WHAT IF Check report

This file was created 2011-12-15 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 pdb2gsq.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

 204 GBI   ( 203-)  A  -         Fragmented
 205 GBI   ( 204-)  A  -         Fragmented
 206 SO4   ( 300-)  A  -         OK

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: 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 197 ARG   ( 197-)  A

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997357  0.001134 -0.000567|
 |  0.001134  0.999302  0.001279|
 | -0.000567  0.001279  0.992958|
Proposed new scale matrix

 |  0.013698  0.007883 -0.000002|
 | -0.000018  0.015796 -0.000020|
 |  0.000006 -0.000014  0.010615|
With corresponding cell

    A    =  72.954  B   =  72.994  C    =  94.209
    Alpha=  89.840  Beta=  90.065  Gamma= 119.854

The CRYST1 cell dimensions

    A    =  73.150  B   =  73.150  C    =  94.880
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 92.304
(Under-)estimated Z-score: 7.081

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.

  10 LEU   (  10-)  A      CA   CB   CG  130.48    4.1
  13 ARG   (  13-)  A      CB   CG   CD  103.42   -5.3
  18 ARG   (  18-)  A      CD   NE   CZ  135.18    7.5
  19 PHE   (  19-)  A      CA   CB   CG  118.88    5.1
  24 HIS   (  24-)  A      CG   ND1  CE1 109.60    4.0
  30 ASP   (  30-)  A      CA   C    O   109.38   -6.7
  31 ARG   (  31-)  A     -O   -C    N   129.66    4.2
  31 ARG   (  31-)  A      N    CA   CB  117.89    4.3
  37 ASP   (  37-)  A     -C    N    CA  129.77    4.5
  43 ALA   (  43-)  A      CA   C    O   113.37   -4.4
  50 MET   (  50-)  A      CG   SD   CE   88.93   -5.4
  54 ASP   (  54-)  A      CA   C    O   113.93   -4.0
  58 THR   (  58-)  A      CA   CB   OG1 100.56   -6.0
  62 GLN   (  62-)  A      NE2  CD   OE1 116.42   -6.2
  72 ARG   (  72-)  A      CA   CB   CG  122.83    4.4
  72 ARG   (  72-)  A      CD   NE   CZ  130.35    4.8
  86 ARG   (  86-)  A      CG   CD   NE  122.70    7.2
  86 ARG   (  86-)  A      CD   NE   CZ  130.38    4.8
  88 ASP   (  88-)  A      CA   CB   CG  118.47    5.9
  92 GLU   (  92-)  A      CG   CD   OE2 105.85   -5.5
  95 GLN   (  95-)  A     -C    N    CA  130.06    4.6
  95 GLN   (  95-)  A      CB   CG   CD  119.85    4.3
  96 ASP   (  96-)  A      CA   CB   CG  122.39    9.8
  96 ASP   (  96-)  A      CB   CG   OD1 128.97    4.6
 100 ASP   ( 100-)  A      N    CA   CB  119.01    5.0
And so on for a total of 61 lines.

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.

 197 ARG   ( 197-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 107 ALA   ( 107-)  A      CA     6.5    42.33    34.09
 178 VAL   ( 178-)  A      CA    -7.7    22.05    33.23
 178 VAL   ( 178-)  A      CB    10.2   -19.65   -32.96
The average deviation= 2.411

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.045

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.

 160 LEU   ( 160-)  A    5.91
 158 VAL   ( 158-)  A    5.64
 177 ILE   ( 177-)  A    4.22
 187 CYS   ( 187-)  A    4.10
  85 TYR   (  85-)  A    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.760

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  30 ASP   (  30-)  A    5.42
  54 ASP   (  54-)  A    4.47
 147 ASN   ( 147-)  A    4.46
   6 HIS   (   6-)  A    4.24
  31 ARG   (  31-)  A    4.21
  26 GLU   (  26-)  A    4.07
 166 HIS   ( 166-)  A    4.04

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.

 200 ARG   ( 200-)  A    -2.4
 106 PHE   ( 106-)  A    -2.4
   7 TYR   (   7-)  A    -2.4
 171 LEU   ( 171-)  A    -2.2
 167 THR   ( 167-)  A    -2.2
 196 LYS   ( 196-)  A    -2.2
  47 SER   (  47-)  A    -2.1
  12 GLY   (  12-)  A    -2.1
   5 LEU   (   5-)  A    -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.

  12 GLY   (  12-)  A  Poor phi/psi
  47 SER   (  47-)  A  Poor phi/psi
  48 ASN   (  48-)  A  Poor phi/psi
  50 MET   (  50-)  A  PRO omega poor
  62 GLN   (  62-)  A  Poor phi/psi
 111 ALA   ( 111-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.303

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.303

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.

 122 SER   ( 122-)  A    0.35

Warning: Unusual backbone conformations

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

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

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

   6 HIS   (   6-)  A      0
   7 TYR   (   7-)  A      0
   8 PHE   (   8-)  A      0
   9 PRO   (   9-)  A      0
  10 LEU   (  10-)  A      0
  11 MET   (  11-)  A      0
  13 ARG   (  13-)  A      0
  35 MET   (  35-)  A      0
  46 TYR   (  46-)  A      0
  47 SER   (  47-)  A      0
  48 ASN   (  48-)  A      0
  49 ALA   (  49-)  A      0
  50 MET   (  50-)  A      0
  61 SER   (  61-)  A      0
  62 GLN   (  62-)  A      0
  76 LEU   (  76-)  A      0
  77 ASP   (  77-)  A      0
  79 LYS   (  79-)  A      0
 110 ALA   ( 110-)  A      0
 111 ALA   ( 111-)  A      0
 137 ASN   ( 137-)  A      0
 141 ASP   ( 141-)  A      0
 143 PHE   ( 143-)  A      0
 144 PHE   ( 144-)  A      0
 145 VAL   ( 145-)  A      0
 147 ASN   ( 147-)  A      0
 149 MET   ( 149-)  A      0
 166 HIS   ( 166-)  A      0
 167 THR   ( 167-)  A      0
 174 CYS   ( 174-)  A      0
 200 ARG   ( 200-)  A      0
  12 GLY   (  12-)  A      1
  24 HIS   (  24-)  A      1
  27 GLU   (  27-)  A      1
  34 GLU   (  34-)  A      1
  45 MET   (  45-)  A      1
  52 VAL   (  52-)  A      1
  55 ILE   (  55-)  A      1
  56 ASP   (  56-)  A      1
  74 PHE   (  74-)  A      1
  80 THR   (  80-)  A      1
 148 SER   ( 148-)  A      1
 173 ASP   ( 173-)  A      1
 186 GLU   ( 186-)  A      1
 196 LYS   ( 196-)  A      1
 106 PHE   ( 106-)  A      2
 112 LYS   ( 112-)  A      2
 187 CYS   ( 187-)  A      2

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 : 3.528

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]

   9 PRO   (   9-)  A    0.19 LOW
  51 PRO   (  51-)  A    0.48 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].

   1 PRO   (   1-)  A   101.3 envelop C-beta (108 degrees)
 108 PRO   ( 108-)  A   102.8 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

  54 ASP   (  54-)  A      OD2 <->   59 LYS   (  59-)  A      NZ     0.31    2.39  INTRA
 116 GLN   ( 116-)  A      NE2 <->  120 GLU   ( 120-)  A      OE2    0.30    2.40  INTRA
  68 ARG   (  68-)  A      NH1 <->  207 HOH   ( 346 )  A      O      0.28    2.42  INTRA
 123 CYS   ( 123-)  A      SG  <->  170 LEU   ( 170-)  A      CD1    0.27    3.13  INTRA
  95 GLN   (  95-)  A      NE2 <->  155 HIS   ( 155-)  A      CE1    0.27    2.83  INTRA BL
  31 ARG   (  31-)  A      NH2 <->  207 HOH   ( 496 )  A      O      0.26    2.44  INTRA
 111 ALA   ( 111-)  A      N   <->  112 LYS   ( 112-)  A      N      0.26    2.34  INTRA B3
 200 ARG   ( 200-)  A      NH2 <->  207 HOH   ( 358 )  A      O      0.25    2.45  INTRA
 196 LYS   ( 196-)  A      NZ  <->  207 HOH   ( 490 )  A      O      0.24    2.46  INTRA
 121 LYS   ( 121-)  A      NZ  <->  207 HOH   ( 494 )  A      O      0.23    2.47  INTRA
  24 HIS   (  24-)  A      ND1 <->   26 GLU   (  26-)  A      OE2    0.22    2.48  INTRA
  31 ARG   (  31-)  A      NE  <->  207 HOH   ( 394 )  A      O      0.21    2.49  INTRA
  47 SER   (  47-)  A      N   <->  207 HOH   ( 325 )  A      O      0.21    2.49  INTRA
  99 ASN   (  99-)  A      ND2 <->  207 HOH   ( 317 )  A      O      0.17    2.53  INTRA BL
  42 LYS   (  42-)  A      NZ  <->  204 GBI   ( 203-)  A      O32    0.16    2.54  INTRA
 127 ALA   ( 127-)  A      N   <->  128 PRO   ( 128-)  A      CD     0.16    2.84  INTRA BL
 187 CYS   ( 187-)  A      O   <->  191 ALA   ( 191-)  A      N      0.15    2.55  INTRA
  68 ARG   (  68-)  A      NH1 <->  207 HOH   ( 333 )  A      O      0.13    2.57  INTRA
  22 ALA   (  22-)  A      O   <->   25 GLY   (  25-)  A      N      0.12    2.58  INTRA
  38 TRP   (  38-)  A      N   <->   39 PRO   (  39-)  A      CD     0.12    2.88  INTRA
   6 HIS   (   6-)  A      CB  <->   50 MET   (  50-)  A      CE     0.12    3.08  INTRA BL
 200 ARG   ( 200-)  A      NH1 <->  207 HOH   ( 484 )  A      O      0.12    2.58  INTRA
 107 ALA   ( 107-)  A      O   <->  112 LYS   ( 112-)  A      NZ     0.10    2.60  INTRA
  88 ASP   (  88-)  A      O   <->   92 GLU   (  92-)  A      N      0.07    2.63  INTRA BL
   4 THR   (   4-)  A      O   <->   54 ASP   (  54-)  A      N      0.06    2.64  INTRA BL
 108 PRO   ( 108-)  A      O   <->  112 LYS   ( 112-)  A      CE     0.05    2.75  INTRA
  71 ALA   (  71-)  A      O   <->   76 LEU   (  76-)  A      N      0.05    2.65  INTRA BL
 149 MET   ( 149-)  A      CE  <->  187 CYS   ( 187-)  A      SG     0.05    3.35  INTRA
 147 ASN   ( 147-)  A      ND2 <->  207 HOH   ( 373 )  A      O      0.05    2.65  INTRA
 190 ILE   ( 190-)  A      O   <->  194 LEU   ( 194-)  A      N      0.04    2.66  INTRA
  10 LEU   (  10-)  A      O   <->   18 ARG   (  18-)  A      NH1    0.04    2.66  INTRA BL
  42 LYS   (  42-)  A      NZ  <->  204 GBI   ( 203-)  A      C3     0.04    3.06  INTRA
  24 HIS   (  24-)  A      N   <->   25 GLY   (  25-)  A      N      0.04    2.56  INTRA B3
  68 ARG   (  68-)  A      NH2 <->  207 HOH   ( 346 )  A      O      0.03    2.67  INTRA
  78 GLY   (  78-)  A      O   <->   84 LYS   (  84-)  A      NZ     0.03    2.67  INTRA
  67 ALA   (  67-)  A      O   <->   71 ALA   (  71-)  A      N      0.02    2.68  INTRA BL
 183 ARG   ( 183-)  A      NH1 <->  207 HOH   ( 302 )  A      O      0.02    2.68  INTRA
 188 PRO   ( 188-)  A      O   <->  192 ALA   ( 192-)  A      N      0.02    2.68  INTRA
  55 ILE   (  55-)  A      N   <->   58 THR   (  58-)  A      O      0.02    2.68  INTRA
 110 ALA   ( 110-)  A      N   <->  111 ALA   ( 111-)  A      N      0.02    2.58  INTRA B3
 137 ASN   ( 137-)  A      ND2 <->  143 PHE   ( 143-)  A      O      0.02    2.68  INTRA
 186 GLU   ( 186-)  A      C   <->  187 CYS   ( 187-)  A      C      0.02    2.78  INTRA B3
 122 SER   ( 122-)  A      O   <->  126 LEU   ( 126-)  A      N      0.02    2.68  INTRA
 125 ARG   ( 125-)  A      NH1 <->  126 LEU   ( 126-)  A      CD2    0.01    3.09  INTRA BL
 113 GLU   ( 113-)  A      C   <->  115 VAL   ( 115-)  A      N      0.01    2.89  INTRA
  82 LEU   (  82-)  A      O   <->   86 ARG   (  86-)  A      N      0.01    2.69  INTRA
 139 GLY   ( 139-)  A      N   <->  140 GLY   ( 140-)  A      N      0.01    2.59  INTRA B3

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.

 166 HIS   ( 166-)  A      -6.00
 199 VAL   ( 199-)  A      -5.20
  48 ASN   (  48-)  A      -5.05

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.

 199 VAL   ( 199-)  A       202 - PHE    202- ( A)         -4.64

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.

 198 PRO   ( 198-)  A   -3.02
  11 MET   (  11-)  A   -2.57
 146 GLY   ( 146-)  A   -2.55
 200 ARG   ( 200-)  A   -2.52

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.

 207 HOH   ( 497 )  A      O     13.55   56.05   14.62

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.

 207 HOH   ( 454 )  A      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.

 118 ASN   ( 118-)  A

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.

   1 PRO   (   1-)  A      N
   3 TYR   (   3-)  A      N
   7 TYR   (   7-)  A      OH
   8 PHE   (   8-)  A      N
  38 TRP   (  38-)  A      NE1
  46 TYR   (  46-)  A      N
  50 MET   (  50-)  A      N
  63 SER   (  63-)  A      N
  69 HIS   (  69-)  A      ND1
  72 ARG   (  72-)  A      NE
  72 ARG   (  72-)  A      NH2
  80 THR   (  80-)  A      N
 110 ALA   ( 110-)  A      N
 112 LYS   ( 112-)  A      N
 119 TYR   ( 119-)  A      OH
 160 LEU   ( 160-)  A      N
 169 GLU   ( 169-)  A      N
 200 ARG   ( 200-)  A      NH1

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.

   6 HIS   (   6-)  A      ND1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  96 ASP   (  96-)  A   H-bonding suggests Asn
 100 ASP   ( 100-)  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 :  -0.405
  2nd generation packing quality :  -1.995
  Ramachandran plot appearance   :  -2.386
  chi-1/chi-2 rotamer normality  :  -4.303 (bad)
  Backbone conformation          :   0.345

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.706
  Omega angle restraints         :   0.642 (tight)
  Side chain planarity           :   2.242 (loose)
  Improper dihedral distribution :   2.045 (loose)
  B-factor distribution          :   0.402
  Inside/Outside distribution    :   0.981

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.706
  Omega angle restraints         :   0.642 (tight)
  Side chain planarity           :   2.242 (loose)
  Improper dihedral distribution :   2.045 (loose)
  B-factor distribution          :   0.402
  Inside/Outside distribution    :   0.981
==============

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.