WHAT IF Check report

This file was created 2012-02-27 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 pdb3nn7.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

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

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

 323 BXA   ( 601-)  A  -         Fragmented

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'.

 128 GLN   ( 128-)  A      CG
 128 GLN   ( 128-)  A      CD
 128 GLN   ( 128-)  A      OE1
 128 GLN   ( 128-)  A      NE2
 158 GLN   ( 158-)  A      CG
 158 GLN   ( 158-)  A      CD
 158 GLN   ( 158-)  A      OE1
 158 GLN   ( 158-)  A      NE2
 182 LYS   ( 182-)  A      CG
 182 LYS   ( 182-)  A      CD
 182 LYS   ( 182-)  A      CE
 182 LYS   ( 182-)  A      NZ
 219 LYS   ( 219-)  A      CG
 219 LYS   ( 219-)  A      CD
 219 LYS   ( 219-)  A      CE
 219 LYS   ( 219-)  A      NZ
 225 GLN   ( 225-)  A      CG
 225 GLN   ( 225-)  A      CD
 225 GLN   ( 225-)  A      OE1
 225 GLN   ( 225-)  A      NE2
 273 GLN   ( 273-)  A      CG
 273 GLN   ( 273-)  A      CD
 273 GLN   ( 273-)  A      OE1
 273 GLN   ( 273-)  A      NE2
 316 LYS   ( 316-)  A      CG
 316 LYS   ( 316-)  A      CD
 316 LYS   ( 316-)  A      CE
 316 LYS   ( 316-)  A      NZ

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

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.808 over 2147 bonds
Average difference in B over a bond : 4.07
RMS difference in B over a bond : 5.49

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

  27 TYR   (  27-)  A
  29 TYR   (  29-)  A
  93 TYR   (  93-)  A
 122 TYR   ( 122-)  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.

  57 ASP   (  57-)  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.

  11 ARG   (  11-)  A      CA   CB   CG  123.20    4.5
  11 ARG   (  11-)  A      CD   NE   CZ  129.60    4.4
  32 ASP   (  32-)  A      CA   CB   CG  116.72    4.1
  35 ARG   (  35-)  A      CD   NE   CZ  129.31    4.2
  74 HIS   (  74-)  A      CA   CB   CG  119.28    5.5
  74 HIS   (  74-)  A      CG   ND1  CE1 112.30    6.7
  74 HIS   (  74-)  A      ND1  CE1  NE2 106.29   -4.2
  88 HIS   (  88-)  A      CG   ND1  CE1 109.63    4.0
 105 HIS   ( 105-)  A      CG   ND1  CE1 109.70    4.1
 111 ASN   ( 111-)  A      CA   CB   CG  116.78    4.2
 114 PHE   ( 114-)  A      CA   CB   CG  118.91    5.1
 138 ASP   ( 138-)  A      CA   CB   CG  119.38    6.8
 142 HIS   ( 142-)  A      CA   CB   CG  118.35    4.6
 142 HIS   ( 142-)  A      CG   ND1  CE1 110.50    4.9
 146 HIS   ( 146-)  A      CG   ND1  CE1 110.35    4.7
 172 PHE   ( 172-)  A     -C    N    CA  114.40   -4.1
 172 PHE   ( 172-)  A      CA   CB   CG  106.72   -7.1
 198 SER   ( 198-)  A     -C    N    CA  113.54   -4.5
 216 HIS   ( 216-)  A      CG   ND1  CE1 110.43    4.8
 233 ASN   ( 233-)  A      CA   CB   CG  107.20   -5.4
 250 HIS   ( 250-)  A      CG   ND1  CE1 109.95    4.3
 260 ARG   ( 260-)  A      CD   NE   CZ  129.47    4.3
 285 ARG   ( 285-)  A      CD   NE   CZ  130.60    4.9
 310 PHE   ( 310-)  A      CA   CB   CG  109.24   -4.6
 313 VAL   ( 313-)  A     -C    N    CA  114.50   -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.

  57 ASP   (  57-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 229 GLY   ( 229-)  A    4.41

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.

 190 GLU   ( 190-)  A   15.05

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.

 107 SER   ( 107-)  A    -2.6
 157 TYR   ( 157-)  A    -2.6
  20 ILE   (  20-)  A    -2.3
   6 THR   (   6-)  A    -2.3
 119 GLN   ( 119-)  A    -2.2
  92 SER   (  92-)  A    -2.1
 132 PRO   ( 132-)  A    -2.1
  25 SER   (  25-)  A    -2.0
 194 THR   ( 194-)  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.

  26 THR   (  26-)  A  Poor phi/psi
  45 LYS   (  45-)  A  Poor phi/psi
  46 TYR   (  46-)  A  Poor phi/psi
  50 LEU   (  50-)  A  PRO omega poor
  60 ASN   (  60-)  A  Poor phi/psi
  67 ASP   (  67-)  A  omega poor
  92 SER   (  92-)  A  Poor phi/psi
 105 HIS   ( 105-)  A  Poor phi/psi
 107 SER   ( 107-)  A  Poor phi/psi
 112 ASN   ( 112-)  A  Poor phi/psi
 118 SER   ( 118-)  A  Poor phi/psi
 130 PHE   ( 130-)  A  omega poor
 132 PRO   ( 132-)  A  omega poor
 152 THR   ( 152-)  A  Poor phi/psi
 157 TYR   ( 157-)  A  Poor phi/psi
 159 ASN   ( 159-)  A  Poor phi/psi
 194 THR   ( 194-)  A  Poor phi/psi
 227 ASN   ( 227-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.022

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 SER   (   5-)  A      0
   9 VAL   (   9-)  A      0
  11 ARG   (  11-)  A      0
  14 LEU   (  14-)  A      0
  24 TYR   (  24-)  A      0
  25 SER   (  25-)  A      0
  26 THR   (  26-)  A      0
  30 LEU   (  30-)  A      0
  34 THR   (  34-)  A      0
  37 ASN   (  37-)  A      0
  44 ALA   (  44-)  A      0
  45 LYS   (  45-)  A      0
  46 TYR   (  46-)  A      0
  49 THR   (  49-)  A      0
  51 PRO   (  51-)  A      0
  53 SER   (  53-)  A      0
  55 TRP   (  55-)  A      0
  60 ASN   (  60-)  A      0
  61 GLN   (  61-)  A      0
  62 PHE   (  62-)  A      0
  63 PHE   (  63-)  A      0
  92 SER   (  92-)  A      0
  96 ASN   (  96-)  A      0
 104 VAL   ( 104-)  A      0
 105 HIS   ( 105-)  A      0
And so on for a total of 121 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  69 PRO   (  69-)  A    0.45 HIGH

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].

 195 PRO   ( 195-)  A  -126.1 half-chair C-delta/C-gamma (-126 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.

 126 ASP   ( 126-)  A      OD1 <->  128 GLN   ( 128-)  A      N      0.20    2.50  INTRA
 257 GLY   ( 257-)  A      N   <->  324 HOH   (1114 )  A      O      0.19    2.51  INTRA
  17 GLN   (  17-)  A      NE2 <->  324 HOH   (1112 )  A      O      0.19    2.51  INTRA
 262 LYS   ( 262-)  A      NZ  <->  302 GLU   ( 302-)  A      OE2    0.18    2.52  INTRA
  37 ASN   (  37-)  A      ND2 <->   97 ASN   (  97-)  A      O      0.18    2.52  INTRA
   8 GLY   (   8-)  A      N   <->   20 ILE   (  20-)  A      O      0.17    2.53  INTRA BL
 186 TRP   ( 186-)  A      N   <->  324 HOH   (1071 )  A      O      0.13    2.57  INTRA
 248 GLY   ( 248-)  A      O   <->  255 VAL   ( 255-)  A      N      0.12    2.58  INTRA BL
 243 LEU   ( 243-)  A      O   <->  247 GLY   ( 247-)  A      N      0.12    2.58  INTRA
  21 ASN   (  21-)  A      O   <->   74 HIS   (  74-)  A      NE2    0.11    2.59  INTRA BL
 215 ASP   ( 215-)  A      O   <->  250 HIS   ( 250-)  A      NE2    0.10    2.60  INTRA
 217 TYR   ( 217-)  A      CE2 <->  220 ARG   ( 220-)  A      NH1    0.10    3.00  INTRA
  14 LEU   (  14-)  A      N   <->  324 HOH   (1004 )  A      O      0.10    2.60  INTRA
  51 PRO   (  51-)  A      O   <->  103 SER   ( 103-)  A      OG     0.09    2.31  INTRA BL
   1 ILE   (   1-)  A      CD1 <->   29 TYR   (  29-)  A      CD2    0.09    3.11  INTRA
 194 THR   ( 194-)  A      OG1 <->  200 ASP   ( 200-)  A      OD2    0.09    2.31  INTRA
 290 GLN   ( 290-)  A      O   <->  294 ASP   ( 294-)  A      N      0.09    2.61  INTRA
 206 SER   ( 206-)  A      O   <->  239 LYS   ( 239-)  A      NZ     0.08    2.62  INTRA
 274 TYR   ( 274-)  A      OH  <->  294 ASP   ( 294-)  A      OD2    0.08    2.32  INTRA
  40 PHE   (  40-)  A      N   <->  100 ILE   ( 100-)  A      O      0.07    2.63  INTRA BL
  30 LEU   (  30-)  A      C   <->   74 HIS   (  74-)  A      CE1    0.07    3.13  INTRA BL
 127 GLY   ( 127-)  A      N   <->  130 PHE   ( 130-)  A      O      0.07    2.63  INTRA
 218 SER   ( 218-)  A      O   <->  324 HOH   (1056 )  A      O      0.06    2.34  INTRA
 239 LYS   ( 239-)  A      NZ  <->  324 HOH   (1034 )  A      O      0.06    2.64  INTRA
 188 ILE   ( 188-)  A      N   <->  203 ARG   ( 203-)  A      O      0.06    2.64  INTRA BL
And so on for a total of 53 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 221 TYR   ( 221-)  A      -6.91
 108 GLN   ( 108-)  A      -5.98
 251 TYR   ( 251-)  A      -5.70
  88 HIS   (  88-)  A      -5.66
 246 GLN   ( 246-)  A      -5.56
 157 TYR   ( 157-)  A      -5.23

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.

 226 ASP   ( 226-)  A       228 - GLY    228- ( A)         -4.21

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.

  44 ALA   (  44-)  A   -2.72
 219 LYS   ( 219-)  A   -2.70
 182 LYS   ( 182-)  A   -2.65
 153 ALA   ( 153-)  A   -2.65

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.

 324 HOH   (1152 )  A      O     49.67   35.70   -6.40

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.

 324 HOH   (1078 )  A      O
 324 HOH   (1140 )  A      O
Metal-coordinating Histidine residue 142 fixed to   1
Metal-coordinating Histidine residue 146 fixed to   1

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.

  31 GLN   (  31-)  A
  33 ASN   (  33-)  A
  60 ASN   (  60-)  A
 216 HIS   ( 216-)  A
 290 GLN   ( 290-)  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 THR   (   4-)  A      OG1
   7 VAL   (   7-)  A      N
  35 ARG   (  35-)  A      N
  49 THR   (  49-)  A      N
  60 ASN   (  60-)  A      ND2
 113 ALA   ( 113-)  A      N
 115 TRP   ( 115-)  A      NE1
 155 LEU   ( 155-)  A      N
 203 ARG   ( 203-)  A      NH2
 204 SER   ( 204-)  A      N
 216 HIS   ( 216-)  A      N
 262 LYS   ( 262-)  A      N
Only metal coordination for  142 HIS  ( 142-) 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.

 143 GLU   ( 143-)  A      OE2
 177 GLU   ( 177-)  A      OE1
 238 ASN   ( 238-)  A      OD1

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+.

 319  CA   ( 501-)  A   -.-  -.-  Part of ionic cluster
 319  CA   ( 501-)  A     0.71   0.94 Scores about as good as NA
 320  CA   ( 502-)  A     0.80   1.03 Scores about as good as NA
 321  CA   ( 503-)  A     0.84   1.09 Scores about as good as NA
 322  CA   ( 504-)  A   -.-  -.-  Part of ionic cluster
 322  CA   ( 504-)  A     0.67   0.90 Scores about as good as NA (Few ligands (4) )

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.

 324 HOH   (1151 )  A      O  1.02  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.

  16 ASP   (  16-)  A   H-bonding suggests Asn
 143 GLU   ( 143-)  A   H-bonding suggests Gln; Ligand-contact
 150 ASP   ( 150-)  A   H-bonding suggests Asn
 294 ASP   ( 294-)  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 :  -0.696
  2nd generation packing quality :  -1.434
  Ramachandran plot appearance   :  -0.973
  chi-1/chi-2 rotamer normality  :  -2.022
  Backbone conformation          :  -0.409

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.289 (tight)
  Bond angles                    :   1.079
  Omega angle restraints         :   0.889
  Side chain planarity           :   1.407
  Improper dihedral distribution :   0.654
  B-factor distribution          :   1.808 (loose)
  Inside/Outside distribution    :   1.020

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.289 (tight)
  Bond angles                    :   1.079
  Omega angle restraints         :   0.889
  Side chain planarity           :   1.407
  Improper dihedral distribution :   0.654
  B-factor distribution          :   1.808 (loose)
  Inside/Outside distribution    :   1.020
==============

WHAT IF
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
    D.Cremer and J.A.Pople,
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    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
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      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.