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 pdb3zge.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.

1834 SO4   (1968-)  A  -
1835 EDO   (1969-)  A  -
1836 SO4   (1968-)  B  -
1837 EDO   (1969-)  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: B-factors outside the range 0.0 - 100.0

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

   8 GLN   (  15-)  A    High
  14 PRO   (  21-)  A    High
  15 GLY   (  22-)  A    High
  16 LYS   (  23-)  A    High
  17 VAL   (  24-)  A    High
  18 SER   (  25-)  A    High
 216 GLU   ( 224-)  A    High
 217 ILE   ( 225-)  A    High
 218 ARG   ( 226-)  A    High
 219 ARG   ( 227-)  A    High
 220 THR   ( 228-)  A    High
 221 PRO   ( 229-)  A    High
 335 ARG   ( 343-)  A    High
 337 HIS   ( 351-)  A    High
 379 ASP   ( 393-)  A    High
 733 ARG   ( 747-)  A    High
 882 PRO   ( 909-)  A    High
 885 HIS   ( 912-)  A    High
 931 GLY   (  22-)  B    High
 932 LYS   (  23-)  B    High
 933 VAL   (  24-)  B    High
 934 SER   (  25-)  B    High
 935 GLU   (  26-)  B    High
1026 ARG   ( 117-)  B    High
1084 GLN   ( 175-)  B    High
1133 PRO   ( 229-)  B    High
1141 ARG   ( 237-)  B    High
1247 HIS   ( 351-)  B    High
1254 ARG   ( 358-)  B    High
1643 ARG   ( 747-)  B    High
1735 GLU   ( 852-)  B    High
1804 LYS   ( 921-)  B    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 5

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

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, 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.

  42 HIS   (  49-)  A      CG   CD2   1.40    4.2
  64 HIS   (  71-)  A      CB   CG    1.58    5.7
  64 HIS   (  71-)  A      CG   CD2   1.41    5.2
 140 HIS   ( 147-)  A      CG   CD2   1.42    6.1
 165 HIS   ( 172-)  A      CG   CD2   1.40    4.2
 178 HIS   ( 185-)  A      CG   CD2   1.40    4.4
 240 TRP   ( 248-)  A      NE1  CE2   1.31   -5.4
 275 TRP   ( 283-)  A      CD2  CE2   1.48    4.2
 337 HIS   ( 351-)  A      CB   CG    1.55    4.1
 337 HIS   ( 351-)  A      CG   CD2   1.42    6.0
 442 HIS   ( 456-)  A      CG   CD2   1.40    4.1
 534 HIS   ( 548-)  A      CG   CD2   1.42    5.8
 537 HIS   ( 551-)  A      CG   CD2   1.41    5.0
 751 THR   ( 778-)  A      CB   CG2   1.37   -4.4
 767 HIS   ( 794-)  A      CG   CD2   1.42    6.0
 844 HIS   ( 871-)  A      CG   CD2   1.42    5.6
 891 HIS   ( 918-)  A      CG   CD2   1.40    4.0
 917 LYS   (   8-)  B      CA   C     1.61    4.2
 980 HIS   (  71-)  B      CG   CD2   1.41    4.9
1009 HIS   ( 100-)  B      CG   CD2   1.40    4.2
1056 HIS   ( 147-)  B      CG   CD2   1.42    5.4
1081 HIS   ( 172-)  B      CB   CG    1.55    4.0
1081 HIS   ( 172-)  B      CG   CD2   1.41    4.7
1094 HIS   ( 185-)  B      CG   CD2   1.41    5.0
1281 HIS   ( 385-)  B      CG   CD2   1.41    4.6
1319 HIS   ( 423-)  B      CG   CD2   1.41    5.2
1444 HIS   ( 548-)  B      CG   CD2   1.43    6.8
1447 HIS   ( 551-)  B      CG   CD2   1.41    5.2
1505 TRP   ( 609-)  B      NE1  CE2   1.32   -4.1
1529 HIS   ( 633-)  B      CG   CD2   1.41    5.3
1664 HIS   ( 781-)  B      CG   CD2   1.41    4.8

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

 |  0.998852  0.000093 -0.000181|
 |  0.000093  0.998567  0.000441|
 | -0.000181  0.000441  0.998768|
Proposed new scale matrix

 |  0.006160  0.000000  0.000001|
 |  0.000000  0.008201 -0.000004|
 |  0.000001 -0.000003  0.007590|
With corresponding cell

    A    = 162.336  B   = 121.940  C    = 131.746
    Alpha=  89.949  Beta=  90.021  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 162.520  B   = 122.110  C    = 131.910
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 102.501
(Under-)estimated Z-score: 7.462

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.

  42 HIS   (  49-)  A      CG   ND1  CE1 109.67    4.1
  64 HIS   (  71-)  A      CG   ND1  CE1 109.85    4.3
  77 THR   (  84-)  A      C    CA   CB  100.35   -5.1
 137 ARG   ( 144-)  A      CG   CD   NE  103.01   -4.4
 236 HIS   ( 244-)  A      CG   ND1  CE1 109.70    4.1
 337 HIS   ( 351-)  A      CG   ND1  CE1 109.91    4.3
 519 SER   ( 533-)  A      C    CA   CB  102.36   -4.1
 570 ARG   ( 584-)  A      CG   CD   NE   98.84   -6.9
 571 ILE   ( 585-)  A      CA   CB   CG2 118.69    4.8
 590 ARG   ( 604-)  A      CG   CD   NE  102.10   -4.9
 633 HIS   ( 647-)  A      CG   ND1  CE1 110.14    4.5
 649 ARG   ( 663-)  A      CD   NE   CZ  129.95    4.6
 697 MET   ( 711-)  A      CG   SD   CE   87.76   -6.0
 791 VAL   ( 818-)  A      N    CA   CB  102.99   -4.4
 791 VAL   ( 818-)  A      C    CA   CB  118.80    4.6
 818 GLU   ( 845-)  A      C    CA   CB  102.11   -4.2
 956 ASP   (  47-)  B      C    CA   CB  102.44   -4.0
 958 HIS   (  49-)  B      CG   ND1  CE1 109.74    4.1
 993 THR   (  84-)  B      N    CA   CB  117.91    4.4
 993 THR   (  84-)  B      C    CA   CB  101.25   -4.7
1053 ARG   ( 144-)  B      CD   NE   CZ  129.66    4.4
1073 THR   ( 164-)  B      CA   CB   CG2 119.29    5.2
1081 HIS   ( 172-)  B      CG   ND1  CE1 109.65    4.0
1148 HIS   ( 244-)  B      CG   ND1  CE1 109.95    4.3
1247 HIS   ( 351-)  B      CG   ND1  CE1 109.75    4.1
1319 HIS   ( 423-)  B      CG   ND1  CE1 109.97    4.4
1340 LEU   ( 444-)  B      CB   CG   CD1  94.18   -5.5
1429 SER   ( 533-)  B      C    CA   CB  101.84   -4.3
1480 ARG   ( 584-)  B      CG   CD   NE   97.56   -7.6
1481 ILE   ( 585-)  B      CA   CB   CG2 120.33    5.8
1535 VAL   ( 639-)  B      N    CA   CB  102.26   -4.8
1559 ARG   ( 663-)  B      CD   NE   CZ  129.09    4.1
1560 VAL   ( 664-)  B      C    CA   CB  100.74   -4.9
1607 MET   ( 711-)  B      CG   SD   CE   81.87   -8.6
1643 ARG   ( 747-)  B     -C    N    CA  128.90    4.0
1643 ARG   ( 747-)  B      CG   CD   NE  117.30    4.0
1701 VAL   ( 818-)  B      N    CA   CB  102.46   -4.7
1701 VAL   ( 818-)  B      CG1  CB   CG2 120.23    4.3
1754 HIS   ( 871-)  B      CG   ND1  CE1 109.86    4.3
1801 HIS   ( 918-)  B      CG   ND1  CE1 109.65    4.1

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.

 791 VAL   ( 818-)  A      CB     6.1   -24.96   -32.96
1481 ILE   ( 585-)  B      CB    -6.2    24.21    32.31
1701 VAL   ( 818-)  B      CB     6.1   -24.93   -32.96
1813 ILE   ( 952-)  B      CB     6.0    40.12    32.31
The average deviation= 1.226

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.

  14 PRO   (  21-)  A    -2.9
 930 PRO   (  21-)  B    -2.8
 534 HIS   ( 548-)  A    -2.7
1444 HIS   ( 548-)  B    -2.6
 571 ILE   ( 585-)  A    -2.5
1481 ILE   ( 585-)  B    -2.5
 894 LYS   ( 921-)  A    -2.4
1796 VAL   ( 913-)  B    -2.4
1637 PRO   ( 741-)  B    -2.4
 385 VAL   ( 399-)  A    -2.4
1295 VAL   ( 399-)  B    -2.3
 929 VAL   (  20-)  B    -2.3
 727 PRO   ( 741-)  A    -2.3
1465 PRO   ( 569-)  B    -2.3
  13 VAL   (  20-)  A    -2.3
 886 VAL   ( 913-)  A    -2.2
 280 ARG   ( 288-)  A    -2.2
1192 ARG   ( 288-)  B    -2.1
1340 LEU   ( 444-)  B    -2.1
1231 MET   ( 327-)  B    -2.1
 580 GLY   ( 594-)  A    -2.1
 649 ARG   ( 663-)  A    -2.1
1490 GLY   ( 594-)  B    -2.1
1559 ARG   ( 663-)  B    -2.1
 192 ILE   ( 200-)  A    -2.1
 751 THR   ( 778-)  A    -2.1
 218 ARG   ( 226-)  A    -2.1
 388 ASN   ( 402-)  A    -2.1
1661 THR   ( 778-)  B    -2.1
1073 THR   ( 164-)  B    -2.1
 430 LEU   ( 444-)  A    -2.1
 510 GLY   ( 524-)  A    -2.0
1253 LYS   ( 357-)  B    -2.0
1298 ASN   ( 402-)  B    -2.0
 343 LYS   ( 357-)  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.

  15 GLY   (  22-)  A  omega poor
  16 LYS   (  23-)  A  Poor phi/psi
  18 SER   (  25-)  A  omega poor
  64 HIS   (  71-)  A  Poor phi/psi
 164 ALA   ( 171-)  A  omega poor
 168 GLN   ( 175-)  A  Poor phi/psi
 214 THR   ( 222-)  A  omega poor
 216 GLU   ( 224-)  A  omega poor
 238 THR   ( 246-)  A  omega poor
 268 PRO   ( 276-)  A  Poor phi/psi
 278 GLY   ( 286-)  A  Poor phi/psi
 342 TRP   ( 356-)  A  omega poor
 384 ALA   ( 398-)  A  omega poor
 388 ASN   ( 402-)  A  omega poor
 480 LEU   ( 494-)  A  omega poor
 486 PRO   ( 500-)  A  omega poor
 487 LYS   ( 501-)  A  omega poor
 502 ALA   ( 516-)  A  omega poor
 516 MET   ( 530-)  A  Poor phi/psi
 518 THR   ( 532-)  A  Poor phi/psi
 519 SER   ( 533-)  A  omega poor
 587 ASP   ( 601-)  A  omega poor
 642 ASP   ( 656-)  A  Poor phi/psi
 651 THR   ( 665-)  A  omega poor
 725 ALA   ( 739-)  A  omega poor
And so on for a total of 70 lines.

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.

 369 SER   ( 383-)  A    0.34
1008 SER   (  99-)  B    0.35
1334 SER   ( 438-)  B    0.36
1279 SER   ( 383-)  B    0.36
  92 SER   (  99-)  A    0.36
 303 SER   ( 311-)  A    0.36
1215 SER   ( 311-)  B    0.36
  74 SER   (  81-)  A    0.38
 173 SER   ( 180-)  A    0.39

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!

  13 VAL   (  20-)  A      0
  14 PRO   (  21-)  A      0
  16 LYS   (  23-)  A      0
  22 LYS   (  29-)  A      0
  42 HIS   (  49-)  A      0
  63 LYS   (  70-)  A      0
 140 HIS   ( 147-)  A      0
 165 HIS   ( 172-)  A      0
 167 THR   ( 174-)  A      0
 168 GLN   ( 175-)  A      0
 189 TYR   ( 196-)  A      0
 190 ALA   ( 197-)  A      0
 191 ASP   ( 199-)  A      0
 192 ILE   ( 200-)  A      0
 214 THR   ( 222-)  A      0
 215 ASP   ( 223-)  A      0
 216 GLU   ( 224-)  A      0
 234 TYR   ( 242-)  A      0
 238 THR   ( 246-)  A      0
 260 ASN   ( 268-)  A      0
 263 PHE   ( 271-)  A      0
 266 ASN   ( 274-)  A      0
 268 PRO   ( 276-)  A      0
 269 LEU   ( 277-)  A      0
 275 TRP   ( 283-)  A      0
And so on for a total of 432 lines.

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]

 166 PRO   ( 173-)  A    0.13 LOW
 224 PRO   ( 232-)  A    0.16 LOW
 505 PRO   ( 519-)  A    0.18 LOW
 743 PRO   ( 770-)  A    0.09 LOW
 890 PRO   ( 917-)  A    0.15 LOW
1082 PRO   ( 173-)  B    0.14 LOW
1136 PRO   ( 232-)  B    0.16 LOW
1260 PRO   ( 364-)  B    0.20 LOW
1415 PRO   ( 519-)  B    0.18 LOW
1653 PRO   ( 770-)  B    0.10 LOW
1800 PRO   ( 917-)  B    0.16 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].

  14 PRO   (  21-)  A     2.1 envelop N (0 degrees)
 146 PRO   ( 153-)  A   106.0 envelop C-beta (108 degrees)
 194 PRO   ( 202-)  A   111.6 envelop C-beta (108 degrees)
 222 PRO   ( 230-)  A   -45.5 half-chair C-beta/C-alpha (-54 degrees)
 244 PRO   ( 252-)  A  -139.0 envelop C-delta (-144 degrees)
 347 PRO   ( 361-)  A   -39.1 envelop C-alpha (-36 degrees)
 350 PRO   ( 364-)  A    36.5 envelop C-delta (36 degrees)
 486 PRO   ( 500-)  A   -48.6 half-chair C-beta/C-alpha (-54 degrees)
 882 PRO   ( 909-)  A    99.6 envelop C-beta (108 degrees)
 930 PRO   (  21-)  B     2.3 envelop N (0 degrees)
1062 PRO   ( 153-)  B   107.9 envelop C-beta (108 degrees)
1109 PRO   ( 202-)  B   119.8 half-chair C-beta/C-alpha (126 degrees)
1134 PRO   ( 230-)  B   -42.1 envelop C-alpha (-36 degrees)
1156 PRO   ( 252-)  B  -134.7 half-chair C-delta/C-gamma (-126 degrees)
1257 PRO   ( 361-)  B   -40.4 envelop C-alpha (-36 degrees)
1396 PRO   ( 500-)  B   -47.6 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1455 PHE   ( 559-)  B      CZ  <-> 1468 MET   ( 572-)  B      CE     0.40    2.80  INTRA BL
1446 LYS   ( 550-)  B      NZ  <-> 1839 HOH   (2046 )  B      O      0.39    2.31  INTRA BF
1314 CYS   ( 418-)  B      SG  <-> 1319 HIS   ( 423-)  B      ND1    0.37    2.93  INTRA BF
 404 CYS   ( 418-)  A      SG  <->  409 HIS   ( 423-)  A      ND1    0.36    2.94  INTRA BF
1477 TYR   ( 581-)  B      CZ  <-> 1481 ILE   ( 585-)  B      CD1    0.36    2.84  INTRA BL
 872 GLN   ( 899-)  A      OE1 <->  904 THR   ( 954-)  A      CG2    0.36    2.44  INTRA BL
 775 ASN   ( 802-)  A      ND2 <-> 1838 HOH   (2107 )  A      O      0.35    2.35  INTRA BF
1796 VAL   ( 913-)  B      CG1 <-> 1797 THR   ( 914-)  B      N      0.32    2.68  INTRA BF
 882 PRO   ( 909-)  A      CD  <-> 1838 HOH   (2115 )  A      O      0.32    2.48  INTRA BF
1688 MET   ( 805-)  B      C   <-> 1692 MET   ( 809-)  B      CE     0.32    2.88  INTRA BL
1782 GLN   ( 899-)  B      OE1 <-> 1815 THR   ( 954-)  B      CG2    0.31    2.49  INTRA BL
1087 ARG   ( 178-)  B      NH2 <-> 1836 SO4   (1968-)  B      O2     0.31    2.39  INTRA BF
 545 PHE   ( 559-)  A      CZ  <->  558 MET   ( 572-)  A      CE     0.30    2.90  INTRA BL
1236 GLU   ( 333-)  B      OE1 <-> 1311 ARG   ( 415-)  B      NH1    0.29    2.41  INTRA BF
1491 TYR   ( 595-)  B      OH  <-> 1529 HIS   ( 633-)  B      ND1    0.28    2.42  INTRA BL
 882 PRO   ( 909-)  A      N   <-> 1838 HOH   (2115 )  A      O      0.27    2.43  INTRA BF
1824 GLN   ( 963-)  B      NE2 <-> 1839 HOH   (2066 )  B      O      0.24    2.46  INTRA BF
1044 GLU   ( 135-)  B      OE1 <-> 1543 HIS   ( 647-)  B      ND1    0.23    2.47  INTRA BL
 567 TYR   ( 581-)  A      CZ  <->  571 ILE   ( 585-)  A      CD1    0.23    2.97  INTRA BL
 581 TYR   ( 595-)  A      OH  <->  619 HIS   ( 633-)  A      ND1    0.23    2.47  INTRA BL
 949 LYS   (  40-)  B      NZ  <-> 1116 ASP   ( 209-)  B      OD2    0.23    2.47  INTRA BF
 802 LYS   ( 829-)  A      NZ  <->  912 MET   ( 962-)  A      O      0.22    2.48  INTRA BL
1689 LEU   ( 806-)  B      N   <-> 1692 MET   ( 809-)  B      CE     0.22    2.88  INTRA BL
 322 CYS   ( 330-)  A      SG  <->  327 ARG   ( 335-)  A      NH2    0.22    3.08  INTRA BF
 599 LYS   ( 613-)  A      NZ  <->  698 ASP   ( 712-)  A      OD1    0.22    2.48  INTRA BL
And so on for a total of 167 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.

 219 ARG   ( 227-)  A      -8.05
1254 ARG   ( 358-)  B      -7.34
 344 ARG   ( 358-)  A      -7.20
1387 LYS   ( 491-)  B      -6.77
 321 ARG   ( 329-)  A      -6.67
 477 LYS   ( 491-)  A      -6.65
 478 ARG   ( 492-)  A      -6.46
1388 ARG   ( 492-)  B      -6.45
1446 LYS   ( 550-)  B      -6.27
 536 LYS   ( 550-)  A      -6.24
1247 HIS   ( 351-)  B      -5.97
1362 HIS   ( 466-)  B      -5.90
 452 HIS   ( 466-)  A      -5.89
1795 HIS   ( 912-)  B      -5.84
 885 HIS   ( 912-)  A      -5.84
 335 ARG   ( 343-)  A      -5.82
 894 LYS   ( 921-)  A      -5.68
 218 ARG   ( 226-)  A      -5.63
1537 ARG   ( 641-)  B      -5.56
 627 ARG   ( 641-)  A      -5.49
1597 ILE   ( 701-)  B      -5.39
 687 ILE   ( 701-)  A      -5.36
 958 HIS   (  49-)  B      -5.28
1790 ARG   ( 907-)  B      -5.27
 155 ASN   ( 162-)  A      -5.27
 880 ARG   ( 907-)  A      -5.26
 140 HIS   ( 147-)  A      -5.23
  42 HIS   (  49-)  A      -5.23
1172 ASN   ( 268-)  B      -5.21
 262 ARG   ( 270-)  A      -5.19
1232 TRP   ( 328-)  B      -5.17
 980 HIS   (  71-)  B      -5.13
1174 ARG   ( 270-)  B      -5.12
1168 ASN   ( 264-)  B      -5.10
 503 GLU   ( 517-)  A      -5.03
 460 GLU   ( 474-)  A      -5.03
1370 GLU   ( 474-)  B      -5.02
1413 GLU   ( 517-)  B      -5.02
1249 ILE   ( 353-)  B      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 216 GLU   ( 224-)  A       220 - THR    228- ( A)         -5.31

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.

 644 ILE   ( 658-)  A   -3.01
1554 ILE   ( 658-)  B   -2.96
1795 HIS   ( 912-)  B   -2.82
1284 VAL   ( 388-)  B   -2.62

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: 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.

1838 HOH   (2115 )  A      O
1839 HOH   (2025 )  B      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.

  64 HIS   (  71-)  A
 140 HIS   ( 147-)  A
 775 ASN   ( 802-)  A
1685 ASN   ( 802-)  B
1782 GLN   ( 899-)  B
1793 ASN   ( 910-)  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.

  21 ASP   (  28-)  A      N
  25 GLU   (  32-)  A      N
  65 ASP   (  72-)  A      N
  80 ASP   (  87-)  A      N
 109 ARG   ( 116-)  A      NH1
 143 ASN   ( 150-)  A      N
 147 GLU   ( 154-)  A      N
 156 GLN   ( 163-)  A      NE2
 172 ARG   ( 179-)  A      NE
 173 SER   ( 180-)  A      N
 178 HIS   ( 185-)  A      NE2
 218 ARG   ( 226-)  A      NH1
 234 TYR   ( 242-)  A      N
 311 GLU   ( 319-)  A      N
 319 MET   ( 327-)  A      N
 320 TRP   ( 328-)  A      N
 321 ARG   ( 329-)  A      N
 338 TYR   ( 352-)  A      N
 341 PHE   ( 355-)  A      N
 342 TRP   ( 356-)  A      N
 351 TYR   ( 365-)  A      N
 352 ARG   ( 366-)  A      NH2
 359 ARG   ( 373-)  A      NE
 359 ARG   ( 373-)  A      NH1
 366 ARG   ( 380-)  A      NH1
And so on for a total of 101 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.

  27 ASP   (  34-)  A      OD1
 527 GLU   ( 541-)  A      OE2
 680 GLU   ( 694-)  A      OE1
 872 GLN   ( 899-)  A      OE1
1094 HIS   ( 185-)  B      NE2
1437 GLU   ( 541-)  B      OE2

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.

1838 HOH   (2112 )  A      O  0.90  K  4
1839 HOH   (2080 )  B      O  1.01  K  4

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.

 191 ASP   ( 199-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.298
  2nd generation packing quality :  -0.366
  Ramachandran plot appearance   :  -0.124
  chi-1/chi-2 rotamer normality  :  -1.699
  Backbone conformation          :   0.661

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.858
  Bond angles                    :   0.910
  Omega angle restraints         :   1.074
  Side chain planarity           :   0.941
  Improper dihedral distribution :   1.014
  B-factor distribution          :   0.648
  Inside/Outside distribution    :   1.000

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 : 2.49


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   1.5
  chi-1/chi-2 rotamer normality  :   0.0
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.858
  Bond angles                    :   0.910
  Omega angle restraints         :   1.074
  Side chain planarity           :   0.941
  Improper dihedral distribution :   1.014
  B-factor distribution          :   0.648
  Inside/Outside distribution    :   1.000
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      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
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      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.