WHAT IF Check report

This file was created 2013-12-10 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 pdb4km4.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.566
CA-only RMS fit for the two chains : 0.214

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

 896 PO4   ( 501-)  A  -
 900 PO4   ( 501-)  B  -

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

Note: Ramachandran plot

Chain identifier: B

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:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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

  84 TYR   (  87-)  A
 437 TYR   ( 440-)  A
 506 TYR   (  64-)  B
 529 TYR   (  87-)  B

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.

  52 ASP   (  55-)  A
 324 ASP   ( 327-)  A
 497 ASP   (  55-)  B
 736 ASP   ( 294-)  B
 769 ASP   ( 327-)  B

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.

 173 GLU   ( 176-)  A
 305 GLU   ( 308-)  A
 404 GLU   ( 407-)  A
 450 GLU   (   8-)  B
 618 GLU   ( 176-)  B
 669 GLU   ( 227-)  B
 783 GLU   ( 341-)  B
 849 GLU   ( 407-)  B

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.995525 -0.000824 -0.000412|
 | -0.000824  0.995561 -0.000403|
 | -0.000412 -0.000403  0.993729|
Proposed new scale matrix

 |  0.006245  0.003608  0.000004|
 |  0.000006  0.007207  0.000003|
 |  0.000003  0.000003  0.007211|
With corresponding cell

    A    = 160.207  B   = 160.326  C    = 138.673
    Alpha=  90.016  Beta=  90.047  Gamma= 120.066

The CRYST1 cell dimensions

    A    = 160.935  B   = 160.935  C    = 139.549
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 700.413
(Under-)estimated Z-score: 19.505

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.

  36 ASP   (  39-)  A     -C    N    CA  131.36    5.4
  36 ASP   (  39-)  A      CA   CB   CG  117.02    4.4
  54 GLU   (  57-)  A     -C    N    CA  129.59    4.4
  54 GLU   (  57-)  A      CB   CG   CD  120.40    4.6
  56 THR   (  59-)  A      N    CA   CB  117.57    4.2
  81 TYR   (  84-)  A      CA   CB   CG  125.99    6.5
  83 HIS   (  86-)  A      CG   ND1  CE1 110.03    4.4
  83 HIS   (  86-)  A      ND1  CE1  NE2 106.37   -4.1
 115 GLY   ( 118-)  A     -C    N    CA  127.43    4.0
 121 ILE   ( 124-)  A      N    CA   CB  118.56    4.7
 122 HIS   ( 125-)  A      CG   ND1  CE1 110.09    4.5
 123 GLU   ( 126-)  A     -C    N    CA  128.96    4.0
 150 ASP   ( 153-)  A      CA   CB   CG  119.71    7.1
 159 HIS   ( 162-)  A      CG   ND1  CE1 110.39    4.8
 217 TRP   ( 220-)  A      CE3  CD2  CG  129.84   -4.1
 218 GLN   ( 221-)  A      CB   CG   CD  121.06    5.0
 223 ARG   ( 226-)  A      CD   NE   CZ  129.38    4.3
 236 ASP   ( 239-)  A      CA   CB   CG  118.49    5.9
 264 ARG   ( 267-)  A      N    CA   CB  118.00    4.4
 265 TRP   ( 268-)  A      CE3  CD2  CG  129.24   -4.7
 273 HIS   ( 276-)  A      CG   ND1  CE1 110.44    4.8
 273 HIS   ( 276-)  A      ND1  CE1  NE2 106.35   -4.1
 277 ASP   ( 280-)  A      CA   CB   CG  117.85    5.2
 324 ASP   ( 327-)  A      CA   CB   CG  118.26    5.7
 327 ASP   ( 330-)  A      CA   CB   CG  119.13    6.5
And so on for a total of 64 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  52 ASP   (  55-)  A
 173 GLU   ( 176-)  A
 305 GLU   ( 308-)  A
 324 ASP   ( 327-)  A
 404 GLU   ( 407-)  A
 450 GLU   (   8-)  B
 497 ASP   (  55-)  B
 618 GLU   ( 176-)  B
 669 GLU   ( 227-)  B
 736 ASP   ( 294-)  B
 769 ASP   ( 327-)  B
 783 GLU   ( 341-)  B
 849 GLU   ( 407-)  B

Error: Side chain planarity problems

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

 367 HIS   ( 370-)  A    6.32
 690 GLU   ( 248-)  B    5.30
 812 HIS   ( 370-)  B    5.16
 245 GLU   ( 248-)  A    4.84
 497 ASP   (  55-)  B    4.33
  36 ASP   (  39-)  A    4.17
 681 ASP   ( 239-)  B    4.10

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.

  61 TYR   (  64-)  A      OH   4.98
 506 TYR   (  64-)  B      OH   4.70
 159 HIS   ( 162-)  A      CB   4.06
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.717

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.

 809 THR   ( 367-)  B    -3.2
 364 THR   ( 367-)  A    -3.0
 557 THR   ( 115-)  B    -2.9
 112 THR   ( 115-)  A    -2.9
 168 PRO   ( 171-)  A    -2.7
 859 LEU   ( 417-)  B    -2.5
 414 LEU   ( 417-)  A    -2.5
 369 HIS   ( 372-)  A    -2.4
 692 ASN   ( 250-)  B    -2.3
 247 ASN   ( 250-)  A    -2.3
 849 GLU   ( 407-)  B    -2.3
   2 PRO   (   5-)  A    -2.2
 814 HIS   ( 372-)  B    -2.2
 871 VAL   ( 429-)  B    -2.0
 451 ASN   (   9-)  B    -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.

   2 PRO   (   5-)  A  omega poor
  38 PRO   (  41-)  A  omega poor
  93 PRO   (  96-)  A  omega poor
  94 ASP   (  97-)  A  omega poor
  97 THR   ( 100-)  A  omega poor
 123 GLU   ( 126-)  A  Poor phi/psi
 146 ALA   ( 149-)  A  omega poor
 174 LYS   ( 177-)  A  Poor phi/psi
 214 ALA   ( 217-)  A  Poor phi/psi
 231 TYR   ( 234-)  A  omega poor
 245 GLU   ( 248-)  A  omega poor
 255 LEU   ( 258-)  A  omega poor
 273 HIS   ( 276-)  A  Poor phi/psi
 281 VAL   ( 284-)  A  omega poor
 320 GLY   ( 323-)  A  omega poor
 330 ALA   ( 333-)  A  Poor phi/psi
 369 HIS   ( 372-)  A  Poor phi/psi, omega poor
 404 GLU   ( 407-)  A  omega poor
 407 GLN   ( 410-)  A  omega poor
 412 SER   ( 415-)  A  omega poor
 415 ARG   ( 418-)  A  omega poor
 422 HIS   ( 425-)  A  Poor phi/psi
 491 ILE   (  49-)  B  omega poor
 506 TYR   (  64-)  B  omega poor
 523 THR   (  81-)  B  omega poor
 530 ALA   (  88-)  B  Poor phi/psi
 531 LEU   (  89-)  B  omega poor
 538 PRO   (  96-)  B  omega poor
 539 ASP   (  97-)  B  omega poor
 542 THR   ( 100-)  B  omega poor
 568 GLU   ( 126-)  B  Poor phi/psi
 591 ALA   ( 149-)  B  omega poor
 610 CYS   ( 168-)  B  Poor phi/psi
 641 ARG   ( 199-)  B  Poor phi/psi
 676 TYR   ( 234-)  B  omega poor
 711 LEU   ( 269-)  B  omega poor
 726 VAL   ( 284-)  B  omega poor
 764 GLU   ( 322-)  B  omega poor
 772 ASP   ( 330-)  B  omega poor
 775 ALA   ( 333-)  B  Poor phi/psi
 814 HIS   ( 372-)  B  Poor phi/psi
 844 TYR   ( 402-)  B  omega poor
 852 GLN   ( 410-)  B  omega poor
 857 SER   ( 415-)  B  omega poor
 860 ARG   ( 418-)  B  omega poor
 867 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.198

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.

 617 SER   ( 175-)  B    0.34
 684 SER   ( 242-)  B    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!

   4 LEU   (   7-)  A      0
   5 GLU   (   8-)  A      0
   6 ASN   (   9-)  A      0
   7 ARG   (  10-)  A      0
  10 GLN   (  13-)  A      0
  12 ASP   (  15-)  A      0
  15 ALA   (  18-)  A      0
  16 PRO   (  19-)  A      0
  20 ARG   (  23-)  A      0
  36 ASP   (  39-)  A      0
  40 LYS   (  43-)  A      0
  41 ASN   (  44-)  A      0
  48 ASP   (  51-)  A      0
  50 MET   (  53-)  A      0
  74 ALA   (  77-)  A      0
  83 HIS   (  86-)  A      0
  95 TYR   (  98-)  A      0
 111 LYS   ( 114-)  A      0
 113 TYR   ( 116-)  A      0
 114 ASN   ( 117-)  A      0
 117 LEU   ( 120-)  A      0
 121 ILE   ( 124-)  A      0
 123 GLU   ( 126-)  A      0
 125 ASP   ( 128-)  A      0
 146 ALA   ( 149-)  A      0
And so on for a total of 335 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 376 PRO   ( 379-)  A   1.68   15
 821 PRO   ( 379-)  B   1.50   14

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]

 538 PRO   (  96-)  B    0.45 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].

 168 PRO   ( 171-)  A   101.6 envelop C-beta (108 degrees)
 262 PRO   ( 265-)  A  -112.7 envelop C-gamma (-108 degrees)
 376 PRO   ( 379-)  A   101.1 envelop C-beta (108 degrees)
 713 PRO   ( 271-)  B    51.9 half-chair C-delta/C-gamma (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.

  88 LYS   (  91-)  A      NZ  <->  123 GLU   ( 126-)  A      OE2    0.13    2.57  INTRA
 618 GLU   ( 176-)  B      OE2 <->  619 LYS   ( 177-)  B      NZ     0.13    2.57  INTRA BF
 570 ASP   ( 128-)  B      OD2 <->  630 LYS   ( 188-)  B      NZ     0.10    2.60  INTRA
 269 LYS   ( 272-)  A      NZ  <->  405 ASP   ( 408-)  A      CG     0.10    3.00  INTRA
 305 GLU   ( 308-)  A      O   <->  309 LYS   ( 312-)  A      NZ     0.09    2.61  INTRA
 482 LYS   (  40-)  B      NZ  <->  803 ASN   ( 361-)  B      OD1    0.09    2.61  INTRA
 367 HIS   ( 370-)  A      C   <->  414 LEU   ( 417-)  A      CD2    0.08    3.12  INTRA BL
 269 LYS   ( 272-)  A      NZ  <->  405 ASP   ( 408-)  A      OD1    0.08    2.62  INTRA
 690 GLU   ( 248-)  B      OE2 <->  695 LYS   ( 253-)  B      NZ     0.07    2.63  INTRA BF
 450 GLU   (   8-)  B      CD  <->  799 LYS   ( 357-)  B      NZ     0.07    3.03  INTRA BF
 485 LYS   (  43-)  B      NZ  <->  756 GLU   ( 314-)  B      O      0.07    2.63  INTRA
 366 ASP   ( 369-)  A      CG  <->  367 HIS   ( 370-)  A      CD2    0.06    3.14  INTRA BL
 581 ALA   ( 139-)  B      O   <->  757 LYS   ( 315-)  B      NZ     0.06    2.64  INTRA
 125 ASP   ( 128-)  A      OD2 <->  185 LYS   ( 188-)  A      NZ     0.06    2.64  INTRA
 690 GLU   ( 248-)  B      CD  <->  695 LYS   ( 253-)  B      NZ     0.06    3.04  INTRA BF
 450 GLU   (   8-)  B      OE1 <->  799 LYS   ( 357-)  B      NZ     0.05    2.65  INTRA BF
  40 LYS   (  43-)  A      NZ  <->  311 GLU   ( 314-)  A      O      0.05    2.65  INTRA
 533 LYS   (  91-)  B      NZ  <->  568 GLU   ( 126-)  B      OE2    0.04    2.66  INTRA
 450 GLU   (   8-)  B      OE2 <->  799 LYS   ( 357-)  B      NZ     0.04    2.66  INTRA BF
 812 HIS   ( 370-)  B      C   <->  859 LEU   ( 417-)  B      CD2    0.04    3.16  INTRA BL
   1 MET   (   4-)  A      N   <->   32 ASP   (  35-)  A      O      0.04    2.66  INTRA BF
 126 HIS   ( 129-)  A      O   <->  159 HIS   ( 162-)  A      CE1    0.04    2.76  INTRA BL
 173 GLU   ( 176-)  A      OE1 <->  174 LYS   ( 177-)  A      NZ     0.03    2.67  INTRA BF
 811 ASP   ( 369-)  B      CG  <->  812 HIS   ( 370-)  B      CD2    0.03    3.17  INTRA BL
 220 LYS   ( 223-)  A      NZ  <->  224 GLU   ( 227-)  A      OE2    0.02    2.68  INTRA BF
 269 LYS   ( 272-)  A      NZ  <->  405 ASP   ( 408-)  A      OD2    0.02    2.68  INTRA
  37 LYS   (  40-)  A      NZ  <->  357 GLY   ( 360-)  A      O      0.02    2.68  INTRA
 152 THR   ( 155-)  A      CB  <->  319 GLU   ( 322-)  A      CD     0.01    3.19  INTRA BL
 404 GLU   ( 407-)  A      OE2 <->  824 LYS   ( 382-)  B      NZ     0.01    2.69  INTRA BF
 245 GLU   ( 248-)  A      OE2 <->  250 LYS   ( 253-)  A      NZ     0.01    2.69  INTRA BF
 592 GLU   ( 150-)  B      OE2 <->  651 LYS   ( 209-)  B      NZ     0.01    2.69  INTRA

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 272 TYR   ( 275-)  A      -7.00
 717 TYR   ( 275-)  B      -6.61
 249 GLN   ( 252-)  A      -6.03
 694 GLN   ( 252-)  B      -5.95
 534 LYS   (  92-)  B      -5.86
  89 LYS   (  92-)  A      -5.84
 185 LYS   ( 188-)  A      -5.17
 756 GLU   ( 314-)  B      -5.10
 450 GLU   (   8-)  B      -5.06
 311 GLU   ( 314-)  A      -5.02
 356 GLU   ( 359-)  A      -5.00

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: 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: B

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.

 122 HIS   ( 125-)  A   -2.77
 321 ALA   ( 324-)  A   -2.54
 567 HIS   ( 125-)  B   -2.52
 766 ALA   ( 324-)  B   -2.51

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

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 335 GLN   ( 338-)  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.

   3 VAL   (   6-)  A      N
   7 ARG   (  10-)  A      N
  59 ARG   (  62-)  A      NH1
  70 LYS   (  73-)  A      N
  75 LEU   (  78-)  A      N
  78 THR   (  81-)  A      N
  80 GLN   (  83-)  A      NE2
  84 TYR   (  87-)  A      OH
  97 THR   ( 100-)  A      N
  99 GLY   ( 102-)  A      N
 100 ALA   ( 103-)  A      N
 110 VAL   ( 113-)  A      N
 111 LYS   ( 114-)  A      NZ
 119 VAL   ( 122-)  A      N
 142 ASN   ( 145-)  A      ND2
 214 ALA   ( 217-)  A      N
 223 ARG   ( 226-)  A      NH2
 245 GLU   ( 248-)  A      N
 265 TRP   ( 268-)  A      N
 267 GLY   ( 270-)  A      N
 297 ALA   ( 300-)  A      N
 322 SER   ( 325-)  A      N
 323 ILE   ( 326-)  A      N
 333 CYS   ( 336-)  A      N
 335 GLN   ( 338-)  A      NE2
And so on for a total of 60 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.

  83 HIS   (  86-)  A      ND1
 142 ASN   ( 145-)  A      OD1
 385 GLN   ( 388-)  A      OE1
 528 HIS   (  86-)  B      ND1
 772 ASP   ( 330-)  B      OD2
 830 GLN   ( 388-)  B      OE1

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.

  54 GLU   (  57-)  A   H-bonding suggests Gln
 277 ASP   ( 280-)  A   H-bonding suggests Asn
 499 GLU   (  57-)  B   H-bonding suggests Gln
 848 GLU   ( 406-)  B   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 :  -0.382
  2nd generation packing quality :  -0.746
  Ramachandran plot appearance   :  -0.717
  chi-1/chi-2 rotamer normality  :  -2.198
  Backbone conformation          :  -0.091

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.847
  Bond angles                    :   1.183
  Omega angle restraints         :   1.176
  Side chain planarity           :   1.578
  Improper dihedral distribution :   1.318
  B-factor distribution          :   0.778
  Inside/Outside distribution    :   0.934

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.847
  Bond angles                    :   1.183
  Omega angle restraints         :   1.176
  Side chain planarity           :   1.578
  Improper dihedral distribution :   1.318
  B-factor distribution          :   0.778
  Inside/Outside distribution    :   0.934
==============

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.