WHAT IF Check report

This file was created 2012-01-12 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 pdb1rp9.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.

 410 DAF   (4000-)  A  -
 411 DAF   (2000-)  A  -
 418 DAF   (3000-)  A  -
 419 BGC   (4001-)  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.

 405 GLC   (4002-)  A  -   O4  bound to  419 BGC   (4001-)  A  -   C1
 406 GLC   (2001-)  A  -   O4  bound to  411 DAF   (2000-)  A  -   C1
 407 GLC   (2002-)  A  -   O4  bound to  406 GLC   (2001-)  A  -   C1
 408 GLC   (3001-)  A  -   O4  bound to  418 DAF   (3000-)  A  -   C1
 409 GLC   (3002-)  A  -   O4  bound to  408 GLC   (3001-)  A  -   C1

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 404 LYS   ( 404-)  A      CB
 404 LYS   ( 404-)  A      CG
 404 LYS   ( 404-)  A      CD
 404 LYS   ( 404-)  A      CE
 404 LYS   ( 404-)  A      NZ

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) :100.000

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

 |  0.996156 -0.000006  0.001111|
 | -0.000006  0.996329 -0.000571|
 |  0.001111 -0.000571  0.997804|
Proposed new scale matrix

 |  0.010710  0.000000 -0.000012|
 |  0.000000  0.013648  0.000008|
 | -0.000018  0.000009  0.016413|
With corresponding cell

    A    =  93.369  B   =  73.270  C    =  60.927
    Alpha=  90.066  Beta=  89.872  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  93.730  B   =  73.540  C    =  61.060
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 150.197
(Under-)estimated Z-score: 9.032

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.

 178 ARG   ( 178-)  A      N    CA   C    99.57   -4.2

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.

 265 LEU   ( 265-)  A    5.30
 178 ARG   ( 178-)  A    4.56
 308 GLN   ( 308-)  A    4.22
 303 SER   ( 303-)  A    4.18

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.530

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.

 181 PHE   ( 181-)  A    -2.8
 201 LEU   ( 201-)  A    -2.5
 299 TRP   ( 299-)  A    -2.4
 294 SER   ( 294-)  A    -2.3
 279 TRP   ( 279-)  A    -2.2
  55 GLY   (  55-)  A    -2.1
 236 VAL   ( 236-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

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

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

   8 PHE   (   8-)  A  Poor phi/psi
 114 ASP   ( 114-)  A  Poor phi/psi
 117 LEU   ( 117-)  A  Poor phi/psi
 131 TYR   ( 131-)  A  Poor phi/psi
 237 GLY   ( 237-)  A  Poor phi/psi
 259 GLU   ( 259-)  A  Poor phi/psi
 294 SER   ( 294-)  A  Poor phi/psi
 361 GLY   ( 361-)  A  Poor phi/psi
 393 SER   ( 393-)  A  Poor phi/psi
 398 ASP   ( 398-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.854

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.

  73 SER   (  73-)  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!

   8 PHE   (   8-)  A      0
  16 SER   (  16-)  A      0
  19 TRP   (  19-)  A      0
  43 PRO   (  43-)  A      0
  45 HIS   (  45-)  A      0
  47 VAL   (  47-)  A      0
  48 SER   (  48-)  A      0
  49 ASN   (  49-)  A      0
  50 GLU   (  50-)  A      0
  52 TYR   (  52-)  A      0
  53 MET   (  53-)  A      0
  54 PRO   (  54-)  A      0
  56 ARG   (  56-)  A      0
  60 ILE   (  60-)  A      0
  65 TYR   (  65-)  A      0
  81 LYS   (  81-)  A      0
  90 VAL   (  90-)  A      0
  91 ILE   (  91-)  A      0
  92 ASN   (  92-)  A      0
 102 ARG   ( 102-)  A      0
 105 TYR   ( 105-)  A      0
 106 CYS   ( 106-)  A      0
 114 ASP   ( 114-)  A      0
 116 ARG   ( 116-)  A      0
 117 LEU   ( 117-)  A      0
And so on for a total of 170 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 : 2.046

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!

 361 GLY   ( 361-)  A   1.69   14

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]

  42 PRO   (  42-)  A    0.46 HIGH

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].

 187 PRO   ( 187-)  A  -130.7 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 405 GLC   (4002-)  A      O4  <->  419 BGC   (4001-)  A      C1     1.02    1.38  INTRA B3
 408 GLC   (3001-)  A      O4  <->  418 DAF   (3000-)  A      C1     1.00    1.40  INTRA B3
 405 GLC   (4002-)  A      C4  <->  419 BGC   (4001-)  A      C1     0.83    2.37  INTRA BF
 408 GLC   (3001-)  A      C4  <->  418 DAF   (3000-)  A      C1     0.76    2.44  INTRA
  22 MET   (  22-)  A      SD  <->   26 LYS   (  26-)  A      NZ     0.22    3.08  INTRA
 100 ASP   ( 100-)  A      OD2 <->  102 ARG   ( 102-)  A      NE     0.21    2.49  INTRA
 310 TYR   ( 310-)  A      OH  <->  326 HIS   ( 326-)  A      ND1    0.19    2.51  INTRA BL
  14 LYS   (  14-)  A      NZ  <->  420 HOH   ( 670 )  A      O      0.18    2.52  INTRA
 102 ARG   ( 102-)  A      NH2 <->  106 CYS   ( 106-)  A      SG     0.17    3.13  INTRA
  36 THR   (  36-)  A      OG1 <->   37 HIS   (  37-)  A      ND1    0.16    2.54  INTRA BL
   1 HIS   (   1-)  A      N   <->  420 HOH   ( 870 )  A      O      0.13    2.57  INTRA
 130 LYS   ( 130-)  A      NZ  <->  420 HOH   ( 896 )  A      O      0.13    2.57  INTRA BF
 209 ASN   ( 209-)  A      N   <->  420 HOH   ( 663 )  A      O      0.13    2.57  INTRA
 215 ASP   ( 215-)  A      OD1 <->  217 LYS   ( 217-)  A      N      0.12    2.58  INTRA
 143 ASP   ( 143-)  A      CG  <->  144 PHE   ( 144-)  A      N      0.10    2.90  INTRA
 269 GLN   ( 269-)  A      NE2 <->  420 HOH   ( 921 )  A      O      0.10    2.60  INTRA
 109 GLU   ( 109-)  A      OE2 <->  111 GLY   ( 111-)  A      N      0.09    2.61  INTRA
  79 HIS   (  79-)  A      NE2 <->  175 ASP   ( 175-)  A      OD2    0.08    2.62  INTRA BL
 251 LYS   ( 251-)  A      NZ  <->  287 VAL   ( 287-)  A      O      0.08    2.62  INTRA BL
  84 GLN   (  84-)  A      NE2 <->  200 SER   ( 200-)  A      OG     0.06    2.64  INTRA BL
 267 ASP   ( 267-)  A      OD1 <->  269 GLN   ( 269-)  A      N      0.05    2.65  INTRA BL
 152 HIS   ( 152-)  A      O   <->  158 GLN   ( 158-)  A      NE2    0.04    2.66  INTRA BL
 342 ILE   ( 342-)  A      O   <->  346 ASN   ( 346-)  A      ND2    0.04    2.66  INTRA
   9 ASN   (   9-)  A      OD1 <->   11 GLU   (  11-)  A      N      0.03    2.67  INTRA BL
 251 LYS   ( 251-)  A      NZ  <->  288 ASP   ( 288-)  A      OD1    0.03    2.67  INTRA BL
 359 HIS   ( 359-)  A      CE1 <->  420 HOH   (1571 )  A      O      0.03    2.77  INTRA
 345 ARG   ( 345-)  A      NH2 <->  403 GLU   ( 403-)  A      OE2    0.03    2.67  INTRA
   2 GLN   (   2-)  A      OE1 <->  420 HOH   ( 945 )  A      O      0.02    2.38  INTRA
 116 ARG   ( 116-)  A      NH1 <->  420 HOH   (1021 )  A      O      0.02    2.68  INTRA
 299 TRP   ( 299-)  A      N   <->  300 PRO   ( 300-)  A      CD     0.02    2.98  INTRA BL
 225 HIS   ( 225-)  A      ND1 <->  249 THR   ( 249-)  A      OG1    0.02    2.68  INTRA
 167 TRP   ( 167-)  A      O   <->  171 ASP   ( 171-)  A      N      0.02    2.68  INTRA
 325 ASP   ( 325-)  A      O   <->  329 ASN   ( 329-)  A      N      0.02    2.68  INTRA
 375 LYS   ( 375-)  A      NZ  <->  379 ARG   ( 379-)  A      O      0.01    2.69  INTRA BL
 370 GLY   ( 370-)  A      N   <->  420 HOH   ( 815 )  A      O      0.01    2.69  INTRA
  56 ARG   (  56-)  A      NH1 <->   97 ASP   (  97-)  A      OD2    0.01    2.69  INTRA
 357 LEU   ( 357-)  A      N   <->  365 VAL   ( 365-)  A      O      0.01    2.69  INTRA BL
  53 MET   (  53-)  A      N   <->   54 PRO   (  54-)  A      CD     0.01    2.99  INTRA BL
 133 ASP   ( 133-)  A      N   <->  134 GLY   ( 134-)  A      N      0.01    2.59  INTRA B3

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.

 380 TYR   ( 380-)  A      -7.14
 345 ARG   ( 345-)  A      -5.55
 269 GLN   ( 269-)  A      -5.55
  52 TYR   (  52-)  A      -5.03
 395 HIS   ( 395-)  A      -5.01

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.

 404 LYS   ( 404-)  A   -2.62
 102 ARG   ( 102-)  A   -2.58

Water, ion, and hydrogenbond related checks

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.

   6 GLN   (   6-)  A
 359 HIS   ( 359-)  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.

   6 GLN   (   6-)  A      NE2
   8 PHE   (   8-)  A      N
  12 SER   (  12-)  A      OG
  84 GLN   (  84-)  A      NE2
  93 HIS   (  93-)  A      N
  94 ARG   (  94-)  A      NH1
  97 ASP   (  97-)  A      N
 114 ASP   ( 114-)  A      N
 178 ARG   ( 178-)  A      NE
 178 ARG   ( 178-)  A      NH1
 193 TYR   ( 193-)  A      OH
 200 SER   ( 200-)  A      OG
 201 LEU   ( 201-)  A      N
 263 TRP   ( 263-)  A      N
 266 ILE   ( 266-)  A      N
 332 PHE   ( 332-)  A      N
 382 VAL   ( 382-)  A      N
 402 TRP   ( 402-)  A      NE1
Only metal coordination for   92 ASN  (  92-) A      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 414  CA   ( 500-)  A     0.85   1.09 Scores about as good as NA
 415  CA   ( 501-)  A     0.65   0.89 Scores about as good as NA
 416  CA   ( 502-)  A     0.81   1.04 Scores about as good as NA

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.

 420 HOH   ( 700 )  A      O  0.92  K  4
 420 HOH   ( 825 )  A      O  1.00  K  4 Ion-B
 420 HOH   ( 904 )  A      O  0.95  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.

 100 ASP   ( 100-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 ASP   ( 291-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.462
  2nd generation packing quality :  -1.803
  Ramachandran plot appearance   :  -1.438
  chi-1/chi-2 rotamer normality  :  -0.854
  Backbone conformation          :  -0.775

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.750
  Omega angle restraints         :   0.372 (tight)
  Side chain planarity           :   0.400 (tight)
  Improper dihedral distribution :   0.739
  B-factor distribution          :   0.785
  Inside/Outside distribution    :   0.968

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.750
  Omega angle restraints         :   0.372 (tight)
  Side chain planarity           :   0.400 (tight)
  Improper dihedral distribution :   0.739
  B-factor distribution          :   0.785
  Inside/Outside distribution    :   0.968
==============

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.