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 pdb1ej7.ent

Checks that need to be done early-on in validation

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 585 HOH   ( 750 )  L      O
 585 HOH   ( 864 )  L      O
 585 HOH   ( 873 )  L      O

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 585 HOH   ( 750 )  L      O       8
 585 HOH   ( 864 )  L      O       8
 585 HOH   ( 873 )  L      O      14

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.

 582 PO4   ( 641-)  L  -
 583 PO4   ( 642-)  L  -
 584 PO4   ( 643-)  L  -

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 319 GLU   ( 336-)  L  -

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 452 ALA   ( 470-)  L  -   CB
 453 ALA   ( 471-)  L  -   CB
 454 VAL   ( 472-)  L  -   CB
 454 VAL   ( 472-)  L  -   CG1
 454 VAL   ( 472-)  L  -   CG2
 455 ASP   ( 473-)  L  -   CB
 455 ASP   ( 473-)  L  -   CG
 455 ASP   ( 473-)  L  -   OD1
 455 ASP   ( 473-)  L  -   OD2
 456 VAL   ( 474-)  L  -   CB
 456 VAL   ( 474-)  L  -   CG1
 456 VAL   ( 474-)  L  -   CG2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 452 ALA   ( 470-)  L  -   N
 452 ALA   ( 470-)  L  -   C
 452 ALA   ( 470-)  L  -   O
 453 ALA   ( 471-)  L  -   N
 453 ALA   ( 471-)  L  -   C
 453 ALA   ( 471-)  L  -   O
 454 VAL   ( 472-)  L  -   N
 454 VAL   ( 472-)  L  -   CA
 454 VAL   ( 472-)  L  -   C
 454 VAL   ( 472-)  L  -   O
 455 ASP   ( 473-)  L  -   N
 455 ASP   ( 473-)  L  -   CA
 455 ASP   ( 473-)  L  -   C
 455 ASP   ( 473-)  L  -   O
 456 VAL   ( 474-)  L  -   N
 456 VAL   ( 474-)  L  -   CA
 456 VAL   ( 474-)  L  -   C
 456 VAL   ( 474-)  L  -   O

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: L

Note: Ramachandran plot

Chain identifier: S

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 LYS   (  18-)  L      CG
   1 LYS   (  18-)  L      CD
   1 LYS   (  18-)  L      CE
   1 LYS   (  18-)  L      NZ
 452 ALA   ( 470-)  L      CA
 453 ALA   ( 471-)  L      CA

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) :295.000

Note: B-factor plot

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

Chain identifier: L

Note: B-factor plot

Chain identifier: S

Nomenclature related problems

Warning: Tyrosine convention problem

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

  80 TYR   (  97-)  L

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.

   2 ASP   (  19-)  L
  16 ASP   (  33-)  L
  61 ASP   (  78-)  L
  78 ASP   (  95-)  L
  89 ASP   ( 106-)  L
 322 ASP   ( 340-)  L
 418 ASP   ( 436-)  L
 476 ASP   ( 520-)  S
 561 ASP   ( 605-)  S

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.

  11 GLU   (  28-)  L
  34 GLU   (  51-)  L
  35 GLU   (  52-)  L
  43 GLU   (  60-)  L
  71 GLU   (  88-)  L
 232 GLU   ( 249-)  L
 319 GLU   ( 336-)  L
 320 GLU   ( 338-)  L
 374 GLU   ( 392-)  L
 442 GLU   ( 460-)  L
 480 GLU   ( 524-)  S
 503 GLU   ( 547-)  S
 545 GLU   ( 589-)  S
 577 GLU   ( 621-)  S

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.

 451 PHE   ( 469-)  L      CA   C     1.40   -5.9
 451 PHE   ( 469-)  L      N   -C     1.42    4.7
 452 ALA   ( 470-)  L      N   -C     1.24   -4.6
 453 ALA   ( 471-)  L      N   -C     1.19   -6.8
 454 VAL   ( 472-)  L      N   -C     1.24   -4.6
 455 ASP   ( 473-)  L      N   -C     1.20   -6.3
 456 VAL   ( 474-)  L      N   -C     1.24   -4.5
 561 ASP   ( 605-)  S      CA   C     1.71    8.7
 562 ASN   ( 606-)  S      N    CA    1.61    7.9
 562 ASN   ( 606-)  S      N   -C     1.43    5.1
 563 VAL   ( 607-)  S      CA   C     1.44   -4.0
 564 ARG   ( 608-)  S      N    CA    1.37   -4.6
 567 GLN   ( 611-)  S      N   -C     1.46    6.4

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

 |  0.998697 -0.000197 -0.000269|
 | -0.000197  0.998414 -0.000272|
 | -0.000269 -0.000272  0.998383|
Proposed new scale matrix

 |  0.006712  0.000001  0.000002|
 |  0.000001  0.006714  0.000002|
 |  0.000002  0.000002  0.007241|
With corresponding cell

    A    = 148.993  B   = 148.950  C    = 138.108
    Alpha=  90.031  Beta=  90.031  Gamma=  90.023

The CRYST1 cell dimensions

    A    = 149.180  B   = 149.180  C    = 138.340
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 45.255
(Under-)estimated Z-score: 4.958

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.

  19 ILE   (  36-)  L      N    CA   C    99.87   -4.0
 246 PRO   ( 263-)  L      N    CA   C   122.67    4.3
 285 ASP   ( 302-)  L      N    CA   C   123.14    4.3
 308 HIS   ( 325-)  L      C    CA   CB  101.52   -4.5
 319 GLU   ( 336-)  L      N    CA   C    88.73   -8.0
 319 GLU   ( 336-)  L      C    CA   CB  119.11    4.7
 451 PHE   ( 469-)  L      N    CA   C   126.53    5.5
 451 PHE   ( 469-)  L      N    CA   CB  122.09    6.8
 451 PHE   ( 469-)  L      C    CA   CB   79.28  -16.2
 451 PHE   ( 469-)  L      CA   CB   CG  105.96   -7.8
 451 PHE   ( 469-)  L      CB   CG   CD2 111.81   -5.2
 452 ALA   ( 470-)  L     -O   -C    N   133.16    6.3
 452 ALA   ( 470-)  L     -CA  -C    N   101.20   -7.5
 453 ALA   ( 471-)  L     -O   -C    N   148.87   16.2
 455 ASP   ( 473-)  L     -C    N    CA  134.79    7.3
 456 VAL   ( 474-)  L     -C    N    CA  134.06    6.9
 561 ASP   ( 605-)  S      C    CA   CB  100.00   -5.3
 562 ASN   ( 606-)  S     -O   -C    N   113.09   -6.2
 562 ASN   ( 606-)  S     -CA  -C    N   124.79    4.3
 562 ASN   ( 606-)  S      C    CA   CB  101.34   -4.6
 565 GLN   ( 609-)  S      C    CA   CB  100.35   -5.1
 567 GLN   ( 611-)  S     -O   -C    N   149.77   16.7
 567 GLN   ( 611-)  S     -CA  -C    N    87.20  -14.5
 567 GLN   ( 611-)  S     -C    N    CA   98.34  -13.0

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.

   2 ASP   (  19-)  L
  11 GLU   (  28-)  L
  16 ASP   (  33-)  L
  34 GLU   (  51-)  L
  35 GLU   (  52-)  L
  43 GLU   (  60-)  L
  61 ASP   (  78-)  L
  71 GLU   (  88-)  L
  78 ASP   (  95-)  L
  89 ASP   ( 106-)  L
 232 GLU   ( 249-)  L
 319 GLU   ( 336-)  L
 320 GLU   ( 338-)  L
 322 ASP   ( 340-)  L
 374 GLU   ( 392-)  L
 418 ASP   ( 436-)  L
 442 GLU   ( 460-)  L
 476 ASP   ( 520-)  S
 480 GLU   ( 524-)  S
 503 GLU   ( 547-)  S
 545 GLU   ( 589-)  S
 561 ASP   ( 605-)  S
 577 GLU   ( 621-)  S

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.

 451 PHE   ( 469-)  L      CA     7.4    45.89    33.98
The average deviation= 0.862

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.

 319 GLU   ( 336-)  L    7.75
 285 ASP   ( 302-)  L    7.29
 451 PHE   ( 469-)  L    5.90
 107 VAL   ( 124-)  L    5.78
 252 TYR   ( 269-)  L    5.23
 566 VAL   ( 610-)  S    4.88
 138 ILE   ( 155-)  L    4.66
 442 GLU   ( 460-)  L    4.51
 332 ARG   ( 350-)  L    4.34
 184 LYS   ( 201-)  L    4.21

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 : 1.534

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.

  58 THR   (  75-)  L    -3.1
 451 PHE   ( 469-)  L    -2.7
 569 ILE   ( 613-)  S    -2.6
 351 VAL   ( 369-)  L    -2.3
 362 GLY   ( 380-)  L    -2.2
 565 GLN   ( 609-)  S    -2.1
  47 GLY   (  64-)  L    -2.1
 283 VAL   ( 300-)  L    -2.1
 385 GLY   ( 403-)  L    -2.0
 423 GLY   ( 441-)  L    -2.0
 564 ARG   ( 608-)  S    -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.

  45 SER   (  62-)  L  Poor phi/psi
  50 THR   (  67-)  L  Poor phi/psi
  78 ASP   (  95-)  L  Poor phi/psi
 106 ASN   ( 123-)  L  Poor phi/psi
 146 ASN   ( 163-)  L  Poor phi/psi
 150 ARG   ( 167-)  L  Poor phi/psi
 158 LYS   ( 175-)  L  PRO omega poor
 190 ASN   ( 207-)  L  Poor phi/psi
 280 MET   ( 297-)  L  Poor phi/psi
 351 VAL   ( 369-)  L  Poor phi/psi
 352 SER   ( 370-)  L  Poor phi/psi
 423 GLY   ( 441-)  L  Poor phi/psi
 450 ASN   ( 468-)  L  Poor phi/psi
 451 PHE   ( 469-)  L  Poor phi/psi
 452 ALA   ( 470-)  L  Impossible phi
 453 ALA   ( 471-)  L  Impossible phi
 454 VAL   ( 472-)  L  omega poor
 455 ASP   ( 473-)  L  omega poor
 464 ASN   ( 508-)  S  Poor phi/psi
 469 GLU   ( 513-)  S  Poor phi/psi
 471 LEU   ( 515-)  S  Poor phi/psi
 527 LYS   ( 571-)  S  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.682

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.

 262 SER   ( 279-)  L    0.36

Warning: Unusual backbone conformations

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

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

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

   3 TYR   (  20-)  L      0
   6 THR   (  23-)  L      0
   8 TYR   (  25-)  L      0
   9 THR   (  26-)  L      0
  29 PRO   (  46-)  L      0
  44 SER   (  61-)  L      0
  45 SER   (  62-)  L      0
  46 THR   (  63-)  L      0
  49 TRP   (  66-)  L      0
  50 THR   (  67-)  L      0
  57 LEU   (  74-)  L      0
  58 THR   (  75-)  L      0
  68 TYR   (  85-)  L      0
  77 LYS   (  94-)  L      0
  78 ASP   (  95-)  L      0
  90 LEU   ( 107-)  L      0
  93 GLU   ( 110-)  L      0
 110 PHE   ( 127-)  L      0
 114 ARG   ( 131-)  L      0
 119 GLU   ( 136-)  L      0
 120 ASP   ( 137-)  L      0
 131 PHE   ( 148-)  L      0
 134 PRO   ( 151-)  L      0
 135 PRO   ( 152-)  L      0
 136 HIS   ( 153-)  L      0
And so on for a total of 221 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.618

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 470 THR   ( 514-)  S   1.73

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.

 451 PHE   ( 469-)  L      CB  <->  452 ALA   ( 470-)  L      N      1.24    1.46  INTRA BF
 321 ARG   ( 339-)  L      NH2 <->  375 ILE   ( 393-)  L      CG1    0.69    2.41  INTRA BF
 451 PHE   ( 469-)  L      CG  <->  452 ALA   ( 470-)  L      N      0.66    2.34  INTRA BF
 452 ALA   ( 470-)  L      C   <->  453 ALA   ( 471-)  L      CB     0.61    2.19  INTRA BL
 452 ALA   ( 470-)  L      CB  <->  453 ALA   ( 471-)  L      N      0.52    2.18  INTRA BL
 318 LEU   ( 335-)  L      C   <->  319 GLU   ( 336-)  L      O      0.43    2.17  INTRA BF
 428 ARG   ( 446-)  L      NH1 <->  453 ALA   ( 471-)  L      O      0.39    2.31  INTRA BF
 454 VAL   ( 472-)  L      CG1 <->  455 ASP   ( 473-)  L      O      0.39    2.31  INTRA BL
 561 ASP   ( 605-)  S      N   <->  566 VAL   ( 610-)  S      O      0.36    2.34  INTRA BF
 451 PHE   ( 469-)  L      CD1 <->  452 ALA   ( 470-)  L      N      0.36    2.64  INTRA BF
 452 ALA   ( 470-)  L      O   <->  453 ALA   ( 471-)  L      CB     0.35    2.25  INTRA BL
 281 HIS   ( 298-)  L      NE2 <->  582 PO4   ( 642-)  L      O1     0.35    2.35  INTRA
 155 CYS   ( 172-)  L      SG  <->  175 CYS   ( 192-)  L      SG     0.33    3.12  INTRA BF
 451 PHE   ( 469-)  L      C   <->  452 ALA   ( 470-)  L      CB     0.29    2.51  INTRA BF
 321 ARG   ( 339-)  L      CZ  <->  375 ILE   ( 393-)  L      CD1    0.28    2.92  INTRA BF
 321 ARG   ( 339-)  L      NH2 <->  375 ILE   ( 393-)  L      CD1    0.27    2.83  INTRA BF
 563 VAL   ( 607-)  S      N   <->  564 ARG   ( 608-)  S      N      0.26    2.34  INTRA BF
 318 LEU   ( 335-)  L      C   <->  319 GLU   ( 336-)  L      C      0.25    2.55  INTRA BF
 141 GLU   ( 158-)  L      OE2 <->  308 HIS   ( 325-)  L      NE2    0.24    2.46  INTRA BL
 321 ARG   ( 339-)  L      NH1 <->  375 ILE   ( 393-)  L      CD1    0.23    2.87  INTRA BF
 562 ASN   ( 606-)  S      C   <->  564 ARG   ( 608-)  S      N      0.22    2.68  INTRA BF
 564 ARG   ( 608-)  S      O   <->  566 VAL   ( 610-)  S      N      0.21    2.49  INTRA BF
 121 LEU   ( 138-)  L      O   <->  299 LYS   ( 316-)  L      NZ     0.18    2.52  INTRA BL
 454 VAL   ( 472-)  L      CG1 <->  455 ASP   ( 473-)  L      N      0.17    2.83  INTRA BL
 451 PHE   ( 469-)  L      CA  <->  452 ALA   ( 470-)  L      N      0.16    2.04  INTRA BF
And so on for a total of 66 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

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.

 522 TYR   ( 566-)  S      -8.24
 531 PHE   ( 575-)  S      -6.05
 463 ILE   ( 507-)  S      -5.83
 132 GLN   ( 149-)  L      -5.76
 451 PHE   ( 469-)  L      -5.75
 114 ARG   ( 131-)  L      -5.72
 527 LYS   ( 571-)  S      -5.72
 513 LYS   ( 557-)  S      -5.68
 158 LYS   ( 175-)  L      -5.51
 421 GLN   ( 439-)  L      -5.50
 459 VAL   ( 503-)  S      -5.34
 492 ASN   ( 536-)  S      -5.30
 332 ARG   ( 350-)  L      -5.23
 177 ARG   ( 194-)  L      -5.19
  77 LYS   (  94-)  L      -5.17
  49 TRP   (  66-)  L      -5.16
 270 ASN   ( 287-)  L      -5.14
 342 ARG   ( 360-)  L      -5.13
 414 ASN   ( 432-)  L      -5.04
 161 LEU   ( 178-)  L      -5.03

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: L

Note: Quality value plot

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

Chain identifier: S

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.

 456 VAL   ( 474-)  L   -2.88
 282 ALA   ( 299-)  L   -2.76
   1 LYS   (  18-)  L   -2.64
 452 ALA   ( 470-)  L   -2.55
 453 ALA   ( 471-)  L   -2.55
 389 LEU   ( 407-)  L   -2.54

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: L

Note: Second generation quality Z-score plot

Chain identifier: S

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.

 584 HOH   ( 723 )  L      O     76.58   93.74   84.46

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.

 584 HOH   ( 819 )  L      O
 584 HOH   ( 831 )  L      O
 584 HOH   ( 863 )  L      O
 585 HOH   ( 875 )  S      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.

 212 GLN   ( 229-)  L
 224 ASN   ( 241-)  L
 265 HIS   ( 282-)  L
 287 GLN   ( 304-)  L
 338 GLN   ( 356-)  L
 368 HIS   ( 386-)  L
 402 ASN   ( 420-)  L
 414 ASN   ( 432-)  L
 512 ASN   ( 556-)  S

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.

   4 LYS   (  21-)  L      N
   5 LEU   (  22-)  L      N
  34 GLU   (  51-)  L      N
  35 GLU   (  52-)  L      N
  48 THR   (  65-)  L      N
  50 THR   (  67-)  L      N
  53 TRP   (  70-)  L      NE1
  58 THR   (  75-)  L      N
  58 THR   (  75-)  L      OG1
  59 SER   (  76-)  L      N
  61 ASP   (  78-)  L      N
  76 GLU   (  93-)  L      N
  78 ASP   (  95-)  L      N
  79 GLN   (  96-)  L      N
 112 ALA   ( 129-)  L      N
 117 ARG   ( 134-)  L      NH1
 117 ARG   ( 134-)  L      NH2
 150 ARG   ( 167-)  L      N
 158 LYS   ( 175-)  L      N
 161 LEU   ( 178-)  L      N
 190 ASN   ( 207-)  L      ND2
 194 PHE   ( 211-)  L      N
 200 ARG   ( 217-)  L      NH1
 222 TYR   ( 239-)  L      OH
 229 THR   ( 246-)  L      N
And so on for a total of 55 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 188 ASN   ( 205-)  L      OD1
 251 ASP   ( 268-)  L      OD1
 383 GLN   ( 401-)  L      OE1
 395 ASN   ( 413-)  L      OD1
 402 ASN   ( 420-)  L      OD1

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.

 251 ASP   ( 268-)  L   H-bonding suggests Asn; but Alt-Rotamer
 285 ASP   ( 302-)  L   H-bonding suggests Asn
 455 ASP   ( 473-)  L   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 :  -1.134
  2nd generation packing quality :  -0.687
  Ramachandran plot appearance   :  -1.140
  chi-1/chi-2 rotamer normality  :  -1.682
  Backbone conformation          :  -0.959

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.476 (tight)
  Side chain planarity           :   0.341 (tight)
  Improper dihedral distribution :   0.751
  B-factor distribution          :   0.801
  Inside/Outside distribution    :   1.079

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 : 2.45


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.476 (tight)
  Side chain planarity           :   0.341 (tight)
  Improper dihedral distribution :   0.751
  B-factor distribution          :   0.801
  Inside/Outside distribution    :   1.079
==============

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.