WHAT IF Check report

This file was created 2012-01-13 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 pdb1urt.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  49 SER   (  73-)  A  -   CB
  49 SER   (  73-)  A  -   OG
  50 CYS   (  74-)  A  -   CB
  50 CYS   (  74-)  A  -   SG
  51 GLU   (  75-)  A  -   CB
  51 GLU   (  75-)  A  -   CG
  51 GLU   (  75-)  A  -   CD
  51 GLU   (  75-)  A  -   OE1
  51 GLU   (  75-)  A  -   OE2
  52 ASP   (  76-)  A  -   CB
  52 ASP   (  76-)  A  -   CG
  52 ASP   (  76-)  A  -   OD1
  52 ASP   (  76-)  A  -   OD2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  49 SER   (  73-)  A  -   CA
  49 SER   (  73-)  A  -   C
  49 SER   (  73-)  A  -   O
  50 CYS   (  74-)  A  -   N
  50 CYS   (  74-)  A  -   CA
  50 CYS   (  74-)  A  -   C
  50 CYS   (  74-)  A  -   O
  51 GLU   (  75-)  A  -   N
  51 GLU   (  75-)  A  -   CA
  51 GLU   (  75-)  A  -   C
  51 GLU   (  75-)  A  -   O
  52 ASP   (  76-)  A  -   N
  52 ASP   (  76-)  A  -   CA
  52 ASP   (  76-)  A  -   C
  52 ASP   (  76-)  A  -   O
Residue with missing backbone atom(s)  237 ARG  ( 261-) A  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

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. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 237 ARG   ( 261-)  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'.

 237 ARG   ( 261-)  A      O
 237 ARG   ( 261-)  A      CG
 237 ARG   ( 261-)  A      CD
 237 ARG   ( 261-)  A      NE
 237 ARG   ( 261-)  A      CZ
 237 ARG   ( 261-)  A      NH1
 237 ARG   ( 261-)  A      NH2

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:

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

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.

  70 HIS   (  94-)  A      ND1  CE1   1.38    4.6
  72 HIS   (  96-)  A      CG   CD2   1.41    4.6
  72 HIS   (  96-)  A      ND1  CE1   1.39    5.2
  95 HIS   ( 119-)  A      ND1  CE1   1.38    4.6

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.

  70 HIS   (  94-)  A      CD2  CG   ND1 114.60    8.5
  72 HIS   (  96-)  A      CD2  CG   ND1 110.35    4.3
  95 HIS   ( 119-)  A      CD2  CG   ND1 111.97    5.9
 184 THR   ( 208-)  A      N    CA   C    99.75   -4.1

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.

 183 VAL   ( 207-)  A    5.92
  12 LYS   (  36-)  A    4.33
 131 GLN   ( 155-)  A    4.17
 184 THR   ( 208-)  A    4.09
 143 VAL   ( 167-)  A    4.05

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 : 1.509

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  72 HIS   (  96-)  A      CB   4.64
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.562

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.

 228 ARG   ( 252-)  A    -2.8
 196 PRO   ( 220-)  A    -2.2
  68 GLN   (  92-)  A    -2.2
  62 ASN   (  86-)  A    -2.2
 206 LEU   ( 230-)  A    -2.1
 190 THR   ( 214-)  A    -2.1
 153 GLY   ( 177-)  A    -2.1
   6 PRO   (  30-)  A    -2.1
 154 ASP   ( 178-)  A    -2.1
  85 VAL   ( 109-)  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.

   5 SER   (  29-)  A  PRO omega poor
  58 GLY   (  82-)  A  Poor phi/psi
  86 ASP   ( 110-)  A  Poor phi/psi
 147 ASP   ( 171-)  A  Poor phi/psi
 152 MET   ( 176-)  A  Poor phi/psi
 154 ASP   ( 178-)  A  Poor phi/psi
 177 PRO   ( 201-)  A  PRO omega poor
 179 LEU   ( 203-)  A  Poor phi/psi
 228 ARG   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.636

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 ARG   (  27-)  A      0
   4 GLN   (  28-)  A      0
   5 SER   (  29-)  A      0
  11 TRP   (  35-)  A      0
  14 SER   (  38-)  A      0
  32 CYS   (  56-)  A      0
  33 ARG   (  57-)  A      0
  34 TYR   (  58-)  A      0
  36 TRP   (  60-)  A      0
  37 ASN   (  61-)  A      0
  38 THR   (  62-)  A      0
  40 HIS   (  64-)  A      0
  48 ASP   (  72-)  A      0
  49 SER   (  73-)  A      0
  50 CYS   (  74-)  A      0
  51 GLU   (  75-)  A      0
  53 SER   (  77-)  A      0
  55 ILE   (  79-)  A      0
  59 PRO   (  83-)  A      0
  67 LYS   (  91-)  A      0
  68 GLN   (  92-)  A      0
  75 ALA   (  99-)  A      0
  76 THR   ( 100-)  A      0
  77 ASP   ( 101-)  A      0
  78 GLU   ( 102-)  A      0
And so on for a total of 112 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 : 1.420

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!

 211 GLY   ( 235-)  A   1.53   80

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]

  18 PRO   (  42-)  A    0.45 HIGH

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.

 159 CYS   ( 183-)  A      SG  <->  239 HOH   ( 295 )  A      O      0.56    2.44  INTRA BL
 164 CYS   ( 188-)  A      SG  <->  239 HOH   ( 297 )  A      O      0.47    2.53  INTRA
   9 ILE   (  33-)  A      O   <->   86 ASP   ( 110-)  A      N      0.28    2.42  INTRA
   9 ILE   (  33-)  A      N   <->   84 ALA   ( 108-)  A      O      0.21    2.49  INTRA
   3 ARG   (  27-)  A      CA  <->  230 ARG   ( 254-)  A      NH1    0.17    2.93  INTRA
   3 ARG   (  27-)  A      C   <->  230 ARG   ( 254-)  A      NH1    0.17    2.93  INTRA
 140 LEU   ( 164-)  A      N   <->  141 PRO   ( 165-)  A      CD     0.13    2.87  INTRA
  37 ASN   (  61-)  A      O   <->  147 ASP   ( 171-)  A      N      0.07    2.63  INTRA
   6 PRO   (  30-)  A      O   <->  225 GLN   ( 249-)  A      N      0.06    2.64  INTRA BL
 153 GLY   ( 177-)  A      C   <->  154 ASP   ( 178-)  A      CG     0.06    3.04  INTRA BF
 113 GLY   ( 137-)  A      O   <->  182 SER   ( 206-)  A      CB     0.06    2.74  INTRA
  88 HIS   ( 112-)  A      CE1 <->   90 TYR   ( 114-)  A      CE1    0.05    3.15  INTRA
 235 SER   ( 259-)  A      N   <->  236 PHE   ( 260-)  A      N      0.04    2.56  INTRA BL
 183 VAL   ( 207-)  A      CG1 <->  185 TRP   ( 209-)  A      NE1    0.03    3.07  INTRA BL
   8 ASN   (  32-)  A      OD1 <->   87 GLY   ( 111-)  A      N      0.03    2.67  INTRA
   5 SER   (  29-)  A      O   <->  222 ARG   ( 246-)  A      NH1    0.03    2.67  INTRA
  52 ASP   (  76-)  A      O   <->   63 HIS   (  87-)  A      NE2    0.02    2.68  INTRA BL
 104 TYR   ( 128-)  A      OH  <->  114 GLU   ( 138-)  A      N      0.02    2.68  INTRA BF
 227 LEU   ( 251-)  A      N   <->  239 HOH   ( 302 )  A      O      0.02    2.68  INTRA
  76 THR   ( 100-)  A      CG2 <->   77 ASP   ( 101-)  A      N      0.02    2.98  INTRA
  27 TYR   (  51-)  A      OH  <->   98 HIS   ( 122-)  A      NE2    0.01    2.69  INTRA BL
  40 HIS   (  64-)  A      ND1 <->  239 HOH   ( 316 )  A      O      0.01    2.69  INTRA
 196 PRO   ( 220-)  A      O   <->  200 SER   ( 224-)  A      N      0.01    2.69  INTRA BL
 199 LEU   ( 223-)  A      CD1 <->  203 ARG   ( 227-)  A      NH2    0.01    3.09  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.

 210 ARG   ( 234-)  A      -6.39
 114 GLU   ( 138-)  A      -5.65
 105 GLU   ( 129-)  A      -5.24
  50 CYS   (  74-)  A      -5.05

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.

 112 VAL   ( 136-)  A   -2.54

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 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.

 239 HOH   ( 295 )  A      O
Metal-coordinating Histidine residue  70 fixed to   1
Metal-coordinating Histidine residue  72 fixed to   1
Metal-coordinating Histidine residue  95 fixed to   1

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.

   7 ILE   (  31-)  A      N
  36 TRP   (  60-)  A      NE1
  42 PHE   (  66-)  A      N
  49 SER   (  73-)  A      N
  62 ASN   (  86-)  A      ND2
  71 PHE   (  95-)  A      N
  76 THR   ( 100-)  A      N
  78 GLU   ( 102-)  A      N
  92 ALA   ( 116-)  A      N
 106 ASN   ( 130-)  A      N
 134 GLN   ( 158-)  A      NE2
 167 TYR   ( 191-)  A      OH
 176 THR   ( 200-)  A      N
 180 ALA   ( 204-)  A      N
 188 GLN   ( 212-)  A      NE2
 198 GLN   ( 222-)  A      NE2
 209 GLY   ( 233-)  A      N
 230 ARG   ( 254-)  A      NH1
 232 LEU   ( 256-)  A      N
Only metal coordination for   72 HIS  (  96-) A      NE2

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 188 GLN   ( 212-)  A      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  51 GLU   (  75-)  A   H-bonding suggests Gln
  86 ASP   ( 110-)  A   H-bonding suggests Asn
 154 ASP   ( 178-)  A   H-bonding suggests Asn; but Alt-Rotamer
 181 GLU   ( 205-)  A   H-bonding suggests Gln

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 :  -0.539
  2nd generation packing quality :  -1.545
  Ramachandran plot appearance   :  -2.562
  chi-1/chi-2 rotamer normality  :  -2.636
  Backbone conformation          :  -1.087

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.515 (tight)
  Bond angles                    :   0.782
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.455 (tight)
  Improper dihedral distribution :   0.900
  B-factor distribution          :   1.460
  Inside/Outside distribution    :   1.026

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.515 (tight)
  Bond angles                    :   0.782
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.455 (tight)
  Improper dihedral distribution :   0.900
  B-factor distribution          :   1.460
  Inside/Outside distribution    :   1.026
==============

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.