WHAT IF Check report

This file was created 2013-12-10 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 pdb4khq.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.

 935 DUP   (1005-)  A  -

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.

 246 ARG   ( 246-)  A  -
 296 ASN   ( 299-)  A  -
 327 ARG   ( 330-)  A  -
 338 ILE   ( 341-)  A  -
 344 MET   ( 347-)  A  -
 704 ARG   ( 707-)  A  -
 769 ARG   ( 772-)  A  -

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.

 246 ARG   ( 246-)  A  -
 296 ASN   ( 299-)  A  -
 327 ARG   ( 330-)  A  -
 338 ILE   ( 341-)  A  -
 344 MET   ( 347-)  A  -
 704 ARG   ( 707-)  A  -
 769 ARG   ( 772-)  A  -

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.

 511 LEU   ( 514-)  A  -

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

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'.

  32 GLU   (  32-)  A      CD
  32 GLU   (  32-)  A      OE1
  32 GLU   (  32-)  A      OE2
  34 LYS   (  34-)  A      NZ
  55 LYS   (  55-)  A      CD
  55 LYS   (  55-)  A      CE
  55 LYS   (  55-)  A      NZ
  66 ARG   (  66-)  A      CG
  66 ARG   (  66-)  A      CD
  66 ARG   (  66-)  A      NE
  66 ARG   (  66-)  A      CZ
  66 ARG   (  66-)  A      NH1
  66 ARG   (  66-)  A      NH2
 130 LYS   ( 130-)  A      CE
 130 LYS   ( 130-)  A      NZ
 195 LYS   ( 195-)  A      CD
 195 LYS   ( 195-)  A      CE
 195 LYS   ( 195-)  A      NZ
 236 GLU   ( 236-)  A      CD
 236 GLU   ( 236-)  A      OE1
 236 GLU   ( 236-)  A      OE2
 251 LYS   ( 251-)  A      CG
 251 LYS   ( 251-)  A      CD
 251 LYS   ( 251-)  A      CE
 251 LYS   ( 251-)  A      NZ
And so on for a total of 129 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.

 253 ILE   ( 253-)  A    High
 254 GLU   ( 254-)  A    High
 255 ASN   ( 255-)  A    High
 256 SER   ( 259-)  A    High
 897 MET   ( 900-)  A    High

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: 16

Crystal temperature (K) : 95.000

Note: B-factor plot

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

Chain identifier: A

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

  49 TYR   (  49-)  A
  53 TYR   (  53-)  A
  92 TYR   (  92-)  A
  97 TYR   (  97-)  A
  99 TYR   (  99-)  A
 139 TYR   ( 139-)  A
 147 TYR   ( 147-)  A
 274 TYR   ( 277-)  A
 285 TYR   ( 288-)  A
 320 TYR   ( 323-)  A
 388 TYR   ( 391-)  A
 461 TYR   ( 464-)  A
 515 TYR   ( 518-)  A
 574 TYR   ( 577-)  A
 575 TYR   ( 578-)  A
 601 TYR   ( 604-)  A
 616 TYR   ( 619-)  A
 760 TYR   ( 763-)  A
 773 TYR   ( 776-)  A
 788 TYR   ( 791-)  A
 888 TYR   ( 891-)  A

Warning: Phenylalanine convention problem

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

  16 PHE   (  16-)  A
  62 PHE   (  62-)  A
 113 PHE   ( 113-)  A
 221 PHE   ( 221-)  A
 234 PHE   ( 234-)  A
 277 PHE   ( 280-)  A
 279 PHE   ( 282-)  A
 293 PHE   ( 296-)  A
 367 PHE   ( 370-)  A
 613 PHE   ( 616-)  A
 638 PHE   ( 641-)  A
 651 PHE   ( 654-)  A
 698 PHE   ( 701-)  A
 764 PHE   ( 767-)  A
 768 PHE   ( 771-)  A
 895 PHE   ( 898-)  A

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.

  86 ASP   (  86-)  A
  95 ASP   (  95-)  A
 408 ASP   ( 411-)  A
 463 ASP   ( 466-)  A
 514 ASP   ( 517-)  A
 521 ASP   ( 524-)  A
 576 ASP   ( 579-)  A
 620 ASP   ( 623-)  A
 646 ASP   ( 649-)  A
 681 ASP   ( 684-)  A
 789 ASP   ( 792-)  A
 853 ASP   ( 856-)  A
 857 ASP   ( 860-)  A
 858 ASP   ( 861-)  A
 896 ASP   ( 899-)  A

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.

   3 GLU   (   3-)  A
  17 GLU   (  17-)  A
  43 GLU   (  43-)  A
  76 GLU   (  76-)  A
 100 GLU   ( 100-)  A
 172 GLU   ( 172-)  A
 194 GLU   ( 194-)  A
 200 GLU   ( 200-)  A
 219 GLU   ( 219-)  A
 258 GLU   ( 261-)  A
 471 GLU   ( 474-)  A
 481 GLU   ( 484-)  A
 522 GLU   ( 525-)  A
 537 GLU   ( 540-)  A
 654 GLU   ( 657-)  A
 683 GLU   ( 686-)  A
 713 GLU   ( 716-)  A
 744 GLU   ( 747-)  A
 754 GLU   ( 757-)  A
 767 GLU   ( 770-)  A
 834 GLU   ( 837-)  A
 889 GLU   ( 892-)  A

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.

 383 HIS   ( 386-)  A      CG   ND1  CE1 109.74    4.1
 903 DGUA  (   4-)  T      N9   C8   N7  113.18    4.2
 904 DGUA  (   5-)  T      N9   C8   N7  113.19    4.2
 906 DADE  (   7-)  T      O4'  C1'  N9  111.04    4.0
 908 DGUA  (   9-)  T      N9   C8   N7  113.42    4.6
 911 DGUA  (  12-)  T      N9   C8   N7  113.40    4.6
 912 DTHY  (  13-)  T      O4   C4   N3  122.47    4.3
 915 DGUA  (  16-)  T      N9   C8   N7  113.52    4.8
 917 DGUA  (  18-)  T      N9   C8   N7  113.53    4.9
 918 DGUA  ( 102-)  P      N9   C8   N7  113.50    4.8
 920 DGUA  ( 104-)  P      N9   C8   N7  113.42    4.6
 921 DGUA  ( 105-)  P      N9   C8   N7  113.37    4.5
 924 DTHY  ( 108-)  P      C5   C4   O4  122.02   -4.1
 924 DTHY  ( 108-)  P      O4   C4   N3  122.51    4.4
 925 DGUA  ( 109-)  P      N9   C8   N7  113.43    4.7
 928 DTHY  ( 112-)  P      O4'  C1'  N1  111.31    4.4
 928 DTHY  ( 112-)  P      C5   C4   O4  122.09   -4.0
 928 DTHY  ( 112-)  P      O4   C4   N3  122.37    4.1
 931 DCYT  ( 115-)  P      C4'  O4'  C1' 103.90   -4.1
 931 DCYT  ( 115-)  P      O4'  C1'  N1  112.01    5.3

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.

   3 GLU   (   3-)  A
  17 GLU   (  17-)  A
  43 GLU   (  43-)  A
  76 GLU   (  76-)  A
  86 ASP   (  86-)  A
  95 ASP   (  95-)  A
 100 GLU   ( 100-)  A
 172 GLU   ( 172-)  A
 194 GLU   ( 194-)  A
 200 GLU   ( 200-)  A
 219 GLU   ( 219-)  A
 258 GLU   ( 261-)  A
 408 ASP   ( 411-)  A
 463 ASP   ( 466-)  A
 471 GLU   ( 474-)  A
 481 GLU   ( 484-)  A
 514 ASP   ( 517-)  A
 521 ASP   ( 524-)  A
 522 GLU   ( 525-)  A
 537 GLU   ( 540-)  A
 576 ASP   ( 579-)  A
 620 ASP   ( 623-)  A
 646 ASP   ( 649-)  A
 654 GLU   ( 657-)  A
 681 ASP   ( 684-)  A
 683 GLU   ( 686-)  A
 713 GLU   ( 716-)  A
 744 GLU   ( 747-)  A
 754 GLU   ( 757-)  A
 767 GLU   ( 770-)  A
 789 ASP   ( 792-)  A
 834 GLU   ( 837-)  A
 853 ASP   ( 856-)  A
 857 ASP   ( 860-)  A
 858 ASP   ( 861-)  A
 889 GLU   ( 892-)  A
 896 ASP   ( 899-)  A

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.

 412 PHE   ( 415-)  A    -2.8
 619 THR   ( 622-)  A    -2.6
 214 THR   ( 214-)  A    -2.4
 594 ILE   ( 597-)  A    -2.3
  47 THR   (  47-)  A    -2.3
 411 SER   ( 414-)  A    -2.1
 113 PHE   ( 113-)  A    -2.1
 683 GLU   ( 686-)  A    -2.1
 615 LEU   ( 618-)  A    -2.1
 852 THR   ( 855-)  A    -2.1
 897 MET   ( 900-)  A    -2.1

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.

  98 ASN   (  98-)  A  Poor phi/psi
 177 GLU   ( 177-)  A  Poor phi/psi
 217 ASN   ( 217-)  A  Poor phi/psi
 246 ARG   ( 246-)  A  Poor phi/psi
 296 ASN   ( 299-)  A  Poor phi/psi
 336 GLN   ( 339-)  A  Poor phi/psi
 349 LYS   ( 352-)  A  Poor phi/psi
 374 ASN   ( 377-)  A  Poor phi/psi
 421 ASN   ( 424-)  A  Poor phi/psi
 619 THR   ( 622-)  A  Poor phi/psi
 683 GLU   ( 686-)  A  Poor phi/psi
 703 LYS   ( 706-)  A  Poor phi/psi
 713 GLU   ( 716-)  A  Poor phi/psi
 726 GLY   ( 729-)  A  Poor phi/psi
 784 ASN   ( 787-)  A  Poor phi/psi
 797 LYS   ( 800-)  A  Poor phi/psi
 885 LYS   ( 888-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.130

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.

 341 SER   ( 344-)  A    0.35
 534 SER   ( 537-)  A    0.36

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!

   7 THR   (   7-)  A      0
   9 GLU   (   9-)  A      0
  11 ILE   (  11-)  A      0
  13 ASP   (  13-)  A      0
  32 GLU   (  32-)  A      0
  33 TYR   (  33-)  A      0
  46 ALA   (  46-)  A      0
  49 TYR   (  49-)  A      0
  53 TYR   (  53-)  A      0
  63 ALA   (  63-)  A      0
  64 ASN   (  64-)  A      0
  65 MET   (  65-)  A      0
  83 LEU   (  83-)  A      0
  85 MET   (  85-)  A      0
  86 ASP   (  86-)  A      0
  97 TYR   (  97-)  A      0
  99 TYR   (  99-)  A      0
 105 HIS   ( 105-)  A      0
 121 ASP   ( 121-)  A      0
 123 PHE   ( 123-)  A      0
 128 GLN   ( 128-)  A      0
 129 ALA   ( 129-)  A      0
 130 LYS   ( 130-)  A      0
 143 ASP   ( 143-)  A      0
 152 LEU   ( 152-)  A      0
And so on for a total of 329 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!

 424 PRO   ( 427-)  A   1.85   11
 726 GLY   ( 729-)  A   1.56   10

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].

 124 PRO   ( 124-)  A    27.1 envelop C-delta (36 degrees)
 126 PRO   ( 126-)  A  -114.4 envelop C-gamma (-108 degrees)
 155 PRO   ( 155-)  A  -112.9 envelop C-gamma (-108 degrees)
 424 PRO   ( 427-)  A  -115.7 envelop C-gamma (-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.

  59 ARG   (  59-)  A      NH2 <->  944 HOH   (1431 )  A      O      0.38    2.32  INTRA BF
 483 LYS   ( 486-)  A      NZ  <->  944 HOH   (1530 )  A      O      0.31    2.39  INTRA BF
 910 DADE  (  11-)  T      N1  <->  924 DTHY  ( 108-)  P      N3     0.29    2.71  INTRA BF
 918 DGUA  ( 102-)  P      N3  <->  946 HOH   ( 224 )  P      O      0.26    2.44  INTRA BF
 907 DADE  (   8-)  T      N1  <->  927 DTHY  ( 111-)  P      N3     0.22    2.78  INTRA BL
 913 DCYT  (  14-)  T      N3  <->  921 DGUA  ( 105-)  P      N1     0.20    2.80  INTRA BF
 902 DADE  (   3-)  T      N1  <->  935 DUP   (1005-)  A      N3     0.19    2.81  INTRA BL
 905 DTHY  (   6-)  T      N3  <->  929 DADE  ( 113-)  P      N1     0.18    2.82  INTRA BL
 702 LYS   ( 705-)  A      NZ  <->  944 HOH   (1576 )  A      O      0.15    2.55  INTRA BF
 262 LEU   ( 265-)  A      N   <->  944 HOH   (1246 )  A      O      0.13    2.57  INTRA BL
 906 DADE  (   7-)  T      N1  <->  928 DTHY  ( 112-)  P      N3     0.13    2.87  INTRA BL
 914 DCYT  (  15-)  T      N3  <->  920 DGUA  ( 104-)  P      N1     0.13    2.87  INTRA BF
 208 LYS   ( 208-)  A      NZ  <->  944 HOH   (1409 )  A      O      0.12    2.58  INTRA BF
 945 HOH   ( 131 )  T      O   <->  946 HOH   ( 225 )  P      O      0.12    2.28  INTRA BF
 704 ARG   ( 707-)  A    A NH2 <->  728 GLU   ( 731-)  A      OE1    0.12    2.58  INTRA BL
 903 DGUA  (   4-)  T      N3  <->  945 HOH   ( 102 )  T      O      0.11    2.59  INTRA BL
 219 GLU   ( 219-)  A      OE1 <->  944 HOH   (1370 )  A      O      0.11    2.29  INTRA BF
 116 GLU   ( 116-)  A      OE2 <->  944 HOH   (1463 )  A      O      0.11    2.29  INTRA BF
 766 LYS   ( 769-)  A      O   <->  944 HOH   (1273 )  A      O      0.11    2.29  INTRA BF
 406 SER   ( 409-)  A      OG  <->  684 ALA   ( 687-)  A      N      0.10    2.60  INTRA BL
 907 DADE  (   8-)  T      N7  <->  945 HOH   ( 141 )  T      O      0.10    2.60  INTRA BF
 773 TYR   ( 776-)  A      OH  <->  850 GLU   ( 853-)  A      OE1    0.10    2.30  INTRA BF
 903 DGUA  (   4-)  T      N1  <->  931 DCYT  ( 115-)  P      N3     0.10    2.90  INTRA BL
 406 SER   ( 409-)  A      O   <->  683 GLU   ( 686-)  A      N      0.10    2.60  INTRA BL
 332 ASP   ( 335-)  A      O   <->  336 GLN   ( 339-)  A      N      0.09    2.61  INTRA BL
And so on for a total of 83 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

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.

 302 TYR   ( 305-)  A      -7.66
 639 ARG   ( 642-)  A      -6.99
  53 TYR   (  53-)  A      -6.97
 156 TYR   ( 156-)  A      -6.78
 388 TYR   ( 391-)  A      -6.49
 797 LYS   ( 800-)  A      -6.39
 464 ARG   ( 467-)  A      -6.34
 128 GLN   ( 128-)  A      -5.98
 507 VAL   ( 510-)  A      -5.69
 173 GLN   ( 173-)  A      -5.61
 770 GLN   ( 773-)  A      -5.50
 730 GLN   ( 733-)  A      -5.47
 898 PHE   ( 901-)  A      -5.41
 102 LYS   ( 102-)  A      -5.26
 862 TRP   ( 865-)  A      -5.24
 385 VAL   ( 388-)  A      -5.23
 751 GLN   ( 754-)  A      -5.12

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.

 232 ASN   ( 232-)  A       234 - PHE    234- ( A)         -4.40
 302 TYR   ( 305-)  A       304 - GLY    307- ( A)         -5.60
 385 VAL   ( 388-)  A       388 - TYR    391- ( A)         -5.15

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

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.

 432 LYS   ( 435-)  A   -2.66
 825 GLU   ( 828-)  A   -2.65
 637 LYS   ( 640-)  A   -2.62
 718 ALA   ( 721-)  A   -2.60
 381 ARG   ( 384-)  A   -2.54
 577 LEU   ( 580-)  A   -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.

 378 PRO   ( 381-)  A     -  381 ARG   ( 384-)  A        -1.56

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

 944 HOH   (1496 )  A      O     11.87   65.75   -5.63
 944 HOH   (1563 )  A      O    -18.47   25.33   37.95

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.

 944 HOH   (1450 )  A      O
 944 HOH   (1567 )  A      O
 945 HOH   ( 134 )  T      O

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 TYR   (   5-)  A      N
  64 ASN   (  64-)  A      N
  98 ASN   (  98-)  A      N
  99 TYR   (  99-)  A      N
 153 ASN   ( 153-)  A      N
 218 VAL   ( 218-)  A      N
 282 GLN   ( 285-)  A      NE2
 284 SER   ( 287-)  A      N
 297 VAL   ( 300-)  A      N
 411 SER   ( 414-)  A    A N
 412 PHE   ( 415-)  A      N
 413 TYR   ( 416-)  A      N
 427 ILE   ( 430-)  A      N
 437 HIS   ( 440-)  A      N
 464 ARG   ( 467-)  A      N
 479 ARG   ( 482-)  A      NH2
 508 ASP   ( 511-)  A      N
 574 TYR   ( 577-)  A      N
 579 ASN   ( 582-)  A      ND2
 617 GLY   ( 620-)  A      N
 629 ILE   ( 632-)  A      N
 640 ASP   ( 643-)  A      N
 699 TRP   ( 702-)  A      NE1
 708 ASN   ( 711-)  A      ND2
 727 LEU   ( 730-)  A      N
 787 LYS   ( 790-)  A      N
 802 ILE   ( 805-)  A      N
 842 CYS   ( 845-)  A      N
 849 THR   ( 852-)  A      N
 857 ASP   ( 860-)  A      N
Only metal coordination for  681 ASP  ( 684-) A      OD1

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.

 555 ASN   ( 558-)  A      OD1
 683 GLU   ( 686-)  A      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+.

 932  CA   (1001-)  A   -.-  -.-  Part of ionic cluster
 933  CA   (1003-)  A     0.81   1.06 Scores about as good as NA *1
 934  CA   (1004-)  A     0.81   1.03 Scores about as good as NA *1
 936  NA   (1006-)  A    0.74  -.-   Poor packing
 937  NA   (1007-)  A     0.40   0.48 Scores about as good as  K (Few ligands (4) )
 939  NA   (1002-)  A   -.-  -.-  Low probability ion. B= 96.4
 940  NA   (1009-)  A   -.-  -.-  Part of ionic cluster
 940  NA   (1009-)  A     0.62   1.32 Scores about as good as  K (Few ligands (4) )
 941  NA   (1010-)  A   -.-  -.-  Part of ionic cluster
 942  NA   (1011-)  A   -.-  -.-  Part of ionic cluster
 943  NA   (1012-)  A    0.73  -.-   Poor packing

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.

 944 HOH   (1477 )  A      O  0.86 NA  4 *1 Ion-B

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.

 134 ASP   ( 134-)  A   H-bonding suggests Asn; but Alt-Rotamer
 269 ASP   ( 272-)  A   H-bonding suggests Asn; but Alt-Rotamer
 311 GLU   ( 314-)  A   H-bonding suggests Gln
 631 ASP   ( 634-)  A   H-bonding suggests Asn; but Alt-Rotamer
 661 ASP   ( 664-)  A   H-bonding suggests Asn
 870 GLU   ( 873-)  A   H-bonding suggests Gln; but Alt-Rotamer
 887 ASP   ( 890-)  A   H-bonding suggests Asn; but Alt-Rotamer
 896 ASP   ( 899-)  A   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 :  -0.348
  2nd generation packing quality :  -1.248
  Ramachandran plot appearance   :  -0.004
  chi-1/chi-2 rotamer normality  :   0.130
  Backbone conformation          :  -0.395

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.238 (tight)
  Bond angles                    :   0.480 (tight)
  Omega angle restraints         :   0.763
  Side chain planarity           :   0.185 (tight)
  Improper dihedral distribution :   0.393
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   1.005

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 : 2.19


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :   1.2
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.238 (tight)
  Bond angles                    :   0.480 (tight)
  Omega angle restraints         :   0.763
  Side chain planarity           :   0.185 (tight)
  Improper dihedral distribution :   0.393
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   1.005
==============

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.