WHAT IF Check report

This file was created 2011-12-15 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 pdb3e2w.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 D

All-atom RMS fit for the two chains : 1.586
CA-only RMS fit for the two chains : 1.287

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

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.

1236 BCT   ( 231-)  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. 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: 6

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

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

  27 TYR   (  37-)  A
 220 TYR   (  12-)  B
 229 TYR   (  37-)  B
 433 TYR   (  37-)  C
 639 TYR   (  37-)  D
 839 TYR   (  37-)  E
1040 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.

  65 PHE   (  75-)  A
 171 PHE   ( 181-)  A
 177 PHE   ( 187-)  A
 267 PHE   (  75-)  B
 373 PHE   ( 181-)  B
 379 PHE   ( 187-)  B
 417 PHE   (   8-)  C
 471 PHE   (  75-)  C
 524 PHE   ( 128-)  C
 577 PHE   ( 181-)  C
 583 PHE   ( 187-)  C
 620 PHE   (   8-)  D
 677 PHE   (  75-)  D
 730 PHE   ( 128-)  D
 783 PHE   ( 181-)  D
 824 PHE   (   8-)  E
 877 PHE   (  75-)  E
 983 PHE   ( 181-)  E
 989 PHE   ( 187-)  E
1078 PHE   (  75-)  F
1131 PHE   ( 128-)  F
1184 PHE   ( 181-)  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.

 175 ASP   ( 185-)  A
 180 ASP   ( 190-)  A
 210 ASP   (   2-)  B
 302 ASP   ( 110-)  B
 336 ASP   ( 144-)  B
 374 ASP   ( 182-)  B
 408 ASP   ( 216-)  B
 411 ASP   (   2-)  C
 506 ASP   ( 110-)  C
 540 ASP   ( 144-)  C
 578 ASP   ( 182-)  C
 581 ASP   ( 185-)  C
 612 ASP   ( 216-)  C
 646 ASP   (  44-)  D
 787 ASP   ( 185-)  D
 818 ASP   (   2-)  E
 846 ASP   (  44-)  E
 912 ASP   ( 110-)  E
 914 ASP   ( 112-)  E
 987 ASP   ( 185-)  E
1047 ASP   (  44-)  F
1113 ASP   ( 110-)  F
1115 ASP   ( 112-)  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.

  21 GLU   (  21-)  A
  81 GLU   (  91-)  A
 159 GLU   ( 169-)  A
 192 GLU   ( 202-)  A
 207 GLU   ( 217-)  A
 208 GLU   ( 218-)  A
 242 GLU   (  50-)  B
 283 GLU   (  91-)  B
 394 GLU   ( 202-)  B
 446 GLU   (  50-)  C
 455 GLU   (  59-)  C
 633 GLU   (  21-)  D
 742 GLU   ( 140-)  D
 771 GLU   ( 169-)  D
 801 GLU   ( 199-)  D
 893 GLU   (  91-)  E
 942 GLU   ( 140-)  E
1001 GLU   ( 199-)  E
1053 GLU   (  50-)  F
1062 GLU   (  59-)  F
1094 GLU   (  91-)  F
1143 GLU   ( 140-)  F
1156 GLU   ( 153-)  F
1172 GLU   ( 169-)  F
1205 GLU   ( 202-)  F

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.

1126 ILE   ( 123-)  F      CA   CB    1.62    4.4

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

 |  0.990229  0.000152 -0.000524|
 |  0.000152  0.996886 -0.000350|
 | -0.000524 -0.000350  0.996628|
Proposed new scale matrix

 |  0.004038  0.000000  0.000267|
 | -0.000001  0.006908  0.000002|
 |  0.000010  0.000007  0.018796|
With corresponding cell

    A    = 247.681  B   = 144.770  C    =  53.320
    Alpha=  90.041  Beta=  93.814  Gamma=  89.991

The CRYST1 cell dimensions

    A    = 250.141  B   = 145.225  C    =  53.499
    Alpha=  90.000  Beta=  93.780  Gamma=  90.000

Variance: 1391.101
(Under-)estimated Z-score: 27.488

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.

 236 ASP   (  44-)  B      C    CA   CB   96.23   -7.3
 440 ASP   (  44-)  C      C    CA   CB  101.94   -4.3
 459 HIS   (  63-)  C      CG   ND1  CE1 109.76    4.2
 665 HIS   (  63-)  D      CG   ND1  CE1 109.63    4.0
 865 HIS   (  63-)  E      CG   ND1  CE1 109.75    4.2
 907 HIS   ( 105-)  E      CG   ND1  CE1 109.61    4.0
1055 LEU   (  52-)  F      CA   CB   CG  131.84    4.4
1066 HIS   (  63-)  F      CG   ND1  CE1 109.89    4.3
1108 HIS   ( 105-)  F      CG   ND1  CE1 109.62    4.0

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.

  21 GLU   (  21-)  A
  81 GLU   (  91-)  A
 159 GLU   ( 169-)  A
 175 ASP   ( 185-)  A
 180 ASP   ( 190-)  A
 192 GLU   ( 202-)  A
 207 GLU   ( 217-)  A
 208 GLU   ( 218-)  A
 210 ASP   (   2-)  B
 242 GLU   (  50-)  B
 283 GLU   (  91-)  B
 302 ASP   ( 110-)  B
 336 ASP   ( 144-)  B
 374 ASP   ( 182-)  B
 394 GLU   ( 202-)  B
 408 ASP   ( 216-)  B
 411 ASP   (   2-)  C
 446 GLU   (  50-)  C
 455 GLU   (  59-)  C
 506 ASP   ( 110-)  C
 540 ASP   ( 144-)  C
 578 ASP   ( 182-)  C
 581 ASP   ( 185-)  C
 612 ASP   ( 216-)  C
 633 GLU   (  21-)  D
 646 ASP   (  44-)  D
 742 GLU   ( 140-)  D
 771 GLU   ( 169-)  D
 787 ASP   ( 185-)  D
 801 GLU   ( 199-)  D
 818 ASP   (   2-)  E
 846 ASP   (  44-)  E
 893 GLU   (  91-)  E
 912 ASP   ( 110-)  E
 914 ASP   ( 112-)  E
 942 GLU   ( 140-)  E
 987 ASP   ( 185-)  E
1001 GLU   ( 199-)  E
1047 ASP   (  44-)  F
1053 GLU   (  50-)  F
1062 GLU   (  59-)  F
1094 GLU   (  91-)  F
1113 ASP   ( 110-)  F
1115 ASP   ( 112-)  F
1143 GLU   ( 140-)  F
1156 GLU   ( 153-)  F
1172 GLU   ( 169-)  F
1205 GLU   ( 202-)  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.

 664 VAL   (  62-)  D    4.76
 312 LEU   ( 120-)  B    4.48
 458 VAL   (  62-)  C    4.33

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.

 891 LYS   (  89-)  E    -2.5
1126 ILE   ( 123-)  F    -2.5
 657 LEU   (  55-)  D    -2.4
1177 LEU   ( 174-)  F    -2.3
  36 ARG   (  46-)  A    -2.3
 836 THR   (  34-)  E    -2.2
 875 THR   (  73-)  E    -2.2
 739 LEU   ( 137-)  D    -2.2
1119 ILE   ( 116-)  F    -2.2
 485 LYS   (  89-)  C    -2.2
1071 ASN   (  68-)  F    -2.1
 370 GLY   ( 178-)  B    -2.1
 574 GLY   ( 178-)  C    -2.1
 980 GLY   ( 178-)  E    -2.1
 691 LYS   (  89-)  D    -2.1
 918 ILE   ( 116-)  E    -2.1
 168 GLY   ( 178-)  A    -2.1
1181 GLY   ( 178-)  F    -2.1
 247 LEU   (  55-)  B    -2.1
 204 ILE   ( 214-)  A    -2.1
 464 ASN   (  68-)  C    -2.1
 780 GLY   ( 178-)  D    -2.1
 131 LYS   ( 141-)  A    -2.1
 985 VAL   ( 183-)  E    -2.1
 512 ILE   ( 116-)  C    -2.1
1020 ASP   (   2-)  F    -2.1
 238 ARG   (  46-)  B    -2.1
 308 ILE   ( 116-)  B    -2.1
  58 ASN   (  68-)  A    -2.0
1058 LEU   (  55-)  F    -2.0
 265 THR   (  73-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  27 TYR   (  37-)  A  omega poor
  50 LEU   (  60-)  A  omega poor
  51 PHE   (  61-)  A  omega poor
  57 ALA   (  67-)  A  Poor phi/psi
  79 LYS   (  89-)  A  Poor phi/psi
  86 CYS   (  96-)  A  omega poor
 210 ASP   (   2-)  B  Poor phi/psi
 236 ASP   (  44-)  B  omega poor
 246 ASN   (  54-)  B  Poor phi/psi
 253 PHE   (  61-)  B  omega poor
 259 ALA   (  67-)  B  Poor phi/psi
 281 LYS   (  89-)  B  Poor phi/psi
 292 ASN   ( 100-)  B  Poor phi/psi
 433 TYR   (  37-)  C  omega poor
 457 PHE   (  61-)  C  omega poor
 463 ALA   (  67-)  C  Poor phi/psi
 465 GLN   (  69-)  C  omega poor
 485 LYS   (  89-)  C  Poor phi/psi
 496 ASN   ( 100-)  C  Poor phi/psi
 593 SER   ( 197-)  C  Poor phi/psi
 630 MET   (  18-)  D  Poor phi/psi
 639 TYR   (  37-)  D  omega poor
 656 ASN   (  54-)  D  Poor phi/psi
 663 PHE   (  61-)  D  omega poor
 669 ALA   (  67-)  D  Poor phi/psi
 856 ASN   (  54-)  E  Poor phi/psi
 863 PHE   (  61-)  E  omega poor
 869 ALA   (  67-)  E  Poor phi/psi
 891 LYS   (  89-)  E  Poor phi/psi
 984 ASP   ( 182-)  E  omega poor
 987 ASP   ( 185-)  E  Poor phi/psi
1040 TYR   (  37-)  F  omega poor
1064 PHE   (  61-)  F  omega poor
1070 ALA   (  67-)  F  Poor phi/psi
1072 GLN   (  69-)  F  omega poor
1092 LYS   (  89-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.843

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.

 806 SER   ( 204-)  D    0.36
  69 SER   (  79-)  A    0.37
 829 SER   (  13-)  E    0.38
1006 SER   ( 204-)  E    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!

  21 GLU   (  21-)  A      0
  22 ASN   (  22-)  A      0
  23 GLN   (  33-)  A      0
  24 THR   (  34-)  A      0
  36 ARG   (  46-)  A      0
  44 ASN   (  54-)  A      0
  47 PRO   (  57-)  A      0
  49 GLU   (  59-)  A      0
  55 ASN   (  65-)  A      0
  56 VAL   (  66-)  A      0
  57 ALA   (  67-)  A      0
  59 GLN   (  69-)  A      0
  63 THR   (  73-)  A      0
  65 PHE   (  75-)  A      0
  76 ASP   (  86-)  A      0
  78 LEU   (  88-)  A      0
  79 LYS   (  89-)  A      0
  81 GLU   (  91-)  A      0
  89 THR   (  99-)  A      0
  91 CYS   ( 101-)  A      0
 100 ASP   ( 110-)  A      0
 103 LEU   ( 113-)  A      0
 105 LEU   ( 115-)  A      0
 181 GLN   ( 191-)  A      0
 186 THR   ( 196-)  A      0
And so on for a total of 356 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!

 980 GLY   ( 178-)  E   1.73   19
 370 GLY   ( 178-)  B   1.53   36

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]

  25 PRO   (  35-)  A    0.18 LOW
  38 PRO   (  48-)  A    0.17 LOW
 431 PRO   (  35-)  C    0.19 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].

 227 PRO   (  35-)  B    42.8 envelop C-delta (36 degrees)
 859 PRO   (  57-)  E    47.7 half-chair C-delta/C-gamma (54 degrees)
1038 PRO   (  35-)  F    -2.5 envelop N (0 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.

 209 MET   (   1-)  B      O   <->  212 ILE   (   4-)  B      N      0.41    2.29  INTRA BF
 272 VAL   (  80-)  B      CG2 <-> 1238 HOH   ( 263 )  B      O      0.35    2.45  INTRA BL
  40 GLU   (  50-)  A      OE1 <-> 1237 HOH   ( 268 )  A      O      0.33    2.07  INTRA BF
1053 GLU   (  50-)  F      OE2 <-> 1236 BCT   ( 231-)  F      O3     0.22    2.18  INTRA BF
 173 VAL   ( 183-)  A      CG1 <-> 1222 SO4   ( 233-)  A      O2     0.21    2.59  INTRA BF
 209 MET   (   1-)  B      N   <-> 1238 HOH   ( 243 )  B      O      0.20    2.50  INTRA BF
 817 MET   (   1-)  E      N   <-> 1241 HOH   ( 268 )  E      O      0.20    2.50  INTRA BF
 238 ARG   (  46-)  B      N   <-> 1224 SO4   ( 231-)  B      O3     0.19    2.51  INTRA BF
 703 CYS   ( 101-)  D      N   <-> 1240 HOH   ( 272 )  D      O      0.18    2.52  INTRA BL
 375 VAL   ( 183-)  B      CG1 <-> 1224 SO4   ( 231-)  B      O4     0.18    2.62  INTRA BF
 767 LYS   ( 165-)  D      CD  <->  800 ARG   ( 198-)  D      NH1    0.17    2.93  INTRA BF
 880 LEU   (  78-)  E      CD2 <->  965 ILE   ( 163-)  E      CD1    0.16    3.04  INTRA BF
 197 ASN   ( 207-)  A      ND2 <-> 1237 HOH   ( 288 )  A      O      0.15    2.55  INTRA BL
 173 VAL   ( 183-)  A      CG1 <-> 1222 SO4   ( 233-)  A      S      0.15    3.25  INTRA BF
 209 MET   (   1-)  B      O   <->  211 LYS   (   3-)  B      N      0.13    2.57  INTRA BF
 364 GLN   ( 172-)  B      NE2 <-> 1238 HOH   ( 242 )  B      O      0.13    2.57  INTRA BL
 146 TYR   ( 156-)  A      OH  <->  192 GLU   ( 202-)  A      OE2    0.13    2.27  INTRA BF
1211 ALA   ( 208-)  F      O   <-> 1215 LEU   ( 212-)  F      CD2    0.13    2.67  INTRA BF
 985 VAL   ( 183-)  E      CG1 <-> 1233 SO4   ( 232-)  E      O2     0.11    2.69  INTRA BF
 162 GLN   ( 172-)  A      NE2 <-> 1237 HOH   ( 257 )  A      O      0.11    2.59  INTRA BL
 732 HIS   ( 130-)  D      NE2 <->  755 GLU   ( 153-)  D      OE2    0.09    2.61  INTRA BL
 122 HIS   ( 132-)  A      CE1 <->  126 LYS   ( 136-)  A      NZ     0.09    3.01  INTRA BF
 316 ARG   ( 124-)  B      NE  <-> 1220 SO4   ( 232-)  A      O4     0.09    2.61  INTRA BF
 121 GLY   ( 131-)  A      O   <->  125 GLY   ( 135-)  A      N      0.09    2.61  INTRA BF
 569 LYS   ( 173-)  C      NZ  <-> 1239 HOH   ( 241 )  C      O      0.09    2.61  INTRA BL
And so on for a total of 69 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.

  36 ARG   (  46-)  A      -7.93
 648 ARG   (  46-)  D      -7.89
 238 ARG   (  46-)  B      -7.64
1049 ARG   (  46-)  F      -7.57
 848 ARG   (  46-)  E      -7.53
 442 ARG   (  46-)  C      -7.48
  54 ARG   (  64-)  A      -6.14
 256 ARG   (  64-)  B      -6.00
 833 ARG   (  17-)  E      -5.85
 224 GLN   (  16-)  B      -5.67
 496 ASN   ( 100-)  C      -5.59
 902 ASN   ( 100-)  E      -5.58
  90 ASN   ( 100-)  A      -5.56
 207 GLU   ( 217-)  A      -5.56
 702 ASN   ( 100-)  D      -5.55
1103 ASN   ( 100-)  F      -5.55
1035 ARG   (  17-)  F      -5.53
 772 ARG   ( 170-)  D      -5.52
 292 ASN   ( 100-)  B      -5.29
1017 LEU   ( 215-)  E      -5.08
  21 GLU   (  21-)  A      -5.07
 460 ARG   (  64-)  C      -5.03
1173 ARG   ( 170-)  F      -5.00

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.

 426 ARG   (  17-)  C       428 - LYS     19- ( C)         -4.40

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

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.

 701 THR   (  99-)  D   -2.69

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.

1237 HOH   ( 261 )  A      O     90.50  122.08   15.84

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.

  22 ASN   (  22-)  A
 120 HIS   ( 130-)  A
 228 HIS   (  36-)  B
 376 ASN   ( 184-)  B
 419 ASN   (  10-)  C
 432 HIS   (  36-)  C
 501 HIS   ( 105-)  C
 580 ASN   ( 184-)  C
 707 HIS   ( 105-)  D
 786 ASN   ( 184-)  D
 835 GLN   (  33-)  E
 838 HIS   (  36-)  E

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.

  16 GLN   (  16-)  A      NE2
  54 ARG   (  64-)  A      N
  62 HIS   (  72-)  A      N
  63 THR   (  73-)  A      N
  67 CYS   (  77-)  A      N
  82 HIS   (  92-)  A      N
 112 HIS   ( 122-)  A      N
 127 LEU   ( 137-)  A      N
 153 ILE   ( 163-)  A      N
 187 SER   ( 197-)  A      N
 256 ARG   (  64-)  B      N
 264 HIS   (  72-)  B      N
 284 HIS   (  92-)  B      N
 305 LEU   ( 113-)  B      N
 314 HIS   ( 122-)  B      N
 377 ASP   ( 185-)  B      N
 465 GLN   (  69-)  C      NE2
 488 HIS   (  92-)  C      N
 500 ILE   ( 104-)  C      N
 507 LYS   ( 111-)  C      N
 518 HIS   ( 122-)  C      N
 579 VAL   ( 183-)  C      N
 593 SER   ( 197-)  C      N
 630 MET   (  18-)  D      N
 632 GLU   (  20-)  D      N
 634 ASN   (  22-)  D      N
 694 HIS   (  92-)  D      N
 715 LEU   ( 113-)  D      N
 785 VAL   ( 183-)  D      N
 789 PHE   ( 187-)  D      N
 874 HIS   (  72-)  E      N
 894 HIS   (  92-)  E      N
 915 LEU   ( 113-)  E      N
 946 ASP   ( 144-)  E      N
 965 ILE   ( 163-)  E      N
1040 TYR   (  37-)  F      N
1053 GLU   (  50-)  F      N
1072 GLN   (  69-)  F      NE2
1076 THR   (  73-)  F      N
1079 ASN   (  76-)  F      ND2
1095 HIS   (  92-)  F      N
1146 ALA   ( 143-)  F      N
1166 ILE   ( 163-)  F      N
Only metal coordination for   88 HIS  (  98-) A      NE2
Only metal coordination for  290 HIS  (  98-) B      NE2
Only metal coordination for  494 HIS  (  98-) C      NE2
Only metal coordination for  700 HIS  (  98-) D      NE2
Only metal coordination for  900 HIS  (  98-) E      NE2
Only metal coordination for 1047 ASP  (  44-) F      OD1
Only metal coordination for 1101 HIS  (  98-) F      NE2

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.

1053 GLU   (  50-)  F      OE2

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.

 266 ASP   (  74-)  B   H-bonding suggests Asn
 361 GLU   ( 169-)  B   H-bonding suggests Gln
 565 GLU   ( 169-)  C   H-bonding suggests Gln
 581 ASP   ( 185-)  C   H-bonding suggests Asn; but Alt-Rotamer
 586 ASP   ( 190-)  C   H-bonding suggests Asn
 746 ASP   ( 144-)  D   H-bonding suggests Asn
1188 ASP   ( 185-)  F   H-bonding suggests Asn; but Alt-Rotamer
1193 ASP   ( 190-)  F   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 :  -0.571
  2nd generation packing quality :  -1.881
  Ramachandran plot appearance   :  -0.048
  chi-1/chi-2 rotamer normality  :  -2.843
  Backbone conformation          :   0.146

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.634 (tight)
  Bond angles                    :   0.735
  Omega angle restraints         :   0.982
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.605
  B-factor distribution          :   0.344
  Inside/Outside distribution    :   1.029

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   1.2
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.634 (tight)
  Bond angles                    :   0.735
  Omega angle restraints         :   0.982
  Side chain planarity           :   0.539 (tight)
  Improper dihedral distribution :   0.605
  B-factor distribution          :   0.344
  Inside/Outside distribution    :   1.029
==============

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.