WHAT IF Check report

This file was created 2011-12-17 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 pdb4pad.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    =  45.000  B   = 104.300  C    =  50.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  45.000  B   = 104.300  C    =  50.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  45.000  B   =  50.800  C    = 104.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  45.000  B   =  50.800  C    = 104.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

Error: Value in second row of scale matrix mistyped

The SCALE matrix is incompatible with the CRYST1 cell.

Possible cause: one or more of the values in the second row of the SCALE matrix are wrong.

Scale matrix as derived from SCALE

 |  0.022222  0.000000  0.000000|
 |  0.000000 -0.009855  0.000208|
 |  0.000000 -0.000427 -0.019680|

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.

 214 TCK   ( 213-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Rounded coordinates detected

At least two atoms were detected with all three coordinates rounded to 1 decimal place. Since this is highly unlikely to occur accidentally, the atoms listed in the table below were probably not refined. It could also be that ALL atomic coordinates were rounded to 1 or 2 decimal places (resulting in considerable loss of accuracy).

 215 HOH   ( 215 )  A      O    22.700    14.600    36.300
 215 HOH   ( 217 )  A      O    25.000    20.400    34.100
 215 HOH   ( 236 )  A      O    17.700    48.100    25.600
 215 HOH   ( 239 )  A      O    12.000    22.800    34.100
 215 HOH   ( 240 )  A      O    19.700    42.100    11.600

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 ILE   (   1-)  A    Zero
   2 PRO   (   2-)  A    Zero
   3 GLU   (   3-)  A    Zero
   4 TYR   (   4-)  A    Zero
   5 VAL   (   5-)  A    Zero
   6 ASP   (   6-)  A    Zero
   7 TRP   (   7-)  A    Zero
   8 ARG   (   8-)  A    Zero
   9 GLN   (   9-)  A    Zero
  10 LYS   (  10-)  A    Zero
  11 GLY   (  11-)  A    Zero
  12 ALA   (  12-)  A    Zero
  13 VAL   (  13-)  A    Zero
  14 THR   (  14-)  A    Zero
  15 PRO   (  15-)  A    Zero
  16 VAL   (  16-)  A    Zero
  17 LYS   (  17-)  A    Zero
  18 ASN   (  18-)  A    Zero
  19 GLN   (  19-)  A    Zero
  20 GLY   (  20-)  A    Zero
  21 SER   (  21-)  A    Zero
  22 CYS   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 SER   (  24-)  A    Zero
  25 CYS   (  25-)  A    Zero
And so on for a total of 212 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

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.

   8 ARG   (   8-)  A
  93 ARG   (  93-)  A
  98 ARG   (  98-)  A
 191 ARG   ( 191-)  A

Warning: Tyrosine convention problem

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

  48 TYR   (  48-)  A
  61 TYR   (  61-)  A
  67 TYR   (  67-)  A
  86 TYR   (  86-)  A
  94 TYR   (  94-)  A
 103 TYR   ( 103-)  A
 123 TYR   ( 123-)  A
 170 TYR   ( 170-)  A
 203 TYR   ( 203-)  A

Warning: Phenylalanine convention problem

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

 141 PHE   ( 141-)  A
 207 PHE   ( 207-)  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.

   7 TRP   (   7-)  A      NE1  CE2   1.28   -8.6
  18 ASN   (  18-)  A      CG   OD1   1.39    8.0
  18 ASN   (  18-)  A      CG   ND2   1.22   -5.2
  25 CYS   (  25-)  A      N   -C     1.57   12.3
  26 TRP   (  26-)  A      NE1  CE2   1.28   -8.6
  44 ASN   (  44-)  A      CG   OD1   1.39    7.9
  44 ASN   (  44-)  A      CG   ND2   1.22   -5.2
  46 ASN   (  46-)  A      CG   OD1   1.39    7.9
  46 ASN   (  46-)  A      CG   ND2   1.22   -5.2
  64 ASN   (  64-)  A      CG   OD1   1.39    7.9
  64 ASN   (  64-)  A      CG   ND2   1.22   -5.2
  69 TRP   (  69-)  A      NE1  CE2   1.28   -8.6
  70 SER   (  70-)  A      N    CA    1.68   11.9
  84 ASN   (  84-)  A      CG   OD1   1.39    8.0
  84 ASN   (  84-)  A      CG   ND2   1.22   -5.2
 117 ASN   ( 117-)  A      CG   OD1   1.39    7.9
 117 ASN   ( 117-)  A      CG   ND2   1.22   -5.2
 127 ASN   ( 127-)  A      CG   OD1   1.39    7.9
 127 ASN   ( 127-)  A      CG   ND2   1.22   -5.2
 152 PRO   ( 152-)  A      CD   N     1.32  -11.3
 152 PRO   ( 152-)  A      N   -C     1.23   -4.9
 155 ASN   ( 155-)  A      CG   OD1   1.39    8.0
 155 ASN   ( 155-)  A      CG   ND2   1.22   -5.0
 169 ASN   ( 169-)  A      CG   OD1   1.39    8.0
 169 ASN   ( 169-)  A      CG   ND2   1.22   -5.1
 175 ASN   ( 175-)  A      CG   OD1   1.39    8.0
 175 ASN   ( 175-)  A      CG   ND2   1.22   -5.0
 177 TRP   ( 177-)  A      NE1  CE2   1.28   -8.4
 181 TRP   ( 181-)  A      NE1  CE2   1.28   -8.3
 184 ASN   ( 184-)  A      CG   OD1   1.39    8.0
 184 ASN   ( 184-)  A      CG   ND2   1.22   -5.0
 195 ASN   ( 195-)  A      CG   OD1   1.39    8.0
 195 ASN   ( 195-)  A      CG   ND2   1.22   -5.1
 212 ASN   ( 212-)  A      CG   OD1   1.39    8.0
 212 ASN   ( 212-)  A      CG   ND2   1.22   -5.1
  56 CYS   (  56-)  A      SG  -SG*   1.69   -8.7
  95 CYS   (  95-)  A      SG  -SG*   1.69   -8.7

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

 |  0.995344  0.000176 -0.000320|
 |  0.000176  0.996457 -0.000291|
 | -0.000320 -0.000291  0.992570|
Proposed new scale matrix

 |  0.022326 -0.000004  0.000007|
 |  0.000002 -0.009619  0.000207|
 | -0.000006 -0.000434 -0.019827|
With corresponding cell

    A    =  44.791  B   = 103.935  C    =  50.423
    Alpha=  90.024  Beta=  89.964  Gamma=  90.021

The CRYST1 cell dimensions

    A    =  45.000  B   = 104.300  C    =  50.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 195.408
(Under-)estimated Z-score: 10.302

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   1 ILE   (   1-)  A      N    CA   C    90.17   -7.5
   1 ILE   (   1-)  A      CA   CB   CG2 101.76   -5.1
   3 GLU   (   3-)  A      CG   CD   OE2 108.00   -4.5
  18 ASN   (  18-)  A      CB   CG   ND2 124.93    5.7
  25 CYS   (  25-)  A     -O   -C    N   129.91    4.3
  34 ILE   (  34-)  A      CA   CB   CG2 101.81   -5.1
  35 GLU   (  35-)  A      CG   CD   OE2 107.99   -4.5
  37 ILE   (  37-)  A      CA   CB   CG2 101.73   -5.2
  38 ILE   (  38-)  A      CA   CB   CG2 101.76   -5.1
  40 ILE   (  40-)  A      CA   CB   CG2 101.74   -5.2
  44 ASN   (  44-)  A      CB   CG   ND2 124.84    5.6
  46 ASN   (  46-)  A      CB   CG   ND2 124.92    5.7
  50 GLU   (  50-)  A      CG   CD   OE2 108.04   -4.5
  52 GLU   (  52-)  A      CG   CD   OE2 107.99   -4.5
  64 ASN   (  64-)  A      CB   CG   ND2 124.91    5.7
  70 SER   (  70-)  A     -C    N    CA  110.00   -6.5
  80 ILE   (  80-)  A      CA   CB   CG2 101.73   -5.2
  84 ASN   (  84-)  A      CB   CG   ND2 124.90    5.7
  89 GLU   (  89-)  A      CG   CD   OE2 108.01   -4.5
  99 GLU   (  99-)  A      CG   CD   OE2 108.01   -4.5
 117 ASN   ( 117-)  A      CB   CG   ND2 124.90    5.7
 125 ILE   ( 125-)  A      CA   CB   CG2 101.72   -5.2
 127 ASN   ( 127-)  A      CB   CG   ND2 124.86    5.6
 148 ILE   ( 148-)  A      CA   CB   CG2 101.79   -5.1
 152 PRO   ( 152-)  A     -O   -C    N   128.98    5.0
 152 PRO   ( 152-)  A      CD   N    CA  117.85    4.2
 155 ASN   ( 155-)  A      CB   CG   ND2 124.91    5.7
 158 ASP   ( 158-)  A      N    CA   C   123.21    4.3
 169 ASN   ( 169-)  A      N    CA   C   128.04    6.0
 169 ASN   ( 169-)  A      C    CA   CB  100.39   -5.1
 169 ASN   ( 169-)  A      CB   CG   ND2 124.90    5.7
 171 ILE   ( 171-)  A      CA   CB   CG2 101.91   -5.1
 173 ILE   ( 173-)  A      CA   CB   CG2 101.92   -5.0
 175 ASN   ( 175-)  A      CB   CG   ND2 124.89    5.7
 183 GLU   ( 183-)  A      CG   CD   OE2 108.04   -4.5
 184 ASN   ( 184-)  A      CB   CG   ND2 124.87    5.6
 187 ILE   ( 187-)  A      CA   CB   CG2 101.95   -5.0
 189 ILE   ( 189-)  A      CA   CB   CG2 101.92   -5.0
 195 ASN   ( 195-)  A      CB   CG   ND2 124.90    5.7
 207 PHE   ( 207-)  A      N    CA   C   133.37    7.9
 207 PHE   ( 207-)  A      C    CA   CB   97.63   -6.6
 208 TYR   ( 208-)  A      N    CA   C   128.29    6.1
 208 TYR   ( 208-)  A      C    CA   CB  101.04   -4.8
 210 VAL   ( 210-)  A      N    CA   C    99.51   -4.2
 212 ASN   ( 212-)  A      CB   CG   ND2 124.92    5.7

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.

   8 ARG   (   8-)  A
  93 ARG   (  93-)  A
  98 ARG   (  98-)  A
 191 ARG   ( 191-)  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.

  69 TRP   (  69-)  A      C      6.6     9.96     0.23
The average deviation= 1.211

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.

 207 PHE   ( 207-)  A   10.51
 208 TYR   ( 208-)  A    8.16
   1 ILE   (   1-)  A    6.85
  70 SER   (  70-)  A    5.41
  40 ILE   (  40-)  A    5.39
 169 ASN   ( 169-)  A    5.35
 137 ALA   ( 137-)  A    4.56
  60 SER   (  60-)  A    4.32
 173 ILE   ( 173-)  A    4.29
 198 GLY   ( 198-)  A    4.08
  50 GLU   (  50-)  A    4.07
 210 VAL   ( 210-)  A    4.07
 158 ASP   ( 158-)  A    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 : 2.121

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.

  59 ARG   (  59-)  A    5.49

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 : -5.473

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.

  86 TYR   (  86-)  A    -3.6
  74 LEU   (  74-)  A    -2.6
  64 ASN   (  64-)  A    -2.4
  93 ARG   (  93-)  A    -2.4
  62 GLY   (  62-)  A    -2.4
 116 TYR   ( 116-)  A    -2.3
 209 PRO   ( 209-)  A    -2.3
 193 THR   ( 193-)  A    -2.3
 134 LEU   ( 134-)  A    -2.2
 128 GLN   ( 128-)  A    -2.2
  83 ARG   (  83-)  A    -2.2
  31 VAL   (  31-)  A    -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.

  25 CYS   (  25-)  A  omega poor
  62 GLY   (  62-)  A  Poor phi/psi
  63 CYS   (  63-)  A  Poor phi/psi
  64 ASN   (  64-)  A  Poor phi/psi
  69 TRP   (  69-)  A  omega poor
  78 TYR   (  78-)  A  Poor phi/psi
  86 TYR   (  86-)  A  Poor phi/psi
  93 ARG   (  93-)  A  Poor phi/psi
  97 SER   (  97-)  A  Poor phi/psi
 119 GLY   ( 119-)  A  Poor phi/psi
 128 GLN   ( 128-)  A  Poor phi/psi
 134 LEU   ( 134-)  A  Poor phi/psi
 137 ALA   ( 137-)  A  Poor phi/psi
 151 GLY   ( 151-)  A  PRO omega poor
 158 ASP   ( 158-)  A  Poor phi/psi
 161 VAL   ( 161-)  A  Poor phi/psi
 169 ASN   ( 169-)  A  Poor phi/psi
 184 ASN   ( 184-)  A  Poor phi/psi
 193 THR   ( 193-)  A  Poor phi/psi
 200 CYS   ( 200-)  A  Poor phi/psi
 208 TYR   ( 208-)  A  Poor phi/psi
 209 PRO   ( 209-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.990

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 : -4.990

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.

  29 SER   (  29-)  A    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!

   3 GLU   (   3-)  A      0
   7 TRP   (   7-)  A      0
  10 LYS   (  10-)  A      0
  12 ALA   (  12-)  A      0
  21 SER   (  21-)  A      0
  24 SER   (  24-)  A      0
  41 ARG   (  41-)  A      0
  46 ASN   (  46-)  A      0
  56 CYS   (  56-)  A      0
  58 ARG   (  58-)  A      0
  61 TYR   (  61-)  A      0
  63 CYS   (  63-)  A      0
  64 ASN   (  64-)  A      0
  78 TYR   (  78-)  A      0
  82 TYR   (  82-)  A      0
  85 THR   (  85-)  A      0
  86 TYR   (  86-)  A      0
  89 GLU   (  89-)  A      0
  92 GLN   (  92-)  A      0
  93 ARG   (  93-)  A      0
  94 TYR   (  94-)  A      0
  95 CYS   (  95-)  A      0
  96 ARG   (  96-)  A      0
 100 LYS   ( 100-)  A      0
 102 PRO   ( 102-)  A      0
And so on for a total of 110 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 : 2.156

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!

 182 GLY   ( 182-)  A   1.54   10

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.

 203 TYR   ( 203-)  A      OH  <->  215 HOH   ( 237 )  A      O      1.32    1.08  INTRA BL
  25 CYS   (  25-)  A      SG  <->  214 TCK   ( 213-)  A      CM     1.12    1.88  INTRA B3
 112 GLN   ( 112-)  A      CB  <->  207 PHE   ( 207-)  A      CE1    1.08    2.12  INTRA BL
 203 TYR   ( 203-)  A      CZ  <->  215 HOH   ( 237 )  A      O      0.93    1.87  INTRA BL
 135 GLN   ( 135-)  A      OE1 <->  154 GLY   ( 154-)  A      N      0.81    1.89  INTRA BL
 144 TYR   ( 144-)  A      CD1 <->  182 GLY   ( 182-)  A      CA     0.70    2.50  INTRA BL
  54 LEU   (  54-)  A      CD2 <->   62 GLY   (  62-)  A      CA     0.69    2.51  INTRA BL
  19 GLN   (  19-)  A      O   <->   88 TYR   (  88-)  A      OH     0.67    1.73  INTRA BL
 144 TYR   ( 144-)  A      CE1 <->  182 GLY   ( 182-)  A      CA     0.67    2.53  INTRA BL
 136 ALA   ( 136-)  A      C   <->  138 GLY   ( 138-)  A      N      0.66    2.24  INTRA BL
 132 VAL   ( 132-)  A      CG1 <->  202 LEU   ( 202-)  A      CD1    0.59    2.61  INTRA BL
  27 ALA   (  27-)  A      O   <->   31 VAL   (  31-)  A      CG1    0.58    2.22  INTRA BL
 136 ALA   ( 136-)  A      O   <->  138 GLY   ( 138-)  A      N      0.57    2.13  INTRA BL
  37 ILE   (  37-)  A      CG2 <->   38 ILE   (  38-)  A      N      0.54    2.46  INTRA BL
  51 GLN   (  51-)  A      OE1 <->   89 GLU   (  89-)  A      CG     0.52    2.28  INTRA BL
  30 ALA   (  30-)  A      O   <->   33 THR   (  33-)  A      OG1    0.50    1.90  INTRA BL
 112 GLN   ( 112-)  A      CG  <->  207 PHE   ( 207-)  A      CE1    0.49    2.71  INTRA BL
 112 GLN   ( 112-)  A      CB  <->  207 PHE   ( 207-)  A      CD1    0.46    2.74  INTRA BL
  28 PHE   (  28-)  A      O   <->   32 VAL   (  32-)  A      CG1    0.44    2.36  INTRA BL
   5 VAL   (   5-)  A      O   <->  165 GLY   ( 165-)  A      CA     0.44    2.36  INTRA BL
 177 TRP   ( 177-)  A      CZ3 <->  181 TRP   ( 181-)  A      NE1    0.42    2.68  INTRA BL
 177 TRP   ( 177-)  A      CE3 <->  181 TRP   ( 181-)  A      CD1    0.41    2.79  INTRA BL
  11 GLY   (  11-)  A      O   <->  215 HOH   ( 218 )  A      O      0.41    1.99  INTRA BL
 112 GLN   ( 112-)  A      CD  <->  207 PHE   ( 207-)  A      CZ     0.40    2.80  INTRA BL
  35 GLU   (  35-)  A      CG  <->   46 ASN   (  46-)  A      O      0.40    2.40  INTRA BL
And so on for a total of 185 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

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.

 145 ARG   ( 145-)  A      -7.05
  41 ARG   (  41-)  A      -5.50
  61 TYR   (  61-)  A      -5.46
 127 ASN   ( 127-)  A      -5.38
  77 GLN   (  77-)  A      -5.35
  94 TYR   (  94-)  A      -5.30
   9 GLN   (   9-)  A      -5.16
 103 TYR   ( 103-)  A      -5.14

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 - 212 : -1.588

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: 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.

 215 HOH   ( 229 )  A      O      8.40    3.80   25.21
  -1.00000  -0.00000  -0.00001   21.80003 ROT=  179.9720
  -0.00001   0.99906  -0.04337   45.04728 DET=    1.0000
   0.00002  -0.04337  -0.99906   55.10504

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.

  44 ASN   (  44-)  A
 118 GLN   ( 118-)  A
 135 GLN   ( 135-)  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.

  10 LYS   (  10-)  A      N
  13 VAL   (  13-)  A      N
  14 THR   (  14-)  A      N
  19 GLN   (  19-)  A      NE2
  22 CYS   (  22-)  A      N
  25 CYS   (  25-)  A      N
  26 TRP   (  26-)  A      N
  33 THR   (  33-)  A      OG1
  53 LEU   (  53-)  A      N
  58 ARG   (  58-)  A      NH1
  58 ARG   (  58-)  A      NH2
  62 GLY   (  62-)  A      N
  63 CYS   (  63-)  A      N
  69 TRP   (  69-)  A      N
  79 GLY   (  79-)  A      N
  84 ASN   (  84-)  A      N
  85 THR   (  85-)  A      OG1
  86 TYR   (  86-)  A      N
  91 VAL   (  91-)  A      N
  93 ARG   (  93-)  A      NE
  94 TYR   (  94-)  A      N
  94 TYR   (  94-)  A      OH
  96 ARG   (  96-)  A      NH1
  98 ARG   (  98-)  A      N
 110 VAL   ( 110-)  A      N
And so on for a total of 54 lines.

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.

  19 GLN   (  19-)  A      OE1
  50 GLU   (  50-)  A      OE2
 159 HIS   ( 159-)  A      ND1

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.

  35 GLU   (  35-)  A   H-bonding suggests Gln
  55 ASP   (  55-)  A   H-bonding suggests Asn
 140 ASP   ( 140-)  A   H-bonding suggests Asn

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 :  -2.720
  2nd generation packing quality :  -2.959
  Ramachandran plot appearance   :  -5.473 (bad)
  chi-1/chi-2 rotamer normality  :  -4.990 (bad)
  Backbone conformation          :  -0.881

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.376
  Bond angles                    :   1.418
  Omega angle restraints         :   0.392 (tight)
  Side chain planarity           :   1.503
  Improper dihedral distribution :   1.170
  Inside/Outside distribution    :   1.048

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 :  -1.3
  Ramachandran plot appearance   :  -2.9
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.376
  Bond angles                    :   1.418
  Omega angle restraints         :   0.392 (tight)
  Side chain planarity           :   1.503
  Improper dihedral distribution :   1.170
  Inside/Outside distribution    :   1.048
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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,
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      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,
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    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.