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 pdb3kw5.ent

Checks that need to be done early-on in validation

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.

 300 GVE   (  76-)  B  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

  90 CYS   (  90-)  A  -   SG   300 GVE   (  76-)  B  -   CB

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: B-factors outside the range 0.0 - 100.0

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

   1 MET   (   1-)  A    High
   2 GLN   (   2-)  A    High
   3 LEU   (   3-)  A    High
   4 LYS   (   4-)  A    High
   5 PRO   (   5-)  A    High
   7 GLU   (   7-)  A    High
   8 ILE   (   8-)  A    High
   9 ASN   (   9-)  A    High
  10 PRO   (  10-)  A    High
  11 GLU   (  11-)  A    High
  12 MET   (  12-)  A    High
  14 ASN   (  14-)  A    High
  15 LYS   (  15-)  A    High
  16 VAL   (  16-)  A    High
  17 LEU   (  17-)  A    High
  18 SER   (  18-)  A    High
  19 ARG   (  19-)  A    High
  20 LEU   (  20-)  A    High
  21 GLY   (  21-)  A    High
  22 VAL   (  22-)  A    High
  23 ALA   (  23-)  A    High
  24 GLY   (  24-)  A    High
  25 GLN   (  25-)  A    High
  26 TRP   (  26-)  A    High
  27 ARG   (  27-)  A    High
And so on for a total of 268 lines.

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.

  11 GLU   (  11-)  A    0.50

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: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

 277 ARG   (  54-)  B

Warning: Tyrosine convention problem

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

 282 TYR   (  59-)  B

Warning: Phenylalanine convention problem

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

  28 PHE   (  28-)  A
  53 PHE   (  53-)  A
 108 PHE   ( 108-)  A
 162 PHE   ( 162-)  A
 165 PHE   ( 165-)  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.

  30 ASP   (  30-)  A
 104 ASP   ( 104-)  A
 144 ASP   ( 144-)  A
 156 ASP   ( 156-)  A
 176 ASP   ( 176-)  A
 196 ASP   ( 196-)  A
 255 ASP   (  32-)  B
 281 ASP   (  58-)  B

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.

  36 GLU   (  36-)  A
  60 GLU   (  60-)  A
  68 GLU   (  68-)  A
 127 GLU   ( 127-)  A
 134 GLU   ( 134-)  A
 174 GLU   ( 174-)  A
 208 GLU   ( 208-)  A
 211 GLU   ( 211-)  A
 239 GLU   (  16-)  B
 247 GLU   (  24-)  B

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

 |  0.997767  0.000030  0.000002|
 |  0.000030  0.997579 -0.000080|
 |  0.000002 -0.000080  0.997734|
Proposed new scale matrix

 |  0.011522  0.006653  0.000000|
 |  0.000000  0.013306  0.000001|
 |  0.000000  0.000000  0.005182|
With corresponding cell

    A    =  86.794  B   =  86.782  C    = 192.985
    Alpha=  90.005  Beta=  89.999  Gamma= 120.003

The CRYST1 cell dimensions

    A    =  86.989  B   =  86.989  C    = 193.434
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 51.120
(Under-)estimated Z-score: 5.269

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.

  30 ASP   (  30-)  A
  36 GLU   (  36-)  A
  60 GLU   (  60-)  A
  68 GLU   (  68-)  A
 104 ASP   ( 104-)  A
 127 GLU   ( 127-)  A
 134 GLU   ( 134-)  A
 144 ASP   ( 144-)  A
 156 ASP   ( 156-)  A
 174 GLU   ( 174-)  A
 176 ASP   ( 176-)  A
 196 ASP   ( 196-)  A
 208 GLU   ( 208-)  A
 211 GLU   ( 211-)  A
 239 GLU   (  16-)  B
 247 GLU   (  24-)  B
 255 ASP   (  32-)  B
 277 ARG   (  54-)  B
 281 ASP   (  58-)  B

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.

 287 GLU   (  64-)  B    -2.2
  10 PRO   (  10-)  A    -2.1
 151 GLN   ( 151-)  A    -2.1
 154 VAL   ( 154-)  A    -2.0
  35 GLU   (  35-)  A    -2.0
 155 ASP   ( 155-)  A    -2.0
 241 GLU   (  18-)  B    -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.

  44 ALA   (  44-)  A  PRO omega poor
  71 LYS   (  71-)  A  Poor phi/psi
  88 ASN   (  88-)  A  Poor phi/psi
 152 CYS   ( 152-)  A  omega poor
 156 ASP   ( 156-)  A  Poor phi/psi
 169 ASP   ( 169-)  A  Poor phi/psi
 208 GLU   ( 208-)  A  omega poor
 213 ARG   ( 213-)  A  Poor phi/psi
 269 ALA   (  46-)  B  Poor phi/psi
 287 GLU   (  64-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.524

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!

   7 GLU   (   7-)  A      0
  20 LEU   (  20-)  A      0
  23 ALA   (  23-)  A      0
  25 GLN   (  25-)  A      0
  26 TRP   (  26-)  A      0
  34 LEU   (  34-)  A      0
  44 ALA   (  44-)  A      0
  47 CYS   (  47-)  A      0
  71 LYS   (  71-)  A      0
  84 GLN   (  84-)  A      0
  88 ASN   (  88-)  A      0
  89 SER   (  89-)  A      0
 102 ASN   ( 102-)  A      0
 110 ASP   ( 110-)  A      0
 151 GLN   ( 151-)  A      0
 153 ARG   ( 153-)  A      0
 154 VAL   ( 154-)  A      0
 156 ASP   ( 156-)  A      0
 157 LYS   ( 157-)  A      0
 158 VAL   ( 158-)  A      0
 166 ASN   ( 166-)  A      0
 168 VAL   ( 168-)  A      0
 179 MET   ( 179-)  A      0
 181 PHE   ( 181-)  A      0
 185 HIS   ( 185-)  A      0
And so on for a total of 84 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 255 ASP   (  32-)  B   1.55   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].

  10 PRO   (  10-)  A  -129.0 half-chair C-delta/C-gamma (-126 degrees)
  45 PRO   (  45-)  A    44.4 envelop C-delta (36 degrees)
 260 PRO   (  37-)  B  -114.9 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 298 GLY   (  75-)  B      C    <->   300 GVE   (  76-)  B      N    1.43    1.27  INTRA BL
  90 CYS   (  90-)  A      SG   <->   300 GVE   (  76-)  B      CB   1.19    1.81  INTRA BL
 298 GLY   (  75-)  B      CA   <->   300 GVE   (  76-)  B      N    0.69    2.41  INTRA BL
  90 CYS   (  90-)  A      CB   <->   300 GVE   (  76-)  B      CB   0.66    2.54  INTRA BL
 298 GLY   (  75-)  B      O    <->   300 GVE   (  76-)  B      N    0.52    2.18  INTRA BL
  92 THR   (  92-)  A      OG1  <->   143 HIS   ( 143-)  A      ND1  0.17    2.53  INTRA BL
  90 CYS   (  90-)  A      SG   <->   300 GVE   (  76-)  B      CA   0.17    2.33  INTRA BL
 155 ASP   ( 155-)  A      O    <->   157 LYS   ( 157-)  A      N    0.13    2.57  INTRA BF
  36 GLU   (  36-)  A      O    <->    40 GLY   (  40-)  A      N    0.08    2.62  INTRA BF
 228 VAL   (   5-)  B      O    <->   236 ILE   (  13-)  B      N    0.06    2.64  INTRA BL
 137 GLU   ( 137-)  A      O    <->   141 ALA   ( 141-)  A      N    0.06    2.64  INTRA BL
 122 GLU   ( 122-)  A      O    <->   129 ARG   ( 129-)  A      NH2  0.06    2.64  INTRA BL
   4 LYS   (   4-)  A      O    <->   143 HIS   ( 143-)  A      NE2  0.06    2.64  INTRA BL
 224 MET   (   1-)  B      O    <->   240 VAL   (  17-)  B      N    0.04    2.66  INTRA BF
  30 ASP   (  30-)  A      OD2  <->   295 ARG   (  72-)  B      NH2  0.02    2.68  INTRA BL
 212 VAL   ( 212-)  A      O    <->   214 PHE   ( 214-)  A      N    0.01    2.69  INTRA BL
  24 GLY   (  24-)  A      O    <->    27 ARG   (  27-)  A      NH2  0.01    2.69  INTRA BL
 298 GLY   (  75-)  B      O    <->   300 GVE   (  76-)  B      CA   0.01    2.79  INTRA BL
  84 GLN   (  84-)  A      N    <->   177 GLY   ( 177-)  A      O    0.01    2.69  INTRA BL
 227 PHE   (   4-)  B      O    <->   290 LEU   (  67-)  B      N    0.01    2.69  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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 178 ARG   ( 178-)  A      -6.64
 152 CYS   ( 152-)  A      -5.74
  19 ARG   (  19-)  A      -5.42
 151 GLN   ( 151-)  A      -5.07

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.

 151 GLN   ( 151-)  A       154 - VAL    154- ( A)         -4.90

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

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.

 157 LYS   ( 157-)  A   -2.74

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

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.

 161 HIS   ( 161-)  A
 171 HIS   ( 171-)  A
 225 GLN   (   2-)  B

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.

   7 GLU   (   7-)  A      N
  19 ARG   (  19-)  A      NE
  26 TRP   (  26-)  A      N
  33 GLY   (  33-)  A      N
  35 GLU   (  35-)  A      N
  56 THR   (  56-)  A      OG1
  81 PHE   (  81-)  A      N
  86 ILE   (  86-)  A      N
  90 CYS   (  90-)  A      N
  91 GLY   (  91-)  A      N
 137 GLU   ( 137-)  A      N
 149 GLU   ( 149-)  A      N
 151 GLN   ( 151-)  A      N
 153 ARG   ( 153-)  A      NH1
 155 ASP   ( 155-)  A      N
 156 ASP   ( 156-)  A      N
 158 VAL   ( 158-)  A      N
 159 ASN   ( 159-)  A      N
 160 PHE   ( 160-)  A      N
 162 PHE   ( 162-)  A      N
 166 ASN   ( 166-)  A      ND2
 167 ASN   ( 167-)  A      N
 181 PHE   ( 181-)  A      N
 192 THR   ( 192-)  A      N
 193 LEU   ( 193-)  A      N
 223 ALA   ( 223-)  A      N
 247 GLU   (  24-)  B      N
 259 ILE   (  36-)  B      N
 270 GLY   (  47-)  B      N
 288 SER   (  65-)  B      N
 296 LEU   (  73-)  B      N

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.

  61 ASN   (  61-)  A      OD1
 161 HIS   ( 161-)  A      ND1
 184 ASN   ( 184-)  A      OD1
 208 GLU   ( 208-)  A      OE2
 264 GLN   (  41-)  B      OE1
 291 HIS   (  68-)  B      ND1

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.

  68 GLU   (  68-)  A   H-bonding suggests Gln
  74 GLU   (  74-)  A   H-bonding suggests Gln
 155 ASP   ( 155-)  A   H-bonding suggests Asn
 196 ASP   ( 196-)  A   H-bonding suggests Asn
 208 GLU   ( 208-)  A   H-bonding suggests Gln
 255 ASP   (  32-)  B   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 :   0.011
  2nd generation packing quality :  -1.221
  Ramachandran plot appearance   :  -0.708
  chi-1/chi-2 rotamer normality  :  -2.524
  Backbone conformation          :   0.539

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.299 (tight)
  Bond angles                    :   0.474 (tight)
  Omega angle restraints         :   0.811
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.365
  B-factor distribution          :   0.406
  Inside/Outside distribution    :   0.913

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 : 2.83


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.299 (tight)
  Bond angles                    :   0.474 (tight)
  Omega angle restraints         :   0.811
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.365
  B-factor distribution          :   0.406
  Inside/Outside distribution    :   0.913
==============

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.