WHAT IF Check report

This file was created 2011-12-22 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 pdb1euu.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.

 604 GAL   (   2-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: What type of B-factor?

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

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

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

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

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

Percentage of buried atoms with B less than 5 : 4.74

Note: B-factor plot

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

Chain identifier: 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.

 345 ILE   ( 391-)  A      CA   CB    1.61    4.0
 305 CYS   ( 351-)  A      SG  -SG*   2.28    6.0
 359 CYS   ( 405-)  A      SG  -SG*   2.28    6.0

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

 |  0.999135 -0.000460 -0.000658|
 | -0.000460  0.999336  0.000430|
 | -0.000658  0.000430  0.998041|
Proposed new scale matrix

 |  0.019676  0.000008  0.001944|
 |  0.000004  0.008554 -0.000004|
 |  0.000011 -0.000007  0.016780|
With corresponding cell

    A    =  50.826  B   = 116.909  C    =  59.889
    Alpha=  89.946  Beta=  95.680  Gamma=  90.053

The CRYST1 cell dimensions

    A    =  50.870  B   = 116.990  C    =  60.000
    Alpha=  90.000  Beta=  95.600  Gamma=  90.000

Variance: 32.675
(Under-)estimated Z-score: 4.213

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.

  17 GLY   (  63-)  A      N    CA   C   125.00    4.3
  39 ASP   (  85-)  A      C    CA   CB  102.37   -4.1
  40 GLY   (  86-)  A      N    CA   C    98.76   -4.7
 140 HIS   ( 186-)  A      CG   ND1  CE1 109.69    4.1
 142 THR   ( 188-)  A      N    CA   C    97.28   -5.0
 153 TRP   ( 199-)  A      CA   CB   CG  122.79    4.8
 171 HIS   ( 217-)  A      CG   ND1  CE1 109.80    4.2
 229 SER   ( 275-)  A      N    CA   C   125.07    5.0
 230 ARG   ( 276-)  A      N    CA   C    99.09   -4.3
 234 ARG   ( 280-)  A      N    CA   C   123.02    4.2
 245 ASP   ( 291-)  A      N    CA   C   125.38    5.1
 247 GLY   ( 293-)  A      N    CA   C    99.93   -4.3
 248 HIS   ( 294-)  A     -C    N    CA  133.38    6.5
 248 HIS   ( 294-)  A      N    CA   C   126.91    5.6
 337 LEU   ( 383-)  A      CA   CB   CG  131.28    4.3
 356 GLY   ( 402-)  A      N    CA   C    98.34   -4.9
 358 ILE   ( 404-)  A      N    CA   C   124.25    4.7
 374 GLN   ( 420-)  A      N    CA   C   123.40    4.4
 375 VAL   ( 421-)  A      N    CA   C   124.13    4.6
 385 SER   ( 431-)  A      N    CA   C   122.74    4.1
 388 ALA   ( 434-)  A      N    CA   C    96.91   -5.1
 468 VAL   ( 514-)  A      C    CA   CB  101.57   -4.5
 480 ALA   ( 526-)  A      N    CA   C    97.21   -5.0
 499 ALA   ( 545-)  A     -C    N    CA  129.24    4.2
 504 TYR   ( 550-)  A      N    CA   C   135.51    8.7
 505 PRO   ( 551-)  A      N    CA   C   100.94   -4.3
 527 GLN   ( 573-)  A      N    CA   C   122.91    4.2
 557 PHE   ( 603-)  A     -C    N    CA  113.68   -4.5
 559 THR   ( 605-)  A      N    CA   CB  103.17   -4.3
 587 HIS   ( 633-)  A      CG   ND1  CE1 110.10    4.5
 588 LYS   ( 634-)  A      N    CA   C   123.88    4.5

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.

 504 TYR   ( 550-)  A      CA    -8.4    20.83    34.03
The average deviation= 1.614

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.

 504 TYR   ( 550-)  A    9.25
 229 SER   ( 275-)  A    6.77
 388 ALA   ( 434-)  A    6.01
 480 ALA   ( 526-)  A    5.89
  40 GLY   (  86-)  A    5.54
 356 GLY   ( 402-)  A    5.47
 375 VAL   ( 421-)  A    5.44
 142 THR   ( 188-)  A    5.13
 248 HIS   ( 294-)  A    5.08
 358 ILE   ( 404-)  A    4.92
 247 GLY   ( 293-)  A    4.90
 588 LYS   ( 634-)  A    4.83
 245 ASP   ( 291-)  A    4.78
 374 GLN   ( 420-)  A    4.72
 505 PRO   ( 551-)  A    4.67
 230 ARG   ( 276-)  A    4.58
 527 GLN   ( 573-)  A    4.53
 234 ARG   ( 280-)  A    4.38
 385 SER   ( 431-)  A    4.25
  84 SER   ( 130-)  A    4.16
 481 SER   ( 527-)  A    4.11
  17 GLY   (  63-)  A    4.10
 498 ARG   ( 544-)  A    4.05

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 : 1.780

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.

 324 TYR   ( 370-)  A      OH   4.24
  83 PHE   ( 129-)  A      CB   4.24
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.857

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.

 341 PRO   ( 387-)  A    -2.9
  27 THR   (  73-)  A    -2.7
 449 THR   ( 495-)  A    -2.7
  23 ILE   (  69-)  A    -2.6
  16 GLU   (  62-)  A    -2.6
 328 THR   ( 374-)  A    -2.5
 156 ARG   ( 202-)  A    -2.5
 387 ILE   ( 433-)  A    -2.5
 394 LEU   ( 440-)  A    -2.4
  45 ILE   (  91-)  A    -2.4
 574 ARG   ( 620-)  A    -2.4
 559 THR   ( 605-)  A    -2.4
 450 THR   ( 496-)  A    -2.4
 315 LYS   ( 361-)  A    -2.4
 495 GLU   ( 541-)  A    -2.4
 103 TYR   ( 149-)  A    -2.3
 262 PRO   ( 308-)  A    -2.3
 442 THR   ( 488-)  A    -2.3
 473 THR   ( 519-)  A    -2.3
 468 VAL   ( 514-)  A    -2.3
 565 ARG   ( 611-)  A    -2.2
 298 GLN   ( 344-)  A    -2.2
 161 GLY   ( 207-)  A    -2.2
 323 SER   ( 369-)  A    -2.2
  26 LEU   (  72-)  A    -2.1
 585 THR   ( 631-)  A    -2.1
 532 GLU   ( 578-)  A    -2.1
 571 ARG   ( 617-)  A    -2.1
 246 GLY   ( 292-)  A    -2.1
 523 TYR   ( 569-)  A    -2.1
 337 LEU   ( 383-)  A    -2.1
 338 LEU   ( 384-)  A    -2.1
 255 ILE   ( 301-)  A    -2.1
 344 GLY   ( 390-)  A    -2.0
 218 VAL   ( 264-)  A    -2.0
 345 ILE   ( 391-)  A    -2.0
 213 ASP   ( 259-)  A    -2.0
  40 GLY   (  86-)  A    -2.0
 322 MET   ( 368-)  A    -2.0
 384 GLN   ( 430-)  A    -2.0
 248 HIS   ( 294-)  A    -2.0
 557 PHE   ( 603-)  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.

  16 GLU   (  62-)  A  Poor phi/psi
  46 ASP   (  92-)  A  Poor phi/psi
  47 ALA   (  93-)  A  PRO omega poor
  50 PRO   (  96-)  A  Poor phi/psi
  78 ALA   ( 124-)  A  PRO omega poor
  85 ASP   ( 131-)  A  Poor phi/psi
 213 ASP   ( 259-)  A  Poor phi/psi
 247 GLY   ( 293-)  A  Poor phi/psi
 248 HIS   ( 294-)  A  Poor phi/psi
 263 THR   ( 309-)  A  Poor phi/psi
 298 GLN   ( 344-)  A  Poor phi/psi
 307 ASP   ( 353-)  A  Poor phi/psi
 323 SER   ( 369-)  A  Poor phi/psi
 358 ILE   ( 404-)  A  Poor phi/psi
 375 VAL   ( 421-)  A  Poor phi/psi
 384 GLN   ( 430-)  A  Poor phi/psi
 385 SER   ( 431-)  A  Poor phi/psi
 481 SER   ( 527-)  A  Poor phi/psi
 498 ARG   ( 544-)  A  Poor phi/psi
 499 ALA   ( 545-)  A  Poor phi/psi
 535 ALA   ( 581-)  A  Poor phi/psi
 550 GLY   ( 596-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -3.917

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.917

Warning: Unusual backbone conformations

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

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

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

   4 LEU   (  50-)  A      0
   5 TYR   (  51-)  A      0
   7 GLU   (  53-)  A      0
  13 ASN   (  59-)  A      0
  15 ARG   (  61-)  A      0
  16 GLU   (  62-)  A      0
  18 PHE   (  64-)  A      0
  19 PRO   (  65-)  A      0
  20 ASN   (  66-)  A      0
  21 TYR   (  67-)  A      0
  22 ARG   (  68-)  A      0
  23 ILE   (  69-)  A      0
  24 PRO   (  70-)  A      0
  43 THR   (  89-)  A      0
  46 ASP   (  92-)  A      0
  47 ALA   (  93-)  A      0
  48 PRO   (  94-)  A      0
  50 PRO   (  96-)  A      0
  60 ASP   ( 106-)  A      0
  63 ARG   ( 109-)  A      0
  64 THR   ( 110-)  A      0
  71 VAL   ( 117-)  A      0
  77 THR   ( 123-)  A      0
  78 ALA   ( 124-)  A      0
  80 ILE   ( 126-)  A      0
And so on for a total of 280 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 : 1.914

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!

 344 GLY   ( 390-)  A   1.69   15

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...

 384 GLN   ( 430-)  A   1.72

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]

   3 PRO   (  49-)  A    0.46 HIGH
  30 PRO   (  76-)  A    0.45 HIGH
  48 PRO   (  94-)  A    0.47 HIGH
  50 PRO   (  96-)  A    0.46 HIGH
 121 PRO   ( 167-)  A    0.45 HIGH
 151 PRO   ( 197-)  A    0.46 HIGH
 410 PRO   ( 456-)  A    0.45 HIGH
 502 PRO   ( 548-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 341 PRO   ( 387-)  A    41.8 envelop C-delta (36 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.

 247 GLY   ( 293-)  A      N   <->  248 HIS   ( 294-)  A      N      0.32    2.28  INTRA B3
 525 ARG   ( 571-)  A      NH1 <->  557 PHE   ( 603-)  A      CE2    0.29    2.81  INTRA
 385 SER   ( 431-)  A      O   <->  387 ILE   ( 433-)  A      N      0.25    2.45  INTRA BF
 504 TYR   ( 550-)  A      O   <->  506 HIS   ( 552-)  A      N      0.24    2.46  INTRA
  56 ARG   ( 102-)  A      NH1 <->   66 GLY   ( 112-)  A      O      0.22    2.48  INTRA BL
 231 ASP   ( 277-)  A      OD1 <->  239 LYS   ( 285-)  A      NZ     0.21    2.49  INTRA
 220 LEU   ( 266-)  A      CD1 <->  224 ARG   ( 270-)  A      NH1    0.20    2.90  INTRA
 585 THR   ( 631-)  A      CG2 <->  587 HIS   ( 633-)  A      ND1    0.20    2.90  INTRA
 481 SER   ( 527-)  A      N   <->  482 ASN   ( 528-)  A      N      0.19    2.41  INTRA B3
 264 ASN   ( 310-)  A      ND2 <->  324 TYR   ( 370-)  A      CE1    0.18    2.92  INTRA BL
 523 TYR   ( 569-)  A      CE2 <->  557 PHE   ( 603-)  A      CZ     0.16    3.04  INTRA
 372 GLY   ( 418-)  A      N   <->  425 VAL   ( 471-)  A      O      0.14    2.56  INTRA
  99 ASN   ( 145-)  A      ND2 <->  101 HIS   ( 147-)  A      CD2    0.13    2.97  INTRA BL
  41 ARG   (  87-)  A      NH1 <->   46 ASP   (  92-)  A      OD1    0.11    2.59  INTRA
 195 SER   ( 241-)  A      OG  <->  199 GLY   ( 245-)  A      N      0.11    2.59  INTRA BL
 171 HIS   ( 217-)  A      CE1 <->  246 GLY   ( 292-)  A      CA     0.11    3.09  INTRA
 501 ALA   ( 547-)  A      CB  <->  502 PRO   ( 548-)  A      CD     0.11    2.99  INTRA
 176 ILE   ( 222-)  A      CG2 <->  178 GLN   ( 224-)  A      NE2    0.10    3.00  INTRA BL
   4 LEU   (  50-)  A      N   <->  351 ASN   ( 397-)  A      ND2    0.10    2.75  INTRA BL
  55 GLN   ( 101-)  A      NE2 <->   88 TYR   ( 134-)  A      OH     0.10    2.60  INTRA BL
 397 ASP   ( 443-)  A      N   <->  437 GLY   ( 483-)  A      O      0.10    2.60  INTRA
 442 THR   ( 488-)  A      CG2 <->  443 SER   ( 489-)  A      N      0.10    2.90  INTRA
 229 SER   ( 275-)  A      N   <->  239 LYS   ( 285-)  A      O      0.10    2.60  INTRA BL
 374 GLN   ( 420-)  A      C   <->  423 ILE   ( 469-)  A      O      0.10    2.70  INTRA
 228 ASN   ( 274-)  A      ND2 <->  238 ARG   ( 284-)  A      NE     0.09    2.76  INTRA BL
And so on for a total of 70 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: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 106 ARG   ( 152-)  A      -7.76
 498 ARG   ( 544-)  A      -7.48
 234 ARG   ( 280-)  A      -6.38
  15 ARG   (  61-)  A      -6.36
 167 ARG   ( 213-)  A      -6.34
 435 ARG   ( 481-)  A      -6.17
 600 GLN   ( 646-)  A      -6.14
 475 ARG   ( 521-)  A      -6.07
 113 ARG   ( 159-)  A      -5.95
  63 ARG   ( 109-)  A      -5.85
 561 LEU   ( 607-)  A      -5.84
 171 HIS   ( 217-)  A      -5.84
 412 MET   ( 458-)  A      -5.80
 462 ARG   ( 508-)  A      -5.76
 200 ARG   ( 246-)  A      -5.68
 441 ARG   ( 487-)  A      -5.66
 543 LEU   ( 589-)  A      -5.62
 257 ARG   ( 303-)  A      -5.22
 384 GLN   ( 430-)  A      -5.15
 391 LYS   ( 437-)  A      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

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.

  55 GLN   ( 101-)  A
  99 ASN   ( 145-)  A
 101 HIS   ( 147-)  A
 125 HIS   ( 171-)  A
 177 GLN   ( 223-)  A
 178 GLN   ( 224-)  A
 198 HIS   ( 244-)  A
 228 ASN   ( 274-)  A
 265 ASN   ( 311-)  A
 309 GLN   ( 355-)  A
 318 GLN   ( 364-)  A
 351 ASN   ( 397-)  A
 373 GLN   ( 419-)  A
 564 GLN   ( 610-)  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.

  26 LEU   (  72-)  A      N
  43 THR   (  89-)  A      OG1
  45 ILE   (  91-)  A      N
  56 ARG   ( 102-)  A      NE
  68 GLN   ( 114-)  A      N
  72 SER   ( 118-)  A      OG
  94 THR   ( 140-)  A      OG1
  99 ASN   ( 145-)  A      ND2
 105 GLN   ( 151-)  A      N
 107 GLN   ( 153-)  A      N
 127 ASN   ( 173-)  A      ND2
 130 THR   ( 176-)  A      OG1
 150 ASP   ( 196-)  A      N
 153 TRP   ( 199-)  A      NE1
 167 ARG   ( 213-)  A      N
 174 ARG   ( 220-)  A      NH1
 184 ALA   ( 230-)  A      N
 202 TRP   ( 248-)  A      NE1
 215 ASN   ( 261-)  A      N
 238 ARG   ( 284-)  A      NH1
 248 HIS   ( 294-)  A      N
 264 ASN   ( 310-)  A      ND2
 265 ASN   ( 311-)  A      N
 272 PHE   ( 318-)  A      N
 290 ALA   ( 336-)  A      N
And so on for a total of 54 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.

  51 ASN   (  97-)  A      OD1
 101 HIS   ( 147-)  A      NE2
 105 GLN   ( 151-)  A      OE1
 248 HIS   ( 294-)  A      NE2
 264 ASN   ( 310-)  A      OD1
 493 HIS   ( 539-)  A      NE2
 533 GLN   ( 579-)  A      OE1
 584 GLN   ( 630-)  A      OE1

Warning: No crystallisation information

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

Warning: Possible wrong residue type

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

 197 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 206 GLU   ( 252-)  A   H-bonding suggests Gln; but Alt-Rotamer
 469 ASP   ( 515-)  A   H-bonding suggests Asn; but Alt-Rotamer
 594 GLU   ( 640-)  A   H-bonding suggests Gln; 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 :  -0.651
  2nd generation packing quality :  -1.006
  Ramachandran plot appearance   :  -1.857
  chi-1/chi-2 rotamer normality  :  -3.917 (poor)
  Backbone conformation          :   0.119

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.615 (tight)
  Bond angles                    :   0.931
  Omega angle restraints         :   0.348 (tight)
  Side chain planarity           :   0.704
  Improper dihedral distribution :   1.362
  B-factor distribution          :   1.424
  Inside/Outside distribution    :   0.978

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.615 (tight)
  Bond angles                    :   0.931
  Omega angle restraints         :   0.348 (tight)
  Side chain planarity           :   0.704
  Improper dihedral distribution :   1.362
  B-factor distribution          :   1.424
  Inside/Outside distribution    :   0.978
==============

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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
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Ion Checks
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      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.