WHAT IF Check report

This file was created 2011-12-21 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 pdb1avn.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.

 261 HSM   ( 264-)  A  -
 262 AZI   ( 265-)  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: 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'.

   1 HIS   (   4-)  A      CB
   1 HIS   (   4-)  A      CG
   1 HIS   (   4-)  A      ND1
   1 HIS   (   4-)  A      CD2
   1 HIS   (   4-)  A      CE1
   1 HIS   (   4-)  A      NE2
  11 GLU   (  14-)  A      CB
  11 GLU   (  14-)  A      CG
  11 GLU   (  14-)  A      CD
  11 GLU   (  14-)  A      OE1
  11 GLU   (  14-)  A      OE2

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) :293.000

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 : 25.48

Note: B-factor plot

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

Chain identifier: 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.

   1 HIS   (   4-)  A      N    CA    1.57    6.0
  26 SER   (  29-)  A      CA   C     1.64    5.4
  27 PRO   (  30-)  A      N    CA    1.37   -6.2
  27 PRO   (  30-)  A      CD   N     1.61    9.9
 123 LYS   ( 127-)  A      N   -C     1.65   16.1

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.

   1 HIS   (   4-)  A      N    CA   C    99.76   -4.1
   1 HIS   (   4-)  A      CA   C    O   113.66   -4.2
   2 TRP   (   5-)  A     -CA  -C    N   127.61    5.7
   3 GLY   (   6-)  A     -C    N    CA  127.90    4.3
   6 LYS   (   9-)  A     -O   -C    N   116.55   -4.0
   6 LYS   (   9-)  A      CA   C    O   110.76   -5.9
   7 HIS   (  10-)  A      CA   CB   CG  106.63   -7.2
   8 ASN   (  11-)  A      CA   CB   CG  119.74    7.1
   8 ASN   (  11-)  A      CB   CG   ND2 123.49    4.7
   8 ASN   (  11-)  A      ND2  CG   OD1 117.05   -5.5
   9 GLY   (  12-)  A     -C    N    CA  131.58    6.5
  11 GLU   (  14-)  A     -C    N    CA  129.07    4.1
  12 HIS   (  15-)  A      CA   C    O   113.99   -4.0
  12 HIS   (  15-)  A      C    CA   CB  102.20   -4.2
  14 HIS   (  17-)  A     -O   -C    N   132.63    6.0
  16 ASP   (  19-)  A      OD2  CG   OD1 133.25    4.3
  17 PHE   (  20-)  A      CA   CB   CG  108.12   -5.7
  20 ALA   (  23-)  A      C    CA   CB  103.60   -4.6
  23 GLU   (  26-)  A      N    CA   CB  103.41   -4.2
  23 GLU   (  26-)  A      CB   CG   CD  132.04   11.4
  23 GLU   (  26-)  A      OE2  CD   OE1 112.85   -4.2
  24 ARG   (  27-)  A      N    CA   CB  117.36    4.0
  25 GLN   (  28-)  A      CA   C    O   129.71    5.2
  25 GLN   (  28-)  A      NE2  CD   OE1 126.82    4.2
  26 SER   (  29-)  A      CA   C    O   105.14   -9.2
And so on for a total of 231 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.232
RMS-deviation in bond angles: 4.124

Warning: Chirality deviations detected

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

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

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

  27 PRO   (  30-)  A      N    -53.4  -177.56    -2.48
  27 PRO   (  30-)  A      CA    -8.1    26.77    38.15
  44 LEU   (  47-)  A      CA     7.3    45.40    34.19
  55 ARG   (  58-)  A      CA     7.2    45.73    33.91
  56 ILE   (  59-)  A      CB     6.5    40.81    32.31
 122 THR   ( 125-)  A      C     12.4    18.85     0.30
 203 VAL   ( 207-)  A      CA     6.2    42.24    33.23
 206 ILE   ( 210-)  A      CB     8.0    42.69    32.31
The average deviation= 2.212

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.5 worries us. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.686

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.

 203 VAL   ( 207-)  A    6.19
  27 PRO   (  30-)  A    5.93
 150 LYS   ( 154-)  A    4.61
 137 LEU   ( 141-)  A    4.40
 160 LEU   ( 164-)  A    4.19
 182 PRO   ( 186-)  A    4.14
  89 GLN   (  92-)  A    4.12
  55 ARG   (  58-)  A    4.08

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.815

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.

 104 HIS   ( 107-)  A    4.93

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.

  57 LEU   (  60-)  A    -2.3
 172 PHE   ( 176-)  A    -2.2
 159 VAL   ( 163-)  A    -2.2
 163 ILE   ( 167-)  A    -2.2
  55 ARG   (  58-)  A    -2.1
  47 SER   (  50-)  A    -2.1
 187 TYR   ( 191-)  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.

  27 PRO   (  30-)  A  Poor phi/psi
  61 HIS   (  64-)  A  Poor phi/psi
 108 LYS   ( 111-)  A  Poor phi/psi
 125 GLY   ( 129-)  A  Poor phi/psi
 174 ASN   ( 178-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 239 ASP   ( 243-)  A  Poor phi/psi
 248 LYS   ( 252-)  A  Poor phi/psi
 249 ASN   ( 253-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.879

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 TYR   (   7-)  A      0
   7 HIS   (  10-)  A      0
  11 GLU   (  14-)  A      0
  16 ASP   (  19-)  A      0
  17 PHE   (  20-)  A      0
  21 LYS   (  24-)  A      0
  23 GLU   (  26-)  A      0
  24 ARG   (  27-)  A      0
  25 GLN   (  28-)  A      0
  26 SER   (  29-)  A      0
  27 PRO   (  30-)  A      0
  35 ALA   (  38-)  A      0
  47 SER   (  50-)  A      0
  51 ALA   (  54-)  A      0
  59 ASN   (  62-)  A      0
  61 HIS   (  64-)  A      0
  69 ASP   (  72-)  A      0
  70 SER   (  73-)  A      0
  73 LYS   (  76-)  A      0
  74 ALA   (  77-)  A      0
  77 LYS   (  80-)  A      0
  80 PRO   (  83-)  A      0
  82 ASP   (  85-)  A      0
  84 THR   (  87-)  A      0
  89 GLN   (  92-)  A      0
And so on for a total of 124 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 : 3.075

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]

  10 PRO   (  13-)  A    0.16 LOW
  39 PRO   (  42-)  A    0.13 LOW
 191 PRO   ( 195-)  A    0.14 LOW
 197 PRO   ( 201-)  A    0.51 HIGH
 198 PRO   ( 202-)  A    0.46 HIGH
 211 PRO   ( 215-)  A    0.18 LOW
 233 PRO   ( 237-)  A    0.10 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].

  43 PRO   (  46-)  A    49.0 half-chair C-delta/C-gamma (54 degrees)
 243 PRO   ( 247-)  A    50.7 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.

 262 AZI   ( 265-)  A      N2  <->  263 HOH   ( 407 )  A      O      2.28    0.32  INTRA
 262 AZI   ( 265-)  A      N3  <->  263 HOH   ( 407 )  A      O      1.53    1.07  INTRA
 262 AZI   ( 265-)  A      N1  <->  263 HOH   ( 407 )  A      O      1.18    1.42  INTRA
  61 HIS   (  64-)  A      CD2 <->  263 HOH   ( 391 )  A      O      0.44    2.36  INTRA
  12 HIS   (  15-)  A      ND1 <->   15 LYS   (  18-)  A      NZ     0.40    2.60  INTRA BL
 261 HSM   ( 264-)  A      CE1 <->  263 HOH   ( 396 )  A      O      0.35    2.45  INTRA
 221 LYS   ( 225-)  A      NZ  <->  263 HOH   ( 321 )  A      O      0.35    2.35  INTRA BF
  89 GLN   (  92-)  A      NE2 <->  261 HSM   ( 264-)  A      NE2    0.35    2.65  INTRA
 235 GLU   ( 239-)  A      OE2 <->  263 HOH   ( 312 )  A      O      0.26    2.14  INTRA BF
  26 SER   (  29-)  A      C   <->   27 PRO   (  30-)  A      CD     0.24    2.06  INTRA BL
  15 LYS   (  18-)  A      NZ  <->  263 HOH   ( 307 )  A      O      0.23    2.47  INTRA BL
 263 HOH   ( 313 )  A      O   <->  263 HOH   ( 420 )  A      O      0.22    1.98  INTRA
 104 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.15    2.55  INTRA BL
 216 SER   ( 220-)  A      OG  <->  263 HOH   ( 387 )  A      O      0.08    2.32  INTRA
 100 GLN   ( 103-)  A      NE2 <->  239 ASP   ( 243-)  A      OD1    0.07    2.63  INTRA BL
 248 LYS   ( 252-)  A      CB  <->  249 ASN   ( 253-)  A      N      0.06    2.64  INTRA B3
  48 TYR   (  51-)  A      OH  <->  119 HIS   ( 122-)  A      NE2    0.06    2.64  INTRA BL
  68 ASP   (  71-)  A      OD2 <->   73 LYS   (  76-)  A      NZ     0.05    2.65  INTRA
  19 ILE   (  22-)  A      O   <->   22 GLY   (  25-)  A      N      0.04    2.66  INTRA BL
  26 SER   (  29-)  A      CA  <->   27 PRO   (  30-)  A      N      0.04    2.16  INTRA BL
 121 ASN   ( 124-)  A      N   <->  136 GLY   ( 140-)  A      O      0.03    2.67  INTRA BL
 255 SER   ( 259-)  A      N   <->  256 PHE   ( 260-)  A      N      0.03    2.57  INTRA BL
 141 GLY   ( 145-)  A      N   <->  206 ILE   ( 210-)  A      O      0.03    2.67  INTRA BL
 101 GLY   ( 104-)  A      N   <->  263 HOH   ( 282 )  A      O      0.03    2.67  INTRA BL
  27 PRO   (  30-)  A      CB  <->  103 GLU   ( 106-)  A      C      0.03    3.17  INTRA BL
 243 PRO   ( 247-)  A      O   <->  245 GLN   ( 249-)  A      NE2    0.03    2.67  INTRA BL
 187 TYR   ( 191-)  A      O   <->  255 SER   ( 259-)  A      N      0.02    2.68  INTRA BL
  64 ASN   (  67-)  A      ND2 <->  263 HOH   ( 396 )  A      O      0.02    2.68  INTRA BL
  53 SER   (  56-)  A      OG  <->  175 PHE   ( 179-)  A      N      0.01    2.69  INTRA BL
  95 GLY   (  98-)  A      O   <->  223 ARG   ( 227-)  A      NE     0.01    2.69  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.

   7 HIS   (  10-)  A      -5.97
  97 LEU   ( 100-)  A      -5.43
 132 GLN   ( 136-)  A      -5.17

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.

   1 HIS   (   4-)  A   -2.92

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.

 263 HOH   ( 301 )  A      O
ERROR. No atoms within 50 A?

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.

 263 HOH   ( 301 )  A      O
Metal-coordinating Histidine residue  91 fixed to   1
Metal-coordinating Histidine residue  93 fixed to   1
Metal-coordinating Histidine residue 116 fixed to   1

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.

   7 HIS   (  10-)  A
  50 GLN   (  53-)  A
  64 ASN   (  67-)  A
 133 GLN   ( 137-)  A
 174 ASN   ( 178-)  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.

  28 VAL   (  31-)  A      N
  49 ASP   (  52-)  A      N
  71 GLN   (  74-)  A      N
  97 LEU   ( 100-)  A      N
 196 THR   ( 200-)  A      N
 200 LEU   ( 204-)  A      N
 228 ASN   ( 232-)  A      N
 229 GLY   ( 233-)  A      N
 240 ASN   ( 244-)  A      ND2
 241 TRP   ( 245-)  A      N
 249 ASN   ( 253-)  A      N
 256 PHE   ( 260-)  A      N
Only metal coordination for   91 HIS  (  94-) A      NE2
Only metal coordination for   93 HIS  (  96-) A      NE2
Only metal coordination for  116 HIS  ( 119-) A      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.

 263 HOH   ( 351 )  A      O  1.04  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 :  -0.299
  2nd generation packing quality :   0.085
  Ramachandran plot appearance   :  -1.534
  chi-1/chi-2 rotamer normality  :  -2.879
  Backbone conformation          :  -1.144

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.932
  Bond angles                    :   2.232 (loose)
  Omega angle restraints         :   0.559 (tight)
  Side chain planarity           :   1.482
  Improper dihedral distribution :   2.686 (loose)
  Inside/Outside distribution    :   0.949

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 :   0.1
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.932
  Bond angles                    :   2.232 (loose)
  Omega angle restraints         :   0.559 (tight)
  Side chain planarity           :   1.482
  Improper dihedral distribution :   2.686 (loose)
  Inside/Outside distribution    :   0.949
==============

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.