WHAT IF Check report

This file was created 2012-01-29 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 pdb3blk.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.

 500 AGL   ( 502-)  A  -
 504 HMC   ( 504-)  A  -
 505 AGL   ( 505-)  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.

 497 GLC   ( 503-)  A  -   O4  bound to  500 AGL   ( 502-)  A  -   C1
 498 GLC   ( 506-)  A  -   O4  bound to  505 AGL   ( 505-)  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: 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: 0

Crystal temperature (K) : 77.000

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

  94 TYR   (  94-)  A
 333 TYR   ( 333-)  A

Warning: Phenylalanine convention problem

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

 327 PHE   ( 327-)  A
 348 PHE   ( 348-)  A
 419 PHE   ( 419-)  A
 429 PHE   ( 429-)  A
 477 PHE   ( 477-)  A

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.

 125 ASP   ( 125-)  A
 147 ASP   ( 147-)  A
 471 ASP   ( 471-)  A

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.

 484 GLU   ( 484-)  A

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

 |  0.993035 -0.000600 -0.000779|
 | -0.000600  0.990253 -0.000244|
 | -0.000779 -0.000244  0.997290|
Proposed new scale matrix

 |  0.019261  0.000012  0.000015|
 |  0.000008  0.013456  0.000003|
 |  0.000006  0.000002  0.007427|
With corresponding cell

    A    =  51.918  B   =  74.315  C    = 134.642
    Alpha=  90.028  Beta=  90.090  Gamma=  90.069

The CRYST1 cell dimensions

    A    =  52.282  B   =  75.046  C    = 135.013
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 773.647
(Under-)estimated Z-score: 20.499

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.

 101 HIS   ( 101-)  A      CG   ND1  CE1 109.61    4.0
 305 HIS   ( 305-)  A      CG   ND1  CE1 109.68    4.1
 346 ARG   ( 346-)  A      CG   CD   NE  117.60    4.2

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.

 125 ASP   ( 125-)  A
 147 ASP   ( 147-)  A
 471 ASP   ( 471-)  A
 484 GLU   ( 484-)  A

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 101 HIS   ( 101-)  A    4.32

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
 124 ARG   ( 124-)  A    -2.9
 486 PRO   ( 486-)  A    -2.7
 350 ASN   ( 350-)  A    -2.6
 240 GLU   ( 240-)  A    -2.3
  45 PRO   (  45-)  A    -2.2
  13 ILE   (  13-)  A    -2.2
 163 SER   ( 163-)  A    -2.2
 458 ILE   ( 458-)  A    -2.1
 196 ILE   ( 196-)  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 ASN   (   5-)  A  Poor phi/psi
  10 ARG   (  10-)  A  omega poor
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
  54 PRO   (  54-)  A  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
 149 GLU   ( 149-)  A  omega poor
 163 SER   ( 163-)  A  Poor phi/psi
 190 GLY   ( 190-)  A  Poor phi/psi
 193 GLY   ( 193-)  A  omega poor
 194 PHE   ( 194-)  A  omega poor
 215 HIS   ( 215-)  A  omega poor
 268 LYS   ( 268-)  A  Poor phi/psi
 270 ASN   ( 270-)  A  Poor phi/psi
 292 ALA   ( 292-)  A  omega poor
 317 ASP   ( 317-)  A  omega poor
 333 TYR   ( 333-)  A  omega poor
 340 SER   ( 340-)  A  omega poor
 345 PRO   ( 345-)  A  Poor phi/psi
 349 GLU   ( 349-)  A  omega poor
 350 ASN   ( 350-)  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
 410 TYR   ( 410-)  A  omega poor
 414 SER   ( 414-)  A  Poor phi/psi
 454 SER   ( 454-)  A  omega poor
 459 ASN   ( 459-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.853

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 ASN   (   5-)  A      0
   8 GLN   (   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
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  32 LEU   (  32-)  A      0
  37 PHE   (  37-)  A      0
  52 HIS   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 PHE   (  55-)  A      0
  56 ARG   (  56-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  66 SER   (  66-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
And so on for a total of 222 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!

 144 GLY   ( 144-)  A   1.77   13

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].

  45 PRO   (  45-)  A   -44.2 envelop C-alpha (-36 degrees)
 228 PRO   ( 228-)  A  -117.3 half-chair C-delta/C-gamma (-126 degrees)
 486 PRO   ( 486-)  A   -62.0 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 504 HMC   ( 504-)  A      C1  <->  505 AGL   ( 505-)  A      N4     1.37    1.33  INTRA BL
 498 GLC   ( 506-)  A      O4  <->  505 AGL   ( 505-)  A      C1     0.95    1.45  INTRA B3
 498 GLC   ( 506-)  A      C4  <->  505 AGL   ( 505-)  A      C1     0.76    2.44  INTRA
 504 HMC   ( 504-)  A      C6  <->  505 AGL   ( 505-)  A      N4     0.59    2.51  INTRA BL
 504 HMC   ( 504-)  A      C2  <->  505 AGL   ( 505-)  A      N4     0.49    2.61  INTRA BL
  27 GLU   (  27-)  A      OE2 <->  386 HIS   ( 386-)  A      NE2    0.22    2.48  INTRA
 170 LEU   ( 170-)  A      CD1 <->  202 MET   ( 202-)  A      SD     0.20    3.20  INTRA
 504 HMC   ( 504-)  A      C6  <->  505 AGL   ( 505-)  A      C4     0.18    3.02  INTRA BL
 149 GLU   ( 149-)  A      N   <->  156 GLN   ( 156-)  A      OE1    0.14    2.56  INTRA
 390 GLN   ( 390-)  A      NE2 <->  485 ASP   ( 485-)  A      OD2    0.09    2.61  INTRA
  11 THR   (  11-)  A      OG1 <->  399 ASN   ( 399-)  A      ND2    0.08    2.62  INTRA
 338 VAL   ( 338-)  A      CG1 <->  506 HOH   ( 665 )  A      O      0.07    2.73  INTRA BF
 337 ARG   ( 337-)  A      NH2 <->  502  CL   ( 498-)  A     CL      0.07    3.03  INTRA
 431 ASN   ( 431-)  A      ND2 <->  506 HOH   ( 581 )  A      O      0.07    2.63  INTRA
 147 ASP   ( 147-)  A      OD1 <->  161 ARG   ( 161-)  A      NH1    0.07    2.63  INTRA BF
  92 ARG   (  92-)  A      NH1 <->  506 HOH   ( 678 )  A      O      0.06    2.64  INTRA BF
  56 ARG   (  56-)  A      N   <->   57 PRO   (  57-)  A      CD     0.05    2.95  INTRA BL
 307 ALA   ( 307-)  A      N   <->  506 HOH   ( 694 )  A      O      0.04    2.66  INTRA BF
 496 LEU   ( 496-)  A      O   <->  506 HOH   ( 583 )  A      O      0.03    2.37  INTRA BF
 201 HIS   ( 201-)  A      NE2 <->  505 AGL   ( 505-)  A      O2     0.03    2.67  INTRA BL
  15 HIS   (  15-)  A      ND1 <->  506 HOH   ( 582 )  A      O      0.02    2.68  INTRA
 470 SER   ( 470-)  A      OG  <->  472 ASP   ( 472-)  A      OD1    0.02    2.38  INTRA BF
 142 LYS   ( 142-)  A      CE  <->  506 HOH   ( 609 )  A      O      0.02    2.78  INTRA BF
 158 ARG   ( 158-)  A      NH2 <->  506 HOH   ( 692 )  A      O      0.02    2.68  INTRA
 258 TYR   ( 258-)  A      CE2 <->  280 TRP   ( 280-)  A      NE1    0.02    3.08  INTRA BL
 446 ALA   ( 446-)  A      N   <->  506 HOH   ( 671 )  A      O      0.01    2.69  INTRA BF
 103 CYS   ( 103-)  A      SG  <->  121 PRO   ( 121-)  A      CG     0.01    3.39  INTRA
  80 ARG   (  80-)  A      NH1 <->  506 HOH   ( 610 )  A      O      0.01    2.69  INTRA

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      -7.41
 343 ARG   ( 343-)  A      -6.60
 142 LYS   ( 142-)  A      -6.26
   8 GLN   (   8-)  A      -6.26
 118 TYR   ( 118-)  A      -5.74
   2 TYR   (   2-)  A      -5.59
   7 GLN   (   7-)  A      -5.47
 284 TRP   ( 284-)  A      -5.38
 279 ASN   ( 279-)  A      -5.34
  53 ASN   (  53-)  A      -5.33
 303 ARG   ( 303-)  A      -5.27
  30 ARG   (  30-)  A      -5.26
 302 GLN   ( 302-)  A      -5.26
 267 ARG   ( 267-)  A      -5.16

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 506 HOH   ( 683 )  A      O
Marked this atom as acceptor  502  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.

 305 HIS   ( 305-)  A
 399 ASN   ( 399-)  A
 441 GLN   ( 441-)  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.

   8 GLN   (   8-)  A      N
  43 SER   (  43-)  A      OG
  46 ASN   (  46-)  A      ND2
  53 ASN   (  53-)  A      N
  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 175 VAL   ( 175-)  A      N
 193 GLY   ( 193-)  A      N
 195 ARG   ( 195-)  A      NH2
 242 ILE   ( 242-)  A      N
 269 TRP   ( 269-)  A      NE1
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 299 HIS   ( 299-)  A      NE2
 300 ASP   ( 300-)  A      N
 337 ARG   ( 337-)  A      NH2
 357 TRP   ( 357-)  A      N
 390 GLN   ( 390-)  A      NE2
 416 GLN   ( 416-)  A      NE2
 421 ARG   ( 421-)  A      NH1
 434 TRP   ( 434-)  A      N
 454 SER   ( 454-)  A      N
 495 LYS   ( 495-)  A      N

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.

 212 ASP   ( 212-)  A      OD1
 240 GLU   ( 240-)  A      OE2

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+.

 501  CA   ( 497-)  A     0.81   1.05 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.

 506 HOH   ( 588 )  A      O  0.98  K  5

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.

 188 ASP   ( 188-)  A   H-bonding suggests Asn; but Alt-Rotamer
 240 GLU   ( 240-)  A   H-bonding suggests Gln; 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 :  -1.140
  2nd generation packing quality :  -1.535
  Ramachandran plot appearance   :  -1.029
  chi-1/chi-2 rotamer normality  :  -1.853
  Backbone conformation          :  -0.930

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.864
  Bond angles                    :   0.817
  Omega angle restraints         :   1.181
  Side chain planarity           :   0.966
  Improper dihedral distribution :   0.929
  B-factor distribution          :   0.480
  Inside/Outside distribution    :   1.004

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 :  -0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.864
  Bond angles                    :   0.817
  Omega angle restraints         :   1.181
  Side chain planarity           :   0.966
  Improper dihedral distribution :   0.929
  B-factor distribution          :   0.480
  Inside/Outside distribution    :   1.004
==============

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.