WHAT IF Check report

This file was created 2011-12-13 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 pdb2dhb.ent

Checks that need to be done early-on in validation

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

  15 SER   (  15-)  A  -   CB      3
  15 SER   (  15-)  A  -   OG      3
  67 THR   (  67-)  A  -   CG2     3

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 290 HEM   ( 142-)  A  -
 291 HEM   ( 147-)  B  -

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

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 VAL   (   1-)  A    Zero
   2 LEU   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 ALA   (   4-)  A    Zero
   5 ALA   (   5-)  A    Zero
   6 ASP   (   6-)  A    Zero
   7 LYS   (   7-)  A    Zero
   8 THR   (   8-)  A    Zero
   9 ASN   (   9-)  A    Zero
  10 VAL   (  10-)  A    Zero
  11 LYS   (  11-)  A    Zero
  12 ALA   (  12-)  A    Zero
  13 ALA   (  13-)  A    Zero
  14 TRP   (  14-)  A    Zero
  15 SER   (  15-)  A    Zero
  16 LYS   (  16-)  A    Zero
  17 VAL   (  17-)  A    Zero
  18 GLY   (  18-)  A    Zero
  19 GLY   (  19-)  A    Zero
  20 HIS   (  20-)  A    Zero
  21 ALA   (  21-)  A    Zero
  22 GLY   (  22-)  A    Zero
  23 GLU   (  23-)  A    Zero
  24 TYR   (  24-)  A    Zero
  25 GLY   (  25-)  A    Zero
And so on for a total of 287 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.

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

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  31 ARG   (  31-)  A
  92 ARG   (  92-)  A
 141 ARG   ( 141-)  A
 171 ARG   (  30-)  B
 181 ARG   (  40-)  B
 245 ARG   ( 104-)  B
 257 ARG   ( 116-)  B

Warning: Tyrosine convention problem

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

  24 TYR   (  24-)  A
 140 TYR   ( 140-)  A
 286 TYR   ( 145-)  B

Warning: Phenylalanine convention problem

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

  36 PHE   (  36-)  A
  43 PHE   (  43-)  A
  46 PHE   (  46-)  A
 182 PHE   (  41-)  B
 183 PHE   (  42-)  B
 186 PHE   (  45-)  B
 212 PHE   (  71-)  B
 226 PHE   (  85-)  B
 259 PHE   ( 118-)  B

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.

  94 ASP   (  94-)  A
 157 ASP   (  16-)  B
 184 ASP   (  43-)  B
 188 ASP   (  47-)  B
 220 ASP   (  79-)  B
 240 ASP   (  99-)  B

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.

  27 GLU   (  27-)  A
  30 GLU   (  30-)  A
 147 GLU   (   6-)  B
 161 GLU   (  20-)  B
 163 GLU   (  22-)  B
 167 GLU   (  26-)  B
 214 GLU   (  73-)  B
 231 GLU   (  90-)  B
 266 GLU   ( 125-)  B

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.

  14 TRP   (  14-)  A      NE1  CE2   1.28   -8.0
 122 HIS   ( 122-)  A      CB   CG    1.56    4.6
 156 TRP   (  15-)  B      NE1  CE2   1.28   -7.8
 178 TRP   (  37-)  B      NE1  CE2   1.28   -7.8
 195 VAL   (  54-)  B      N    CA    1.53    4.0

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.987650 -0.000043 -0.000852|
 | -0.000043  0.985583 -0.000366|
 | -0.000852 -0.000366  0.987817|
Proposed new scale matrix

 |  0.000000 -0.013184 -0.000005|
 |  0.007357  0.000004  0.009984|
 | -0.008796  0.000002  0.006473|
With corresponding cell

    A    =  75.849  B   =  80.632  C    =  91.564
    Alpha=  89.963  Beta=  89.976  Gamma=  89.965

The CRYST1 cell dimensions

    A    =  76.960  B   =  81.700  C    =  92.630
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1604.620
(Under-)estimated Z-score: 29.522

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.

   2 LEU   (   2-)  A     -C    N    CA  129.45    4.3
   5 ALA   (   5-)  A     -C    N    CA  133.80    6.7
   6 ASP   (   6-)  A      CA   C    O   110.63   -6.0
   6 ASP   (   6-)  A      N    CA   CB  118.10    4.5
   6 ASP   (   6-)  A      C    CA   CB  118.57    4.5
   8 THR   (   8-)  A     -C    N    CA  130.49    4.9
   8 THR   (   8-)  A      CA   CB   CG2 117.34    4.0
  10 VAL   (  10-)  A     -C    N    CA  132.31    5.9
  11 LYS   (  11-)  A      CA   C    O   113.37   -4.4
  11 LYS   (  11-)  A      N    CA   CB  119.93    5.5
  17 VAL   (  17-)  A     -C    N    CA  133.50    6.6
  18 GLY   (  18-)  A     -C    N    CA  129.57    5.3
  20 HIS   (  20-)  A     -C    N    CA  131.19    5.3
  22 GLY   (  22-)  A     -C    N    CA  128.69    4.8
  23 GLU   (  23-)  A      CA   C    O   113.42   -4.3
  25 GLY   (  25-)  A     -C    N    CA  128.23    4.5
  27 GLU   (  27-)  A      N    CA   CB  100.46   -5.9
  28 ALA   (  28-)  A     -C    N    CA  130.78    5.0
  29 LEU   (  29-)  A      CA   C    O   113.74   -4.2
  31 ARG   (  31-)  A      CB   CG   CD  102.22   -5.9
  32 MET   (  32-)  A      CA   C    O   112.85   -4.7
  33 PHE   (  33-)  A      CA   C    O   113.69   -4.2
  34 LEU   (  34-)  A     -CA  -C    N   108.08   -4.1
  37 PRO   (  37-)  A      CD   N    CA  101.25   -7.7
  38 THR   (  38-)  A     -C    N    CA  132.08    5.8
And so on for a total of 207 lines.

Warning: High bond angle deviations

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

RMS Z-score for bond angles: 2.167
RMS-deviation in bond angles: 4.003

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.

  27 GLU   (  27-)  A
  30 GLU   (  30-)  A
  31 ARG   (  31-)  A
  92 ARG   (  92-)  A
  94 ASP   (  94-)  A
 141 ARG   ( 141-)  A
 147 GLU   (   6-)  B
 157 ASP   (  16-)  B
 161 GLU   (  20-)  B
 163 GLU   (  22-)  B
 167 GLU   (  26-)  B
 171 ARG   (  30-)  B
 181 ARG   (  40-)  B
 184 ASP   (  43-)  B
 188 ASP   (  47-)  B
 214 GLU   (  73-)  B
 220 ASP   (  79-)  B
 231 GLU   (  90-)  B
 240 ASP   (  99-)  B
 245 ARG   ( 104-)  B
 257 ARG   ( 116-)  B
 266 GLU   ( 125-)  B

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.

   1 VAL   (   1-)  A      C     10.8    14.97     0.15
   2 LEU   (   2-)  A      C     -9.5   -14.77     0.20
   3 SER   (   3-)  A      C     -8.4   -13.42     0.37
   4 ALA   (   4-)  A      C     15.6    24.02     0.08
   6 ASP   (   6-)  A      CA    -8.6    16.66    33.73
   6 ASP   (   6-)  A      C     15.3    23.56    -0.01
   7 LYS   (   7-)  A      C     13.1    19.84     0.11
   9 ASN   (   9-)  A      C     13.7    21.80     0.27
  11 LYS   (  11-)  A      CA    -6.1    23.87    33.92
  11 LYS   (  11-)  A      C     11.3    17.15     0.11
  12 ALA   (  12-)  A      C     14.8    22.77     0.08
  13 ALA   (  13-)  A      C     10.3    15.79     0.08
  14 TRP   (  14-)  A      C      6.8    10.21     0.23
  16 LYS   (  16-)  A      C     10.4    15.74     0.11
  18 GLY   (  18-)  A      C     13.3    17.66     0.06
  19 GLY   (  19-)  A      C     10.8    14.28     0.06
  21 ALA   (  21-)  A      C      8.0    12.38     0.08
  23 GLU   (  23-)  A      C     15.2    22.03    -0.03
  25 GLY   (  25-)  A      C      7.8    10.39     0.06
  26 ALA   (  26-)  A      C      6.8    10.50     0.08
  27 GLU   (  27-)  A      C      8.2    11.91    -0.03
  28 ALA   (  28-)  A      C      7.2    11.07     0.08
  29 LEU   (  29-)  A      C     14.2    22.64     0.20
  32 MET   (  32-)  A      C     13.8    20.70     0.17
  33 PHE   (  33-)  A      C     15.3    25.20     0.23
And so on for a total of 199 lines.

Error: High improper dihedral angle deviations

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

Improper dihedral RMS Z-score : 6.477

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.

 108 THR   ( 108-)  A   12.41
 183 PHE   (  42-)  B    8.09
 194 ALA   (  53-)  B    7.78
 147 GLU   (   6-)  B    5.95
 227 ALA   (  86-)  B    5.58
  34 LEU   (  34-)  A    5.23
 190 SER   (  49-)  B    5.11
 237 LEU   (  96-)  B    5.04
 199 PRO   (  58-)  B    4.92
 151 ALA   (  10-)  B    4.67
 267 LEU   ( 126-)  B    4.60
 154 ALA   (  13-)  B    4.59
 265 PRO   ( 124-)  B    4.58
 138 SER   ( 138-)  A    4.51
  88 ALA   (  88-)  A    4.37
 169 LEU   (  28-)  B    4.31
 209 LEU   (  68-)  B    4.23
 164 VAL   (  23-)  B    4.21
 258 HIS   ( 117-)  B    4.17
 119 PRO   ( 119-)  A    4.14
 226 PHE   (  85-)  B    4.14
 235 ASP   (  94-)  B    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 : 2.399

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.

 180 GLN   (  39-)  B   13.51
 160 ASN   (  19-)  B   12.90
 220 ASP   (  79-)  B   12.62
 268 GLN   ( 127-)  B   12.25
 157 ASP   (  16-)  B   11.50
 242 GLU   ( 101-)  B   11.41
 240 ASP   (  99-)  B   11.16
  85 ASN   (  85-)  A   10.72
   9 ASN   (   9-)  A   10.70
 191 ASN   (  50-)  B   10.56
  82 ASP   (  82-)  A   10.51
  94 ASP   (  94-)  A   10.16
  74 ASP   (  74-)  A    9.86
 272 GLN   ( 131-)  B    9.82
 167 GLU   (  26-)  B    9.22
 148 GLU   (   7-)  B    9.14
 249 ASN   ( 108-)  B    8.54
 163 GLU   (  22-)  B    8.18
  27 GLU   (  27-)  A    7.99
 221 ASN   (  80-)  B    7.62
  30 GLU   (  30-)  A    6.28
 184 ASP   (  43-)  B    6.26
  47 ASP   (  47-)  A    6.15
  75 ASP   (  75-)  A    6.03
  42 TYR   (  42-)  A    5.89
  97 ASN   (  97-)  A    5.89
 161 GLU   (  20-)  B    5.71
 262 ASP   ( 121-)  B    5.51
 280 ASN   ( 139-)  B    4.80
 147 GLU   (   6-)  B    4.79
 214 GLU   (  73-)  B    4.47

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.

 286 TYR   ( 145-)  B      OH   7.86
 271 TYR   ( 130-)  B      OH   7.70
 176 TYR   (  35-)  B      OH   5.38
 140 TYR   ( 140-)  A      OH   4.44
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -6.639

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 : -6.639

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.

 265 PRO   ( 124-)  B    -3.1
  52 SER   (  52-)  A    -2.7
  37 PRO   (  37-)  A    -2.7
  92 ARG   (  92-)  A    -2.7
  18 GLY   (  18-)  A    -2.4
  90 LYS   (  90-)  A    -2.4
 119 PRO   ( 119-)  A    -2.4
  36 PHE   (  36-)  A    -2.3
 153 LEU   (  12-)  B    -2.3
 159 VAL   (  18-)  B    -2.2
   2 LEU   (   2-)  A    -2.2
  41 THR   (  41-)  A    -2.1
 186 PHE   (  45-)  B    -2.1
 143 GLN   (   2-)  B    -2.1
 160 ASN   (  19-)  B    -2.0
  66 LEU   (  66-)  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.

  18 GLY   (  18-)  A  Poor phi/psi
  36 PHE   (  36-)  A  PRO omega poor
  37 PRO   (  37-)  A  Poor phi/psi
  49 SER   (  49-)  A  Poor phi/psi
  52 SER   (  52-)  A  Poor phi/psi
  63 ALA   (  63-)  A  omega poor
  76 LEU   (  76-)  A  Poor phi/psi, PRO omega poor
  84 SER   (  84-)  A  Poor phi/psi, omega poor
  89 HIS   (  89-)  A  omega poor
  95 PRO   (  95-)  A  Poor phi/psi
 108 THR   ( 108-)  A  Poor phi/psi, omega poor
 109 LEU   ( 109-)  A  Poor phi/psi, omega poor
 117 PHE   ( 117-)  A  omega poor
 119 PRO   ( 119-)  A  omega poor
 145 SER   (   4-)  B  omega poor
 146 GLY   (   5-)  B  Poor phi/psi
 158 LYS   (  17-)  B  omega poor
 159 VAL   (  18-)  B  omega poor
 160 ASN   (  19-)  B  omega poor
 161 GLU   (  20-)  B  Poor phi/psi
 162 GLU   (  21-)  B  Poor phi/psi
 176 TYR   (  35-)  B  PRO omega poor
 179 THR   (  38-)  B  omega poor
 182 PHE   (  41-)  B  omega poor
 183 PHE   (  42-)  B  omega poor
 184 ASP   (  43-)  B  omega poor
 186 PHE   (  45-)  B  Poor phi/psi
 190 SER   (  49-)  B  Poor phi/psi
 191 ASN   (  50-)  B  PRO omega poor
 194 ALA   (  53-)  B  omega poor
 223 LYS   (  82-)  B  Poor phi/psi
 236 LYS   (  95-)  B  omega poor
 238 HIS   (  97-)  B  Poor phi/psi
 241 PRO   ( 100-)  B  omega poor
 264 THR   ( 123-)  B  PRO omega poor
 265 PRO   ( 124-)  B  Poor phi/psi
 284 HIS   ( 143-)  B  Poor phi/psi
 285 LYS   ( 144-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.345

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 : -5.345

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.

 270 SER   ( 129-)  B    0.36
 131 SER   ( 131-)  A    0.39

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!

  14 TRP   (  14-)  A      0
  17 VAL   (  17-)  A      0
  20 HIS   (  20-)  A      0
  27 GLU   (  27-)  A      0
  36 PHE   (  36-)  A      0
  37 PRO   (  37-)  A      0
  42 TYR   (  42-)  A      0
  43 PHE   (  43-)  A      0
  45 HIS   (  45-)  A      0
  48 LEU   (  48-)  A      0
  49 SER   (  49-)  A      0
  50 HIS   (  50-)  A      0
  52 SER   (  52-)  A      0
  53 ALA   (  53-)  A      0
  72 HIS   (  72-)  A      0
  73 LEU   (  73-)  A      0
  75 ASP   (  75-)  A      0
  76 LEU   (  76-)  A      0
  80 LEU   (  80-)  A      0
  84 SER   (  84-)  A      0
  91 LEU   (  91-)  A      0
  92 ARG   (  92-)  A      0
  94 ASP   (  94-)  A      0
 113 LEU   ( 113-)  A      0
 117 PHE   ( 117-)  A      0
And so on for a total of 89 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 9.152

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!

 173 LEU   (  32-)  B   1.53   34

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  33 PHE   (  33-)  A   1.50
  80 LEU   (  80-)  A   1.60
  87 HIS   (  87-)  A   2.16
 161 GLU   (  20-)  B   1.96
 171 ARG   (  30-)  B   1.59
 226 PHE   (  85-)  B   2.48
 237 LEU   (  96-)  B   2.13
 261 LYS   ( 120-)  B   2.17
 270 SER   ( 129-)  B   1.56

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].

  37 PRO   (  37-)  A   158.1 half-chair C-alpha/N (162 degrees)
  95 PRO   (  95-)  A  -121.5 half-chair C-delta/C-gamma (-126 degrees)
 119 PRO   ( 119-)  A   -44.7 envelop C-alpha (-36 degrees)
 265 PRO   ( 124-)  B  -120.8 half-chair C-delta/C-gamma (-126 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.

  34 LEU   (  34-)  A      CD1 <->  265 PRO   ( 124-)  B      CB     0.55    2.65  INTRA BL
  34 LEU   (  34-)  A      CD1 <->  265 PRO   ( 124-)  B      CA     0.40    2.80  INTRA BL
  34 LEU   (  34-)  A      CD1 <->  265 PRO   ( 124-)  B      C      0.38    2.82  INTRA BL
 103 HIS   ( 103-)  A      CE1 <->  272 GLN   ( 131-)  B      NE2    0.37    2.73  INTRA BL
 145 SER   (   4-)  B      C   <->  147 GLU   (   6-)  B      N      0.23    2.67  INTRA BL
 118 THR   ( 118-)  A      O   <->  171 ARG   (  30-)  B      NH1    0.21    2.49  INTRA BL
  85 ASN   (  85-)  A      CG  <->   89 HIS   (  89-)  A      NE2    0.19    2.91  INTRA BL
 107 SER   ( 107-)  A      O   <->  110 ALA   ( 110-)  A      N      0.19    2.51  INTRA BL
 111 VAL   ( 111-)  A      CG1 <->  260 GLY   ( 119-)  B      C      0.17    3.03  INTRA BL
 106 LEU   ( 106-)  A      CD1 <->  122 HIS   ( 122-)  A      CD2    0.17    3.03  INTRA BL
  95 PRO   (  95-)  A      CB  <->  137 THR   ( 137-)  A      CG2    0.16    3.04  INTRA BL
 148 GLU   (   7-)  B      O   <->  152 VAL   (  11-)  B      N      0.15    2.55  INTRA BL
  21 ALA   (  21-)  A      C   <->   63 ALA   (  63-)  A      CB     0.15    3.05  INTRA BL
 255 VAL   ( 114-)  B      CG1 <->  263 PHE   ( 122-)  B      CE1    0.15    3.05  INTRA BL
  29 LEU   (  29-)  A      CD1 <->   58 HIS   (  58-)  A      CD2    0.14    3.06  INTRA BL
 167 GLU   (  26-)  B      CD  <->  257 ARG   ( 116-)  B      NH1    0.13    2.97  INTRA BL
 153 LEU   (  12-)  B      CD1 <->  217 HIS   (  76-)  B      CD2    0.13    3.07  INTRA BL
 167 GLU   (  26-)  B      OE2 <->  171 ARG   (  30-)  B      NE     0.13    2.57  INTRA BL
 150 ALA   (   9-)  B      O   <->  154 ALA   (  13-)  B      N      0.13    2.57  INTRA BL
 201 VAL   (  60-)  B      O   <->  205 GLY   (  64-)  B      N      0.12    2.58  INTRA BL
 229 LEU   (  88-)  B      O   <->  233 HIS   (  92-)  B      N      0.09    2.61  INTRA BL
  94 ASP   (  94-)  A      O   <->   96 VAL   (  96-)  A      N      0.09    2.61  INTRA BL
  27 GLU   (  27-)  A      OE2 <->   31 ARG   (  31-)  A      NH2    0.09    2.61  INTRA BL
  82 ASP   (  82-)  A      CG  <->   83 LEU   (  83-)  A      N      0.09    2.91  INTRA BL
  83 LEU   (  83-)  A      CD1 <->  290 HEM   ( 142-)  A      CMA    0.08    3.12  INTRA BL
And so on for a total of 53 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

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  89 HIS   (  89-)  A      -5.77
 143 GLN   (   2-)  B      -5.65
 258 HIS   ( 117-)  B      -5.60
  50 HIS   (  50-)  A      -5.05

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 287 : -1.580

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

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.

 157 ASP   (  16-)  B   -2.53

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.

 161 GLU   (  20-)  B     -  164 VAL   (  23-)  B        -1.66

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

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.

 292 HOH   ( 144 )  A      O      1.17    0.25   -0.76

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.

  97 ASN   (  97-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   5 ALA   (   5-)  A      N
  18 GLY   (  18-)  A      N
  19 GLY   (  19-)  A      N
  31 ARG   (  31-)  A      N
  38 THR   (  38-)  A      N
  39 THR   (  39-)  A      OG1
  40 LYS   (  40-)  A      N
  41 THR   (  41-)  A      N
  43 PHE   (  43-)  A      N
  55 VAL   (  55-)  A      N
  62 VAL   (  62-)  A      N
  71 GLY   (  71-)  A      N
  72 HIS   (  72-)  A      NE2
  75 ASP   (  75-)  A      N
  76 LEU   (  76-)  A      N
  84 SER   (  84-)  A      N
  87 HIS   (  87-)  A      N
  88 ALA   (  88-)  A      N
  98 PHE   (  98-)  A      N
 102 SER   ( 102-)  A      OG
 109 LEU   ( 109-)  A      N
 112 HIS   ( 112-)  A      N
 120 ALA   ( 120-)  A      N
 121 VAL   ( 121-)  A      N
 122 HIS   ( 122-)  A      N
 139 LYS   ( 139-)  A      N
 147 GLU   (   6-)  B      N
 164 VAL   (  23-)  B      N
 171 ARG   (  30-)  B      NH1
 178 TRP   (  37-)  B      NE1
 181 ARG   (  40-)  B      N
 194 ALA   (  53-)  B      N
 198 ASN   (  57-)  B      N
 220 ASP   (  79-)  B      N
 223 LYS   (  82-)  B      N
 228 ALA   (  87-)  B      N
 238 HIS   (  97-)  B      N
 240 ASP   (  99-)  B      N
 253 LEU   ( 112-)  B      N
 257 ARG   ( 116-)  B      NH1
 266 GLU   ( 125-)  B      N
 267 LEU   ( 126-)  B      N
 268 GLN   ( 127-)  B      NE2
 270 SER   ( 129-)  B      N
 276 ALA   ( 135-)  B      N
 287 HIS   ( 146-)  B      N
Only metal coordination for   87 HIS  (  87-) A      NE2
Only metal coordination for  233 HIS  (  92-) B      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.

  75 ASP   (  75-)  A      OD1
  85 ASN   (  85-)  A      OD1
 122 HIS   ( 122-)  A      ND1
 184 ASP   (  43-)  B      OD1
 238 HIS   (  97-)  B      ND1
 240 ASP   (  99-)  B      OD2
 258 HIS   ( 117-)  B      ND1
 272 GLN   ( 131-)  B      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.

   6 ASP   (   6-)  A   H-bonding suggests Asn; but Alt-Rotamer
  23 GLU   (  23-)  A   H-bonding suggests Gln; 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 :  -2.700
  2nd generation packing quality :  -3.014 (poor)
  Ramachandran plot appearance   :  -6.639 (bad)
  chi-1/chi-2 rotamer normality  :  -5.345 (bad)
  Backbone conformation          :  -1.785

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.221
  Bond angles                    :   2.167 (loose)
  Omega angle restraints         :   1.664 (loose)
  Side chain planarity           :   5.379 (loose)
  Improper dihedral distribution :   6.477 (loose)
  Inside/Outside distribution    :   0.939

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 :  -2.1
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -4.0 (bad)
  chi-1/chi-2 rotamer normality  :  -2.9
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.221
  Bond angles                    :   2.167 (loose)
  Omega angle restraints         :   1.664 (loose)
  Side chain planarity           :   5.379 (loose)
  Improper dihedral distribution :   6.477 (loose)
  Inside/Outside distribution    :   0.939
==============

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.