WHAT IF Check report

This file was created 2012-01-04 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 pdb1m9y.ent

Checks that need to be done early-on in validation

Warning: Triclinic cell with mixed acute and obtuse angles

The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I).

The CRYST1 cell dimensions

    A    =  38.426  B   = 111.223  C    =  67.780
    Alpha=  89.990  Beta= 101.450  Gamma=  89.750

Warning: Class of conventional cell differs from CRYST1 cell

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

The CRYST1 cell dimensions

    A    =  38.426  B   = 111.223  C    =  67.780
    Alpha=  89.990  Beta= 101.450  Gamma=  89.750

Dimensions of a reduced cell

    A    =  38.426  B   =  67.780  C    = 111.223
    Alpha=  90.010  Beta=  90.250  Gamma= 101.450

Dimensions of the conventional cell

    A    =  38.426  B   = 111.223  C    =  67.780
    Alpha=  89.990  Beta= 101.450  Gamma=  89.750

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: TRICLINIC

Crystal class of the conventional CELL: MONOCLINIC

Space group name: P 1

Bravais type of conventional cell is: P

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.912
CA-only RMS fit for the two chains : 0.496

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 E

All-atom RMS fit for the two chains : 0.330
CA-only RMS fit for the two chains : 0.103

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.944
CA-only RMS fit for the two chains : 0.477

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and F

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 E

All-atom RMS fit for the two chains : 0.929
CA-only RMS fit for the two chains : 0.499

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 E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and F

All-atom RMS fit for the two chains : 0.527
CA-only RMS fit for the two chains : 0.182

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 F

Warning: Conventional cell is pseudo-cell

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

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

 429 ARG   ( 100-)  C

Warning: Phenylalanine convention problem

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

  36 PHE   (  36-)  A
 171 PHE   (   7-)  B
 200 PHE   (  36-)  B
 210 PHE   (  46-)  B
 276 PHE   ( 112-)  B
 646 PHE   (  36-)  E
 820 PHE   (  46-)  F
 886 PHE   ( 112-)  F

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 298 GLU   ( 134-)  B
 408 GLU   (  79-)  C
 753 GLU   ( 143-)  E
 797 GLU   (  23-)  F
 855 GLU   (  81-)  F
 968 GLU   (  29-)  G
1037 GLU   (  98-)  G
1102 GLU   (  28-)  H

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.

1142 MET   (  68-)  H      SD   CE    1.45   -5.8

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.

  44 LYS   (  44-)  A      N    CA   CB  117.53    4.1
  53 PHE   (  53-)  A      N    CA   C    99.83   -4.1
  68 THR   (  68-)  A      N    CA   CB  117.33    4.0
  92 HIS   (  92-)  A      CG   ND1  CE1 109.80    4.2
 143 GLU   ( 143-)  A      N    CA   CB  118.89    4.9
 143 GLU   ( 143-)  A      CA   CB   CG  123.03    4.5
 169 THR   (   5-)  B     -C    N    CA  129.78    4.5
 172 PHE   (   8-)  B      CA   CB   CG  118.00    4.2
 179 GLU   (  15-)  B      C    CA   CB  101.16   -4.7
 184 VAL   (  20-)  B      C    CA   CB   99.46   -5.6
 233 ARG   (  69-)  B      CG   CD   NE  117.65    4.2
 233 ARG   (  69-)  B      CD   NE   CZ  129.01    4.1
 244 GLY   (  80-)  B      N    CA   C    96.61   -5.5
 259 PRO   (  95-)  B      CG   CD   N    96.61   -4.4
 281 ALA   ( 117-)  B     -C    N    CA  129.28    4.2
 307 GLU   ( 143-)  B      N    CA   CB  117.66    4.2
 329 GLU   ( 165-)  B      CA   C    O   129.05    4.9
 344 ILE   (  15-)  C      CB   CG1  CD1 104.72   -4.3
 348 THR   (  19-)  C      N    CA   CB  102.97   -4.4
 348 THR   (  19-)  C      CA   CB   OG1 103.48   -4.1
 357 GLU   (  28-)  C      CB   CG   CD  119.75    4.2
 365 VAL   (  36-)  C      CG1  CB   CG2 101.85   -4.1
 370 SER   (  41-)  C      C    CA   CB  118.39    4.4
 387 THR   (  58-)  C      N    CA   CB   97.57   -7.6
 387 THR   (  58-)  C      CA   CB   OG1 117.76    5.4
And so on for a total of 91 lines.

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.

 298 GLU   ( 134-)  B
 408 GLU   (  79-)  C
 429 ARG   ( 100-)  C
 753 GLU   ( 143-)  E
 797 GLU   (  23-)  F
 855 GLU   (  81-)  F
 968 GLU   (  29-)  G
1037 GLU   (  98-)  G
1102 GLU   (  28-)  H

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.

 202 ALA   (  38-)  B      C      6.5    10.10     0.08
 294 GLY   ( 130-)  B      C      6.5     8.65     0.06
 331 ILE   (   2-)  C      CB     6.1    40.20    32.31
 475 SER   ( 146-)  C      CA    -6.7    21.88    34.32
1068 ILE   ( 129-)  G      C      6.8     8.87     0.03
1119 GLU   (  45-)  H      C     -6.3    -9.11    -0.03
The average deviation= 2.050

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.

 120 GLU   ( 120-)  A    6.77
 244 GLY   (  80-)  B    6.09
 553 ALA   (  89-)  D    5.82
1003 ALA   (  64-)  G    5.52
1163 ALA   (  89-)  H    5.12
1189 ILE   ( 115-)  H    5.05
1152 ALA   (  78-)  H    4.57
1075 LEU   ( 136-)  G    4.55
 398 LEU   (  69-)  C    4.42
 484 LEU   (  20-)  D    4.40
  53 PHE   (  53-)  A    4.39
 590 VAL   ( 126-)  D    4.31
 359 LYS   (  30-)  C    4.14
 393 ALA   (  64-)  C    4.11
1110 VAL   (  36-)  H    4.11
 273 GLY   ( 109-)  B    4.10
 443 GLN   ( 114-)  C    4.06
1027 ALA   (  88-)  G    4.06
 544 TRP   (  80-)  D    4.05
 849 GLY   (  75-)  F    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.584

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.

1158 HIS   (  84-)  H    8.60
 712 ASN   ( 102-)  E    8.47
 989 GLN   (  50-)  G    8.02
 736 HIS   ( 126-)  E    7.72
 960 ASN   (  21-)  G    7.63
 126 HIS   ( 126-)  A    6.97
 702 HIS   (  92-)  E    6.30
 653 GLU   (  43-)  E    6.10
 380 ASP   (  51-)  C    6.01
  63 GLN   (  63-)  A    6.00
 396 GLN   (  67-)  C    5.95
 646 PHE   (  36-)  E    5.82
1136 HIS   (  62-)  H    5.38
 290 HIS   ( 126-)  B    5.32
1213 ASN   ( 139-)  H    5.21
 992 ASN   (  53-)  G    5.11
 990 ASP   (  51-)  G    5.09
 379 GLN   (  50-)  C    5.05
 450 ASN   ( 121-)  C    4.88
 413 HIS   (  84-)  C    4.85
 275 GLN   ( 111-)  B    4.83
 235 ASN   (  71-)  B    4.81
 230 ASP   (  66-)  B    4.75
1023 HIS   (  84-)  G    4.75
 386 ASN   (  57-)  C    4.72
 676 ASP   (  66-)  E    4.56
  92 HIS   (  92-)  A    4.48
 664 HIS   (  54-)  E    4.37
 441 GLN   ( 112-)  C    4.27
 341 HIS   (  12-)  C    4.24
 250 GLU   (  86-)  B    4.21
 468 ASN   ( 139-)  C    4.19
 718 ASN   ( 108-)  E    4.15
 410 ASP   (  81-)  C    4.09
 952 GLN   (  13-)  G    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.

 479 ILE   (  15-)  D    -2.7
 671 MET   (  61-)  E    -2.4
 855 GLU   (  81-)  F    -2.4
  61 MET   (  61-)  A    -2.4
1199 PRO   ( 125-)  H    -2.4
 835 MET   (  61-)  F    -2.3
 225 MET   (  61-)  B    -2.3
 493 GLU   (  29-)  D    -2.2
 834 PHE   (  60-)  F    -2.2
1080 ILE   ( 141-)  G    -2.2
 803 VAL   (  29-)  F    -2.2
 193 VAL   (  29-)  B    -2.2
 331 ILE   (   2-)  C    -2.2
 883 GLY   ( 109-)  F    -2.2
 719 GLY   ( 109-)  E    -2.1
 273 GLY   ( 109-)  B    -2.1
 109 GLY   ( 109-)  A    -2.1
 589 PRO   ( 125-)  D    -2.1
1165 ILE   (  91-)  H    -2.1
 454 PRO   ( 125-)  C    -2.1
 387 THR   (  58-)  C    -2.0
  29 VAL   (  29-)  A    -2.0
 332 VAL   (   3-)  C    -2.0
 564 ARG   ( 100-)  D    -2.0
 997 THR   (  58-)  G    -2.0
 189 PHE   (  25-)  B    -2.0
 224 PHE   (  60-)  B    -2.0
1035 MET   (  96-)  G    -2.0
 483 THR   (  19-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  12 VAL   (  12-)  A  omega poor
  22 PHE   (  22-)  A  omega poor
  70 HIS   (  70-)  A  Poor phi/psi
  92 HIS   (  92-)  A  omega poor
 106 ASN   ( 106-)  A  Poor phi/psi
 125 LYS   ( 125-)  A  Poor phi/psi
 172 PHE   (   8-)  B  omega poor
 234 HIS   (  70-)  B  Poor phi/psi
 243 TYR   (  79-)  B  omega poor
 244 GLY   (  80-)  B  omega poor
 256 HIS   (  92-)  B  omega poor
 270 ASN   ( 106-)  B  Poor phi/psi
 360 ALA   (  31-)  C  Poor phi/psi
 450 ASN   ( 121-)  C  PRO omega poor
 479 ILE   (  15-)  D  Poor phi/psi
 493 GLU   (  29-)  D  Poor phi/psi
 495 ALA   (  31-)  D  Poor phi/psi
 553 ALA   (  89-)  D  PRO omega poor
 563 PRO   (  99-)  D  omega poor
 585 ASN   ( 121-)  D  PRO omega poor
 632 PHE   (  22-)  E  omega poor
 680 HIS   (  70-)  E  Poor phi/psi
 702 HIS   (  92-)  E  omega poor
 716 ASN   ( 106-)  E  Poor phi/psi
 735 LYS   ( 125-)  E  Poor phi/psi
 774 LEU   ( 164-)  E  omega poor
 787 ASP   (  13-)  F  Poor phi/psi
 845 ASN   (  71-)  F  Poor phi/psi
 880 ASN   ( 106-)  F  Poor phi/psi
 891 ALA   ( 117-)  F  Poor phi/psi
 944 ASN   (   5-)  G  Poor phi/psi
 970 ALA   (  31-)  G  Poor phi/psi
1040 GLY   ( 101-)  G  Poor phi/psi
1060 ASN   ( 121-)  G  PRO omega poor
1105 ALA   (  31-)  H  Poor phi/psi
1163 ALA   (  89-)  H  PRO omega poor
1173 PRO   (  99-)  H  omega poor
1195 ASN   ( 121-)  H  PRO omega poor
1197 PRO   ( 123-)  H  omega poor
 chi-1/chi-2 correlation Z-score : -1.837

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 ASN   (   3-)  A      0
  12 VAL   (  12-)  A      0
  16 PRO   (  16-)  A      0
  25 PHE   (  25-)  A      0
  26 ALA   (  26-)  A      0
  28 LYS   (  28-)  A      0
  29 VAL   (  29-)  A      0
  43 GLU   (  43-)  A      0
  44 LYS   (  44-)  A      0
  46 PHE   (  46-)  A      0
  48 TYR   (  48-)  A      0
  49 LYS   (  49-)  A      0
  51 SER   (  51-)  A      0
  53 PHE   (  53-)  A      0
  54 HIS   (  54-)  A      0
  55 ARG   (  55-)  A      0
  58 PRO   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  68 THR   (  68-)  A      0
  69 ARG   (  69-)  A      0
  70 HIS   (  70-)  A      0
  71 ASN   (  71-)  A      0
  73 THR   (  73-)  A      0
  79 TYR   (  79-)  A      0
And so on for a total of 479 lines.

Warning: Backbone oxygen evaluation

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

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

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

 999 GLY   (  60-)  G   2.67   13
 389 GLY   (  60-)  C   2.58   11

Warning: Unusual PRO puckering amplitudes

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

   4 PRO   (   4-)  A    0.18 LOW
  58 PRO   (  58-)  A    0.20 LOW
 168 PRO   (   4-)  B    0.09 LOW
 346 PRO   (  17-)  C    0.19 LOW
 414 PRO   (  85-)  C    0.17 LOW
 419 PRO   (  90-)  C    0.10 LOW
 498 PRO   (  34-)  D    0.46 HIGH
 502 PRO   (  38-)  D    0.19 LOW
 614 PRO   (   4-)  E    0.20 LOW
 832 PRO   (  58-)  F    0.18 LOW
 956 PRO   (  17-)  G    0.11 LOW
1029 PRO   (  90-)  G    0.18 LOW
1032 PRO   (  93-)  G    0.19 LOW
1062 PRO   ( 123-)  G    0.47 HIGH
1123 PRO   (  49-)  H    0.46 HIGH
1197 PRO   ( 123-)  H    0.19 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].

 194 PRO   (  30-)  B  -118.2 half-chair C-delta/C-gamma (-126 degrees)
 330 PRO   (   1-)  C  -112.4 envelop C-gamma (-108 degrees)
 451 PRO   ( 122-)  C   -60.8 half-chair C-beta/C-alpha (-54 degrees)
 454 PRO   ( 125-)  C   -39.8 envelop C-alpha (-36 degrees)
 549 PRO   (  85-)  D   105.3 envelop C-beta (108 degrees)
 586 PRO   ( 122-)  D    43.6 envelop C-delta (36 degrees)
 587 PRO   ( 123-)  D   -56.3 half-chair C-beta/C-alpha (-54 degrees)
 589 PRO   ( 125-)  D   -18.1 half-chair C-alpha/N (-18 degrees)
 778 PRO   (   4-)  F   106.9 envelop C-beta (108 degrees)
 973 PRO   (  34-)  G   109.7 envelop C-beta (108 degrees)
1024 PRO   (  85-)  G  -123.2 half-chair C-delta/C-gamma (-126 degrees)
1159 PRO   (  85-)  H    44.7 envelop C-delta (36 degrees)
1164 PRO   (  90-)  H   -58.2 half-chair C-beta/C-alpha (-54 degrees)
1196 PRO   ( 122-)  H    42.7 envelop C-delta (36 degrees)
1199 PRO   ( 125-)  H   -44.3 envelop C-alpha (-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.

 359 LYS   (  30-)  C      NZ  <->  364 GLU   (  35-)  C      CG     0.63    2.47  INTRA BF
  44 LYS   (  44-)  A      NZ  <-> 1229 HOH   ( 334 )  A      O      0.53    2.17  INTRA BF
 335 LEU   (   6-)  C      CD2 <->  336 GLN   (   7-)  C      NE2    0.53    2.57  INTRA BF
 747 ASN   ( 137-)  E      ND2 <-> 1233 HOH   ( 264 )  E      O      0.49    2.21  INTRA
  49 LYS   (  49-)  A      NZ  <-> 1229 HOH   ( 282 )  A      O      0.49    2.21  INTRA
1136 HIS   (  62-)  H      N   <-> 1236 HOH   ( 165 )  H      O      0.48    2.22  INTRA
 118 LYS   ( 118-)  A      NZ  <-> 1229 HOH   ( 321 )  A      O      0.46    2.24  INTRA BF
1001 HIS   (  62-)  G      NE2 <-> 1235 HOH   ( 220 )  G      O      0.44    2.26  INTRA
 686 LYS   (  76-)  E      NZ  <-> 1233 HOH   ( 353 )  E      O      0.42    2.28  INTRA BF
1142 MET   (  68-)  H      CE  <-> 1236 HOH   ( 160 )  H      O      0.42    2.38  INTRA
 611 MET   (   1-)  E      N   <-> 1233 HOH   ( 340 )  E      O      0.41    2.29  INTRA BF
 400 GLU   (  71-)  C      OE1 <-> 1231 HOH   ( 175 )  C      O      0.40    2.00  INTRA BL
1081 VAL   ( 142-)  G      CG2 <-> 1217 ARG   ( 143-)  H      CD     0.40    2.80  INTRA
 213 LYS   (  49-)  B      NZ  <-> 1230 HOH   ( 231 )  B      O      0.38    2.32  INTRA
1214 LYS   ( 140-)  H      NZ  <-> 1236 HOH   ( 212 )  H      O      0.38    2.32  INTRA
1010 GLU   (  71-)  G      OE1 <-> 1235 HOH   ( 169 )  G      O      0.37    2.03  INTRA
1188 GLN   ( 114-)  H      NE2 <-> 1236 HOH   ( 185 )  H      O      0.37    2.33  INTRA
 686 LYS   (  76-)  E      NZ  <-> 1233 HOH   ( 362 )  E      O      0.36    2.34  INTRA BF
 195 LYS   (  31-)  B      NZ  <->  248 GLU   (  84-)  B      OE2    0.36    2.34  INTRA
 449 HIS   ( 120-)  C      ND1 <->  450 ASN   ( 121-)  C      N      0.35    2.55  INTRA BF
 526 HIS   (  62-)  D      N   <-> 1232 HOH   ( 183 )  D      O      0.34    2.36  INTRA BF
 535 GLU   (  71-)  D      OE1 <-> 1232 HOH   ( 180 )  D      O      0.33    2.07  INTRA BF
 521 ASN   (  57-)  D      ND2 <-> 1232 HOH   ( 201 )  D      O      0.31    2.39  INTRA BF
 195 LYS   (  31-)  B      NZ  <->  248 GLU   (  84-)  B      CD     0.31    2.79  INTRA
 472 ARG   ( 143-)  C      NE  <-> 1231 HOH   ( 233 )  C      O      0.31    2.39  INTRA BF
And so on for a total of 215 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 922 ARG   ( 148-)  F      -7.71
 758 ARG   ( 148-)  E      -7.66
 148 ARG   ( 148-)  A      -7.42
 312 ARG   ( 148-)  B      -7.01
1171 ARG   (  97-)  H      -6.76
 561 ARG   (  97-)  D      -6.65
 335 LEU   (   6-)  C      -6.62
 945 LEU   (   6-)  G      -6.49
1036 ARG   (  97-)  G      -6.14
 426 ARG   (  97-)  C      -5.95
1195 ASN   ( 121-)  H      -5.82
 585 ASN   ( 121-)  D      -5.80
 450 ASN   ( 121-)  C      -5.78
1060 ASN   ( 121-)  G      -5.77
1169 GLN   (  95-)  H      -5.72
1194 HIS   ( 120-)  H      -5.59
1034 GLN   (  95-)  G      -5.58
 144 ARG   ( 144-)  A      -5.37
 584 HIS   ( 120-)  D      -5.26
1170 MET   (  96-)  H      -5.20
 943 GLN   (   4-)  G      -5.08
 946 GLN   (   7-)  G      -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.

1034 GLN   (  95-)  G      1036 - ARG     97- ( G)         -5.25
1169 GLN   (  95-)  H      1171 - ARG     97- ( H)         -5.89
1193 THR   ( 119-)  H      1195 - ASN    121- ( H)         -5.16

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

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: G

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: H

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.

  87 ASN   (  87-)  A   -2.95
 861 ASN   (  87-)  F   -2.94
 697 ASN   (  87-)  E   -2.93
 691 GLU   (  81-)  E   -2.73
 894 GLU   ( 120-)  F   -2.71
1134 GLY   (  60-)  H   -2.71
  81 GLU   (  81-)  A   -2.67
 120 GLU   ( 120-)  A   -2.56
 730 GLU   ( 120-)  E   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 471 VAL   ( 142-)  C     -  474 TYR   ( 145-)  C        -1.83
1102 GLU   (  28-)  H     - 1105 ALA   (  31-)  H        -1.70

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

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.

1230 HOH   ( 341 )  B      O     19.61   30.09   37.13
1231 HOH   ( 319 )  C      O     32.95   25.20   66.47
1233 HOH   ( 364 )  E      O     29.85   12.51    6.19

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.

1231 HOH   ( 293 )  C      O
1235 HOH   ( 212 )  G      O
1235 HOH   ( 256 )  G      O
1235 HOH   ( 257 )  G      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.

 350 ASN   (  21-)  C
 396 GLN   (  67-)  C
 441 GLN   ( 112-)  C
 449 HIS   ( 120-)  C
 514 GLN   (  50-)  D
 526 HIS   (  62-)  D
 538 ASN   (  74-)  D
 559 GLN   (  95-)  D
 948 GLN   (   9-)  G
 952 GLN   (  13-)  G

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.

  87 ASN   (  87-)  A      N
  94 GLY   (  94-)  A      N
 121 TRP   ( 121-)  A      N
 210 PHE   (  46-)  B      N
 263 SER   (  99-)  B      OG
 266 ASN   ( 102-)  B      N
 281 ALA   ( 117-)  B      N
 283 THR   ( 119-)  B      OG1
 285 TRP   ( 121-)  B      N
 318 LYS   ( 154-)  B      N
 336 GLN   (   7-)  C      N
 361 PHE   (  32-)  C      N
 377 THR   (  48-)  C      OG1
 438 SER   ( 109-)  C      N
 479 ILE   (  15-)  D      N
 482 ARG   (  18-)  D      N
 482 ARG   (  18-)  D      NH2
 512 THR   (  48-)  D      OG1
 556 ALA   (  92-)  D      N
 596 ARG   ( 132-)  D      NH2
 656 PHE   (  46-)  E      N
 673 GLN   (  63-)  E      NE2
 697 ASN   (  87-)  E      N
 709 SER   (  99-)  E      OG
 727 ALA   ( 117-)  E      N
 731 TRP   ( 121-)  E      N
 764 LYS   ( 154-)  E      N
 820 PHE   (  46-)  F      N
 851 SER   (  77-)  F      OG
 861 ASN   (  87-)  F      N
 868 GLY   (  94-)  F      N
 876 ASN   ( 102-)  F      N
 885 GLN   ( 111-)  F      NE2
 891 ALA   ( 117-)  F      N
 894 GLU   ( 120-)  F      N
 895 TRP   ( 121-)  F      N
 928 LYS   ( 154-)  F      N
 951 HIS   (  12-)  G      NE2
 971 PHE   (  32-)  G      N
 987 THR   (  48-)  G      OG1
1031 ALA   (  92-)  G      N
1084 TYR   ( 145-)  G      OH
1107 SER   (  33-)  H      OG
1166 ALA   (  92-)  H      N
1206 ARG   ( 132-)  H      NH1

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.

1229 HOH   ( 197 )  A      O  0.85  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.

 123 ASP   ( 123-)  A   H-bonding suggests Asn
 250 GLU   (  86-)  B   H-bonding suggests Gln
 696 GLU   (  86-)  E   H-bonding suggests Gln; but Alt-Rotamer
 733 ASP   ( 123-)  E   H-bonding suggests Asn
 860 GLU   (  86-)  F   H-bonding suggests Gln
 984 GLU   (  45-)  G   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 :  -0.639
  2nd generation packing quality :  -1.029
  Ramachandran plot appearance   :  -0.452
  chi-1/chi-2 rotamer normality  :  -1.837
  Backbone conformation          :   0.162

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   1.318
  Omega angle restraints         :   0.997
  Side chain planarity           :   2.298 (loose)
  Improper dihedral distribution :   1.695 (loose)
  B-factor distribution          :   0.817
  Inside/Outside distribution    :   0.957

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   1.318
  Omega angle restraints         :   0.997
  Side chain planarity           :   2.298 (loose)
  Improper dihedral distribution :   1.695 (loose)
  B-factor distribution          :   0.817
  Inside/Outside distribution    :   0.957
==============

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.