WHAT IF Check report

This file was created 2012-08-12 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 pdb1lnc.ent

Checks that need to be done early-on in validation

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.

 326 DMS   ( 320-)  E  -

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.

  11 ARG   (  11-)  E  -
 143 GLU   ( 143-)  E  -
 144 LEU   ( 144-)  E  -

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.

  11 ARG   (  11-)  E  -
 143 GLU   ( 143-)  E  -
 144 LEU   ( 144-)  E  -

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: E

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  11 ARG   (  11-)  E    1.31
 120 MET   ( 120-)  E    0.86
 143 GLU   ( 143-)  E    1.05
 161 SER   ( 161-)  E    0.85

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) :298.000

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

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

RMS Z-score : 2.445 over 2126 bonds
Average difference in B over a bond : 5.12
RMS difference in B over a bond : 7.75

Note: B-factor plot

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

Chain identifier: E

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.

 126 ASP   ( 126-)  E      CG   OD1   1.33    4.0
 166 GLU   ( 166-)  E      CD   OE2   1.16   -4.7
 177 GLU   ( 177-)  E      CD   OE2   1.35    5.5
 187 GLU   ( 187-)  E      CD   OE1   1.33    4.5
 190 GLU   ( 190-)  E      CD   OE2   1.33    4.2

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

 |  0.996634  0.000882 -0.001122|
 |  0.000882  0.996742 -0.000164|
 | -0.001122 -0.000164  1.003383|
Proposed new scale matrix

 |  0.010681  0.006160  0.000013|
 | -0.000011  0.012337  0.000002|
 |  0.000009  0.000001  0.007596|
With corresponding cell

    A    =  93.581  B   =  93.522  C    = 131.643
    Alpha=  89.952  Beta=  90.129  Gamma= 119.922

The CRYST1 cell dimensions

    A    =  93.900  B   =  93.900  C    = 131.200
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 59.749
(Under-)estimated Z-score: 5.697

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.

  32 ASP   (  32-)  E      CA   CB   CG  118.35    5.8
  65 SER   (  65-)  E     -C    N    CA  112.90   -4.9
  69 PRO   (  69-)  E      N    CA   CB  107.71    4.3
 112 ASN   ( 112-)  E      CA   CB   CG  117.97    5.4
 156 ILE   ( 156-)  E      N    CA   CB  117.53    4.1
 172 PHE   ( 172-)  E      CA   CB   CG  107.81   -6.0
 173 GLY   ( 173-)  E     -C    N    CA  113.67   -4.1
 215 ASP   ( 215-)  E      CA   CB   CG  108.14   -4.5
 227 ASN   ( 227-)  E      CA   CB   CG  107.24   -5.4
 231 HIS   ( 231-)  E      N    CA   CB  117.33    4.0
 310 PHE   ( 310-)  E      CA   CB   CG  109.70   -4.1

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.

 156 ILE   ( 156-)  E      CA    -6.5    23.39    33.24
The average deviation= 1.918

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.

 227 ASN   ( 227-)  E    7.21
  89 ASN   (  89-)  E    6.62
 119 GLU   ( 119-)  E    5.22
  74 HIS   (  74-)  E    5.19
 108 GLN   ( 108-)  E    5.13
 142 HIS   ( 142-)  E    5.08
 290 GLN   ( 290-)  E    4.91
  33 ASN   (  33-)  E    4.78
  88 HIS   (  88-)  E    4.32
 143 GLU   ( 143-)  E    4.14

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  66 TYR   (  66-)  E      OH   4.23
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.327

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.

   6 THR   (   6-)  E    -2.8
 182 LYS   ( 182-)  E    -2.6
  46 TYR   (  46-)  E    -2.5
 107 SER   ( 107-)  E    -2.4
  92 SER   (  92-)  E    -2.4
 157 TYR   ( 157-)  E    -2.4
 183 ASN   ( 183-)  E    -2.2
  25 SER   (  25-)  E    -2.2
 185 ASP   ( 185-)  E    -2.1
  20 ILE   (  20-)  E    -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.

  26 THR   (  26-)  E  Poor phi/psi
  46 TYR   (  46-)  E  Poor phi/psi
  50 LEU   (  50-)  E  PRO omega poor
  60 ASN   (  60-)  E  Poor phi/psi
  89 ASN   (  89-)  E  Poor phi/psi
  92 SER   (  92-)  E  Poor phi/psi
  97 ASN   (  97-)  E  Poor phi/psi
 105 HIS   ( 105-)  E  Poor phi/psi
 107 SER   ( 107-)  E  Poor phi/psi
 118 SER   ( 118-)  E  Poor phi/psi
 130 PHE   ( 130-)  E  omega poor
 152 THR   ( 152-)  E  Poor phi/psi
 157 TYR   ( 157-)  E  Poor phi/psi
 159 ASN   ( 159-)  E  Poor phi/psi
 181 ASN   ( 181-)  E  Poor phi/psi
 227 ASN   ( 227-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.845

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!

   5 SER   (   5-)  E      0
  14 LEU   (  14-)  E      0
  24 TYR   (  24-)  E      0
  25 SER   (  25-)  E      0
  26 THR   (  26-)  E      0
  27 TYR   (  27-)  E      0
  30 LEU   (  30-)  E      0
  34 THR   (  34-)  E      0
  35 ARG   (  35-)  E      0
  37 ASP   (  37-)  E      0
  45 LYS   (  45-)  E      0
  46 TYR   (  46-)  E      0
  49 THR   (  49-)  E      0
  51 PRO   (  51-)  E      0
  53 SER   (  53-)  E      0
  55 TRP   (  55-)  E      0
  60 ASN   (  60-)  E      0
  61 GLN   (  61-)  E      0
  62 PHE   (  62-)  E      0
  63 PHE   (  63-)  E      0
  88 HIS   (  88-)  E      0
  89 ASN   (  89-)  E      0
  91 LEU   (  91-)  E      0
  92 SER   (  92-)  E      0
  96 ASN   (  96-)  E      0
And so on for a total of 124 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!

 277 PRO   ( 277-)  E   1.58   10

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]

  69 PRO   (  69-)  E    0.10 LOW
 184 PRO   ( 184-)  E    0.14 LOW
 195 PRO   ( 195-)  E    0.13 LOW
 208 PRO   ( 208-)  E    0.18 LOW

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.

 120 MET   ( 120-)  E    A SD  <->  143 GLU   ( 143-)  E      CB     0.56    2.84  INTRA BL
   1 ILE   (   1-)  E      CD1 <->   29 TYR   (  29-)  E      CE2    0.55    2.65  INTRA BF
   1 ILE   (   1-)  E      CD1 <->   29 TYR   (  29-)  E      CD2    0.43    2.77  INTRA BF
   1 ILE   (   1-)  E      CD1 <->   29 TYR   (  29-)  E      CZ     0.37    2.83  INTRA BF
 126 ASP   ( 126-)  E      OD1 <->  128 GLN   ( 128-)  E      N      0.24    2.46  INTRA
 317 VAL   (1321-)  E      N   <->  327 HOH   ( 389 )  E      O      0.22    2.48  INTRA BF
 262 LYS   ( 262-)  E      NZ  <->  302 GLU   ( 302-)  E      OE2    0.20    2.50  INTRA
 194 THR   ( 194-)  E      CA  <->  195 PRO   ( 195-)  E      CD     0.16    2.64  INTRA B3
   1 ILE   (   1-)  E      CD1 <->   29 TYR   (  29-)  E      CG     0.15    3.05  INTRA BF
 120 MET   ( 120-)  E    A CE  <->  143 GLU   ( 143-)  E      CB     0.12    3.08  INTRA BL
 269 ARG   ( 269-)  E      NE  <->  294 ASP   ( 294-)  E      OD2    0.11    2.59  INTRA
 292 ALA   ( 292-)  E      O   <->  296 TYR   ( 296-)  E      N      0.11    2.59  INTRA
  13 VAL   (  13-)  E      N   <->   72 ASP   (  72-)  E      OD2    0.10    2.60  INTRA BL
 262 LYS   ( 262-)  E      NZ  <->  327 HOH   (1026 )  E      O      0.09    2.61  INTRA
 126 ASP   ( 126-)  E      N   <->  127 GLY   ( 127-)  E      N      0.09    2.51  INTRA B3
  25 SER   (  25-)  E      O   <->   27 TYR   (  27-)  E      N      0.09    2.61  INTRA
 187 GLU   ( 187-)  E      OE2 <->  327 HOH   (1056 )  E      O      0.06    2.34  INTRA
 225 GLN   ( 225-)  E      O   <->  228 GLY   ( 228-)  E      N      0.06    2.64  INTRA
 313 VAL   ( 313-)  E      N   <->  314 GLY   ( 314-)  E      N      0.06    2.54  INTRA BL
 129 THR   ( 129-)  E      O   <->  194 THR   ( 194-)  E      N      0.05    2.65  INTRA
 146 HIS   ( 146-)  E      ND1 <->  165 ASN   ( 165-)  E      OD1    0.05    2.65  INTRA BL
  45 LYS   (  45-)  E      NZ  <->  327 HOH   ( 962 )  E      O      0.05    2.65  INTRA
  49 THR   (  49-)  E      CG2 <->  327 HOH   (1071 )  E      O      0.04    2.76  INTRA
 149 THR   ( 149-)  E      O   <->  154 GLY   ( 154-)  E      N      0.04    2.66  INTRA BL
   8 GLY   (   8-)  E      N   <->   20 ILE   (  20-)  E      O      0.04    2.66  INTRA BL
  32 ASP   (  32-)  E      OD2 <->   35 ARG   (  35-)  E      NH1    0.04    2.66  INTRA BL
 180 ALA   ( 180-)  E      N   <->  181 ASN   ( 181-)  E      N      0.04    2.56  INTRA BL
 299 THR   ( 299-)  E      N   <->  300 SER   ( 300-)  E      N      0.03    2.57  INTRA B3
 243 LEU   ( 243-)  E      O   <->  247 GLY   ( 247-)  E      N      0.03    2.67  INTRA BL
   1 ILE   (   1-)  E      CD1 <->   29 TYR   (  29-)  E      CE1    0.02    3.18  INTRA BF
 233 ASN   ( 233-)  E      C   <->  235 GLY   ( 235-)  E      N      0.02    2.88  INTRA BL
  24 TYR   (  24-)  E      CD1 <->   28 TYR   (  28-)  E      CE1    0.02    3.18  INTRA BL
 216 HIS   ( 216-)  E      ND1 <->  218 SER   ( 218-)  E      N      0.02    2.98  INTRA BL
 226 ASP   ( 226-)  E      OD2 <->  231 HIS   ( 231-)  E      N      0.02    2.68  INTRA
 242 TYR   ( 242-)  E      O   <->  246 GLN   ( 246-)  E      N      0.02    2.68  INTRA BL
 206 SER   ( 206-)  E      O   <->  239 LYS   ( 239-)  E      NZ     0.02    2.68  INTRA BL
 138 ASP   ( 138-)  E      N   <->  327 HOH   ( 982 )  E      O      0.02    2.68  INTRA
 217 TYR   ( 217-)  E      O   <->  220 ARG   ( 220-)  E      NH1    0.02    2.68  INTRA
 327 HOH   (1011 )  E      O   <->  327 HOH   (1069 )  E      O      0.02    2.18  INTRA BF
  54 LEU   (  54-)  E      N   <->  327 HOH   (1010 )  E      O      0.02    2.68  INTRA
 211 TYR   ( 211-)  E      N   <->  212 GLY   ( 212-)  E      N      0.01    2.59  INTRA B3
  64 ALA   (  64-)  E      C   <->   65 SER   (  65-)  E      CA     0.01    2.29  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: E

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.

 225 GLN   ( 225-)  E      -5.95
  88 HIS   (  88-)  E      -5.80
 108 GLN   ( 108-)  E      -5.70
 251 TYR   ( 251-)  E      -5.51
 246 GLN   ( 246-)  E      -5.50
 221 TYR   ( 221-)  E      -5.48
 157 TYR   ( 157-)  E      -5.43
 182 LYS   ( 182-)  E      -5.12
 273 GLN   ( 273-)  E      -5.10
  50 LEU   (  50-)  E      -5.04

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

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.

  44 ALA   (  44-)  E   -2.78

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: E

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.

 327 HOH   ( 968 )  E      O     56.35   40.57   -5.42
 327 HOH   ( 986 )  E      O     61.88   41.40  -11.53
 327 HOH   ( 994 )  E      O      6.31   48.56   13.38
 327 HOH   ( 996 )  E      O     29.93   52.10   20.28
 327 HOH   (1039 )  E      O     34.02   44.53  -12.17
 327 HOH   (1059 )  E      O     14.42   58.96   15.79

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.

 327 HOH   (1057 )  E      O
Metal-coordinating Histidine residue 142 fixed to   1
Metal-coordinating Histidine residue 146 fixed to   1

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.

  31 GLN   (  31-)  E
  33 ASN   (  33-)  E
 290 GLN   ( 290-)  E
 301 GLN   ( 301-)  E
 308 GLN   ( 308-)  E

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.

  35 ARG   (  35-)  E      N
  97 ASN   (  97-)  E      ND2
 112 ASN   ( 112-)  E      N
 155 LEU   ( 155-)  E      N
 216 HIS   ( 216-)  E      N
Only metal coordination for  142 HIS  ( 142-) E      NE2
Only metal coordination for  190 GLU  ( 190-) E      OE2

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.

 238 ASN   ( 238-)  E      OD1

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+.

 321  CA   ( 901-)  E   -.-  -.-  Part of ionic cluster
 321  CA   ( 901-)  E     0.81   1.05 Scores about as good as NA

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.

  37 ASP   (  37-)  E   H-bonding suggests Asn
 119 GLU   ( 119-)  E   H-bonding suggests Gln
 294 ASP   ( 294-)  E   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.886
  2nd generation packing quality :  -1.224
  Ramachandran plot appearance   :  -0.327
  chi-1/chi-2 rotamer normality  :  -0.845
  Backbone conformation          :  -0.104

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.954
  Bond angles                    :   1.064
  Omega angle restraints         :   0.743
  Side chain planarity           :   2.315 (loose)
  Improper dihedral distribution :   1.588 (loose)
  B-factor distribution          :   2.445 (loose)
  Inside/Outside distribution    :   1.016

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 : 1.80

Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.954
  Bond angles                    :   1.064
  Omega angle restraints         :   0.743
  Side chain planarity           :   2.315 (loose)
  Improper dihedral distribution :   1.588 (loose)
  B-factor distribution          :   2.445 (loose)
  Inside/Outside distribution    :   1.016

      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
    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).

    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
      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
    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.