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 pdb1cx2.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

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

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

2221 S58   ( 701-)  A  -         Fragmented
2224 S58   ( 701-)  C  -         OK
2226 S58   ( 701-)  D  -         OK
2228 S58   ( 701-)  B  -         OK

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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:

Crystal temperature (K) :113.000

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 : 48.86

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Geometric checks

Warning: Unusual bond 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.

 357 HIS   ( 388-)  A      CG   CD2   1.40    4.3
1352 ILE   ( 279-)  C      CA   CB    1.61    4.0
2013 HIS   ( 388-)  D      CG   CD2   1.41    4.5

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

 |  0.999420 -0.000040  0.000013|
 | -0.000040  0.999506 -0.000003|
 |  0.000013 -0.000003  0.999265|
Proposed new scale matrix

 |  0.005548  0.000000  0.000000|
 |  0.000000  0.007471  0.000000|
 |  0.000000  0.000000  0.008261|
With corresponding cell

    A    = 180.238  B   = 133.856  C    = 121.050
    Alpha=  90.001  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 180.340  B   = 133.920  C    = 121.140
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 27.947
(Under-)estimated Z-score: 3.896

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.

  30 THR   (  62-)  A      N    CA   C    97.89   -4.8
  41 GLU   (  73-)  A      N    CA   C    96.88   -5.1
 107 SER   ( 138-)  A      N    CA   C   122.41    4.0
 117 TYR   ( 148-)  A      N    CA   C    99.30   -4.3
 203 TYR   ( 234-)  A      N    CA   C   123.69    4.5
 211 HIS   ( 242-)  A      CG   ND1  CE1 109.63    4.0
 256 VAL   ( 287-)  A      N    CA   C   126.12    5.3
 278 HIS   ( 309-)  A      CG   ND1  CE1 109.81    4.2
 289 HIS   ( 320-)  A      CG   ND1  CE1 109.69    4.1
 325 HIS   ( 356-)  A      N    CA   C    99.94   -4.0
 355 HIS   ( 386-)  A      CG   ND1  CE1 109.66    4.1
 357 HIS   ( 388-)  A      CA   CB   CG  107.22   -6.6
 357 HIS   ( 388-)  A      NE2  CD2  CG  102.41   -4.1
 357 HIS   ( 388-)  A      CD2  CG   ND1 111.83    5.7
 391 PHE   ( 422-)  A      N    CA   C    98.86   -4.4
 451 THR   ( 482-)  A      N    CA   C   124.04    4.6
 482 ARG   ( 513-)  A      N    CA   C    98.88   -4.4
 527 ILE   ( 558-)  A      N    CA   C    99.59   -4.1
 544 CYS   ( 575-)  A      N    CA   C    93.02   -6.5
 582 THR   (  62-)  B      N    CA   C    97.97   -4.7
 593 GLU   (  73-)  B      N    CA   C    97.42   -4.9
 610 HIS   (  90-)  B      CG   ND1  CE1 109.66    4.1
 659 SER   ( 138-)  B      N    CA   C   123.46    4.4
 669 TYR   ( 148-)  B      N    CA   C    99.05   -4.3
 728 HIS   ( 207-)  B      CG   ND1  CE1 109.65    4.1
And so on for a total of 78 lines.

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.

2183 ILE   ( 558-)  D    7.80
1631 ILE   ( 558-)  C    7.79
 943 PHE   ( 422-)  B    7.62
1495 PHE   ( 422-)  C    7.56
 527 ILE   ( 558-)  A    7.48
1003 THR   ( 482-)  B    7.46
 451 THR   ( 482-)  A    7.46
1859 TYR   ( 234-)  D    7.42
1079 ILE   ( 558-)  B    7.33
1626 GLU   ( 553-)  C    7.23
2047 PHE   ( 422-)  D    7.19
 755 TYR   ( 234-)  B    7.15
 544 CYS   ( 575-)  A    7.12
2107 THR   ( 482-)  D    7.11
1555 THR   ( 482-)  C    7.10
 522 GLU   ( 553-)  A    7.05
 391 PHE   ( 422-)  A    7.05
2200 CYS   ( 575-)  D    6.91
1648 CYS   ( 575-)  C    6.82
 203 TYR   ( 234-)  A    6.81
1096 CYS   ( 575-)  B    6.79
1307 TYR   ( 234-)  C    6.77
1912 VAL   ( 287-)  D    6.56
 808 VAL   ( 287-)  B    6.50
1360 VAL   ( 287-)  C    6.43
And so on for a total of 97 lines.

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 : 2.077

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.

 869 TYR   ( 348-)  B      CB   4.63
1740 TYR   ( 115-)  D      CB   4.57
1887 TYR   ( 262-)  D      CB   4.22
 317 TYR   ( 348-)  A      CB   4.15
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.935

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 : -4.935

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.

 904 THR   ( 383-)  B    -3.2
1456 THR   ( 383-)  C    -3.2
 352 THR   ( 383-)  A    -3.2
1035 PRO   ( 514-)  B    -3.1
1587 PRO   ( 514-)  C    -3.1
2139 PRO   ( 514-)  D    -3.1
 483 PRO   ( 514-)  A    -3.1
 775 TYR   ( 254-)  B    -3.1
1879 TYR   ( 254-)  D    -3.1
 930 TYR   ( 409-)  B    -3.0
1327 TYR   ( 254-)  C    -3.0
 223 TYR   ( 254-)  A    -3.0
2008 THR   ( 383-)  D    -3.0
1482 TYR   ( 409-)  C    -3.0
 378 TYR   ( 409-)  A    -3.0
2034 TYR   ( 409-)  D    -2.9
1168 PHE   (  96-)  C    -2.9
 959 ARG   ( 438-)  B    -2.8
2063 ARG   ( 438-)  D    -2.8
1154 LEU   (  82-)  C    -2.7
 602 LEU   (  82-)  B    -2.7
  50 LEU   (  82-)  A    -2.7
1706 LEU   (  82-)  D    -2.7
1511 ARG   ( 438-)  C    -2.7
 877 HIS   ( 356-)  B    -2.7
And so on for a total of 149 lines.

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.

  12 ARG   (  44-)  A  Poor phi/psi
  19 GLY   (  51-)  A  Poor phi/psi
  20 PHE   (  52-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  35 GLU   (  67-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  38 THR   (  70-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  99 TYR   ( 130-)  A  Poor phi/psi
 100 ASN   ( 131-)  A  Poor phi/psi
 107 SER   ( 138-)  A  Poor phi/psi
 154 ARG   ( 185-)  A  Poor phi/psi
 181 THR   ( 212-)  A  Poor phi/psi
 195 HIS   ( 226-)  A  Poor phi/psi
 197 VAL   ( 228-)  A  Poor phi/psi
 206 THR   ( 237-)  A  Poor phi/psi
 213 LEU   ( 244-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 227 GLY   ( 258-)  A  Poor phi/psi
 228 GLY   ( 259-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 246 PRO   ( 277-)  A  Poor phi/psi
 247 HIS   ( 278-)  A  Poor phi/psi
 249 PRO   ( 280-)  A  Poor phi/psi
And so on for a total of 171 lines.

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 : -5.088

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.

 489 GLU   ( 520-)  A    0.33
1593 GLU   ( 520-)  C    0.33
 394 SER   ( 425-)  A    0.34
2050 SER   ( 425-)  D    0.35
 946 SER   ( 425-)  B    0.35
1498 SER   ( 425-)  C    0.35
1041 GLU   ( 520-)  B    0.36

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!

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  12 ARG   (  44-)  A      0
  18 THR   (  50-)  A      0
  20 PHE   (  52-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  50 LEU   (  82-)  A      0
  64 PHE   (  96-)  A      0
  90 SER   ( 121-)  A      0
  91 TYR   ( 122-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
And so on for a total of 908 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.645

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!

1611 PRO   ( 538-)  C   2.17   13
1883 GLY   ( 258-)  D   2.15   12
 779 GLY   ( 258-)  B   2.10   12
 227 GLY   ( 258-)  A   2.08   12
1331 GLY   ( 258-)  C   2.05   12
2161 GLY   ( 536-)  D   1.91   12
1609 GLY   ( 536-)  C   1.90   12
1057 GLY   ( 536-)  B   1.89   14
 505 GLY   ( 536-)  A   1.86   11
 586 GLY   (  66-)  B   1.61   12
  34 GLY   (  66-)  A   1.60   13
1690 GLY   (  66-)  D   1.52   13

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...

 541 VAL   ( 572-)  A   2.01
1093 VAL   ( 572-)  B   1.92
1120 MET   (  48-)  C   1.69
1645 VAL   ( 572-)  C   1.84
2197 VAL   ( 572-)  D   1.83

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  54 PRO   (  86-)  A    0.45 HIGH
  75 PRO   ( 106-)  A    0.46 HIGH
  96 PRO   ( 127-)  A    0.47 HIGH
 606 PRO   (  86-)  B    0.46 HIGH
 627 PRO   ( 106-)  B    0.47 HIGH
 817 PRO   ( 296-)  B    0.45 HIGH
1144 PRO   (  72-)  C    0.45 HIGH
1158 PRO   (  86-)  C    0.47 HIGH
1179 PRO   ( 106-)  C    0.47 HIGH
1200 PRO   ( 127-)  C    0.45 HIGH
1353 PRO   ( 280-)  C    0.46 HIGH
1601 PRO   ( 528-)  C    0.46 HIGH
1664 PRO   (  40-)  D    0.46 HIGH
1696 PRO   (  72-)  D    0.45 HIGH
1731 PRO   ( 106-)  D    0.46 HIGH
1752 PRO   ( 127-)  D    0.46 HIGH
1814 PRO   ( 189-)  D    0.45 HIGH
1905 PRO   ( 280-)  D    0.45 HIGH
1921 PRO   ( 296-)  D    0.45 HIGH
1946 PRO   ( 321-)  D    0.45 HIGH
1988 PRO   ( 363-)  D    0.46 HIGH
2017 PRO   ( 392-)  D    0.45 HIGH

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].

  97 PRO   ( 128-)  A  -114.5 envelop C-gamma (-108 degrees)
 249 PRO   ( 280-)  A  -116.1 envelop C-gamma (-108 degrees)
 358 PRO   ( 389-)  A   106.4 envelop C-beta (108 degrees)
 410 PRO   ( 441-)  A   106.5 envelop C-beta (108 degrees)
 483 PRO   ( 514-)  A   133.1 half-chair C-beta/C-alpha (126 degrees)
 507 PRO   ( 538-)  A  -116.4 envelop C-gamma (-108 degrees)
 649 PRO   ( 128-)  B  -113.1 envelop C-gamma (-108 degrees)
 910 PRO   ( 389-)  B   102.1 envelop C-beta (108 degrees)
 962 PRO   ( 441-)  B   102.3 envelop C-beta (108 degrees)
1035 PRO   ( 514-)  B   134.4 half-chair C-beta/C-alpha (126 degrees)
1059 PRO   ( 538-)  B  -115.4 envelop C-gamma (-108 degrees)
1201 PRO   ( 128-)  C  -112.2 envelop C-gamma (-108 degrees)
1462 PRO   ( 389-)  C   103.8 envelop C-beta (108 degrees)
1514 PRO   ( 441-)  C   102.0 envelop C-beta (108 degrees)
1587 PRO   ( 514-)  C   129.7 half-chair C-beta/C-alpha (126 degrees)
1611 PRO   ( 538-)  C  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1753 PRO   ( 128-)  D  -115.4 envelop C-gamma (-108 degrees)
1905 PRO   ( 280-)  D  -113.6 envelop C-gamma (-108 degrees)
2014 PRO   ( 389-)  D   102.4 envelop C-beta (108 degrees)
2066 PRO   ( 441-)  D   102.2 envelop C-beta (108 degrees)
2139 PRO   ( 514-)  D   133.0 half-chair C-beta/C-alpha (126 degrees)
2163 PRO   ( 538-)  D  -114.5 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 634 MET   ( 113-)  B      SD  <->  881 LYS   ( 360-)  B      N      0.66    2.64  INTRA BL
1745 ARG   ( 120-)  D      NH1 <-> 2226 S58   ( 701-)  D      F3     0.55    2.55  INTRA
1162 HIS   (  90-)  C      NE2 <-> 2224 S58   ( 701-)  C      N3     0.49    2.51  INTRA BL
 641 ARG   ( 120-)  B      NH1 <-> 2228 S58   ( 701-)  B      F3     0.48    2.62  INTRA
1186 MET   ( 113-)  C      SD  <-> 1433 LYS   ( 360-)  C      N      0.48    2.82  INTRA BL
1738 MET   ( 113-)  D      SD  <-> 1985 LYS   ( 360-)  D      N      0.46    2.84  INTRA BL
  82 MET   ( 113-)  A      SD  <->  329 LYS   ( 360-)  A      N      0.46    2.84  INTRA BL
 111 PHE   ( 142-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.42    2.28  INTRA BL
 552 GLN   ( 583-)  A      NE2 <-> 1907 ASN   ( 282-)  D      CG     0.41    2.69  INTRA
1215 PHE   ( 142-)  C      O   <-> 1449 ARG   ( 376-)  C      NH2    0.41    2.29  INTRA BL
 552 GLN   ( 583-)  A      NE2 <-> 1907 ASN   ( 282-)  D      ND2    0.37    2.48  INTRA
 557 CYS   (  37-)  B      O   <->  559 ASN   (  39-)  B      ND2    0.36    2.34  INTRA BL
 238 THR   ( 269-)  A      O   <->  240 VAL   ( 271-)  A      N      0.36    2.34  INTRA BL
 655 TYR   ( 134-)  B      CD1 <->  657 TYR   ( 136-)  B      CE1    0.36    2.84  INTRA BL
 210 GLN   ( 241-)  A      NE2 <->  298 PHE   ( 329-)  A      CE1    0.36    2.74  INTRA BL
1894 THR   ( 269-)  D      O   <-> 1896 VAL   ( 271-)  D      N      0.35    2.35  INTRA BL
1866 GLN   ( 241-)  D      NE2 <-> 1954 PHE   ( 329-)  D      CE1    0.35    2.75  INTRA BL
 105 TYR   ( 136-)  A      CD2 <->  848 GLN   ( 327-)  B      NE2    0.34    2.76  INTRA BL
 568 MET   (  48-)  B      SD  <->  569 SER   (  49-)  B      N      0.34    2.86  INTRA
1395 GLU   ( 322-)  C      CG  <-> 1676 PHE   (  52-)  D      N      0.34    2.76  INTRA BL
1124 PHE   (  52-)  C      N   <-> 1947 GLU   ( 322-)  D      CG     0.34    2.76  INTRA BL
 902 PHE   ( 381-)  B      CD1 <-> 1050 PHE   ( 529-)  B      CB     0.33    2.87  INTRA BL
 663 PHE   ( 142-)  B      O   <->  897 ARG   ( 376-)  B      NH2    0.33    2.37  INTRA BL
 219 GLY   ( 250-)  A      C   <->  282 CYS   ( 313-)  A      SG     0.33    3.07  INTRA BL
1767 PHE   ( 142-)  D      O   <-> 2001 ARG   ( 376-)  D      NH2    0.33    2.37  INTRA BL
And so on for a total of 1020 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

1685 ARG   (  61-)  D      -6.83
1133 ARG   (  61-)  C      -6.80
 581 ARG   (  61-)  B      -6.79
  29 ARG   (  61-)  A      -6.70
 799 HIS   ( 278-)  B      -6.62
1903 HIS   ( 278-)  D      -6.60
1351 HIS   ( 278-)  C      -6.59
 247 HIS   ( 278-)  A      -6.57
1794 LYS   ( 169-)  D      -6.23
 138 LYS   ( 169-)  A      -6.16
1242 LYS   ( 169-)  C      -6.14
 690 LYS   ( 169-)  B      -6.09
 891 GLN   ( 370-)  B      -5.58
 339 GLN   ( 370-)  A      -5.54
2202 PHE   ( 577-)  D      -5.48
1490 HIS   ( 417-)  C      -5.46
 386 HIS   ( 417-)  A      -5.46
2042 HIS   ( 417-)  D      -5.46
 938 HIS   ( 417-)  B      -5.45
  12 ARG   (  44-)  A      -5.42
2198 LYS   ( 573-)  D      -5.41
 572 PHE   (  52-)  B      -5.40
1646 LYS   ( 573-)  C      -5.39
1995 GLN   ( 370-)  D      -5.39
1900 TYR   ( 275-)  D      -5.38
And so on for a total of 68 lines.

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.

  20 PHE   (  52-)  A        22 - GLN     54- ( A)         -4.51
 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -5.11
 572 PHE   (  52-)  B       574 - GLN     54- ( B)         -4.54
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -5.04
1124 PHE   (  52-)  C      1126 - GLN     54- ( C)         -4.47
1242 LYS   ( 169-)  C      1244 - LEU    171- ( C)         -5.15
1676 PHE   (  52-)  D      1678 - GLN     54- ( D)         -4.54
1794 LYS   ( 169-)  D      1796 - LEU    171- ( D)         -5.08

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 153 ARG   ( 184-)  A   -2.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

  22 GLN   (  54-)  A
 319 GLN   ( 350-)  A
 320 HIS   ( 351-)  A
 355 HIS   ( 386-)  A
 433 ASN   ( 464-)  A
 574 GLN   (  54-)  B
 762 GLN   ( 241-)  B
 872 HIS   ( 351-)  B
 985 ASN   ( 464-)  B
1126 GLN   (  54-)  C
1314 GLN   ( 241-)  C
1423 GLN   ( 350-)  C
1424 HIS   ( 351-)  C
1459 HIS   ( 386-)  C
1537 ASN   ( 464-)  C
1678 GLN   (  54-)  D
1866 GLN   ( 241-)  D
1976 HIS   ( 351-)  D
1994 GLN   ( 369-)  D
2089 ASN   ( 464-)  D

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   9 CYS   (  41-)  A      N
  20 PHE   (  52-)  A      N
  22 GLN   (  54-)  A      N
  23 TYR   (  55-)  A      N
  28 THR   (  60-)  A      OG1
  45 ARG   (  77-)  A      NE
  55 ASN   (  87-)  A      N
  92 LEU   ( 123-)  A      N
  99 TYR   ( 130-)  A      N
 100 ASN   ( 131-)  A      ND2
 101 VAL   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 119 ARG   ( 150-)  A      N
 119 ARG   ( 150-)  A      NE
 119 ARG   ( 150-)  A      NH1
 135 LYS   ( 166-)  A      N
 139 GLU   ( 170-)  A      N
 153 ARG   ( 184-)  A      NH1
 153 ARG   ( 184-)  A      NH2
 161 GLN   ( 192-)  A      N
 164 ASN   ( 195-)  A      ND2
 172 GLN   ( 203-)  A      NE2
 173 HIS   ( 204-)  A      ND1
 177 GLN   ( 208-)  A      NE2
And so on for a total of 342 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.

  58 HIS   (  90-)  A      NE2
 109 GLU   ( 140-)  A      OE2
 159 ASP   ( 190-)  A      OD1
 308 GLU   ( 339-)  A      OE1
 338 GLN   ( 369-)  A      OE1
 380 ASN   ( 411-)  A      OD1
 386 HIS   ( 417-)  A      ND1
 610 HIS   (  90-)  B      NE2
 661 GLU   ( 140-)  B      OE2
 711 ASP   ( 190-)  B      OD1
 725 HIS   ( 204-)  B      ND1
 729 GLN   ( 208-)  B      OE1
 803 ASN   ( 282-)  B      OD1
 860 GLU   ( 339-)  B      OE1
 890 GLN   ( 369-)  B      OE1
 901 GLU   ( 380-)  B      OE1
 932 ASN   ( 411-)  B      OD1
1213 GLU   ( 140-)  C      OE2
1263 ASP   ( 190-)  C      OD1
1412 GLU   ( 339-)  C      OE1
1442 GLN   ( 369-)  C      OE1
1484 ASN   ( 411-)  C      OD1
1490 HIS   ( 417-)  C      ND1
1714 HIS   (  90-)  D      NE2
1765 GLU   ( 140-)  D      OE2
1815 ASP   ( 190-)  D      OD1
1829 HIS   ( 204-)  D      ND1
1833 GLN   ( 208-)  D      OE1
1947 GLU   ( 322-)  D      OE2
1964 GLU   ( 339-)  D      OE1
2036 ASN   ( 411-)  D      OD1

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.

  21 ASP   (  53-)  A   H-bonding suggests Asn
  26 ASP   (  58-)  A   H-bonding suggests Asn
 259 GLU   ( 290-)  A   H-bonding suggests Gln
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 422 ASP   ( 453-)  A   H-bonding suggests Asn
 573 ASP   (  53-)  B   H-bonding suggests Asn
 578 ASP   (  58-)  B   H-bonding suggests Asn
 661 GLU   ( 140-)  B   H-bonding suggests Gln; but Alt-Rotamer
 811 GLU   ( 290-)  B   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln
 974 ASP   ( 453-)  B   H-bonding suggests Asn
1130 ASP   (  58-)  C   H-bonding suggests Asn
1363 GLU   ( 290-)  C   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1471 GLU   ( 398-)  C   H-bonding suggests Gln; but Alt-Rotamer
1526 ASP   ( 453-)  C   H-bonding suggests Asn
1677 ASP   (  53-)  D   H-bonding suggests Asn
1682 ASP   (  58-)  D   H-bonding suggests Asn
1915 GLU   ( 290-)  D   H-bonding suggests Gln
1947 GLU   ( 322-)  D   H-bonding suggests Gln
2078 ASP   ( 453-)  D   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 :  -2.153
  2nd generation packing quality :  -2.180
  Ramachandran plot appearance   :  -4.935 (bad)
  chi-1/chi-2 rotamer normality  :  -5.088 (bad)
  Backbone conformation          :  -1.192

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.635 (tight)
  Bond angles                    :   0.897
  Omega angle restraints         :   0.299 (tight)
  Side chain planarity           :   0.671
  Improper dihedral distribution :   1.156
  Inside/Outside distribution    :   1.099

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.0
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.635 (tight)
  Bond angles                    :   0.897
  Omega angle restraints         :   0.299 (tight)
  Side chain planarity           :   0.671
  Improper dihedral distribution :   1.156
  Inside/Outside distribution    :   1.099
==============

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.