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 pdb2nnv.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 259 CMH   ( 206-)  A  -         Atom types
 261 M29   ( 301-)  A  -         OK
 263 M29   ( 302-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 111 LYS   ( 112-)  A  -
 168 LYS   ( 170-)  A  -
 185 GLU   ( 187-)  A  -
 210 LYS   ( 213-)  A  -
 211 GLU   ( 214-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 111 LYS   ( 112-)  A  -
 185 GLU   ( 187-)  A  -
 210 LYS   ( 213-)  A  -
 211 GLU   ( 214-)  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: 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.

 168 LYS   ( 170-)  A    0.81

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 113 TYR   ( 114-)  A

Warning: Phenylalanine convention problem

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

  65 PHE   (  66-)  A
 129 PHE   ( 131-)  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.

 163 ASP   ( 165-)  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.

 105 GLU   ( 106-)  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.

  14 HIS   (  15-)  A      ND1  CE1   1.22   -7.4
  61 ASN   (  62-)  A      CG   ND2   1.23   -4.5
 211 GLU   ( 214-)  A      CD   OE2   2.76   79.7

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.

   2 HIS   (   3-)  A      CG   ND1  CE1 110.76    5.2
   8 LYS   (   9-)  A      CB   CG   CD  121.78    4.6
   9 HIS   (  10-)  A      CG   ND1  CE1 109.98    4.4
  14 HIS   (  15-)  A      CB   CG   ND1 128.33    4.5
  14 HIS   (  15-)  A      CG   ND1  CE1 122.26   16.7
  14 HIS   (  15-)  A      ND1  CE1  NE2 101.05   -8.2
  14 HIS   (  15-)  A      CD2  CG   ND1  99.22   -6.9
  33 ASP   (  34-)  A      CA   CB   CG  105.51   -7.1
  35 HIS   (  36-)  A      CA   CB   CG  109.28   -4.5
  35 HIS   (  36-)  A      CG   ND1  CE1 111.21    5.6
  38 LYS   (  39-)  A     -C    N    CA  113.90   -4.3
  42 SER   (  43-)  A     -C    N    CA  113.69   -4.4
  61 ASN   (  62-)  A      CB   CG   ND2 105.53   -7.2
  61 ASN   (  62-)  A      ND2  CG   OD1 129.52    6.9
  66 ASN   (  67-)  A      CA   CB   CG  117.50    4.9
  66 ASN   (  67-)  A      ND2  CG   OD1 118.39   -4.2
  73 GLN   (  74-)  A      CA   C    O   113.63   -4.2
  73 GLN   (  74-)  A      CB   CG   CD  104.43   -4.8
  73 GLN   (  74-)  A      NE2  CD   OE1 129.29    6.7
  75 LYS   (  76-)  A     -O   -C    N   116.01   -4.4
  75 LYS   (  76-)  A      CA   C    O   128.63    4.6
  76 ALA   (  77-)  A     -O   -C    N   114.57   -5.3
  84 ASP   (  85-)  A      CA   CB   CG  119.27    6.7
  95 HIS   (  96-)  A      NE2  CD2  CG  111.49    5.0
  99 LEU   ( 100-)  A     -C    N    CA  129.14    4.1
 100 ASP   ( 101-)  A      CA   CB   CG  119.68    7.1
 106 HIS   ( 107-)  A      NE2  CD2  CG  112.18    5.7
 121 HIS   ( 122-)  A      NE2  CD2  CG  110.76    4.3
 128 ASP   ( 130-)  A      CA   CB   CG  121.83    9.2
 160 ASP   ( 162-)  A      CA   CB   CG  106.91   -5.7
 170 LYS   ( 172-)  A      CB   CG   CD  122.84    5.0
 176 ASN   ( 178-)  A      CA   CB   CG  107.83   -4.8
 188 ASP   ( 190-)  A     -O   -C    N   113.78   -5.8
 188 ASP   ( 190-)  A     -C    N    CA  131.53    5.5
 211 GLU   ( 214-)  A      CG   CD   OE2  47.31  -30.9
 211 GLU   ( 214-)  A      OE2  CD   OE1 166.98   18.4
 218 GLU   ( 221-)  A      CB   CG   CD  122.36    5.7
 218 GLU   ( 221-)  A      CG   CD   OE1 128.48    4.4
 223 PHE   ( 226-)  A      CA   CB   CG  120.06    6.3
 224 ARG   ( 227-)  A      CD   NE   CZ  130.76    5.0
 225 LYS   ( 228-)  A      CG   CD   CE  121.45    4.4
 228 PHE   ( 231-)  A      CA   CB   CG  119.54    5.7
 236 GLU   ( 239-)  A      CA   CB   CG  127.68    6.8
 249 LYS   ( 252-)  A      CB   CG   CD  123.60    5.3
 250 ASN   ( 253-)  A      CA   C    O   112.46   -4.9
 252 GLN   ( 255-)  A      NE2  CD   OE1 118.58   -4.0

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 105 GLU   ( 106-)  A
 163 ASP   ( 165-)  A

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 211 GLU   ( 214-)  A   10.21
  61 ASN   (  62-)  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.

 161 VAL   ( 163-)  A    -2.1
 149 GLY   ( 151-)  A    -2.0
  91 GLN   (  92-)  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.

  28 SER   (  29-)  A  PRO omega poor
  56 LEU   (  57-)  A  omega poor
  74 ASP   (  75-)  A  Poor phi/psi
  91 GLN   (  92-)  A  omega poor
 110 LYS   ( 111-)  A  Poor phi/psi
 176 ASN   ( 178-)  A  Poor phi/psi
 189 TYR   ( 191-)  A  omega poor
 195 SER   ( 197-)  A  omega poor
 199 PRO   ( 201-)  A  PRO omega poor
 201 LEU   ( 203-)  A  Poor phi/psi
 212 PRO   ( 215-)  A  omega poor
 240 ASP   ( 243-)  A  Poor phi/psi
 249 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.111

Warning: Unusual backbone conformations

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

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

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

   3 HIS   (   4-)  A      0
   4 TRP   (   5-)  A      0
   6 TYR   (   7-)  A      0
   9 HIS   (  10-)  A      0
  18 ASP   (  19-)  A      0
  19 PHE   (  20-)  A      0
  23 LYS   (  24-)  A      0
  26 ARG   (  27-)  A      0
  27 GLN   (  28-)  A      0
  28 SER   (  29-)  A      0
  37 ALA   (  38-)  A      0
  49 SER   (  50-)  A      0
  53 ALA   (  54-)  A      0
  61 ASN   (  62-)  A      0
  63 HIS   (  64-)  A      0
  71 ASP   (  72-)  A      0
  72 SER   (  73-)  A      0
  74 ASP   (  75-)  A      0
  75 LYS   (  76-)  A      0
  76 ALA   (  77-)  A      0
  79 LYS   (  80-)  A      0
  82 PRO   (  83-)  A      0
  84 ASP   (  85-)  A      0
  91 GLN   (  92-)  A      0
  98 SER   (  99-)  A      0
And so on for a total of 122 lines.

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].

  20 PRO   (  21-)  A  -114.3 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 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.

 254 LYS   ( 257-)  A      NZ  <->  264 HOH   ( 571 )  A      O      0.21    2.49  INTRA BF
 157 LYS   ( 159-)  A      NZ  <->  264 HOH   ( 607 )  A      O      0.21    2.49  INTRA
 125 LYS   ( 127-)  A      NZ  <->  264 HOH   ( 505 )  A      O      0.20    2.50  INTRA
  35 HIS   (  36-)  A      ND1 <->  264 HOH   ( 650 )  A      O      0.20    2.50  INTRA
  40 ASP   (  41-)  A      OD1 <->   42 SER   (  43-)  A      N      0.20    2.50  INTRA BF
  44 LYS   (  45-)  A      NZ  <->  264 HOH   ( 490 )  A      O      0.17    2.53  INTRA
  75 LYS   (  76-)  A      NZ  <->  264 HOH   ( 637 )  A      O      0.17    2.53  INTRA BF
  25 GLU   (  26-)  A      OE1 <->  264 HOH   ( 636 )  A      O      0.10    2.30  INTRA
 252 GLN   ( 255-)  A      OE1 <->  264 HOH   ( 597 )  A      O      0.10    2.30  INTRA BF
 106 HIS   ( 107-)  A      NE2 <->  192 TYR   ( 194-)  A      OH     0.08    2.62  INTRA BL
  17 LYS   (  18-)  A      NZ  <->  264 HOH   ( 440 )  A      O      0.06    2.64  INTRA
 160 ASP   ( 162-)  A      O   <->  163 ASP   ( 165-)  A      OD1    0.05    2.35  INTRA BF
 249 LYS   ( 252-)  A      NZ  <->  264 HOH   ( 457 )  A      O      0.05    2.65  INTRA BF
 116 GLU   ( 117-)  A      OE2 <->  118 HIS   ( 119-)  A      NE2    0.03    2.67  INTRA BL
 112 LYS   ( 113-)  A      NZ  <->  264 HOH   ( 566 )  A      O      0.03    2.67  INTRA
  88 ARG   (  89-)  A      NH1 <->  264 HOH   ( 467 )  A      O      0.02    2.68  INTRA
   2 HIS   (   3-)  A      ND1 <->  264 HOH   ( 530 )  A      O      0.02    2.68  INTRA
  66 ASN   (  67-)  A      ND2 <->  262 GOL   ( 311-)  A      O2     0.01    2.69  INTRA BL
  23 LYS   (  24-)  A      NZ  <->  264 HOH   ( 508 )  A      O      0.01    2.69  INTRA
  50 TYR   (  51-)  A      OH  <->  121 HIS   ( 122-)  A      NE2    0.01    2.69  INTRA BL

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.

   9 HIS   (  10-)  A      -5.96
   3 HIS   (   4-)  A      -5.24
  99 LEU   ( 100-)  A      -5.15
 134 GLN   ( 136-)  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.

 125 LYS   ( 127-)  A   -2.92
  17 LYS   (  18-)  A   -2.61

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.

 264 HOH   ( 438 )  A      O     10.41  -10.92   16.06

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.

   9 HIS   (  10-)  A
 135 GLN   ( 137-)  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.

   4 TRP   (   5-)  A      N
  30 VAL   (  31-)  A      N
  66 ASN   (  67-)  A      ND2
  99 LEU   ( 100-)  A      N
 139 LEU   ( 141-)  A      N
 198 THR   ( 200-)  A      N
 202 LEU   ( 204-)  A      N
 227 ASN   ( 230-)  A      ND2
 241 ASN   ( 244-)  A      ND2
 242 TRP   ( 245-)  A      N
 257 PHE   ( 260-)  A      N
 262 GOL   ( 311-)  A      O2
Only metal coordination for   93 HIS  (  94-) A      NE2
Only metal coordination for   95 HIS  (  96-) A      NE2
Only metal coordination for  118 HIS  ( 119-) A      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 264 HOH   ( 465 )  A      O  0.93  K  4 H2O-B
 264 HOH   ( 537 )  A      O  0.90  K  4
 264 HOH   ( 546 )  A      O  1.11  K  4 Ion-B

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.

 163 ASP   ( 165-)  A   H-bonding suggests Asn; but Alt-Rotamer
 211 GLU   ( 214-)  A   H-bonding suggests Gln

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 :  -0.130
  2nd generation packing quality :   0.567
  Ramachandran plot appearance   :  -0.875
  chi-1/chi-2 rotamer normality  :   0.111
  Backbone conformation          :  -1.024

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.716
  Bond angles                    :   1.296
  Omega angle restraints         :   1.160
  Side chain planarity           :   1.546
  Improper dihedral distribution :   0.986
  B-factor distribution          :   0.888
  Inside/Outside distribution    :   0.952

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 : 1.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.716
  Bond angles                    :   1.296
  Omega angle restraints         :   1.160
  Side chain planarity           :   1.546
  Improper dihedral distribution :   0.986
  B-factor distribution          :   0.888
  Inside/Outside distribution    :   0.952
==============

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.