WHAT IF Check report

This file was created 2013-05-02 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 pdb3w09.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.

 395 MAN   ( 504-)  A  -
 396 MAN   ( 505-)  A  -
 397 MAN   ( 506-)  A  -
 398 MAN   ( 507-)  A  -
 399 MAN   ( 508-)  A  -
 408 ZGE   ( 520-)  A  -
 409 MAN   ( 509-)  A  -
 410 BMA   ( 503-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  31 SER   ( 112-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  31 SER   ( 112-)  A  -

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 389 NAG   ( 501-)  A  -   O4  bound to  390 NAG   ( 502-)  A  -   C1
 390 NAG   ( 502-)  A  -   O4  bound to  410 BMA   ( 503-)  A  -   C1
 391 NAG   ( 510-)  A  -   O4  bound to  392 NAG   ( 511-)  A  -   C1

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 336 GLU   ( 416-)  A    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

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.

   1 ARG   (  82-)  A
  60 ARG   ( 141-)  A
 129 ARG   ( 209-)  A
 140 ARG   ( 220-)  A
 204 ARG   ( 284-)  A
 283 ARG   ( 364-)  A

Warning: Tyrosine convention problem

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

 176 TYR   ( 256-)  A
 343 TYR   ( 423-)  A

Warning: Phenylalanine convention problem

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

 161 PHE   ( 241-)  A
 342 PHE   ( 422-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  70 ASP   ( 151-)  A
 258 ASP   ( 339-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 334 GLU   ( 414-)  A
 336 GLU   ( 416-)  A

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.

  25 VAL   ( 106-)  A      N    CA    1.54    4.2
  89 TYR   ( 169-)  A      N   -C     1.46    6.7
 106 GLY   ( 186-)  A      N    CA    1.52    4.2
 235 GLN   ( 315-)  A      CD   NE2   1.42    4.6
 252 THR   ( 332-)  A      N   -C     1.22   -5.4
 254 GLY   ( 335-)  A      C    O     1.32    4.2
 331 TYR   ( 412-)  A      N   -C     1.44    5.5

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

 |  0.995355 -0.001473 -0.000736|
 | -0.001473  0.993355 -0.001758|
 | -0.000736 -0.001758  0.993255|
Proposed new scale matrix

 |  0.005556  0.000008  0.000004|
 |  0.000008  0.005567  0.000010|
 |  0.000004  0.000010  0.005568|
With corresponding cell

    A    = 179.992  B   = 179.631  C    = 179.613
    Alpha=  90.203  Beta=  90.085  Gamma=  90.170

The CRYST1 cell dimensions

    A    = 180.836  B   = 180.836  C    = 180.836
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 501.639
(Under-)estimated Z-score: 16.507

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.

  89 TYR   ( 169-)  A     -O   -C    N   115.12   -4.9
 140 ARG   ( 220-)  A      CB   CG   CD  105.79   -4.2
 153 HIS   ( 233-)  A      CG   ND1  CE1 109.62    4.0
 212 ARG   ( 292-)  A      CB   CG   CD  104.63   -4.7
 224 ARG   ( 304-)  A      CG   CD   NE  118.30    4.6
 233 THR   ( 313-)  A      C    CA   CB   98.33   -6.2
 252 THR   ( 332-)  A     -C    N    CA  128.96    4.0
 252 THR   ( 332-)  A      CA   CB   CG2 117.56    4.2
 253 VAL   ( 333-)  A      CA   CB   CG1 119.05    5.0
 253 VAL   ( 333-)  A      CA   CB   CG2 118.13    4.5
 310 THR   ( 391-)  A     -C    N    CA  113.18   -4.7
 313 GLN   ( 395-)  A     -O   -C    N   129.41    4.0
 331 TYR   ( 412-)  A     -O   -C    N   105.02  -11.2
 331 TYR   ( 412-)  A     -CA  -C    N   127.02    5.4
 331 TYR   ( 412-)  A     -C    N    CA  131.24    5.3
 332 TRP   ( 412-)  A     -O   -C    N   110.86   -7.6
 332 TRP   ( 412-)  A     -CA  -C    N   128.06    5.9
 366 MET   ( 446-)  A      CG   SD   CE  112.03    5.1

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.

   1 ARG   (  82-)  A
  60 ARG   ( 141-)  A
  70 ASP   ( 151-)  A
 129 ARG   ( 209-)  A
 140 ARG   ( 220-)  A
 204 ARG   ( 284-)  A
 258 ASP   ( 339-)  A
 283 ARG   ( 364-)  A
 334 GLU   ( 414-)  A
 336 GLU   ( 416-)  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.

  88 VAL   ( 169-)  A      C    -13.9   -18.91     0.15
 253 VAL   ( 333-)  A      CB     6.6   -24.26   -32.96
 313 GLN   ( 395-)  A      C     -7.0   -10.81     0.15
 330 ASP   ( 412-)  A      C    -10.4   -15.99    -0.01
The average deviation= 1.547

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.

 108 THR   ( 188-)  A    -2.9
 204 ARG   ( 284-)  A    -2.8
 145 THR   ( 225-)  A    -2.6
  37 ARG   ( 118-)  A    -2.5
  57 THR   ( 138-)  A    -2.4
 129 ARG   ( 209-)  A    -2.4
 233 THR   ( 313-)  A    -2.3
 101 THR   ( 181-)  A    -2.2
 379 PRO   ( 459-)  A    -2.2
 137 THR   ( 217-)  A    -2.1
 268 VAL   ( 349-)  A    -2.1
  95 CYS   ( 175-)  A    -2.1
  82 LEU   ( 163-)  A    -2.1
 366 MET   ( 446-)  A    -2.0
 360 SER   ( 440-)  A    -2.0
  98 TRP   ( 178-)  A    -2.0
 251 PRO   ( 331-)  A    -2.0
 376 TRP   ( 456-)  A    -2.0
 203 GLU   ( 283-)  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.

  23 ASN   ( 104-)  A  Poor phi/psi, omega poor
  31 SER   ( 112-)  A  omega poor
  36 THR   ( 117-)  A  omega poor
  38 GLU   ( 119-)  A  Poor phi/psi
  70 ASP   ( 151-)  A  omega poor
  83 SER   ( 164-)  A  Poor phi/psi, omega poor
  88 VAL   ( 169-)  A  omega poor
  97 GLY   ( 177-)  A  omega poor
 100 SER   ( 180-)  A  omega poor
 129 ARG   ( 209-)  A  Poor phi/psi
 140 ARG   ( 220-)  A  Poor phi/psi
 142 ILE   ( 222-)  A  Poor phi/psi
 145 THR   ( 225-)  A  Poor phi/psi, omega poor
 147 GLU   ( 227-)  A  Poor phi/psi
 149 GLU   ( 229-)  A  omega poor
 179 GLU   ( 259-)  A  Poor phi/psi
 184 LYS   ( 264-)  A  omega poor
 205 ALA   ( 285-)  A  Poor phi/psi
 216 GLN   ( 296-)  A  Poor phi/psi, omega poor
 218 SER   ( 298-)  A  omega poor
 232 HIS   ( 312-)  A  omega poor
 235 GLN   ( 315-)  A  Poor phi/psi
 236 TYR   ( 316-)  A  omega poor
 245 ASN   ( 325-)  A  PRO omega poor
 251 PRO   ( 331-)  A  Poor phi/psi
 264 ASN   ( 345-)  A  omega poor
 265 ASN   ( 346-)  A  Poor phi/psi
 278 ASN   ( 359-)  A  Poor phi/psi
 300 ASN   ( 381-)  A  Poor phi/psi
 322 SER   ( 404-)  A  Poor phi/psi
 331 TYR   ( 412-)  A  Poor phi/psi
 335 GLY   ( 415-)  A  omega poor
 350 ARG   ( 430-)  A  PRO omega poor
 361 ASN   ( 441-)  A  omega poor
 363 ILE   ( 443-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.501

Warning: Unusual backbone conformations

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

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

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

   7 THR   (  88-)  A      0
  12 THR   (  93-)  A      0
  14 ASN   (  95-)  A      0
  22 ASP   ( 103-)  A      0
  30 ASP   ( 111-)  A      0
  31 SER   ( 112-)  A      0
  32 ASP   ( 113-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  40 TYR   ( 121-)  A      0
  46 ASP   ( 127-)  A      0
  47 GLU   ( 128-)  A      0
  55 GLN   ( 136-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  67 THR   ( 148-)  A      0
  68 ILE   ( 149-)  A      0
  71 ARG   ( 152-)  A      0
  80 TRP   ( 161-)  A      0
  82 LEU   ( 163-)  A      0
  83 SER   ( 164-)  A      0
  94 GLU   ( 174-)  A      0
  95 CYS   ( 175-)  A      0
  96 ILE   ( 176-)  A      0
  98 TRP   ( 178-)  A      0
And so on for a total of 226 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.819

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!

  20 GLY   ( 101-)  A   1.64   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]

 221 PRO   ( 301-)  A    0.18 LOW

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].

  85 PRO   ( 166-)  A    -3.2 envelop N (0 degrees)
 251 PRO   ( 331-)  A   -53.7 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 390 NAG   ( 502-)  A      O4  <->  410 BMA   ( 503-)  A      C1     0.97    1.43  INTRA B3
 324 TYR   ( 406-)  A      OH  <->  408 ZGE   ( 520-)  A      C2     0.96    1.44  INTRA BL
 398 MAN   ( 507-)  A      O6  <->  409 MAN   ( 509-)  A      C1     0.94    1.46  INTRA BF
 390 NAG   ( 502-)  A      C4  <->  410 BMA   ( 503-)  A      C1     0.82    2.38  INTRA
 398 MAN   ( 507-)  A      C6  <->  409 MAN   ( 509-)  A      C1     0.80    2.40  INTRA BF
 324 TYR   ( 406-)  A      CZ  <->  408 ZGE   ( 520-)  A      C2     0.54    2.66  INTRA BL
 263 ASN   ( 344-)  A      CB  <->  411 HOH   ( 623 )  A      O      0.44    2.36  INTRA BF
  87 THR   ( 168-)  A      OG1 <->   90 ASN   ( 170-)  A    A ND2    0.40    2.30  INTRA BL
   6 LEU   (  87-)  A      N   <->  153 HIS   ( 233-)  A      CD2    0.38    2.72  INTRA BL
 129 ARG   ( 209-)  A      NH1 <->  411 HOH   ( 709 )  A      O      0.32    2.38  INTRA BF
  92 ARG   ( 172-)  A      CD  <->  129 ARG   ( 209-)  A      NH2    0.27    2.83  INTRA BF
 263 ASN   ( 344-)  A      ND2 <->  411 HOH   ( 715 )  A      O      0.26    2.44  INTRA BF
 208 THR   ( 288-)  A      OG1 <->  224 ARG   ( 304-)  A      NH1    0.25    2.45  INTRA BF
 104 HIS   ( 184-)  A      NE2 <->  411 HOH   ( 947 )  A      O      0.19    2.51  INTRA
  87 THR   ( 168-)  A      N   <->   90 ASN   ( 170-)  A    A ND2    0.19    2.66  INTRA BL
 324 TYR   ( 406-)  A      CZ  <->  408 ZGE   ( 520-)  A      F1     0.19    3.01  INTRA BL
 411 HOH   ( 619 )  A      O   <->  411 HOH   ( 864 )  A      O      0.19    2.01  INTRA BF
 257 ASN   ( 338-)  A      N   <->  405 GOL   ( 518-)  A      C3     0.18    2.92  INTRA BF
 214 ASN   ( 294-)  A      ND2 <->  266 ASN   ( 347-)  A      C      0.17    2.93  INTRA
 411 HOH   ( 709 )  A      O   <->  411 HOH   ( 729 )  A      O      0.16    2.04  INTRA BF
  17 HIS   (  98-)  A      CE1 <->  339 ARG   ( 419-)  A      NH1    0.16    2.94  INTRA BL
 411 HOH   ( 709 )  A      O   <->  411 HOH   ( 890 )  A      O      0.14    2.06  INTRA BF
 401 GOL   ( 514-)  A      C1  <->  411 HOH   ( 896 )  A      O      0.14    2.66  INTRA BF
  38 GLU   ( 119-)  A      N   <->   39 PRO   ( 120-)  A      CD     0.13    2.87  INTRA BL
  92 ARG   ( 172-)  A      NH2 <->  411 HOH   ( 703 )  A      O      0.13    2.57  INTRA BF
And so on for a total of 71 lines.

Packing, accessibility and threading

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.

 375 GLN   ( 455-)  A      -6.07
 334 GLU   ( 414-)  A      -6.01
  74 TYR   ( 155-)  A      -5.94
  71 ARG   ( 152-)  A      -5.68
 372 PHE   ( 452-)  A      -5.43
  89 TYR   ( 169-)  A      -5.33
 336 GLU   ( 416-)  A      -5.26
 260 TYR   ( 341-)  A      -5.24

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.

  65 ASN   ( 146-)  A   -2.85
 228 VAL   ( 308-)  A   -2.65
   5 ASN   (  86-)  A   -2.64

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 372 PHE   ( 452-)  A     -  375 GLN   ( 455-)  A        -1.90

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.

 411 HOH   ( 611 )  A      O     28.97   24.64   29.34
 411 HOH   ( 636 )  A      O     37.33   14.18   38.62
 411 HOH   ( 646 )  A      O     44.92   -6.44   55.78
 411 HOH   ( 735 )  A      O     41.31   -1.73   62.07
 411 HOH   ( 796 )  A      O      0.85   30.88   57.59
 411 HOH   ( 798 )  A      O      0.65   31.91   55.06
 411 HOH   ( 968 )  A      O      7.95    2.62   77.01
 411 HOH   ( 970 )  A      O     17.70   28.99   31.11

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.

 411 HOH   ( 614 )  A      O
 411 HOH   ( 630 )  A      O
 411 HOH   ( 687 )  A      O
 411 HOH   ( 718 )  A      O
 411 HOH   ( 734 )  A      O
 411 HOH   ( 750 )  A      O
 411 HOH   ( 876 )  A      O
 411 HOH   ( 919 )  A      O
 411 HOH   ( 963 )  A      O
 411 HOH   ( 973 )  A      O
 411 HOH   ( 979 )  A      O
Bound group on Asn; dont flip    5 ASN  (  86-) A
Bound to:  391 NAG  ( 510-) A
Bound group on Asn; dont flip   65 ASN  ( 146-) A
Bound to:  393 NAG  ( 512-) A
Bound group on Asn; dont flip  120 ASN  ( 200-) A
Bound to:  389 NAG  ( 501-) A
Marked this atom as acceptor  408 ZGE  ( 520-) A      F1

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.

  14 ASN   (  95-)  A
  17 HIS   (  98-)  A
  63 HIS   ( 144-)  A
  90 ASN   ( 170-)  A
 136 ASN   ( 216-)  A
 153 HIS   ( 233-)  A
 214 ASN   ( 294-)  A
 263 ASN   ( 344-)  A
 311 GLN   ( 392-)  A
 313 GLN   ( 395-)  A
 318 ASN   ( 400-)  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.

  16 TRP   (  97-)  A      NE1
  41 VAL   ( 122-)  A      N
  57 THR   ( 138-)  A      N
  72 SER   ( 153-)  A    A N
  83 SER   ( 164-)  A      N
  87 THR   ( 168-)  A      OG1
 116 GLY   ( 196-)  A      N
 146 GLN   ( 226-)  A      NE2
 148 SER   ( 228-)  A      N
 168 GLY   ( 248-)  A      N
 194 HIS   ( 274-)  A      N
 201 TYR   ( 281-)  A      OH
 212 ARG   ( 292-)  A      NH1
 212 ARG   ( 292-)  A      NH2
 215 TRP   ( 295-)  A      NE1
 217 GLY   ( 297-)  A      N
 234 SER   ( 314-)  A      N
 247 ARG   ( 327-)  A      NH2
 250 ASP   ( 330-)  A      N
 257 ASN   ( 338-)  A      N
 258 ASP   ( 339-)  A      N
 263 ASN   ( 344-)  A      ND2
 269 LYS   ( 350-)  A      N
 283 ARG   ( 364-)  A      NH1
 323 GLY   ( 405-)  A      N
 337 CYS   ( 417-)  A      N
 358 TRP   ( 438-)  A      N
 365 SER   ( 445-)  A    A OG
 393 NAG   ( 512-)  A      N2

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.

 196 GLU   ( 276-)  A      OE1
 318 ASN   ( 400-)  A      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+.

 406  CA   ( 521-)  A     0.48   1.35 Is perhaps  K

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 411 HOH   ( 684 )  A      O  0.92  K  4
 411 HOH   ( 827 )  A      O  1.02  K  4
 411 HOH   ( 945 )  A      O  0.99  K 10 Ion-B

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 105 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 163 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 186 GLU   ( 266-)  A   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 :  -0.626
  2nd generation packing quality :  -2.182
  Ramachandran plot appearance   :  -2.054
  chi-1/chi-2 rotamer normality  :  -1.501
  Backbone conformation          :  -1.598

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.003
  Bond angles                    :   0.990
  Omega angle restraints         :   1.422 (loose)
  Side chain planarity           :   1.156
  Improper dihedral distribution :   1.359
  B-factor distribution          :   0.836
  Inside/Outside distribution    :   1.073

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -1.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.003
  Bond angles                    :   0.990
  Omega angle restraints         :   1.422 (loose)
  Side chain planarity           :   1.156
  Improper dihedral distribution :   1.359
  B-factor distribution          :   0.836
  Inside/Outside distribution    :   1.073
==============

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.