WHAT IF Check report

This file was created 2011-12-18 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 pdb2ya5.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.615
CA-only RMS fit for the two chains : 0.310

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

 943 SIA   (1778-)  A  -
 951 SIA   (1777-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 293 LYS   ( 599-)  A    0.10
 764 LYS   ( 599-)  B    0.10

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: A

Note: B-factor plot

Chain identifier: B

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

 |  0.997392 -0.000796 -0.000508|
 | -0.000796  0.996595 -0.000770|
 | -0.000508 -0.000770  0.997279|
Proposed new scale matrix

 |  0.006068  0.000006  0.001610|
 |  0.000016  0.020373  0.000016|
 |  0.000004  0.000006  0.008282|
With corresponding cell

    A    = 164.831  B   =  49.084  C    = 124.948
    Alpha=  90.062  Beta= 104.894  Gamma=  90.091

The CRYST1 cell dimensions

    A    = 165.272  B   =  49.251  C    = 125.255
    Alpha=  90.000  Beta= 104.840  Gamma=  90.000

Variance: 280.406
(Under-)estimated Z-score: 12.341

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.

 276 HIS   ( 582-)  A      CG   ND1  CE1 109.61    4.0

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.

 747 HIS   ( 582-)  B    -2.8
 845 TYR   ( 680-)  B    -2.7
 276 HIS   ( 582-)  A    -2.7
 498 ILE   ( 333-)  B    -2.7
  27 ILE   ( 333-)  A    -2.7
 705 THR   ( 540-)  B    -2.6
 374 TYR   ( 680-)  A    -2.6
 922 LYS   ( 757-)  B    -2.6
 856 GLU   ( 691-)  B    -2.4
 234 THR   ( 540-)  A    -2.3
 401 GLU   ( 707-)  A    -2.3
 325 THR   ( 631-)  A    -2.2
  59 ILE   ( 365-)  A    -2.2
 530 ILE   ( 365-)  B    -2.2
 846 VAL   ( 681-)  B    -2.2
 858 LYS   ( 693-)  B    -2.2
 375 VAL   ( 681-)  A    -2.2
 853 THR   ( 688-)  B    -2.1
 571 VAL   ( 406-)  B    -2.1
 501 LEU   ( 336-)  B    -2.1
 504 THR   ( 339-)  B    -2.1
 100 VAL   ( 406-)  A    -2.1
 410 VAL   ( 716-)  A    -2.0
 412 GLU   ( 718-)  A    -2.0
  48 HIS   ( 354-)  A    -2.0
 795 ASN   ( 630-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  23 LYS   ( 329-)  A  omega poor
  27 ILE   ( 333-)  A  Poor phi/psi
  42 ALA   ( 348-)  A  omega poor
  45 ARG   ( 351-)  A  omega poor
  59 ILE   ( 365-)  A  omega poor
  65 ASN   ( 371-)  A  Poor phi/psi
  89 ILE   ( 395-)  A  omega poor
  93 VAL   ( 399-)  A  omega poor
  96 ASP   ( 402-)  A  Poor phi/psi
 106 LYS   ( 412-)  A  Poor phi/psi
 109 PHE   ( 415-)  A  omega poor
 136 ASP   ( 442-)  A  Poor phi/psi
 155 ARG   ( 461-)  A  Poor phi/psi
 157 ASN   ( 463-)  A  Poor phi/psi
 164 ASP   ( 470-)  A  omega poor
 180 ALA   ( 486-)  A  Poor phi/psi
 181 TYR   ( 487-)  A  Poor phi/psi
 206 PRO   ( 512-)  A  omega poor
 223 ASP   ( 529-)  A  Poor phi/psi
 237 VAL   ( 543-)  A  Poor phi/psi
 243 LYS   ( 549-)  A  Poor phi/psi
 244 PHE   ( 550-)  A  omega poor
 247 VAL   ( 553-)  A  omega poor
 270 THR   ( 576-)  A  omega poor
 276 HIS   ( 582-)  A  Poor phi/psi
And so on for a total of 88 lines.

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!

   4 GLU   ( 310-)  A      0
   9 PHE   ( 315-)  A      0
  13 ARG   ( 319-)  A      0
  19 LYS   ( 325-)  A      0
  22 ILE   ( 328-)  A      0
  26 ARG   ( 332-)  A      0
  27 ILE   ( 333-)  A      0
  28 PRO   ( 334-)  A      0
  35 LYS   ( 341-)  A      0
  46 ARG   ( 352-)  A      0
  47 LEU   ( 353-)  A      0
  48 HIS   ( 354-)  A      0
  51 ASP   ( 357-)  A      0
  52 TRP   ( 358-)  A      0
  54 ASP   ( 360-)  A      0
  57 MET   ( 363-)  A      0
  65 ASN   ( 371-)  A      0
  68 THR   ( 374-)  A      0
  72 ARG   ( 378-)  A      0
  76 THR   ( 382-)  A      0
  81 ASN   ( 387-)  A      0
  89 ILE   ( 395-)  A      0
  93 VAL   ( 399-)  A      0
  95 ILE   ( 401-)  A      0
  96 ASP   ( 402-)  A      0
And so on for a total of 441 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!

 719 GLY   ( 554-)  B   1.75   10
 403 GLY   ( 709-)  A   1.68   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]

  17 PRO   ( 323-)  A    0.15 LOW
 235 PRO   ( 541-)  A    0.19 LOW
 587 PRO   ( 422-)  B    0.06 LOW
 720 PRO   ( 555-)  B    0.01 LOW
 894 PRO   ( 729-)  B    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 206 PRO   ( 512-)  A    51.0 half-chair C-delta/C-gamma (54 degrees)
 677 PRO   ( 512-)  B    51.4 half-chair C-delta/C-gamma (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.

 856 GLU   ( 691-)  B      CB  <->  858 LYS   ( 693-)  B      NZ     0.37    2.73  INTRA BF
  54 ASP   ( 360-)  A      OD1 <->  952 HOH   (2032 )  A      O      0.35    2.05  INTRA BL
 383 MET   ( 689-)  A      CE  <->  388 GLU   ( 694-)  A      CA     0.29    2.91  INTRA BF
 635 ASP   ( 470-)  B      OD2 <->  637 LYS   ( 472-)  B      NZ     0.25    2.45  INTRA BF
  23 LYS   ( 329-)  A      NZ  <->  952 HOH   (2013 )  A      O      0.22    2.48  INTRA
 608 GLY   ( 443-)  B      N   <->  953 HOH   (2086 )  B      O      0.21    2.49  INTRA BF
 384 HIS   ( 690-)  A      O   <->  389 TYR   ( 695-)  A      CE2    0.20    2.60  INTRA BF
 674 LYS   ( 509-)  B      NZ  <->  949  CL   (1780-)  B     CL      0.18    2.92  INTRA BL
 212 ASP   ( 518-)  A      OD2 <->  952 HOH   (2138 )  A      O      0.18    2.22  INTRA
 572 GLN   ( 407-)  B      NE2 <->  577 LYS   ( 412-)  B      O      0.18    2.52  INTRA
 411 GLU   ( 717-)  A      C   <->  413 ASN   ( 719-)  A      N      0.15    2.75  INTRA BF
 128 LYS   ( 434-)  A      NZ  <->  952 HOH   (2069 )  A      O      0.15    2.55  INTRA BL
 363 ASP   ( 669-)  A      O   <->  952 HOH   (2230 )  A      O      0.13    2.27  INTRA BF
 333 ASN   ( 639-)  A      N   <->  388 GLU   ( 694-)  A      OE2    0.13    2.57  INTRA BF
 528 MET   ( 363-)  B      CE  <->  568 MET   ( 403-)  B      CB     0.12    3.08  INTRA BL
 411 GLU   ( 717-)  A      O   <->  413 ASN   ( 719-)  A      N      0.12    2.58  INTRA BF
 284 ARG   ( 590-)  A      NE  <->  952 HOH   (2176 )  A      O      0.12    2.58  INTRA BL
 309 GLY   ( 615-)  A      N   <->  952 HOH   (2195 )  A      O      0.12    2.58  INTRA BF
 910 ASN   ( 745-)  B      N   <->  911 GLY   ( 746-)  B      CA     0.12    2.78  INTRA BF
 856 GLU   ( 691-)  B      C   <->  858 LYS   ( 693-)  B      NZ     0.12    2.98  INTRA BF
 411 GLU   ( 717-)  A      O   <->  414 GLY   ( 720-)  A      N      0.11    2.59  INTRA BF
 599 LYS   ( 434-)  B      NZ  <->  953 HOH   (2071 )  B      O      0.11    2.59  INTRA
 877 HIS   ( 712-)  B      CD2 <->  892 HIS   ( 727-)  B      CD2    0.11    3.09  INTRA BF
 338 LYS   ( 644-)  A      NZ  <->  952 HOH   (2212 )  A      O      0.11    2.59  INTRA BF
 103 PRO   ( 409-)  A      O   <->  106 LYS   ( 412-)  A      NZ     0.11    2.59  INTRA BF
And so on for a total of 100 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 490 LYS   ( 325-)  B      -6.35
 727 ARG   ( 562-)  B      -6.28
 256 ARG   ( 562-)  A      -6.28
 897 LYS   ( 732-)  B      -6.15
  19 LYS   ( 325-)  A      -6.07
 426 LYS   ( 732-)  A      -5.68
 385 GLU   ( 691-)  A      -5.51
 412 GLU   ( 718-)  A      -5.51
 910 ASN   ( 745-)  B      -5.47
 344 LEU   ( 650-)  A      -5.28
 815 LEU   ( 650-)  B      -5.10
 883 GLU   ( 718-)  B      -5.06
  47 LEU   ( 353-)  A      -5.06
 628 ASN   ( 463-)  B      -5.06
 518 LEU   ( 353-)  B      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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.

 674 LYS   ( 509-)  B   -3.19
 203 LYS   ( 509-)  A   -3.09

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

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.

  77 ASN   ( 383-)  A
 548 ASN   ( 383-)  B

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.

  26 ARG   ( 332-)  A      NH2
  45 ARG   ( 351-)  A      NH2
  48 HIS   ( 354-)  A      N
  72 ARG   ( 378-)  A      NH1
  91 SER   ( 397-)  A      N
  94 ASN   ( 400-)  A      ND2
 164 ASP   ( 470-)  A      N
 213 SER   ( 519-)  A      N
 321 ARG   ( 627-)  A      NH2
 342 ARG   ( 648-)  A      NE
 376 GLN   ( 682-)  A      N
 387 LYS   ( 693-)  A      N
 402 ASN   ( 708-)  A      ND2
 413 ASN   ( 719-)  A      N
 415 GLU   ( 721-)  A      N
 418 TRP   ( 724-)  A      NE1
 471 ASN   ( 777-)  A      N
 476 LYS   ( 311-)  B      N
 497 ARG   ( 332-)  B      NH2
 516 ARG   ( 351-)  B      NH2
 519 HIS   ( 354-)  B      N
 523 TRP   ( 358-)  B      N
 562 SER   ( 397-)  B      N
 565 ASN   ( 400-)  B      ND2
 589 GLY   ( 424-)  B      N
 627 GLU   ( 462-)  B      N
 633 THR   ( 468-)  B      OG1
 684 SER   ( 519-)  B      N
 813 ARG   ( 648-)  B      NE
 847 GLN   ( 682-)  B      N
 889 TRP   ( 724-)  B      NE1
 892 HIS   ( 727-)  B      NE2
 912 GLU   ( 747-)  B      N
 920 THR   ( 755-)  B      N
 924 GLN   ( 759-)  B      NE2
 937 GLU   ( 772-)  B      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.

  96 ASP   ( 402-)  A      OD1
 113 ASP   ( 419-)  A      OD2
 567 ASP   ( 402-)  B      OD1
 852 HIS   ( 687-)  B      NE2
 877 HIS   ( 712-)  B      ND1

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.

 952 HOH   (2032 )  A      O  0.96 NA  6
 952 HOH   (2061 )  A      O  1.01  K  4 *2
 952 HOH   (2187 )  A      O  1.22  K  4 *2
 952 HOH   (2266 )  A      O  1.00  K  4 *2 Ion-B
 953 HOH   (2062 )  B      O  1.16  K  4 *2

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.

 290 ASP   ( 596-)  A   H-bonding suggests Asn
 355 ASP   ( 661-)  A   H-bonding suggests Asn; but Alt-Rotamer
 535 ASP   ( 370-)  B   H-bonding suggests Asn; but Alt-Rotamer
 693 ASP   ( 528-)  B   H-bonding suggests Asn; Ligand-contact
 761 ASP   ( 596-)  B   H-bonding suggests Asn; but Alt-Rotamer
 826 ASP   ( 661-)  B   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 :  -0.218
  2nd generation packing quality :  -0.760
  Ramachandran plot appearance   :  -0.790
  chi-1/chi-2 rotamer normality  :  -1.965
  Backbone conformation          :  -0.621

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.501 (tight)
  Bond angles                    :   0.675
  Omega angle restraints         :   1.224
  Side chain planarity           :   0.503 (tight)
  Improper dihedral distribution :   0.665
  B-factor distribution          :   0.415
  Inside/Outside distribution    :   0.967

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 :   0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.501 (tight)
  Bond angles                    :   0.675
  Omega angle restraints         :   1.224
  Side chain planarity           :   0.503 (tight)
  Improper dihedral distribution :   0.665
  B-factor distribution          :   0.415
  Inside/Outside distribution    :   0.967
==============

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.