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 pdb1q4n.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 TAM   ( 900-)  X  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: X

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: X

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

 468 TYR   ( 468-)  X

Warning: Phenylalanine convention problem

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

 419 PHE   ( 419-)  X

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.

 471 ASP   ( 471-)  X

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-)  X

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

 |  0.998147 -0.000480 -0.000867|
 | -0.000480  0.997803 -0.000593|
 | -0.000867 -0.000593  0.997387|
Proposed new scale matrix

 |  0.019303  0.000009  0.000017|
 |  0.000006  0.013507  0.000008|
 |  0.000006  0.000004  0.007436|
With corresponding cell

    A    =  51.806  B   =  74.037  C    = 134.473
    Alpha=  90.068  Beta=  90.100  Gamma=  90.055

The CRYST1 cell dimensions

    A    =  51.900  B   =  74.200  C    = 134.820
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 89.594
(Under-)estimated Z-score: 6.976

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.

  99 ILE   (  99-)  X      N    CA   CB  103.17   -4.3
  99 ILE   (  99-)  X      C    CA   CB  117.71    4.0
  99 ILE   (  99-)  X      CA   CB   CG2 120.35    5.8
 101 HIS   ( 101-)  X      CG   ND1  CE1 109.81    4.2
 303 ARG   ( 303-)  X      CG   CD   NE  118.18    4.5
 407 THR   ( 407-)  X      CG2  CB   OG1 101.21   -4.0

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 471 ASP   ( 471-)  X
 484 GLU   ( 484-)  X

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  99 ILE   (  99-)  X      CB    -7.3    22.84    32.31
The average deviation= 1.069

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-)  X    -3.1
  99 ILE   (  99-)  X    -2.6
 486 PRO   ( 486-)  X    -2.4
 124 ARG   ( 124-)  X    -2.4
 243 LYS   ( 243-)  X    -2.3
 163 SER   ( 163-)  X    -2.2
 273 LYS   ( 273-)  X    -2.2
  56 ARG   (  56-)  X    -2.2
 422 GLY   ( 422-)  X    -2.1
  45 PRO   (  45-)  X    -2.1
 461 ASN   ( 461-)  X    -2.1
 452 VAL   ( 452-)  X    -2.1
 306 GLY   ( 306-)  X    -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-)  X  Poor phi/psi
  10 ARG   (  10-)  X  omega poor
  18 GLU   (  18-)  X  Poor phi/psi
  53 ASN   (  53-)  X  PRO omega poor
  69 LEU   (  69-)  X  omega poor
  98 VAL   (  98-)  X  omega poor
  99 ILE   (  99-)  X  Poor phi/psi
 100 ASN   ( 100-)  X  omega poor
 102 MET   ( 102-)  X  Poor phi/psi
 124 ARG   ( 124-)  X  Poor phi/psi
 129 VAL   ( 129-)  X  PRO omega poor
 194 PHE   ( 194-)  X  omega poor
 198 ALA   ( 198-)  X  Poor phi/psi
 215 HIS   ( 215-)  X  omega poor
 270 ASN   ( 270-)  X  Poor phi/psi
 295 PHE   ( 295-)  X  Poor phi/psi
 306 GLY   ( 306-)  X  Poor phi/psi
 340 SER   ( 340-)  X  omega poor
 345 PRO   ( 345-)  X  Poor phi/psi
 349 GLU   ( 349-)  X  omega poor
 350 ASN   ( 350-)  X  Poor phi/psi
 376 THR   ( 376-)  X  Poor phi/psi, omega poor
 380 ASN   ( 380-)  X  Poor phi/psi
 381 ASP   ( 381-)  X  Poor phi/psi
 405 PRO   ( 405-)  X  omega poor
 414 SER   ( 414-)  X  Poor phi/psi
 422 GLY   ( 422-)  X  Poor phi/psi
 437 SER   ( 437-)  X  omega poor
 450 CYS   ( 450-)  X  omega poor
 456 ASP   ( 456-)  X  omega poor
 459 ASN   ( 459-)  X  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.039

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-)  X      0
   8 GLN   (   8-)  X      0
  12 SER   (  12-)  X      0
  17 PHE   (  17-)  X      0
  18 GLU   (  18-)  X      0
  19 TRP   (  19-)  X      0
  30 ARG   (  30-)  X      0
  31 TYR   (  31-)  X      0
  32 LEU   (  32-)  X      0
  37 PHE   (  37-)  X      0
  52 HIS   (  52-)  X      0
  53 ASN   (  53-)  X      0
  54 PRO   (  54-)  X      0
  55 PHE   (  55-)  X      0
  56 ARG   (  56-)  X      0
  62 TYR   (  62-)  X      0
  63 GLN   (  63-)  X      0
  64 PRO   (  64-)  X      0
  66 SER   (  66-)  X      0
  67 TYR   (  67-)  X      0
  69 LEU   (  69-)  X      0
  70 CYS   (  70-)  X      0
  73 SER   (  73-)  X      0
  75 ASN   (  75-)  X      0
  89 VAL   (  89-)  X      0
And so on for a total of 223 lines.

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].

 228 PRO   ( 228-)  X  -117.2 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.

 290 ASP   ( 290-)  X      OD2 <->  501 HOH   ( 724 )  X      O      0.34    2.06  INTRA
 500 TAM   ( 900-)  X      N   <->  501 HOH   ( 697 )  X      O      0.25    2.45  INTRA
  11 THR   (  11-)  X      OG1 <->  399 ASN   ( 399-)  X      ND2    0.24    2.46  INTRA BL
 140 LYS   ( 140-)  X      NZ  <->  501 HOH   ( 816 )  X      O      0.23    2.47  INTRA BF
  99 ILE   (  99-)  X      CG1 <->  179 ILE   ( 179-)  X      CG2    0.17    3.03  INTRA
 256 TRP   ( 256-)  X      CH2 <->  298 ASN   ( 298-)  X      ND2    0.16    2.94  INTRA
 461 ASN   ( 461-)  X      ND2 <->  466 LYS   ( 466-)  X      NZ     0.15    2.70  INTRA
 213 LYS   ( 213-)  X      NZ  <->  501 HOH   ( 688 )  X      O      0.15    2.55  INTRA
 101 HIS   ( 101-)  X      CE1 <->  500 TAM   ( 900-)  X      C6     0.11    3.09  INTRA
  30 ARG   (  30-)  X      CZ  <->  372 ILE   ( 372-)  X      CD1    0.11    3.09  INTRA
  35 LYS   (  35-)  X      NZ  <->  501 HOH   ( 667 )  X      O      0.11    2.59  INTRA
 170 LEU   ( 170-)  X      CD1 <->  202 MET   ( 202-)  X      SD     0.10    3.30  INTRA
 461 ASN   ( 461-)  X      ND2 <->  462 CYS   ( 462-)  X      N      0.10    2.65  INTRA
 103 CYS   ( 103-)  X      SG  <->  121 PRO   ( 121-)  X      CG     0.07    3.33  INTRA
 322 LYS   ( 322-)  X      NZ  <->  485 ASP   ( 485-)  X      OD1    0.05    2.65  INTRA BL
 352 LYS   ( 352-)  X      NZ  <->  356 ASP   ( 356-)  X      OD2    0.05    2.65  INTRA BF
 240 GLU   ( 240-)  X      OE2 <->  501 HOH   ( 623 )  X      O      0.05    2.35  INTRA
 390 GLN   ( 390-)  X      NE2 <->  485 ASP   ( 485-)  X      OD2    0.04    2.66  INTRA BL
 201 HIS   ( 201-)  X      NE2 <->  501 HOH   ( 673 )  X      O      0.04    2.66  INTRA
 501 HOH   ( 631 )  X      O   <->  501 HOH   ( 696 )  X      O      0.04    2.16  INTRA
 200 LYS   ( 200-)  X      NZ  <->  501 HOH   ( 570 )  X      O      0.04    2.66  INTRA
  52 HIS   (  52-)  X      O   <->  501 HOH   ( 665 )  X      O      0.04    2.36  INTRA
  40 VAL   (  40-)  X      O   <->   94 TYR   (  94-)  X      N      0.03    2.67  INTRA BL
 153 ASP   ( 153-)  X      OD2 <->  156 GLN   ( 156-)  X      NE2    0.03    2.67  INTRA
  27 GLU   (  27-)  X      OE2 <->  386 HIS   ( 386-)  X      NE2    0.02    2.68  INTRA BL
 278 LYS   ( 278-)  X      NZ  <->  501 HOH   ( 598 )  X      O      0.02    2.68  INTRA
 501 HOH   ( 696 )  X      O   <->  501 HOH   ( 748 )  X      O      0.02    2.18  INTRA
  27 GLU   (  27-)  X      OE2 <->  387 ARG   ( 387-)  X      NE     0.01    2.69  INTRA BL
  95 VAL   (  95-)  X      CG1 <->   96 ASP   (  96-)  X      N      0.01    2.99  INTRA BL
  76 GLU   (  76-)  X      OE1 <->  501 HOH   ( 539 )  X      O      0.01    2.39  INTRA
 178 LYS   ( 178-)  X      NZ  <->  181 GLU   ( 181-)  X      OE1    0.01    2.69  INTRA
 492 ALA   ( 492-)  X      O   <->  501 HOH   ( 763 )  X      O      0.01    2.39  INTRA
 200 LYS   ( 200-)  X      NZ  <->  240 GLU   ( 240-)  X      OE1    0.01    2.69  INTRA
 485 ASP   ( 485-)  X      OD2 <->  501 HOH   ( 639 )  X      O      0.01    2.39  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: X

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-)  X      -7.35
 142 LYS   ( 142-)  X      -6.28
   8 GLN   (   8-)  X      -6.27
 118 TYR   ( 118-)  X      -5.63
   2 TYR   (   2-)  X      -5.41
 284 TRP   ( 284-)  X      -5.38
 343 ARG   ( 343-)  X      -5.38
 279 ASN   ( 279-)  X      -5.31
  30 ARG   (  30-)  X      -5.28
  88 ASN   (  88-)  X      -5.28
 302 GLN   ( 302-)  X      -5.21
 303 ARG   ( 303-)  X      -5.19
  53 ASN   (  53-)  X      -5.15
   7 GLN   (   7-)  X      -5.13
 224 GLU   ( 224-)  X      -5.08
  55 PHE   (  55-)  X      -5.08

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: X

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: X

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.

 501 HOH   ( 516 )  X      O     16.65   40.84    2.58
 501 HOH   ( 630 )  X      O     -8.65   54.73   33.28
 501 HOH   ( 767 )  X      O     -6.24   34.29   30.19

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.

 501 HOH   ( 785 )  X      O
 501 HOH   ( 797 )  X      O
 501 HOH   ( 802 )  X      O
Marked this atom as acceptor  499  CL  ( 951-) X     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.

 105 ASN   ( 105-)  X
 396 ASN   ( 396-)  X
 399 ASN   ( 399-)  X
 461 ASN   ( 461-)  X

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-)  X      N
  87 ASN   (  87-)  X      ND2
 101 HIS   ( 101-)  X      N
 138 ASP   ( 138-)  X      N
 164 GLY   ( 164-)  X      N
 193 GLY   ( 193-)  X      N
 242 ILE   ( 242-)  X      N
 269 TRP   ( 269-)  X      NE1
 273 LYS   ( 273-)  X      N
 281 GLY   ( 281-)  X      N
 295 PHE   ( 295-)  X      N
 298 ASN   ( 298-)  X      ND2
 300 ASP   ( 300-)  X      N
 307 ALA   ( 307-)  X      N
 314 THR   ( 314-)  X      N
 316 TRP   ( 316-)  X      NE1
 337 ARG   ( 337-)  X      NH2
 344 TRP   ( 344-)  X      N
 355 ASN   ( 355-)  X      ND2
 370 VAL   ( 370-)  X      N
 416 GLN   ( 416-)  X      NE2
 434 TRP   ( 434-)  X      N
 471 ASP   ( 471-)  X      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.

 147 ASP   ( 147-)  X      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+.

 498  CA   ( 950-)  X     0.73   0.97 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.

 501 HOH   ( 542 )  X      O  1.04  K  4
 501 HOH   ( 547 )  X      O  0.96  K  6
 501 HOH   ( 590 )  X      O  0.97  K  4
 501 HOH   ( 595 )  X      O  1.14  K  4
 501 HOH   ( 662 )  X      O  0.86  K  6 Ion-B
 501 HOH   ( 680 )  X      O  0.92  K  4 Ion-B
 501 HOH   ( 786 )  X      O  0.88  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.

 188 ASP   ( 188-)  X   H-bonding suggests Asn; but Alt-Rotamer
 212 ASP   ( 212-)  X   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 :  -0.841
  2nd generation packing quality :  -1.610
  Ramachandran plot appearance   :  -1.281
  chi-1/chi-2 rotamer normality  :  -2.039
  Backbone conformation          :  -1.121

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.701
  Bond angles                    :   0.820
  Omega angle restraints         :   1.254
  Side chain planarity           :   0.896
  Improper dihedral distribution :   0.898
  B-factor distribution          :   0.493
  Inside/Outside distribution    :   1.009

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 : 2.07


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.1
  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                   :   0.701
  Bond angles                    :   0.820
  Omega angle restraints         :   1.254
  Side chain planarity           :   0.896
  Improper dihedral distribution :   0.898
  B-factor distribution          :   0.493
  Inside/Outside distribution    :   1.009
==============

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.