WHAT IF Check report

This file was created 2012-01-25 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 pdb2hc1.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.

 294 ACT   ( 601-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  41 ASN   (1716-)  A  -
 202 GLN   (1882-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  41 ASN   (1716-)  A  -
 123 GLN   (1803-)  A  -
 202 GLN   (1882-)  A  -
 239 ARG   (1919-)  A  -

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: 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.

  33 GLU   (1708-)  A    0.66
 169 CYS   (1849-)  A    0.66
 195 GLU   (1875-)  A    0.66

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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  53 ARG   (1728-)  A
  89 ARG   (1769-)  A

Warning: Tyrosine convention problem

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

  92 TYR   (1772-)  A
 145 TYR   (1825-)  A
 210 TYR   (1890-)  A
 253 TYR   (1933-)  A

Warning: Phenylalanine convention problem

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

 166 PHE   (1846-)  A
 183 PHE   (1863-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 133 ASP   (1813-)  A
 209 ASP   (1889-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  91 GLU   (1771-)  A
 195 GLU   (1875-)  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.

  11 ASN   (1686-)  A      CB   CG    1.63    4.6

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.431
RMS-deviation in bond distances: 0.010

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.

  16 HIS   (1691-)  A      CG   ND1  CE1 109.70    4.1

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.

  53 ARG   (1728-)  A
  89 ARG   (1769-)  A
  91 GLU   (1771-)  A
 133 ASP   (1813-)  A
 195 GLU   (1875-)  A
 209 ASP   (1889-)  A

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.

 216 GLY   (1896-)  A    -2.1
  24 SER   (1699-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

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

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

  23 ASP   (1698-)  A  Poor phi/psi
  25 ASN   (1700-)  A  Poor phi/psi
  35 LEU   (1710-)  A  omega poor
  51 GLU   (1726-)  A  omega poor
  61 ILE   (1736-)  A  omega poor
  73 GLY   (1748-)  A  omega poor
  75 SER   (1755-)  A  omega poor
  77 TYR   (1757-)  A  omega poor
  89 ARG   (1769-)  A  omega poor
  90 ARG   (1770-)  A  Poor phi/psi
  92 TYR   (1772-)  A  omega poor
 114 ASN   (1794-)  A  Poor phi/psi
 122 THR   (1802-)  A  omega poor
 134 HIS   (1814-)  A  omega poor
 144 TYR   (1824-)  A  omega poor
 166 PHE   (1846-)  A  omega poor
 173 GLN   (1853-)  A  Poor phi/psi
 185 TYR   (1865-)  A  omega poor
 191 HIS   (1871-)  A  omega poor
 216 GLY   (1896-)  A  omega poor
 223 HIS   (1903-)  A  omega poor
 224 CYS   (1904-)  A  Poor phi/psi
 228 VAL   (1908-)  A  Poor phi/psi
 248 ASP   (1928-)  A  omega poor
 265 HIS   (1945-)  A  Poor phi/psi
 266 MET   (1946-)  A  omega poor
 267 VAL   (1947-)  A  Poor phi/psi, omega poor
 chi-1/chi-2 correlation Z-score : 0.940

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!

   3 LYS   (1678-)  A      0
   5 SER   (1680-)  A      0
   6 CYS   (1681-)  A      0
  23 ASP   (1698-)  A      0
  24 SER   (1699-)  A      0
  25 ASN   (1700-)  A      0
  38 VAL   (1713-)  A      0
  44 CYS   (1719-)  A      0
  49 LEU   (1724-)  A      0
  57 ARG   (1732-)  A      0
  58 TYR   (1733-)  A      0
  61 ILE   (1736-)  A      0
  67 THR   (1742-)  A      0
  72 SER   (1747-)  A      0
  75 SER   (1755-)  A      0
  78 ILE   (1758-)  A      0
  79 ASN   (1759-)  A      0
  87 ASN   (1767-)  A      0
  88 PHE   (1768-)  A      0
  89 ARG   (1769-)  A      0
  90 ARG   (1770-)  A      0
  92 TYR   (1772-)  A      0
 102 THR   (1782-)  A      0
 113 GLN   (1793-)  A      0
 114 ASN   (1794-)  A      0
And so on for a total of 114 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.357

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!

 227 GLY   (1907-)  A   1.50   62

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].

   7 PRO   (1682-)  A    40.7 envelop C-delta (36 degrees)
  50 PRO   (1725-)  A    52.1 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.

  19 LYS   (1694-)  A    A NZ  <->  295 HOH   ( 531 )  A      O      0.59    2.11  INTRA
  53 ARG   (1728-)  A    A CD  <->  295 HOH   ( 430 )  A      O      0.51    2.29  INTRA
 243 GLN   (1923-)  A      NE2 <->  295 HOH   ( 151 )  A      O      0.47    2.23  INTRA
 295 HOH   ( 462 )  A      O   <->  295 HOH   ( 585 )  A      O      0.46    1.74  INTRA
  16 HIS   (1691-)  A      CE1 <->  295 HOH   ( 538 )  A      O      0.41    2.39  INTRA
  19 LYS   (1694-)  A    A CE  <->  295 HOH   ( 531 )  A      O      0.37    2.43  INTRA
  16 HIS   (1691-)  A      NE2 <->  295 HOH   ( 538 )  A      O      0.29    2.41  INTRA
 295 HOH   ( 385 )  A      O   <->  295 HOH   ( 426 )  A      O      0.27    1.93  INTRA
 258 ASP   (1938-)  A    A OD2 <->  295 HOH   ( 441 )  A      O      0.26    2.14  INTRA
 127 LYS   (1807-)  A      CG  <->  190 ASP   (1870-)  A      OD2    0.20    2.60  INTRA
  92 TYR   (1772-)  A    A CE2 <->  239 ARG   (1919-)  A    B NE     0.19    2.91  INTRA BL
 144 TYR   (1824-)  A      CE1 <->  149 ILE   (1829-)  A    A CG1    0.18    3.02  INTRA BL
 288 LYS   (1968-)  A    A CD  <->  295 HOH   ( 383 )  A      O      0.17    2.63  INTRA
 190 ASP   (1870-)  A      O   <->  191 HIS   (1871-)  A    A CG     0.17    2.53  INTRA
  55 LYS   (1730-)  A      NZ  <->  295 HOH   (  41 )  A      O      0.16    2.54  INTRA
  12 GLN   (1687-)  A    A NE2 <->  295 HOH   ( 147 )  A      O      0.15    2.55  INTRA
 268 GLN   (1948-)  A      NE2 <->  295 HOH   ( 186 )  A      O      0.14    2.56  INTRA
 148 LEU   (1828-)  A      CD2 <->  170 GLY   (1850-)  A      CA     0.13    3.07  INTRA
 249 SER   (1929-)  A    B OG  <->  295 HOH   ( 414 )  A      O      0.11    2.29  INTRA
 213 ARG   (1893-)  A      CG  <->  295 HOH   ( 374 )  A      O      0.11    2.69  INTRA
  37 ASP   (1712-)  A      OD1 <->  295 HOH   ( 225 )  A      O      0.10    2.30  INTRA
  14 GLU   (1689-)  A      OE2 <->   18 MET   (1693-)  A    A CE     0.09    2.71  INTRA
 181 ARG   (1861-)  A    A NH2 <->  213 ARG   (1893-)  A      NH2    0.09    2.76  INTRA
 295 HOH   ( 463 )  A      O   <->  295 HOH   ( 477 )  A      O      0.09    2.11  INTRA
 196 THR   (1876-)  A      OG1 <->  198 GLN   (1878-)  A      CG     0.09    2.71  INTRA
  16 HIS   (1691-)  A      ND1 <->  295 HOH   ( 531 )  A      O      0.09    2.61  INTRA
 295 HOH   (  76 )  A      O   <->  295 HOH   ( 226 )  A      O      0.08    2.12  INTRA
 295 HOH   ( 268 )  A      O   <->  295 HOH   ( 529 )  A      O      0.07    2.13  INTRA
 181 ARG   (1861-)  A    A NH2 <->  295 HOH   ( 550 )  A      O      0.07    2.63  INTRA
 284 LEU   (1964-)  A      O   <->  288 LYS   (1968-)  A    A CG     0.06    2.74  INTRA
 173 GLN   (1853-)  A      NE2 <->  295 HOH   ( 497 )  A      O      0.06    2.64  INTRA
  54 GLY   (1729-)  A      N   <->  295 HOH   ( 140 )  A      O      0.06    2.64  INTRA
 103 LYS   (1783-)  A    A NZ  <->  295 HOH   ( 468 )  A      O      0.05    2.65  INTRA
  70 LYS   (1745-)  A      NZ  <->  295 HOH   ( 439 )  A      O      0.02    2.68  INTRA
  92 TYR   (1772-)  A    A CE2 <->  239 ARG   (1919-)  A    B NH2    0.02    3.08  INTRA BL
 196 THR   (1876-)  A      CB  <->  198 GLN   (1878-)  A      CG     0.02    3.18  INTRA
  36 LYS   (1711-)  A      NZ  <->  295 HOH   ( 532 )  A      O      0.01    2.69  INTRA
 208 ARG   (1888-)  A      NH2 <->  295 HOH   (  44 )  A      O      0.01    2.69  INTRA
 224 CYS   (1904-)  A      SG  <->  227 GLY   (1907-)  A      N      0.01    3.29  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.

  89 ARG   (1769-)  A      -7.10
 191 HIS   (1871-)  A      -6.83
 174 LEU   (1854-)  A      -6.55
 213 ARG   (1893-)  A      -5.59
  87 ASN   (1767-)  A      -5.30
  88 PHE   (1768-)  A      -5.18
   2 ARG   (1677-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  86 ASN   (1766-)  A        90 - ARG   1770- ( A)         -5.37

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.

 173 GLN   (1853-)  A   -2.83

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

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 295 HOH   ( 436 )  A      O
 295 HOH   ( 523 )  A      O
ERROR. No atoms within 50 A?
ERROR. No atoms within 50 A?

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.

 295 HOH   (   2 )  A      O    -14.98   33.18   28.11
 295 HOH   ( 505 )  A      O    -15.13   18.92   31.17
 295 HOH   ( 516 )  A      O     -7.86   25.16    1.36
 295 HOH   ( 517 )  A      O    -14.99   27.53   14.60
 295 HOH   ( 518 )  A      O    -15.39   31.35   15.02
 295 HOH   ( 519 )  A      O    -14.20   28.68   16.94
 295 HOH   ( 521 )  A      O    -14.27   30.21   18.70
 295 HOH   ( 594 )  A      O      6.96   36.77  -10.43

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.

 295 HOH   ( 436 )  A      O
 295 HOH   ( 523 )  A      O
 295 HOH   ( 587 )  A      O
Marked this atom as acceptor  292  CL  ( 602-) A     CL
Marked this atom as acceptor  293  CL  ( 603-) A     CL

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.

  25 ASN   (1700-)  A
  86 ASN   (1766-)  A
 117 ASN   (1797-)  A
 242 GLN   (1922-)  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.

   5 SER   (1680-)  A      N
  11 ASN   (1686-)  A      N
  53 ARG   (1728-)  A      N
 122 THR   (1802-)  A      N
 136 TRP   (1816-)  A      N
 139 ASP   (1819-)  A      N
 170 GLY   (1850-)  A      N
 187 VAL   (1867-)  A      N
 249 SER   (1929-)  A      N
 266 MET   (1946-)  A      N
 287 ARG   (1967-)  A      NE
 287 ARG   (1967-)  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.

 295 HOH   (   5 )  A      O  0.96  K  4
 295 HOH   (  29 )  A      O  1.02  K  4
 295 HOH   ( 130 )  A      O  1.14  K  4
 295 HOH   ( 402 )  A      O  0.98  K  4 Ion-B
 295 HOH   ( 475 )  A      O  0.90  K  5

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 :  -0.290
  2nd generation packing quality :  -1.232
  Ramachandran plot appearance   :   0.220
  chi-1/chi-2 rotamer normality  :   0.940
  Backbone conformation          :  -0.026

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.431 (tight)
  Bond angles                    :   0.681
  Omega angle restraints         :   1.338 (loose)
  Side chain planarity           :   0.631 (tight)
  Improper dihedral distribution :   0.731
  B-factor distribution          :   0.771
  Inside/Outside distribution    :   1.036

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 : 1.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.431 (tight)
  Bond angles                    :   0.681
  Omega angle restraints         :   1.338 (loose)
  Side chain planarity           :   0.631 (tight)
  Improper dihedral distribution :   0.731
  B-factor distribution          :   0.771
  Inside/Outside distribution    :   1.036
==============

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.