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 pdb6cox.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 181.170  B   = 132.810  C    = 122.740
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 127.990  B   = 122.740  C    = 127.990
    Alpha=  61.348  Beta=  62.507  Gamma=  61.348

Dimensions of the conventional cell

    A    = 122.740  B   = 132.810  C    = 181.170
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

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.

1111 S58   ( 701-)  A  -         Fragmented
1112 HEM   ( 682-)  A  -         OK
1113 S58   ( 701-)  B  -         Fragmented
1114 HEM   ( 682-)  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

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 : 13.17

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

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    4.7
 909 HIS   ( 388-)  B      CG   CD2   1.41    5.3

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.

 117 TYR   ( 148-)  A      N    CA   C    98.03   -4.7
 173 HIS   ( 204-)  A      CG   ND1  CE1 109.70    4.1
 187 PRO   ( 218-)  A      N    CA   C   100.62   -4.5
 195 HIS   ( 226-)  A      CG   ND1  CE1 109.63    4.0
 201 HIS   ( 232-)  A      CG   ND1  CE1 109.60    4.0
 238 THR   ( 269-)  A      N    CA   C    98.61   -4.5
 256 VAL   ( 287-)  A      N    CA   C   125.97    5.3
 287 GLN   ( 318-)  A     -C    N    CA  114.12   -4.2
 357 HIS   ( 388-)  A      CD2  CG   ND1 112.33    6.2
 391 PHE   ( 422-)  A      N    CA   C    97.78   -4.8
 482 ARG   ( 513-)  A      N    CA   C    97.92   -4.7
 669 TYR   ( 148-)  B      N    CA   C    97.74   -4.8
 739 PRO   ( 218-)  B      N    CA   C   100.41   -4.6
 753 HIS   ( 232-)  B      CG   ND1  CE1 109.67    4.1
 790 THR   ( 269-)  B      N    CA   C    97.72   -4.8
 808 VAL   ( 287-)  B      N    CA   C   125.29    5.0
 909 HIS   ( 388-)  B      CD2  CG   ND1 111.22    5.1
 943 PHE   ( 422-)  B      N    CA   C    99.01   -4.4
 958 GLY   ( 437-)  B      N    CA   C   100.17   -4.3
1007 GLU   ( 486-)  B     -C    N    CA  114.15   -4.2
1034 ARG   ( 513-)  B      N    CA   C    98.17   -4.7

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.

 391 PHE   ( 422-)  A    7.64
 943 PHE   ( 422-)  B    6.96
 315 GLU   ( 346-)  A    6.45
 867 GLU   ( 346-)  B    6.43
 256 VAL   ( 287-)  A    6.15
 948 THR   ( 427-)  B    5.97
 808 VAL   ( 287-)  B    5.89
 622 ILE   ( 102-)  B    5.66
 396 THR   ( 427-)  A    5.61
 493 GLU   ( 524-)  A    5.53
  70 ILE   ( 102-)  A    5.48
 975 GLN   ( 454-)  B    5.38
1045 GLU   ( 524-)  B    5.19
 392 VAL   ( 423-)  A    5.18
 669 TYR   ( 148-)  B    5.13
 381 SER   ( 412-)  A    5.07
 117 TYR   ( 148-)  A    5.02
 482 ARG   ( 513-)  A    5.01
1047 GLY   ( 526-)  B    4.94
 495 GLY   ( 526-)  A    4.92
1034 ARG   ( 513-)  B    4.92
 702 VAL   ( 181-)  B    4.92
 423 GLN   ( 454-)  A    4.88
 150 VAL   ( 181-)  A    4.88
 295 GLU   ( 326-)  A    4.88
And so on for a total of 53 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 : 1.999

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 : -5.000

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.

 616 PHE   (  96-)  B    -3.2
  64 PHE   (  96-)  A    -3.1
 483 PRO   ( 514-)  A    -3.1
1035 PRO   ( 514-)  B    -3.1
 594 PHE   (  74-)  B    -3.1
  42 PHE   (  74-)  A    -2.8
 381 SER   ( 412-)  A    -2.7
 933 SER   ( 412-)  B    -2.7
 671 ARG   ( 150-)  B    -2.6
 119 ARG   ( 150-)  A    -2.6
 352 THR   ( 383-)  A    -2.6
 751 LEU   ( 230-)  B    -2.5
 453 GLU   ( 484-)  A    -2.5
1005 GLU   ( 484-)  B    -2.5
 199 LEU   ( 230-)  A    -2.4
 533 ILE   ( 564-)  A    -2.4
1085 ILE   ( 564-)  B    -2.4
 454 LYS   ( 485-)  A    -2.4
  49 LEU   (  81-)  A    -2.4
 601 LEU   (  81-)  B    -2.3
1059 PRO   ( 538-)  B    -2.3
 904 THR   ( 383-)  B    -2.3
 507 PRO   ( 538-)  A    -2.3
1094 LYS   ( 573-)  B    -2.3
 542 LYS   ( 573-)  A    -2.3
And so on for a total of 60 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
  20 PHE   (  52-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  33 TYR   (  65-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  50 LEU   (  82-)  A  Poor phi/psi
  63 HIS   (  95-)  A  Poor phi/psi
  64 PHE   (  96-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  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
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 256 VAL   ( 287-)  A  Poor phi/psi
 288 GLU   ( 319-)  A  Poor phi/psi
 298 PHE   ( 329-)  A  Poor phi/psi
 316 ASP   ( 347-)  A  Poor phi/psi
 317 TYR   ( 348-)  A  Poor phi/psi
 340 PHE   ( 371-)  A  Poor phi/psi
 342 TYR   ( 373-)  A  Poor phi/psi
 356 TRP   ( 387-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
And so on for a total of 78 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 : -4.644

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.

 946 SER   ( 425-)  B    0.34
 394 SER   ( 425-)  A    0.34
 420 SER   ( 451-)  A    0.35
 972 SER   ( 451-)  B    0.37
 976 SER   ( 455-)  B    0.38
 631 SER   ( 110-)  B    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   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
  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
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  36 ASN   (  68-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  39 THR   (  71-)  A      0
  50 LEU   (  82-)  A      0
  56 THR   (  88-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
And so on for a total of 447 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 : 1.654

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!

 953 GLY   ( 432-)  B   1.56   21

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...

 929 LEU   ( 408-)  B   1.75

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]

  96 PRO   ( 127-)  A    0.46 HIGH
 158 PRO   ( 189-)  A    0.46 HIGH
 245 PRO   ( 276-)  A    0.45 HIGH
 410 PRO   ( 441-)  A    0.45 HIGH
 497 PRO   ( 528-)  A    0.47 HIGH
 648 PRO   ( 127-)  B    0.45 HIGH
 797 PRO   ( 276-)  B    0.46 HIGH
 962 PRO   ( 441-)  B    0.46 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].

   3 PRO   (  35-)  A  -113.2 envelop C-gamma (-108 degrees)
 141 PRO   ( 172-)  A   105.5 envelop C-beta (108 degrees)
 187 PRO   ( 218-)  A    51.9 half-chair C-delta/C-gamma (54 degrees)
 249 PRO   ( 280-)  A   106.3 envelop C-beta (108 degrees)
 358 PRO   ( 389-)  A   108.9 envelop C-beta (108 degrees)
 481 PRO   ( 512-)  A    99.6 envelop C-beta (108 degrees)
 483 PRO   ( 514-)  A   128.5 half-chair C-beta/C-alpha (126 degrees)
 507 PRO   ( 538-)  A  -123.1 half-chair C-delta/C-gamma (-126 degrees)
 555 PRO   (  35-)  B  -113.2 envelop C-gamma (-108 degrees)
 693 PRO   ( 172-)  B   107.3 envelop C-beta (108 degrees)
 739 PRO   ( 218-)  B    52.4 half-chair C-delta/C-gamma (54 degrees)
 801 PRO   ( 280-)  B   105.3 envelop C-beta (108 degrees)
 910 PRO   ( 389-)  B   111.4 envelop C-beta (108 degrees)
1033 PRO   ( 512-)  B   101.0 envelop C-beta (108 degrees)
1035 PRO   ( 514-)  B   132.5 half-chair C-beta/C-alpha (126 degrees)
1059 PRO   ( 538-)  B  -121.3 half-chair C-delta/C-gamma (-126 degrees)
1097 PRO   ( 576-)  B    52.1 half-chair C-delta/C-gamma (54 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.

 328 LEU   ( 359-)  A      CD1 <-> 1111 S58   ( 701-)  A      F1     0.56    2.64  INTRA BL
 677 ALA   ( 156-)  B      CB  <->  680 CYS   ( 159-)  B      SG     0.45    2.95  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  427 MET   ( 458-)  A      O      0.43    2.27  INTRA BL
 125 ALA   ( 156-)  A      CB  <->  128 CYS   ( 159-)  A      SG     0.42    2.98  INTRA BL
  92 LEU   ( 123-)  A      O   <->  438 ARG   ( 469-)  A      NH2    0.41    2.29  INTRA BL
 671 ARG   ( 150-)  B      NH2 <->  979 MET   ( 458-)  B      O      0.37    2.33  INTRA BL
 641 ARG   ( 120-)  B      NH1 <-> 1113 S58   ( 701-)  B      F3     0.36    2.74  INTRA
 644 LEU   ( 123-)  B      O   <->  990 ARG   ( 469-)  B      NH2    0.34    2.36  INTRA
 561 CYS   (  41-)  B      SG  <->  567 CYS   (  47-)  B      CB     0.34    3.06  INTRA BL
 111 PHE   ( 142-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.33    2.37  INTRA BL
   9 CYS   (  41-)  A      SG  <->   15 CYS   (  47-)  A      CB     0.33    3.07  INTRA
 464 TYR   ( 495-)  A      CE2 <->  470 MET   ( 501-)  A      SD     0.33    3.07  INTRA
1099 THR   ( 578-)  B      CG2 <-> 1100 SER   ( 579-)  B      N      0.31    2.69  INTRA BL
 547 THR   ( 578-)  A      CG2 <->  548 SER   ( 579-)  A      N      0.31    2.69  INTRA BL
  62 THR   (  94-)  A      O   <->  325 HIS   ( 356-)  A      ND1    0.30    2.40  INTRA
 804 LEU   ( 283-)  B      CB  <->  932 ASN   ( 411-)  B      ND2    0.29    2.81  INTRA BF
 714 GLY   ( 193-)  B      O   <-> 1103 VAL   ( 582-)  B      N      0.29    2.41  INTRA
 773 LEU   ( 252-)  B      O   <->  831 GLN   ( 310-)  B      NE2    0.29    2.41  INTRA BL
 100 ASN   ( 131-)  A      ND2 <->  116 TYR   ( 147-)  A      CD2    0.29    2.81  INTRA BL
 654 HIS   ( 133-)  B      ND1 <->  668 TYR   ( 147-)  B      CE2    0.28    2.82  INTRA BL
 804 LEU   ( 283-)  B      CB  <->  932 ASN   ( 411-)  B      CG     0.28    2.92  INTRA BF
1016 TYR   ( 495-)  B      CE2 <-> 1022 MET   ( 501-)  B      SD     0.28    3.12  INTRA BL
 427 MET   ( 458-)  A      CE  <->  429 TYR   ( 460-)  A      CE1    0.27    2.93  INTRA BL
 979 MET   ( 458-)  B      CE  <->  981 TYR   ( 460-)  B      CE1    0.27    2.93  INTRA BL
 880 LEU   ( 359-)  B      CD1 <-> 1113 S58   ( 701-)  B      F1     0.27    2.93  INTRA
And so on for a total of 440 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 581 ARG   (  61-)  B      -6.87
  29 ARG   (  61-)  A      -6.82
 799 HIS   ( 278-)  B      -6.48
 247 HIS   ( 278-)  A      -6.43
 339 GLN   ( 370-)  A      -6.07
 891 GLN   ( 370-)  B      -6.03
 138 LYS   ( 169-)  A      -5.84
 397 ARG   ( 428-)  A      -5.84
 690 LYS   ( 169-)  B      -5.71
 949 ARG   ( 428-)  B      -5.69
 938 HIS   ( 417-)  B      -5.52
 386 HIS   ( 417-)  A      -5.51
  20 PHE   (  52-)  A      -5.39
 572 PHE   (  52-)  B      -5.36
 564 ARG   (  44-)  B      -5.31
  12 ARG   (  44-)  A      -5.30
 930 TYR   ( 409-)  B      -5.28
 585 TYR   (  65-)  B      -5.26
 563 ASN   (  43-)  B      -5.25
 140 LEU   ( 171-)  A      -5.24
  11 ASN   (  43-)  A      -5.23
 378 TYR   ( 409-)  A      -5.21
 216 PHE   ( 247-)  A      -5.21
 692 LEU   ( 171-)  B      -5.19
 737 ARG   ( 216-)  B      -5.18
 736 LYS   ( 215-)  B      -5.17
 185 ARG   ( 216-)  A      -5.14
 184 LYS   ( 215-)  A      -5.11
 768 PHE   ( 247-)  B      -5.05

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.

  10 GLN   (  42-)  A        12 - ARG     44- ( A)         -5.02
 138 LYS   ( 169-)  A       140 - LEU    171- ( A)         -5.28
 183 HIS   ( 214-)  A       185 - ARG    216- ( A)         -4.78
 562 GLN   (  42-)  B       564 - ARG     44- ( B)         -5.03
 690 LYS   ( 169-)  B       692 - LEU    171- ( B)         -5.16
 735 HIS   ( 214-)  B       737 - ARG    216- ( B)         -4.84

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 804 LEU   ( 283-)  B   -2.77
 252 LEU   ( 283-)  A   -2.76
  92 LEU   ( 123-)  A   -2.59

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

  10 GLN   (  42-)  A
 247 HIS   ( 278-)  A
 319 GLN   ( 350-)  A
 320 HIS   ( 351-)  A
 386 HIS   ( 417-)  A
 799 HIS   ( 278-)  B
 871 GLN   ( 350-)  B
 872 HIS   ( 351-)  B
 890 GLN   ( 369-)  B
 938 HIS   ( 417-)  B

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.

  20 PHE   (  52-)  A      N
  22 GLN   (  54-)  A      N
  55 ASN   (  87-)  A      N
  57 VAL   (  89-)  A      N
  58 HIS   (  90-)  A      NE2
  76 PHE   ( 107-)  A      N
  89 ARG   ( 120-)  A      NH1
 100 ASN   ( 131-)  A      ND2
 101 VAL   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 119 ARG   ( 150-)  A      NE
 119 ARG   ( 150-)  A      NH1
 119 ARG   ( 150-)  A      NH2
 134 VAL   ( 165-)  A      N
 135 LYS   ( 166-)  A      N
 154 ARG   ( 185-)  A      N
 161 GLN   ( 192-)  A      N
 166 MET   ( 197-)  A      N
 172 GLN   ( 203-)  A      NE2
 173 HIS   ( 204-)  A      NE2
 176 HIS   ( 207-)  A      N
 177 GLN   ( 208-)  A      NE2
 178 PHE   ( 209-)  A      N
 180 LYS   ( 211-)  A      NZ
 190 THR   ( 221-)  A      OG1
And so on for a total of 154 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.

 159 ASP   ( 190-)  A      OD1
 173 HIS   ( 204-)  A      ND1
 177 GLN   ( 208-)  A      OE1
 289 HIS   ( 320-)  A      ND1
 308 GLU   ( 339-)  A      OE1
 338 GLN   ( 369-)  A      OE1
 430 GLN   ( 461-)  A      OE1
 661 GLU   ( 140-)  B      OE2
 711 ASP   ( 190-)  B      OD1
 725 HIS   ( 204-)  B      ND1
 729 GLN   ( 208-)  B      OE1
 829 GLU   ( 308-)  B      OE2
 841 HIS   ( 320-)  B      ND1
 860 GLU   ( 339-)  B      OE2
 932 ASN   ( 411-)  B      OD1
 982 GLN   ( 461-)  B      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.

  21 ASP   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
 126 ASP   ( 157-)  A   H-bonding suggests Asn; but Alt-Rotamer
 283 ASP   ( 314-)  A   H-bonding suggests Asn
 422 ASP   ( 453-)  A   H-bonding suggests Asn
 573 ASP   (  53-)  B   H-bonding suggests Asn
 678 ASP   ( 157-)  B   H-bonding suggests Asn; but Alt-Rotamer
 835 ASP   ( 314-)  B   H-bonding suggests Asn
 974 ASP   ( 453-)  B   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 :  -2.176
  2nd generation packing quality :  -2.054
  Ramachandran plot appearance   :  -5.000 (bad)
  chi-1/chi-2 rotamer normality  :  -4.644 (bad)
  Backbone conformation          :  -1.157

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.579 (tight)
  Bond angles                    :   0.860
  Omega angle restraints         :   0.301 (tight)
  Side chain planarity           :   0.639 (tight)
  Improper dihedral distribution :   1.137
  Inside/Outside distribution    :   1.103

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 :  -1.4
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -2.5
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.579 (tight)
  Bond angles                    :   0.860
  Omega angle restraints         :   0.301 (tight)
  Side chain planarity           :   0.639 (tight)
  Improper dihedral distribution :   1.137
  Inside/Outside distribution    :   1.103
==============

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Protein side chain planarity
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Quality Control
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Ion Checks
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    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
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Checking checks
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      Who checks the checkers
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