WHAT IF Check report

This file was created 2011-12-21 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 pdb1bgg.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.043
CA-only RMS fit for the two chains : 0.013

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.047
CA-only RMS fit for the two chains : 0.017

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.054
CA-only RMS fit for the two chains : 0.017

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.052
CA-only RMS fit for the two chains : 0.018

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

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.

1793 GCO   ( 500-)  B  -
1794 GCO   ( 500-)  C  -
1795 GCO   ( 500-)  D  -

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  93 ASN   (  94-)  A
 570 LEU   ( 124-)  B

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 441 ASN   ( 442-)  A    0.50
 888 ASN   ( 442-)  B    0.50
1335 ASN   ( 442-)  C    0.50
1782 ASN   ( 442-)  D    0.50

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) :176.000

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 : 6.17

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

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.

 876 GLU   ( 430-)  B      CD   OE2   1.33    4.3

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.

 115 PHE   ( 116-)  A      N    CA   C    99.54   -4.2
 278 GLY   ( 279-)  A     -C    N    CA  127.42    4.0
 349 ILE   ( 350-)  A      N    CA   C    99.66   -4.1
 397 TRP   ( 398-)  A      N    CA   CB  118.25    4.6
 398 SER   ( 399-)  A     -C    N    CA  130.20    4.7
 398 SER   ( 399-)  A      N    CA   C   127.66    5.9
 562 PHE   ( 116-)  B      N    CA   C    99.98   -4.0
 796 ILE   ( 350-)  B      N    CA   C    99.83   -4.1
 837 HIS   ( 391-)  B      CG   ND1  CE1 109.64    4.0
 844 TRP   ( 398-)  B      N    CA   CB  118.39    4.6
 845 SER   ( 399-)  B     -CA  -C    N   107.98   -4.1
 845 SER   ( 399-)  B     -C    N    CA  130.46    4.9
 845 SER   ( 399-)  B      N    CA   C   127.22    5.7
 933 HIS   (  40-)  C      CG   ND1  CE1 109.65    4.1
1009 PHE   ( 116-)  C      N    CA   C    99.96   -4.0
1243 ILE   ( 350-)  C      N    CA   C    99.83   -4.1
1291 TRP   ( 398-)  C      N    CA   CB  118.20    4.5
1292 SER   ( 399-)  C     -C    N    CA  130.14    4.7
1292 SER   ( 399-)  C      N    CA   C   127.52    5.8
1380 HIS   (  40-)  D      CG   ND1  CE1 109.66    4.1
1399 HIS   (  59-)  D      CG   ND1  CE1 109.65    4.0
1456 PHE   ( 116-)  D      N    CA   C    99.59   -4.1
1535 HIS   ( 195-)  D      CG   ND1  CE1 109.61    4.0
1541 HIS   ( 201-)  D      CG   ND1  CE1 109.68    4.1
1690 ILE   ( 350-)  D      N    CA   C    99.90   -4.0
1738 TRP   ( 398-)  D      N    CA   CB  118.19    4.5
1739 SER   ( 399-)  D     -C    N    CA  130.26    4.8
1739 SER   ( 399-)  D      N    CA   C   127.57    5.8

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 398 SER   ( 399-)  A      CA    -7.9    19.64    34.32
 845 SER   ( 399-)  B      CA    -7.6    20.23    34.32
1292 SER   ( 399-)  C      CA    -8.0    19.53    34.32
1739 SER   ( 399-)  D      CA    -8.0    19.49    34.32
The average deviation= 1.121

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.

 398 SER   ( 399-)  A    6.12
1739 SER   ( 399-)  D    6.09
1292 SER   ( 399-)  C    6.07
 845 SER   ( 399-)  B    5.95
 914 ILE   (  21-)  C    5.56
 467 ILE   (  21-)  B    5.44
1361 ILE   (  21-)  D    5.40
  20 ILE   (  21-)  A    5.24
 500 ALA   (  54-)  B    5.22
 482 ASP   (  36-)  B    5.11
1394 ALA   (  54-)  D    5.05
  35 ASP   (  36-)  A    5.04
  53 ALA   (  54-)  A    5.01
 929 ASP   (  36-)  C    4.98
 911 ALA   (  18-)  C    4.93
1286 LYS   ( 393-)  C    4.85
 947 ALA   (  54-)  C    4.84
 839 LYS   ( 393-)  B    4.83
1376 ASP   (  36-)  D    4.81
1733 LYS   ( 393-)  D    4.79
  17 ALA   (  18-)  A    4.77
 392 LYS   ( 393-)  A    4.72
1358 ALA   (  18-)  D    4.70
 464 ALA   (  18-)  B    4.68
 690 SER   ( 244-)  B    4.53
1457 CYS   ( 117-)  D    4.43
 563 CYS   ( 117-)  B    4.41
1137 SER   ( 244-)  C    4.39
1584 SER   ( 244-)  D    4.39
 115 PHE   ( 116-)  A    4.38
1456 PHE   ( 116-)  D    4.36
 243 SER   ( 244-)  A    4.35
1632 GLY   ( 292-)  D    4.33
1010 CYS   ( 117-)  C    4.31
 738 GLY   ( 292-)  B    4.27
 116 CYS   ( 117-)  A    4.26
1009 PHE   ( 116-)  C    4.19
 562 PHE   ( 116-)  B    4.18
 291 GLY   ( 292-)  A    4.18
 121 TRP   ( 122-)  A    4.13
1185 GLY   ( 292-)  C    4.08
1462 TRP   ( 122-)  D    4.07
  59 ARG   (  60-)  A    4.01
 506 ARG   (  60-)  B    4.00

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 : 1.599

Torsion-related checks

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.

1292 SER   ( 399-)  C    -2.6
 398 SER   ( 399-)  A    -2.6
1739 SER   ( 399-)  D    -2.6
 845 SER   ( 399-)  B    -2.6
1495 HIS   ( 155-)  D    -2.4
1048 HIS   ( 155-)  C    -2.4
 601 HIS   ( 155-)  B    -2.4
 154 HIS   ( 155-)  A    -2.4
 289 MET   ( 290-)  A    -2.3
1630 MET   ( 290-)  D    -2.3
1183 MET   ( 290-)  C    -2.3
 736 MET   ( 290-)  B    -2.3
1462 TRP   ( 122-)  D    -2.2
 568 TRP   ( 122-)  B    -2.2
 121 TRP   ( 122-)  A    -2.2
1015 TRP   ( 122-)  C    -2.2
1745 GLU   ( 405-)  D    -2.1
1014 HIS   ( 121-)  C    -2.0
1461 HIS   ( 121-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  23 ALA   (  24-)  A  Poor phi/psi
  46 ASN   (  47-)  A  Poor phi/psi
  53 ALA   (  54-)  A  Poor phi/psi
  54 CYS   (  55-)  A  Poor phi/psi
 121 TRP   ( 122-)  A  Poor phi/psi
 180 ALA   ( 181-)  A  PRO omega poor
 274 PRO   ( 275-)  A  Poor phi/psi
 306 ALA   ( 307-)  A  Poor phi/psi
 362 ASN   ( 363-)  A  Poor phi/psi
 366 GLN   ( 367-)  A  Poor phi/psi
 367 ASP   ( 368-)  A  Poor phi/psi
 390 HIS   ( 391-)  A  Poor phi/psi
 398 SER   ( 399-)  A  Poor phi/psi
 405 TRP   ( 406-)  A  Poor phi/psi
 406 ALA   ( 407-)  A  Poor phi/psi
 423 GLN   ( 424-)  A  Poor phi/psi
 441 ASN   ( 442-)  A  Poor phi/psi
 470 ALA   (  24-)  B  Poor phi/psi
 493 ASN   (  47-)  B  Poor phi/psi
 500 ALA   (  54-)  B  Poor phi/psi
 501 CYS   (  55-)  B  Poor phi/psi
 502 ASP   (  56-)  B  Poor phi/psi
 568 TRP   ( 122-)  B  Poor phi/psi
 612 GLU   ( 166-)  B  Poor phi/psi
 627 ALA   ( 181-)  B  PRO omega poor
And so on for a total of 68 lines.

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.

1266 SER   ( 373-)  C    0.39
1713 SER   ( 373-)  D    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!

   8 ASP   (   9-)  A      0
  11 TRP   (  12-)  A      0
  20 ILE   (  21-)  A      0
  23 ALA   (  24-)  A      0
  26 GLU   (  27-)  A      0
  27 ASP   (  28-)  A      0
  39 HIS   (  40-)  A      0
  41 PRO   (  42-)  A      0
  45 PHE   (  46-)  A      0
  46 ASN   (  47-)  A      0
  48 ASP   (  49-)  A      0
  51 ASN   (  52-)  A      0
  52 VAL   (  53-)  A      0
  53 ALA   (  54-)  A      0
  54 CYS   (  55-)  A      0
  55 ASP   (  56-)  A      0
  56 SER   (  57-)  A      0
  58 HIS   (  59-)  A      0
  72 ILE   (  73-)  A      0
  74 THR   (  75-)  A      0
  81 TRP   (  82-)  A      0
  84 ILE   (  85-)  A      0
  85 PHE   (  86-)  A      0
  91 GLU   (  92-)  A      0
  94 GLN   (  95-)  A      0
And so on for a total of 689 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 : 1.711

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]

  86 PRO   (  87-)  A    0.46 HIGH
 533 PRO   (  87-)  B    0.46 HIGH
 980 PRO   (  87-)  C    0.46 HIGH
1427 PRO   (  87-)  D    0.46 HIGH

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.

 567 HIS   ( 121-)  B      CE1 <-> 1793 GCO   ( 500-)  B      O2     0.74    2.06  INTRA
 821 MET   ( 375-)  B      SD  <-> 1797 HOH   ( 758 )  B      O      0.60    2.40  INTRA
1715 MET   ( 375-)  D      SD  <-> 1799 HOH   ( 639 )  D      O      0.58    2.42  INTRA
 374 MET   ( 375-)  A      SD  <-> 1796 HOH   ( 655 )  A      O      0.57    2.43  INTRA
1268 MET   ( 375-)  C      SD  <-> 1798 HOH   ( 755 )  C      O      0.56    2.44  INTRA
1059 GLU   ( 166-)  C      CD  <-> 1794 GCO   ( 500-)  C      O11    0.44    2.36  INTRA
 466 GLN   (  20-)  B      NE2 <-> 1793 GCO   ( 500-)  B      O3     0.39    2.31  INTRA
1102 ARG   ( 209-)  C      NH1 <-> 1798 HOH   ( 722 )  C      O      0.37    2.33  INTRA
 208 ARG   ( 209-)  A      NH1 <-> 1796 HOH   ( 727 )  A      O      0.36    2.34  INTRA
1589 TRP   ( 249-)  D      NE1 <-> 1799 HOH   ( 856 )  D      O      0.30    2.40  INTRA
1142 TRP   ( 249-)  C      NE1 <-> 1798 HOH   ( 874 )  C      O      0.28    2.42  INTRA
 913 GLN   (  20-)  C      NE2 <-> 1794 GCO   ( 500-)  C      O3     0.27    2.43  INTRA
1461 HIS   ( 121-)  D      CE1 <-> 1795 GCO   ( 500-)  D      O2     0.26    2.54  INTRA
 567 HIS   ( 121-)  B      NE2 <-> 1793 GCO   ( 500-)  B      O2     0.25    2.45  INTRA
1059 GLU   ( 166-)  C      OE1 <-> 1794 GCO   ( 500-)  C      O11    0.24    2.16  INTRA
 852 TRP   ( 406-)  B      NE1 <-> 1793 GCO   ( 500-)  B      O3     0.24    2.46  INTRA
1442 HIS   ( 102-)  D      CD2 <-> 1497 LYS   ( 157-)  D      NZ     0.23    2.87  INTRA BL
 101 HIS   ( 102-)  A      CD2 <->  156 LYS   ( 157-)  A      NZ     0.23    2.87  INTRA BL
 995 HIS   ( 102-)  C      CD2 <-> 1050 LYS   ( 157-)  C      NZ     0.23    2.87  INTRA BL
1589 TRP   ( 249-)  D      CZ3 <-> 1799 HOH   ( 713 )  D      O      0.22    2.58  INTRA
 548 HIS   ( 102-)  B      CD2 <->  603 LYS   ( 157-)  B      NZ     0.22    2.88  INTRA BL
1031 ARG   ( 138-)  C      NE  <-> 1798 HOH   ( 867 )  C      O      0.21    2.49  INTRA BF
 547 TYR   ( 101-)  B      CE2 <-> 1797 HOH   ( 768 )  B      O      0.21    2.59  INTRA BF
1014 HIS   ( 121-)  C      CE1 <-> 1794 GCO   ( 500-)  C      O2     0.20    2.60  INTRA
1360 GLN   (  20-)  D      NE2 <-> 1795 GCO   ( 500-)  D      O3     0.20    2.50  INTRA
And so on for a total of 200 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.

1340 ARG   ( 447-)  C      -7.05
 893 ARG   ( 447-)  B      -7.02
1787 ARG   ( 447-)  D      -6.98
 446 ARG   ( 447-)  A      -6.97
 833 HIS   ( 387-)  B      -6.18
 386 HIS   ( 387-)  A      -6.18
1727 HIS   ( 387-)  D      -6.18
1280 HIS   ( 387-)  C      -6.18
 245 HIS   ( 246-)  A      -5.94
 692 HIS   ( 246-)  B      -5.94
1139 HIS   ( 246-)  C      -5.94
1586 HIS   ( 246-)  D      -5.93
 868 ARG   ( 422-)  B      -5.78
 421 ARG   ( 422-)  A      -5.66
1365 TYR   (  25-)  D      -5.58
1762 ARG   ( 422-)  D      -5.56
 702 GLN   ( 256-)  B      -5.55
 918 TYR   (  25-)  C      -5.55
1596 GLN   ( 256-)  D      -5.54
 471 TYR   (  25-)  B      -5.54
 255 GLN   ( 256-)  A      -5.54
1149 GLN   ( 256-)  C      -5.54
 723 GLN   ( 277-)  B      -5.52
  24 TYR   (  25-)  A      -5.51
1617 GLN   ( 277-)  D      -5.48
1315 ARG   ( 422-)  C      -5.47
1170 GLN   ( 277-)  C      -5.43
 675 TYR   ( 229-)  B      -5.42
 276 GLN   ( 277-)  A      -5.42
 440 ASN   ( 441-)  A      -5.38
 887 ASN   ( 441-)  B      -5.37
1781 ASN   ( 441-)  D      -5.37
1334 ASN   ( 441-)  C      -5.36
1387 ASN   (  47-)  D      -5.35
1122 TYR   ( 229-)  C      -5.34
  46 ASN   (  47-)  A      -5.34
 228 TYR   ( 229-)  A      -5.33
 940 ASN   (  47-)  C      -5.32
 493 ASN   (  47-)  B      -5.32
1569 TYR   ( 229-)  D      -5.26
1656 ASN   ( 316-)  D      -5.09
 762 ASN   ( 316-)  B      -5.06
1209 ASN   ( 316-)  C      -5.06
 315 ASN   ( 316-)  A      -5.06
 752 GLU   ( 306-)  B      -5.03

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.

  24 TYR   (  25-)  A        28 - GLY     29- ( A)         -4.48
  45 PHE   (  46-)  A        47 - GLY     48- ( A)         -4.63
 471 TYR   (  25-)  B       475 - GLY     29- ( B)         -4.47
 492 PHE   (  46-)  B       494 - GLY     48- ( B)         -4.63
 918 TYR   (  25-)  C       922 - GLY     29- ( C)         -4.50
 939 PHE   (  46-)  C       941 - GLY     48- ( C)         -4.66
1365 TYR   (  25-)  D      1369 - GLY     29- ( D)         -4.50
1386 PHE   (  46-)  D      1388 - GLY     48- ( D)         -4.67

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.

 318 LEU   ( 319-)  A   -2.93
1659 LEU   ( 319-)  D   -2.92
1393 VAL   (  53-)  D   -2.78
 946 VAL   (  53-)  C   -2.77
 499 VAL   (  53-)  B   -2.76
  52 VAL   (  53-)  A   -2.74
 945 ASN   (  52-)  C   -2.58
 498 ASN   (  52-)  B   -2.53
  51 ASN   (  52-)  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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1796 HOH   ( 570 )  A      O      8.39   45.13   36.83
1796 HOH   ( 573 )  A      O     10.14   33.66   31.98
1796 HOH   ( 577 )  A      O      1.25   34.24   38.03
1796 HOH   ( 670 )  A      O     10.52   23.76   30.30
1796 HOH   ( 684 )  A      O     11.19   31.89   26.28
1797 HOH   ( 532 )  B      O     26.19   98.38   38.85
1797 HOH   ( 664 )  B      O     18.06   80.06   74.32
1797 HOH   ( 665 )  B      O     17.83   77.27   74.32
1797 HOH   ( 669 )  B      O     22.90   75.81   74.09
1797 HOH   ( 749 )  B      O     44.12   77.32   72.59
1797 HOH   ( 750 )  B      O     50.33   93.42   34.96
1797 HOH   ( 754 )  B      O     45.49   92.36   36.64
1797 HOH   ( 828 )  B      O     20.79   84.35   78.63
1797 HOH   ( 844 )  B      O     31.44   98.52   35.26
1797 HOH   ( 847 )  B      O     34.27   90.20   31.69
1798 HOH   ( 872 )  C      O     89.98   71.83   29.08
1799 HOH   ( 531 )  D      O     75.28    0.50   38.00
1799 HOH   ( 561 )  D      O     65.47   18.02   77.52
1799 HOH   ( 650 )  D      O     77.61   24.90   74.36
1799 HOH   ( 654 )  D      O     82.53   20.46   74.91
1799 HOH   ( 661 )  D      O     82.23   16.35   77.21
1799 HOH   ( 787 )  D      O     55.95   22.73   72.49
1799 HOH   ( 789 )  D      O     79.91   16.39   79.02

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1796 HOH   ( 456 )  A      O
1796 HOH   ( 515 )  A      O
1796 HOH   ( 596 )  A      O
1797 HOH   ( 581 )  B      O
1797 HOH   ( 645 )  B      O
1797 HOH   ( 693 )  B      O
1797 HOH   ( 760 )  B      O
1797 HOH   ( 776 )  B      O
1797 HOH   ( 842 )  B      O
1798 HOH   ( 555 )  C      O
1798 HOH   ( 585 )  C      O
1798 HOH   ( 592 )  C      O
1798 HOH   ( 644 )  C      O
1798 HOH   ( 756 )  C      O
1798 HOH   ( 779 )  C      O
1798 HOH   ( 796 )  C      O
1798 HOH   ( 830 )  C      O
1798 HOH   ( 859 )  C      O
1799 HOH   ( 693 )  D      O
1799 HOH   ( 727 )  D      O
1799 HOH   ( 745 )  D      O
1799 HOH   ( 771 )  D      O

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.

  19 GLN   (  20-)  A
  46 ASN   (  47-)  A
  51 ASN   (  52-)  A
  94 GLN   (  95-)  A
 101 HIS   ( 102-)  A
 120 HIS   ( 121-)  A
 125 GLN   ( 126-)  A
 128 GLN   ( 129-)  A
 164 ASN   ( 165-)  A
 200 HIS   ( 201-)  A
 215 GLN   ( 216-)  A
 260 GLN   ( 261-)  A
 315 ASN   ( 316-)  A
 337 HIS   ( 338-)  A
 366 GLN   ( 367-)  A
 376 GLN   ( 377-)  A
 380 GLN   ( 381-)  A
 390 HIS   ( 391-)  A
 441 ASN   ( 442-)  A
 466 GLN   (  20-)  B
 486 HIS   (  40-)  B
 493 ASN   (  47-)  B
 541 GLN   (  95-)  B
 548 HIS   ( 102-)  B
 567 HIS   ( 121-)  B
And so on for a total of 69 lines.

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.

  11 TRP   (  12-)  A      N
  13 THR   (  14-)  A      OG1
  16 ALA   (  17-)  A      N
  18 TYR   (  19-)  A      OH
  19 GLN   (  20-)  A      NE2
  22 GLY   (  23-)  A      N
  23 ALA   (  24-)  A      N
  54 CYS   (  55-)  A      N
  57 TYR   (  58-)  A      N
  80 SER   (  81-)  A      OG
  89 ASP   (  90-)  A      N
  91 GLU   (  92-)  A      N
 121 TRP   ( 122-)  A      N
 136 ARG   ( 137-)  A      NH1
 159 HIS   ( 160-)  A      N
 164 ASN   ( 165-)  A      ND2
 167 TRP   ( 168-)  A      NE1
 180 ALA   ( 181-)  A      N
 218 ILE   ( 219-)  A      N
 223 SER   ( 224-)  A      N
 225 ALA   ( 226-)  A      N
 240 ARG   ( 241-)  A      NH2
 248 TRP   ( 249-)  A      NE1
 277 ASP   ( 278-)  A      N
 289 MET   ( 290-)  A      N
And so on for a total of 147 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.

 377 HIS   ( 378-)  A      NE2
 466 GLN   (  20-)  B      OE1
 567 HIS   ( 121-)  B      NE2
 587 GLN   ( 141-)  B      OE1
 913 GLN   (  20-)  C      OE1
1014 HIS   ( 121-)  C      NE2
1170 GLN   ( 277-)  C      OE1
1360 GLN   (  20-)  D      OE1
1461 HIS   ( 121-)  D      NE2
1550 GLU   ( 210-)  D      OE2
1617 GLN   ( 277-)  D      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1796 HOH   ( 816 )  A      O  0.95  K  4
1797 HOH   ( 607 )  B      O  0.96  K  4
1797 HOH   ( 752 )  B      O  0.92  K  4 ION-B H2O-B
1799 HOH   ( 648 )  D      O  0.89  K  4 H2O-B

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.

  55 ASP   (  56-)  A   H-bonding suggests Asn
  98 ASP   (  99-)  A   H-bonding suggests Asn
 109 ASP   ( 110-)  A   H-bonding suggests Asn
 264 ASP   ( 265-)  A   H-bonding suggests Asn; but Alt-Rotamer
 358 ASP   ( 359-)  A   H-bonding suggests Asn
 502 ASP   (  56-)  B   H-bonding suggests Asn
 545 ASP   (  99-)  B   H-bonding suggests Asn
 556 ASP   ( 110-)  B   H-bonding suggests Asn
 711 ASP   ( 265-)  B   H-bonding suggests Asn; but Alt-Rotamer
 805 ASP   ( 359-)  B   H-bonding suggests Asn
 949 ASP   (  56-)  C   H-bonding suggests Asn
 992 ASP   (  99-)  C   H-bonding suggests Asn; but Alt-Rotamer
1003 ASP   ( 110-)  C   H-bonding suggests Asn
1158 ASP   ( 265-)  C   H-bonding suggests Asn; but Alt-Rotamer
1252 ASP   ( 359-)  C   H-bonding suggests Asn
1396 ASP   (  56-)  D   H-bonding suggests Asn
1439 ASP   (  99-)  D   H-bonding suggests Asn; but Alt-Rotamer
1450 ASP   ( 110-)  D   H-bonding suggests Asn
1692 GLU   ( 352-)  D   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1699 ASP   ( 359-)  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 :  -0.432
  2nd generation packing quality :  -0.677
  Ramachandran plot appearance   :  -1.207
  chi-1/chi-2 rotamer normality  :  -1.129
  Backbone conformation          :  -0.687

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.407 (tight)
  Bond angles                    :   0.754
  Omega angle restraints         :   0.311 (tight)
  Side chain planarity           :   0.428 (tight)
  Improper dihedral distribution :   0.958
  Inside/Outside distribution    :   1.012

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.407 (tight)
  Bond angles                    :   0.754
  Omega angle restraints         :   0.311 (tight)
  Side chain planarity           :   0.428 (tight)
  Improper dihedral distribution :   0.958
  Inside/Outside distribution    :   1.012
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
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WHAT_CHECK (verification routines from WHAT IF)
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      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.