   ( 244-)  C      C    CA   CB  117.82    4.1
 811 ASN   (  72-)  D      CA   C    O   130.07    5.5
 812 LYS   (  76-)  D     -CA  -C    N   102.10   -7.0
 862 LYS   ( 126-)  D      CA   C    O   113.29   -4.4
 919 ARG   ( 189-)  D      CB   CG   CD  105.10   -4.5
 949 HIS   ( 219-)  D      CG   ND1  CE1 109.83    4.2
 965 GLU   ( 236-)  D     -O   -C    N   106.66  -10.2

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.

   4 GLU   (   8-)  A
   8 GLU   (  11-)  A
  24 ARG   (  27-)  A
  50 ASP   (  52-)  A
 120 GLU   ( 125-)  A
 124 ASP   ( 139-)  A
 157 GLU   ( 171-)  A
 174 GLU   ( 187-)  A
 175 GLU   ( 187-)  A
 210 GLU   ( 221-)  A
 224 GLU   ( 236-)  A
 255 GLU   (  11-)  B
 270 ASP   (  26-)  B
 271 ARG   (  27-)  B
 354 GLU   ( 112-)  B
 371 ASP   ( 139-)  B
 388 GLU   ( 155-)  B
 404 GLU   ( 171-)  B
 411 GLU   ( 178-)  B
 421 GLU   ( 187-)  B
 422 GLU   ( 187-)  B
 450 GLU   ( 214-)  B
 471 GLU   ( 236-)  B
 498 GLU   (   8-)  C
 502 GLU   (  11-)  C
 518 ARG   (  27-)  C
 617 GLU   ( 138-)  C
 618 ASP   ( 139-)  C
 619 GLU   ( 140-)  C
 651 GLU   ( 171-)  C
 658 GLU   ( 178-)  C
 668 GLU   ( 187-)  C
 669 GLU   ( 187-)  C
 697 GLU   ( 214-)  C
 704 GLU   ( 221-)  C
 718 GLU   ( 236-)  C
 745 GLU   (   8-)  D
 749 GLU   (  11-)  D
 765 ARG   (  27-)  D
 810 GLU   (  71-)  D
 861 GLU   ( 125-)  D
 864 GLU   ( 138-)  D
 865 ASP   ( 139-)  D
 866 GLU   ( 140-)  D
 898 GLU   ( 171-)  D
 905 GLU   ( 178-)  D
 915 GLU   ( 187-)  D
 944 GLU   ( 214-)  D
 951 GLU   ( 221-)  D
 965 GLU   ( 236-)  D

Warning: Chirality deviations detected

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

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

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

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  16 TRP   (  16-)  A      C      9.2    13.70     0.23
 223 LYS   ( 233-)  A      C     -8.6   -12.92     0.11
 263 TRP   (  16-)  B      C     12.5    18.67     0.23
 382 ALA   ( 150-)  B      C      7.0    10.77     0.08
 717 LYS   ( 233-)  C      C     12.7    19.33     0.11
 964 LYS   ( 233-)  D      C     15.8    23.95     0.11
The average deviation= 1.542

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.

 346 GLY   ( 104-)  B    6.46
 592 LYS   ( 103-)  C    5.86
 382 ALA   ( 150-)  B    5.39
 759 GLY   (  21-)  D    4.65
 712 LYS   ( 228-)  C    4.62
 565 LYS   (  76-)  C    4.53
 385 GLN   ( 152-)  B    4.39
 345 LYS   ( 103-)  B    4.21
  98 LYS   ( 103-)  A    4.10
 465 LYS   ( 228-)  B    4.03

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.

 583 HIS   (  94-)  C    5.36
 455 HIS   ( 219-)  B    4.28
  19 ASN   (  22-)  A    4.20
 596 HIS   ( 107-)  C    4.18
  89 HIS   (  94-)  A    4.02

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.

 901 THR   ( 174-)  D    -2.7
 274 PRO   (  30-)  B    -2.7
 160 THR   ( 174-)  A    -2.6
 407 THR   ( 174-)  B    -2.5
 521 PRO   (  30-)  C    -2.4
 265 GLY   (  21-)  B    -2.4
 689 LYS   ( 206-)  C    -2.3
  11 LEU   (  11-)  A    -2.3
 654 THR   ( 174-)  C    -2.3
 923 ARG   ( 193-)  D    -2.2
 182 ARG   ( 193-)  A    -2.2
 429 ARG   ( 193-)  B    -2.2
 821 PRO   (  85-)  D    -2.2
 768 PRO   (  30-)  D    -2.2
 505 LEU   (  11-)  C    -2.2
 810 GLU   (  71-)  D    -2.2
 454 LEU   ( 218-)  B    -2.2
 815 ILE   (  79-)  D    -2.1
  98 LYS   ( 103-)  A    -2.1
 334 GLN   (  92-)  B    -2.1
 438 THR   ( 202-)  B    -2.1
 828 GLN   (  92-)  D    -2.1
 581 GLN   (  92-)  C    -2.1
  27 PRO   (  30-)  A    -2.1
 310 SER   (  65-)  B    -2.0
 191 THR   ( 202-)  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.

   8 GLU   (  11-)  A  Poor phi/psi, omega poor
  22 LYS   (  25-)  A  omega poor
  26 SER   (  29-)  A  PRO omega poor
  93 SER   (  98-)  A  Poor phi/psi
  97 TYR   ( 102-)  A  omega poor
 157 GLU   ( 171-)  A  Poor phi/psi
 170 LEU   ( 184-)  A  omega poor
 180 TYR   ( 191-)  A  omega poor
 186 SER   ( 197-)  A  omega poor
 190 PRO   ( 201-)  A  omega poor
 192 CYS   ( 203-)  A  Poor phi/psi
 196 VAL   ( 207-)  A  omega poor
 231 ASP   ( 243-)  A  Poor phi/psi
 232 ASN   ( 244-)  A  Poor phi/psi
 255 GLU   (  11-)  B  Poor phi/psi, omega poor
 264 GLY   (  20-)  B  omega poor
 265 GLY   (  21-)  B  Poor phi/psi
 269 LYS   (  25-)  B  omega poor
 273 SER   (  29-)  B  PRO omega poor
 297 ASP   (  52-)  B  omega poor
 300 GLN   (  55-)  B  omega poor
 309 HIS   (  64-)  B  Poor phi/psi
 315 LEU   (  70-)  B  omega poor
 316 GLU   (  71-)  B  Poor phi/psi
 317 ASN   (  72-)  B  Poor phi/psi
And so on for a total of 83 lines.

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.

 422 GLU   ( 187-)  B    0.38

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 TYR   (   7-)  A      0
   8 GLU   (  11-)  A      0
   9 SER   (  11-)  A      0
  10 CYS   (  11-)  A      0
  11 LEU   (  11-)  A      0
  19 ASN   (  22-)  A      0
  20 CYS   (  23-)  A      0
  24 ARG   (  27-)  A      0
  26 SER   (  29-)  A      0
  47 SER   (  50-)  A      0
  52 LYS   (  54-)  A      0
  60 ASN   (  62-)  A      0
  62 HIS   (  64-)  A      0
  69 GLU   (  71-)  A      0
  70 ASN   (  72-)  A      0
  71 LYS   (  76-)  A      0
  72 ALA   (  77-)  A      0
  75 SER   (  80-)  A      0
  80 PRO   (  85-)  A      0
  86 LYS   (  91-)  A      0
  91 HIS   (  96-)  A      0
  92 TRP   (  97-)  A      0
  93 SER   (  98-)  A      0
  94 ASP   (  99-)  A      0
  97 TYR   ( 102-)  A      0
And so on for a total of 491 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 : 7.586

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]

  27 PRO   (  30-)  A    0.46 HIGH
  96 PRO   ( 101-)  A    0.17 LOW
 327 PRO   (  85-)  B    0.12 LOW
 369 PRO   ( 137-)  B    0.46 HIGH
 401 PRO   ( 168-)  B    0.48 HIGH
 403 PRO   ( 170-)  B    0.14 LOW
 639 PRO   ( 159-)  C    0.47 HIGH
 650 PRO   ( 170-)  C    0.13 LOW
 729 PRO   ( 247-)  C    0.20 LOW
 821 PRO   (  85-)  D    0.47 HIGH
 886 PRO   ( 159-)  D    0.49 HIGH
 897 PRO   ( 170-)  D    0.18 LOW
 976 PRO   ( 247-)  D    0.08 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].

 122 PRO   ( 137-)  A    17.5 half-chair N/C-delta (18 degrees)
 369 PRO   ( 137-)  B   111.9 envelop C-beta (108 degrees)
 482 PRO   ( 247-)  B  -115.4 envelop C-gamma (-108 degrees)
 507 PRO   (  13-)  C   101.9 envelop C-beta (108 degrees)
 639 PRO   ( 159-)  C    99.2 envelop C-beta (108 degrees)
 698 PRO   ( 215-)  C    41.0 envelop C-delta (36 degrees)
 863 PRO   ( 137-)  D  -173.6 envelop N (180 degrees)
 895 PRO   ( 168-)  D  -114.0 envelop C-gamma (-108 degrees)
 945 PRO   ( 215-)  D    27.7 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 615 LYS   ( 126-)  C      NZ  <->  616 PRO   ( 137-)  C      CG     0.75    2.35  INTRA BF
 312 MET   (  67-)  B      CE  <->  314 LEU   (  69-)  B      CD2    0.68    2.52  INTRA
 615 LYS   ( 126-)  C      NZ  <->  616 PRO   ( 137-)  C      CB     0.49    2.51  INTRA BF
  57 VAL   (  59-)  A      CG2 <->   64 VAL   (  66-)  A      CG2    0.48    2.72  INTRA
 898 GLU   ( 171-)  D      OE2 <->  964 LYS   ( 233-)  D      NZ     0.38    2.32  INTRA
 385 GLN   ( 152-)  B      CB  <->  755 VAL   (  14-)  D      O      0.37    2.43  INTRA
 628 GLU   ( 149-)  C      CG  <->  700 GLN   ( 217-)  C      NE2    0.35    2.75  INTRA
 144 GLN   ( 158-)  A      NE2 <->  148 GLU   ( 162-)  A      OE2    0.35    2.35  INTRA
 179 HIS   ( 190-)  A      ND1 <->  202 ARG   ( 213-)  A      NH2    0.34    2.66  INTRA
 384 THR   ( 151-)  B      OG1 <->  385 GLN   ( 152-)  B      CD     0.33    2.47  INTRA
 949 HIS   ( 219-)  D      ND1 <->  951 GLU   ( 221-)  D      N      0.30    2.70  INTRA
 384 THR   ( 151-)  B      C   <->  385 GLN   ( 152-)  B      CG     0.29    2.81  INTRA
  58 GLN   (  60-)  A      NE2 <->   65 MET   (  67-)  A      CE     0.29    2.81  INTRA
 254 ALA   (  11-)  B      O   <->  256 SER   (  11-)  B      N      0.27    2.43  INTRA
 254 ALA   (  11-)  B      C   <->  256 SER   (  11-)  B      N      0.26    2.64  INTRA
 345 LYS   ( 103-)  B      O   <->  346 GLY   ( 104-)  B      CA     0.25    2.15  INTRA B3
 297 ASP   (  52-)  B      OD1 <->  298 LYS   (  53-)  B      N      0.24    2.36  INTRA
 553 ASN   (  61-)  C      O   <->  651 GLU   ( 171-)  C      N      0.20    2.50  INTRA
 385 GLN   ( 152-)  B      CB  <->  386 VAL   ( 153-)  B      N      0.17    2.53  INTRA B3
 551 VAL   (  59-)  C      CG2 <->  558 VAL   (  66-)  C      CG2    0.17    3.03  INTRA
   1 TRP   (   5-)  A      N   <-> 1001 HOH   ( 510 )  A      O      0.17    2.53  INTRA
 894 ILE   ( 167-)  D      N   <->  895 PRO   ( 168-)  D      CD     0.16    2.84  INTRA BL
 434 LEU   ( 198-)  B      CD2 <->  996 AG4   ( 266-)  B      C3     0.15    3.05  INTRA
 379 LEU   ( 147-)  B      O   <->  452 ILE   ( 216-)  B      N      0.14    2.56  INTRA BL
 638 GLN   ( 158-)  C      N   <->  639 PRO   ( 159-)  C      CD     0.14    2.86  INTRA BL
And so on for a total of 111 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.

 591 TYR   ( 102-)  C      -6.98
 485 GLN   ( 250-)  B      -6.65
 344 TYR   ( 102-)  B      -6.47
 838 TYR   ( 102-)  D      -6.39
  97 TYR   ( 102-)  A      -6.28
 732 GLN   ( 250-)  C      -6.19
 449 ARG   ( 213-)  B      -6.17
 943 ARG   ( 213-)  D      -6.13
 696 ARG   ( 213-)  C      -6.12
 202 ARG   ( 213-)  A      -5.86
 238 GLN   ( 250-)  A      -5.83
 241 GLN   ( 253-)  A      -5.75
 762 GLN   (  24-)  D      -5.49
 488 GLN   ( 253-)  B      -5.48
 893 ASN   ( 166-)  D      -5.35
  40 LYS   (  43-)  A      -5.30
 646 ASN   ( 166-)  C      -5.27
 399 ASN   ( 166-)  B      -5.27
 287 LYS   (  43-)  B      -5.26
 515 GLN   (  24-)  C      -5.24
 979 GLN   ( 250-)  D      -5.24
 534 LYS   (  43-)  C      -5.16
 367 GLU   ( 125-)  B      -5.02

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.

 575 ALA   (  86-)  C   -2.76
 836 LEU   ( 100-)  D   -2.67
 822 ALA   (  86-)  D   -2.56
 589 LEU   ( 100-)  C   -2.56

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

1001 HOH   ( 288 )  A      O     17.81   74.70  154.37
1001 HOH   ( 304 )  A      O     14.71   75.55  153.25
1002 HOH   ( 348 )  B      O     82.72   75.82   75.22
1003 HOH   ( 307 )  C      O     21.50   48.06   78.48
1003 HOH   ( 342 )  C      O     83.19   51.60  140.30
1003 HOH   ( 352 )  C      O     81.54   53.65  138.00

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.

1001 HOH   ( 375 )  A      O
1002 HOH   ( 360 )  B      O
1002 HOH   ( 377 )  B      O
1002 HOH   ( 389 )  B      O
1002 HOH   ( 432 )  B      O
1002 HOH   ( 491 )  B      O
1002 HOH   ( 508 )  B      O
1002 HOH   ( 522 )  B      O
1002 HOH   ( 550 )  B      O
1002 HOH   ( 559 )  B      O
1003 HOH   ( 292 )  C      O
1003 HOH   ( 321 )  C      O
1003 HOH   ( 422 )  C      O
1003 HOH   ( 423 )  C      O
1003 HOH   ( 467 )  C      O
1003 HOH   ( 476 )  C      O
1003 HOH   ( 526 )  C      O
1003 HOH   ( 539 )  C      O
1003 HOH   ( 557 )  C      O
1004 HOH   ( 413 )  D      O
1004 HOH   ( 429 )  D      O
1004 HOH   ( 472 )  D      O
Metal-coordinating Histidine residue  89 fixed to   1
Metal-coordinating Histidine residue  91 fixed to   1
Metal-coordinating Histidine residue 114 fixed to   1
Metal-coordinating Histidine residue 336 fixed to   1
Metal-coordinating Histidine residue 338 fixed to   1
Metal-coordinating Histidine residue 361 fixed to   1
Metal-coordinating Histidine residue 583 fixed to   1
Metal-coordinating Histidine residue 585 fixed to   1
Metal-coordinating Histidine residue 608 fixed to   1
Metal-coordinating Histidine residue 830 fixed to   1
Metal-coordinating Histidine residue 832 fixed to   1
Metal-coordinating Histidine residue 855 fixed to   1

Error: HIS, ASN, GLN side chain flips

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

  58 GLN   (  60-)  A
 241 GLN   ( 253-)  A
 305 GLN   (  60-)  B
 385 GLN   ( 152-)  B
 794 GLN   (  55-)  D
 803 HIS   (  64-)  D
 982 GLN   ( 253-)  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.

   3 TYR   (   7-)  A      OH
  14 VAL   (  14-)  A      N
  28 ILE   (  31-)  A      N
  29 ASN   (  32-)  A      N
  55 TRP   (  57-)  A      N
  78 GLY   (  83-)  A      N
  97 TYR   ( 102-)  A      N
 175 GLU   ( 187-)  A      N
 179 HIS   ( 190-)  A      N
 189 THR   ( 200-)  A      N
 193 ASP   ( 204-)  A      N
 216 SER   ( 227-)  A      N
 223 LYS   ( 233-)  A      N
 228 SER   ( 240-)  A      OG
 250 TYR   (   7-)  B      OH
 261 VAL   (  14-)  B      N
 275 ILE   (  31-)  B      N
 276 ASN   (  32-)  B      N
 302 TRP   (  57-)  B      N
 319 ALA   (  77-)  B      N
 344 TYR   ( 102-)  B      N
 346 GLY   ( 104-)  B      N
 398 SER   ( 165-)  B      N
 436 THR   ( 200-)  B      N
 440 ASP   ( 204-)  B      N
And so on for a total of 53 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.

  62 HIS   (  64-)  A      ND1
 309 HIS   (  64-)  B      ND1
 619 GLU   ( 140-)  C      OE1
 658 GLU   ( 178-)  C      OE1

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.

 745 GLU   (   8-)  D   H-bonding suggests Gln
 905 GLU   ( 178-)  D   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 :  -0.294
  2nd generation packing quality :  -1.590
  Ramachandran plot appearance   :  -1.540
  chi-1/chi-2 rotamer normality  :  -1.583
  Backbone conformation          :  -1.864

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.089
  Bond angles                    :   1.035
  Omega angle restraints         :   1.379 (loose)
  Side chain planarity           :   1.268
  Improper dihedral distribution :   1.335
  B-factor distribution          :   0.756
  Inside/Outside distribution    :   0.985

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -2.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.089
  Bond angles                    :   1.035
  Omega angle restraints         :   1.379 (loose)
  Side chain planarity           :   1.268
  Improper dihedral distribution :   1.335
  B-factor distribution          :   0.756
  Inside/Outside distribution    :   0.985
==============

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.