WHAT IF Check report

This file was created 2011-12-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1bwv.ent

Checks that need to be done early-on in validation

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

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.

2446 CAP   ( 491-)  A  -
2448 CAP   ( 491-)  C  -
2450 CAP   ( 491-)  E  -
2452 CAP   ( 491-)  G  -

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: S

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: Y

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

Warning: What type of B-factor?

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

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

Crystal temperature (K) :293.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.26

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

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

RMS Z-score : 2.215 over 17368 bonds
Average difference in B over a bond : 4.71
RMS difference in B over a bond : 6.18

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: S

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: Y

Nomenclature related problems

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 196 KCX   ( 201-)  A      CH     CX
 196 KCX   ( 201-)  A      OX1    OQ1
 196 KCX   ( 201-)  A      OX2    OQ2
 806 KCX   ( 201-)  C      CH     CX
 806 KCX   ( 201-)  C      OX1    OQ1
 806 KCX   ( 201-)  C      OX2    OQ2
1416 KCX   ( 201-)  E      CH     CX
1416 KCX   ( 201-)  E      OX1    OQ1
1416 KCX   ( 201-)  E      OX2    OQ2
2026 KCX   ( 201-)  G      CH     CX
2026 KCX   ( 201-)  G      OX1    OQ1
2026 KCX   ( 201-)  G      OX2    OQ2

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 199 GLU   ( 204-)  A      CD   OE1   1.09   -8.5
 808 ASP   ( 203-)  C      CG   OD1   1.15   -5.1
 809 GLU   ( 204-)  C      CD   OE1   1.10   -7.7
1419 GLU   ( 204-)  E      CD   OE1   1.11   -7.4
2028 ASP   ( 203-)  G      CG   OD1   1.16   -4.4
2029 GLU   ( 204-)  G      CD   OE1   1.04  -10.9

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.

   6 ARG   (  12-)  A      CA   CB   CG  127.24    6.6
   8 GLU   (  14-)  A      CA   CB   CG  123.71    4.8
  20 TRP   (  25-)  A      CB   CG   CD1 119.95   -4.6
  20 TRP   (  25-)  A      CE3  CD2  CG  138.75    4.8
  20 TRP   (  25-)  A      CG   CD2  CE2 101.31   -4.9
  30 ASP   (  35-)  A      CA   CB   CG  117.60    5.0
  44 ASP   (  49-)  A      CA   CB   CG  117.99    5.4
  60 THR   (  65-)  A      CA   CB   CG2 118.36    4.6
  60 THR   (  65-)  A      CA   CB   OG1 101.79   -5.2
  61 TRP   (  66-)  A      CD1  CG   CD2 113.29    4.4
  61 TRP   (  66-)  A      CG   CD1  NE1 104.90   -4.1
  61 TRP   (  66-)  A      CE3  CD2  CG  138.35    4.4
  61 TRP   (  66-)  A      CG   CD2  CE2 100.98   -5.2
  65 TRP   (  70-)  A      CB   CG   CD1 120.43   -4.3
  65 TRP   (  70-)  A      CE3  CD2  CG  138.66    4.8
  65 TRP   (  70-)  A      CG   CD2  CE2 101.47   -4.8
  67 ASP   (  72-)  A      CA   CB   CG  118.94    6.3
  87 ASN   (  92-)  A      CB   CG   ND2 122.50    4.1
  87 ASN   (  92-)  A      ND2  CG   OD1 116.98   -5.6
 101 ASP   ( 106-)  A      CA   CB   CG  116.70    4.1
 118 ASN   ( 123-)  A      CA   CB   CG  117.55    5.0
 118 ASN   ( 123-)  A      ND2  CG   OD1 117.30   -5.3
 171 PRO   ( 176-)  A     -CA  -C    N   123.83    4.6
 194 PHE   ( 199-)  A      CA   CB   CG  117.94    4.1
 196 KCX   ( 201-)  A      CG   CD   CE  123.35    5.2
And so on for a total of 342 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 729 VAL   ( 124-)  C    5.55
1949 VAL   ( 124-)  G    5.51
1339 VAL   ( 124-)  E    5.40
 119 VAL   ( 124-)  A    5.40
1564 LEU   ( 350-)  E    5.34
 954 LEU   ( 350-)  C    5.34
1084 ARG   (   9-)  U    5.33
2304 ARG   (   9-)  Y    5.32
2174 LEU   ( 350-)  G    5.32
 344 LEU   ( 350-)  A    5.32
 906 SER   ( 302-)  C    5.23
2126 SER   ( 302-)  G    5.15
1516 SER   ( 302-)  E    5.02
 296 SER   ( 302-)  A    4.97
1694 ARG   (   9-)  W    4.75
 474 ARG   (   9-)  S    4.75
 227 THR   ( 232-)  A    4.29
1447 THR   ( 232-)  E    4.24
2057 THR   ( 232-)  G    4.11
 837 THR   ( 232-)  C    4.09

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.

1916 PRO   (  91-)  G    -2.8
 696 PRO   (  91-)  C    -2.8
1306 PRO   (  91-)  E    -2.8
  86 PRO   (  91-)  A    -2.8
1733 ILE   (  48-)  W    -2.7
 513 ILE   (  48-)  S    -2.7
2343 ILE   (  48-)  Y    -2.7
1123 ILE   (  48-)  U    -2.7
 289 ARG   ( 295-)  A    -2.6
1509 ARG   ( 295-)  E    -2.6
2119 ARG   ( 295-)  G    -2.6
 899 ARG   ( 295-)  C    -2.6
2340 THR   (  45-)  Y    -2.6
 510 THR   (  45-)  S    -2.6
1730 THR   (  45-)  W    -2.6
1120 THR   (  45-)  U    -2.6
1642 ILE   ( 428-)  E    -2.3
 422 ILE   ( 428-)  A    -2.3
2252 ILE   ( 428-)  G    -2.3
1032 ILE   ( 428-)  C    -2.3
 670 THR   (  65-)  C    -2.3
1280 THR   (  65-)  E    -2.3
  60 THR   (  65-)  A    -2.3
1890 THR   (  65-)  G    -2.3
 476 THR   (  11-)  S    -2.3
And so on for a total of 60 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.

   5 SER   (  11-)  A  Poor phi/psi
  58 THR   (  63-)  A  Poor phi/psi
 118 ASN   ( 123-)  A  Poor phi/psi
 158 ASP   ( 163-)  A  Poor phi/psi
 170 LYS   ( 175-)  A  PRO omega poor
 202 ASN   ( 207-)  A  Poor phi/psi
 289 ARG   ( 295-)  A  Poor phi/psi
 364 SER   ( 370-)  A  Poor phi/psi
 428 ASN   ( 434-)  A  Poor phi/psi
 435 GLY   ( 441-)  A  Poor phi/psi
 588 ASP   ( 133-)  S  Poor phi/psi
 590 SER   ( 135-)  S  Poor phi/psi
 615 SER   (  11-)  C  Poor phi/psi
 668 THR   (  63-)  C  Poor phi/psi
 728 ASN   ( 123-)  C  Poor phi/psi
 768 ASP   ( 163-)  C  Poor phi/psi
 780 LYS   ( 175-)  C  PRO omega poor
 812 ASN   ( 207-)  C  Poor phi/psi
 899 ARG   ( 295-)  C  Poor phi/psi
 974 SER   ( 370-)  C  Poor phi/psi
1038 ASN   ( 434-)  C  Poor phi/psi
1045 GLY   ( 441-)  C  Poor phi/psi
1198 ASP   ( 133-)  U  Poor phi/psi
1200 SER   ( 135-)  U  Poor phi/psi
1225 SER   (  11-)  E  Poor phi/psi
1278 THR   (  63-)  E  Poor phi/psi
1338 ASN   ( 123-)  E  Poor phi/psi
1378 ASP   ( 163-)  E  Poor phi/psi
1390 LYS   ( 175-)  E  PRO omega poor
1422 ASN   ( 207-)  E  Poor phi/psi
1509 ARG   ( 295-)  E  Poor phi/psi
1584 SER   ( 370-)  E  Poor phi/psi
1648 ASN   ( 434-)  E  Poor phi/psi
1655 GLY   ( 441-)  E  Poor phi/psi
1808 ASP   ( 133-)  W  Poor phi/psi
1810 SER   ( 135-)  W  Poor phi/psi
1835 SER   (  11-)  G  Poor phi/psi
1888 THR   (  63-)  G  Poor phi/psi
1948 ASN   ( 123-)  G  Poor phi/psi
1988 ASP   ( 163-)  G  Poor phi/psi
2000 LYS   ( 175-)  G  PRO omega poor
2032 ASN   ( 207-)  G  Poor phi/psi
2119 ARG   ( 295-)  G  Poor phi/psi
2194 SER   ( 370-)  G  Poor phi/psi
2258 ASN   ( 434-)  G  Poor phi/psi
2265 GLY   ( 441-)  G  Poor phi/psi
2418 ASP   ( 133-)  Y  Poor phi/psi
2420 SER   ( 135-)  Y  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.817

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.

 224 SER   ( 229-)  A    0.36
 834 SER   ( 229-)  C    0.36
1444 SER   ( 229-)  E    0.36
2054 SER   ( 229-)  G    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!

   4 ASN   (  10-)  A      0
   5 SER   (  11-)  A      0
   6 ARG   (  12-)  A      0
   9 SER   (  15-)  A      0
  17 MET   (  22-)  A      0
  19 TYR   (  24-)  A      0
  20 TRP   (  25-)  A      0
  41 PRO   (  46-)  A      0
  56 SER   (  61-)  A      0
  57 SER   (  62-)  A      0
  58 THR   (  63-)  A      0
  59 ALA   (  64-)  A      0
  61 TRP   (  66-)  A      0
  65 TRP   (  70-)  A      0
  69 LEU   (  74-)  A      0
  71 ALA   (  76-)  A      0
  72 ALA   (  77-)  A      0
  80 TYR   (  85-)  A      0
  87 ASN   (  92-)  A      0
  91 GLN   (  96-)  A      0
 105 GLU   ( 110-)  A      0
 115 ILE   ( 120-)  A      0
 116 ILE   ( 121-)  A      0
 118 ASN   ( 123-)  A      0
 119 VAL   ( 124-)  A      0
And so on for a total of 895 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 3.813

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!

1551 GLY   ( 337-)  E   2.17   11
 331 GLY   ( 337-)  A   2.17   11
2161 GLY   ( 337-)  G   2.16   11
 941 GLY   ( 337-)  C   2.16   11

Warning: Unusual PRO puckering amplitudes

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

  86 PRO   (  91-)  A    0.45 HIGH
 146 PRO   ( 151-)  A    0.45 HIGH
 696 PRO   (  91-)  C    0.45 HIGH
1306 PRO   (  91-)  E    0.45 HIGH
1366 PRO   ( 151-)  E    0.45 HIGH
1916 PRO   (  91-)  G    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].

  41 PRO   (  46-)  A  -118.8 half-chair C-delta/C-gamma (-126 degrees)
  45 PRO   (  50-)  A  -122.6 half-chair C-delta/C-gamma (-126 degrees)
  86 PRO   (  91-)  A    99.2 envelop C-beta (108 degrees)
 333 PRO   ( 339-)  A  -112.0 envelop C-gamma (-108 degrees)
 515 PRO   (  50-)  S  -122.9 half-chair C-delta/C-gamma (-126 degrees)
 605 PRO   ( 150-)  S  -116.0 envelop C-gamma (-108 degrees)
 651 PRO   (  46-)  C  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 655 PRO   (  50-)  C  -123.5 half-chair C-delta/C-gamma (-126 degrees)
 696 PRO   (  91-)  C    99.7 envelop C-beta (108 degrees)
1125 PRO   (  50-)  U  -122.5 half-chair C-delta/C-gamma (-126 degrees)
1143 PRO   (  80-)  U  -112.2 envelop C-gamma (-108 degrees)
1215 PRO   ( 150-)  U  -116.0 envelop C-gamma (-108 degrees)
1261 PRO   (  46-)  E  -119.0 half-chair C-delta/C-gamma (-126 degrees)
1265 PRO   (  50-)  E  -122.6 half-chair C-delta/C-gamma (-126 degrees)
1306 PRO   (  91-)  E    99.2 envelop C-beta (108 degrees)
1553 PRO   ( 339-)  E  -112.0 envelop C-gamma (-108 degrees)
1735 PRO   (  50-)  W  -122.9 half-chair C-delta/C-gamma (-126 degrees)
1825 PRO   ( 150-)  W  -116.1 envelop C-gamma (-108 degrees)
1871 PRO   (  46-)  G  -119.1 half-chair C-delta/C-gamma (-126 degrees)
1875 PRO   (  50-)  G  -123.4 half-chair C-delta/C-gamma (-126 degrees)
1916 PRO   (  91-)  G    99.5 envelop C-beta (108 degrees)
2345 PRO   (  50-)  Y  -122.6 half-chair C-delta/C-gamma (-126 degrees)
2363 PRO   (  80-)  Y  -112.2 envelop C-gamma (-108 degrees)
2435 PRO   ( 150-)  Y  -116.1 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.

1374 ARG   ( 159-)  E      NH2 <-> 1382 ARG   ( 167-)  E      O      0.17    2.53  INTRA
 764 ARG   ( 159-)  C      NH2 <->  772 ARG   ( 167-)  C      O      0.17    2.53  INTRA
 154 ARG   ( 159-)  A      NH2 <->  162 ARG   ( 167-)  A      O      0.17    2.53  INTRA
1984 ARG   ( 159-)  G      NH2 <-> 1992 ARG   ( 167-)  G      O      0.17    2.53  INTRA
 305 PHE   ( 311-)  A      CE2 <->  309 CYS   ( 315-)  A      SG     0.15    3.25  INTRA BL
1525 PHE   ( 311-)  E      CE2 <-> 1529 CYS   ( 315-)  E      SG     0.15    3.25  INTRA BL
 915 PHE   ( 311-)  C      CE2 <->  919 CYS   ( 315-)  C      SG     0.12    3.28  INTRA BL
2135 PHE   ( 311-)  G      CE2 <-> 2139 CYS   ( 315-)  G      SG     0.12    3.28  INTRA BL
1903 ASP   (  78-)  G      O   <-> 1908 LYS   (  83-)  G      NZ     0.09    2.61  INTRA BL
 683 ASP   (  78-)  C      O   <->  688 LYS   (  83-)  C      NZ     0.08    2.62  INTRA BL
1965 LEU   ( 140-)  G      CD1 <-> 2144 MET   ( 320-)  G      SD     0.08    3.32  INTRA BL
 135 LEU   ( 140-)  A      CD1 <->  314 MET   ( 320-)  A      SD     0.08    3.32  INTRA BL
1355 LEU   ( 140-)  E      CD1 <-> 1534 MET   ( 320-)  E      SD     0.08    3.32  INTRA BL
 745 LEU   ( 140-)  C      CD1 <->  924 MET   ( 320-)  C      SD     0.08    3.32  INTRA BL
  73 ASP   (  78-)  A      O   <->   78 LYS   (  83-)  A      NZ     0.07    2.63  INTRA
1293 ASP   (  78-)  E      O   <-> 1298 LYS   (  83-)  E      NZ     0.07    2.63  INTRA
 377 HIS   ( 383-)  A      ND1 <-> 2453 HOH   ( 582 )  A      O      0.05    2.65  INTRA BF
2433 TYR   ( 148-)  Y      N   <-> 2434 LYS   ( 149-)  Y      N      0.03    2.57  INTRA B3
1213 TYR   ( 148-)  U      N   <-> 1214 LYS   ( 149-)  U      N      0.03    2.57  INTRA B3
 603 TYR   ( 148-)  S      N   <->  604 LYS   ( 149-)  S      N      0.02    2.58  INTRA B3
1823 TYR   ( 148-)  W      N   <-> 1824 LYS   ( 149-)  W      N      0.02    2.58  INTRA B3
 477 GLN   (  12-)  S      NE2 <-> 2454 HOH   ( 164 )  S      O      0.02    2.68  INTRA BL
2119 ARG   ( 295-)  G      N   <-> 2459 HOH   ( 577 )  G      O      0.01    2.69  INTRA BL

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: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

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.

1549 LEU   ( 335-)  E      -6.37
2159 LEU   ( 335-)  G      -6.37
 329 LEU   ( 335-)  A      -6.37
 939 LEU   ( 335-)  C      -6.36
 577 HIS   ( 122-)  S      -6.32
1797 HIS   ( 122-)  W      -6.32
2407 HIS   ( 122-)  Y      -6.31
1187 HIS   ( 122-)  U      -6.31
2406 LYS   ( 121-)  Y      -5.67
1186 LYS   ( 121-)  U      -5.67
 576 LYS   ( 121-)  S      -5.62
1745 LEU   (  72-)  W      -5.62
1796 LYS   ( 121-)  W      -5.62
 525 LEU   (  72-)  S      -5.62
1135 LEU   (  72-)  U      -5.60
2355 LEU   (  72-)  Y      -5.59
  87 ASN   (  92-)  A      -5.46
1917 ASN   (  92-)  G      -5.46
 697 ASN   (  92-)  C      -5.45
1307 ASN   (  92-)  E      -5.44
2000 LYS   ( 175-)  G      -5.39
 780 LYS   ( 175-)  C      -5.39
1390 LYS   ( 175-)  E      -5.36
1834 ASN   (  10-)  G      -5.36
 170 LYS   ( 175-)  A      -5.36
1224 ASN   (  10-)  E      -5.36
   4 ASN   (  10-)  A      -5.36
 614 ASN   (  10-)  C      -5.36
1364 GLN   ( 149-)  E      -5.21
 144 GLN   ( 149-)  A      -5.19
1974 GLN   ( 149-)  G      -5.16
 754 GLN   ( 149-)  C      -5.14

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.

   2 ILE   (   8-)  A         4 - ASN     10- ( A)         -4.97
 328 LYS   ( 334-)  A       330 - GLU    336- ( A)         -5.17
 576 LYS   ( 121-)  S       578 - GLU    123- ( S)         -5.42
 608 GLU   ( 153-)  S       610 - TYR    155- ( S)         -4.38
 612 ILE   (   8-)  C       614 - ASN     10- ( C)         -4.96
 938 LYS   ( 334-)  C       940 - GLU    336- ( C)         -5.15
1186 LYS   ( 121-)  U      1188 - GLU    123- ( U)         -5.44
1218 GLU   ( 153-)  U      1220 - TYR    155- ( U)         -4.35
1222 ILE   (   8-)  E      1224 - ASN     10- ( E)         -4.97
1548 LYS   ( 334-)  E      1550 - GLU    336- ( E)         -5.15
1796 LYS   ( 121-)  W      1798 - GLU    123- ( W)         -5.42
1828 GLU   ( 153-)  W      1830 - TYR    155- ( W)         -4.38
1832 ILE   (   8-)  G      1834 - ASN     10- ( G)         -4.96
2158 LYS   ( 334-)  G      2160 - GLU    336- ( G)         -5.15
2406 LYS   ( 121-)  Y      2408 - GLU    123- ( Y)         -5.44
2438 GLU   ( 153-)  Y      2440 - TYR    155- ( Y)         -4.35

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: S

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: U

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: Y

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.

2355 LEU   (  72-)  Y   -2.90
1135 LEU   (  72-)  U   -2.89
1745 LEU   (  72-)  W   -2.87
 525 LEU   (  72-)  S   -2.87
 613 LYS   (   9-)  C   -2.84
1833 LYS   (   9-)  G   -2.83
   3 LYS   (   9-)  A   -2.82
1223 LYS   (   9-)  E   -2.81
2186 LEU   ( 362-)  G   -2.79
 966 LEU   ( 362-)  C   -2.78
 356 LEU   ( 362-)  A   -2.78
1576 LEU   ( 362-)  E   -2.78
 100 LEU   ( 105-)  A   -2.71
1320 LEU   ( 105-)  E   -2.70
 710 LEU   ( 105-)  C   -2.70
1930 LEU   ( 105-)  G   -2.70

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: Y

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.

2453 HOH   ( 609 )  A      O     -6.47   -3.18    6.95
2457 HOH   ( 492 )  E      O     21.92  -14.12  -14.80
2457 HOH   ( 591 )  E      O      0.62   -7.03  -41.77
2459 HOH   ( 590 )  G      O     -4.06    5.14  -38.13
2459 HOH   ( 592 )  G      O     -0.17    4.11  -37.72

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.

2454 HOH   ( 174 )  S      O
2455 HOH   ( 563 )  C      O
2455 HOH   ( 582 )  C      O
2455 HOH   ( 585 )  C      O
2457 HOH   ( 575 )  E      O
2459 HOH   ( 563 )  G      O
2459 HOH   ( 587 )  G      O
2459 HOH   ( 591 )  G      O
2459 HOH   ( 594 )  G      O

Error: HIS, ASN, GLN side chain flips

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

 236 ASN   ( 241-)  A
 250 ASN   ( 255-)  A
 292 ASN   ( 298-)  A
 477 GLN   (  12-)  S
 541 ASN   (  88-)  S
 573 ASN   ( 118-)  S
 586 GLN   ( 131-)  S
 846 ASN   ( 241-)  C
 902 ASN   ( 298-)  C
1087 GLN   (  12-)  U
1151 ASN   (  88-)  U
1183 ASN   ( 118-)  U
1208 HIS   ( 143-)  U
1456 ASN   ( 241-)  E
1470 ASN   ( 255-)  E
1512 ASN   ( 298-)  E
1697 GLN   (  12-)  W
1761 ASN   (  88-)  W
1793 ASN   ( 118-)  W
1806 GLN   ( 131-)  W
2066 ASN   ( 241-)  G
2080 ASN   ( 255-)  G
2122 ASN   ( 298-)  G
2307 GLN   (  12-)  Y
2403 ASN   ( 118-)  Y
2428 HIS   ( 143-)  Y

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.

  20 TRP   (  25-)  A      N
  46 ILE   (  51-)  A      N
  60 THR   (  65-)  A      OG1
  62 THR   (  67-)  A      N
  73 ASP   (  78-)  A      N
 154 ARG   ( 159-)  A      NH1
 154 ARG   ( 159-)  A      NH2
 162 ARG   ( 167-)  A      N
 168 THR   ( 173-)  A      OG1
 170 LYS   ( 175-)  A      N
 173 LEU   ( 178-)  A      N
 174 GLY   ( 179-)  A      N
 200 ASN   ( 205-)  A      ND2
 210 ARG   ( 215-)  A      NE
 233 HIS   ( 238-)  A      N
 239 ALA   ( 244-)  A      N
 243 GLU   ( 248-)  A      N
 265 VAL   ( 271-)  A      N
 292 ASN   ( 298-)  A      ND2
 294 THR   ( 300-)  A      OG1
 297 ARG   ( 303-)  A      N
 298 GLN   ( 304-)  A      NE2
 306 ARG   ( 312-)  A      NH1
 319 HIS   ( 325-)  A      NE2
 321 HIS   ( 327-)  A      N
And so on for a total of 208 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.

 153 GLU   ( 158-)  A      OE2
 233 HIS   ( 238-)  A      ND1
 263 ASP   ( 268-)  A      OD1
 263 ASP   ( 268-)  A      OD2
 598 HIS   ( 143-)  S      ND1
 763 GLU   ( 158-)  C      OE2
 843 HIS   ( 238-)  C      ND1
 873 ASP   ( 268-)  C      OD2
 996 HIS   ( 392-)  C      ND1
1373 GLU   ( 158-)  E      OE2
1453 HIS   ( 238-)  E      ND1
1483 ASP   ( 268-)  E      OD1
1483 ASP   ( 268-)  E      OD2
1606 HIS   ( 392-)  E      ND1
1818 HIS   ( 143-)  W      ND1
1983 GLU   ( 158-)  G      OE2
2063 HIS   ( 238-)  G      ND1
2093 ASP   ( 268-)  G      OD2
2216 HIS   ( 392-)  G      ND1

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+.

2445  MG   ( 490-)  A     0.62   1.01 Is perhaps CA
2447  MG   ( 490-)  C     0.65   1.08 Is perhaps CA
2449  MG   ( 490-)  E     0.58   0.93 Is perhaps CA
2451  MG   ( 490-)  G     0.63   1.05 Is perhaps CA

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.

 211 GLU   ( 216-)  A   H-bonding suggests Gln
 263 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 454 ASP   ( 460-)  A   H-bonding suggests Asn
 564 GLU   ( 109-)  S   H-bonding suggests Gln
 873 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1064 ASP   ( 460-)  C   H-bonding suggests Asn
1174 GLU   ( 109-)  U   H-bonding suggests Gln
1431 GLU   ( 216-)  E   H-bonding suggests Gln
1483 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1674 ASP   ( 460-)  E   H-bonding suggests Asn
1784 GLU   ( 109-)  W   H-bonding suggests Gln
2093 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
2284 ASP   ( 460-)  G   H-bonding suggests Asn
2394 GLU   ( 109-)  Y   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.518
  2nd generation packing quality :  -0.806
  Ramachandran plot appearance   :  -0.550
  chi-1/chi-2 rotamer normality  :  -1.817
  Backbone conformation          :  -0.270

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.610 (tight)
  Bond angles                    :   1.254
  Omega angle restraints         :   0.693 (tight)
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   1.016
  B-factor distribution          :   2.215 (loose)
  Inside/Outside distribution    :   1.075

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.610 (tight)
  Bond angles                    :   1.254
  Omega angle restraints         :   0.693 (tight)
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   1.016
  B-factor distribution          :   2.215 (loose)
  Inside/Outside distribution    :   1.075
==============

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.