WHAT IF Check report

This file was created 2011-12-28 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 pdb1gnh.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 : 0.438
CA-only RMS fit for the two chains : 0.018

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 : 0.491
CA-only RMS fit for the two chains : 0.019

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 : 2.137
CA-only RMS fit for the two chains : 1.707

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

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 E

All-atom RMS fit for the two chains : 0.483
CA-only RMS fit for the two chains : 0.019

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 F

All-atom RMS fit for the two chains : 0.516
CA-only RMS fit for the two chains : 0.019

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 231052.875
Volume of the Unit Cell V= 3787327.3
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.098
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.100

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  28 LYS   (  28-)  A    High
  58 ARG   (  58-)  A    High
  88 GLU   (  88-)  A    High
 130 GLU   ( 130-)  A    High
 234 LYS   (  28-)  B    High
 294 GLU   (  88-)  B    High
 336 GLU   ( 130-)  B    High
 440 LYS   (  28-)  C    High
 500 GLU   (  88-)  C    High
 542 GLU   ( 130-)  C    High
 646 LYS   (  28-)  D    High
 665 ARG   (  47-)  D    High
 675 LYS   (  57-)  D    High
 706 GLU   (  88-)  D    High
 707 VAL   (  89-)  D    High
 748 GLU   ( 130-)  D    High
 759 SER   ( 141-)  D    High
 760 PHE   ( 142-)  D    High
 761 GLY   ( 143-)  D    High
 825 GLN   (   1-)  E    High
 852 LYS   (  28-)  E    High
 912 GLU   (  88-)  E    High
 954 GLU   ( 130-)  E    High
1058 LYS   (  28-)  F    High
1118 GLU   (  88-)  F    High
1160 GLU   ( 130-)  F    High
1264 LYS   (  28-)  G    High
1294 ARG   (  58-)  G    High
1324 GLU   (  88-)  G    High
1366 GLU   ( 130-)  G    High
1424 ARG   ( 188-)  G    High
1470 LYS   (  28-)  H    High
1530 GLU   (  88-)  H    High
1572 GLU   ( 130-)  H    High
1589 GLU   ( 147-)  H    High
1676 LYS   (  28-)  I    High
1736 GLU   (  88-)  I    High
1778 GLU   ( 130-)  I    High
1882 LYS   (  28-)  J    High
1901 ARG   (  47-)  J    High
1912 ARG   (  58-)  J    High
1942 GLU   (  88-)  J    High
1984 GLU   ( 130-)  J    High
1995 SER   ( 141-)  J    High
1996 PHE   ( 142-)  J    High
1997 GLY   ( 143-)  J    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.845 over 14568 bonds
Average difference in B over a bond : 4.26
RMS difference in B over a bond : 6.08

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

 887 ILE   (  63-)  E      CA   CB    1.61    4.1

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.

 759 SER   ( 141-)  D      N    CA   C   123.42    4.4
 862 HIS   (  38-)  E      CG   ND1  CE1 109.71    4.1
 940 ARG   ( 116-)  E      N    CA   C    99.89   -4.0
1352 ARG   ( 116-)  G      N    CA   C    99.79   -4.1
1480 HIS   (  38-)  H      CG   ND1  CE1 109.72    4.1
1743 HIS   (  95-)  I      CG   ND1  CE1 109.62    4.0
1764 ARG   ( 116-)  I      N    CA   C    99.70   -4.1
1995 SER   ( 141-)  J      N    CA   C   124.47    4.7

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.

 660 GLU   (  42-)  D      C     13.5    19.57    -0.03
1896 GLU   (  42-)  J      C     13.6    19.63    -0.03
The average deviation= 1.142

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.

1995 SER   ( 141-)  J    4.90
 759 SER   ( 141-)  D    4.50
1764 ARG   ( 116-)  I    4.35
 189 ALA   ( 189-)  A    4.33
1352 ARG   ( 116-)  G    4.31
 807 ALA   ( 189-)  D    4.30
 395 ALA   ( 189-)  B    4.28
 940 ARG   ( 116-)  E    4.27
1146 ARG   ( 116-)  F    4.22
1558 ARG   ( 116-)  H    4.22
1631 ALA   ( 189-)  H    4.22
2043 ALA   ( 189-)  J    4.20
1425 ALA   ( 189-)  G    4.16
 601 ALA   ( 189-)  C    4.14
 528 ARG   ( 116-)  C    4.11
1970 ARG   ( 116-)  J    4.10
 322 ARG   ( 116-)  B    4.02

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 : 1.501

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.

 830 ARG   (   6-)  E    -3.0
1448 ARG   (   6-)  H    -2.9
1897 LEU   (  43-)  J    -2.8
 661 LEU   (  43-)  D    -2.8
1036 ARG   (   6-)  F    -2.8
   6 ARG   (   6-)  A    -2.8
1242 ARG   (   6-)  G    -2.7
 449 LEU   (  37-)  C    -2.7
 243 LEU   (  37-)  B    -2.7
 861 LEU   (  37-)  E    -2.7
1273 LEU   (  37-)  G    -2.7
  37 LEU   (  37-)  A    -2.7
1067 LEU   (  37-)  F    -2.7
1479 LEU   (  37-)  H    -2.7
1654 ARG   (   6-)  I    -2.7
1891 LEU   (  37-)  J    -2.7
 655 LEU   (  37-)  D    -2.7
1685 LEU   (  37-)  I    -2.7
1980 THR   ( 126-)  J    -2.6
 126 THR   ( 126-)  A    -2.6
 950 THR   ( 126-)  E    -2.6
1774 THR   ( 126-)  I    -2.6
 538 THR   ( 126-)  C    -2.6
1568 THR   ( 126-)  H    -2.6
 332 THR   ( 126-)  B    -2.6
And so on for a total of 109 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.

   6 ARG   (   6-)  A  Poor phi/psi
  32 ALA   (  32-)  A  Poor phi/psi
  70 ASP   (  70-)  A  Poor phi/psi
  92 ALA   (  92-)  A  Poor phi/psi
 104 SER   ( 104-)  A  Poor phi/psi
 124 GLY   ( 124-)  A  Poor phi/psi
 145 ASN   ( 145-)  A  Poor phi/psi
 212 ARG   (   6-)  B  Poor phi/psi
 238 ALA   (  32-)  B  Poor phi/psi
 276 ASP   (  70-)  B  Poor phi/psi
 298 ALA   (  92-)  B  Poor phi/psi
 310 SER   ( 104-)  B  Poor phi/psi
 318 ASP   ( 112-)  B  Poor phi/psi
 351 ASN   ( 145-)  B  Poor phi/psi
 418 ARG   (   6-)  C  Poor phi/psi
 444 ALA   (  32-)  C  Poor phi/psi
 445 PHE   (  33-)  C  Poor phi/psi
 482 ASP   (  70-)  C  Poor phi/psi
 504 ALA   (  92-)  C  Poor phi/psi
 516 SER   ( 104-)  C  Poor phi/psi
 524 ASP   ( 112-)  C  Poor phi/psi
 536 GLY   ( 124-)  C  Poor phi/psi
 557 ASN   ( 145-)  C  Poor phi/psi
 624 ARG   (   6-)  D  Poor phi/psi
 650 ALA   (  32-)  D  Poor phi/psi
And so on for a total of 82 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.074

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 MET   (   4-)  A      0
   5 SER   (   5-)  A      0
   6 ARG   (   6-)  A      0
  12 PRO   (  12-)  A      0
  16 ASP   (  16-)  A      0
  18 SER   (  18-)  A      0
  19 TYR   (  19-)  A      0
  26 LEU   (  26-)  A      0
  31 LYS   (  31-)  A      0
  32 ALA   (  32-)  A      0
  36 CYS   (  36-)  A      0
  38 HIS   (  38-)  A      0
  42 GLU   (  42-)  A      0
  45 SER   (  45-)  A      0
  47 ARG   (  47-)  A      0
  52 PHE   (  52-)  A      0
  58 ARG   (  58-)  A      0
  59 GLN   (  59-)  A      0
  60 ASP   (  60-)  A      0
  62 GLU   (  62-)  A      0
  63 ILE   (  63-)  A      0
  69 LYS   (  69-)  A      0
  71 ILE   (  71-)  A      0
  77 VAL   (  77-)  A      0
  84 PHE   (  84-)  A      0
And so on for a total of 1027 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 : 1.383

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!

1998 GLY   ( 144-)  J   2.59   10
 762 GLY   ( 144-)  D   2.56   10

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]

1557 PRO   ( 115-)  H    0.45 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.

1850 PRO   ( 202-)  I      O   <-> 1972 ARG   ( 118-)  J      NH2    0.52    2.18  INTRA BL
 408 PRO   ( 202-)  B      O   <->  530 ARG   ( 118-)  C      NH2    0.40    2.30  INTRA BL
 820 PRO   ( 202-)  D      O   <->  942 ARG   ( 118-)  E      NH2    0.35    2.35  INTRA BL
1177 GLU   ( 147-)  F      CD  <-> 2080  CA   ( 502-)  F     CA      0.33    2.87  INTRA BF
 614 PRO   ( 202-)  C      O   <->  736 ARG   ( 118-)  D      NH2    0.31    2.39  INTRA BL
1438 PRO   ( 202-)  G      O   <-> 1560 ARG   ( 118-)  H      NH2    0.29    2.41  INTRA BL
1644 PRO   ( 202-)  H      O   <-> 1766 ARG   ( 118-)  I      NH2    0.26    2.44  INTRA BL
 726 GLU   ( 108-)  D      OE2 <->  736 ARG   ( 118-)  D      NH1    0.25    2.45  INTRA
1962 GLU   ( 108-)  J      OE2 <-> 1972 ARG   ( 118-)  J      NH1    0.23    2.47  INTRA BL
1550 GLU   ( 108-)  H      OE2 <-> 1560 ARG   ( 118-)  H      NH1    0.22    2.48  INTRA BL
 108 GLU   ( 108-)  A      OE2 <->  118 ARG   ( 118-)  A      NH1    0.21    2.49  INTRA
 202 PRO   ( 202-)  A      O   <->  324 ARG   ( 118-)  B      NH2    0.21    2.49  INTRA BL
 932 GLU   ( 108-)  E      OE2 <->  942 ARG   ( 118-)  E      NH1    0.21    2.49  INTRA
1344 GLU   ( 108-)  G      OE2 <-> 1354 ARG   ( 118-)  G      NH1    0.21    2.49  INTRA
 520 GLU   ( 108-)  C      OE2 <->  530 ARG   ( 118-)  C      NH1    0.20    2.50  INTRA
 691 TYR   (  73-)  D      N   <->  702 PHE   (  84-)  D      O      0.20    2.50  INTRA BL
1912 ARG   (  58-)  J      NH2 <-> 1979 TYR   ( 125-)  J      OH     0.20    2.50  INTRA BF
1138 GLU   ( 108-)  F      OE2 <-> 1148 ARG   ( 118-)  F      NH1    0.20    2.50  INTRA
1927 TYR   (  73-)  J      N   <-> 1938 PHE   (  84-)  J      O      0.20    2.50  INTRA BL
 314 GLU   ( 108-)  B      OE2 <->  324 ARG   ( 118-)  B      NH1    0.20    2.50  INTRA
1148 ARG   ( 118-)  F      NH2 <-> 2056 PRO   ( 202-)  J      O      0.19    2.51  INTRA BL
1756 GLU   ( 108-)  I      OE2 <-> 1766 ARG   ( 118-)  I      NH1    0.19    2.51  INTRA
 116 ARG   ( 116-)  A      NH1 <->  866 GLU   (  42-)  E      OE2    0.19    2.51  INTRA BF
1498 THR   (  56-)  H      CB  <-> 1500 ARG   (  58-)  H      NH1    0.17    2.93  INTRA BF
 701 LEU   (  83-)  D      O   <->  737 LYS   ( 119-)  D      NZ     0.16    2.54  INTRA BL
And so on for a total of 167 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

 764 PHE   ( 146-)  D      -7.57
2000 PHE   ( 146-)  J      -7.52
 665 ARG   (  47-)  D      -6.91
 760 PHE   ( 142-)  D      -6.84
1901 ARG   (  47-)  J      -6.84
1996 PHE   ( 142-)  J      -6.77
 676 ARG   (  58-)  D      -6.27
1706 ARG   (  58-)  I      -6.22
1088 ARG   (  58-)  F      -6.04
1210 PHE   ( 180-)  F      -6.01
 386 PHE   ( 180-)  B      -6.00
1828 PHE   ( 180-)  I      -6.00
1500 ARG   (  58-)  H      -5.99
1004 PHE   ( 180-)  E      -5.99
 798 PHE   ( 180-)  D      -5.99
 264 ARG   (  58-)  B      -5.97
1622 PHE   ( 180-)  H      -5.96
1416 PHE   ( 180-)  G      -5.96
 180 PHE   ( 180-)  A      -5.95
 592 PHE   ( 180-)  C      -5.95
2034 PHE   ( 180-)  J      -5.95
 470 ARG   (  58-)  C      -5.89
 882 ARG   (  58-)  E      -5.87
  58 ARG   (  58-)  A      -5.85
1912 ARG   (  58-)  J      -5.74
1860 ARG   (   6-)  J      -5.59
 212 ARG   (   6-)  B      -5.56
1294 ARG   (  58-)  G      -5.49
1654 ARG   (   6-)  I      -5.44
 624 ARG   (   6-)  D      -5.39
 418 ARG   (   6-)  C      -5.28
1242 ARG   (   6-)  G      -5.19
1036 ARG   (   6-)  F      -5.18
   6 ARG   (   6-)  A      -5.18
1448 ARG   (   6-)  H      -5.18
1028 LEU   ( 204-)  E      -5.16
2058 LEU   ( 204-)  J      -5.16
 830 ARG   (   6-)  E      -5.15
  23 LYS   (  23-)  A      -5.11
1440 LEU   ( 204-)  G      -5.08
1945 VAL   (  91-)  J      -5.06
1234 LEU   ( 204-)  F      -5.05
 709 VAL   (  91-)  D      -5.05
1646 LEU   ( 204-)  H      -5.02

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

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: E

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: F

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: G

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: H

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: I

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: J

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.

 202 PRO   ( 202-)  A     -  205 TRP   ( 205-)  A        -1.15
 820 PRO   ( 202-)  D     -  823 TRP   ( 205-)  D        -1.18
1026 PRO   ( 202-)  E     - 1029 TRP   ( 205-)  E        -1.24
1232 PRO   ( 202-)  F     - 1235 TRP   ( 205-)  F        -1.20
1438 PRO   ( 202-)  G     - 1441 TRP   ( 205-)  G        -1.14
1644 PRO   ( 202-)  H     - 1647 TRP   ( 205-)  H        -1.23
1850 PRO   ( 202-)  I     - 1853 TRP   ( 205-)  I        -1.13
2056 PRO   ( 202-)  J     - 2059 TRP   ( 205-)  J        -1.25

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

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.

 137 GLN   ( 137-)  A
 160 ASN   ( 160-)  A
 343 GLN   ( 137-)  B
 366 ASN   ( 160-)  B
 473 ASN   (  61-)  C
 549 GLN   ( 137-)  C
 572 ASN   ( 160-)  C
 778 ASN   ( 160-)  D
 961 GLN   ( 137-)  E
 984 ASN   ( 160-)  E
1167 GLN   ( 137-)  F
1190 ASN   ( 160-)  F
1373 GLN   ( 137-)  G
1396 ASN   ( 160-)  G
1579 GLN   ( 137-)  H
1602 ASN   ( 160-)  H
1649 GLN   (   1-)  I
1709 ASN   (  61-)  I
1785 GLN   ( 137-)  I
1808 ASN   ( 160-)  I
1855 GLN   (   1-)  J
2014 ASN   ( 160-)  J

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.

  13 LYS   (  13-)  A      N
  15 SER   (  15-)  A      N
  47 ARG   (  47-)  A      NH2
  57 LYS   (  57-)  A      N
  58 ARG   (  58-)  A      NE
  59 GLN   (  59-)  A      N
  85 GLU   (  85-)  A      N
 109 PHE   ( 109-)  A      N
 126 THR   ( 126-)  A      N
 137 GLN   ( 137-)  A      N
 139 GLN   ( 139-)  A      NE2
 143 GLY   ( 143-)  A      N
 147 GLU   ( 147-)  A      N
 153 VAL   ( 153-)  A      N
 158 ASN   ( 158-)  A      N
 159 VAL   ( 159-)  A      N
 164 PHE   ( 164-)  A      N
 169 ASP   ( 169-)  A      N
 204 LEU   ( 204-)  A      N
 205 TRP   ( 205-)  A      N
 219 LYS   (  13-)  B      N
 251 SER   (  45-)  B      N
 253 ARG   (  47-)  B      NH2
 259 SER   (  53-)  B      OG
 263 LYS   (  57-)  B      N
And so on for a total of 240 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.

 139 GLN   ( 139-)  A      OE1
 155 ASP   ( 155-)  A      OD1
 345 GLN   ( 139-)  B      OE1
 361 ASP   ( 155-)  B      OD1
 551 GLN   ( 139-)  C      OE1
 567 ASP   ( 155-)  C      OD1
 609 GLU   ( 197-)  C      OE2
 688 ASP   (  70-)  D      OD1
 773 ASP   ( 155-)  D      OD1
 919 HIS   (  95-)  E      ND1
 963 GLN   ( 139-)  E      OE1
 979 ASP   ( 155-)  E      OD1
 996 ASN   ( 172-)  E      OD1
1125 HIS   (  95-)  F      ND1
1169 GLN   ( 139-)  F      OE1
1185 ASP   ( 155-)  F      OD1
1375 GLN   ( 139-)  G      OE1
1386 GLN   ( 150-)  G      OE1
1391 ASP   ( 155-)  G      OD1
1581 GLN   ( 139-)  H      OE1
1597 ASP   ( 155-)  H      OD1
1639 GLU   ( 197-)  H      OE2
1787 GLN   ( 139-)  I      OE1
1803 ASP   ( 155-)  I      OD1
1820 ASN   ( 172-)  I      OD1
1924 ASP   (  70-)  J      OD1
2009 ASP   ( 155-)  J      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

2071  CA   ( 501-)  A   -.-  -.-  Low probability ion. B= 81.0
2072  CA   ( 502-)  A   -.-  -.-  Part of ionic cluster
2072  CA   ( 502-)  A     0.85   1.04 Scores about as good as NA (Few ligands (4) )
2073  CA   ( 501-)  B   -.-  -.-  Low probability ion. B= 84.7
2074  CA   ( 502-)  B   -.-  -.-  Part of ionic cluster
2075  CA   ( 501-)  C   -.-  -.-  Part of ionic cluster
2075  CA   ( 501-)  C     0.84   1.03 Scores about as good as NA
2076  CA   ( 502-)  C   -.-  -.-  Part of ionic cluster
2076  CA   ( 502-)  C     1.64   0.90 Scores about as good as MG
2077  CA   ( 501-)  E   -.-  -.-  Part of ionic cluster
2077  CA   ( 501-)  E     0.82   0.99 Scores about as good as NA
2078  CA   ( 502-)  E   -.-  -.-  Part of ionic cluster
2079  CA   ( 501-)  F   -.-  -.-  Part of ionic cluster
2079  CA   ( 501-)  F     0.78   0.97 Scores about as good as NA (Few ligands (4) )
2080  CA   ( 502-)  F   -.-  -.-  Part of ionic cluster
2080  CA   ( 502-)  F     0.90   1.09 Scores about as good as NA
2081  CA   ( 501-)  G   -.-  -.-  Part of ionic cluster
2081  CA   ( 501-)  G     0.55   0.75 Scores about as good as NA
2082  CA   ( 502-)  G   -.-  -.-  Part of ionic cluster
2082  CA   ( 502-)  G     0.59   0.79 Scores about as good as NA (Few ligands (4) )
2083  CA   ( 501-)  H   -.-  -.-  Low probability ion. B= 99.3
2084  CA   ( 502-)  H   -.-  -.-  Part of ionic cluster
2085  CA   ( 501-)  I   -.-  -.-  Part of ionic cluster
2085  CA   ( 501-)  I     0.79   1.00 Scores about as good as NA
2086  CA   ( 502-)  I   -.-  -.-  Part of ionic cluster
Since there are no waters, the water check has been skipped.

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.

  16 ASP   (  16-)  A   H-bonding suggests Asn; but Alt-Rotamer
 222 ASP   (  16-)  B   H-bonding suggests Asn; but Alt-Rotamer
 353 GLU   ( 147-)  B   H-bonding suggests Gln
 428 ASP   (  16-)  C   H-bonding suggests Asn; but Alt-Rotamer
 840 ASP   (  16-)  E   H-bonding suggests Asn; but Alt-Rotamer
1046 ASP   (  16-)  F   H-bonding suggests Asn; but Alt-Rotamer
1252 ASP   (  16-)  G   H-bonding suggests Asn; but Alt-Rotamer
1458 ASP   (  16-)  H   H-bonding suggests Asn; but Alt-Rotamer
1664 ASP   (  16-)  I   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.706
  2nd generation packing quality :  -1.966
  Ramachandran plot appearance   :  -2.393
  chi-1/chi-2 rotamer normality  :  -5.074 (bad)
  Backbone conformation          :  -0.826

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.454 (tight)
  Bond angles                    :   0.716
  Omega angle restraints         :   0.251 (tight)
  Side chain planarity           :   0.449 (tight)
  Improper dihedral distribution :   0.977
  B-factor distribution          :   1.845 (loose)
  Inside/Outside distribution    :   0.959

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.454 (tight)
  Bond angles                    :   0.716
  Omega angle restraints         :   0.251 (tight)
  Side chain planarity           :   0.449 (tight)
  Improper dihedral distribution :   0.977
  B-factor distribution          :   1.845 (loose)
  Inside/Outside distribution    :   0.959
==============

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.