WHAT IF Check report

This file was created 2012-01-13 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 pdb1tx3.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

  74 PRO   (  23-)  A  -
 301 LEU   ( 258-)  A  -
 555 ILE   ( 257-)  B  -
 810 ILE   ( 257-)  C  -
 831 ARG   (  22-)  D  -
1054 ILE   ( 257-)  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: Missing atoms

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

  72 LYS   (  21-)  A      CG
  72 LYS   (  21-)  A      CD
  72 LYS   (  21-)  A      CE
  72 LYS   (  21-)  A      NZ
  73 ARG   (  22-)  A      CG
  73 ARG   (  22-)  A      CD
  73 ARG   (  22-)  A      NE
  73 ARG   (  22-)  A      CZ
  73 ARG   (  22-)  A      NH1
  73 ARG   (  22-)  A      NH2
  74 PRO   (  23-)  A      O
  93 SER   (  50-)  A      OG
 145 GLU   ( 102-)  A      CG
 145 GLU   ( 102-)  A      CD
 145 GLU   ( 102-)  A      OE1
 145 GLU   ( 102-)  A      OE2
 163 ASP   ( 120-)  A      CG
 163 ASP   ( 120-)  A      OD1
 163 ASP   ( 120-)  A      OD2
 202 LYS   ( 159-)  A      CG
 202 LYS   ( 159-)  A      CD
 202 LYS   ( 159-)  A      CE
 202 LYS   ( 159-)  A      NZ
 271 LYS   ( 228-)  A      CG
 271 LYS   ( 228-)  A      CD
And so on for a total of 182 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

  26 DGUA  (  13-)  F    High
  27 DGUA  (   1-)  G    High
  28 DCYT  (   2-)  G    High
  39 DGUA  (  13-)  G    High
  52 DGUA  (  13-)  H    High
 322 ARG   (  22-)  B    High
 324 LYS   (  24-)  B    High
 325 THR   (  27-)  B    High
 326 LEU   (  28-)  B    High
 327 SER   (  29-)  B    High
 328 GLY   (  30-)  B    High
 329 HIS   (  31-)  B    High
 330 ALA   (  32-)  B    High
 331 ALA   (  33-)  B    High
 332 GLY   (  34-)  B    High
 563 GLN   (   9-)  C    High
 575 LYS   (  21-)  C    High
 576 ARG   (  22-)  C    High
 577 PRO   (  23-)  C    High
 578 LYS   (  24-)  C    High
 579 SER   (  25-)  C    High
 580 GLY   (  26-)  C    High
 581 THR   (  27-)  C    High
 582 LEU   (  28-)  C    High
 583 SER   (  29-)  C    High
And so on for a total of 58 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 2.096 over 7023 bonds
Average difference in B over a bond : 5.29
RMS difference in B over a bond : 6.93

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.

 134 ARG   (  91-)  A

Warning: Tyrosine convention problem

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

  85 TYR   (  42-)  A
 357 TYR   (  59-)  B
 752 TYR   ( 199-)  C
 996 TYR   ( 199-)  D

Warning: Phenylalanine convention problem

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

  80 PHE   (  37-)  A
 148 PHE   ( 105-)  A
 207 PHE   ( 164-)  A
 234 PHE   ( 191-)  A
 277 PHE   ( 234-)  A
 296 PHE   ( 253-)  A
 335 PHE   (  37-)  B
 403 PHE   ( 105-)  B
 489 PHE   ( 191-)  B
 532 PHE   ( 234-)  B
 551 PHE   ( 253-)  B
 744 PHE   ( 191-)  C
 806 PHE   ( 253-)  C
 877 PHE   (  80-)  D
 902 PHE   ( 105-)  D
 988 PHE   ( 191-)  D
1031 PHE   ( 234-)  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.

 157 ASP   ( 114-)  A
 200 ASP   ( 157-)  A
 257 ASP   ( 214-)  A
 290 ASP   ( 247-)  A
 310 ASP   (  10-)  B
 412 ASP   ( 114-)  B
 425 ASP   ( 127-)  B
 463 ASP   ( 165-)  B
 470 ASP   ( 172-)  B
 514 ASP   ( 216-)  B
 710 ASP   ( 157-)  C
 725 ASP   ( 172-)  C
 819 ASP   (  10-)  D
 848 ASP   (  51-)  D
 859 ASP   (  62-)  D
 911 ASP   ( 114-)  D
 924 ASP   ( 127-)  D
1044 ASP   ( 247-)  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.

  81 GLU   (  38-)  A
  90 GLU   (  47-)  A
 117 GLU   (  74-)  A
 140 GLU   (  97-)  A
 149 GLU   ( 106-)  A
 167 GLU   ( 124-)  A
 217 GLU   ( 174-)  A
 221 GLU   ( 178-)  A
 232 GLU   ( 189-)  A
 240 GLU   ( 197-)  A
 267 GLU   ( 224-)  A
 336 GLU   (  38-)  B
 356 GLU   (  58-)  B
 372 GLU   (  74-)  B
 405 GLU   ( 107-)  B
 422 GLU   ( 124-)  B
 458 GLU   ( 160-)  B
 468 GLU   ( 170-)  B
 472 GLU   ( 174-)  B
 476 GLU   ( 178-)  B
 495 GLU   ( 197-)  B
 592 GLU   (  38-)  C
 651 GLU   (  97-)  C
 660 GLU   ( 106-)  C
 677 GLU   ( 124-)  C
 727 GLU   ( 174-)  C
 792 GLU   ( 239-)  C
 835 GLU   (  38-)  D
 894 GLU   (  97-)  D
 967 GLU   ( 170-)  D
 971 GLU   ( 174-)  D
 975 GLU   ( 178-)  D
 986 GLU   ( 189-)  D
 991 GLU   ( 194-)  D
1021 GLU   ( 224-)  D
1022 GLU   ( 225-)  D
1036 GLU   ( 239-)  D

Geometric checks

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.

   4 DGUA  (   4-)  E      N9   C8   N7  113.12    4.0
   5 DGUA  (   5-)  E      N9   C8   N7  113.18    4.2
  13 DGUA  (  13-)  E      N9   C8   N7  113.20    4.2
  14 DGUA  (   1-)  F      N9   C8   N7  113.13    4.1
  17 DGUA  (   4-)  F      N9   C8   N7  113.10    4.0
  18 DGUA  (   5-)  F      N9   C8   N7  113.13    4.1
  21 DGUA  (   8-)  F      N9   C8   N7  113.21    4.2
  23 DCYT  (  10-)  F      C2'  C1'  N1  107.03   -4.5
  26 DGUA  (  13-)  F      N9   C8   N7  113.15    4.1
  31 DGUA  (   5-)  G      N9   C8   N7  113.11    4.0
  34 DGUA  (   8-)  G      N9   C8   N7  113.24    4.3
  38 DGUA  (  12-)  G      N9   C8   N7  113.33    4.5
  40 DGUA  (   1-)  H      N9   C8   N7  113.11    4.0
  43 DGUA  (   4-)  H      N9   C8   N7  113.10    4.0
  47 DGUA  (   8-)  H      N9   C8   N7  113.13    4.1
  51 DGUA  (  12-)  H      N9   C8   N7  113.14    4.1
 353 LYS   (  55-)  B      N    CA   C    98.96   -4.4

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.

  81 GLU   (  38-)  A
  90 GLU   (  47-)  A
 117 GLU   (  74-)  A
 134 ARG   (  91-)  A
 140 GLU   (  97-)  A
 149 GLU   ( 106-)  A
 157 ASP   ( 114-)  A
 167 GLU   ( 124-)  A
 200 ASP   ( 157-)  A
 217 GLU   ( 174-)  A
 221 GLU   ( 178-)  A
 232 GLU   ( 189-)  A
 240 GLU   ( 197-)  A
 257 ASP   ( 214-)  A
 267 GLU   ( 224-)  A
 290 ASP   ( 247-)  A
 310 ASP   (  10-)  B
 336 GLU   (  38-)  B
 356 GLU   (  58-)  B
 372 GLU   (  74-)  B
 405 GLU   ( 107-)  B
 412 ASP   ( 114-)  B
 422 GLU   ( 124-)  B
 425 ASP   ( 127-)  B
 458 GLU   ( 160-)  B
And so on for a total of 56 lines.

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.

 353 LYS   (  55-)  B    4.76
  98 LYS   (  55-)  A    4.30
 886 LEU   (  89-)  D    4.07

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.

 696 ILE   ( 143-)  C    -2.8
 631 TYR   (  77-)  C    -2.6
 849 LEU   (  52-)  D    -2.5
 389 ARG   (  91-)  B    -2.3
 577 PRO   (  23-)  C    -2.3
 164 GLN   ( 121-)  A    -2.2
 771 GLY   ( 218-)  C    -2.2
 400 GLU   ( 102-)  B    -2.1
 307 ILE   (   7-)  B    -2.1
 606 LEU   (  52-)  C    -2.1
 625 ILE   (  71-)  C    -2.1
 508 PHE   ( 210-)  B    -2.0
1015 GLY   ( 218-)  D    -2.0
 970 TRP   ( 173-)  D    -2.0
 888 ARG   (  91-)  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.

 134 ARG   (  91-)  A  Poor phi/psi
 163 ASP   ( 120-)  A  Poor phi/psi
 164 GLN   ( 121-)  A  Poor phi/psi
 331 ALA   (  33-)  B  Poor phi/psi
 334 PRO   (  36-)  B  Poor phi/psi
 379 ASN   (  81-)  B  Poor phi/psi
 398 SER   ( 100-)  B  Poor phi/psi
 418 ASP   ( 120-)  B  Poor phi/psi
 419 GLN   ( 121-)  B  Poor phi/psi
 457 LYS   ( 159-)  B  Poor phi/psi
 502 ALA   ( 204-)  B  Poor phi/psi
 503 ALA   ( 205-)  B  Poor phi/psi
 508 PHE   ( 210-)  B  Poor phi/psi
 602 ASN   (  48-)  C  Poor phi/psi
 610 GLN   (  56-)  C  Poor phi/psi
 618 PHE   (  64-)  C  Poor phi/psi
 619 MET   (  65-)  C  Poor phi/psi
 627 HIS   (  73-)  C  Poor phi/psi
 628 GLU   (  74-)  C  Poor phi/psi
 643 LEU   (  89-)  C  Poor phi/psi
 645 ARG   (  91-)  C  Poor phi/psi
 744 PHE   ( 191-)  C  Poor phi/psi
 758 ALA   ( 205-)  C  Poor phi/psi
 801 LYS   ( 248-)  C  Poor phi/psi
 828 LYS   (  19-)  D  Poor phi/psi
 829 VAL   (  20-)  D  Poor phi/psi
 830 LYS   (  21-)  D  Poor phi/psi
 878 ASN   (  81-)  D  Poor phi/psi
 888 ARG   (  91-)  D  Poor phi/psi
 917 ASP   ( 120-)  D  Poor phi/psi
 918 GLN   ( 121-)  D  Poor phi/psi
 959 ASP   ( 162-)  D  Poor phi/psi
 971 GLU   ( 174-)  D  Poor phi/psi
 972 LEU   ( 175-)  D  Poor phi/psi
 973 ASN   ( 176-)  D  Poor phi/psi
 975 GLU   ( 178-)  D  Poor phi/psi
1002 ALA   ( 205-)  D  Poor phi/psi
1007 PHE   ( 210-)  D  Poor phi/psi
1011 ASP   ( 214-)  D  Poor phi/psi
1047 VAL   ( 250-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.838

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.

 313 SER   (  13-)  B    0.36
  56 LYS   (   5-)  A    0.38
 305 LYS   (   5-)  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 DCYT  (   3-)  E      0
   4 DGUA  (   4-)  E      0
   5 DGUA  (   5-)  E      0
   6 DTHY  (   6-)  E      0
   7 DCYT  (   7-)  E      0
   8 DGUA  (   8-)  E      0
   9 DADE  (   9-)  E      0
  10 DCYT  (  10-)  E      0
  11 DCYT  (  11-)  E      0
  12 DGUA  (  12-)  E      0
  13 DGUA  (  13-)  E      0
  14 DGUA  (   1-)  F      0
  15 DCYT  (   2-)  F      0
  16 DCYT  (   3-)  F      0
  17 DGUA  (   4-)  F      0
  18 DGUA  (   5-)  F      0
  19 DTHY  (   6-)  F      0
  20 DCYT  (   7-)  F      0
  21 DGUA  (   8-)  F      0
  22 DADE  (   9-)  F      0
  23 DCYT  (  10-)  F      0
  24 DCYT  (  11-)  F      0
  25 DGUA  (  12-)  F      0
  26 DGUA  (  13-)  F      0
  27 DGUA  (   1-)  G      0
And so on for a total of 433 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.879

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!

 332 GLY   (  34-)  B   2.18   12

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]

 438 PRO   ( 140-)  B    0.46 HIGH
 833 PRO   (  36-)  D    0.00 LOW

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.

 862 MET   (  65-)  D      SD  <-> 1066 HOH   ( 904 )  D      O      0.50    2.50  INTRA BF
 135 GLY   (  92-)  A      N   <-> 1063 HOH   ( 819 )  A      O      0.39    2.31  INTRA BL
 134 ARG   (  91-)  A      C   <-> 1063 HOH   ( 819 )  A      O      0.35    2.45  INTRA
 288 MET   ( 245-)  A      SD  <-> 1064 HOH   (1113 )  B      O      0.35    2.65  INTRA BF
 888 ARG   (  91-)  D      C   <-> 1066 HOH   ( 851 )  D      O      0.33    2.47  INTRA
 389 ARG   (  91-)  B      NH2 <->  404 GLU   ( 106-)  B      O      0.31    2.39  INTRA BL
 254 HIS   ( 211-)  A      ND1 <-> 1063 HOH   ( 867 )  A      O      0.31    2.39  INTRA BL
 333 GLU   (  35-)  B      C   <->  335 PHE   (  37-)  B      N      0.29    2.61  INTRA BF
  34 DGUA  (   8-)  G      N7  <->  938 ASN   ( 141-)  D      ND2    0.28    2.72  INTRA BL
 878 ASN   (  81-)  D      N   <-> 1066 HOH   ( 827 )  D      O      0.27    2.43  INTRA BF
 889 GLY   (  92-)  D      N   <-> 1066 HOH   ( 851 )  D      O      0.26    2.44  INTRA BL
 618 PHE   (  64-)  C      O   <->  620 LYS   (  66-)  C      N      0.26    2.44  INTRA BF
 134 ARG   (  91-)  A      N   <-> 1063 HOH   ( 819 )  A      O      0.25    2.45  INTRA BL
  38 DGUA  (  12-)  G      C8  <-> 1061 HOH   ( 708 )  G      O      0.25    2.55  INTRA BL
 134 ARG   (  91-)  A      NH2 <->  149 GLU   ( 106-)  A      O      0.25    2.45  INTRA
 918 GLN   ( 121-)  D      N   <-> 1066 HOH   ( 866 )  D      O      0.24    2.46  INTRA BF
 453 MET   ( 155-)  B      SD  <-> 1064 HOH   (1005 )  B      O      0.22    2.78  INTRA BL
 877 PHE   (  80-)  D      O   <->  879 SER   (  82-)  D      N      0.21    2.49  INTRA BF
  35 DADE  (   9-)  G      N1  <->   45 DTHY  (   6-)  H      N3     0.21    2.79  INTRA BL
  78 GLU   (  35-)  A      N   <->   79 PRO   (  36-)  A      CD     0.21    2.79  INTRA BL
 116 HIS   (  73-)  A      ND1 <->  140 GLU   (  97-)  A      OE1    0.21    2.49  INTRA BL
  37 DCYT  (  11-)  G      N3  <->   43 DGUA  (   4-)  H      N1     0.20    2.80  INTRA BL
  44 DGUA  (   5-)  H      N7  <->  998 ASN   ( 201-)  D      ND2    0.20    2.80  INTRA BL
 431 ILE   ( 133-)  B      O   <->  433 LYS   ( 135-)  B      N      0.20    2.50  INTRA BL
 888 ARG   (  91-)  D      NH2 <->  903 GLU   ( 106-)  D      O      0.20    2.50  INTRA BF
And so on for a total of 206 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.

 935 GLN   ( 138-)  D      -7.10
 436 GLN   ( 138-)  B      -6.94
 181 GLN   ( 138-)  A      -6.47
 691 GLN   ( 138-)  C      -6.45
 134 ARG   (  91-)  A      -5.92
 731 GLU   ( 178-)  C      -5.66
 888 ARG   (  91-)  D      -5.49
 868 ILE   (  71-)  D      -5.45
 773 ASN   ( 220-)  C      -5.43
 845 ASN   (  48-)  D      -5.41
 808 LYS   ( 255-)  C      -5.41
1016 PHE   ( 219-)  D      -5.40
 553 LYS   ( 255-)  B      -5.39
  91 ASN   (  48-)  A      -5.38
 906 GLN   ( 109-)  D      -5.36
 456 ASN   ( 158-)  B      -5.33
 201 ASN   ( 158-)  A      -5.32
1052 LYS   ( 255-)  D      -5.31
 645 ARG   (  91-)  C      -5.31
 772 PHE   ( 219-)  C      -5.29
 625 ILE   (  71-)  C      -5.26
 895 ASN   (  98-)  D      -5.21
 114 ILE   (  71-)  A      -5.17
 396 ASN   (  98-)  B      -5.16
 321 LYS   (  21-)  B      -5.15
 663 GLN   ( 109-)  C      -5.14
 221 GLU   ( 178-)  A      -5.14
 518 ASN   ( 220-)  B      -5.10
 635 ASN   (  81-)  C      -5.05
 827 GLN   (  18-)  D      -5.02
 369 ILE   (  71-)  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.

 153 ASN   ( 110-)  A   -3.99
 408 ASN   ( 110-)  B   -3.94
 906 GLN   ( 109-)  D   -3.39
  73 ARG   (  22-)  A   -3.35
 576 ARG   (  22-)  C   -3.19
 907 ASN   ( 110-)  D   -3.13
 407 GLN   ( 109-)  B   -3.13
 647 LYS   (  93-)  C   -2.94
 152 GLN   ( 109-)  A   -2.92
 333 GLU   (  35-)  B   -2.91
 573 LYS   (  19-)  C   -2.85
 609 LYS   (  55-)  C   -2.78
 181 GLN   ( 138-)  A   -2.72
 691 GLN   ( 138-)  C   -2.70
 436 GLN   ( 138-)  B   -2.59
 163 ASP   ( 120-)  A   -2.58
 935 GLN   ( 138-)  D   -2.58
 301 LEU   ( 258-)  A   -2.56
 578 LYS   (  24-)  C   -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.

 330 ALA   (  32-)  B     -  333 GLU   (  35-)  B        -2.04
 432 SER   ( 134-)  B     -  436 GLN   ( 138-)  B        -1.97
 582 LEU   (  28-)  C     -  585 HIS   (  31-)  C        -1.81

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

1063 HOH   ( 942 )  A      O
1064 HOH   ( 992 )  B      O
1066 HOH   ( 837 )  D      O

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.

1060 HOH   ( 269 )  F      O     26.92    1.23  182.47
1062 HOH   ( 351 )  H      O     21.71  -22.70  250.83
1063 HOH   ( 840 )  A      O     58.28   21.17  205.45
1063 HOH   ( 897 )  A      O     44.57   35.16  183.54
1063 HOH   ( 906 )  A      O     58.98   22.15  201.14
1063 HOH   ( 937 )  A      O     56.87   25.10  210.19
1063 HOH   ( 940 )  A      O     57.64   23.88  205.44
1063 HOH   ( 942 )  A      O     -6.01   26.33  173.72
1063 HOH   ( 962 )  A      O     23.20    1.42  192.32
1063 HOH   ( 971 )  A      O     10.24   -1.97  202.23
1063 HOH   ( 983 )  A      O     10.07    0.95  196.62
1063 HOH   ( 987 )  A      O     60.58   25.01  206.52
1063 HOH   ( 989 )  A      O     59.22   17.09  204.15
1064 HOH   ( 991 )  B      O     -3.48   26.86  213.73
1064 HOH   (1000 )  B      O     -4.10   13.44  186.92
1064 HOH   (1001 )  B      O     -4.64   16.38  185.49
1064 HOH   (1008 )  B      O     -3.29    9.20  227.11
1064 HOH   (1030 )  B      O     24.45   47.20  190.91
1066 HOH   ( 831 )  D      O     50.89    8.62  225.49
1066 HOH   ( 837 )  D      O     51.96   20.10  175.41
1066 HOH   ( 839 )  D      O     54.85    2.86  206.85
1066 HOH   ( 845 )  D      O     54.53  -16.66  230.90

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.

1060 HOH   ( 616 )  F      O
1061 HOH   ( 412 )  G      O
1063 HOH   ( 830 )  A      O
1063 HOH   ( 883 )  A      O
1063 HOH   ( 897 )  A      O
1063 HOH   ( 942 )  A      O
1063 HOH   ( 949 )  A      O
1063 HOH   ( 960 )  A      O
1063 HOH   ( 972 )  A      O
1063 HOH   (1005 )  A      O
1064 HOH   ( 906 )  B      O
1064 HOH   ( 962 )  B      O
1064 HOH   ( 985 )  B      O
1064 HOH   ( 992 )  B      O
1064 HOH   (1040 )  B      O
1065 HOH   ( 820 )  C      O
1065 HOH   ( 827 )  C      O
1065 HOH   ( 836 )  C      O
1065 HOH   ( 842 )  C      O
1065 HOH   ( 865 )  C      O
1066 HOH   ( 837 )  D      O
1066 HOH   ( 867 )  D      O
1066 HOH   ( 882 )  D      O
1066 HOH   ( 899 )  D      O

Error: HIS, ASN, GLN side chain flips

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

 396 ASN   (  98-)  B
 509 HIS   ( 211-)  B
 615 ASN   (  61-)  C
 657 ASN   ( 103-)  C
 853 GLN   (  56-)  D
 878 ASN   (  81-)  D
1037 GLN   ( 240-)  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.

  48 DADE  (   9-)  H      N6
 120 TYR   (  77-)  A      OH
 134 ARG   (  91-)  A      NH1
 135 GLY   (  92-)  A      N
 204 PHE   ( 161-)  A      N
 228 THR   ( 185-)  A      OG1
 250 GLN   ( 207-)  A      NE2
 253 PHE   ( 210-)  A      N
 259 ASP   ( 216-)  A      N
 265 THR   ( 222-)  A      N
 267 GLU   ( 224-)  A      N
 268 GLU   ( 225-)  A      N
 300 ILE   ( 257-)  A      N
 322 ARG   (  22-)  B      NE
 335 PHE   (  37-)  B      N
 355 TYR   (  57-)  B      N
 372 GLU   (  74-)  B      N
 380 SER   (  82-)  B      OG
 389 ARG   (  91-)  B      NH1
 400 GLU   ( 102-)  B      N
 427 LYS   ( 129-)  B      NZ
 436 GLN   ( 138-)  B      NE2
 460 ASP   ( 162-)  B      N
 466 TYR   ( 168-)  B      OH
 473 LEU   ( 175-)  B      N
And so on for a total of 66 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.

 152 GLN   ( 109-)  A      OE1
 170 ASP   ( 127-)  A      OD1
 336 GLU   (  38-)  B      OE1
 470 ASP   ( 172-)  B      OD1
 505 GLN   ( 207-)  B      OE1
 677 GLU   ( 124-)  C      OE1
 680 ASP   ( 127-)  C      OD2
 711 ASN   ( 158-)  C      OD1
 725 ASP   ( 172-)  C      OD1
 906 GLN   ( 109-)  D      OE1

Warning: Unusual ion packing

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

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

1056  NA   ( 802-)  B     1.39   1.17 Scores about as good as CA

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1059 HOH   ( 776 )  E      O  0.98  K  7
1062 HOH   ( 780 )  H      O  1.04  K  4 Ion-B
1063 HOH   ( 812 )  A      O  0.89  K  6 ION-B
1063 HOH   ( 868 )  A      O  0.91  K  4 NCS 1/1
1064 HOH   ( 902 )  B      O  0.99  K  4 Ion-B
1064 HOH   ( 923 )  B      O  0.87  K  4 Ion-B
1064 HOH   ( 932 )  B      O  1.10  K  6 Ion-B
1064 HOH   (1027 )  B      O  0.98  K  4
1064 HOH   (1065 )  B      O  0.88  K  4 Ion-B
1064 HOH   (1067 )  B      O  0.95  K  4
1064 HOH   (1118 )  B      O  0.88 NA  6 *1 and *2
1066 HOH   ( 812 )  D      O  1.04  K  4
1066 HOH   ( 906 )  D      O  0.84 NA  6 *1 and *2 NCS 1/1

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.

 157 ASP   ( 114-)  A   H-bonding suggests Asn; but Alt-Rotamer
 170 ASP   ( 127-)  A   H-bonding suggests Asn; but Alt-Rotamer
 222 ASP   ( 179-)  A   H-bonding suggests Asn; but Alt-Rotamer
 425 ASP   ( 127-)  B   H-bonding suggests Asn; but Alt-Rotamer
 477 ASP   ( 179-)  B   H-bonding suggests Asn; but Alt-Rotamer
 545 ASP   ( 247-)  B   H-bonding suggests Asn
 616 ASP   (  62-)  C   H-bonding suggests Asn; but Alt-Rotamer
 668 ASP   ( 114-)  C   H-bonding suggests Asn
 732 ASP   ( 179-)  C   H-bonding suggests Asn; but Alt-Rotamer
 800 ASP   ( 247-)  C   H-bonding suggests Asn
 911 ASP   ( 114-)  D   H-bonding suggests Asn
 954 ASP   ( 157-)  D   H-bonding suggests Asn; but Alt-Rotamer
 962 ASP   ( 165-)  D   H-bonding suggests Asn; but Alt-Rotamer
 976 ASP   ( 179-)  D   H-bonding suggests Asn; but Alt-Rotamer
1011 ASP   ( 214-)  D   H-bonding suggests Asn
1044 ASP   ( 247-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.405
  2nd generation packing quality :  -2.763
  Ramachandran plot appearance   :  -2.913
  chi-1/chi-2 rotamer normality  :  -1.838
  Backbone conformation          :  -1.030

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.288 (tight)
  Bond angles                    :   0.522 (tight)
  Omega angle restraints         :   0.160 (tight)
  Side chain planarity           :   0.208 (tight)
  Improper dihedral distribution :   0.540
  B-factor distribution          :   2.096 (loose)
  Inside/Outside distribution    :   0.992

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.288 (tight)
  Bond angles                    :   0.522 (tight)
  Omega angle restraints         :   0.160 (tight)
  Side chain planarity           :   0.208 (tight)
  Improper dihedral distribution :   0.540
  B-factor distribution          :   2.096 (loose)
  Inside/Outside distribution    :   0.992
==============

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.