WHAT IF Check report

This file was created 2011-12-17 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 pdb3rzf.ent

Checks that need to be done early-on in validation

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: 62774.723
Volume of the Unit Cell V= 7414272.0
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.382
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 5.940

Warning: Ligands for which topology could not be determined

The 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 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.

 542 XNM   ( 676-)  A  -

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

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'.

  36 SER   (  51-)  A      OG
  64 VAL   (  79-)  A      CG1
  64 VAL   (  79-)  A      CG2
  75 ASP   (  90-)  A      CG
  75 ASP   (  90-)  A      OD1
  75 ASP   (  90-)  A      OD2
 267 ASP   ( 291-)  A      CG
 267 ASP   ( 291-)  A      OD1
 267 ASP   ( 291-)  A      OD2

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 GLU   (  16-)  A    High
   2 MET   (  17-)  A    High
   3 LYS   (  18-)  A    High
   4 GLU   (  19-)  A    High
   5 ARG   (  20-)  A    High
   6 LEU   (  21-)  A    High
   7 GLY   (  22-)  A    High
   8 THR   (  23-)  A    High
   9 GLY   (  24-)  A    High
  10 GLY   (  25-)  A    High
  11 PHE   (  26-)  A    High
  12 GLY   (  27-)  A    High
  13 TYR   (  28-)  A    High
  14 VAL   (  29-)  A    High
  15 LEU   (  30-)  A    High
  16 ARG   (  31-)  A    High
  17 TRP   (  32-)  A    High
  18 ILE   (  33-)  A    High
  19 HIS   (  34-)  A    High
  20 GLN   (  35-)  A    High
  21 ASP   (  36-)  A    High
  22 THR   (  37-)  A    High
  23 GLY   (  38-)  A    High
  24 GLU   (  39-)  A    High
  25 GLN   (  40-)  A    High
And so on for a total of 541 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: 10

Crystal temperature (K) : 83.000

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

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

  92 TYR   ( 107-)  A
 120 TYR   ( 135-)  A
 154 TYR   ( 169-)  A
 190 TYR   ( 205-)  A
 225 TYR   ( 246-)  A
 386 TYR   ( 423-)  A
 475 TYR   ( 571-)  A

Warning: Phenylalanine convention problem

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

  96 PHE   ( 111-)  A
 198 PHE   ( 213-)  A
 276 PHE   ( 300-)  A
 505 PHE   ( 601-)  A

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.

  66 ASP   (  81-)  A
 130 ASP   ( 145-)  A
 280 ASP   ( 304-)  A
 354 ASP   ( 385-)  A
 466 ASP   ( 562-)  A

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.

   1 GLU   (  16-)  A
  24 GLU   (  39-)  A
  82 GLU   (  97-)  A
  97 GLU   ( 112-)  A
 104 GLU   ( 119-)  A
 123 GLU   ( 138-)  A
 134 GLU   ( 149-)  A
 177 GLU   ( 192-)  A
 326 GLU   ( 350-)  A
 469 GLU   ( 565-)  A
 535 GLU   ( 631-)  A

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.

  88 ASP   ( 103-)  A      CA   C     1.43   -4.7
  89 LEU   ( 104-)  A      N    CA    1.37   -4.6
  89 LEU   ( 104-)  A      N   -C     1.22   -5.4
 153 GLY   ( 168-)  A      CA   C     1.59    5.2
 154 TYR   ( 169-)  A      N    CA    1.56    5.5
 154 TYR   ( 169-)  A      CA   C     1.63    4.9

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

 |  0.996373 -0.000330  0.000201|
 | -0.000330  0.996432 -0.000144|
 |  0.000201 -0.000144  0.996460|
Proposed new scale matrix

 |  0.006095  0.000002 -0.000001|
 |  0.000002  0.006095  0.000000|
 |  0.000000  0.000000  0.003670|
With corresponding cell

    A    = 164.066  B   = 164.076  C    = 272.480
    Alpha=  90.003  Beta=  89.990  Gamma=  90.038

The CRYST1 cell dimensions

    A    = 164.656  B   = 164.656  C    = 273.458
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 235.056
(Under-)estimated Z-score: 11.299

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.

  84 CYS   (  99-)  A      N    CA   C   122.60    4.1
  84 CYS   (  99-)  A      N    CA   CB  103.66   -4.0
  85 GLU   ( 100-)  A     -CA  -C    N   127.75    5.8
  89 LEU   ( 104-)  A      N    CA   CB  103.44   -4.2
  89 LEU   ( 104-)  A      C    CA   CB  121.30    5.9
 154 TYR   ( 169-)  A      N    CA   C   122.78    4.1
 213 PRO   ( 228-)  A      N    CA   C   127.63    6.3
 214 VAL   ( 229-)  A     -CA  -C    N   127.19    5.5
 214 VAL   ( 229-)  A     -C    N    CA  134.82    7.3
 217 HIS   ( 232-)  A      CG   ND1  CE1 109.60    4.0

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.

   1 GLU   (  16-)  A
  24 GLU   (  39-)  A
  66 ASP   (  81-)  A
  82 GLU   (  97-)  A
  97 GLU   ( 112-)  A
 104 GLU   ( 119-)  A
 123 GLU   ( 138-)  A
 130 ASP   ( 145-)  A
 134 GLU   ( 149-)  A
 177 GLU   ( 192-)  A
 280 ASP   ( 304-)  A
 326 GLU   ( 350-)  A
 354 ASP   ( 385-)  A
 466 ASP   ( 562-)  A
 469 GLU   ( 565-)  A
 535 GLU   ( 631-)  A

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.

 214 VAL   ( 229-)  A      CA    -7.2    22.82    33.23
The average deviation= 0.760

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.

 213 PRO   ( 228-)  A    5.79
 154 TYR   ( 169-)  A    4.41
  84 CYS   (  99-)  A    4.33

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -6.866

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.

 207 PHE   ( 222-)  A    -3.4
 165 THR   ( 180-)  A    -3.2
 320 THR   ( 344-)  A    -3.1
 241 PRO   ( 262-)  A    -3.1
 206 PRO   ( 221-)  A    -3.0
 187 THR   ( 202-)  A    -2.9
  73 PRO   (  88-)  A    -2.9
 302 PRO   ( 326-)  A    -2.9
 120 TYR   ( 135-)  A    -2.9
 109 THR   ( 124-)  A    -2.8
 211 TRP   ( 226-)  A    -2.8
 176 PRO   ( 191-)  A    -2.8
 228 LEU   ( 249-)  A    -2.7
 304 THR   ( 328-)  A    -2.7
 251 LYS   ( 272-)  A    -2.7
 204 PHE   ( 219-)  A    -2.7
 247 ILE   ( 268-)  A    -2.6
 300 THR   ( 324-)  A    -2.6
 263 HIS   ( 284-)  A    -2.6
 344 THR   ( 368-)  A    -2.6
 322 ILE   ( 346-)  A    -2.6
 174 LEU   ( 189-)  A    -2.6
  65 PRO   (  80-)  A    -2.6
 205 ARG   ( 220-)  A    -2.6
 229 THR   ( 250-)  A    -2.6
And so on for a total of 69 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.

   2 MET   (  17-)  A  omega poor
   3 LYS   (  18-)  A  Poor phi/psi, omega poor
  33 GLN   (  48-)  A  Poor phi/psi
  35 LEU   (  50-)  A  Poor phi/psi
  36 SER   (  51-)  A  PRO omega poor
  56 PRO   (  71-)  A  Poor phi/psi, omega poor
  62 ARG   (  77-)  A  Poor phi/psi
  63 GLU   (  78-)  A  Poor phi/psi
  68 LEU   (  83-)  A  Poor phi/psi
  69 GLN   (  84-)  A  Poor phi/psi
  72 ALA   (  87-)  A  Poor phi/psi
  74 ASN   (  89-)  A  omega poor
  83 TYR   (  98-)  A  omega poor
  85 GLU   ( 100-)  A  Poor phi/psi
 103 LYS   ( 118-)  A  omega poor
 104 GLU   ( 119-)  A  Poor phi/psi
 105 GLY   ( 120-)  A  PRO omega poor
 106 PRO   ( 121-)  A  omega poor
 120 TYR   ( 135-)  A  Poor phi/psi
 125 ARG   ( 140-)  A  Poor phi/psi
 130 ASP   ( 145-)  A  Poor phi/psi
 131 LEU   ( 146-)  A  Poor phi/psi
 137 VAL   ( 152-)  A  omega poor
 145 LEU   ( 160-)  A  omega poor
 151 ASP   ( 166-)  A  Poor phi/psi
And so on for a total of 119 lines.

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

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

chi-1/chi-2 correlation Z-score : -5.901

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.

 115 SER   ( 130-)  A    0.37

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!

   3 LYS   (  18-)  A      0
   4 GLU   (  19-)  A      0
   6 LEU   (  21-)  A      0
   8 THR   (  23-)  A      0
  11 PHE   (  26-)  A      0
  13 TYR   (  28-)  A      0
  19 HIS   (  34-)  A      0
  20 GLN   (  35-)  A      0
  21 ASP   (  36-)  A      0
  22 THR   (  37-)  A      0
  32 ARG   (  47-)  A      0
  33 GLN   (  48-)  A      0
  34 GLU   (  49-)  A      0
  35 LEU   (  50-)  A      0
  36 SER   (  51-)  A      0
  37 PRO   (  52-)  A      0
  38 LYS   (  53-)  A      0
  52 LYS   (  67-)  A      0
  53 LEU   (  68-)  A      0
  54 ASN   (  69-)  A      0
  55 HIS   (  70-)  A      0
  57 ASN   (  72-)  A      0
  62 ARG   (  77-)  A      0
  63 GLU   (  78-)  A      0
  64 VAL   (  79-)  A      0
And so on for a total of 289 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.540

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 8.672

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!

   9 GLY   (  24-)  A   2.40   15
 246 GLY   ( 267-)  A   1.63   14

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].

  37 PRO   (  52-)  A   -10.9 half-chair C-alpha/N (-18 degrees)
  65 PRO   (  80-)  A   -32.8 envelop C-alpha (-36 degrees)
  73 PRO   (  88-)  A   -20.4 half-chair C-alpha/N (-18 degrees)
 106 PRO   ( 121-)  A   106.0 envelop C-beta (108 degrees)
 176 PRO   ( 191-)  A   148.6 envelop C-alpha (144 degrees)
 206 PRO   ( 221-)  A   -48.4 half-chair C-beta/C-alpha (-54 degrees)
 209 PRO   ( 224-)  A   100.1 envelop C-beta (108 degrees)
 241 PRO   ( 262-)  A   -27.5 envelop C-alpha (-36 degrees)
 302 PRO   ( 326-)  A   -20.3 half-chair C-alpha/N (-18 degrees)
 342 PRO   ( 366-)  A    99.6 envelop C-beta (108 degrees)
 367 PRO   ( 404-)  A    53.0 half-chair C-delta/C-gamma (54 degrees)
 383 PRO   ( 420-)  A   -19.3 half-chair C-alpha/N (-18 degrees)
 488 PRO   ( 584-)  A   110.7 envelop C-beta (108 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.

  50 MET   (  65-)  A      CE  <->  152 LEU   ( 167-)  A      CD1    1.88    1.32  INTRA BF
  50 MET   (  65-)  A      SD  <->  152 LEU   ( 167-)  A      CD1    1.45    1.95  INTRA BF
  87 GLY   ( 102-)  A      CA  <->  542 XNM   ( 676-)  A      CAT    1.08    2.12  INTRA BF
  87 GLY   ( 102-)  A      CA  <->  542 XNM   ( 676-)  A      CAS    1.06    2.14  INTRA BF
  84 CYS   (  99-)  A      O   <->   85 GLU   ( 100-)  A      CG     1.03    1.67  INTRA BF
 129 ARG   ( 144-)  A      CD  <->  154 TYR   ( 169-)  A      O      0.91    1.89  INTRA BL
  50 MET   (  65-)  A      SD  <->  152 LEU   ( 167-)  A      CG     0.77    2.63  INTRA BF
  27 ALA   (  42-)  A      CB  <->  542 XNM   ( 676-)  A      CAE    0.74    2.46  INTRA BL
  81 MET   (  96-)  A      CE  <->  542 XNM   ( 676-)  A     CLAA    0.67    2.53  INTRA BF
 117 ALA   ( 132-)  A      CB  <->  149 ILE   ( 164-)  A      CD1    0.65    2.55  INTRA BL
  50 MET   (  65-)  A      SD  <->  152 LEU   ( 167-)  A      CB     0.60    2.80  INTRA BF
  84 CYS   (  99-)  A      N   <->  542 XNM   ( 676-)  A      CAQ    0.59    2.51  INTRA BF
 153 GLY   ( 168-)  A      O   <->  164 CYS   ( 179-)  A      SG     0.54    2.31  INTRA BF
 129 ARG   ( 144-)  A      CB  <->  154 TYR   ( 169-)  A      O      0.51    2.29  INTRA BL
 129 ARG   ( 144-)  A      CG  <->  154 TYR   ( 169-)  A      O      0.50    2.30  INTRA BL
  84 CYS   (  99-)  A      C   <->   85 GLU   ( 100-)  A      CG     0.49    2.61  INTRA BF
  50 MET   (  65-)  A      CE  <->  152 LEU   ( 167-)  A      CG     0.47    2.73  INTRA BF
  84 CYS   (  99-)  A      O   <->   85 GLU   ( 100-)  A      CB     0.45    2.15  INTRA BF
 129 ARG   ( 144-)  A      CD  <->  154 TYR   ( 169-)  A      C      0.43    2.77  INTRA BL
 251 LYS   ( 272-)  A      O   <->  255 TRP   ( 276-)  A      N      0.42    2.28  INTRA BL
 150 ILE   ( 165-)  A      CG2 <->  151 ASP   ( 166-)  A      N      0.41    2.59  INTRA BL
 397 TRP   ( 434-)  A      CD1 <->  398 GLN   ( 435-)  A      N      0.40    2.60  INTRA BL
 137 VAL   ( 152-)  A      CG2 <->  542 XNM   ( 676-)  A      NAK    0.39    2.71  INTRA BL
  87 GLY   ( 102-)  A      C   <->  542 XNM   ( 676-)  A      CAS    0.38    2.82  INTRA BF
 215 GLN   ( 230-)  A      O   <->  218 GLY   ( 233-)  A      N      0.36    2.34  INTRA BL
And so on for a total of 199 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

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.

 460 ARG   ( 549-)  A      -8.25
 269 GLN   ( 293-)  A      -7.55
 362 ARG   ( 393-)  A      -7.45
 486 ARG   ( 582-)  A      -6.98
  32 ARG   (  47-)  A      -6.88
 483 ARG   ( 579-)  A      -6.64
 204 PHE   ( 219-)  A      -6.41
 143 GLN   ( 158-)  A      -6.30
 173 TYR   ( 188-)  A      -6.29
 144 ARG   ( 159-)  A      -6.27
 539 LEU   ( 635-)  A      -6.26
 264 GLN   ( 285-)  A      -6.21
 540 MET   ( 636-)  A      -6.17
 390 ARG   ( 427-)  A      -6.14
 183 LYS   ( 198-)  A      -6.08
  62 ARG   (  77-)  A      -6.04
 205 ARG   ( 220-)  A      -5.98
 167 PHE   ( 182-)  A      -5.95
  85 GLU   ( 100-)  A      -5.91
  71 LEU   (  86-)  A      -5.87
  20 GLN   (  35-)  A      -5.71
   5 ARG   (  20-)  A      -5.66
 184 TYR   ( 199-)  A      -5.61
 160 GLN   ( 175-)  A      -5.59
 238 LEU   ( 259-)  A      -5.58
 318 GLN   ( 342-)  A      -5.54
  33 GLN   (  48-)  A      -5.44
 346 TYR   ( 370-)  A      -5.41
 228 LEU   ( 249-)  A      -5.36
 129 ARG   ( 144-)  A      -5.36
  76 LEU   (  91-)  A      -5.35
  83 TYR   (  98-)  A      -5.33
  34 GLU   (  49-)  A      -5.29
 369 HIS   ( 406-)  A      -5.22
  53 LEU   (  68-)  A      -5.20
 350 CYS   ( 374-)  A      -5.19
 447 LYS   ( 536-)  A      -5.11
 262 TRP   ( 283-)  A      -5.09
 272 ASN   ( 296-)  A      -5.07
  63 GLU   (  78-)  A      -5.04
 225 TYR   ( 246-)  A      -5.03

Warning: Abnormal packing environment for sequential residues

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

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

  32 ARG   (  47-)  A        35 - LEU     50- ( A)         -5.57
  52 LYS   (  67-)  A        54 - ASN     69- ( A)         -4.81
  83 TYR   (  98-)  A        85 - GLU    100- ( A)         -5.34
 143 GLN   ( 158-)  A       145 - LEU    160- ( A)         -5.69
 261 MET   ( 282-)  A       264 - GLN    285- ( A)         -5.01
 459 GLN   ( 548-)  A       462 - PRO    551- ( A)         -5.38

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 541 : -2.211

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

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.

  74 ASN   (  89-)  A   -3.58
  59 VAL   (  74-)  A   -2.58
 376 VAL   ( 413-)  A   -2.54
 258 CYS   ( 279-)  A   -2.51

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.

 204 PHE   ( 219-)  A     -  208 LEU   ( 223-)  A        -2.01
 240 THR   ( 261-)  A     -  243 HIS   ( 264-)  A        -1.79
 357 PHE   ( 388-)  A     -  361 ASN   ( 392-)  A        -1.75
 537 MET   ( 633-)  A     -  540 MET   ( 636-)  A        -1.59

Note: Second generation quality Z-score plot

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

Chain identifier: A

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.

  57 ASN   (  72-)  A
 215 GLN   ( 230-)  A
 270 ASN   ( 294-)  A
 361 ASN   ( 392-)  A
 388 HIS   ( 425-)  A
 395 GLN   ( 432-)  A
 452 GLN   ( 541-)  A
 515 GLN   ( 611-)  A

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.

   3 LYS   (  18-)  A      N
   4 GLU   (  19-)  A      N
  11 PHE   (  26-)  A      N
  18 ILE   (  33-)  A      N
  23 GLY   (  38-)  A      N
  24 GLU   (  39-)  A      N
  33 GLN   (  48-)  A      N
  39 ASN   (  54-)  A      N
  40 ARG   (  55-)  A      N
  63 GLU   (  78-)  A      N
  67 GLY   (  82-)  A      N
  74 ASN   (  89-)  A      ND2
  76 LEU   (  91-)  A      N
  80 ALA   (  95-)  A      N
  84 CYS   (  99-)  A      N
  85 GLU   ( 100-)  A      N
  86 GLY   ( 101-)  A      N
  88 ASP   ( 103-)  A      N
 104 GLU   ( 119-)  A      N
 105 GLY   ( 120-)  A      N
 107 ILE   ( 122-)  A      N
 108 ARG   ( 123-)  A      N
 122 HIS   ( 137-)  A      NE2
 129 ARG   ( 144-)  A      NE
 132 LYS   ( 147-)  A      N
And so on for a total of 147 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  19 HIS   (  34-)  A      ND1
  46 GLU   (  61-)  A      OE1
 122 HIS   ( 137-)  A      ND1
 135 ASN   ( 150-)  A      OD1
 139 GLN   ( 154-)  A      OE1
 147 HIS   ( 162-)  A      ND1
 166 GLU   ( 181-)  A      OE2
 189 ASP   ( 204-)  A      OD1
 189 ASP   ( 204-)  A      OD2
 226 ASP   ( 247-)  A      OD2
 242 ASN   ( 263-)  A      OD1
 306 ASN   ( 330-)  A      OD1
 327 GLN   ( 351-)  A      OE1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  46 GLU   (  61-)  A   H-bonding suggests Gln; but Alt-Rotamer
  88 ASP   ( 103-)  A   H-bonding suggests Asn; Ligand-contact
 113 ASP   ( 128-)  A   H-bonding suggests Asn; but Alt-Rotamer
 166 GLU   ( 181-)  A   H-bonding suggests Gln
 189 ASP   ( 204-)  A   H-bonding suggests Asn; but Alt-Rotamer
 226 ASP   ( 247-)  A   H-bonding suggests Asn
 227 ASP   ( 248-)  A   H-bonding suggests Asn
 253 GLU   ( 274-)  A   H-bonding suggests Gln
 280 ASP   ( 304-)  A   H-bonding suggests Asn
 319 ASP   ( 343-)  A   H-bonding suggests Asn
 326 GLU   ( 350-)  A   H-bonding suggests Gln; but Alt-Rotamer
 349 ASP   ( 373-)  A   H-bonding suggests Asn; but Alt-Rotamer
 354 ASP   ( 385-)  A   H-bonding suggests Asn
 360 ASP   ( 391-)  A   H-bonding suggests Asn
 379 ASP   ( 416-)  A   H-bonding suggests Asn; but Alt-Rotamer
 446 ASP   ( 535-)  A   H-bonding suggests Asn; but Alt-Rotamer
 457 ASP   ( 546-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -4.276 (poor)
  2nd generation packing quality :  -4.627 (bad)
  Ramachandran plot appearance   :  -6.866 (bad)
  chi-1/chi-2 rotamer normality  :  -5.901 (bad)
  Backbone conformation          :  -2.540

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.519 (tight)
  Bond angles                    :   0.743
  Omega angle restraints         :   1.577 (loose)
  Side chain planarity           :   0.347 (tight)
  Improper dihedral distribution :   0.695
  Inside/Outside distribution    :   1.129

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 :  -2.7
  2nd generation packing quality :  -2.0
  Ramachandran plot appearance   :  -3.5 (poor)
  chi-1/chi-2 rotamer normality  :  -3.3 (poor)
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.519 (tight)
  Bond angles                    :   0.743
  Omega angle restraints         :   1.577 (loose)
  Side chain planarity           :   0.347 (tight)
  Improper dihedral distribution :   0.695
  Inside/Outside distribution    :   1.129
==============

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.