WHAT IF Check report

This file was created 2012-01-05 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 pdb1ppi.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.

 502 BGC   ( 993-)  A  -
 503 DAF   ( 992-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 498 GLC   ( 991-)  A  -   O4  bound to  497 GLC   ( 990-)  A  -   C1

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 23.58

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.

 157 VAL   ( 157-)  A      CA   CB    1.63    5.1
 323 VAL   ( 323-)  A      CA   CB    1.63    4.8
 349 VAL   ( 349-)  A      CA   CB    1.62    4.6
 366 VAL   ( 366-)  A      CA   CB    1.62    4.6
 376 THR   ( 376-)  A      CA   CB    1.62    4.6
 383 VAL   ( 383-)  A      CA   CB    1.67    6.8
 386 HIS   ( 386-)  A      CG   CD2   1.31   -4.3
 469 VAL   ( 469-)  A      CA   CB    1.65    6.0
 491 HIS   ( 491-)  A      CG   CD2   1.31   -4.2

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

 |  1.001206  0.001885 -0.000733|
 |  0.001885  0.999691 -0.000694|
 | -0.000733 -0.000694  1.002295|
Proposed new scale matrix

 |  0.017741 -0.000033  0.000013|
 | -0.000021  0.011394  0.000008|
 |  0.000007  0.000007  0.009649|
With corresponding cell

    A    =  56.368  B   =  87.769  C    = 103.639
    Alpha=  90.080  Beta=  90.084  Gamma=  89.784

The CRYST1 cell dimensions

    A    =  56.300  B   =  87.800  C    = 103.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 48.917
(Under-)estimated Z-score: 5.155

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.

   1 GLN   (   1-)  A      NE2  CD   OE1 118.60   -4.0
   2 TYR   (   2-)  A     -CA  -C    N   126.78    5.3
   7 GLN   (   7-)  A      CG   CD   NE2 122.48    4.1
   7 GLN   (   7-)  A      NE2  CD   OE1 116.51   -6.1
  10 ARG   (  10-)  A      CA   CB   CG  104.08   -5.0
  13 ILE   (  13-)  A      CB   CG1  CD1 105.07   -4.2
  14 VAL   (  14-)  A      N    CA   CB  118.68    4.8
  14 VAL   (  14-)  A      C    CA   CB  100.30   -5.2
  19 TRP   (  19-)  A      CD1  CG   CD2 113.70    4.6
  19 TRP   (  19-)  A      CG   CD2  CE2 101.56   -4.7
  20 ARG   (  20-)  A      CB   CG   CD  103.69   -5.2
  21 TRP   (  21-)  A      CB   CG   CD1 120.51   -4.3
  21 TRP   (  21-)  A      CE3  CD2  CG  139.44    5.5
  21 TRP   (  21-)  A      CG   CD2  CE2 101.83   -4.5
  22 VAL   (  22-)  A      CA   CB   CG1 103.58   -4.1
  25 ALA   (  25-)  A     -CA  -C    N   124.58    4.2
  41 GLN   (  41-)  A      CG   CD   NE2 124.50    5.4
  41 GLN   (  41-)  A      NE2  CD   OE1 116.54   -6.1
  48 ASN   (  48-)  A      CB   CG   ND2 122.43    4.0
  48 ASN   (  48-)  A      ND2  CG   OD1 116.66   -5.9
  53 ASN   (  53-)  A      CA   CB   CG  107.34   -5.3
  53 ASN   (  53-)  A      ND2  CG   OD1 118.33   -4.3
  54 PRO   (  54-)  A     -CA  -C    N   126.15    6.2
  58 TRP   (  58-)  A      CB   CG   CD1 120.02   -4.6
  58 TRP   (  58-)  A      CD1  CG   CD2 113.45    4.5
And so on for a total of 161 lines.

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.

 310 SER   ( 310-)  A    6.41
 318 ALA   ( 318-)  A    4.71
 162 LEU   ( 162-)  A    4.59
 163 VAL   ( 163-)  A    4.50
 439 THR   ( 439-)  A    4.37
 395 VAL   ( 395-)  A    4.21
 224 ALA   ( 224-)  A    4.11

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.

 376 THR   ( 376-)  A    -3.0
 163 VAL   ( 163-)  A    -2.2
 383 VAL   ( 383-)  A    -2.2
 417 VAL   ( 417-)  A    -2.2
  69 LEU   (  69-)  A    -2.2
 435 GLN   ( 435-)  A    -2.1
  56 ARG   (  56-)  A    -2.1
 440 LEU   ( 440-)  A    -2.1
 157 VAL   ( 157-)  A    -2.0
  13 ILE   (  13-)  A    -2.0
 237 LEU   ( 237-)  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.

   5 GLN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 100 ASN   ( 100-)  A  omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 124 ARG   ( 124-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 163 VAL   ( 163-)  A  Poor phi/psi
 268 LYS   ( 268-)  A  Poor phi/psi
 270 SER   ( 270-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 416 GLN   ( 416-)  A  omega poor
 486 PRO   ( 486-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.626

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.

 246 GLU   ( 246-)  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!

   5 GLN   (   5-)  A      0
   8 SER   (   8-)  A      0
  10 ARG   (  10-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  21 TRP   (  21-)  A      0
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  32 LEU   (  32-)  A      0
  48 ASN   (  48-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 SER   (  55-)  A      0
  56 ARG   (  56-)  A      0
  57 PRO   (  57-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
And so on for a total of 218 lines.

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.

 502 BGC   ( 993-)  A      O4  <->  503 DAF   ( 992-)  A      C1     0.98    1.42  INTRA B3
 502 BGC   ( 993-)  A      C4  <->  503 DAF   ( 992-)  A      C1     0.73    2.37  INTRA
 195 ARG   ( 195-)  A      NH1 <->  500  CL   ( 498-)  A     CL      0.24    2.86  INTRA BL
 215 HIS   ( 215-)  A      C   <->  227 ARG   ( 227-)  A      NH2    0.20    2.90  INTRA
   1 GLN   (   1-)  A      N   <->  504 HOH   ( 625 )  A      O      0.14    2.56  INTRA
   1 GLN   (   1-)  A      N   <->  228 PRO   ( 228-)  A      O      0.10    2.60  INTRA
 137 ASN   ( 137-)  A      ND2 <->  504 HOH   ( 556 )  A      O      0.07    2.63  INTRA BL
  11 THR   (  11-)  A      OG1 <->  399 ASN   ( 399-)  A      ND2    0.06    2.64  INTRA BL
 200 LYS   ( 200-)  A      NZ  <->  235 ILE   ( 235-)  A      O      0.05    2.65  INTRA BL
  15 HIS   (  15-)  A      ND1 <->  504 HOH   ( 521 )  A      O      0.03    2.67  INTRA BL
 195 ARG   ( 195-)  A      NH2 <->  197 ASP   ( 197-)  A      OD1    0.03    2.67  INTRA BL
 149 GLU   ( 149-)  A      N   <->  156 GLN   ( 156-)  A      OE1    0.03    2.67  INTRA BL
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      ND1    0.02    2.98  INTRA BL
  15 HIS   (  15-)  A      NE2 <->  504 HOH   ( 526 )  A      O      0.02    2.68  INTRA BL
 497 GLC   ( 990-)  A      C1  <->  498 GLC   ( 991-)  A      C4     0.02    2.28  INTRA BL
 201 HIS   ( 201-)  A      NE2 <->  503 DAF   ( 992-)  A      O2     0.02    2.68  INTRA
 170 LEU   ( 170-)  A      O   <->  176 ARG   ( 176-)  A      CD     0.01    2.79  INTRA BL

Packing, accessibility and threading

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.

  72 ARG   (  72-)  A      -6.99
   7 GLN   (   7-)  A      -5.53
 284 TRP   ( 284-)  A      -5.38
 118 TYR   ( 118-)  A      -5.34
  30 ARG   (  30-)  A      -5.33
 279 ASN   ( 279-)  A      -5.32
  88 ASN   (  88-)  A      -5.29
  53 ASN   (  53-)  A      -5.27
 302 GLN   ( 302-)  A      -5.25
 484 GLU   ( 484-)  A      -5.24
 303 ARG   ( 303-)  A      -5.21
 267 ARG   ( 267-)  A      -5.18

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 355 ASN   ( 355-)  A     -  358 ILE   ( 358-)  A        -1.59

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.

 504 HOH   ( 588 )  A      O      4.60   28.24   27.40
 504 HOH   ( 719 )  A      O      4.85   72.54   20.76
 504 HOH   ( 724 )  A      O     35.33   47.21   12.64
 504 HOH   ( 733 )  A      O     35.60   50.68    4.36
 504 HOH   ( 735 )  A      O     15.63   49.49   42.68
 504 HOH   ( 761 )  A      O     36.62   20.44   13.88
 504 HOH   ( 782 )  A      O     10.70   64.95   31.62
 504 HOH   ( 795 )  A      O     41.27   21.68   10.27
 504 HOH   ( 798 )  A      O     42.65   23.36   -1.48
 504 HOH   ( 815 )  A      O     45.68   25.37   17.96
 505 HOH   ( 877 )  A      O     32.70   18.55    5.09
 505 HOH   ( 915 )  A      O      2.19   58.84   35.07
 505 HOH   ( 928 )  A      O     34.30   46.96   15.47
 505 HOH   ( 933 )  A      O     44.39   42.92    3.34
 505 HOH   ( 941 )  A      O     48.35   35.50   13.60

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.

 504 HOH   ( 808 )  A      O
 505 HOH   ( 871 )  A      O
 505 HOH   ( 874 )  A      O
 505 HOH   ( 886 )  A      O
 505 HOH   ( 894 )  A      O
 505 HOH   ( 907 )  A      O
 505 HOH   ( 913 )  A      O
 505 HOH   ( 924 )  A      O
 505 HOH   ( 925 )  A      O
 505 HOH   ( 929 )  A      O
Marked this atom as acceptor  500  CL  ( 498-) A     CL
Strange metal coordination for HIS 201

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.

  75 ASN   (  75-)  A
 279 ASN   ( 279-)  A
 347 ASN   ( 347-)  A
 350 ASN   ( 350-)  A
 399 ASN   ( 399-)  A
 408 ASN   ( 408-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
  96 ASP   (  96-)  A      N
 101 HIS   ( 101-)  A      N
 138 ASP   ( 138-)  A      N
 193 GLY   ( 193-)  A      N
 195 ARG   ( 195-)  A      NH1
 251 GLY   ( 251-)  A      N
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 299 HIS   ( 299-)  A      NE2
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 344 TRP   ( 344-)  A      N
 357 TRP   ( 357-)  A      N
 370 VAL   ( 370-)  A      N
 384 CYS   ( 384-)  A      N
 434 TRP   ( 434-)  A      N
 462 CYS   ( 462-)  A      N
 485 ASP   ( 485-)  A      N
Only metal coordination for  100 ASN  ( 100-) A      OD1

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.

 201 HIS   ( 201-)  A      NE2
 300 ASP   ( 300-)  A      OD1
 435 GLN   ( 435-)  A      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual water packing

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

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

 504 HOH   ( 529 )  A      O  0.87  K  5
 504 HOH   ( 574 )  A      O  0.91  K  4
 504 HOH   ( 615 )  A      O  0.88  K  4
 504 HOH   ( 753 )  A      O  1.02  K  4 Ion-B
 504 HOH   ( 792 )  A      O  0.92  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.

 356 ASP   ( 356-)  A   H-bonding suggests Asn
 484 GLU   ( 484-)  A   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.949
  2nd generation packing quality :  -1.854
  Ramachandran plot appearance   :  -1.372
  chi-1/chi-2 rotamer normality  :  -2.626
  Backbone conformation          :  -1.170

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.863
  Bond angles                    :   1.573
  Omega angle restraints         :   0.871
  Side chain planarity           :   0.653 (tight)
  Improper dihedral distribution :   1.053
  Inside/Outside distribution    :   0.999

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.863
  Bond angles                    :   1.573
  Omega angle restraints         :   0.871
  Side chain planarity           :   0.653 (tight)
  Improper dihedral distribution :   1.053
  Inside/Outside distribution    :   0.999
==============

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.