WHAT IF Check report

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

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

Verification log for pdb3nb0.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

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

The CRYST1 cell dimensions

    A    = 192.739  B   = 206.982  C    = 205.799
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 174.888  B   = 174.888  C    = 174.888
    Alpha= 107.917  Beta= 113.124  Gamma= 107.437

Dimensions of the conventional cell

    A    = 205.799  B   = 206.982  C    = 192.739
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: I 2 2 2

Bravais type of conventional cell is: I

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.168
CA-only RMS fit for the two chains : 1.002

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Warning: Conventional cell is pseudo-cell

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

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2566 G6P   ( 901-)  A  -
2567 G6P   ( 902-)  A  -
2568 PEG   (1001-)  A  -
2569 PEG   (1002-)  A  -
2570 G6P   ( 901-)  B  -
2571 G6P   ( 902-)  B  -
2572 PEG   (1001-)  B  -
2573 PEG   ( 706-)  D  -
2574 G6P   ( 901-)  C  -
2575 PEG   (1001-)  C  -
2576 PEG   (1002-)  D  -
2577 G6P   ( 901-)  D  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

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

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

 371 GLN   ( 372-)  A  -
 382 HIS   ( 383-)  A  -
 894 HIS   ( 257-)  B  -
1020 HIS   ( 383-)  B  -
1654 GLN   ( 372-)  C  -

Warning: Alternate atom problems quasi solved

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

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

 371 GLN   ( 372-)  A  -
 382 HIS   ( 383-)  A  -
 894 HIS   ( 257-)  B  -
1020 HIS   ( 383-)  B  -
1654 GLN   ( 372-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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'.

1172 SER   ( 535-)  B      OG

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.

  54 GLN   (  55-)  A    High
  64 LYS   (  65-)  A    High
  65 PRO   (  66-)  A    High
  66 GLU   (  67-)  A    High
 182 ARG   ( 183-)  A    High
 623 GLU   ( 624-)  A    High
 625 VAL   ( 626-)  A    High
 626 GLY   ( 627-)  A    High
 627 GLU   ( 628-)  A    High
 628 GLU   ( 629-)  A    High
 704 GLU   (  67-)  B    High
 820 ARG   ( 183-)  B    High
1346 LYS   (  64-)  C    High
1347 LYS   (  65-)  C    High
1349 GLU   (  67-)  C    High
1368 ARG   (  86-)  C    High
1371 HIS   (  89-)  C    High
1930 SER   (   2-)  D    High
1931 ARG   (   3-)  D    High
1932 ASP   (   4-)  D    High
1933 LEU   (   5-)  D    High
1934 GLN   (   6-)  D    High
1979 LYS   (  51-)  D    High
1982 TYR   (  54-)  D    High
1983 GLN   (  55-)  D    High
And so on for a total of 113 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. 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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  24 TYR   (  25-)  A
  38 TYR   (  39-)  A
  53 TYR   (  54-)  A
 199 TYR   ( 200-)  A
 322 TYR   ( 323-)  A
 551 TYR   ( 552-)  A
 570 TYR   ( 571-)  A
 605 TYR   ( 606-)  A
 617 TYR   ( 618-)  A
 662 TYR   (  25-)  B
 691 TYR   (  54-)  B
 751 TYR   ( 114-)  B
 782 TYR   ( 145-)  B
 960 TYR   ( 323-)  B
1173 TYR   ( 536-)  B
1186 TYR   ( 549-)  B
1189 TYR   ( 552-)  B
1208 TYR   ( 571-)  B
1243 TYR   ( 606-)  B
1255 TYR   ( 618-)  B
1307 TYR   (  25-)  C
1396 TYR   ( 114-)  C
1427 TYR   ( 145-)  C
1482 TYR   ( 200-)  C
1605 TYR   ( 323-)  C
1831 TYR   ( 549-)  C
1834 TYR   ( 552-)  C
1853 TYR   ( 571-)  C
1888 TYR   ( 606-)  C
1900 TYR   ( 618-)  C
1953 TYR   (  25-)  D
1982 TYR   (  54-)  D
2128 TYR   ( 200-)  D
2249 TYR   ( 323-)  D
2266 TYR   ( 340-)  D
2497 TYR   ( 571-)  D
2532 TYR   ( 606-)  D
2544 TYR   ( 618-)  D

Warning: Phenylalanine convention problem

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

  10 PHE   (  11-)  A
  68 PHE   (  69-)  A
  89 PHE   (  90-)  A
 166 PHE   ( 167-)  A
 208 PHE   ( 209-)  A
 252 PHE   ( 253-)  A
 281 PHE   ( 282-)  A
 300 PHE   ( 301-)  A
 306 PHE   ( 307-)  A
 706 PHE   (  69-)  B
 772 PHE   ( 135-)  B
 804 PHE   ( 167-)  B
 938 PHE   ( 301-)  B
 944 PHE   ( 307-)  B
 991 PHE   ( 354-)  B
1372 PHE   (  90-)  C
1449 PHE   ( 167-)  C
1491 PHE   ( 209-)  C
1535 PHE   ( 253-)  C
1558 PHE   ( 276-)  C
1583 PHE   ( 301-)  C
1589 PHE   ( 307-)  C
1997 PHE   (  69-)  D
2063 PHE   ( 135-)  D
2078 PHE   ( 150-)  D
2095 PHE   ( 167-)  D
2135 PHE   ( 209-)  D
2205 PHE   ( 279-)  D
2227 PHE   ( 301-)  D
2233 PHE   ( 307-)  D
2501 PHE   ( 575-)  D
2548 PHE   ( 622-)  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.

 108 ASP   ( 109-)  A
 216 ASP   ( 217-)  A
 218 ASP   ( 219-)  A
 328 ASP   ( 329-)  A
 394 ASP   ( 395-)  A
 631 ASP   ( 632-)  A
 699 ASP   (  62-)  B
 854 ASP   ( 217-)  B
 945 ASP   ( 308-)  B
 966 ASP   ( 329-)  B
1176 ASP   ( 539-)  B
1199 ASP   ( 562-)  B
1269 ASP   ( 632-)  B
1391 ASP   ( 109-)  C
1499 ASP   ( 217-)  C
1501 ASP   ( 219-)  C
1590 ASP   ( 308-)  C
1611 ASP   ( 329-)  C
1677 ASP   ( 395-)  C
1703 ASP   ( 421-)  C
1844 ASP   ( 562-)  C
1914 ASP   ( 632-)  C
1969 ASP   (  41-)  D
2145 ASP   ( 219-)  D
2234 ASP   ( 308-)  D
2255 ASP   ( 329-)  D
2375 ASP   ( 449-)  D
2419 ASP   ( 493-)  D
2481 ASP   ( 555-)  D
2488 ASP   ( 562-)  D
2524 ASP   ( 598-)  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.

  71 GLU   (  72-)  A
  97 GLU   (  98-)  A
 116 GLU   ( 117-)  A
 168 GLU   ( 169-)  A
 220 GLU   ( 221-)  A
 233 GLU   ( 234-)  A
 253 GLU   ( 254-)  A
 255 GLU   ( 256-)  A
 604 GLU   ( 605-)  A
 627 GLU   ( 628-)  A
 653 GLU   (  16-)  B
 735 GLU   (  98-)  B
 754 GLU   ( 117-)  B
 806 GLU   ( 169-)  B
 858 GLU   ( 221-)  B
 871 GLU   ( 234-)  B
 893 GLU   ( 256-)  B
 918 GLU   ( 281-)  B
 928 GLU   ( 291-)  B
1011 GLU   ( 374-)  B
1045 GLU   ( 408-)  B
1146 GLU   ( 509-)  B
1154 GLU   ( 517-)  B
1242 GLU   ( 605-)  B
1265 GLU   ( 628-)  B
1380 GLU   (  98-)  C
1451 GLU   ( 169-)  C
1503 GLU   ( 221-)  C
1516 GLU   ( 234-)  C
1536 GLU   ( 254-)  C
1538 GLU   ( 256-)  C
1573 GLU   ( 291-)  C
1666 GLU   ( 384-)  C
1690 GLU   ( 408-)  C
1761 GLU   ( 479-)  C
1791 GLU   ( 509-)  C
1845 GLU   ( 563-)  C
1887 GLU   ( 605-)  C
1944 GLU   (  16-)  D
2000 GLU   (  72-)  D
2012 GLU   (  84-)  D
2060 GLU   ( 132-)  D
2097 GLU   ( 169-)  D
2147 GLU   ( 221-)  D
2160 GLU   ( 234-)  D
2180 GLU   ( 254-)  D
2217 GLU   ( 291-)  D
2334 GLU   ( 408-)  D
2435 GLU   ( 509-)  D
2554 GLU   ( 628-)  D

Geometric checks

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.

  71 GLU   (  72-)  A
  97 GLU   (  98-)  A
 108 ASP   ( 109-)  A
 116 GLU   ( 117-)  A
 168 GLU   ( 169-)  A
 216 ASP   ( 217-)  A
 218 ASP   ( 219-)  A
 220 GLU   ( 221-)  A
 233 GLU   ( 234-)  A
 253 GLU   ( 254-)  A
 255 GLU   ( 256-)  A
 328 ASP   ( 329-)  A
 394 ASP   ( 395-)  A
 604 GLU   ( 605-)  A
 627 GLU   ( 628-)  A
 631 ASP   ( 632-)  A
 653 GLU   (  16-)  B
 699 ASP   (  62-)  B
 735 GLU   (  98-)  B
 754 GLU   ( 117-)  B
 806 GLU   ( 169-)  B
 854 ASP   ( 217-)  B
 858 GLU   ( 221-)  B
 871 GLU   ( 234-)  B
 893 GLU   ( 256-)  B
And so on for a total of 81 lines.

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.

1825 THR   ( 543-)  C    -3.6
1683 PRO   ( 401-)  C    -3.1
1038 PRO   ( 401-)  B    -3.0
 400 PRO   ( 401-)  A    -3.0
2327 PRO   ( 401-)  D    -3.0
 857 HIS   ( 220-)  B    -2.9
  32 PRO   (  33-)  A    -2.9
 844 PHE   ( 207-)  B    -2.8
1282 LYS   ( 645-)  B    -2.7
2039 VAL   ( 111-)  D    -2.6
2469 THR   ( 543-)  D    -2.5
2139 LEU   ( 213-)  D    -2.5
 397 ILE   ( 398-)  A    -2.4
2324 ILE   ( 398-)  D    -2.4
 627 GLU   ( 628-)  A    -2.3
2289 SER   ( 363-)  D    -2.3
1000 SER   ( 363-)  B    -2.3
2112 ILE   ( 184-)  D    -2.3
2247 TYR   ( 321-)  D    -2.3
1645 SER   ( 363-)  C    -2.3
  18 ASN   (  19-)  A    -2.3
 362 SER   ( 363-)  A    -2.3
1680 ILE   ( 398-)  C    -2.3
1787 PRO   ( 505-)  C    -2.3
 273 ILE   ( 274-)  A    -2.2
And so on for a total of 58 lines.

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.

  17 ALA   (  18-)  A  Poor phi/psi
  39 LYS   (  40-)  A  Poor phi/psi
  52 THR   (  53-)  A  Poor phi/psi
  85 ARG   (  86-)  A  Poor phi/psi
  95 LEU   (  96-)  A  Poor phi/psi
  99 ALA   ( 100-)  A  Poor phi/psi
 168 GLU   ( 169-)  A  Poor phi/psi
 184 ASP   ( 185-)  A  Poor phi/psi
 193 ALA   ( 194-)  A  Poor phi/psi, omega poor
 259 LYS   ( 260-)  A  Poor phi/psi
 315 PHE   ( 316-)  A  omega poor
 362 SER   ( 363-)  A  Poor phi/psi
 399 TYR   ( 400-)  A  PRO omega poor
 402 ASN   ( 403-)  A  Poor phi/psi
 462 GLN   ( 463-)  A  Poor phi/psi
 465 ASN   ( 466-)  A  Poor phi/psi
 477 PRO   ( 478-)  A  Poor phi/psi
 504 PRO   ( 505-)  A  Poor phi/psi
 624 LEU   ( 625-)  A  Poor phi/psi
 625 VAL   ( 626-)  A  Poor phi/psi
 626 GLY   ( 627-)  A  Poor phi/psi
 654 VAL   (  17-)  B  Poor phi/psi
 657 ARG   (  20-)  B  Poor phi/psi
 677 LYS   (  40-)  B  Poor phi/psi
 690 THR   (  53-)  B  Poor phi/psi
And so on for a total of 74 lines.

Warning: Unusual rotamers

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

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

 667 SER   (  30-)  B    0.36
2490 SER   ( 564-)  D    0.37
1057 SER   ( 420-)  B    0.38
1172 SER   ( 535-)  B    0.39
1308 SER   (  26-)  C    0.40

Warning: Unusual backbone conformations

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

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

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

   6 ASN   (   7-)  A      0
  16 VAL   (  17-)  A      0
  17 ALA   (  18-)  A      0
  18 ASN   (  19-)  A      0
  19 ARG   (  20-)  A      0
  20 VAL   (  21-)  A      0
  39 LYS   (  40-)  A      0
  40 ASP   (  41-)  A      0
  41 HIS   (  42-)  A      0
  42 TYR   (  43-)  A      0
  52 THR   (  53-)  A      0
  62 TRP   (  63-)  A      0
  67 ALA   (  68-)  A      0
  72 MET   (  73-)  A      0
  91 TYR   (  92-)  A      0
  95 LEU   (  96-)  A      0
  96 ILE   (  97-)  A      0
  97 GLU   (  98-)  A      0
  99 ALA   ( 100-)  A      0
 110 VAL   ( 111-)  A      0
 124 LEU   ( 125-)  A      0
 125 VAL   ( 126-)  A      0
 156 LEU   ( 157-)  A      0
 158 SER   ( 159-)  A      0
 159 GLN   ( 160-)  A      0
And so on for a total of 759 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!

 109 SER   ( 110-)  A   1.60   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]

 477 PRO   ( 478-)  A    0.45 HIGH

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].

  32 PRO   (  33-)  A   108.2 envelop C-beta (108 degrees)
 100 PRO   ( 101-)  A    36.4 envelop C-delta (36 degrees)
 176 PRO   ( 177-)  A  -123.3 half-chair C-delta/C-gamma (-126 degrees)
 400 PRO   ( 401-)  A    22.3 half-chair N/C-delta (18 degrees)
 485 PRO   ( 486-)  A    41.5 envelop C-delta (36 degrees)
 504 PRO   ( 505-)  A    52.4 half-chair C-delta/C-gamma (54 degrees)
 685 PRO   (  48-)  B    42.4 envelop C-delta (36 degrees)
 712 PRO   (  75-)  B   102.4 envelop C-beta (108 degrees)
 738 PRO   ( 101-)  B   -59.1 half-chair C-beta/C-alpha (-54 degrees)
 768 PRO   ( 131-)  B   104.4 envelop C-beta (108 degrees)
1038 PRO   ( 401-)  B   -53.4 half-chair C-beta/C-alpha (-54 degrees)
1072 PRO   ( 435-)  B   101.9 envelop C-beta (108 degrees)
1142 PRO   ( 505-)  B    39.4 envelop C-delta (36 degrees)
1198 PRO   ( 561-)  B   100.4 envelop C-beta (108 degrees)
1330 PRO   (  48-)  C    37.7 envelop C-delta (36 degrees)
1383 PRO   ( 101-)  C    36.8 envelop C-delta (36 degrees)
1411 PRO   ( 129-)  C    48.0 half-chair C-delta/C-gamma (54 degrees)
1683 PRO   ( 401-)  C    14.6 half-chair N/C-delta (18 degrees)
1768 PRO   ( 486-)  C  -112.7 envelop C-gamma (-108 degrees)
1787 PRO   ( 505-)  C    30.4 envelop C-delta (36 degrees)
1843 PRO   ( 561-)  C   104.3 envelop C-beta (108 degrees)
2003 PRO   (  75-)  D   109.3 envelop C-beta (108 degrees)
2059 PRO   ( 131-)  D   102.3 envelop C-beta (108 degrees)
2105 PRO   ( 177-)  D  -118.2 half-chair C-delta/C-gamma (-126 degrees)
2327 PRO   ( 401-)  D    19.8 half-chair N/C-delta (18 degrees)
2361 PRO   ( 435-)  D   106.7 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1732 ASP   ( 450-)  C      OD1 <-> 1742 ARG   ( 460-)  C      NH2    0.44    2.26  INTRA BL
1770 LEU   ( 488-)  C      N   <-> 2580 HOH   ( 706 )  C      O      0.37    2.33  INTRA BL
1767 ASN   ( 485-)  C      CG  <-> 2580 HOH   ( 706 )  C      O      0.37    2.43  INTRA BL
 932 ASP   ( 295-)  B      OD1 <-> 1013 ARG   ( 376-)  B      NH2    0.35    2.35  INTRA BL
1087 ASP   ( 450-)  B      OD1 <-> 1097 ARG   ( 460-)  B      NH2    0.34    2.36  INTRA BL
 748 VAL   ( 111-)  B      CG1 <->  755 TRP   ( 118-)  B      CH2    0.33    2.87  INTRA BF
 932 ASP   ( 295-)  B      CG  <-> 1013 ARG   ( 376-)  B      NH2    0.33    2.77  INTRA BL
2414 LEU   ( 488-)  D      N   <-> 2581 HOH   ( 710 )  D      O      0.33    2.37  INTRA BL
 294 ASP   ( 295-)  A    A OD1 <->  375 ARG   ( 376-)  A      NH2    0.31    2.39  INTRA BL
1654 GLN   ( 372-)  C    A NE2 <-> 1658 ARG   ( 376-)  C      NH2    0.30    2.55  INTRA BL
 449 ASP   ( 450-)  A      OD1 <->  459 ARG   ( 460-)  A      NH2    0.30    2.40  INTRA BL
 487 LEU   ( 488-)  A      N   <-> 2578 HOH   ( 722 )  A      O      0.29    2.41  INTRA BL
1860 LYS   ( 578-)  C      NZ  <-> 1868 GLN   ( 586-)  C      NE2    0.29    2.56  INTRA BL
   2 ARG   (   3-)  A      NH2 <->  157 ASP   ( 158-)  A      O      0.29    2.41  INTRA BF
 297 ARG   ( 298-)  A      NH1 <-> 2578 HOH   ( 791 )  A      O      0.29    2.41  INTRA BL
1767 ASN   ( 485-)  C      ND2 <-> 2580 HOH   ( 706 )  C      O      0.29    2.41  INTRA BL
1247 ARG   ( 610-)  B      NH2 <-> 2579 HOH   ( 729 )  B      O      0.26    2.44  INTRA BL
2360 ARG   ( 434-)  D      NH1 <-> 2581 HOH   ( 763 )  D      O      0.26    2.44  INTRA BL
2408 ASN   ( 482-)  D      ND2 <-> 2410 ASN   ( 484-)  D      N      0.25    2.60  INTRA BL
 297 ARG   ( 298-)  A      NH2 <-> 2578 HOH   ( 760 )  A      O      0.24    2.46  INTRA BL
 294 ASP   ( 295-)  A    A CG  <->  375 ARG   ( 376-)  A      NH2    0.23    2.87  INTRA BL
2287 ASN   ( 361-)  D      N   <-> 2581 HOH   ( 746 )  D      O      0.22    2.48  INTRA BL
 555 ARG   ( 556-)  A      NH2 <-> 2578 HOH   ( 762 )  A      O      0.22    2.48  INTRA BL
2376 ASP   ( 450-)  D      OD1 <-> 2386 ARG   ( 460-)  D      NH2    0.21    2.49  INTRA BL
 762 LEU   ( 125-)  B      O   <->  818 LYS   ( 181-)  B      NZ     0.21    2.49  INTRA BF
And so on for a total of 329 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.

  19 ARG   (  20-)  A      -7.39
1302 ARG   (  20-)  C      -7.12
1948 ARG   (  20-)  D      -6.98
1070 ARG   ( 433-)  B      -6.97
 657 ARG   (  20-)  B      -6.74
1720 GLN   ( 438-)  C      -6.48
2364 GLN   ( 438-)  D      -6.22
2359 ARG   ( 433-)  D      -6.09
 437 GLN   ( 438-)  A      -6.08
 957 ARG   ( 320-)  B      -5.92
1715 ARG   ( 433-)  C      -5.83
1075 GLN   ( 438-)  B      -5.79
 319 ARG   ( 320-)  A      -5.79
2360 ARG   ( 434-)  D      -5.72
2150 ARG   ( 224-)  D      -5.68
 155 HIS   ( 156-)  A      -5.62
1464 ARG   ( 182-)  C      -5.59
 432 ARG   ( 433-)  A      -5.59
2110 ARG   ( 182-)  D      -5.56
1840 PHE   ( 558-)  C      -5.55
1506 ARG   ( 224-)  C      -5.53
 223 ARG   ( 224-)  A      -5.51
 861 ARG   ( 224-)  B      -5.50
1602 ARG   ( 320-)  C      -5.47
1716 ARG   ( 434-)  C      -5.45
1762 PHE   ( 480-)  C      -5.44
1071 ARG   ( 434-)  B      -5.38
1282 LYS   ( 645-)  B      -5.30
1195 PHE   ( 558-)  B      -5.28
  41 HIS   (  42-)  A      -5.28
 438 LEU   ( 439-)  A      -5.28
  63 LYS   (  64-)  A      -5.24
2365 LEU   ( 439-)  D      -5.21
1076 LEU   ( 439-)  B      -5.11
1681 ARG   ( 399-)  C      -5.07
1036 ARG   ( 399-)  B      -5.04
 557 PHE   ( 558-)  A      -5.03
 479 PHE   ( 480-)  A      -5.03
2325 ARG   ( 399-)  D      -5.01
1338 ASN   (  56-)  C      -5.01

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.

1278 GLY   ( 641-)  B      1282 - LYS    645- ( B)         -4.60
2186 LYS   ( 260-)  D      2188 - LYS    262- ( D)         -4.19

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.

1713 ALA   ( 431-)  C   -2.85
 125 VAL   ( 126-)  A   -2.63
1684 HIS   ( 402-)  C   -2.60
2388 VAL   ( 462-)  D   -2.55

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2578 HOH   ( 785 )  A      O
2578 HOH   ( 799 )  A      O
2578 HOH   ( 814 )  A      O
2578 HOH   ( 833 )  A      O
2578 HOH   ( 834 )  A      O
2578 HOH   ( 835 )  A      O
2578 HOH   ( 856 )  A      O
2579 HOH   ( 733 )  B      O
2579 HOH   ( 773 )  B      O
2579 HOH   ( 779 )  B      O
2579 HOH   ( 780 )  B      O
2579 HOH   ( 791 )  B      O
2579 HOH   ( 794 )  B      O
2579 HOH   ( 805 )  B      O
2581 HOH   ( 765 )  D      O
2581 HOH   ( 808 )  D      O
2581 HOH   ( 815 )  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.

 282 GLN   ( 283-)  A
 310 ASN   ( 311-)  A
 402 ASN   ( 403-)  A
 715 HIS   (  78-)  B
1033 HIS   ( 396-)  B
1089 ASN   ( 452-)  B
1219 GLN   ( 582-)  B
1271 ASN   ( 634-)  B
1521 HIS   ( 239-)  C
1554 ASN   ( 272-)  C
1566 ASN   ( 284-)  C
1654 GLN   ( 372-)  C
1685 ASN   ( 403-)  C
1767 ASN   ( 485-)  C
2006 HIS   (  78-)  D
2017 HIS   (  89-)  D
2096 HIS   ( 168-)  D
2209 GLN   ( 283-)  D
2328 HIS   ( 402-)  D
2329 ASN   ( 403-)  D
2408 ASN   ( 482-)  D
2560 ASN   ( 634-)  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.

   4 LEU   (   5-)  A      N
   6 ASN   (   7-)  A      N
  15 GLU   (  16-)  A      N
  25 SER   (  26-)  A      N
  54 GLN   (  55-)  A      N
  62 TRP   (  63-)  A      N
  63 LYS   (  64-)  A      N
  73 ARG   (  74-)  A      N
  75 VAL   (  76-)  A      N
 115 ASN   ( 116-)  A      N
 127 ILE   ( 128-)  A      N
 162 ILE   ( 163-)  A      N
 170 LEU   ( 171-)  A      N
 174 ALA   ( 175-)  A      N
 193 ALA   ( 194-)  A      N
 218 ASP   ( 219-)  A      N
 246 VAL   ( 247-)  A      N
 247 SER   ( 248-)  A      N
 264 GLY   ( 265-)  A      N
 268 ASN   ( 269-)  A      N
 269 GLY   ( 270-)  A      N
 279 HIS   ( 280-)  A      NE2
 281 PHE   ( 282-)  A      N
 306 PHE   ( 307-)  A      N
 317 ALA   ( 318-)  A      N
And so on for a total of 171 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.

  43 HIS   (  44-)  A      ND1
 285 HIS   ( 286-)  A      NE2
 310 ASN   ( 311-)  A      OD1
 906 ASN   ( 269-)  B      OD1
 923 HIS   ( 286-)  B      NE2
 962 ASN   ( 325-)  B      OD1
1011 GLU   ( 374-)  B      OE1
1475 HIS   ( 193-)  C      ND1
1568 HIS   ( 286-)  C      NE2
1607 ASN   ( 325-)  C      OD1
1799 GLU   ( 517-)  C      OE1
2212 HIS   ( 286-)  D      NE2
2558 ASP   ( 632-)  D      OD1

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.

2578 HOH   ( 798 )  A      O  1.10  K  4
2578 HOH   ( 820 )  A      O  1.00  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.

  15 GLU   (  16-)  A   H-bonding suggests Gln; but Alt-Rotamer
 590 GLU   ( 591-)  A   H-bonding suggests Gln; but Alt-Rotamer
 597 ASP   ( 598-)  A   H-bonding suggests Asn; but Alt-Rotamer
 776 ASP   ( 139-)  B   H-bonding suggests Asn
 966 ASP   ( 329-)  B   H-bonding suggests Asn
1011 GLU   ( 374-)  B   H-bonding suggests Gln; but Alt-Rotamer
1852 ASP   ( 570-)  C   H-bonding suggests Asn
1880 ASP   ( 598-)  C   H-bonding suggests Asn; but Alt-Rotamer
1985 GLU   (  57-)  D   H-bonding suggests Gln; but Alt-Rotamer
2465 ASP   ( 539-)  D   H-bonding suggests Asn
2496 ASP   ( 570-)  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 :   0.084
  2nd generation packing quality :  -0.834
  Ramachandran plot appearance   :  -1.443
  chi-1/chi-2 rotamer normality  :  -2.125
  Backbone conformation          :  -0.049

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.201 (tight)
  Bond angles                    :   0.481 (tight)
  Omega angle restraints         :   0.784
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.406
  B-factor distribution          :   0.464
  Inside/Outside distribution    :   1.010

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 : 2.41


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.201 (tight)
  Bond angles                    :   0.481 (tight)
  Omega angle restraints         :   0.784
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.406
  B-factor distribution          :   0.464
  Inside/Outside distribution    :   1.010
==============

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.