WHAT IF Check report

This file was created 2012-01-30 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 pdb3hmj.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 : 0.524
CA-only RMS fit for the two chains : 0.521

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 B

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 : 0.368
CA-only RMS fit for the two chains : 0.363

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 C

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 C

All-atom RMS fit for the two chains : 0.470
CA-only RMS fit for the two chains : 0.465

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: B and C

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: G and H

All-atom RMS fit for the two chains : 0.834
CA-only RMS fit for the two chains : 0.830

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: G and H

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: G and I

All-atom RMS fit for the two chains : 0.484
CA-only RMS fit for the two chains : 0.479

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: G and I

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 43 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 6
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 24
Polymer chain multiplicity and SEQRES multiplicity disagree 3 6
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very 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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 1261693.9
Volume of the Unit Cell V= 40694740.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 8.064
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.890 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

1135  CER  (2748-) B  -
1135  CER  (2748-) C  -
1135  CER  (2748-) A  -          OK

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

1365 GLU   (1498-)  A  -
3115 GLU   (1498-)  B  -
4861 HIS   (1494-)  C  -
4865 GLU   (1498-)  C  -

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1327 LYS   (1460-)  A  -   NZ  bound to 1638 GLU   (1774-)  A  -   OE2
1361 HIS   (1494-)  A  -   NE2 bound to 1740 GLN   (1877-)  A  -   OE1
1638 GLU   (1774-)  A  -   OE2 bound to 1327 LYS   (1460-)  A  -   NZ
3110 HIS   (1494-)  B  -   NE2 bound to 3489 GLN   (1877-)  B  -   OE1

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: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

1613 ASN   (1748-)  A  -   CG
1613 ASN   (1748-)  A  -   OD1
1613 ASN   (1748-)  A  -   ND2
1614 THR   (1749-)  A  -   OG1
1614 THR   (1749-)  A  -   CG2
1615 ILE   (1750-)  A  -   CG1
1615 ILE   (1750-)  A  -   CG2
1615 ILE   (1750-)  A  -   CD1
1616 GLU   (1751-)  A  -   CG
1616 GLU   (1751-)  A  -   CD
1616 GLU   (1751-)  A  -   OE1
1616 GLU   (1751-)  A  -   OE2
1617 THR   (1752-)  A  -   OG1
1617 THR   (1752-)  A  -   CG2
1619 LYS   (1754-)  A  -   CG
1619 LYS   (1754-)  A  -   CD
1619 LYS   (1754-)  A  -   CE
1619 LYS   (1754-)  A  -   NZ
1620 MET   (1755-)  A  -   CG
1620 MET   (1755-)  A  -   SD
1620 MET   (1755-)  A  -   CE
1621 ILE   (1756-)  A  -   CG1
1621 ILE   (1756-)  A  -   CG2
1621 ILE   (1756-)  A  -   CD1
1622 GLU   (1757-)  A  -   CG
And so on for a total of 168 lines.

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.

   1 MET   (   1-)  A  -   High
   2 LYS   (   2-)  A  -   High
   3 PRO   (   3-)  A  -   High
   4 GLU   (   4-)  A  -   High
   5 VAL   (   5-)  A  -   High
   6 GLU   (   6-)  A  -   High
   7 GLN   (   7-)  A  -   High
   8 GLU   (   8-)  A  -   High
   9 LEU   (   9-)  A  -   High
  10 ALA   (  10-)  A  -   High
  11 HIS   (  11-)  A  -   High
  12 ILE   (  12-)  A  -   High
  13 LEU   (  13-)  A  -   High
  14 LEU   (  14-)  A  -   High
  15 THR   (  15-)  A  -   High
  16 GLU   (  16-)  A  -   High
  17 LEU   (  17-)  A  -   High
  18 LEU   (  18-)  A  -   High
  19 ALA   (  19-)  A  -   High
  20 TYR   (  20-)  A  -   High
  21 GLN   (  21-)  A  -   High
  22 PHE   (  22-)  A  -   High
  23 ALA   (  23-)  A  -   High
  24 SER   (  24-)  A  -   High
  25 PRO   (  25-)  A  -   High
And so on for a total of 11345 lines.

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 1

Crystal temperature (K) :100.000

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: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Nomenclature related problems

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  20 TYR   (  20-)  A  -
  65 TYR   (  65-)  A  -
  81 TYR   (  81-)  A  -
 383 TYR   ( 453-)  A  -
 549 TYR   ( 677-)  A  -
 844 TYR   ( 977-)  A  -
1104 TYR   (1237-)  A  -
1305 TYR   (1438-)  A  -
1490 TYR   (1623-)  A  -
1527 TYR   (1660-)  A  -
1662 TYR   (1798-)  A  -
1769 TYR   (  20-)  B  -
1814 TYR   (  65-)  B  -
1830 TYR   (  81-)  B  -
2132 TYR   ( 453-)  B  -
2204 TYR   ( 525-)  B  -
2298 TYR   ( 677-)  B  -
2593 TYR   ( 977-)  B  -
2853 TYR   (1237-)  B  -
3054 TYR   (1438-)  B  -
3239 TYR   (1623-)  B  -
3276 TYR   (1660-)  B  -
3411 TYR   (1798-)  B  -
3518 TYR   (  20-)  C  -
3563 TYR   (  65-)  C  -
And so on for a total of 86 lines.

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 168 PHE   ( 213-)  A  -
 196 PHE   ( 241-)  A  -
 316 PHE   ( 386-)  A  -
 540 PHE   ( 668-)  A  -
 582 PHE   ( 710-)  A  -
 799 PHE   ( 932-)  A  -
 891 PHE   (1024-)  A  -
 909 PHE   (1042-)  A  -
1001 PHE   (1134-)  A  -
1202 PHE   (1335-)  A  -
1243 PHE   (1376-)  A  -
1379 PHE   (1512-)  A  -
1443 PHE   (1576-)  A  -
1565 PHE   (1698-)  A  -
1655 PHE   (1791-)  A  -
1917 PHE   ( 213-)  B  -
1945 PHE   ( 241-)  B  -
2065 PHE   ( 386-)  B  -
2289 PHE   ( 668-)  B  -
2331 PHE   ( 710-)  B  -
2454 PHE   ( 833-)  B  -
2548 PHE   ( 932-)  B  -
2640 PHE   (1024-)  B  -
2658 PHE   (1042-)  B  -
2750 PHE   (1134-)  B  -
And so on for a total of 158 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

6071 ASP   ( 829-)  G  -
6747 ASP   (1518-)  G  -
8104 ASP   ( 829-)  H  -
8780 ASP   (1518-)  H  -
1013  ASP  ( 829-) I  -
1081  ASP  (1518-) I  -

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

   4 GLU   (   4-)  A  -
   8 GLU   (   8-)  A  -
  16 GLU   (  16-)  A  -
 458 GLU   ( 528-)  A  -
 648 GLU   ( 776-)  A  -
 756 GLU   ( 889-)  A  -
 819 GLU   ( 952-)  A  -
1420 GLU   (1553-)  A  -
1646 GLU   (1782-)  A  -
1753 GLU   (   4-)  B  -
1757 GLU   (   8-)  B  -
1765 GLU   (  16-)  B  -
2207 GLU   ( 528-)  B  -
2397 GLU   ( 776-)  B  -
2505 GLU   ( 889-)  B  -
2568 GLU   ( 952-)  B  -
3169 GLU   (1553-)  B  -
3395 GLU   (1782-)  B  -
3502 GLU   (   4-)  C  -
3506 GLU   (   8-)  C  -
3514 GLU   (  16-)  C  -
3812 GLU   ( 384-)  C  -
3956 GLU   ( 528-)  C  -
4146 GLU   ( 776-)  C  -
4254 GLU   ( 889-)  C  -
And so on for a total of 62 lines.

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

1134  FMN  (3051-) G  -    OP1    O1P
1134  FMN  (3051-) G  -    OP2    O2P
1134  FMN  (3051-) G  -    OP3    O3P
1134  FMN  (3051-) H  -    OP1    O1P
1134  FMN  (3051-) H  -    OP2    O2P
1134  FMN  (3051-) H  -    OP3    O3P
1135  FMN  (3051-) I  -    OP1    O1P
1135  FMN  (3051-) I  -    OP2    O2P
1135  FMN  (3051-) I  -    OP3    O3P

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.

 137 VAL   ( 182-)  A  -   N   -C     1.50    8.5
 541 ASN   ( 669-)  A  -   N   -C     1.51    9.2
 860 PRO   ( 993-)  A  -   N   -C     1.59   13.1
1049 ASP   (1182-)  A  -   N   -C     1.45    6.2
1388 PRO   (1521-)  A  -   N   -C     1.45    6.0
1886 VAL   ( 182-)  B  -   N   -C     1.21   -6.1
2165 VAL   ( 486-)  B  -   N   -C     1.44    5.5
2290 ASN   ( 669-)  B  -   N   -C     1.46    6.4
2549 VAL   ( 933-)  B  -   N   -C     1.22   -5.2
2735 LYS   (1119-)  B  -   N   -C     1.23   -4.7
2798 ASP   (1182-)  B  -   N   -C     1.45    6.1
3047 GLU   (1431-)  B  -   N   -C     1.22   -5.6
3137 PRO   (1521-)  B  -   N   -C     1.25   -4.1
3914 VAL   ( 486-)  C  -   N   -C     1.56   11.4
4007 PHE   ( 637-)  C  -   N   -C     1.21   -5.7
4358 PRO   ( 993-)  C  -   N   -C     1.59   13.0
4482 GLU   (1117-)  C  -   N   -C     1.43    4.9
4484 LYS   (1119-)  C  -   N   -C     1.42    4.3
4886 PRO   (1521-)  C  -   N   -C     1.22   -5.6
5380 ASP   ( 138-)  G  -   N   -C     1.43    5.2
5381 LYS   ( 139-)  G  -   N   -C     1.41    4.2
5558 ASN   ( 316-)  G  -   N   -C     1.58   12.4
5665 VAL   ( 423-)  G  -   N   -C     1.50    8.4
6085 ILE   ( 843-)  G  -   N   -C     1.48    7.3
6146 PHE   ( 904-)  G  -   N   -C     1.45    6.0
6486 ASP   (1257-)  G  -   N   -C     1.48    7.7
6759 LYS   (1530-)  G  -   N   -C     1.21   -6.0
6760 VAL   (1531-)  G  -   N   -C     1.44    5.4
6887 GLU   (1658-)  G  -   N   -C     1.52    9.7
7210 LEU   (1981-)  G  -   N   -C     1.46    6.5
7413 ASP   ( 138-)  H  -   N   -C     1.47    7.2
7414 LYS   ( 139-)  H  -   N   -C     1.54   10.8
7415 LYS   ( 140-)  H  -   N   -C     1.42    4.6
7698 VAL   ( 423-)  H  -   N   -C     1.48    7.6
8329 LEU   (1054-)  H  -   N   -C     1.48    7.6
8519 ASP   (1257-)  H  -   N   -C     1.55   11.1
9102 VAL   (1840-)  H  -   N   -C     1.43    5.1
9103 ALA   (1841-)  H  -   N   -C     1.53   10.1
9243 LEU   (1981-)  H  -   N   -C     1.42    4.7
9245 ASN   (1983-)  H  -   N   -C     1.47    6.9
9446 ASP   ( 138-)  I  -   N   -C     1.43    5.1
9624 ASN   ( 316-)  I  -   N   -C     1.52    9.4
9731 VAL   ( 423-)  I  -   N   -C     1.42    4.4
1015  ILE  ( 843-) I  -    N   -C     1.59   13.1
1021  PHE  ( 904-) I  -    N   -C     1.48    7.6
1032  PRO  (1019-) I  -    N   -C     1.21   -5.8
1055  ASP  (1257-) I  -    N   -C     1.42    4.6
1127  LEU  (1981-) I  -    N   -C     1.51    9.2
1127  ASN  (1983-) I  -    N   -C     1.22   -5.2

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999495  0.000027 -0.000180|
 |  0.000027  0.999710  0.000083|
 | -0.000180  0.000083  0.999577|
Proposed new scale matrix

 |  0.004315  0.000000  0.000000|
 |  0.000000  0.004314  0.000000|
 |  0.000000  0.000000  0.001322|
With corresponding cell

    A    = 231.740  B   = 231.790  C    = 756.682
    Alpha=  90.006  Beta=  90.006  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 231.857  B   = 231.857  C    = 757.002
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 65.330
(Under-)estimated Z-score: 5.957

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.

 134 LYS   ( 179-)  A  -  -O   -C    N   115.19   -4.9
 134 LYS   ( 179-)  A  -  -C    N    CA  132.38    5.9
 334 SER   ( 404-)  A  -  -C    N    CA  129.65    4.4
 470 GLN   ( 540-)  A  -   N    CA   C    95.77   -5.5
 471 MET   ( 599-)  A  -   N    CA   C    92.37   -6.7
 664 HIS   ( 792-)  A  -   CG   ND1  CE1 109.81    4.2
 860 PRO   ( 993-)  A  -  -O   -C    N   132.45    7.5
 860 PRO   ( 993-)  A  -  -CA  -C    N   106.47   -7.0
 860 PRO   ( 993-)  A  -  -C    N    CD  142.37    4.2
1298 GLU   (1431-)  A  -  -O   -C    N   110.85   -7.6
1298 GLU   (1431-)  A  -  -CA  -C    N   125.42    4.6
1298 GLU   (1431-)  A  -  -C    N    CA  129.63    4.4
1388 PRO   (1521-)  A  -  -O   -C    N   131.44    6.7
1388 PRO   (1521-)  A  -  -CA  -C    N   106.56   -6.9
1883 LYS   ( 179-)  B  -  -O   -C    N   131.61    5.4
1883 LYS   ( 179-)  B  -  -CA  -C    N   107.71   -4.1
1886 VAL   ( 182-)  B  -  -C    N    CA  129.48    4.3
2061 LEU   ( 382-)  B  -  -O   -C    N   115.94   -4.4
2219 GLN   ( 540-)  B  -   N    CA   C    95.74   -5.5
2220 MET   ( 599-)  B  -   N    CA   C    92.27   -6.8
2413 HIS   ( 792-)  B  -   CG   ND1  CE1 109.60    4.0
2550 PRO   ( 934-)  B  -  -O   -C    N   116.37   -4.0
2609 PRO   ( 993-)  B  -  -O   -C    N   137.19   10.8
2609 PRO   ( 993-)  B  -  -CA  -C    N    99.99  -11.3
2609 PRO   ( 993-)  B  -  -C    N    CD  145.52    5.0
And so on for a total of 80 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   4 GLU   (   4-)  A  -
   8 GLU   (   8-)  A  -
  16 GLU   (  16-)  A  -
 458 GLU   ( 528-)  A  -
 648 GLU   ( 776-)  A  -
 756 GLU   ( 889-)  A  -
 819 GLU   ( 952-)  A  -
1420 GLU   (1553-)  A  -
1646 GLU   (1782-)  A  -
1753 GLU   (   4-)  B  -
1757 GLU   (   8-)  B  -
1765 GLU   (  16-)  B  -
2207 GLU   ( 528-)  B  -
2397 GLU   ( 776-)  B  -
2505 GLU   ( 889-)  B  -
2568 GLU   ( 952-)  B  -
3169 GLU   (1553-)  B  -
3395 GLU   (1782-)  B  -
3502 GLU   (   4-)  C  -
3506 GLU   (   8-)  C  -
3514 GLU   (  16-)  C  -
3812 GLU   ( 384-)  C  -
3956 GLU   ( 528-)  C  -
4146 GLU   ( 776-)  C  -
4254 GLU   ( 889-)  C  -
And so on for a total of 68 lines.

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

5380 ASP   ( 138-)  G  -   C      6.2     9.58    -0.01
7590 PRO   ( 315-)  H  -   N     -8.1   -29.20    -2.48
8518 GLU   (1256-)  H  -   C    -14.4   -20.98    -0.03
1055  GLU  (1256-) I  -    C     -7.4   -10.76    -0.03
The average deviation= 0.675

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.

2219 GLN   ( 540-)  B  -   6.14
 470 GLN   ( 540-)  A  -   6.13
3968 GLN   ( 540-)  C  -   6.12
2008 GLU   ( 329-)  B  -   6.04
3757 GLU   ( 329-)  C  -   6.03
 259 GLU   ( 329-)  A  -   5.98
2220 MET   ( 599-)  B  -   5.71
3969 MET   ( 599-)  C  -   5.70
 471 MET   ( 599-)  A  -   5.69
2333 LYS   ( 712-)  B  -   5.09
 584 LYS   ( 712-)  A  -   4.86
8384 VAL   (1109-)  H  -   4.82
1041  VAL  (1109-) I  -   4.74
6351 VAL   (1109-)  G  -   4.69
5057 MET   (1692-)  C  -   4.59
4983 LEU   (1618-)  C  -   4.55
9542 ILE   ( 234-)  I  -   4.53
7509 ILE   ( 234-)  H  -   4.39
5476 ILE   ( 234-)  G  -   4.34
4082 LYS   ( 712-)  C  -   4.34
1559 MET   (1692-)  A  -   4.21
1128  LYS  (1986-) I  -   4.12
9248 LYS   (1986-)  H  -   4.12
2007 LEU   ( 328-)  B  -   4.01

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.459

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.

6646 THR   (1417-)  G  -   -3.4
 807 THR   ( 940-)  A  -   -3.2
1071  THR  (1422-) I  -   -3.1
 940 THR   (1073-)  A  -   -3.1
2556 THR   ( 940-)  B  -   -3.1
4438 THR   (1073-)  C  -   -3.1
2689 THR   (1073-)  B  -   -3.1
4305 THR   ( 940-)  C  -   -3.0
5287 THR   (  45-)  G  -   -3.0
3590 PRO   (  92-)  C  -   -3.0
  92 PRO   (  92-)  A  -   -3.0
1841 PRO   (  92-)  B  -   -3.0
9353 THR   (  45-)  I  -   -3.0
7320 THR   (  45-)  H  -   -2.9
9219 PRO   (1957-)  H  -   -2.9
1125  PRO  (1957-) I  -   -2.9
7186 PRO   (1957-)  G  -   -2.9
6614 PRO   (1385-)  G  -   -2.8
7837 LEU   ( 562-)  H  -   -2.8
2914 ILE   (1298-)  B  -   -2.8
4949 PRO   (1584-)  C  -   -2.8
3200 PRO   (1584-)  B  -   -2.8
1451 PRO   (1584-)  A  -   -2.8
1165 ILE   (1298-)  A  -   -2.8
5513 THR   ( 271-)  G  -   -2.8
And so on for a total of 463 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.

  27 ARG   (  27-)  A  - Poor phi/psi
  40 ASN   (  40-)  A  - Poor phi/psi
  64 LYS   (  64-)  A  - Poor phi/psi
  90 TYR   (  90-)  A  - Poor phi/psi
 115 LYS   ( 160-)  A  - Poor phi/psi
 133 GLY   ( 178-)  A  - Poor phi/psi
 256 ASP   ( 301-)  A  - omega poor
 281 LYS   ( 351-)  A  - Poor phi/psi
 323 SER   ( 393-)  A  - Poor phi/psi
 332 PHE   ( 402-)  A  - omega poor
 333 ASP   ( 403-)  A  - omega poor
 334 SER   ( 404-)  A  - Poor phi/psi
 374 ASN   ( 444-)  A  - omega poor
 415 ASP   ( 485-)  A  - Poor phi/psi
 418 PRO   ( 488-)  A  - Poor phi/psi
 434 ASP   ( 504-)  A  - Poor phi/psi
 467 LYS   ( 537-)  A  - Poor phi/psi
 468 GLU   ( 538-)  A  - Poor phi/psi
 469 SER   ( 539-)  A  - omega poor
 476 ALA   ( 604-)  A  - omega poor
 477 LEU   ( 605-)  A  - Poor phi/psi
 505 GLU   ( 633-)  A  - Poor phi/psi
 547 ASP   ( 675-)  A  - Poor phi/psi
 574 LYS   ( 702-)  A  - omega poor
 642 PRO   ( 770-)  A  - Poor phi/psi
And so on for a total of 473 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 : -4.460

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.

6814 SER   (1585-)  G  -   0.34
8847 SER   (1585-)  H  -   0.34
4212 SER   ( 842-)  C  -   0.35
1678 SER   (1814-)  A  -   0.35
3427 SER   (1814-)  B  -   0.35
5176 SER   (1814-)  C  -   0.35
 714 SER   ( 842-)  A  -   0.35
2091 SER   ( 412-)  B  -   0.35
7914 SER   ( 639-)  H  -   0.35
2113 SER   ( 434-)  B  -   0.36
9947 SER   ( 639-)  I  -   0.36
1088  SER  (1585-) I  -   0.36
3862 SER   ( 434-)  C  -   0.36
5881 SER   ( 639-)  G  -   0.36
7471 SER   ( 196-)  H  -   0.36
2463 SER   ( 842-)  B  -   0.36
3299 SER   (1683-)  B  -   0.36
5048 SER   (1683-)  C  -   0.36
6815 SER   (1586-)  G  -   0.36
8848 SER   (1586-)  H  -   0.36
 364 SER   ( 434-)  A  -   0.37
2432 SER   ( 811-)  B  -   0.37
 683 SER   ( 811-)  A  -   0.38
1545 SER   (1678-)  A  -   0.38
3294 SER   (1678-)  B  -   0.38
4181 SER   ( 811-)  C  -   0.38
2094 SER   ( 415-)  B  -   0.38
 342 SER   ( 412-)  A  -   0.38
3840 SER   ( 412-)  C  -   0.39
5438 SER   ( 196-)  G  -   0.39
9504 SER   ( 196-)  I  -   0.39
ERROR. Too many residues to use DSSP

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!

  24 SER   (  24-)  A  -     0
  27 ARG   (  27-)  A  -     0
  28 TRP   (  28-)  A  -     0
  38 ASP   (  38-)  A  -     0
  41 THR   (  41-)  A  -     0
  43 ARG   (  43-)  A  -     0
  47 ILE   (  47-)  A  -     0
  49 PRO   (  49-)  A  -     0
  51 PRO   (  51-)  A  -     0
  63 ASN   (  63-)  A  -     0
  64 LYS   (  64-)  A  -     0
  65 TYR   (  65-)  A  -     0
  84 ASP   (  84-)  A  -     0
  93 ASP   (  93-)  A  -     0
  94 PRO   (  94-)  A  -     0
  95 ILE   ( 140-)  A  -     0
  96 ALA   ( 141-)  A  -     0
 115 LYS   ( 160-)  A  -     0
 118 LEU   ( 163-)  A  -     0
 122 PRO   ( 167-)  A  -     0
 123 MET   ( 168-)  A  -     0
 125 LYS   ( 170-)  A  -     0
 131 VAL   ( 176-)  A  -     0
 134 LYS   ( 179-)  A  -     0
 135 SER   ( 180-)  A  -     0
And so on for a total of 3795 lines.

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!

 194 GLY   ( 239-)  A  -  3.18   28
3692 GLY   ( 239-)  C  -  3.15   25
1943 GLY   ( 239-)  B  -  3.15   25
2647 GLY   (1031-)  B  -  2.03   17
4396 GLY   (1031-)  C  -  2.00   17
 898 GLY   (1031-)  A  -  1.98   19
6516 GLY   (1287-)  G  -  1.97   21
1058  GLY  (1287-) I  -  1.96   20
8549 GLY   (1287-)  H  -  1.94   22
5074 GLU   (1709-)  C  -  1.74   10
1576 GLU   (1709-)  A  -  1.74   10
3325 GLU   (1709-)  B  -  1.72   10
8101 GLY   ( 826-)  H  -  1.69   25
6068 GLY   ( 826-)  G  -  1.67   26
1013  GLY  ( 826-) I  -  1.67   25
3648 GLY   ( 195-)  C  -  1.52   12
2471 PHE   ( 850-)  B  -  1.51   13

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   (   3-)  A  -  107.5 envelop C-beta (108 degrees)
  51 PRO   (  51-)  A  -   40.9 envelop C-delta (36 degrees)
  92 PRO   (  92-)  A  -   24.5 half-chair N/C-delta (18 degrees)
  94 PRO   (  94-)  A  -  145.2 envelop C-alpha (144 degrees)
 122 PRO   ( 167-)  A  -   38.5 envelop C-delta (36 degrees)
 153 PRO   ( 198-)  A  - -112.8 envelop C-gamma (-108 degrees)
 429 PRO   ( 499-)  A  -   31.9 envelop C-delta (36 degrees)
 608 PRO   ( 736-)  A  -   40.8 envelop C-delta (36 degrees)
 642 PRO   ( 770-)  A  -   26.3 half-chair N/C-delta (18 degrees)
 647 PRO   ( 775-)  A  -   49.0 half-chair C-delta/C-gamma (54 degrees)
 697 PRO   ( 825-)  A  -   28.8 envelop C-delta (36 degrees)
 700 PRO   ( 828-)  A  -   38.9 envelop C-delta (36 degrees)
 860 PRO   ( 993-)  A  -   46.4 half-chair C-delta/C-gamma (54 degrees)
 938 PRO   (1071-)  A  -   43.5 envelop C-delta (36 degrees)
 950 PRO   (1083-)  A  -   51.8 half-chair C-delta/C-gamma (54 degrees)
1077 PRO   (1210-)  A  -  115.8 envelop C-beta (108 degrees)
1168 PRO   (1301-)  A  -   47.1 half-chair C-delta/C-gamma (54 degrees)
1229 PRO   (1362-)  A  -  100.5 envelop C-beta (108 degrees)
1288 PRO   (1421-)  A  -   39.5 envelop C-delta (36 degrees)
1384 PRO   (1517-)  A  -   38.1 envelop C-delta (36 degrees)
1438 PRO   (1571-)  A  -   42.2 envelop C-delta (36 degrees)
1451 PRO   (1584-)  A  -   28.1 envelop C-delta (36 degrees)
1494 PRO   (1627-)  A  -   47.3 half-chair C-delta/C-gamma (54 degrees)
1711 PRO   (1847-)  A  -   32.5 envelop C-delta (36 degrees)
1752 PRO   (   3-)  B  -  107.7 envelop C-beta (108 degrees)
And so on for a total of 161 lines.

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.

1172 CYS   (1305-)  A  -   SG  <-> 1135  CER  (2748-) A  -    C2     1.15    1.85  INTRA BF
3363 THR   (1749-)  B  -   CB  <-> 3486 HIS   (1873-)  B  -   O      1.05    1.75  INTRA BF
5112 THR   (1749-)  C  -   CB  <-> 5236 ASP   (1874-)  C  -   CA     1.00    2.20  INTRA BF
5112 THR   (1749-)  C  -   CB  <-> 5236 ASP   (1874-)  C  -   CB     0.98    2.22  INTRA BF
1614 THR   (1749-)  A  -   CB  <-> 1737 HIS   (1873-)  A  -   O      0.92    1.88  INTRA BF
4825 LYS   (1460-)  C  -   NZ  <-> 5136 GLU   (1774-)  C  -   OE2    0.90    1.80  INTRA BF
1614 THR   (1749-)  A  -   CB  <-> 1738 ASP   (1874-)  A  -   CB     0.89    2.31  INTRA BF
3363 THR   (1749-)  B  -   CB  <-> 3487 ASP   (1874-)  B  -   CB     0.88    2.32  INTRA BF
3076 LYS   (1460-)  B  -   NZ  <-> 3387 GLU   (1774-)  B  -   OE2    0.85    1.85  INTRA BF
3363 THR   (1749-)  B  -   CB  <-> 3486 HIS   (1873-)  B  -   C      0.83    2.37  INTRA BF
1004  HIS  ( 741-) I  -    NE2 <-> 1016  HIS  ( 855-) I  -    CE1    0.80    2.30  INTRA BF
4866 LEU   (1501-)  C  -   CD1 <-> 5137 LEU   (1775-)  C  -   CD2    0.73    2.47  INTRA BF
5983 HIS   ( 741-)  G  -   NE2 <-> 6097 HIS   ( 855-)  G  -   CE1    0.72    2.38  INTRA BF
8461 GLU   (1199-)  H  -   OE2 <-> 8829 ARG   (1567-)  H  -   NH1    0.70    2.00  INTRA BF
4825 LYS   (1460-)  C  -   CE  <-> 5136 GLU   (1774-)  C  -   CD     0.70    2.50  INTRA BF
3363 THR   (1749-)  B  -   CB  <-> 3487 ASP   (1874-)  B  -   CA     0.69    2.51  INTRA BF
8052 THR   ( 777-)  H  -   CG2 <-> 8356 HIS   (1081-)  H  -   NE2    0.69    2.41  INTRA BF
6019 THR   ( 777-)  G  -   CG2 <-> 6323 HIS   (1081-)  G  -   NE2    0.69    2.41  INTRA BF
1331 GLU   (1464-)  A  -   CG  <-> 1637 VAL   (1773-)  A  -   CG1    0.68    2.52  INTRA BF
1004  HIS  ( 741-) I  -    CE1 <-> 1015  THR  ( 845-) I  -    CG2    0.68    2.52  INTRA BF
7406 ILE   ( 131-)  H  -   CB  <-> 7457 VAL   ( 182-)  H  -   CG1    0.67    2.53  INTRA BF
1008  THR  ( 777-) I  -    CG2 <-> 1038  HIS  (1081-) I  -    NE2    0.67    2.43  INTRA BF
3076 LYS   (1460-)  B  -   CE  <-> 3386 VAL   (1773-)  B  -   O      0.65    2.15  INTRA BF
1004  HIS  ( 741-) I  -    CE1 <-> 1016  HIS  ( 855-) I  -    CE1    0.65    2.55  INTRA BF
1614 THR   (1749-)  A  -   CB  <-> 1738 ASP   (1874-)  A  -   CA     0.65    2.55  INTRA BF
And so on for a total of 2033 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: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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.

1305 TYR   (1438-)  A  -     -7.29
4803 TYR   (1438-)  C  -     -7.28
3054 TYR   (1438-)  B  -     -7.25
6253 MET   (1011-)  G  -     -7.21
1031  MET  (1011-) I  -     -7.18
8286 MET   (1011-)  H  -     -7.18
1382 ARG   (1515-)  A  -     -6.90
3131 ARG   (1515-)  B  -     -6.88
4880 ARG   (1515-)  C  -     -6.85
1125  ARG  (1962-) I  -     -6.73
9224 ARG   (1962-)  H  -     -6.67
7191 ARG   (1962-)  G  -     -6.65
4778 LYS   (1413-)  C  -     -6.54
1280 LYS   (1413-)  A  -     -6.54
3029 LYS   (1413-)  B  -     -6.52
3319 HIS   (1703-)  B  -     -6.38
5068 HIS   (1703-)  C  -     -6.36
1570 HIS   (1703-)  A  -     -6.36
6642 ARG   (1413-)  G  -     -6.33
1070  ARG  (1413-) I  -     -6.30
7900 PHE   ( 625-)  H  -     -6.28
2253 ARG   ( 632-)  B  -     -6.22
4002 ARG   ( 632-)  C  -     -6.21
1690 LYS   (1826-)  A  -     -6.21
5188 LYS   (1826-)  C  -     -6.21
And so on for a total of 270 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

1013 HIS   (1146-)  A  -   1015 - HIS   1148- ( A)  -      -5.30
1342 GLU   (1475-)  A  -   1344 - ILE   1477- ( A)  -      -4.63
1692 LEU   (1828-)  A  -   1694 - GLY   1830- ( A)  -      -4.20
2762 HIS   (1146-)  B  -   2764 - HIS   1148- ( B)  -      -5.24
3441 LEU   (1828-)  B  -   3443 - GLY   1830- ( B)  -      -4.20
4511 HIS   (1146-)  C  -   4513 - HIS   1148- ( C)  -      -5.30
4778 LYS   (1413-)  C  -   4781 - ARG   1416- ( C)  -      -5.51
4840 GLU   (1475-)  C  -   4842 - ILE   1477- ( C)  -      -4.62
5190 LEU   (1828-)  C  -   5192 - GLY   1830- ( C)  -      -4.21
5235 HIS   (1873-)  C  -   5237 - ASP   1875- ( C)  -      -4.76
5380 ASP   ( 138-)  G  -   5382 - LYS    140- ( G)  -      -4.26
6330 GLN   (1088-)  G  -   6332 - TYR   1090- ( G)  -      -4.60
7898 GLY   ( 623-)  H  -   7900 - PHE    625- ( H)  -      -4.89
8363 GLN   (1088-)  H  -   8365 - TYR   1090- ( H)  -      -4.59
1039  GLN  (1088-) I  -    1039 -  TYR  1090- (I ) -       -4.61

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: 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

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.

3368 LYS   (1754-)  B  -  -3.26
3375 LYS   (1761-)  B  -  -3.19
1626 LYS   (1761-)  A  -  -3.16
1619 LYS   (1754-)  A  -  -3.16
5124 LYS   (1761-)  C  -  -3.11
5117 LYS   (1754-)  C  -  -3.08
1624 MET   (1759-)  A  -  -2.97
5122 MET   (1759-)  C  -  -2.97
3373 MET   (1759-)  B  -  -2.97
4945 LEU   (1580-)  C  -  -2.92
3196 LEU   (1580-)  B  -  -2.92
1447 LEU   (1580-)  A  -  -2.89
8384 VAL   (1109-)  H  -  -2.69
1041  VAL  (1109-) I  -  -2.69
6351 VAL   (1109-)  G  -  -2.69
6075 GLU   ( 833-)  G  -  -2.67
8108 GLU   ( 833-)  H  -  -2.65
1014  GLU  ( 833-) I  -  -2.65
7862 ILE   ( 587-)  H  -  -2.59
5113 ILE   (1750-)  C  -  -2.58
 667 MET   ( 795-)  A  -  -2.58
4165 MET   ( 795-)  C  -  -2.57
3488 ASP   (1875-)  B  -  -2.56
2416 MET   ( 795-)  B  -  -2.56
1739 ASP   (1875-)  A  -  -2.56
  23 ALA   (  23-)  A  -  -2.52
8315 LEU   (1040-)  H  -  -2.51
1034  LEU  (1040-) I  -  -2.50
3376 GLU   (1762-)  B  -  -2.50

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.

 650 GLY   ( 778-)  A  -  -  653 LEU   ( 781-)  A  -     -1.76
1443 PHE   (1576-)  A  -  - 1447 LEU   (1580-)  A  -     -2.05
1613 ASN   (1748-)  A  -  - 1616 GLU   (1751-)  A  -     -1.75
1625 THR   (1760-)  A  -  - 1629 VAL   (1764-)  A  -     -2.24
2399 GLY   ( 778-)  B  -  - 2402 LEU   ( 781-)  B  -     -1.76
3192 PHE   (1576-)  B  -  - 3196 LEU   (1580-)  B  -     -2.04
3362 ASN   (1748-)  B  -  - 3365 GLU   (1751-)  B  -     -1.70
3374 THR   (1760-)  B  -  - 3378 VAL   (1764-)  B  -     -2.37
4148 GLY   ( 778-)  C  -  - 4151 LEU   ( 781-)  C  -     -1.73
4878 TYR   (1513-)  C  -  - 4881 ASP   (1516-)  C  -     -1.83
4941 PHE   (1576-)  C  -  - 4945 LEU   (1580-)  C  -     -2.05
5111 ASN   (1748-)  C  -  - 5114 GLU   (1751-)  C  -     -1.97
5123 THR   (1760-)  C  -  - 5127 VAL   (1764-)  C  -     -2.21
5672 HIS   ( 430-)  G  -  - 5675 VAL   ( 433-)  G  -     -1.72
7705 HIS   ( 430-)  H  -  - 7708 VAL   ( 433-)  H  -     -1.70
9122 GLY   (1860-)  H  -  - 9125 ALA   (1863-)  H  -     -1.61
9738 HIS   ( 430-)  I  -  - 9741 VAL   ( 433-)  I  -     -1.72
ERROR. Too many residues to use DSSP

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: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

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.

  11 HIS   (  11-)  A  -
  21 GLN   (  21-)  A  -
 309 ASN   ( 379-)  A  -
 337 ASN   ( 407-)  A  -
 341 GLN   ( 411-)  A  -
 357 ASN   ( 427-)  A  -
 368 ASN   ( 438-)  A  -
 405 GLN   ( 475-)  A  -
 610 ASN   ( 738-)  A  -
 655 HIS   ( 783-)  A  -
 664 HIS   ( 792-)  A  -
 854 ASN   ( 987-)  A  -
 856 GLN   ( 989-)  A  -
1106 HIS   (1239-)  A  -
1138 GLN   (1271-)  A  -
1299 HIS   (1432-)  A  -
1309 ASN   (1442-)  A  -
1325 GLN   (1458-)  A  -
1349 GLN   (1482-)  A  -
1377 ASN   (1510-)  A  -
1409 HIS   (1542-)  A  -
1477 ASN   (1610-)  A  -
1562 ASN   (1695-)  A  -
1666 GLN   (1802-)  A  -
1760 HIS   (  11-)  B  -
And so on for a total of 162 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.

  15 THR   (  15-)  A  -   OG1
  28 TRP   (  28-)  A  -   NE1
  30 GLU   (  30-)  A  -   N
  43 ARG   (  43-)  A  -   NE
  48 GLY   (  48-)  A  -   N
  50 SER   (  50-)  A  -   N
  63 ASN   (  63-)  A  -   ND2
  87 GLU   (  87-)  A  -   N
  98 GLU   ( 143-)  A  -   N
 100 VAL   ( 145-)  A  -   N
 126 THR   ( 171-)  A  -   N
 129 ASP   ( 174-)  A  -   N
 151 THR   ( 196-)  A  -   N
 157 GLU   ( 202-)  A  -   N
 171 THR   ( 216-)  A  -   N
 175 ALA   ( 220-)  A  -   N
 180 SER   ( 225-)  A  -   OG
 198 ILE   ( 243-)  A  -   N
 199 THR   ( 244-)  A  -   N
 200 VAL   ( 245-)  A  -   N
 209 TRP   ( 254-)  A  -   N
 237 ASP   ( 282-)  A  -   N
 259 GLU   ( 329-)  A  -   N
 262 THR   ( 332-)  A  -   N
 289 ARG   ( 359-)  A  -   NE
And so on for a total of 1199 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.

  33 ASP   (  33-)  A  -   OD1
  40 ASN   (  40-)  A  -   OD1
 148 GLU   ( 193-)  A  -   OE2
 216 GLN   ( 261-)  A  -   OE1
 648 GLU   ( 776-)  A  -   OE2
 702 HIS   ( 830-)  A  -   ND1
 930 HIS   (1063-)  A  -   ND1
1143 GLN   (1276-)  A  -   OE1
1177 GLU   (1310-)  A  -   OE1
1222 GLU   (1355-)  A  -   OE1
1245 GLU   (1378-)  A  -   OE1
1252 GLN   (1385-)  A  -   OE1
1409 HIS   (1542-)  A  -   NE2
1450 HIS   (1583-)  A  -   NE2
1636 ASP   (1772-)  A  -   OD2
1648 ASP   (1784-)  A  -   OD2
1765 GLU   (  16-)  B  -   OE1
1770 GLN   (  21-)  B  -   OE1
1897 GLU   ( 193-)  B  -   OE2
2397 GLU   ( 776-)  B  -   OE2
2543 ASN   ( 927-)  B  -   OD1
2679 HIS   (1063-)  B  -   ND1
2971 GLU   (1355-)  B  -   OE1
3158 HIS   (1542-)  B  -   NE2
3199 HIS   (1583-)  B  -   ND1
And so on for a total of 88 lines.

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.

  46 GLU   (  46-)  A  -  H-bonding suggests Gln; but Alt-Rotamer
 148 GLU   ( 193-)  A  -  H-bonding suggests Gln
 170 ASP   ( 215-)  A  -  H-bonding suggests Asn
 243 ASP   ( 288-)  A  -  H-bonding suggests Asn
 306 ASP   ( 376-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 415 ASP   ( 485-)  A  -  H-bonding suggests Asn
 753 GLU   ( 886-)  A  -  H-bonding suggests Gln
 792 ASP   ( 925-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1200 ASP   (1333-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1328 ASP   (1461-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1331 GLU   (1464-)  A  -  H-bonding suggests Gln; but Alt-Rotamer
1479 ASP   (1612-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1738 ASP   (1874-)  A  -  H-bonding suggests Asn
1795 GLU   (  46-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
1897 GLU   ( 193-)  B  -  H-bonding suggests Gln
1919 ASP   ( 215-)  B  -  H-bonding suggests Asn
1992 ASP   ( 288-)  B  -  H-bonding suggests Asn
2055 ASP   ( 376-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
2502 GLU   ( 886-)  B  -  H-bonding suggests Gln
2541 ASP   ( 925-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
2949 ASP   (1333-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
3077 ASP   (1461-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
3080 GLU   (1464-)  B  -  H-bonding suggests Gln
3228 ASP   (1612-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
3487 ASP   (1874-)  B  -  H-bonding suggests Asn
And so on for a total of 83 lines.

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 :  -0.958
  2nd generation packing quality :  -1.635
  Ramachandran plot appearance   :  -3.459 (poor)
  chi-1/chi-2 rotamer normality  :  -4.460 (bad)
  Backbone conformation          :  -0.547

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.580 (tight)
  Omega angle restraints         :   0.970
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   1.125
  Inside/Outside distribution    :   1.005

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 : 4.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.580 (tight)
  Omega angle restraints         :   0.970
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   1.125
  Inside/Outside distribution    :   1.005
==============

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.