WHAT IF Check report

This file was created 2012-01-19 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 pdb2a8d.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 : 0.847
CA-only RMS fit for the two chains : 0.504

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

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 C

All-atom RMS fit for the two chains : 0.891
CA-only RMS fit for the two chains : 0.408

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 C

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 D

All-atom RMS fit for the two chains : 0.778
CA-only RMS fit for the two chains : 0.438

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 D

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 E

All-atom RMS fit for the two chains : 0.903
CA-only RMS fit for the two chains : 0.420

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 E

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 F

All-atom RMS fit for the two chains : 0.776
CA-only RMS fit for the two chains : 0.403

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 F

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.

1317 BCT   (1001-)  A  -
1319 BCT   (1002-)  B  -
1322 BCT   (1003-)  C  -
1325 BCT   (1004-)  D  -
1328 BCT   (1005-)  E  -
1333 BCT   (1006-)  F  -

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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) : 95.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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

  37 TYR   (  37-)  A
 258 TYR   (  37-)  B
 479 TYR   (  37-)  C
 698 TYR   (  37-)  D
 913 TYR   (  37-)  E
1133 TYR   (  37-)  F

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 247 PHE   (  26-)  B
 296 PHE   (  75-)  B
 517 PHE   (  75-)  C
 629 PHE   ( 187-)  C
 687 PHE   (  26-)  D
 736 PHE   (  75-)  D
 902 PHE   (  26-)  E
 951 PHE   (  75-)  E
1063 PHE   ( 187-)  E
1122 PHE   (  26-)  F
1171 PHE   (  75-)  F

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.

 144 ASP   ( 144-)  A
 223 ASP   (   2-)  B
 365 ASP   ( 144-)  B
 437 ASP   ( 216-)  B
 444 ASP   (   2-)  C
 586 ASP   ( 144-)  C
 627 ASP   ( 185-)  C
 878 ASP   (   2-)  E
1020 ASP   ( 144-)  E
1061 ASP   ( 185-)  E
1098 ASP   (   2-)  F
1240 ASP   ( 144-)  F

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.

  91 GLU   (  91-)  A
 169 GLU   ( 169-)  A
 218 GLU   ( 218-)  A
 249 GLU   (  28-)  B
 312 GLU   (  91-)  B
 438 GLU   ( 217-)  B
 659 GLU   ( 217-)  C
 752 GLU   (  91-)  D
 932 GLU   (  56-)  E
 967 GLU   (  91-)  E
1075 GLU   ( 199-)  E
1093 GLU   ( 217-)  E
1116 GLU   (  20-)  F
1187 GLU   (  91-)  F

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

 |  0.998596  0.000064 -0.000053|
 |  0.000064  0.998813  0.000135|
 | -0.000053  0.000135  0.998909|
Proposed new scale matrix

 |  0.004301  0.000000  0.000309|
 |  0.000000  0.006924  0.000000|
 |  0.000001 -0.000003  0.019264|
With corresponding cell

    A    = 232.502  B   = 144.421  C    =  52.044
    Alpha=  89.993  Beta=  94.106  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 232.807  B   = 144.602  C    =  52.101
    Alpha=  90.000  Beta=  94.100  Gamma=  90.000

Variance: 68.273
(Under-)estimated Z-score: 6.090

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.

  61 PHE   (  61-)  A      N    CA   C    97.07   -5.0
 282 PHE   (  61-)  B      N    CA   C    97.19   -5.0
 503 PHE   (  61-)  C      N    CA   C    96.82   -5.1
 722 PHE   (  61-)  D      N    CA   C    97.76   -4.8
 937 PHE   (  61-)  E      N    CA   C    96.52   -5.2
1157 PHE   (  61-)  F      N    CA   C    97.83   -4.8

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.

  91 GLU   (  91-)  A
 144 ASP   ( 144-)  A
 169 GLU   ( 169-)  A
 218 GLU   ( 218-)  A
 223 ASP   (   2-)  B
 249 GLU   (  28-)  B
 312 GLU   (  91-)  B
 365 ASP   ( 144-)  B
 437 ASP   ( 216-)  B
 438 GLU   ( 217-)  B
 444 ASP   (   2-)  C
 586 ASP   ( 144-)  C
 627 ASP   ( 185-)  C
 659 GLU   ( 217-)  C
 752 GLU   (  91-)  D
 878 ASP   (   2-)  E
 932 GLU   (  56-)  E
 967 GLU   (  91-)  E
1020 ASP   ( 144-)  E
1061 ASP   ( 185-)  E
1075 GLU   ( 199-)  E
1093 GLU   ( 217-)  E
1098 ASP   (   2-)  F
1116 GLU   (  20-)  F
1187 GLU   (  91-)  F
1240 ASP   ( 144-)  F

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.

 937 PHE   (  61-)  E    5.71
 503 PHE   (  61-)  C    5.58
  61 PHE   (  61-)  A    5.46
 282 PHE   (  61-)  B    5.41
1158 VAL   (  62-)  F    5.24
 722 PHE   (  61-)  D    5.16
1157 PHE   (  61-)  F    5.13
 723 VAL   (  62-)  D    5.07
  62 VAL   (  62-)  A    4.87
 504 VAL   (  62-)  C    4.79
 283 VAL   (  62-)  B    4.75
   2 ASP   (   2-)  A    4.23
 938 VAL   (  62-)  E    4.10

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.

 581 PRO   ( 139-)  C    -2.9
1015 PRO   ( 139-)  E    -2.6
 360 PRO   ( 139-)  B    -2.5
1235 PRO   ( 139-)  F    -2.5
 510 ASN   (  68-)  C    -2.4
 558 ILE   ( 116-)  C    -2.4
 139 PRO   ( 139-)  A    -2.4
1164 ASN   (  68-)  F    -2.3
 992 ILE   ( 116-)  E    -2.3
 777 ILE   ( 116-)  D    -2.3
 337 ILE   ( 116-)  B    -2.3
  68 ASN   (  68-)  A    -2.3
 289 ASN   (  68-)  B    -2.2
 399 GLY   ( 178-)  B    -2.2
 944 ASN   (  68-)  E    -2.2
1212 ILE   ( 116-)  F    -2.1
1054 GLY   ( 178-)  E    -2.1
 620 GLY   ( 178-)  C    -2.1
1274 GLY   ( 178-)  F    -2.1
 729 ASN   (  68-)  D    -2.1
 178 GLY   ( 178-)  A    -2.1
 515 THR   (  73-)  C    -2.1
 266 SER   (  45-)  B    -2.1
 706 SER   (  45-)  D    -2.1
 839 GLY   ( 178-)  D    -2.1
1141 SER   (  45-)  F    -2.0
  45 SER   (  45-)  A    -2.0
 116 ILE   ( 116-)  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.

  67 ALA   (  67-)  A  Poor phi/psi
  89 LYS   (  89-)  A  Poor phi/psi
 100 ASN   ( 100-)  A  Poor phi/psi
 275 ASN   (  54-)  B  Poor phi/psi
 288 ALA   (  67-)  B  Poor phi/psi
 310 LYS   (  89-)  B  Poor phi/psi
 321 ASN   ( 100-)  B  Poor phi/psi
 437 ASP   ( 216-)  B  Poor phi/psi
 438 GLU   ( 217-)  B  Poor phi/psi
 459 ARG   (  17-)  C  Poor phi/psi
 496 ASN   (  54-)  C  Poor phi/psi
 509 ALA   (  67-)  C  Poor phi/psi
 510 ASN   (  68-)  C  Poor phi/psi
 531 LYS   (  89-)  C  Poor phi/psi
 728 ALA   (  67-)  D  Poor phi/psi
 750 LYS   (  89-)  D  Poor phi/psi
 761 ASN   ( 100-)  D  Poor phi/psi
 846 ASP   ( 185-)  D  Poor phi/psi
 898 ASN   (  22-)  E  Poor phi/psi
 943 ALA   (  67-)  E  Poor phi/psi
 944 ASN   (  68-)  E  Poor phi/psi
 965 LYS   (  89-)  E  Poor phi/psi
 976 ASN   ( 100-)  E  Poor phi/psi
1118 ASN   (  22-)  F  Poor phi/psi
1163 ALA   (  67-)  F  Poor phi/psi
1185 LYS   (  89-)  F  Poor phi/psi
1196 ASN   ( 100-)  F  Poor phi/psi
1281 ASP   ( 185-)  F  Poor phi/psi
1314 GLU   ( 218-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.187

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.

1042 SER   ( 166-)  E    0.35
1109 SER   (  13-)  F    0.35
1080 SER   ( 204-)  E    0.36
 674 SER   (  13-)  D    0.36
  13 SER   (  13-)  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!

  24 THR   (  24-)  A      0
  36 HIS   (  36-)  A      0
  44 ASP   (  44-)  A      0
  45 SER   (  45-)  A      0
  46 ARG   (  46-)  A      0
  47 VAL   (  47-)  A      0
  57 PRO   (  57-)  A      0
  59 GLU   (  59-)  A      0
  65 ASN   (  65-)  A      0
  66 VAL   (  66-)  A      0
  67 ALA   (  67-)  A      0
  68 ASN   (  68-)  A      0
  69 GLN   (  69-)  A      0
  73 THR   (  73-)  A      0
  86 ASP   (  86-)  A      0
  88 LEU   (  88-)  A      0
  89 LYS   (  89-)  A      0
  91 GLU   (  91-)  A      0
  99 THR   (  99-)  A      0
 101 CYS   ( 101-)  A      0
 110 ASP   ( 110-)  A      0
 113 LEU   ( 113-)  A      0
 115 LEU   ( 115-)  A      0
 179 TRP   ( 179-)  A      0
 191 GLN   ( 191-)  A      0
And so on for a total of 406 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.213

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!

 360 PRO   ( 139-)  B   1.52   11
1054 GLY   ( 178-)  E   1.50   47

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.

 194 MET   ( 194-)  A      CE  <->  195 ALA   ( 195-)  A      N      0.57    2.43  INTRA BL
 834 LYS   ( 173-)  D      NZ  <-> 1097 MET   (   1-)  F      SD     0.46    2.84  INTRA BF
 290 GLN   (  69-)  B      NE2 <->  344 ILE   ( 123-)  B      CD1    0.46    2.64  INTRA BL
 640 ARG   ( 198-)  C      NH1 <->  644 GLU   ( 202-)  C      CG     0.31    2.79  INTRA BF
 443 MET   (   1-)  C      SD  <->  444 ASP   (   2-)  C      N      0.30    2.90  INTRA BF
 334 LEU   ( 113-)  B      N   <->  338 ASN   ( 117-)  B      OD1    0.28    2.42  INTRA BL
 983 ALA   ( 107-)  E      O   <-> 1000 ARG   ( 124-)  E      NH1    0.28    2.42  INTRA BF
 345 ARG   ( 124-)  B      NE  <-> 1320 SO4   (2001-)  B      O3     0.28    2.42  INTRA BF
 662 MET   (   1-)  D      N   <-> 1337 HOH   (4286 )  D      O      0.27    2.43  INTRA BF
 877 MET   (   1-)  E      SD  <->  878 ASP   (   2-)  E      N      0.26    2.94  INTRA BF
 194 MET   ( 194-)  A      CE  <->  195 ALA   ( 195-)  A      C      0.25    2.85  INTRA BL
  51 LYS   (  51-)  A      NZ  <-> 1334 HOH   (1296 )  A      O      0.23    2.47  INTRA BF
  22 ASN   (  22-)  A      ND2 <-> 1334 HOH   (1252 )  A      O      0.22    2.48  INTRA BF
 989 LEU   ( 113-)  E      N   <->  993 ASN   ( 117-)  E      OD1    0.22    2.48  INTRA BF
 728 ALA   (  67-)  D      C   <->  729 ASN   (  68-)  D      CG     0.21    2.89  INTRA BL
 859 ARG   ( 198-)  D      NH1 <-> 1337 HOH   (4245 )  D      O      0.21    2.49  INTRA BF
1138 CYS   (  42-)  F      SG  <-> 1139 SER   (  43-)  F      N      0.21    2.99  INTRA BL
  36 HIS   (  36-)  A      CD2 <->   59 GLU   (  59-)  A      OE1    0.21    2.59  INTRA BF
 572 HIS   ( 130-)  C      NE2 <->  595 GLU   ( 153-)  C      OE2    0.20    2.50  INTRA BL
 386 LYS   ( 165-)  B      NZ  <-> 1335 HOH   (2243 )  B      O      0.20    2.50  INTRA BF
 707 ARG   (  46-)  D      NH2 <-> 1125 LEU   (  29-)  F      CD2    0.20    2.90  INTRA BF
1332 SO4   (2006-)  E      S   <-> 1338 HOH   (5237 )  E      O      0.19    2.81  INTRA BF
1312 ASP   ( 216-)  F      O   <-> 1314 GLU   ( 218-)  F      N      0.19    2.51  INTRA BF
  86 ASP   (  86-)  A      O   <->   89 LYS   (  89-)  A      NZ     0.19    2.51  INTRA BL
 554 ASP   ( 112-)  C      CA  <->  559 ASN   ( 117-)  C      ND2    0.19    2.91  INTRA BF
And so on for a total of 219 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

  46 ARG   (  46-)  A      -6.67
 267 ARG   (  46-)  B      -6.65
 475 GLN   (  33-)  C      -6.62
 694 GLN   (  33-)  D      -6.44
  64 ARG   (  64-)  A      -6.37
 285 ARG   (  64-)  B      -6.32
  33 GLN   (  33-)  A      -6.19
1129 GLN   (  33-)  F      -6.05
 909 GLN   (  33-)  E      -5.81
 254 GLN   (  33-)  B      -5.69
1142 ARG   (  46-)  F      -5.62
 922 ARG   (  46-)  E      -5.53
 707 ARG   (  46-)  D      -5.47
 488 ARG   (  46-)  C      -5.41
 321 ASN   ( 100-)  B      -5.08
 100 ASN   ( 100-)  A      -5.05
 725 ARG   (  64-)  D      -5.04
 542 ASN   ( 100-)  C      -5.03
1196 ASN   ( 100-)  F      -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.

1313 GLU   ( 217-)  F      1315 - ASN    219- ( F)         -4.59

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

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: C

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: D

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: E

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: F

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

1334 HOH   (1283 )  A      O     -9.50   47.56   38.68
1335 HOH   (2245 )  B      O     -1.01   67.79   27.21
1335 HOH   (2252 )  B      O      0.25   93.00   25.36
1339 HOH   (6276 )  F      O     56.06  149.34    7.86

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.

 237 GLN   (  16-)  B
 475 GLN   (  33-)  C
1196 ASN   ( 100-)  F

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 LYS   (   3-)  A      N
  16 GLN   (  16-)  A      NE2
  26 PHE   (  26-)  A      N
  39 TRP   (  39-)  A      NE1
  56 GLU   (  56-)  A      N
  64 ARG   (  64-)  A      NH1
  73 THR   (  73-)  A      N
  77 CYS   (  77-)  A      N
  92 HIS   (  92-)  A      N
 163 ILE   ( 163-)  A      N
 207 ASN   ( 207-)  A      ND2
 225 ILE   (   4-)  B      N
 246 TYR   (  25-)  B      OH
 254 GLN   (  33-)  B      N
 255 THR   (  34-)  B      N
 260 TRP   (  39-)  B      NE1
 285 ARG   (  64-)  B      NH1
 294 THR   (  73-)  B      N
 298 CYS   (  77-)  B      N
 313 HIS   (  92-)  B      N
 384 ILE   ( 163-)  B      N
 440 ASN   ( 219-)  B      N
 441 ILE   ( 220-)  B      N
 445 LYS   (   3-)  C      N
 460 MET   (  18-)  C      N
And so on for a total of 67 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.

 249 GLU   (  28-)  B      OE1
 290 GLN   (  69-)  B      OE1
 297 ASN   (  76-)  B      OD1
 534 HIS   (  92-)  C      NE2
 559 ASN   ( 117-)  C      OD1
 644 GLU   ( 202-)  C      OE1
 659 GLU   ( 217-)  C      OE1
 737 ASN   (  76-)  D      OD1
 968 HIS   (  92-)  E      NE2
1155 GLU   (  59-)  F      OE1
1188 HIS   (  92-)  F      NE2

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.

1334 HOH   (1259 )  A      O  0.89  K  4
1335 HOH   (2265 )  B      O  0.87  K  6 ION-B
1337 HOH   (4252 )  D      O  1.00  K  5
1339 HOH   (6244 )  F      O  0.92  K  5
1339 HOH   (6250 )  F      O  0.96  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.

  50 GLU   (  50-)  A   H-bonding suggests Gln; but Alt-Rotamer
 252 ASP   (  31-)  B   H-bonding suggests Asn
 346 ASP   ( 125-)  B   H-bonding suggests Asn
 463 GLU   (  21-)  C   H-bonding suggests Gln; but Alt-Rotamer
 473 ASP   (  31-)  C   H-bonding suggests Asn
 627 ASP   ( 185-)  C   H-bonding suggests Asn; but Alt-Rotamer
 692 ASP   (  31-)  D   H-bonding suggests Asn
 907 ASP   (  31-)  E   H-bonding suggests Asn
1001 ASP   ( 125-)  E   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 :   0.439
  2nd generation packing quality :  -1.306
  Ramachandran plot appearance   :  -1.205
  chi-1/chi-2 rotamer normality  :  -2.187
  Backbone conformation          :   0.247

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.284 (tight)
  Bond angles                    :   0.616 (tight)
  Omega angle restraints         :   0.221 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.542
  B-factor distribution          :   0.478
  Inside/Outside distribution    :   1.012

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 :   1.0
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.284 (tight)
  Bond angles                    :   0.616 (tight)
  Omega angle restraints         :   0.221 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.542
  B-factor distribution          :   0.478
  Inside/Outside distribution    :   1.012
==============

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.