WHAT IF Check report

This file was created 2011-12-17 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 pdb1qpc.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 273 SO4   ( 901-)  A  -         OK
 274 SO4   ( 902-)  A  -         OK
 275 ANP   ( 904-)  A  -
 276 SO4   ( 903-)  A  -         OK
 277 EDO   ( 905-)  A  -         OK

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

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

Warning: Missing atoms

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

  47 GLN   ( 277-)  A      CG
  47 GLN   ( 277-)  A      CD
  47 GLN   ( 277-)  A      OE1
  47 GLN   ( 277-)  A      NE2
  79 GLN   ( 309-)  A      CG
  79 GLN   ( 309-)  A      CD
  79 GLN   ( 309-)  A      OE1
  79 GLN   ( 309-)  A      NE2
 167 ARG   ( 397-)  A      CG
 167 ARG   ( 397-)  A      CD
 167 ARG   ( 397-)  A      NE
 167 ARG   ( 397-)  A      CZ
 167 ARG   ( 397-)  A      NH1
 167 ARG   ( 397-)  A      NH2
 171 LYS   ( 401-)  A      CG
 171 LYS   ( 401-)  A      CD
 171 LYS   ( 401-)  A      CE
 171 LYS   ( 401-)  A      NZ

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 272 GLU   ( 502-)  A

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.

  17 LEU   ( 247-)  A    0.60
  29 VAL   ( 259-)  A    0.77
  37 HIS   ( 267-)  A    0.49
  44 SER   ( 274-)  A    0.65
  52 PRO   ( 282-)  A    0.51
  76 VAL   ( 306-)  A    0.75
  84 ILE   ( 314-)  A    0.82
  93 SER   ( 323-)  A    0.43
  98 LEU   ( 328-)  A    0.40
 127 GLU   ( 357-)  A    0.36
 191 SER   ( 421-)  A    0.84
 195 SER   ( 425-)  A    0.74
 208 ARG   ( 438-)  A    0.58
 210 PRO   ( 440-)  A    0.43
 220 ILE   ( 450-)  A    0.60
 238 GLU   ( 468-)  A    0.51
 262 SER   ( 492-)  A    0.71

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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

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

Percentage of buried atoms with B less than 5 : 18.40

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

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.

 163 GLU   ( 393-)  A
 238 GLU   ( 468-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 159 ILE   ( 389-)  A      CA   CB    1.61    4.2

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.994819 -0.000138 -0.000621|
 | -0.000138  0.994067  0.000227|
 | -0.000621  0.000227  1.001723|
Proposed new scale matrix

 |  0.023871  0.000003  0.000015|
 |  0.000002  0.013648 -0.000003|
 |  0.000007 -0.000002  0.010885|
With corresponding cell

    A    =  41.892  B   =  73.271  C    =  91.867
    Alpha=  89.974  Beta=  90.071  Gamma=  90.016

The CRYST1 cell dimensions

    A    =  42.110  B   =  73.710  C    =  91.710
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 130.687
(Under-)estimated Z-score: 8.425

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.

  67 HIS   ( 297-)  A      CG   ND1  CE1 110.59    5.0
 132 HIS   ( 362-)  A      CG   ND1  CE1 110.42    4.8
 159 ILE   ( 389-)  A      C    CA   CB  121.17    5.8
 160 GLU   ( 390-)  A      CA   CB   CG  104.07   -5.0
 163 GLU   ( 393-)  A      N    CA   C   123.41    4.4
 163 GLU   ( 393-)  A      N    CA   CB  103.65   -4.0
 206 HIS   ( 436-)  A      CG   ND1  CE1 110.00    4.4

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.

 163 GLU   ( 393-)  A
 238 GLU   ( 468-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

  18 VAL   ( 248-)  A    4.34
 163 GLU   ( 393-)  A    4.08

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.

 258 ASP   ( 488-)  A    4.10

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.

 159 ILE   ( 389-)  A    -2.4
 189 ILE   ( 419-)  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.

  80 GLU   ( 310-)  A  PRO omega poor
 129 ASN   ( 359-)  A  Poor phi/psi
 133 ARG   ( 363-)  A  Poor phi/psi
 146 LEU   ( 376-)  A  Poor phi/psi
 152 ASP   ( 382-)  A  Poor phi/psi
 166 ALA   ( 396-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.395

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 102 SER   ( 332-)  A    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   8 TRP   ( 238-)  A      0
  26 PHE   ( 256-)  A      0
  30 TRP   ( 260-)  A      0
  31 MET   ( 261-)  A      0
  34 TYR   ( 264-)  A      0
  37 HIS   ( 267-)  A      0
  47 GLN   ( 277-)  A      0
  49 SER   ( 279-)  A      0
  50 MET   ( 280-)  A      0
  64 GLN   ( 294-)  A      0
  65 LEU   ( 295-)  A      0
  66 GLN   ( 296-)  A      0
  67 HIS   ( 297-)  A      0
  74 TYR   ( 304-)  A      0
  75 ALA   ( 305-)  A      0
  79 GLN   ( 309-)  A      0
  80 GLU   ( 310-)  A      0
  82 ILE   ( 312-)  A      0
  91 ASN   ( 321-)  A      0
 129 ASN   ( 359-)  A      0
 132 HIS   ( 362-)  A      0
 133 ARG   ( 363-)  A      0
 134 ASP   ( 364-)  A      0
 135 LEU   ( 365-)  A      0
 136 ARG   ( 366-)  A      0
And so on for a total of 88 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 3.005

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.

 114 MET   ( 344-)  A      SD  <->  277 HOH   (1132 )  A      O      0.65    2.35  INTRA
 229 MET   ( 459-)  A      SD  <->  277 HOH   (1145 )  A      O      0.57    2.43  INTRA
 156 ALA   ( 386-)  A      O   <->  277 HOH   (1104 )  A      O      0.27    2.13  INTRA
 161 ASP   ( 391-)  A      N   <->  277 HOH   (1086 )  A      O      0.23    2.47  INTRA
 164 PTR   ( 394-)  A      O1P <->  277 HOH   (1052 )  A      O      0.23    2.17  INTRA
 222 ASN   ( 452-)  A      ND2 <->  277 HOH   ( 993 )  A      O      0.19    2.51  INTRA
 114 MET   ( 344-)  A      CB  <->  277 HOH   (1132 )  A      O      0.13    2.67  INTRA
 249 GLU   ( 479-)  A      OE1 <->  277 HOH   (1138 )  A      O      0.11    2.29  INTRA
 179 PRO   ( 409-)  A      CB  <->  275 SO4   ( 903-)  A      O1     0.10    2.70  INTRA
 161 ASP   ( 391-)  A      O   <->  163 GLU   ( 393-)  A      N      0.10    2.60  INTRA
 105 LYS   ( 335-)  A      NZ  <->  277 HOH   (1026 )  A      O      0.07    2.63  INTRA
 244 ARG   ( 474-)  A      NH2 <->  277 HOH   (1136 )  A      O      0.06    2.64  INTRA
  37 HIS   ( 267-)  A      CD2 <->  277 HOH   ( 942 )  A      O      0.06    2.74  INTRA BL
  16 LYS   ( 246-)  A      NZ  <->  277 HOH   (1130 )  A      O      0.05    2.65  INTRA
 167 ARG   ( 397-)  A      O   <->  170 ALA   ( 400-)  A      N      0.04    2.66  INTRA
  99 LYS   ( 329-)  A      NZ  <->  277 HOH   (1100 )  A      O      0.04    2.66  INTRA
  20 ARG   ( 250-)  A      CZ  <->  277 HOH   ( 980 )  A      O      0.03    2.77  INTRA
   3 TRP   ( 233-)  A      O   <->  277 HOH   (1077 )  A      O      0.03    2.37  INTRA
  67 HIS   ( 297-)  A      ND1 <->   69 ARG   ( 299-)  A      N      0.02    2.98  INTRA BL
 109 ASN   ( 339-)  A      ND2 <->  268 PHE   ( 498-)  A      CE1    0.01    3.09  INTRA
  89 MET   ( 319-)  A      N   <->  274 ANP   ( 904-)  A      N1     0.01    2.99  INTRA BL

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

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.

 208 ARG   ( 438-)  A      -6.03
  80 GLU   ( 310-)  A      -5.71
 227 TYR   ( 457-)  A      -5.52
 183 ASN   ( 413-)  A      -5.47
 230 VAL   ( 460-)  A      -5.12
 209 ILE   ( 439-)  A      -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

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.

  47 GLN   ( 277-)  A   -2.98
 167 ARG   ( 397-)  A   -2.68
 171 LYS   ( 401-)  A   -2.52

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

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.

 277 HOH   ( 913 )  A      O     24.97   20.04   88.48
 277 HOH   ( 926 )  A      O     28.29   53.13   78.90
 277 HOH   ( 941 )  A      O     29.01   34.61   64.92
 277 HOH   ( 948 )  A      O     25.95   56.77   57.38
 277 HOH   ( 951 )  A      O     27.25   50.61   82.07
 277 HOH   ( 967 )  A      O      1.89   40.24   77.12
 277 HOH   ( 982 )  A      O     15.76   35.93   66.84
 277 HOH   ( 990 )  A      O     22.58   52.46   54.43
 277 HOH   (1096 )  A      O     27.84   55.69   55.71
 277 HOH   (1144 )  A      O     38.95   39.82   77.37

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.

 277 HOH   (1106 )  A      O

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.

  37 HIS   ( 267-)  A
 109 ASN   ( 339-)  A
 162 ASN   ( 392-)  A
 216 ASN   ( 446-)  A
 222 ASN   ( 452-)  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.

   4 TRP   ( 234-)  A      N
   8 TRP   ( 238-)  A      N
  12 ARG   ( 242-)  A      NH1
  50 MET   ( 280-)  A      N
  68 GLN   ( 298-)  A      NE2
  69 ARG   ( 299-)  A      NH2
  89 MET   ( 319-)  A      N
 102 SER   ( 332-)  A      N
 109 ASN   ( 339-)  A      N
 133 ARG   ( 363-)  A      NH1
 136 ARG   ( 366-)  A      N
 147 SER   ( 377-)  A      OG
 228 ARG   ( 458-)  A      N
 231 ARG   ( 461-)  A      NH2

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.

 277 HOH   (1041 )  A      O  1.11  K  4 Ion-B

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 :  -0.416
  2nd generation packing quality :  -1.001
  Ramachandran plot appearance   :   0.765
  chi-1/chi-2 rotamer normality  :   0.395
  Backbone conformation          :   0.028

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.728
  Bond angles                    :   0.926
  Omega angle restraints         :   0.546 (tight)
  Side chain planarity           :   1.200
  Improper dihedral distribution :   1.333
  Inside/Outside distribution    :   1.014

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.728
  Bond angles                    :   0.926
  Omega angle restraints         :   0.546 (tight)
  Side chain planarity           :   1.200
  Improper dihedral distribution :   1.333
  Inside/Outside distribution    :   1.014
==============

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.