WHAT IF Check report

This file was created 2014-04-24 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 pdb4cej.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2380 ANP   (2233-)  A  -
2382 SF4   (2160-)  B  -         Atom types
2383 ANP   (2161-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

2379 DTHY  (  69-)  X      C3'
2379 DTHY  (  69-)  X      O3'
2379 DTHY  (  69-)  X      C5'
2379 DTHY  (  69-)  X      C4'
2379 DTHY  (  69-)  X      O4'
2379 DTHY  (  69-)  X      C1'
2379 DTHY  (  69-)  X      C2'
2379 DTHY  (  69-)  X      N1
2379 DTHY  (  69-)  X      C6
2379 DTHY  (  69-)  X      C5
2379 DTHY  (  69-)  X      C4
2379 DTHY  (  69-)  X      O4
2379 DTHY  (  69-)  X      N3
2379 DTHY  (  69-)  X      C2
2379 DTHY  (  69-)  X      O2
2379 DTHY  (  69-)  X      C7

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.

   4 ASP   (  13-)  A    High
   8 ASN   (  17-)  A    High
  15 GLN   (  24-)  A    High
  39 ILE   (  48-)  A    High
  40 THR   (  49-)  A    High
  41 ALA   (  50-)  A    High
  42 GLU   (  51-)  A    High
  43 GLU   (  52-)  A    High
  44 ASN   (  53-)  A    High
  45 PRO   (  54-)  A    High
  49 ASP   (  58-)  A    High
  63 GLU   (  72-)  A    High
  64 MET   (  73-)  A    High
  65 LYS   (  74-)  A    High
  66 HIS   (  75-)  A    High
  67 ARG   (  76-)  A    High
  70 GLU   (  79-)  A    High
  71 ALA   (  80-)  A    High
  72 LEU   (  81-)  A    High
  73 GLU   (  82-)  A    High
  74 LYS   (  83-)  A    High
  75 GLU   (  84-)  A    High
  76 LEU   (  85-)  A    High
  77 VAL   (  86-)  A    High
  78 GLN   (  87-)  A    High
And so on for a total of 919 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

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 : 1.538 over 12370 bonds
Average difference in B over a bond : 6.06
RMS difference in B over a bond : 7.78

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

Nomenclature related problems

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

2366 DTHY  (  56-)  X
2367 DTHY  (  57-)  X
2370 DTHY  (  60-)  X
2371 DTHY  (  61-)  X
2372 DADE  (  62-)  X
2374 DCYT  (  64-)  X

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.

 953 GLY   ( 986-)  A      N    CA   C   125.67    4.5
1035 TYR   (1090-)  A      CA   CB   CG  123.18    5.0
1961 ARG   ( 787-)  B      CG   CD   NE  117.46    4.1
2334 DTHY  (   7-)  X      O4   C4   N3  122.51    4.3
2336 DTHY  (   9-)  X      O4   C4   N3  122.50    4.3
2339 DTHY  (  12-)  X      O4   C4   N3  122.53    4.4
2340 DGUA  (  13-)  X      N9   C8   N7  113.35    4.5
2342 DGUA  (  15-)  X      N9   C8   N7  113.14    4.1
2344 DGUA  (  17-)  X      N9   C8   N7  113.35    4.5
2347 DTHY  (  37-)  X      O4   C4   N3  122.63    4.5
2350 DTHY  (  40-)  X      O4   C4   N3  122.54    4.4
2352 DGUA  (  42-)  X      N9   C8   N7  113.37    4.5
2355 DTHY  (  45-)  X      O4   C4   N3  122.35    4.1
2356 DTHY  (  46-)  X      O4   C4   N3  122.60    4.5
2358 DGUA  (  48-)  X      N9   C8   N7  113.80    5.4
2362 DTHY  (  52-)  X      O4   C4   N3  122.40    4.2
2363 DTHY  (  53-)  X      O4   C4   N3  122.35    4.1
2364 DGUA  (  54-)  X      N9   C8   N7  113.43    4.7
2365 DTHY  (  55-)  X      O4   C4   N3  122.42    4.2
2366 DTHY  (  56-)  X      O4'  C1'  N1  112.68    6.1
2367 DTHY  (  57-)  X      C4'  C3'  C2'  99.19   -4.0
2369 DTHY  (  59-)  X      O4   C4   N3  122.33    4.1
2371 DTHY  (  61-)  X      O4   C4   N3  122.35    4.1
2373 DGUA  (  63-)  X      N9   C8   N7  113.31    4.4
2375 DGUA  (  65-)  X      N9   C8   N7  113.33    4.5
2376 DGUA  (  66-)  X      N9   C8   N7  113.48    4.8
2378 DTHY  (  68-)  X      O4   C4   N3  122.37    4.1

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.

 571 MET   ( 592-)  A    4.71
 953 GLY   ( 986-)  A    4.34
1656 VAL   ( 482-)  B    4.01

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.

 952 PRO   ( 985-)  A    -3.0
  13 THR   (  22-)  A    -2.8
1809 ILE   ( 635-)  B    -2.6
 934 ARG   ( 967-)  A    -2.6
 732 THR   ( 753-)  A    -2.6
 493 GLU   ( 502-)  A    -2.5
1074 GLU   (1129-)  A    -2.5
1122 ARG   (1177-)  A    -2.5
 819 ARG   ( 840-)  A    -2.5
 208 PRO   ( 217-)  A    -2.4
1213 PHE   (  37-)  B    -2.4
1493 ASN   ( 319-)  B    -2.4
1474 ARG   ( 300-)  B    -2.4
 802 LEU   ( 823-)  A    -2.4
 438 ARG   ( 447-)  A    -2.4
 362 LEU   ( 371-)  A    -2.3
 554 LYS   ( 575-)  A    -2.3
2171 LEU   ( 997-)  B    -2.3
2186 HIS   (1012-)  B    -2.2
 161 THR   ( 170-)  A    -2.2
  15 GLN   (  24-)  A    -2.2
1048 ILE   (1103-)  A    -2.2
2242 LYS   (1068-)  B    -2.2
2237 ILE   (1063-)  B    -2.2
2215 LEU   (1041-)  B    -2.2
1890 VAL   ( 716-)  B    -2.2
2313 ASN   (1139-)  B    -2.2
 811 THR   ( 832-)  A    -2.2
2138 SER   ( 964-)  B    -2.2
2119 ARG   ( 945-)  B    -2.2
1355 LEU   ( 181-)  B    -2.1
2177 PRO   (1003-)  B    -2.1
1037 LYS   (1092-)  A    -2.1
1782 GLY   ( 608-)  B    -2.1
 758 ARG   ( 779-)  A    -2.1
 252 LEU   ( 261-)  A    -2.1
2191 GLN   (1017-)  B    -2.1
  40 THR   (  49-)  A    -2.1
1285 VAL   ( 109-)  B    -2.1
2172 GLY   ( 998-)  B    -2.1
 441 GLU   ( 450-)  A    -2.1
 937 GLU   ( 970-)  A    -2.1
 488 GLY   ( 497-)  A    -2.0
1410 THR   ( 236-)  B    -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.

  22 ALA   (  31-)  A  Poor phi/psi
 115 ILE   ( 124-)  A  Poor phi/psi
 163 ARG   ( 172-)  A  Poor phi/psi
 288 PHE   ( 297-)  A  Poor phi/psi
 358 ASP   ( 367-)  A  omega poor
 399 GLU   ( 408-)  A  Poor phi/psi
 439 LEU   ( 448-)  A  Poor phi/psi
 459 THR   ( 468-)  A  Poor phi/psi
 493 GLU   ( 502-)  A  Poor phi/psi
 505 GLY   ( 514-)  A  Poor phi/psi
 554 LYS   ( 575-)  A  Poor phi/psi
 616 TYR   ( 637-)  A  Poor phi/psi
 733 ALA   ( 754-)  A  Poor phi/psi
 819 ARG   ( 840-)  A  Poor phi/psi
 917 PRO   ( 946-)  A  Poor phi/psi
 953 GLY   ( 986-)  A  omega poor
1000 LEU   (1055-)  A  Poor phi/psi
1032 HIS   (1087-)  A  omega poor
1038 GLU   (1093-)  A  Poor phi/psi
1089 ASP   (1144-)  A  Poor phi/psi
1219 MET   (  43-)  B  Poor phi/psi
1242 PHE   (  66-)  B  omega poor
1257 GLY   (  81-)  B  Poor phi/psi
1285 VAL   ( 109-)  B  Poor phi/psi
1350 LEU   ( 176-)  B  omega poor
1351 ALA   ( 177-)  B  Poor phi/psi
1353 GLN   ( 179-)  B  Poor phi/psi
1444 ASN   ( 270-)  B  Poor phi/psi
1474 ARG   ( 300-)  B  PRO omega poor
1541 GLU   ( 367-)  B  Poor phi/psi
1571 ASN   ( 397-)  B  Poor phi/psi
1578 PHE   ( 404-)  B  omega poor
1584 GLU   ( 410-)  B  Poor phi/psi
1590 ASN   ( 416-)  B  Poor phi/psi
1761 GLN   ( 587-)  B  omega poor
1788 LEU   ( 614-)  B  PRO omega poor
1794 GLU   ( 620-)  B  omega poor
1910 GLU   ( 736-)  B  Poor phi/psi
1982 SER   ( 808-)  B  Poor phi/psi
1986 HIS   ( 812-)  B  Poor phi/psi
2047 LYS   ( 873-)  B  Poor phi/psi
2048 GLU   ( 874-)  B  Poor phi/psi
2238 ASN   (1064-)  B  Poor phi/psi
2290 LYS   (1116-)  B  Poor phi/psi
2291 ASN   (1117-)  B  Poor phi/psi
2305 GLN   (1131-)  B  Poor phi/psi
2312 GLU   (1138-)  B  Poor phi/psi
2320 ALA   (1146-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.435

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

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

chi-1/chi-2 correlation Z-score : -3.435

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.

 840 SER   ( 861-)  A    0.35
1898 SER   ( 724-)  B    0.35
2006 SER   ( 832-)  B    0.36
1349 SER   ( 175-)  B    0.36
1902 SER   ( 728-)  B    0.36
1197 SER   (  21-)  B    0.37

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!

  12 SER   (  21-)  A      0
  13 THR   (  22-)  A      0
  20 ALA   (  29-)  A      0
  22 ALA   (  31-)  A      0
  23 ALA   (  32-)  A      0
  41 ALA   (  50-)  A      0
  44 ASN   (  53-)  A      0
  51 LEU   (  60-)  A      0
  56 PHE   (  65-)  A      0
  57 THR   (  66-)  A      0
  83 LEU   (  92-)  A      0
  94 ARG   ( 103-)  A      0
  96 SER   ( 105-)  A      0
  98 SER   ( 107-)  A      0
 111 TYR   ( 120-)  A      0
 113 TYR   ( 122-)  A      0
 114 LEU   ( 123-)  A      0
 115 ILE   ( 124-)  A      0
 116 ASP   ( 125-)  A      0
 147 LYS   ( 156-)  A      0
 149 GLU   ( 158-)  A      0
 159 TYR   ( 168-)  A      0
 163 ARG   ( 172-)  A      0
 164 HIS   ( 173-)  A      0
 165 ASP   ( 174-)  A      0
And so on for a total of 710 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!

 488 GLY   ( 497-)  A   2.58   10
1620 GLY   ( 446-)  B   1.97   13
2217 GLY   (1043-)  B   1.89   14
1067 GLY   (1122-)  A   1.52   33

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].

  45 PRO   (  54-)  A   -58.1 half-chair C-beta/C-alpha (-54 degrees)
 208 PRO   ( 217-)  A   104.9 envelop C-beta (108 degrees)
 238 PRO   ( 247-)  A  -114.8 envelop C-gamma (-108 degrees)
 572 PRO   ( 593-)  A   164.0 half-chair C-alpha/N (162 degrees)
 587 PRO   ( 608-)  A    52.3 half-chair C-delta/C-gamma (54 degrees)
 901 PRO   ( 922-)  A  -112.4 envelop C-gamma (-108 degrees)
 952 PRO   ( 985-)  A   114.5 envelop C-beta (108 degrees)
1313 PRO   ( 137-)  B   106.3 envelop C-beta (108 degrees)
1389 PRO   ( 215-)  B   101.3 envelop C-beta (108 degrees)
2286 PRO   (1112-)  B    47.4 half-chair C-delta/C-gamma (54 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.

 158 ARG   ( 167-)  A      NH1 <->  814 ILE   ( 835-)  A      O      0.48    2.22  INTRA BL
 835 ARG   ( 856-)  A      NH1 <->  890 TYR   ( 911-)  A      O      0.45    2.25  INTRA BL
 123 ILE   ( 132-)  A      N   <-> 2367 DTHY  (  57-)  X      O4     0.45    2.25  INTRA BL
 557 ARG   ( 578-)  A      NH2 <->  563 ASP   ( 584-)  A      OD1    0.44    2.26  INTRA BF
1190 LYS   (  14-)  B      NZ  <-> 2383 ANP   (2161-)  B      O2B    0.43    2.27  INTRA BL
1877 GLU   ( 703-)  B      OE1 <-> 1880 GLN   ( 706-)  B      NE2    0.43    2.27  INTRA BL
2009 LYS   ( 835-)  B      NZ  <-> 2013 ASP   ( 839-)  B      OD2    0.40    2.30  INTRA BL
2104 GLN   ( 930-)  B      O   <-> 2271 GLN   (1097-)  B      NE2    0.40    2.30  INTRA BF
 557 ARG   ( 578-)  A      NH1 <->  560 GLN   ( 581-)  A      OE1    0.39    2.31  INTRA BF
 399 GLU   ( 408-)  A      OE1 <->  401 GLN   ( 410-)  A      NE2    0.39    2.31  INTRA BL
1695 GLU   ( 521-)  B      OE2 <-> 1698 ARG   ( 524-)  B      NH1    0.38    2.32  INTRA BL
 122 ARG   ( 131-)  A      NH2 <->  128 GLU   ( 137-)  A      OE2    0.37    2.33  INTRA BL
1559 GLU   ( 385-)  B      OE2 <-> 1579 ARG   ( 405-)  B      NH1    0.37    2.33  INTRA BL
 550 ASP   ( 571-)  A      O   <->  554 LYS   ( 575-)  A      N      0.36    2.34  INTRA BF
1463 GLU   ( 289-)  B      OE1 <-> 1869 HIS   ( 695-)  B      NE2    0.36    2.34  INTRA BL
1504 GLU   ( 330-)  B      OE1 <-> 1872 ARG   ( 698-)  B      NH2    0.36    2.34  INTRA BL
 863 CYS   ( 884-)  A      SG  <->  864 LYS   ( 885-)  A      N      0.35    2.85  INTRA BF
1186 SER   (  10-)  B      OG  <-> 1457 ARG   ( 283-)  B      NH2    0.35    2.35  INTRA BL
1307 LYS   ( 131-)  B      NZ  <-> 1347 GLU   ( 173-)  B      OE2    0.35    2.35  INTRA BF
1069 LYS   (1124-)  A      NZ  <-> 1108 GLU   (1163-)  A      OE1    0.35    2.35  INTRA BF
 304 LYS   ( 313-)  A      NZ  <-> 2352 DGUA  (  42-)  X      OP2    0.34    2.36  INTRA BF
1587 PHE   ( 413-)  B      O   <-> 1691 LYS   ( 517-)  B      NZ     0.34    2.36  INTRA BL
 690 SER   ( 711-)  A      N   <->  730 GLU   ( 751-)  A      OE2    0.34    2.36  INTRA BL
 472 ARG   ( 481-)  A      NH2 <->  509 PRO   ( 518-)  A      O      0.34    2.36  INTRA BF
1675 LYS   ( 501-)  B      NZ  <-> 1734 ILE   ( 560-)  B      O      0.34    2.36  INTRA BL
And so on for a total of 261 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

1474 ARG   ( 300-)  B      -7.86
2095 LYS   ( 921-)  B      -7.06
1128 GLN   (1183-)  A      -6.94
 990 ARG   (1045-)  A      -6.82
 934 ARG   ( 967-)  A      -6.69
 997 LYS   (1052-)  A      -6.55
 569 ARG   ( 590-)  A      -6.48
1122 ARG   (1177-)  A      -6.45
1627 ARG   ( 453-)  B      -6.42
 998 LYS   (1053-)  A      -6.41
1418 ARG   ( 244-)  B      -6.39
2230 GLN   (1056-)  B      -6.35
 735 ARG   ( 756-)  A      -6.29
1773 TYR   ( 599-)  B      -6.29
1771 ARG   ( 597-)  B      -6.29
 284 LYS   ( 293-)  A      -6.26
1254 HIS   (  78-)  B      -5.96
 646 LYS   ( 667-)  A      -5.94
1791 ARG   ( 617-)  B      -5.83
1385 TYR   ( 211-)  B      -5.82
1772 MET   ( 598-)  B      -5.81
1204 ARG   (  28-)  B      -5.80
2233 ARG   (1059-)  B      -5.75
 438 ARG   ( 447-)  A      -5.75
1015 HIS   (1070-)  A      -5.71
And so on for a total of 61 lines.

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.

 989 TYR   (1044-)  A       991 - ARG   1046- ( A)         -5.77
1771 ARG   ( 597-)  B      1773 - TYR    599- ( B)         -6.13

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 793 ASN   ( 814-)  A   -3.58
 506 ALA   ( 515-)  A   -2.88
 279 ARG   ( 288-)  A   -2.75
 795 MET   ( 816-)  A   -2.61
 437 PHE   ( 446-)  A   -2.60
1157 ALA   (1212-)  A   -2.54

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 591 ASN   ( 612-)  A
 617 GLN   ( 638-)  A
 906 HIS   ( 927-)  A
1010 HIS   (1065-)  A
1091 HIS   (1146-)  A
1466 HIS   ( 292-)  B
2029 GLN   ( 855-)  B
2046 GLN   ( 872-)  B
2077 HIS   ( 903-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   5 ASP   (  14-)  A      N
   6 GLN   (  15-)  A      N
   6 GLN   (  15-)  A      NE2
  12 SER   (  21-)  A      OG
  15 GLN   (  24-)  A      N
  24 GLY   (  33-)  A      N
  25 SER   (  34-)  A      N
  26 GLY   (  35-)  A      N
  27 LYS   (  36-)  A      N
  27 LYS   (  36-)  A      NZ
  29 ALA   (  38-)  A      N
  57 THR   (  66-)  A      N
  85 ILE   (  94-)  A      N
  86 ARG   (  95-)  A      N
  87 ARG   (  96-)  A      NE
  87 ARG   (  96-)  A      NH2
  95 ALA   ( 104-)  A      N
  96 SER   ( 105-)  A      N
 101 HIS   ( 110-)  A      N
 113 TYR   ( 122-)  A      N
 117 LEU   ( 126-)  A      N
 149 GLU   ( 158-)  A      N
 163 ARG   ( 172-)  A      N
 164 HIS   ( 173-)  A      N
 167 ASP   ( 176-)  A      N
And so on for a total of 211 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.

 101 HIS   ( 110-)  A      ND1
 233 GLU   ( 242-)  A      OE1
 251 ASP   ( 260-)  A      OD1
 773 HIS   ( 794-)  A      ND1
 866 HIS   ( 887-)  A      ND1
 869 GLN   ( 890-)  A      OE1
 916 HIS   ( 945-)  A      ND1
 937 GLU   ( 970-)  A      OE2
 964 GLN   ( 997-)  A      OE1
1014 GLN   (1069-)  A      OE1
1121 ASP   (1176-)  A      OD2
1218 GLN   (  42-)  B      OE1
1224 GLU   (  48-)  B      OE1
1506 HIS   ( 332-)  B      ND1
1784 ASN   ( 610-)  B      OD1
1876 ASN   ( 702-)  B      OD1
2077 HIS   ( 903-)  B      ND1
2121 ASP   ( 947-)  B      OD1
2265 HIS   (1091-)  B      NE2

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+.

2381  MG   (2234-)  A   -.-  -.-  Low probability ion. B= 85.1

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   ( 166-)  A   H-bonding suggests Asn
 298 ASP   ( 307-)  A   H-bonding suggests Asn
 477 ASP   ( 486-)  A   H-bonding suggests Asn; but Alt-Rotamer
 522 ASP   ( 531-)  A   H-bonding suggests Asn
 724 ASP   ( 745-)  A   H-bonding suggests Asn; but Alt-Rotamer
 753 ASP   ( 774-)  A   H-bonding suggests Asn
 958 ASP   ( 991-)  A   H-bonding suggests Asn; but Alt-Rotamer
1004 GLU   (1059-)  A   H-bonding suggests Gln
1036 GLU   (1091-)  A   H-bonding suggests Gln; but Alt-Rotamer
1329 GLU   ( 155-)  B   H-bonding suggests Gln; but Alt-Rotamer
1338 ASP   ( 164-)  B   H-bonding suggests Asn; but Alt-Rotamer
1518 ASP   ( 344-)  B   H-bonding suggests Asn; but Alt-Rotamer
1633 ASP   ( 459-)  B   H-bonding suggests Asn
1650 ASP   ( 476-)  B   H-bonding suggests Asn
1701 ASP   ( 527-)  B   H-bonding suggests Asn; but Alt-Rotamer
1768 ASP   ( 594-)  B   H-bonding suggests Asn
2260 ASP   (1086-)  B   H-bonding suggests Asn
2279 ASP   (1105-)  B   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 :   0.068
  2nd generation packing quality :  -1.009
  Ramachandran plot appearance   :  -0.673
  chi-1/chi-2 rotamer normality  :  -3.435 (poor)
  Backbone conformation          :   0.289

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.506 (tight)
  Omega angle restraints         :   0.798
  Side chain planarity           :   0.205 (tight)
  Improper dihedral distribution :   0.342
  B-factor distribution          :   1.538 (loose)
  Inside/Outside distribution    :   0.974

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   1.9
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.506 (tight)
  Omega angle restraints         :   0.798
  Side chain planarity           :   0.205 (tight)
  Improper dihedral distribution :   0.342
  B-factor distribution          :   1.538 (loose)
  Inside/Outside distribution    :   0.974
==============

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.