WHAT IF Check report

This file was created 2011-12-22 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 pdb1efn.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.878
CA-only RMS fit for the two chains : 0.594

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.943
CA-only RMS fit for the two chains : 0.716

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 38273.473
Volume of the Unit Cell V= 2305602.8
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.020
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.920

Warning: Ligands for which topology could not be determined

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

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

 323 PBM   ( 710-)  B  -         Atom types
 324 PBM   ( 720-)  D  -         Atom types

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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'.

   2 LEU   (  86-)  A      CG
   2 LEU   (  86-)  A      CD1
   2 LEU   (  86-)  A      CD2
  14 GLU   (  98-)  A      CG
  14 GLU   (  98-)  A      CD
  14 GLU   (  98-)  A      OE1
  14 GLU   (  98-)  A      OE2
  24 LYS   ( 108-)  A      CG
  24 LYS   ( 108-)  A      CD
  24 LYS   ( 108-)  A      CE
  24 LYS   ( 108-)  A      NZ
  28 LEU   ( 112-)  A      CG
  28 LEU   ( 112-)  A      CD1
  28 LEU   ( 112-)  A      CD2
  31 SER   ( 115-)  A      OG
  37 GLU   ( 121-)  A      CG
  37 GLU   ( 121-)  A      CD
  37 GLU   ( 121-)  A      OE1
  37 GLU   ( 121-)  A      OE2
  39 ARG   ( 123-)  A      CZ
  39 ARG   ( 123-)  A      NH1
  39 ARG   ( 123-)  A      NH2
  41 LEU   ( 125-)  A      CG
  41 LEU   ( 125-)  A      CD1
  41 LEU   ( 125-)  A      CD2
And so on for a total of 55 lines.

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

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Geometric checks

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.

 237 HIS   (  89-)  D      CG   ND1  CE1 109.61    4.0
 318 HIS   ( 199-)  D      CG   ND1  CE1 109.62    4.0

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.

  60 GLN   (  73-)  B    4.44
 266 GLN   ( 118-)  D    4.22
 211 PRO   ( 134-)  C    4.09
 105 GLN   ( 118-)  B    4.04

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 : 1.539

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.

 118 PRO   ( 131-)  B    -2.5
  13 THR   (  97-)  A    -2.4
  10 GLU   (  94-)  A    -2.4
  53 TYR   ( 137-)  A    -2.2
  61 VAL   (  74-)  B    -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.

  29 ASN   ( 113-)  A  Poor phi/psi
  43 THR   ( 127-)  A  Poor phi/psi
  81 LYS   (  94-)  B  Poor phi/psi
  82 GLY   (  95-)  B  Poor phi/psi
 109 PRO   ( 122-)  B  Poor phi/psi
 112 GLN   ( 125-)  B  Poor phi/psi
 117 GLY   ( 130-)  B  PRO omega poor
 247 GLY   (  99-)  D  Poor phi/psi
 270 PRO   ( 122-)  D  Poor phi/psi
 273 GLN   ( 125-)  D  Poor phi/psi
 278 GLY   ( 130-)  D  PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.573

Warning: Unusual rotamers

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

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

  75 SER   (  88-)  B    0.35

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!

   7 TYR   (  91-)  A      0
  11 ALA   (  95-)  A      0
  13 THR   (  97-)  A      0
  18 SER   ( 102-)  A      0
  21 LYS   ( 105-)  A      0
  28 LEU   ( 112-)  A      0
  29 ASN   ( 113-)  A      0
  30 SER   ( 114-)  A      0
  32 GLU   ( 116-)  A      0
  34 ASP   ( 118-)  A      0
  35 TRP   ( 119-)  A      0
  48 TYR   ( 132-)  A      0
  53 TYR   ( 137-)  A      0
  55 ALA   ( 139-)  A      0
  56 PRO   ( 140-)  A      0
  57 VAL   ( 141-)  A      0
  58 ARG   (  71-)  B      0
  59 PRO   (  72-)  B      0
  63 LEU   (  76-)  B      0
  66 MET   (  79-)  B      0
  81 LYS   (  94-)  B      0
  85 GLU   (  98-)  B      0
  87 LEU   ( 100-)  B      0
 104 THR   ( 117-)  B      0
 105 GLN   ( 118-)  B      0
And so on for a total of 154 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 : 1.462

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!

 247 GLY   (  99-)  D   1.52   53

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].

  50 PRO   ( 134-)  A    52.3 half-chair C-delta/C-gamma (54 degrees)
 134 PRO   ( 147-)  B   100.7 envelop C-beta (108 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.

 121 ARG   ( 134-)  B      NH1 <->  139 LEU   ( 181-)  B      CD1    0.24    2.86  INTRA
  88 ILE   ( 101-)  B      O   <->   93 ARG   ( 106-)  B      NH1    0.19    2.51  INTRA BF
 135 VAL   ( 148-)  B      N   <->  138 VAL   ( 180-)  B      O      0.17    2.53  INTRA
 264 HIS   ( 116-)  D      ND1 <->  328 HOH   ( 825 )  D      O      0.16    2.54  INTRA BF
  92 ARG   ( 105-)  B      NH1 <->  271 ASP   ( 123-)  D      OD2    0.16    2.54  INTRA
   7 TYR   (  91-)  A      CE2 <->   59 PRO   (  72-)  B      CD     0.15    3.05  INTRA BF
  98 ASP   ( 111-)  B      OD1 <->  112 GLN   ( 125-)  B      NE2    0.15    2.55  INTRA BL
  89 HIS   ( 102-)  B      NE2 <->   94 GLN   ( 107-)  B      OE1    0.15    2.55  INTRA BL
   8 ASP   (  92-)  A      OD1 <->   21 LYS   ( 105-)  A      N      0.14    2.56  INTRA BF
  58 ARG   (  71-)  B      NH2 <->  326 HOH   ( 846 )  B      O      0.14    2.56  INTRA BF
  69 LYS   (  82-)  B      NZ  <->  326 HOH   ( 886 )  B      O      0.13    2.57  INTRA
 247 GLY   (  99-)  D      O   <->  301 GLU   ( 182-)  D      CD     0.12    2.68  INTRA BF
 275 TYR   ( 127-)  D      CD2 <->  293 LEU   ( 145-)  D      CD1    0.11    3.09  INTRA BL
   3 PHE   (  87-)  A      O   <->   25 PHE   ( 109-)  A      N      0.11    2.59  INTRA BF
  40 SER   ( 124-)  A      O   <->   44 GLY   ( 128-)  A      N      0.10    2.60  INTRA BF
  92 ARG   ( 105-)  B      N   <->  326 HOH   ( 868 )  B      O      0.10    2.60  INTRA BF
  35 TRP   ( 119-)  A      CZ2 <->   61 VAL   (  74-)  B      CG1    0.10    3.10  INTRA BL
 200 ARG   ( 123-)  C      NH2 <->  327 HOH   ( 822 )  C      O      0.10    2.60  INTRA
  89 HIS   ( 102-)  B      N   <->  139 LEU   ( 181-)  B      O      0.09    2.61  INTRA
  36 TRP   ( 120-)  A      O   <->   49 ILE   ( 133-)  A      N      0.09    2.61  INTRA BF
 288 GLY   ( 140-)  D      N   <->  328 HOH   ( 807 )  D      O      0.09    2.61  INTRA BL
   4 VAL   (  88-)  A      N   <->   55 ALA   ( 139-)  A      O      0.09    2.61  INTRA BF
 115 THR   ( 128-)  B      CG2 <->  157 HIS   ( 199-)  B      CD2    0.08    3.12  INTRA BL
 250 HIS   ( 102-)  D      NE2 <->  255 GLN   ( 107-)  D      OE1    0.08    2.62  INTRA
   5 ALA   (  89-)  A      O   <->   22 GLY   ( 106-)  A      N      0.07    2.63  INTRA BF
And so on for a total of 56 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

  63 LEU   (  76-)  B      -6.50
 221 GLN   (  73-)  D      -5.67
  26 GLN   ( 110-)  A      -5.59
 224 LEU   (  76-)  D      -5.36
  32 GLU   ( 116-)  A      -5.24
  60 GLN   (  73-)  B      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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: C

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: D

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.

 308 LEU   ( 189-)  D   -2.55
 147 LEU   ( 189-)  B   -2.54

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 145 SER   ( 187-)  B     -  148 ALA   ( 190-)  B        -2.05
 306 SER   ( 187-)  D     -  309 ALA   ( 190-)  D        -1.98

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 327 HOH   ( 837 )  C      O     42.62   44.58   40.56
 328 HOH   ( 878 )  D      O     44.53   34.24    7.87

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.

 326 HOH   ( 815 )  B      O
 326 HOH   ( 834 )  B      O
 326 HOH   ( 887 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 103 HIS   ( 116-)  B
 311 HIS   ( 192-)  D
 318 HIS   ( 199-)  D

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.

   2 LEU   (  86-)  A      N
  10 GLU   (  94-)  A      N
  32 GLU   ( 116-)  A      N
  90 SER   ( 103-)  B      N
 105 GLN   ( 118-)  B      NE2
 112 GLN   ( 125-)  B      NE2
 121 ARG   ( 134-)  B      NE
 130 TYR   ( 143-)  B      N
 168 TYR   (  91-)  C      N
 173 ILE   (  96-)  C      N
 177 ASP   ( 100-)  C      N
 193 GLU   ( 116-)  C      N
 224 LEU   (  76-)  D      N
 251 SER   ( 103-)  D      N
 273 GLN   ( 125-)  D      NE2
 291 TYR   ( 143-)  D      N
 291 TYR   ( 143-)  D      OH
 315 ARG   ( 196-)  D      NE

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.

  52 ASN   ( 136-)  A      OD1
 234 ASP   (  86-)  D      OD1
 266 GLN   ( 118-)  D      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.

 110 ASP   ( 123-)  B   H-bonding suggests Asn
 234 ASP   (  86-)  D   H-bonding suggests Asn
 256 ASP   ( 108-)  D   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 259 ASP   ( 111-)  D   H-bonding suggests Asn
 271 ASP   ( 123-)  D   H-bonding suggests Asn
 301 GLU   ( 182-)  D   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 :  -1.068
  2nd generation packing quality :  -0.035
  Ramachandran plot appearance   :  -2.140
  chi-1/chi-2 rotamer normality  :  -2.573
  Backbone conformation          :  -0.896

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.432 (tight)
  Bond angles                    :   0.739
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.450 (tight)
  Improper dihedral distribution :   0.940
  B-factor distribution          :   0.627
  Inside/Outside distribution    :   1.073

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.432 (tight)
  Bond angles                    :   0.739
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.450 (tight)
  Improper dihedral distribution :   0.940
  B-factor distribution          :   0.627
  Inside/Outside distribution    :   1.073
==============

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.