WHAT IF Check report

This file was created 2011-12-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2dgl.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 : 0.511
CA-only RMS fit for the two chains : 0.227

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 : 0.511
CA-only RMS fit for the two chains : 0.166

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: A and D

All-atom RMS fit for the two chains : 0.523
CA-only RMS fit for the two chains : 0.181

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 : 0.510
CA-only RMS fit for the two chains : 0.179

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 E

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 : 0.525
CA-only RMS fit for the two chains : 0.171

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 F

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: 309090.344
Volume of the Unit Cell V= 17866134.0
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.817
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.700

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2709 PLP   ( 500-)  A  -
2710 ACY   ( 568-)  B  -
2716 PLP   ( 500-)  B  -
2717 ACY   ( 558-)  A  -
2722 PLP   ( 501-)  C  -
2723 ACY   ( 538-)  C  -
2724 ACY   ( 548-)  C  -
2728 PLP   ( 501-)  D  -
2733 PLP   ( 502-)  E  -
2734 ACY   ( 518-)  E  -
2739 ACY   ( 528-)  F  -
2740 PLP   ( 502-)  F  -

Administrative problems that can generate validation failures

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.

 274 LYS   ( 276-)  A  -   NZ  bound to 2709 PLP   ( 500-)  A  -   C4A
 724 LYS   ( 276-)  B  -   NZ  bound to 2716 PLP   ( 500-)  B  -   C4A
1174 LYS   ( 276-)  C  -   NZ  bound to 2722 PLP   ( 501-)  C  -   C4A
1625 LYS   ( 276-)  D  -   NZ  bound to 2728 PLP   ( 501-)  D  -   C4A
2075 LYS   ( 276-)  E  -   NZ  bound to 2733 PLP   ( 502-)  E  -   C4A
2527 LYS   ( 276-)  F  -   NZ  bound to 2740 PLP   ( 502-)  F  -   C4A

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

2713  BR   ( 469-)  B  -

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

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

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

 872 MET   ( 424-)  B    0.80
1322 MET   ( 424-)  C    0.80

Warning: What type of B-factor?

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

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

Crystal temperature (K) : 90.000

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: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Geometric checks

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

 |  1.000881  0.000091  0.000087|
 |  0.000091  1.000938  0.000105|
 |  0.000087  0.000105  1.001040|
Proposed new scale matrix

 |  0.003363  0.001942  0.000000|
 |  0.000000  0.003883  0.000000|
 |  0.000000  0.000000  0.004274|
With corresponding cell

    A    = 297.370  B   = 297.363  C    = 233.997
    Alpha=  90.001  Beta=  90.002  Gamma= 120.006

The CRYST1 cell dimensions

    A    = 297.051  B   = 297.051  C    = 233.731
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 82.752
(Under-)estimated Z-score: 6.704

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.

1966 HIS   ( 167-)  E      CG   ND1  CE1 109.65    4.1

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.

1062 ILE   ( 164-)  C    5.05
 912 LEU   (  14-)  C    4.96
2415 ILE   ( 164-)  F    4.77
 612 ILE   ( 164-)  B    4.64
1963 ILE   ( 164-)  E    4.61
1513 ILE   ( 164-)  D    4.58
 541 SER   (  93-)  B    4.52
 162 ILE   ( 164-)  A    4.45
2053 VAL   ( 254-)  E    4.41
 991 SER   (  93-)  C    4.36
2505 VAL   ( 254-)  F    4.34
1892 SER   (  93-)  E    4.28
1442 SER   (  93-)  D    4.28
  91 SER   (  93-)  A    4.27
1603 VAL   ( 254-)  D    4.18
 702 VAL   ( 254-)  B    4.17
1152 VAL   ( 254-)  C    4.05
1327 PHE   ( 429-)  C    4.00

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

2492 HIS   ( 241-)  F      CB   4.22
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.646

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.

 186 PHE   ( 188-)  A    -3.0
2116 PHE   ( 317-)  E    -2.8
2557 LEU   ( 306-)  F    -2.6
 612 ILE   ( 164-)  B    -2.5
1513 ILE   ( 164-)  D    -2.5
 162 ILE   ( 164-)  A    -2.5
1106 THR   ( 208-)  C    -2.5
1062 ILE   ( 164-)  C    -2.5
2415 ILE   ( 164-)  F    -2.4
1963 ILE   ( 164-)  E    -2.4
 311 PHE   ( 313-)  A    -2.4
1286 PRO   ( 388-)  C    -2.4
2459 THR   ( 208-)  F    -2.4
 983 ILE   (  85-)  C    -2.4
1557 THR   ( 208-)  D    -2.3
1884 ILE   (  85-)  E    -2.3
 657 PHE   ( 209-)  B    -2.3
  83 ILE   (  85-)  A    -2.3
2362 PRO   ( 111-)  F    -2.3
1203 TYR   ( 305-)  C    -2.3
1278 PHE   ( 380-)  C    -2.3
1737 PRO   ( 388-)  D    -2.3
1434 ILE   (  85-)  D    -2.3
 182 PRO   ( 184-)  A    -2.3
1533 PRO   ( 184-)  D    -2.3
And so on for a total of 75 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.

  14 SER   (  16-)  A  Poor phi/psi
 159 PRO   ( 161-)  A  Poor phi/psi
 186 PHE   ( 188-)  A  Poor phi/psi
 246 GLY   ( 248-)  A  Poor phi/psi
 258 TRP   ( 260-)  A  Poor phi/psi
 259 ASP   ( 261-)  A  Poor phi/psi
 274 LYS   ( 276-)  A  Poor phi/psi
 277 LEU   ( 279-)  A  Poor phi/psi
 281 GLY   ( 283-)  A  Poor phi/psi
 304 LEU   ( 306-)  A  Poor phi/psi
 305 GLY   ( 307-)  A  Poor phi/psi
 315 PHE   ( 317-)  A  Poor phi/psi
 360 PRO   ( 362-)  A  Poor phi/psi
 374 PRO   ( 376-)  A  Poor phi/psi
 557 HIS   ( 109-)  B  Poor phi/psi
 562 LYS   ( 114-)  B  Poor phi/psi
 563 ASN   ( 115-)  B  Poor phi/psi
 609 PRO   ( 161-)  B  Poor phi/psi
 696 GLY   ( 248-)  B  Poor phi/psi
 708 TRP   ( 260-)  B  Poor phi/psi
 709 ASP   ( 261-)  B  Poor phi/psi
 724 LYS   ( 276-)  B  Poor phi/psi
 727 LEU   ( 279-)  B  Poor phi/psi
 731 GLY   ( 283-)  B  Poor phi/psi
 754 LEU   ( 306-)  B  Poor phi/psi
And so on for a total of 78 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1745 SER   ( 396-)  D    0.37
1892 SER   (  93-)  E    0.39
 442 SER   ( 444-)  A    0.39
1342 SER   ( 444-)  C    0.39
1793 SER   ( 444-)  D    0.39
1442 SER   (  93-)  D    0.40
2344 SER   (  93-)  F    0.40

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!

  12 LEU   (  14-)  A      0
  21 ILE   (  23-)  A      0
  22 SER   (  24-)  A      0
  26 GLU   (  28-)  A      0
  27 SER   (  29-)  A      0
  28 LYS   (  30-)  A      0
  29 ARG   (  31-)  A      0
  31 PRO   (  33-)  A      0
  32 LEU   (  34-)  A      0
  33 HIS   (  35-)  A      0
  35 MET   (  37-)  A      0
  36 ARG   (  38-)  A      0
  49 TYR   (  51-)  A      0
  51 ASP   (  53-)  A      0
  53 ASN   (  55-)  A      0
  58 LEU   (  60-)  A      0
  60 THR   (  62-)  A      0
  61 PHE   (  63-)  A      0
  65 TRP   (  67-)  A      0
  77 SER   (  79-)  A      0
  82 TRP   (  84-)  A      0
  83 ILE   (  85-)  A      0
  88 TYR   (  90-)  A      0
 106 TRP   ( 108-)  A      0
 108 ALA   ( 110-)  A      0
And so on for a total of 964 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 : 1.114

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!

1540 PRO   ( 191-)  D   1.94   11
2442 PRO   ( 191-)  F   1.86   12
1089 PRO   ( 191-)  C   1.86   12
1990 PRO   ( 191-)  E   1.84   12
 639 PRO   ( 191-)  B   1.77   13
 189 PRO   ( 191-)  A   1.71   14
 383 GLY   ( 385-)  A   1.56   80

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]

1711 PRO   ( 362-)  D    0.46 HIGH
2051 PRO   ( 252-)  E    0.46 HIGH
2064 PRO   ( 265-)  E    0.45 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 279 PRO   ( 281-)  A    47.4 half-chair C-delta/C-gamma (54 degrees)
1154 PRO   ( 256-)  C    32.8 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

2527 LYS   ( 276-)  F      NZ  <-> 2740 PLP   ( 502-)  F      C4A    1.37    1.33  INTRA BL
2527 LYS   ( 276-)  F      CE  <-> 2740 PLP   ( 502-)  F      C4A    0.75    2.45  INTRA BL
 562 LYS   ( 114-)  B      O   <->  564 GLY   ( 116-)  B      N      0.36    2.34  INTRA BL
 296 GLU   ( 298-)  A      O   <->  619 ARG   ( 171-)  B      NH1    0.34    2.36  INTRA BF
1837 ARG   (  38-)  E      NH2 <-> 1839 ASP   (  40-)  E      OD2    0.33    2.37  INTRA
1061 GLN   ( 163-)  C      OE1 <-> 1063 CYS   ( 165-)  C      N      0.33    2.37  INTRA
 914 SER   (  16-)  C      OG  <-> 2713  BR   ( 469-)  B     BR      0.30    2.50  INTRA
1213 ILE   ( 315-)  C      CG2 <-> 1480 MET   ( 131-)  D      SD     0.28    3.12  INTRA
2599 GLN   ( 348-)  F      NE2 <-> 2682 MET   ( 431-)  F      CE     0.28    2.82  INTRA
 575 SER   ( 127-)  B      N   <-> 2716 PLP   ( 500-)  B      O1P    0.27    2.43  INTRA BL
1097 ASP   ( 199-)  C      OD1 <-> 1099 ASN   ( 201-)  C      N      0.27    2.43  INTRA BF
2174 ILE   ( 375-)  E      O   <-> 2176 ALA   ( 377-)  E      N      0.26    2.44  INTRA BL
 723 HIS   ( 275-)  B      ND1 <->  731 GLY   ( 283-)  B      N      0.26    2.74  INTRA BL
2023 HIS   ( 224-)  E      NE2 <-> 2065 ARG   ( 266-)  E      N      0.26    2.74  INTRA BL
 229 GLN   ( 231-)  A      NE2 <->  235 ASP   ( 237-)  A      CG     0.25    2.85  INTRA BF
1433 TRP   (  84-)  D      NE1 <-> 1446 ASP   (  97-)  D      OD2    0.25    2.45  INTRA BF
 273 HIS   ( 275-)  A      NE2 <-> 2709 PLP   ( 500-)  A      O1P    0.25    2.45  INTRA BL
 229 GLN   ( 231-)  A      NE2 <->  235 ASP   ( 237-)  A      CB     0.25    2.85  INTRA BF
2040 HIS   ( 241-)  E      ND1 <-> 2068 SER   ( 269-)  E      OG     0.24    2.46  INTRA BL
1993 MET   ( 194-)  E      SD  <-> 2022 LEU   ( 223-)  E      CD2    0.24    3.16  INTRA
1908 HIS   ( 109-)  E      ND1 <-> 2060 ASP   ( 261-)  E      OD2    0.24    2.46  INTRA BL
1042 ARG   ( 144-)  C      NH1 <-> 1135 ASP   ( 237-)  C      O      0.24    2.46  INTRA BF
2526 HIS   ( 275-)  F      NE2 <-> 2740 PLP   ( 502-)  F      O2P    0.23    2.47  INTRA BL
1624 HIS   ( 275-)  D      ND1 <-> 1632 GLY   ( 283-)  D      N      0.23    2.77  INTRA BL
 499 TYR   (  51-)  B      CD1 <->  953 ASN   (  55-)  C      ND2    0.23    2.87  INTRA BF
And so on for a total of 409 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

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.

 754 LEU   ( 306-)  B      -6.47
1204 LEU   ( 306-)  C      -6.47
1913 LYS   ( 114-)  E      -6.40
2105 LEU   ( 306-)  E      -6.39
1655 LEU   ( 306-)  D      -6.35
 304 LEU   ( 306-)  A      -6.34
2365 LYS   ( 114-)  F      -6.33
1012 LYS   ( 114-)  C      -6.30
1463 LYS   ( 114-)  D      -6.26
2089 ARG   ( 290-)  E      -6.17
1111 TYR   ( 213-)  C      -6.17
 562 LYS   ( 114-)  B      -6.08
2557 LEU   ( 306-)  F      -6.07
 211 TYR   ( 213-)  A      -6.01
 112 LYS   ( 114-)  A      -5.98
1562 TYR   ( 213-)  D      -5.94
 661 TYR   ( 213-)  B      -5.94
2252 LYS   ( 453-)  E      -5.93
 738 ARG   ( 290-)  B      -5.93
2464 TYR   ( 213-)  F      -5.92
1639 ARG   ( 290-)  D      -5.92
2541 ARG   ( 290-)  F      -5.83
 288 ARG   ( 290-)  A      -5.75
1188 ARG   ( 290-)  C      -5.59
2012 TYR   ( 213-)  E      -5.50
  29 ARG   (  31-)  A      -5.43
 838 TYR   ( 390-)  B      -5.40
2062 ARG   ( 263-)  E      -5.35
2282 ARG   (  31-)  F      -5.31
 261 ARG   ( 263-)  A      -5.24
1830 ARG   (  31-)  E      -5.19
 388 TYR   ( 390-)  A      -5.16
1739 TYR   ( 390-)  D      -5.08
2185 GLU   ( 386-)  E      -5.02
1612 ARG   ( 263-)  D      -5.01
1380 ARG   (  31-)  D      -5.00

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.

 448 ASP   ( 450-)  A       450 - PRO    452- ( A)         -4.25
 898 ASP   ( 450-)  B       900 - PRO    452- ( B)         -4.23
1799 ASP   ( 450-)  D      1801 - PRO    452- ( D)         -4.32

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

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.

1879 ILE   (  80-)  E   -2.88
 528 ILE   (  80-)  B   -2.87
 462 LEU   (  14-)  B   -2.82
  78 ILE   (  80-)  A   -2.80
2331 ILE   (  80-)  F   -2.79
  12 LEU   (  14-)  A   -2.78
 978 ILE   (  80-)  C   -2.73
1363 LEU   (  14-)  D   -2.70
 500 LEU   (  52-)  B   -2.66
2265 LEU   (  14-)  F   -2.65
 912 LEU   (  14-)  C   -2.62
 950 LEU   (  52-)  C   -2.62
2431 ILE   ( 180-)  F   -2.56
1401 LEU   (  52-)  D   -2.56
  50 LEU   (  52-)  A   -2.54
 178 ILE   ( 180-)  A   -2.54
2303 LEU   (  52-)  F   -2.54
1851 LEU   (  52-)  E   -2.54
1979 ILE   ( 180-)  E   -2.52
 628 ILE   ( 180-)  B   -2.52

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

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

2745 HOH   ( 542 )  E      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  79 ASN   (  81-)  A
 120 ASN   ( 122-)  A
 529 ASN   (  81-)  B
 979 ASN   (  81-)  C
1430 ASN   (  81-)  D
2332 ASN   (  81-)  F

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.

  14 SER   (  16-)  A      OG
  15 ARG   (  17-)  A      NE
  18 ALA   (  20-)  A      N
  23 THR   (  25-)  A      N
  36 ARG   (  38-)  A      N
  55 ARG   (  57-)  A      NH2
  56 GLN   (  58-)  A      NE2
  64 THR   (  66-)  A      N
  65 TRP   (  67-)  A      N
  66 ASP   (  68-)  A      N
  67 ASP   (  69-)  A      N
  69 ASN   (  71-)  A      N
  81 ASN   (  83-)  A      N
  97 ARG   (  99-)  A      NH1
 113 ASN   ( 115-)  A      N
 115 GLN   ( 117-)  A      N
 120 ASN   ( 122-)  A      N
 124 SER   ( 126-)  A      OG
 125 SER   ( 127-)  A      N
 126 GLU   ( 128-)  A      N
 138 ARG   ( 140-)  A      NH1
 138 ARG   ( 140-)  A      NH2
 158 GLY   ( 160-)  A      N
 169 ARG   ( 171-)  A      NE
 186 PHE   ( 188-)  A      N
And so on for a total of 317 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.

  66 ASP   (  68-)  A      OD1
  95 ASP   (  97-)  A      OD1
 214 ASN   ( 216-)  A      OD1
 239 HIS   ( 241-)  A      NE2
 484 GLU   (  36-)  B      OE2
 534 ASP   (  86-)  B      OD2
 689 HIS   ( 241-)  B      NE2
 878 GLU   ( 430-)  B      OE2
 910 GLU   (  12-)  C      OE1
 966 ASP   (  68-)  C      OD2
 984 ASP   (  86-)  C      OD2
 986 GLU   (  88-)  C      OE1
 995 ASP   (  97-)  C      OD1
1139 HIS   ( 241-)  C      NE2
1385 GLU   (  36-)  D      OE1
1417 ASP   (  68-)  D      OD1
1435 ASP   (  86-)  D      OD2
1446 ASP   (  97-)  D      OD1
1516 HIS   ( 167-)  D      ND1
1590 HIS   ( 241-)  D      NE2
1847 ASP   (  48-)  E      OD2
1867 ASP   (  68-)  E      OD1
1880 ASN   (  81-)  E      OD1
1896 ASP   (  97-)  E      OD1
1966 HIS   ( 167-)  E      ND1
2287 GLU   (  36-)  F      OE2
2299 ASP   (  48-)  F      OD2
2319 ASP   (  68-)  F      OD1
2337 ASP   (  86-)  F      OD2
2348 ASP   (  97-)  F      OD1
2492 HIS   ( 241-)  F      NE2

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.

  51 ASP   (  53-)  A   H-bonding suggests Asn
  84 ASP   (  86-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
  86 GLU   (  88-)  A   H-bonding suggests Gln
 226 ASP   ( 228-)  A   H-bonding suggests Asn
 231 ASP   ( 233-)  A   H-bonding suggests Asn
 259 ASP   ( 261-)  A   H-bonding suggests Asn
 448 ASP   ( 450-)  A   H-bonding suggests Asn; but Alt-Rotamer
 456 ASP   (   8-)  B   H-bonding suggests Asn
 516 ASP   (  68-)  B   H-bonding suggests Asn; but Alt-Rotamer
 534 ASP   (  86-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 627 GLU   ( 179-)  B   H-bonding suggests Gln; but Alt-Rotamer
 966 ASP   (  68-)  C   H-bonding suggests Asn; but Alt-Rotamer
 984 ASP   (  86-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1338 ASP   ( 440-)  C   H-bonding suggests Asn; but Alt-Rotamer
1357 ASP   (   8-)  D   H-bonding suggests Asn
1364 ASP   (  15-)  D   H-bonding suggests Asn
1385 GLU   (  36-)  D   H-bonding suggests Gln; but Alt-Rotamer
1402 ASP   (  53-)  D   H-bonding suggests Asn
1417 ASP   (  68-)  D   H-bonding suggests Asn; but Alt-Rotamer
1435 ASP   (  86-)  D   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1437 GLU   (  88-)  D   H-bonding suggests Gln
1574 ASP   ( 225-)  D   H-bonding suggests Asn
1807 ASP   (   8-)  E   H-bonding suggests Asn; but Alt-Rotamer
1814 ASP   (  15-)  E   H-bonding suggests Asn
1885 ASP   (  86-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1978 GLU   ( 179-)  E   H-bonding suggests Gln; but Alt-Rotamer
2032 ASP   ( 233-)  E   H-bonding suggests Asn
2249 ASP   ( 450-)  E   H-bonding suggests Asn
2304 ASP   (  53-)  F   H-bonding suggests Asn
2319 ASP   (  68-)  F   H-bonding suggests Asn; but Alt-Rotamer
2337 ASP   (  86-)  F   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2681 GLU   ( 430-)  F   H-bonding suggests Gln
2701 ASP   ( 450-)  F   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.429
  2nd generation packing quality :  -1.160
  Ramachandran plot appearance   :  -2.646
  chi-1/chi-2 rotamer normality  :  -2.767
  Backbone conformation          :   0.182

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.339 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.203 (tight)
  Side chain planarity           :   0.253 (tight)
  Improper dihedral distribution :   0.650
  B-factor distribution          :   0.451
  Inside/Outside distribution    :   1.000

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 : 3.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.339 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.203 (tight)
  Side chain planarity           :   0.253 (tight)
  Improper dihedral distribution :   0.650
  B-factor distribution          :   0.451
  Inside/Outside distribution    :   1.000
==============

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.