WHAT IF Check report

This file was created 2012-01-05 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 pdb1oo3.ent

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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 GLY   (   1-)  A    Zero
   2 MET   (   2-)  A    Zero
   3 ASN   (   3-)  A    Zero
   4 ASN   (   4-)  A    Zero
   5 ASN   (   5-)  A    Zero
   6 MET   (   6-)  A    Zero
   7 SER   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 GLN   (   9-)  A    Zero
  10 ASP   (  10-)  A    Zero
  11 ALA   (  11-)  A    Zero
  12 GLU   (  12-)  A    Zero
  13 TRP   (  13-)  A    Zero
  14 TYR   (  14-)  A    Zero
  15 TRP   (  15-)  A    Zero
  16 GLY   (  16-)  A    Zero
  17 ASP   (  17-)  A    Zero
  18 ILE   (  18-)  A    Zero
  19 SER   (  19-)  A    Zero
  20 ARG   (  20-)  A    Zero
  21 GLU   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  23 VAL   (  23-)  A    Zero
  24 ASN   (  24-)  A    Zero
  25 GLU   (  25-)  A    Zero
And so on for a total of 111 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 not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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 : 100.00

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: A

Nomenclature related problems

Warning: Aspartic acid convention problem

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

  29 ASP   (  29-)  A
  32 ASP   (  32-)  A
  39 ASP   (  39-)  A
  47 ASP   (  47-)  A
  74 ASP   (  74-)  A
 101 ASP   ( 101-)  A

Warning: Glutamic acid convention problem

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

  22 GLU   (  22-)  A
  91 GLU   (  91-)  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.

  10 ASP   (  10-)  A      CG   OD2   1.36    6.0
  12 GLU   (  12-)  A      CD   OE2   1.37    6.1
  17 ASP   (  17-)  A      CG   OD2   1.36    5.8
  21 GLU   (  21-)  A      CD   OE2   1.37    6.1
  22 GLU   (  22-)  A      CD   OE1   1.37    6.3
  25 GLU   (  25-)  A      CD   OE2   1.37    6.3
  29 ASP   (  29-)  A      CG   OD1   1.37    6.3
  32 ASP   (  32-)  A      CG   OD1   1.37    6.3
  39 ASP   (  39-)  A      CG   OD1   1.36    5.9
  45 HIS   (  45-)  A      CG   CD2   1.41    4.5
  45 HIS   (  45-)  A      ND1  CE1   1.37    4.1
  47 ASP   (  47-)  A      CG   OD1   1.36    6.1
  67 ASP   (  67-)  A      CG   OD2   1.37    6.3
  74 ASP   (  74-)  A      CG   OD1   1.36    5.9
  83 GLU   (  83-)  A      CD   OE2   1.36    5.9
  87 HIS   (  87-)  A      CG   CD2   1.40    4.3
  91 GLU   (  91-)  A      CD   OE1   1.36    6.0
 101 ASP   ( 101-)  A      CG   OD1   1.37    6.2

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.501
RMS-deviation in bond distances: 0.030

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

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.

   3 ASN   (   3-)  A      CA   CB   CG  120.10    7.5
   3 ASN   (   3-)  A      ND2  CG   OD1 118.41   -4.2
   4 ASN   (   4-)  A      CA   CB   CG  120.18    7.6
  10 ASP   (  10-)  A      CA   CB   CG  118.01    5.4
  13 TRP   (  13-)  A      N    CA   CB  103.44   -4.2
  15 TRP   (  15-)  A      CA   CB   CG  121.58    4.2
  17 ASP   (  17-)  A      CA   CB   CG  116.73    4.1
  21 GLU   (  21-)  A      N    CA   CB  102.48   -4.7
  31 ALA   (  31-)  A      C    CA   CB  118.54    5.4
  32 ASP   (  32-)  A      CA   CB   CG  121.16    8.6
  34 THR   (  34-)  A      CA   CB   CG2 118.92    5.0
  45 HIS   (  45-)  A      C    CA   CB  118.74    4.5
  45 HIS   (  45-)  A      CG   ND1  CE1  99.90   -5.7
  45 HIS   (  45-)  A      ND1  CE1  NE2 120.09    6.5
  45 HIS   (  45-)  A      CE1  NE2  CD2  99.04   -6.0
  45 HIS   (  45-)  A      NE2  CD2  CG  111.13    4.6
  47 ASP   (  47-)  A      C    CA   CB  118.35    4.3
  47 ASP   (  47-)  A      CA   CB   CG  121.43    8.8
  49 THR   (  49-)  A      CA   CB   CG2 118.35    4.6
  61 ILE   (  61-)  A      CA   CB   CG1 119.63    5.4
  64 PHE   (  64-)  A      CA   CB   CG  118.04    4.2
  65 HIS   (  65-)  A      CA   CB   CG  119.53    5.7
  65 HIS   (  65-)  A      CG   ND1  CE1 100.05   -5.6
  65 HIS   (  65-)  A      ND1  CE1  NE2 119.93    6.3
  65 HIS   (  65-)  A      CE1  NE2  CD2  98.84   -6.2
  65 HIS   (  65-)  A      NE2  CD2  CG  111.30    4.8
  69 LYS   (  69-)  A      CB   CG   CD  121.22    4.3
  72 PHE   (  72-)  A      CA   CB   CG  118.94    5.1
  74 ASP   (  74-)  A      C    CA   CB  119.77    5.1
  78 PHE   (  78-)  A      CA   CB   CG  119.17    5.4
  85 ILE   (  85-)  A      CA   CB   CG1 118.55    4.8
  86 ASN   (  86-)  A      CA   CB   CG  120.46    7.9
  87 HIS   (  87-)  A      CG   ND1  CE1 100.12   -5.5
  87 HIS   (  87-)  A      ND1  CE1  NE2 119.95    6.3
  87 HIS   (  87-)  A      CE1  NE2  CD2  98.92   -6.1
  87 HIS   (  87-)  A      NE2  CD2  CG  111.03    4.5
  90 ASN   (  90-)  A      ND2  CG   OD1 118.33   -4.3
  94 ALA   (  94-)  A      N    CA   CB  103.76   -4.4
  98 PRO   (  98-)  A     -CA  -C    N   123.90    4.7
 101 ASP   ( 101-)  A      CA   CB   CG  117.49    4.9
 107 PRO   ( 107-)  A     -CA  -C    N   123.95    4.7

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  22 GLU   (  22-)  A
  29 ASP   (  29-)  A
  32 ASP   (  32-)  A
  39 ASP   (  39-)  A
  47 ASP   (  47-)  A
  74 ASP   (  74-)  A
  91 GLU   (  91-)  A
 101 ASP   ( 101-)  A

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  31 ALA   (  31-)  A      CA    -6.9    25.28    34.09
The average deviation= 1.650

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.

  94 ALA   (  94-)  A    5.89

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 : 1.561

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.

  58 ASN   (  58-)  A    4.95

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -6.194

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.

  64 PHE   (  64-)  A    -3.2
  48 TYR   (  48-)  A    -2.9
 104 LEU   ( 104-)  A    -2.8
  34 THR   (  34-)  A    -2.7
  36 LEU   (  36-)  A    -2.6
  52 LEU   (  52-)  A    -2.5
  18 ILE   (  18-)  A    -2.5
  54 LYS   (  54-)  A    -2.4
  71 GLY   (  71-)  A    -2.2
  86 ASN   (  86-)  A    -2.0
  38 ARG   (  38-)  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.

   7 SER   (   7-)  A  Poor phi/psi
   8 LEU   (   8-)  A  omega poor
   9 GLN   (   9-)  A  Poor phi/psi
  13 TRP   (  13-)  A  omega poor
  14 TYR   (  14-)  A  omega poor
  15 TRP   (  15-)  A  omega poor
  20 ARG   (  20-)  A  Poor phi/psi
  21 GLU   (  21-)  A  Poor phi/psi, omega poor
  22 GLU   (  22-)  A  Poor phi/psi
  26 LYS   (  26-)  A  omega poor
  31 ALA   (  31-)  A  Poor phi/psi
  37 VAL   (  37-)  A  omega poor
  39 ASP   (  39-)  A  omega poor
  44 MET   (  44-)  A  Poor phi/psi
  45 HIS   (  45-)  A  Poor phi/psi
  47 ASP   (  47-)  A  omega poor
  48 TYR   (  48-)  A  Poor phi/psi
  61 ILE   (  61-)  A  omega poor
  64 PHE   (  64-)  A  Poor phi/psi
  66 ARG   (  66-)  A  Poor phi/psi
  67 ASP   (  67-)  A  Poor phi/psi, omega poor
  74 ASP   (  74-)  A  Poor phi/psi
  77 THR   (  77-)  A  Poor phi/psi
  79 ASN   (  79-)  A  omega poor
  80 SER   (  80-)  A  omega poor
  88 TYR   (  88-)  A  Poor phi/psi
  90 ASN   (  90-)  A  omega poor
  92 SER   (  92-)  A  omega poor
 101 ASP   ( 101-)  A  Poor phi/psi
 102 VAL   ( 102-)  A  Poor phi/psi
 107 PRO   ( 107-)  A  omega poor
 108 VAL   ( 108-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -5.360

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.360

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 SER   (   7-)  A      0
   8 LEU   (   8-)  A      0
   9 GLN   (   9-)  A      0
  10 ASP   (  10-)  A      0
  14 TYR   (  14-)  A      0
  15 TRP   (  15-)  A      0
  17 ASP   (  17-)  A      0
  18 ILE   (  18-)  A      0
  19 SER   (  19-)  A      0
  20 ARG   (  20-)  A      0
  21 GLU   (  21-)  A      0
  22 GLU   (  22-)  A      0
  30 THR   (  30-)  A      0
  31 ALA   (  31-)  A      0
  32 ASP   (  32-)  A      0
  34 THR   (  34-)  A      0
  36 LEU   (  36-)  A      0
  43 LYS   (  43-)  A      0
  44 MET   (  44-)  A      0
  45 HIS   (  45-)  A      0
  47 ASP   (  47-)  A      0
  48 TYR   (  48-)  A      0
  49 THR   (  49-)  A      0
  54 LYS   (  54-)  A      0
  63 ILE   (  63-)  A      0
And so on for a total of 77 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -3.382

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 11.729

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!

  56 GLY   (  56-)  A   1.77   27

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.280

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.

  96 TYR   (  96-)  A      -7.17
  43 LYS   (  43-)  A      -6.00
 100 LEU   ( 100-)  A      -5.99
 105 LEU   ( 105-)  A      -5.82
   9 GLN   (   9-)  A      -5.67
  72 PHE   (  72-)  A      -5.64
  63 ILE   (  63-)  A      -5.55
  44 MET   (  44-)  A      -5.44
  66 ARG   (  66-)  A      -5.33
  88 TYR   (  88-)  A      -5.29
  95 GLN   (  95-)  A      -5.20
   2 MET   (   2-)  A      -5.12
  70 TYR   (  70-)  A      -5.10

Warning: Abnormal packing environment for sequential residues

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

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

  43 LYS   (  43-)  A        45 - HIS     45- ( A)         -5.26
  70 TYR   (  70-)  A        72 - PHE     72- ( A)         -4.94

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 111 : -2.539

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: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: 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.

  10 ASP   (  10-)  A      N
  12 GLU   (  12-)  A      N
  13 TRP   (  13-)  A      N
  13 TRP   (  13-)  A      NE1
  17 ASP   (  17-)  A      N
  18 ILE   (  18-)  A      N
  35 PHE   (  35-)  A      N
  37 VAL   (  37-)  A      N
  45 HIS   (  45-)  A      N
  52 LEU   (  52-)  A      N
  55 GLY   (  55-)  A      N
  58 ASN   (  58-)  A      N
  61 ILE   (  61-)  A      N
  62 LYS   (  62-)  A      NZ
  63 ILE   (  63-)  A      N
  65 HIS   (  65-)  A      N
  66 ARG   (  66-)  A      N
  69 LYS   (  69-)  A      N
  70 TYR   (  70-)  A      N
  77 THR   (  77-)  A      N
  78 PHE   (  78-)  A      N
  84 LEU   (  84-)  A      N
  85 ILE   (  85-)  A      N
  90 ASN   (  90-)  A      N
  92 SER   (  92-)  A      N
  95 GLN   (  95-)  A      NE2
  99 LYS   (  99-)  A      N
 102 VAL   ( 102-)  A      N
 103 LYS   ( 103-)  A      N
 105 LEU   ( 105-)  A      N

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.

  29 ASP   (  29-)  A      OD1
  91 GLU   (  91-)  A      OE1
  95 GLN   (  95-)  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.

  10 ASP   (  10-)  A   H-bonding suggests Asn
  12 GLU   (  12-)  A   H-bonding suggests Gln
  22 GLU   (  22-)  A   H-bonding suggests Gln
  47 ASP   (  47-)  A   H-bonding suggests Asn; but Alt-Rotamer
  67 ASP   (  67-)  A   H-bonding suggests Asn
 101 ASP   ( 101-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :  -5.097 (poor)
  2nd generation packing quality :  -3.894 (poor)
  Ramachandran plot appearance   :  -6.194 (bad)
  chi-1/chi-2 rotamer normality  :  -5.360 (bad)
  Backbone conformation          :  -3.382 (poor)

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.501 (loose)
  Bond angles                    :   1.701
  Omega angle restraints         :   2.133 (loose)
  Side chain planarity           :   1.192
  Improper dihedral distribution :   1.471
  Inside/Outside distribution    :   1.280 (unusual)
==============

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.