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 pdb4cox.ent

Checks that need to be done early-on in validation

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.

2222 IMN   ( 701-)  B  -
2224 IMN   ( 701-)  C  -
2226 IMN   ( 701-)  D  -
2228 IMN   ( 701-)  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

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 : 23.39

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   1.41    4.8
 909 HIS   ( 388-)  B      CG   CD2   1.41    5.2
2013 HIS   ( 388-)  D      CG   CD2   1.41    4.7

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.

 107 SER   ( 138-)  A      N    CA   C   123.60    4.4
 117 TYR   ( 148-)  A      N    CA   C    95.93   -5.5
 201 HIS   ( 232-)  A      CG   ND1  CE1 109.65    4.1
 227 GLY   ( 258-)  A      N    CA   C    99.48   -4.5
 250 GLU   ( 281-)  A      N    CA   C    98.16   -4.7
 256 VAL   ( 287-)  A      N    CA   C   126.74    5.5
 289 HIS   ( 320-)  A      CG   ND1  CE1 109.64    4.0
 355 HIS   ( 386-)  A      CG   ND1  CE1 109.68    4.1
 357 HIS   ( 388-)  A      CA   CB   CG  106.42   -7.4
 357 HIS   ( 388-)  A      NE2  CD2  CG  102.19   -4.3
 357 HIS   ( 388-)  A      CD2  CG   ND1 111.24    5.1
 387 GLY   ( 418-)  A      N    CA   C   127.49    5.2
 391 PHE   ( 422-)  A      N    CA   C    98.41   -4.6
 482 ARG   ( 513-)  A      N    CA   C    96.70   -5.2
 543 GLY   ( 574-)  A      N    CA   C    98.66   -4.8
 654 HIS   ( 133-)  B      CG   ND1  CE1 109.64    4.0
 659 SER   ( 138-)  B      N    CA   C   122.86    4.2
 669 TYR   ( 148-)  B      N    CA   C    97.54   -4.9
 763 HIS   ( 242-)  B      CG   ND1  CE1 109.87    4.3
 779 GLY   ( 258-)  B      N    CA   C    98.18   -4.9
 802 GLU   ( 281-)  B      N    CA   C    99.71   -4.1
 808 VAL   ( 287-)  B      N    CA   C   126.02    5.3
 841 HIS   ( 320-)  B      CG   ND1  CE1 110.10    4.5
 909 HIS   ( 388-)  B      CA   CB   CG  106.09   -7.7
 909 HIS   ( 388-)  B      CD2  CG   ND1 111.52    5.4
And so on for a total of 59 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.

2046 GLN   ( 421-)  D    8.15
 390 GLN   ( 421-)  A    7.37
 391 PHE   ( 422-)  A    7.29
1495 PHE   ( 422-)  C    7.13
2047 PHE   ( 422-)  D    7.10
 943 PHE   ( 422-)  B    6.83
 942 GLN   ( 421-)  B    6.82
1494 GLN   ( 421-)  C    6.80
 256 VAL   ( 287-)  A    6.45
1360 VAL   ( 287-)  C    6.22
 808 VAL   ( 287-)  B    6.17
1912 VAL   ( 287-)  D    6.04
 117 TYR   ( 148-)  A    5.82
1034 ARG   ( 513-)  B    5.67
1971 GLU   ( 346-)  D    5.61
 315 GLU   ( 346-)  A    5.60
2138 ARG   ( 513-)  D    5.58
 779 GLY   ( 258-)  B    5.52
 867 GLU   ( 346-)  B    5.48
 482 ARG   ( 513-)  A    5.47
1883 GLY   ( 258-)  D    5.42
1419 GLU   ( 346-)  C    5.37
 543 GLY   ( 574-)  A    5.35
1647 GLY   ( 574-)  C    5.28
 669 TYR   ( 148-)  B    5.21
And so on for a total of 83 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 : 1.895

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.

  76 PHE   ( 107-)  A      CB   4.55
 628 PHE   ( 107-)  B      CB   4.49
1180 PHE   ( 107-)  C      CB   4.41
1732 PHE   ( 107-)  D      CB   4.31
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.355

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 : -4.355

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.

2139 PRO   ( 514-)  D    -3.1
1587 PRO   ( 514-)  C    -3.1
 483 PRO   ( 514-)  A    -3.1
1035 PRO   ( 514-)  B    -3.1
  75 PRO   ( 106-)  A    -3.1
 627 PRO   ( 106-)  B    -3.1
 941 THR   ( 420-)  B    -3.1
1731 PRO   ( 106-)  D    -3.0
2045 THR   ( 420-)  D    -3.0
1179 PRO   ( 106-)  C    -3.0
1493 THR   ( 420-)  C    -3.0
 547 THR   ( 578-)  A    -2.9
2172 PRO   ( 547-)  D    -2.9
1620 PRO   ( 547-)  C    -2.9
2203 THR   ( 578-)  D    -2.9
 516 PRO   ( 547-)  A    -2.9
1651 THR   ( 578-)  C    -2.8
1099 THR   ( 578-)  B    -2.8
1068 PRO   ( 547-)  B    -2.7
 389 THR   ( 420-)  A    -2.7
  50 LEU   (  82-)  A    -2.7
1154 LEU   (  82-)  C    -2.7
 397 ARG   ( 428-)  A    -2.7
1706 LEU   (  82-)  D    -2.7
 602 LEU   (  82-)  B    -2.7
And so on for a total of 137 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
  29 ARG   (  61-)  A  Poor phi/psi
  49 LEU   (  81-)  A  Poor phi/psi
  50 LEU   (  82-)  A  Poor phi/psi
  63 HIS   (  95-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  99 TYR   ( 130-)  A  Poor phi/psi
 107 SER   ( 138-)  A  Poor phi/psi
 164 ASN   ( 195-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 239 GLN   ( 270-)  A  Poor phi/psi
 249 PRO   ( 280-)  A  Poor phi/psi
 250 GLU   ( 281-)  A  Poor phi/psi
 251 ASN   ( 282-)  A  Poor phi/psi
 252 LEU   ( 283-)  A  Poor phi/psi
 256 VAL   ( 287-)  A  Poor phi/psi
 294 ASP   ( 325-)  A  Poor phi/psi
 342 TYR   ( 373-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 368 ASP   ( 399-)  A  Poor phi/psi
 385 GLU   ( 416-)  A  Poor phi/psi
 388 LEU   ( 419-)  A  Poor phi/psi
 391 PHE   ( 422-)  A  Poor phi/psi
And so on for a total of 133 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.949

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.

  79 SER   ( 110-)  A    0.36
 631 SER   ( 110-)  B    0.36
1183 SER   ( 110-)  C    0.36
1735 SER   ( 110-)  D    0.38
 976 SER   ( 455-)  B    0.38

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!

   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
  21 ASP   (  53-)  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
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  49 LEU   (  81-)  A      0
  50 LEU   (  82-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  75 PRO   ( 106-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
And so on for a total of 916 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 : 1.669

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!

2043 GLY   ( 418-)  D   2.87   17
 939 GLY   ( 418-)  B   2.85   21
1491 GLY   ( 418-)  C   2.84   20
 387 GLY   ( 418-)  A   2.81   18

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...

1114 GLN   (  42-)  C   1.61
1471 GLU   ( 398-)  C   1.59
2023 GLU   ( 398-)  D   1.53

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]

 122 PRO   ( 153-)  A    0.46 HIGH
 158 PRO   ( 189-)  A    0.46 HIGH
 249 PRO   ( 280-)  A    0.46 HIGH
 497 PRO   ( 528-)  A    0.45 HIGH
 507 PRO   ( 538-)  A    0.45 HIGH
 710 PRO   ( 189-)  B    0.46 HIGH
 785 PRO   ( 264-)  B    0.45 HIGH
 801 PRO   ( 280-)  B    0.49 HIGH
 884 PRO   ( 363-)  B    0.46 HIGH
1144 PRO   (  72-)  C    0.45 HIGH
1262 PRO   ( 189-)  C    0.46 HIGH
1353 PRO   ( 280-)  C    0.46 HIGH
1436 PRO   ( 363-)  C    0.46 HIGH
1578 PRO   ( 505-)  C    0.45 HIGH
1585 PRO   ( 512-)  C    0.45 HIGH
1601 PRO   ( 528-)  C    0.45 HIGH
1752 PRO   ( 127-)  D    0.46 HIGH
1814 PRO   ( 189-)  D    0.45 HIGH
1905 PRO   ( 280-)  D    0.46 HIGH
1988 PRO   ( 363-)  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].

 131 PRO   ( 162-)  A   101.3 envelop C-beta (108 degrees)
 141 PRO   ( 172-)  A  -120.3 half-chair C-delta/C-gamma (-126 degrees)
 246 PRO   ( 277-)  A  -112.4 envelop C-gamma (-108 degrees)
 410 PRO   ( 441-)  A   102.8 envelop C-beta (108 degrees)
 483 PRO   ( 514-)  A   143.1 envelop C-alpha (144 degrees)
 683 PRO   ( 162-)  B   100.5 envelop C-beta (108 degrees)
 693 PRO   ( 172-)  B  -121.6 half-chair C-delta/C-gamma (-126 degrees)
 798 PRO   ( 277-)  B  -112.0 envelop C-gamma (-108 degrees)
 962 PRO   ( 441-)  B   103.9 envelop C-beta (108 degrees)
1035 PRO   ( 514-)  B   144.5 envelop C-alpha (144 degrees)
1235 PRO   ( 162-)  C   101.1 envelop C-beta (108 degrees)
1245 PRO   ( 172-)  C  -123.4 half-chair C-delta/C-gamma (-126 degrees)
1350 PRO   ( 277-)  C  -113.8 envelop C-gamma (-108 degrees)
1514 PRO   ( 441-)  C   107.5 envelop C-beta (108 degrees)
1587 PRO   ( 514-)  C   144.4 envelop C-alpha (144 degrees)
1787 PRO   ( 162-)  D   101.6 envelop C-beta (108 degrees)
1797 PRO   ( 172-)  D  -124.3 half-chair C-delta/C-gamma (-126 degrees)
1902 PRO   ( 277-)  D  -114.7 envelop C-gamma (-108 degrees)
2066 PRO   ( 441-)  D   103.6 envelop C-beta (108 degrees)
2139 PRO   ( 514-)  D   143.5 envelop C-alpha (144 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.

 641 ARG   ( 120-)  B      NH1 <-> 2222 IMN   ( 701-)  B      C18    0.57    2.53  INTRA BL
 802 GLU   ( 281-)  B      O   <->  804 LEU   ( 283-)  B      N      0.50    2.20  INTRA
1196 LEU   ( 123-)  C      O   <-> 1542 ARG   ( 469-)  C      NH2    0.48    2.22  INTRA BL
 250 GLU   ( 281-)  A      O   <->  252 LEU   ( 283-)  A      N      0.46    2.24  INTRA
  92 LEU   ( 123-)  A      O   <->  438 ARG   ( 469-)  A      NH2    0.46    2.24  INTRA BL
1223 ARG   ( 150-)  C      NH2 <-> 1531 MET   ( 458-)  C      O      0.44    2.26  INTRA BL
1906 GLU   ( 281-)  D      O   <-> 1908 LEU   ( 283-)  D      N      0.44    2.26  INTRA
1354 GLU   ( 281-)  C      O   <-> 1356 LEU   ( 283-)  C      N      0.44    2.26  INTRA
 671 ARG   ( 150-)  B      NH2 <->  979 MET   ( 458-)  B      O      0.43    2.27  INTRA BL
  89 ARG   ( 120-)  A      NH1 <-> 2228 IMN   ( 701-)  A      C18    0.42    2.68  INTRA
1745 ARG   ( 120-)  D      NH1 <-> 2226 IMN   ( 701-)  D      C18    0.42    2.68  INTRA
1748 LEU   ( 123-)  D      O   <-> 2094 ARG   ( 469-)  D      NH2    0.41    2.29  INTRA BL
 644 LEU   ( 123-)  B      O   <->  990 ARG   ( 469-)  B      NH2    0.41    2.29  INTRA BL
1568 TYR   ( 495-)  C      CE2 <-> 1574 MET   ( 501-)  C      SD     0.40    3.00  INTRA BL
1775 ARG   ( 150-)  D      NH2 <-> 2083 MET   ( 458-)  D      O      0.39    2.31  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  427 MET   ( 458-)  A      O      0.39    2.31  INTRA BL
1193 ARG   ( 120-)  C      NH1 <-> 2224 IMN   ( 701-)  C      C18    0.32    2.78  INTRA
1485 SER   ( 412-)  C      O   <-> 1489 GLU   ( 416-)  C      N      0.32    2.38  INTRA BL
1616 GLN   ( 543-)  C      NE2 <-> 1752 PRO   ( 127-)  D      O      0.32    2.38  INTRA
1016 TYR   ( 495-)  B      CE2 <-> 1022 MET   ( 501-)  B      SD     0.32    3.08  INTRA BL
1756 ASN   ( 131-)  D      ND2 <-> 1772 TYR   ( 147-)  D      CD2    0.31    2.79  INTRA BL
 945 GLU   ( 424-)  B      O   <->  949 ARG   ( 428-)  B      NE     0.30    2.40  INTRA
1334 VAL   ( 261-)  C      O   <-> 1380 ARG   ( 307-)  C      NH1    0.29    2.41  INTRA BL
 125 ALA   ( 156-)  A      CB  <->  128 CYS   ( 159-)  A      SG     0.29    3.11  INTRA BL
 393 GLU   ( 424-)  A      O   <->  397 ARG   ( 428-)  A      NE     0.29    2.41  INTRA
And so on for a total of 712 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.

 581 ARG   (  61-)  B      -6.57
1685 ARG   (  61-)  D      -6.56
  29 ARG   (  61-)  A      -6.51
1133 ARG   (  61-)  C      -6.47
 799 HIS   ( 278-)  B      -6.32
 247 HIS   ( 278-)  A      -6.30
1242 LYS   ( 169-)  C      -6.22
1903 HIS   ( 278-)  D      -6.21
1351 HIS   ( 278-)  C      -6.21
 138 LYS   ( 169-)  A      -6.16
 690 LYS   ( 169-)  B      -6.14
1794 LYS   ( 169-)  D      -6.13
2202 PHE   ( 577-)  D      -5.86
1650 PHE   ( 577-)  C      -5.78
1490 HIS   ( 417-)  C      -5.65
1098 PHE   ( 577-)  B      -5.63
 386 HIS   ( 417-)  A      -5.61
 938 HIS   ( 417-)  B      -5.60
2042 HIS   ( 417-)  D      -5.59
 572 PHE   (  52-)  B      -5.52
  20 PHE   (  52-)  A      -5.48
1676 PHE   (  52-)  D      -5.47
1137 TYR   (  65-)  C      -5.44
 542 LYS   ( 573-)  A      -5.42
2053 ARG   ( 428-)  D      -5.39
And so on for a total of 52 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.

 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -4.53
1287 HIS   ( 214-)  C      1289 - ARG    216- ( C)         -4.55
1839 HIS   ( 214-)  D      1841 - ARG    216- ( D)         -4.69

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.

1990 LEU   ( 365-)  D   -2.67
1438 LEU   ( 365-)  C   -2.66
 334 LEU   ( 365-)  A   -2.66
 886 LEU   ( 365-)  B   -2.66

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.

1437 GLU   ( 364-)  C     - 1440 PHE   ( 367-)  C        -1.96
1989 GLU   ( 364-)  D     - 1992 PHE   ( 367-)  D        -2.00

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.

  73 ASN   ( 105-)  A
 102 HIS   ( 133-)  A
 251 ASN   ( 282-)  A
 289 HIS   ( 320-)  A
 320 HIS   ( 351-)  A
 380 ASN   ( 411-)  A
 386 HIS   ( 417-)  A
 433 ASN   ( 464-)  A
 654 HIS   ( 133-)  B
 841 HIS   ( 320-)  B
 872 HIS   ( 351-)  B
 932 ASN   ( 411-)  B
 938 HIS   ( 417-)  B
 985 ASN   ( 464-)  B
1177 ASN   ( 105-)  C
1206 HIS   ( 133-)  C
1393 HIS   ( 320-)  C
1424 HIS   ( 351-)  C
1484 ASN   ( 411-)  C
1537 ASN   ( 464-)  C
1758 HIS   ( 133-)  D
1943 GLN   ( 318-)  D
1945 HIS   ( 320-)  D
1976 HIS   ( 351-)  D
1993 ASN   ( 368-)  D
1994 GLN   ( 369-)  D
2036 ASN   ( 411-)  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.

  36 ASN   (  68-)  A      N
  38 THR   (  70-)  A      OG1
  55 ASN   (  87-)  A      N
  89 ARG   ( 120-)  A      NH1
  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      NE
 119 ARG   ( 150-)  A      NH1
 119 ARG   ( 150-)  A      NH2
 135 LYS   ( 166-)  A      N
 154 ARG   ( 185-)  A      N
 161 GLN   ( 192-)  A      N
 172 GLN   ( 203-)  A      NE2
 173 HIS   ( 204-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 190 THR   ( 221-)  A      OG1
 201 HIS   ( 232-)  A      N
 205 GLU   ( 236-)  A      N
 206 THR   ( 237-)  A      N
 209 ARG   ( 240-)  A      NH2
 214 ARG   ( 245-)  A      NH1
 214 ARG   ( 245-)  A      NH2
And so on for a total of 285 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.

 109 GLU   ( 140-)  A      OE2
 159 ASP   ( 190-)  A      OD1
 173 HIS   ( 204-)  A      ND1
 205 GLU   ( 236-)  A      OE2
 294 ASP   ( 325-)  A      OD2
 308 GLU   ( 339-)  A      OE1
 380 ASN   ( 411-)  A      OD1
 479 GLU   ( 510-)  A      OE1
 711 ASP   ( 190-)  B      OD1
 725 HIS   ( 204-)  B      ND1
 757 GLU   ( 236-)  B      OE2
 789 ASP   ( 268-)  B      OD1
 860 GLU   ( 339-)  B      OE1
 932 ASN   ( 411-)  B      OD1
1031 GLU   ( 510-)  B      OE1
1213 GLU   ( 140-)  C      OE2
1263 ASP   ( 190-)  C      OD1
1277 HIS   ( 204-)  C      ND1
1309 GLU   ( 236-)  C      OE2
1412 GLU   ( 339-)  C      OE1
1484 ASN   ( 411-)  C      OD1
1552 GLU   ( 479-)  C      OE1
1583 GLU   ( 510-)  C      OE1
1765 GLU   ( 140-)  D      OE2
1815 ASP   ( 190-)  D      OD1
1829 HIS   ( 204-)  D      ND1
1861 GLU   ( 236-)  D      OE2
1964 GLU   ( 339-)  D      OE1
2036 ASN   ( 411-)  D      OD1
2135 GLU   ( 510-)  D      OE1

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.

 205 GLU   ( 236-)  A   H-bonding suggests Gln
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 316 ASP   ( 347-)  A   H-bonding suggests Asn; but Alt-Rotamer
 661 GLU   ( 140-)  B   H-bonding suggests Gln
 757 GLU   ( 236-)  B   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln
1243 GLU   ( 170-)  C   H-bonding suggests Gln; but Alt-Rotamer
1309 GLU   ( 236-)  C   H-bonding suggests Gln
1345 GLU   ( 272-)  C   H-bonding suggests Gln
1395 GLU   ( 322-)  C   H-bonding suggests Gln
1420 ASP   ( 347-)  C   H-bonding suggests Asn; but Alt-Rotamer
1497 GLU   ( 424-)  C   H-bonding suggests Gln; but Alt-Rotamer
1861 GLU   ( 236-)  D   H-bonding suggests Gln
1947 GLU   ( 322-)  D   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.825
  2nd generation packing quality :  -1.898
  Ramachandran plot appearance   :  -4.355 (bad)
  chi-1/chi-2 rotamer normality  :  -3.949 (poor)
  Backbone conformation          :  -0.969

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.610 (tight)
  Bond angles                    :   0.860
  Omega angle restraints         :   0.303 (tight)
  Side chain planarity           :   0.694
  Improper dihedral distribution :   1.126
  Inside/Outside distribution    :   1.107

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -1.8
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.610 (tight)
  Bond angles                    :   0.860
  Omega angle restraints         :   0.303 (tight)
  Side chain planarity           :   0.694
  Improper dihedral distribution :   1.126
  Inside/Outside distribution    :   1.107
==============

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.