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 pdb3mx1.ent

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'.

  85 GLN   (  87-)  A      CB
  85 GLN   (  87-)  A      CG
  85 GLN   (  87-)  A      CD
  85 GLN   (  87-)  A      OE1
  85 GLN   (  87-)  A      NE2
  86 SER   (  88-)  A      CB
  86 SER   (  88-)  A      OG
  87 ARG   (  89-)  A      CB
  87 ARG   (  89-)  A      CG
  87 ARG   (  89-)  A      CD
  87 ARG   (  89-)  A      NE
  87 ARG   (  89-)  A      CZ
  87 ARG   (  89-)  A      NH1
  87 ARG   (  89-)  A      NH2
  88 ILE   (  90-)  A      CB
  88 ILE   (  90-)  A      CG1
  88 ILE   (  90-)  A      CG2
  88 ILE   (  90-)  A      CD1
  89 SER   (  91-)  A      CB
  89 SER   (  91-)  A      OG
  90 ASP   (  92-)  A      CB
  90 ASP   (  92-)  A      CG
  90 ASP   (  92-)  A      OD1
  90 ASP   (  92-)  A      OD2
  92 GLU   (  94-)  A      CB
  92 GLU   (  94-)  A      CG
  92 GLU   (  94-)  A      CD
  92 GLU   (  94-)  A      OE1
  92 GLU   (  94-)  A      OE2
  93 THR   (  95-)  A      OG1
  93 THR   (  95-)  A      CG2
  94 ARG   (  96-)  A      CB
  94 ARG   (  96-)  A      CG
  94 ARG   (  96-)  A      CD
  94 ARG   (  96-)  A      NE
  94 ARG   (  96-)  A      CZ
  94 ARG   (  96-)  A      NH1
  94 ARG   (  96-)  A      NH2
  95 ALA   (  97-)  A      CB
 165 ALA   ( 167-)  A      CB
 186 GLU   ( 188-)  A      CB
 186 GLU   ( 188-)  A      CG
 186 GLU   ( 188-)  A      CD
 186 GLU   ( 188-)  A      OE1
 186 GLU   ( 188-)  A      OE2
 208 LYS   ( 210-)  A      CG
 208 LYS   ( 210-)  A      CD
 208 LYS   ( 210-)  A      CE
 208 LYS   ( 210-)  A      NZ

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.

  84 ARG   (  86-)  A    High
  85 GLN   (  87-)  A    High
  86 SER   (  88-)  A    High
  87 ARG   (  89-)  A    High
  88 ILE   (  90-)  A    High
  89 SER   (  91-)  A    High
  90 ASP   (  92-)  A    High
  91 HIS   (  93-)  A    High
  92 GLU   (  94-)  A    High
  93 THR   (  95-)  A    High
 164 GLY   ( 166-)  A    High
 165 ALA   ( 167-)  A    High
 166 GLY   ( 168-)  A    High
 167 ARG   ( 169-)  A    High
 168 PHE   ( 170-)  A    High
 169 ALA   ( 171-)  A    High
 170 GLN   ( 172-)  A    High
 187 LYS   ( 189-)  A    High
 188 CYS   ( 190-)  A    High
 189 THR   ( 191-)  A    High
 190 GLY   ( 192-)  A    High
 191 VAL   ( 193-)  A    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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

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

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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  63 ARG   (  65-)  A

Warning: Tyrosine convention problem

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

  47 TYR   (  49-)  A
  50 TYR   (  52-)  A

Warning: Phenylalanine convention problem

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

  41 PHE   (  43-)  A
 121 PHE   ( 123-)  A
 128 PHE   ( 130-)  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.

  14 ASP   (  16-)  A
  59 ASP   (  61-)  A
 117 ASP   ( 119-)  A
 174 ASP   ( 176-)  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.

   8 GLU   (  10-)  A
  18 GLU   (  20-)  A
 105 GLU   ( 107-)  A
 199 GLU   ( 201-)  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.

   8 GLU   (  10-)  A      CG   CD    1.62    4.0
 192 HIS   ( 194-)  A      ND1  CE1   1.40    6.0
 192 HIS   ( 194-)  A      CE1  NE2   1.23   -5.7

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

 |  0.994044 -0.000567 -0.000355|
 | -0.000567  0.996036  0.000187|
 | -0.000355  0.000187  0.993374|
Proposed new scale matrix

 |  0.011444  0.000007  0.000004|
 |  0.000006  0.011146 -0.000002|
 |  0.000004 -0.000002  0.011330|
With corresponding cell

    A    =  87.381  B   =  89.717  C    =  88.261
    Alpha=  89.978  Beta=  90.041  Gamma=  90.065

The CRYST1 cell dimensions

    A    =  87.906  B   =  90.074  C    =  88.850
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 219.684
(Under-)estimated Z-score: 10.924

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.

   8 GLU   (  10-)  A      N    CA   CB  103.47   -4.1
   8 GLU   (  10-)  A      CB   CG   CD  119.68    4.2
  96 GLY   (  98-)  A     -C    N    CA  130.56    5.9
  96 GLY   (  98-)  A      N    CA   C   125.10    4.3
 106 HIS   ( 108-)  A      CG   ND1  CE1 109.69    4.1
 129 GLU   ( 131-)  A      N    CA   C   123.08    4.2
 130 ALA   ( 132-)  A     -C    N    CA  109.45   -6.8
 130 ALA   ( 132-)  A      N    CA   C    99.61   -4.1
 177 VAL   ( 179-)  A      N    CA   CB  117.43    4.1
 192 HIS   ( 194-)  A      NE2  CD2  CG  112.70    6.2

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.

   8 GLU   (  10-)  A
  14 ASP   (  16-)  A
  18 GLU   (  20-)  A
  59 ASP   (  61-)  A
  63 ARG   (  65-)  A
 105 GLU   ( 107-)  A
 117 ASP   ( 119-)  A
 174 ASP   ( 176-)  A
 199 GLU   ( 201-)  A

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.

 130 ALA   ( 132-)  A    4.89
 206 PHE   ( 208-)  A    4.62
  96 GLY   (  98-)  A    4.14
 187 LYS   ( 189-)  A    4.11

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.

 167 ARG   ( 169-)  A    -2.6
 195 PRO   ( 197-)  A    -2.5
  96 GLY   (  98-)  A    -2.2
 162 THR   ( 164-)  A    -2.1
 181 GLY   ( 183-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  35 LEU   (  37-)  A  PRO omega poor
  53 GLY   (  55-)  A  omega poor
  55 TYR   (  57-)  A  omega poor
  58 TYR   (  60-)  A  omega poor
  59 ASP   (  61-)  A  omega poor
  83 TRP   (  85-)  A  omega poor
  86 SER   (  88-)  A  Poor phi/psi, omega poor
  90 ASP   (  92-)  A  Poor phi/psi
  92 GLU   (  94-)  A  Poor phi/psi
  93 THR   (  95-)  A  Poor phi/psi
  95 ALA   (  97-)  A  omega poor
  96 GLY   (  98-)  A  Poor phi/psi
 128 PHE   ( 130-)  A  omega poor
 129 GLU   ( 131-)  A  omega poor
 130 ALA   ( 132-)  A  Poor phi/psi
 135 MET   ( 137-)  A  omega poor
 152 ASN   ( 154-)  A  omega poor
 165 ALA   ( 167-)  A  Poor phi/psi
 166 GLY   ( 168-)  A  omega poor
 180 PRO   ( 182-)  A  omega poor
 181 GLY   ( 183-)  A  omega poor
 187 LYS   ( 189-)  A  omega poor
 189 THR   ( 191-)  A  omega poor
 196 TYR   ( 198-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.392

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.

 100 SER   ( 102-)  A    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  30 THR   (  32-)  A      0
  34 SER   (  36-)  A      0
  35 LEU   (  37-)  A      0
  36 PRO   (  38-)  A      0
  37 PRO   (  39-)  A      0
  42 GLN   (  44-)  A      0
  44 ALA   (  46-)  A      0
  46 VAL   (  48-)  A      0
  52 THR   (  54-)  A      0
  54 HIS   (  56-)  A      0
  55 TYR   (  57-)  A      0
  58 TYR   (  60-)  A      0
  59 ASP   (  61-)  A      0
  65 ASN   (  67-)  A      0
  67 LEU   (  69-)  A      0
  69 TYR   (  71-)  A      0
  70 ASN   (  72-)  A      0
  73 ILE   (  75-)  A      0
  79 VAL   (  81-)  A      0
  83 TRP   (  85-)  A      0
  84 ARG   (  86-)  A      0
  85 GLN   (  87-)  A      0
  86 SER   (  88-)  A      0
  87 ARG   (  89-)  A      0
  88 ILE   (  90-)  A      0
And so on for a total of 88 lines.

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 : 7.666

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!

 164 GLY   ( 166-)  A   2.88   29
  96 GLY   (  98-)  A   1.99   15

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   (  39-)  A  -114.3 envelop C-gamma (-108 degrees)
  80 PRO   (  82-)  A    46.1 half-chair C-delta/C-gamma (54 degrees)
 163 PRO   ( 165-)  A    34.5 envelop C-delta (36 degrees)
 195 PRO   ( 197-)  A   103.9 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.

 101 ASN   ( 103-)  A      ND2 <->  209 HOH   ( 353 )  A      O      0.39    2.31  INTRA
 104 ARG   ( 106-)  A      NH1 <->  209 HOH   ( 343 )  A      O      0.22    2.48  INTRA BF
 172 LYS   ( 174-)  A      CD  <->  192 HIS   ( 194-)  A      CD2    0.12    3.08  INTRA BF
 109 ASN   ( 111-)  A      ND2 <->  209 HOH   ( 351 )  A      O      0.11    2.59  INTRA
  54 HIS   (  56-)  A      N   <->  209 HOH   ( 303 )  A      O      0.11    2.59  INTRA BL
  73 ILE   (  75-)  A      N   <->   74 TYR   (  76-)  A      N      0.08    2.52  INTRA BL
  80 PRO   (  82-)  A      CD  <->   83 TRP   (  85-)  A      CE3    0.06    3.14  INTRA BF
  47 TYR   (  49-)  A      OH  <->  106 HIS   ( 108-)  A      NE2    0.05    2.65  INTRA BL
  86 SER   (  88-)  A      N   <->   87 ARG   (  89-)  A      CA     0.04    2.86  INTRA BF
  33 HIS   (  35-)  A      CD2 <->  209 HOH   ( 263 )  A      O      0.04    2.76  INTRA BL
 125 PHE   ( 127-)  A      N   <->  209 HOH   ( 231 )  A      O      0.03    2.67  INTRA BL
  54 HIS   (  56-)  A      C   <->   55 TYR   (  57-)  A      C      0.03    2.77  INTRA BL
  58 TYR   (  60-)  A      OH  <->  179 HIS   ( 181-)  A      NE2    0.02    2.68  INTRA BL
 129 GLU   ( 131-)  A      C   <->  130 ALA   ( 132-)  A      CA     0.01    2.29  INTRA BL
 194 GLU   ( 196-)  A      O   <->  195 PRO   ( 197-)  A      C      0.01    2.59  INTRA BF

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.

  84 ARG   (  86-)  A      -7.48
  91 HIS   (  93-)  A      -7.04
  40 ARG   (  42-)  A      -6.43
  67 LEU   (  69-)  A      -6.39
 161 HIS   ( 163-)  A      -6.13
   9 HIS   (  11-)  A      -6.01
 167 ARG   ( 169-)  A      -5.90
  42 GLN   (  44-)  A      -5.80
  11 TYR   (  13-)  A      -5.71
   4 PHE   (   6-)  A      -5.14

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.

 160 ASN   ( 162-)  A       162 - THR    164- ( A)         -5.02

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

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.

  94 ARG   (  96-)  A   -3.91
  87 ARG   (  89-)  A   -3.04
  85 GLN   (  87-)  A   -2.99
 186 GLU   ( 188-)  A   -2.70
  88 ILE   (  90-)  A   -2.64
  90 ASP   (  92-)  A   -2.52

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.

  83 TRP   (  85-)  A     -   88 ILE   (  90-)  A        -2.26
 184 TRP   ( 186-)  A     -  188 CYS   ( 190-)  A        -2.06

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

Warning: Water molecules need moving

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

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

 209 HOH   ( 382 )  A      O    -11.77  -44.60    8.71

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.

 209 HOH   ( 340 )  A      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.

  33 HIS   (  35-)  A
  65 ASN   (  67-)  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.

  39 GLU   (  41-)  A      N
  53 GLY   (  55-)  A      N
  68 ALA   (  70-)  A      N
  91 HIS   (  93-)  A      N
  98 GLU   ( 100-)  A      N
 104 ARG   ( 106-)  A      NH2
 130 ALA   ( 132-)  A      N
 132 GLY   ( 134-)  A      N
 138 THR   ( 140-)  A      N
 164 GLY   ( 166-)  A      N
 167 ARG   ( 169-)  A      N
 168 PHE   ( 170-)  A      N
 169 ALA   ( 171-)  A      N
 175 TRP   ( 177-)  A      NE1

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.

  98 GLU   ( 100-)  A      OE1

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 :  -1.644
  2nd generation packing quality :  -2.232
  Ramachandran plot appearance   :  -1.978
  chi-1/chi-2 rotamer normality  :  -1.392
  Backbone conformation          :  -0.974

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.995
  Bond angles                    :   1.011
  Omega angle restraints         :   1.394 (loose)
  Side chain planarity           :   0.993
  Improper dihedral distribution :   1.145
  B-factor distribution          :   0.713
  Inside/Outside distribution    :   1.039

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.2
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.995
  Bond angles                    :   1.011
  Omega angle restraints         :   1.394 (loose)
  Side chain planarity           :   0.993
  Improper dihedral distribution :   1.145
  B-factor distribution          :   0.713
  Inside/Outside distribution    :   1.039
==============

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.