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 pdb1q3c.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.

 255 GOL   ( 351-)  A  -
 256 GOL   ( 352-)  A  -
 257 GOL   ( 353-)  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'.

   5 ILE   (   6-)  A      CG1
   5 ILE   (   6-)  A      CG2
   5 ILE   (   6-)  A      CD1
  10 ASP   (  11-)  A      CG
  10 ASP   (  11-)  A      OD1
  10 ASP   (  11-)  A      OD2
  80 GLU   (  81-)  A      CG
  80 GLU   (  81-)  A      CD
  80 GLU   (  81-)  A      OE1
  80 GLU   (  81-)  A      OE2
 181 LYS   ( 185-)  A      CG
 181 LYS   ( 185-)  A      CD
 181 LYS   ( 185-)  A      CE
 181 LYS   ( 185-)  A      NZ
 203 PHE   ( 207-)  A      CG
 203 PHE   ( 207-)  A      CD1
 203 PHE   ( 207-)  A      CD2
 203 PHE   ( 207-)  A      CE1
 203 PHE   ( 207-)  A      CE2
 203 PHE   ( 207-)  A      CZ
 205 TYR   ( 209-)  A      CG
 205 TYR   ( 209-)  A      CD1
 205 TYR   ( 209-)  A      CD2
 205 TYR   ( 209-)  A      CE1
 205 TYR   ( 209-)  A      CE2
 205 TYR   ( 209-)  A      CZ
 205 TYR   ( 209-)  A      OH
 212 LYS   ( 219-)  A      CG
 212 LYS   ( 219-)  A      CD
 212 LYS   ( 219-)  A      CE
 212 LYS   ( 219-)  A      NZ
 239 LYS   ( 246-)  A      CG
 239 LYS   ( 246-)  A      CD
 239 LYS   ( 246-)  A      CE
 239 LYS   ( 246-)  A      NZ

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.

   1 ALA   (   2-)  A    0.30
   2 GLY   (   3-)  A    0.30
   3 PRO   (   4-)  A    0.40
   4 GLU   (   5-)  A    0.40
   5 ILE   (   6-)  A    0.40
   6 ARG   (   7-)  A    0.40
 206 ALA   ( 210-)  A    0.50
 207 THR   ( 211-)  A    0.50
 208 ARG   ( 212-)  A    0.50
 209 GLY   ( 213-)  A    0.50
 210 GLU   ( 217-)  A    0.50
 211 ASN   ( 218-)  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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Geometric checks

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.

 224 HIS   ( 231-)  A      N    CA   C    99.52   -4.2

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.

  16 ILE   (  17-)  A    4.99
  15 ALA   (  16-)  A    4.13
  70 TYR   (  71-)  A    4.07

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.305

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 THR   ( 211-)  A    -3.1
  82 THR   (  86-)  A    -2.9
 109 PRO   ( 113-)  A    -2.7
  76 VAL   (  77-)  A    -2.2
 113 THR   ( 117-)  A    -2.1
 174 VAL   ( 178-)  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.

   5 ILE   (   6-)  A  Poor phi/psi
  45 HIS   (  46-)  A  Poor phi/psi
  60 ASP   (  61-)  A  Poor phi/psi
  68 GLN   (  69-)  A  Poor phi/psi
  82 THR   (  86-)  A  Poor phi/psi
 100 SER   ( 104-)  A  Poor phi/psi
 144 PHE   ( 148-)  A  Poor phi/psi
 206 ALA   ( 210-)  A  Poor phi/psi
 207 THR   ( 211-)  A  Poor phi/psi
 208 ARG   ( 212-)  A  Poor phi/psi
 222 VAL   ( 229-)  A  Poor phi/psi
 224 HIS   ( 231-)  A  Poor phi/psi
 225 ARG   ( 232-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.609

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!

   5 ILE   (   6-)  A      0
  16 ILE   (  17-)  A      0
  17 LYS   (  18-)  A      0
  25 TRP   (  26-)  A      0
  27 ALA   (  28-)  A      0
  35 GLN   (  36-)  A      0
  39 ILE   (  40-)  A      0
  44 THR   (  45-)  A      0
  45 HIS   (  46-)  A      0
  49 ARG   (  50-)  A      0
  51 LYS   (  52-)  A      0
  60 ASP   (  61-)  A      0
  67 ASN   (  68-)  A      0
  68 GLN   (  69-)  A      0
  69 LEU   (  70-)  A      0
  70 TYR   (  71-)  A      0
  78 THR   (  79-)  A      0
  79 GLY   (  80-)  A      0
  80 GLU   (  81-)  A      0
  81 THR   (  85-)  A      0
  82 THR   (  86-)  A      0
  99 TYR   ( 103-)  A      0
 100 SER   ( 104-)  A      0
 101 ALA   ( 105-)  A      0
 104 ILE   ( 108-)  A      0
And so on for a total of 90 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.250

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.

 156 GLN   ( 160-)  A      NE2 <->  258 HOH   ( 419 )  A      O      0.49    2.21  INTRA BF
 119 GLN   ( 123-)  A      O   <->  143 ARG   ( 147-)  A      NH2    0.43    2.27  INTRA BF
 224 HIS   ( 231-)  A      O   <->  226 ASP   ( 233-)  A      N      0.37    2.33  INTRA BF
  81 THR   (  85-)  A      O   <->   83 ARG   (  87-)  A      N      0.30    2.40  INTRA BF
 150 ALA   ( 154-)  A      O   <->  167 ARG   ( 171-)  A      NH1    0.25    2.45  INTRA BF
 205 TYR   ( 209-)  A      O   <->  207 THR   ( 211-)  A      N      0.22    2.48  INTRA BF
  86 ARG   (  90-)  A    A NH1 <->  258 HOH   ( 453 )  A      O      0.22    2.48  INTRA BF
 164 ASN   ( 168-)  A      OD1 <->  167 ARG   ( 171-)  A      NH2    0.22    2.48  INTRA BF
 178 GLY   ( 182-)  A      N   <->  258 HOH   ( 420 )  A      O      0.19    2.51  INTRA BF
 224 HIS   ( 231-)  A      N   <->  243 TYR   ( 255-)  A      CE2    0.18    2.92  INTRA BF
 224 HIS   ( 231-)  A      C   <->  226 ASP   ( 233-)  A      N      0.17    2.73  INTRA BF
 232 ARG   ( 239-)  A      CD  <->  248 CYS   ( 260-)  A      SG     0.17    3.23  INTRA BF
  81 THR   (  85-)  A      C   <->   82 THR   (  86-)  A      CG2    0.16    2.94  INTRA BF
 156 GLN   ( 160-)  A      N   <->  258 HOH   ( 429 )  A      O      0.14    2.56  INTRA BF
   6 ARG   (   7-)  A      NH1 <->  127 ASP   ( 131-)  A      OD1    0.14    2.56  INTRA BF
  81 THR   (  85-)  A      O   <->   82 THR   (  86-)  A      CG2    0.13    2.57  INTRA BF
 144 PHE   ( 148-)  A      O   <->  146 ASN   ( 150-)  A      N      0.12    2.58  INTRA BF
 224 HIS   ( 231-)  A      N   <->  243 TYR   ( 255-)  A      CD2    0.12    2.98  INTRA BF
 233 CYS   ( 240-)  A      SG  <->  245 CYS   ( 257-)  A      SG     0.12    3.33  INTRA BF
 216 ALA   ( 223-)  A      O   <->  219 ARG   ( 226-)  A      NE     0.11    2.59  INTRA BF
 137 GLU   ( 141-)  A      O   <->  141 SER   ( 145-)  A      N      0.10    2.60  INTRA BF
 163 GLY   ( 167-)  A      O   <->  166 LEU   ( 170-)  A      N      0.10    2.60  INTRA BF
 245 CYS   ( 257-)  A      SG  <->  247 GLY   ( 259-)  A      N      0.10    3.20  INTRA BF
 230 CYS   ( 237-)  A      SG  <->  232 ARG   ( 239-)  A      N      0.10    3.20  INTRA BF
 224 HIS   ( 231-)  A      CA  <->  243 TYR   ( 255-)  A      CE2    0.09    3.11  INTRA BF
  81 THR   (  85-)  A      C   <->   83 ARG   (  87-)  A      N      0.09    2.81  INTRA BF
 102 SER   ( 106-)  A      N   <->  258 HOH   ( 414 )  A      O      0.08    2.62  INTRA BL
 186 ASN   ( 190-)  A      ND2 <->  189 GLN   ( 193-)  A      OE1    0.07    2.63  INTRA BF
 144 PHE   ( 148-)  A      C   <->  146 ASN   ( 150-)  A      N      0.07    2.83  INTRA BF
 240 THR   ( 247-)  A      OG1 <->  242 PHE   ( 254-)  A      N      0.06    2.64  INTRA BF
 180 HIS   ( 184-)  A      CE1 <->  250 HIS   ( 262-)  A      O      0.05    2.75  INTRA BF
  13 GLU   (  14-)  A      OE2 <->   46 VAL   (  47-)  A      N      0.05    2.65  INTRA BL
   6 ARG   (   7-)  A      N   <->    7 ARG   (   8-)  A      N      0.04    2.56  INTRA BL
 144 PHE   ( 148-)  A      O   <->  147 ARG   ( 151-)  A      N      0.03    2.67  INTRA BF
  49 ARG   (  50-)  A    A NE  <->  122 GLY   ( 126-)  A      C      0.03    3.07  INTRA BL
 205 TYR   ( 209-)  A      C   <->  207 THR   ( 211-)  A      N      0.03    2.87  INTRA BF
 154 LEU   ( 158-)  A      N   <->  155 ASP   ( 159-)  A      N      0.03    2.57  INTRA BF
 246 PRO   ( 258-)  A      N   <->  247 GLY   ( 259-)  A      N      0.02    2.58  INTRA BF
 164 ASN   ( 168-)  A      C   <->  166 LEU   ( 170-)  A      N      0.02    2.88  INTRA BF
  40 GLY   (  41-)  A      N   <->   41 GLN   (  42-)  A      N      0.02    2.58  INTRA BL
 245 CYS   ( 257-)  A      C   <->  247 GLY   ( 259-)  A      N      0.01    2.89  INTRA BF
  75 VAL   (  76-)  A      N   <->  258 HOH   ( 478 )  A      O      0.01    2.69  INTRA BL
 165 TYR   ( 169-)  A      CE1 <->  166 LEU   ( 170-)  A      CG     0.01    3.19  INTRA BF
 199 GLU   ( 203-)  A      O   <->  203 PHE   ( 207-)  A      N      0.01    2.69  INTRA BF
  78 THR   (  79-)  A      N   <->   93 ASP   (  97-)  A      O      0.01    2.69  INTRA BF
 181 LYS   ( 185-)  A      C   <->  183 LYS   ( 187-)  A      N      0.01    2.89  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.

 208 ARG   ( 212-)  A      -8.30
 232 ARG   ( 239-)  A      -6.56
  69 LEU   (  70-)  A      -6.03
  70 TYR   (  71-)  A      -5.67
 173 GLN   ( 177-)  A      -5.40
 213 HIS   ( 220-)  A      -5.15
 126 LEU   ( 130-)  A      -5.08

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: 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.

 258 HOH   ( 423 )  A      O      9.23   15.91   33.17
 258 HOH   ( 457 )  A      O      9.40   13.35   31.76
 258 HOH   ( 477 )  A      O      7.48   27.79   32.47

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.

 258 HOH   ( 470 )  A      O
 258 HOH   ( 473 )  A      O
Metal-coordinating Histidine residue 180 fixed to   1
Strange metal coordination for HIS 250
Metal-coordinating Histidine residue 250 fixed to   1
Metal-coordinating Histidine residue 213 fixed to   1
Metal-coordinating Histidine residue 195 fixed to   1

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.

   4 GLU   (   5-)  A      N
   6 ARG   (   7-)  A      NH1
   7 ARG   (   8-)  A      N
  50 GLY   (  51-)  A      N
  59 ASN   (  60-)  A      ND2
  69 LEU   (  70-)  A      N
  83 ARG   (  87-)  A      N
  86 ARG   (  90-)  A    A NE
 124 ASP   ( 128-)  A      N
 126 LEU   ( 130-)  A    A N
 146 ASN   ( 150-)  A      N
 164 ASN   ( 168-)  A      N
 212 LYS   ( 219-)  A      N
 217 LEU   ( 224-)  A      N
 221 LYS   ( 228-)  A      N
 224 HIS   ( 231-)  A      N
 243 TYR   ( 255-)  A      N
 249 GLN   ( 261-)  A      NE2
 250 HIS   ( 262-)  A      ND1
Only metal coordination for  250 HIS  ( 262-) A      NE2

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.

 214 HIS   ( 221-)  A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 253  MG   ( 302-)  A   -.-  -.-  Part of ionic cluster
 253  MG   ( 302-)  A     0.58   1.02 Is perhaps CA (Few ligands (4) )
 254  MG   ( 303-)  A   -.-  -.-  Too few ligands (3)

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.

 124 ASP   ( 128-)  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 :  -1.031
  2nd generation packing quality :  -0.447
  Ramachandran plot appearance   :  -3.305 (poor)
  chi-1/chi-2 rotamer normality  :  -1.609
  Backbone conformation          :   0.264

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.670
  Omega angle restraints         :   0.227 (tight)
  Side chain planarity           :   0.212 (tight)
  Improper dihedral distribution :   0.546
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   1.004

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 :  -0.5
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.670
  Omega angle restraints         :   0.227 (tight)
  Side chain planarity           :   0.212 (tight)
  Improper dihedral distribution :   0.546
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   1.004
==============

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.