WHAT IF Check report

This file was created 2012-03-13 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 pdb2xfq.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 131.510  B   = 223.380  C    =  86.550
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  86.550  B   = 129.609  C    = 129.609
    Alpha= 119.027  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 129.609  B   = 129.609  C    =  86.550
    Alpha=  90.000  Beta=  90.000  Gamma= 119.027

Transformation to conventional cell

 | -0.500000  0.500000  0.000000|
 | -0.500000 -0.500000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: HEXAGONAL

Space group name: C 2 2 2

Bravais type of conventional cell is: P

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 : 0.489
CA-only RMS fit for the two chains : 0.283

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: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 994 FAD   ( 600-)  A  -
 995 RAS   ( 601-)  A  -         OK
 996 XCG   ( 602-)  A  -         OK
 997 XCG   ( 602-)  B  -         OK
 998 RAS   ( 601-)  B  -         OK
 999 RAS   ( 600-)  B  -         OK
1000 C15   (1503-)  A  -         OK

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

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

  58 TYR   (  60-)  A
 110 TYR   ( 112-)  A
 257 TYR   ( 259-)  A
 299 TYR   ( 301-)  A
 309 TYR   ( 311-)  A
 366 TYR   ( 368-)  A
 391 TYR   ( 393-)  A
 408 TYR   ( 410-)  A
 550 TYR   (  53-)  B
 557 TYR   (  60-)  B
 577 TYR   (  80-)  B
 594 TYR   (  97-)  B
 756 TYR   ( 259-)  B
 798 TYR   ( 301-)  B
 808 TYR   ( 311-)  B
 865 TYR   ( 368-)  B
 890 TYR   ( 393-)  B
 907 TYR   ( 410-)  B

Warning: Phenylalanine convention problem

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

  97 PHE   (  99-)  A
 101 PHE   ( 103-)  A
 208 PHE   ( 210-)  A
 303 PHE   ( 305-)  A
 341 PHE   ( 343-)  A
 421 PHE   ( 423-)  A
 596 PHE   (  99-)  B
 600 PHE   ( 103-)  B
 707 PHE   ( 210-)  B
 771 PHE   ( 274-)  B
 802 PHE   ( 305-)  B
 840 PHE   ( 343-)  B
 920 PHE   ( 423-)  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.

 469 ASP   ( 471-)  A
 968 ASP   ( 471-)  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.

  72 GLU   (  74-)  A
 139 GLU   ( 141-)  A
 140 GLU   ( 142-)  A
 205 GLU   ( 207-)  A
 254 GLU   ( 256-)  A
 318 GLU   ( 320-)  A
 319 GLU   ( 321-)  A
 383 GLU   ( 385-)  A
 388 GLU   ( 390-)  A
 435 GLU   ( 437-)  A
 447 GLU   ( 449-)  A
 571 GLU   (  74-)  B
 575 GLU   (  78-)  B
 639 GLU   ( 142-)  B
 753 GLU   ( 256-)  B
 817 GLU   ( 320-)  B
 818 GLU   ( 321-)  B
 855 GLU   ( 358-)  B
 876 GLU   ( 379-)  B
 882 GLU   ( 385-)  B
 887 GLU   ( 390-)  B
 934 GLU   ( 437-)  B
 946 GLU   ( 449-)  B
 965 GLU   ( 468-)  B

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.

 405 LEU   ( 407-)  A      CG   CD1   1.65    4.0
 589 VAL   (  92-)  B      CA   CB    1.61    4.0

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

 |  0.991290  0.000138 -0.000355|
 |  0.000138  0.993867 -0.000180|
 | -0.000355 -0.000180  0.994899|
Proposed new scale matrix

 |  0.007671 -0.000001  0.000003|
 |  0.000000  0.004505  0.000000|
 |  0.000004  0.000002  0.011613|
With corresponding cell

    A    = 130.364  B   = 221.994  C    =  86.109
    Alpha=  90.012  Beta=  90.041  Gamma=  89.993

The CRYST1 cell dimensions

    A    = 131.510  B   = 223.380  C    =  86.550
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1510.162
(Under-)estimated Z-score: 28.640

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.

  34 ARG   (  36-)  A      CG   CD   NE  117.72    4.2
 125 ARG   ( 127-)  A      CG   CD   NE  102.37   -4.8
 144 MET   ( 146-)  A      C    CA   CB   99.13   -5.8
 380 HIS   ( 382-)  A      CG   ND1  CE1 109.60    4.0
 410 ARG   ( 412-)  A      CG   CD   NE  118.01    4.4
 413 ARG   ( 415-)  A      CG   CD   NE   99.97   -6.2
 429 HIS   ( 431-)  A      CG   ND1  CE1 109.69    4.1
 443 ARG   ( 445-)  A      CB   CG   CD  105.65   -4.2
 443 ARG   ( 445-)  A      CD   NE   CZ  129.61    4.4
 446 ARG   ( 448-)  A      CB   CG   CD  105.45   -4.3
 544 ARG   (  47-)  B      CB   CG   CD  126.58    6.2
 587 HIS   (  90-)  B      CG   ND1  CE1 109.82    4.2
 643 MET   ( 146-)  B      C    CA   CB  100.82   -4.9
 696 ILE   ( 199-)  B      C    CA   CB  100.77   -4.9
 879 HIS   ( 382-)  B      CG   ND1  CE1 109.63    4.0
 928 HIS   ( 431-)  B      CG   ND1  CE1 109.68    4.1
 942 ARG   ( 445-)  B      CB   CG   CD  105.93   -4.1
 945 ARG   ( 448-)  B      CB   CG   CD  103.23   -5.4
 945 ARG   ( 448-)  B      NE   CZ   NH2 112.28   -4.1

Error: Nomenclature error(s)

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

  72 GLU   (  74-)  A
 139 GLU   ( 141-)  A
 140 GLU   ( 142-)  A
 205 GLU   ( 207-)  A
 254 GLU   ( 256-)  A
 318 GLU   ( 320-)  A
 319 GLU   ( 321-)  A
 383 GLU   ( 385-)  A
 388 GLU   ( 390-)  A
 435 GLU   ( 437-)  A
 447 GLU   ( 449-)  A
 469 ASP   ( 471-)  A
 571 GLU   (  74-)  B
 575 GLU   (  78-)  B
 639 GLU   ( 142-)  B
 753 GLU   ( 256-)  B
 817 GLU   ( 320-)  B
 818 GLU   ( 321-)  B
 855 GLU   ( 358-)  B
 876 GLU   ( 379-)  B
 882 GLU   ( 385-)  B
 887 GLU   ( 390-)  B
 934 GLU   ( 437-)  B
 946 GLU   ( 449-)  B
 965 GLU   ( 468-)  B
 968 ASP   ( 471-)  B

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.

 197 ILE   ( 199-)  A    4.43
 343 LEU   ( 345-)  A    4.07

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.

 397 THR   ( 399-)  A    -3.0
 896 THR   ( 399-)  B    -2.9
  62 THR   (  64-)  A    -2.5
 696 ILE   ( 199-)  B    -2.5
 876 GLU   ( 379-)  B    -2.4
 749 HIS   ( 252-)  B    -2.3
 302 PRO   ( 304-)  A    -2.3
 575 GLU   (  78-)  B    -2.3
 730 ARG   ( 233-)  B    -2.3
  50 LYS   (  52-)  A    -2.3
 561 THR   (  64-)  B    -2.1
 786 VAL   ( 289-)  B    -2.1
 791 VAL   ( 294-)  B    -2.1
 411 VAL   ( 413-)  A    -2.1
 292 VAL   ( 294-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  10 GLY   (  12-)  A  omega poor
  40 ARG   (  42-)  A  omega poor
  49 VAL   (  51-)  A  omega poor
  50 LYS   (  52-)  A  Poor phi/psi
  56 GLY   (  58-)  A  omega poor
  62 THR   (  64-)  A  Poor phi/psi
 126 GLU   ( 128-)  A  omega poor
 197 ILE   ( 199-)  A  omega poor
 199 THR   ( 201-)  A  Poor phi/psi
 201 ASN   ( 203-)  A  Poor phi/psi
 230 GLU   ( 232-)  A  Poor phi/psi
 250 HIS   ( 252-)  A  Poor phi/psi
 273 ASN   ( 275-)  A  PRO omega poor
 308 ASP   ( 310-)  A  Poor phi/psi
 342 ILE   ( 344-)  A  omega poor
 343 LEU   ( 345-)  A  omega poor
 344 ALA   ( 346-)  A  Poor phi/psi
 395 CYS   ( 397-)  A  omega poor
 417 ASP   ( 419-)  A  Poor phi/psi
 422 ALA   ( 424-)  A  Poor phi/psi
 430 TRP   ( 432-)  A  Poor phi/psi
 498 THR   ( 500-)  A  Poor phi/psi
 539 ARG   (  42-)  B  omega poor
 548 VAL   (  51-)  B  omega poor
 549 LYS   (  52-)  B  Poor phi/psi
 561 THR   (  64-)  B  Poor phi/psi
 586 ILE   (  89-)  B  omega poor
 676 GLU   ( 179-)  B  omega poor
 700 ASN   ( 203-)  B  Poor phi/psi
 705 ARG   ( 208-)  B  omega poor
 729 GLU   ( 232-)  B  Poor phi/psi
 749 HIS   ( 252-)  B  Poor phi/psi
 765 LEU   ( 268-)  B  omega poor
 772 ASN   ( 275-)  B  PRO omega poor
 785 ARG   ( 288-)  B  omega poor
 791 VAL   ( 294-)  B  omega poor
 807 ASP   ( 310-)  B  Poor phi/psi
 813 ILE   ( 316-)  B  omega poor
 833 ASN   ( 336-)  B  omega poor
 841 ILE   ( 344-)  B  omega poor
 842 LEU   ( 345-)  B  omega poor
 843 ALA   ( 346-)  B  Poor phi/psi
 894 CYS   ( 397-)  B  omega poor
 902 GLY   ( 405-)  B  omega poor
 916 ASP   ( 419-)  B  Poor phi/psi
 921 ALA   ( 424-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.081

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.

  13 SER   (  15-)  A    0.36
 216 SER   ( 218-)  A    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 CYS   (   5-)  A      0
   4 ASP   (   6-)  A      0
   8 VAL   (  10-)  A      0
  12 ILE   (  14-)  A      0
  24 SER   (  26-)  A      0
  33 ALA   (  35-)  A      0
  34 ARG   (  36-)  A      0
  36 ARG   (  38-)  A      0
  37 VAL   (  39-)  A      0
  40 ARG   (  42-)  A      0
  41 THR   (  43-)  A      0
  45 ARG   (  47-)  A      0
  49 VAL   (  51-)  A      0
  50 LYS   (  52-)  A      0
  51 TYR   (  53-)  A      0
  54 LEU   (  56-)  A      0
  57 SER   (  59-)  A      0
  61 PRO   (  63-)  A      0
  62 THR   (  64-)  A      0
  63 GLN   (  65-)  A      0
  64 ASN   (  66-)  A      0
  73 LEU   (  75-)  A      0
  81 ASN   (  83-)  A      0
  82 GLU   (  84-)  A      0
  83 VAL   (  85-)  A      0
And so on for a total of 340 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!

 555 GLY   (  58-)  B   1.93   10
 136 PRO   ( 138-)  A   1.63   10

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 402 PRO   ( 404-)  A    0.14 LOW
 560 PRO   (  63-)  B    0.11 LOW
 776 PRO   ( 279-)  B    0.17 LOW
 830 PRO   ( 333-)  B    0.10 LOW

Warning: Unusual PRO puckering phases

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

  61 PRO   (  63-)  A  -116.6 envelop C-gamma (-108 degrees)
 132 PRO   ( 134-)  A  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 264 PRO   ( 266-)  A   101.7 envelop C-beta (108 degrees)
 277 PRO   ( 279-)  A    51.0 half-chair C-delta/C-gamma (54 degrees)
 635 PRO   ( 138-)  B   123.6 half-chair C-beta/C-alpha (126 degrees)
 762 PRO   ( 265-)  B    99.9 envelop C-beta (108 degrees)
 763 PRO   ( 266-)  B   120.3 half-chair C-beta/C-alpha (126 degrees)
 901 PRO   ( 404-)  B  -119.7 half-chair C-delta/C-gamma (-126 degrees)
 964 PRO   ( 467-)  B  -122.1 half-chair C-delta/C-gamma (-126 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.

 539 ARG   (  42-)  B      CB  <->  999 RAS   ( 600-)  B      C1     1.16    1.14  INTRA B2
 539 ARG   (  42-)  B      CG  <->  999 RAS   ( 600-)  B      C9     1.08    2.12  INTRA
 539 ARG   (  42-)  B      CB  <->  999 RAS   ( 600-)  B      C9     1.04    1.76  INTRA B3
 539 ARG   (  42-)  B      CG  <->  999 RAS   ( 600-)  B      C8     0.88    2.32  INTRA
 539 ARG   (  42-)  B      CD  <->  999 RAS   ( 600-)  B      C3     0.70    2.50  INTRA
 539 ARG   (  42-)  B      CB  <->  999 RAS   ( 600-)  B      C8     0.64    2.16  INTRA B3
 539 ARG   (  42-)  B      NH1 <->  999 RAS   ( 600-)  B      C5     0.61    2.09  INTRA B3
 539 ARG   (  42-)  B      N   <->  999 RAS   ( 600-)  B      C11    0.58    2.12  INTRA B3
 539 ARG   (  42-)  B      NH2 <->  999 RAS   ( 600-)  B      C6     0.57    1.63  INTRA B2
 539 ARG   (  42-)  B      N   <->  999 RAS   ( 600-)  B      C1     0.54    1.66  INTRA B2
 538 GLY   (  41-)  B      C   <->  999 RAS   ( 600-)  B      C11    0.49    2.31  INTRA B3
 539 ARG   (  42-)  B      C   <->  999 RAS   ( 600-)  B      C1     0.45    1.85  INTRA B2
 883 LYS   ( 386-)  B      NZ  <-> 1002 HOH   (2196 )  B      O      0.42    2.28  INTRA
 384 LYS   ( 386-)  A      NZ  <-> 1001 HOH   (2163 )  A      O      0.41    2.29  INTRA
 385 ASN   ( 387-)  A      ND2 <->  777 MET   ( 280-)  B      CE     0.40    2.70  INTRA
 539 ARG   (  42-)  B      CD  <->  999 RAS   ( 600-)  B      C8     0.39    2.41  INTRA B3
 538 GLY   (  41-)  B      CA  <->  999 RAS   ( 600-)  B      C11    0.37    1.93  INTRA B2
 539 ARG   (  42-)  B      CG  <->  999 RAS   ( 600-)  B      C1     0.32    2.48  INTRA B3
 539 ARG   (  42-)  B      CB  <->  999 RAS   ( 600-)  B      C3     0.31    1.99  INTRA B2
 539 ARG   (  42-)  B      CD  <->  999 RAS   ( 600-)  B      C4     0.28    2.92  INTRA
 961 GLN   ( 464-)  B      NE2 <-> 1002 HOH   (2236 )  B      O      0.27    2.43  INTRA
 539 ARG   (  42-)  B      NH2 <->  999 RAS   ( 600-)  B      C7     0.27    2.43  INTRA B3
 539 ARG   (  42-)  B      NE  <->  999 RAS   ( 600-)  B      C6     0.26    1.94  INTRA B2
 539 ARG   (  42-)  B      C   <->  999 RAS   ( 600-)  B      C2     0.26    2.54  INTRA B3
 539 ARG   (  42-)  B      CZ  <->  999 RAS   ( 600-)  B      C5     0.26    2.04  INTRA B2
And so on for a total of 102 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

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.

  98 ARG   ( 100-)  A      -7.09
 597 ARG   ( 100-)  B      -6.75
 600 PHE   ( 103-)  B      -6.38
 483 HIS   ( 485-)  A      -6.28
 101 PHE   ( 103-)  A      -6.27
 982 HIS   ( 485-)  B      -6.22
 799 LYS   ( 302-)  B      -6.10
 535 ARG   (  38-)  B      -6.10
  36 ARG   (  38-)  A      -6.08
 300 LYS   ( 302-)  A      -6.01
 396 TYR   ( 398-)  A      -6.00
 895 TYR   ( 398-)  B      -5.99
 319 GLU   ( 321-)  A      -5.62
 105 TRP   ( 107-)  A      -5.58
 851 ARG   ( 354-)  B      -5.53
 352 ARG   ( 354-)  A      -5.53
 604 TRP   ( 107-)  B      -5.50
 953 LYS   ( 456-)  B      -5.43
 906 GLN   ( 409-)  B      -5.43
 407 GLN   ( 409-)  A      -5.42
 818 GLU   ( 321-)  B      -5.41
 890 TYR   ( 393-)  B      -5.36
 912 ARG   ( 415-)  B      -5.35
 391 TYR   ( 393-)  A      -5.34
  45 ARG   (  47-)  A      -5.21
   2 LYS   (   4-)  A      -5.15
 454 LYS   ( 456-)  A      -5.15
 413 ARG   ( 415-)  A      -5.13
 501 LYS   (   4-)  B      -5.06
 785 ARG   ( 288-)  B      -5.04
 676 GLU   ( 179-)  B      -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: 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.

 197 ILE   ( 199-)  A   -2.62
 696 ILE   ( 199-)  B   -2.57

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

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.

1001 HOH   (2052 )  A      O     13.60  151.40   23.05

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.

1001 HOH   (2020 )  A      O
1001 HOH   (2204 )  A      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.

 114 ASN   ( 116-)  A
 115 ASN   ( 117-)  A
 161 GLN   ( 163-)  A
 204 GLN   ( 206-)  A
 249 ASN   ( 251-)  A
 587 HIS   (  90-)  B
 613 ASN   ( 116-)  B
 614 ASN   ( 117-)  B
 748 ASN   ( 251-)  B
 913 GLN   ( 416-)  B

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.

  13 SER   (  15-)  A      N
  33 ALA   (  35-)  A      N
  34 ARG   (  36-)  A      NH1
  36 ARG   (  38-)  A      N
  40 ARG   (  42-)  A      N
  40 ARG   (  42-)  A      NE
  57 SER   (  59-)  A      N
  58 TYR   (  60-)  A      N
  63 GLN   (  65-)  A      NE2
 133 TRP   ( 135-)  A      N
 173 ALA   ( 175-)  A      N
 178 VAL   ( 180-)  A      N
 233 VAL   ( 235-)  A      N
 262 ILE   ( 264-)  A      N
 292 VAL   ( 294-)  A      N
 294 LYS   ( 296-)  A      NZ
 304 TRP   ( 306-)  A      N
 322 VAL   ( 324-)  A      N
 324 TYR   ( 326-)  A      N
 381 TYR   ( 383-)  A      N
 394 GLY   ( 396-)  A      N
 400 PHE   ( 402-)  A      N
 410 ARG   ( 412-)  A      N
 424 THR   ( 426-)  A      N
 428 THR   ( 430-)  A      N
 434 MET   ( 436-)  A      N
 443 ARG   ( 445-)  A      NE
 535 ARG   (  38-)  B      N
 562 GLN   (  65-)  B      NE2
 563 ASN   (  66-)  B      N
 632 TRP   ( 135-)  B      N
 672 ALA   ( 175-)  B      N
 717 ARG   ( 220-)  B      NH1
 761 ILE   ( 264-)  B      N
 791 VAL   ( 294-)  B      N
 803 TRP   ( 306-)  B      N
 818 GLU   ( 321-)  B      N
 821 VAL   ( 324-)  B      N
 823 TYR   ( 326-)  B      N
 823 TYR   ( 326-)  B      OH
 835 ALA   ( 338-)  B      N
 855 GLU   ( 358-)  B      N
 893 GLY   ( 396-)  B      N
 899 PHE   ( 402-)  B      N
 927 THR   ( 430-)  B      N
 954 ILE   ( 457-)  B      N

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: Unusual water packing

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

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

1001 HOH   (2075 )  A      O  1.09  K  4 H2O-B
1001 HOH   (2083 )  A      O  0.92  K  4 Ion-B
1002 HOH   (2080 )  B      O  1.04  K  4
1002 HOH   (2248 )  B      O  1.03  K  4 Ion-B

Warning: Possible wrong residue type

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

 301 GLU   ( 303-)  A   H-bonding suggests Gln
 435 GLU   ( 437-)  A   H-bonding suggests Gln
 720 ASP   ( 223-)  B   H-bonding suggests Asn; but Alt-Rotamer
 800 GLU   ( 303-)  B   H-bonding suggests Gln
 876 GLU   ( 379-)  B   H-bonding suggests Gln
 934 GLU   ( 437-)  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 :  -0.510
  2nd generation packing quality :  -1.610
  Ramachandran plot appearance   :  -0.680
  chi-1/chi-2 rotamer normality  :  -1.081
  Backbone conformation          :  -0.404

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.925
  Bond angles                    :   0.854
  Omega angle restraints         :   1.093
  Side chain planarity           :   0.843
  Improper dihedral distribution :   0.941
  B-factor distribution          :   0.667
  Inside/Outside distribution    :   1.053

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.925
  Bond angles                    :   0.854
  Omega angle restraints         :   1.093
  Side chain planarity           :   0.843
  Improper dihedral distribution :   0.941
  B-factor distribution          :   0.667
  Inside/Outside distribution    :   1.053
==============

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.