WHAT IF Check report

This file was created 2013-03-18 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 pdb3w6i.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.136
CA-only RMS fit for the two chains : 0.020

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.

 514 FLB   ( 301-)  A  -
 517 FLB   ( 301-)  E  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

  63 HIS   (  67-)  A  -   ND1 bound to  514 FLB   ( 301-)  A  -   C1
 319 HIS   (  67-)  E  -   ND1 bound to  517 FLB   ( 301-)  E  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  41 LYS   (  45-)  A  -   CE
  41 LYS   (  45-)  A  -   NZ
  69 ASN   (  73-)  A  -   OD1
  69 ASN   (  73-)  A  -   ND2
  76 LYS   (  80-)  A  -   CE
  76 LYS   (  80-)  A  -   NZ
  98 GLU   ( 102-)  A  -   CG
  98 GLU   ( 102-)  A  -   CD
  98 GLU   ( 102-)  A  -   OE1
  98 GLU   ( 102-)  A  -   OE2
 161 GLN   ( 165-)  A  -   CG
 161 GLN   ( 165-)  A  -   CD
 161 GLN   ( 165-)  A  -   OE1
 161 GLN   ( 165-)  A  -   NE2
 164 LYS   ( 168-)  A  -   CD
 164 LYS   ( 168-)  A  -   CE
 164 LYS   ( 168-)  A  -   NZ
 168 LYS   ( 172-)  A  -   CD
 168 LYS   ( 172-)  A  -   CE
 168 LYS   ( 172-)  A  -   NZ
 209 LYS   ( 213-)  A  -   CG
 209 LYS   ( 213-)  A  -   CD
 209 LYS   ( 213-)  A  -   CE
 209 LYS   ( 213-)  A  -   NZ
 271 LEU   (  19-)  E  -   CG
And so on for a total of 59 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: E

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: E

Nomenclature related problems

Warning: Phenylalanine convention problem

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

  87 PHE   (  91-)  A
 343 PHE   (  91-)  E

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.

  70 ASP   (  74-)  A
 326 ASP   (  74-)  E

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.

  54 GLU   (  58-)  A
 217 GLU   ( 221-)  A
 310 GLU   (  58-)  E
 473 GLU   ( 221-)  E

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.

  63 HIS   (  67-)  A      CB   CG   ND1 127.77    4.1
 402 VAL   ( 150-)  E      C    CA   CB  101.52   -4.5

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.

  54 GLU   (  58-)  A
  70 ASP   (  74-)  A
 217 GLU   ( 221-)  A
 310 GLU   (  58-)  E
 326 ASP   (  74-)  E
 473 GLU   ( 221-)  E

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 402 VAL   ( 150-)  E      CB     7.1   -23.70   -32.96
The average deviation= 0.447

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.

  79 PRO   (  83-)  A    -2.3
 335 PRO   (  83-)  E    -2.3
 109 LYS   ( 113-)  A    -2.2
  15 LEU   (  19-)  A    -2.2
 271 LEU   (  19-)  E    -2.2
 365 LYS   ( 113-)  E    -2.1
  90 HIS   (  94-)  A    -2.0
 346 HIS   (  94-)  E    -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.

  25 SER   (  29-)  A  PRO omega poor
  61 SER   (  65-)  A  Poor phi/psi
  87 PHE   (  91-)  A  Poor phi/psi
 106 ASP   ( 110-)  A  Poor phi/psi
 174 ASN   ( 178-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 199 LEU   ( 203-)  A  Poor phi/psi
 281 SER   (  29-)  E  PRO omega poor
 317 SER   (  65-)  E  Poor phi/psi
 343 PHE   (  91-)  E  Poor phi/psi
 362 ASP   ( 110-)  E  Poor phi/psi
 430 ASN   ( 178-)  E  Poor phi/psi
 453 PRO   ( 201-)  E  PRO omega poor
 455 LEU   ( 203-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.793

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 TYR   (   7-)  A      0
  12 TRP   (  16-)  A      0
  15 LEU   (  19-)  A      0
  23 ASN   (  27-)  A      0
  24 GLN   (  28-)  A      0
  25 SER   (  29-)  A      0
  53 LYS   (  57-)  A      0
  54 GLU   (  58-)  A      0
  58 VAL   (  62-)  A      0
  60 HIS   (  64-)  A      0
  61 SER   (  65-)  A      0
  68 ASP   (  72-)  A      0
  69 ASN   (  73-)  A      0
  71 ASN   (  75-)  A      0
  73 SER   (  77-)  A      0
  76 LYS   (  80-)  A      0
  79 PRO   (  83-)  A      0
  80 PHE   (  84-)  A      0
  87 PHE   (  91-)  A      0
  88 GLN   (  92-)  A      0
  90 HIS   (  94-)  A      0
  96 THR   ( 100-)  A      0
  97 ASN   ( 101-)  A      0
  99 HIS   ( 103-)  A      0
 105 VAL   ( 109-)  A      0
And so on for a total of 242 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].

  26 PRO   (  30-)  A    46.6 half-chair C-delta/C-gamma (54 degrees)
  79 PRO   (  83-)  A    42.2 envelop C-delta (36 degrees)
 197 PRO   ( 201-)  A   103.0 envelop C-beta (108 degrees)
 282 PRO   (  30-)  E    46.5 half-chair C-delta/C-gamma (54 degrees)
 335 PRO   (  83-)  E    42.3 envelop C-delta (36 degrees)
 453 PRO   ( 201-)  E   103.0 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 319 HIS   (  67-)  E      ND1 <->  517 FLB   ( 301-)  E      C1     1.24    1.46  INTRA BL
 319 HIS   (  67-)  E      CE1 <->  517 FLB   ( 301-)  E      C1     0.71    2.49  INTRA BL
 319 HIS   (  67-)  E      CG  <->  517 FLB   ( 301-)  E      C1     0.70    2.50  INTRA BL
 450 LEU   ( 198-)  E      CD2 <->  517 FLB   ( 301-)  E      F6     0.25    2.95  INTRA BL
 387 ALA   ( 135-)  E      CB  <->  517 FLB   ( 301-)  E      F2     0.21    2.99  INTRA BL
 109 LYS   ( 113-)  A      NZ  <->  518 HOH   ( 431 )  A      O      0.17    2.53  INTRA
 353 ASN   ( 101-)  E      ND2 <->  472 SER   ( 220-)  E      CB     0.14    2.96  INTRA
  97 ASN   ( 101-)  A      ND2 <->  216 SER   ( 220-)  A      CB     0.13    2.97  INTRA
 367 SER   ( 115-)  E      OG  <->  402 VAL   ( 150-)  E      CG2    0.12    2.68  INTRA
 155 LYS   ( 159-)  A      NZ  <->  173 THR   ( 177-)  A      O      0.09    2.61  INTRA
 411 LYS   ( 159-)  E      NZ  <->  429 THR   ( 177-)  E      O      0.08    2.62  INTRA BL
 495 HIS   ( 243-)  E      ND1 <->  519 HOH   ( 405 )  E      O      0.07    2.63  INTRA BL
   4 ASP   (   8-)  A      O   <->    8 GLY   (  12-)  A      N      0.07    2.63  INTRA
 260 ASP   (   8-)  E      O   <->  264 GLY   (  12-)  E      N      0.07    2.63  INTRA
  92 HIS   (  96-)  A      CD2 <->  115 HIS   ( 119-)  A      ND1    0.06    3.04  INTRA BL
 348 HIS   (  96-)  E      CD2 <->  371 HIS   ( 119-)  E      ND1    0.06    3.04  INTRA BL
  88 GLN   (  92-)  A      CG  <->   89 PHE   (  93-)  A      N      0.06    2.94  INTRA BL
 344 GLN   (  92-)  E      CG  <->  345 PHE   (  93-)  E      N      0.05    2.95  INTRA BL
 356 GLY   ( 104-)  E      N   <->  366 TYR   ( 114-)  E      O      0.05    2.65  INTRA
  63 HIS   (  67-)  A      CB  <->  514 FLB   ( 301-)  A      C2     0.05    3.15  INTRA
  88 GLN   (  92-)  A      OE1 <->  514 FLB   ( 301-)  A      F1     0.04    2.76  INTRA
 100 GLY   ( 104-)  A      N   <->  110 TYR   ( 114-)  A      O      0.04    2.66  INTRA
 120 ASN   ( 124-)  A      N   <->  136 GLY   ( 140-)  A      O      0.03    2.67  INTRA BL
 376 ASN   ( 124-)  E      N   <->  392 GLY   ( 140-)  E      O      0.03    2.67  INTRA BL
 270 LYS   (  18-)  E      NZ  <->  519 HOH   ( 423 )  E      O      0.03    2.67  INTRA
  26 PRO   (  30-)  A      O   <->  245 GLN   ( 249-)  A      N      0.03    2.67  INTRA BL
 282 PRO   (  30-)  E      O   <->  501 GLN   ( 249-)  E      N      0.02    2.68  INTRA BL
 303 TYR   (  51-)  E      OH  <->  374 HIS   ( 122-)  E      NE2    0.01    2.69  INTRA BL
 103 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.01    2.69  INTRA BL
  47 TYR   (  51-)  A      OH  <->  118 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

 276 ASN   (  24-)  E      -5.35
  20 ASN   (  24-)  A      -5.35

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: E

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.

 297 LYS   (  45-)  E   -2.54

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: E

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  36 HIS   (  40-)  A
  60 HIS   (  64-)  A
 316 HIS   (  64-)  E
 497 ASN   ( 245-)  E
Atom is not a donor   63 HIS  (  67-) A      ND1
Atom is not a donor  319 HIS  (  67-) E      ND1

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.

  10 GLU   (  14-)  A      N
  18 ILE   (  22-)  A      N
  27 VAL   (  31-)  A      N
  51 THR   (  55-)  A      OG1
  61 SER   (  65-)  A      N
  69 ASN   (  73-)  A      N
  70 ASP   (  74-)  A      N
  83 SER   (  87-)  A      OG
  88 GLN   (  92-)  A      NE2
  98 GLU   ( 102-)  A      N
  99 HIS   ( 103-)  A      N
 126 SER   ( 130-)  A      N
 184 SER   ( 188-)  A      N
 196 HIS   ( 200-)  A      N
 200 TYR   ( 204-)  A      N
 241 ASN   ( 245-)  A      N
 252 VAL   ( 256-)  A      N
 256 PHE   ( 260-)  A      N
 266 GLU   (  14-)  E      N
 274 ILE   (  22-)  E      N
 280 GLN   (  28-)  E      N
 283 VAL   (  31-)  E      N
 307 THR   (  55-)  E      OG1
 317 SER   (  65-)  E      N
 325 ASN   (  73-)  E      N
 326 ASP   (  74-)  E      N
 339 SER   (  87-)  E      OG
 344 GLN   (  92-)  E      NE2
 352 THR   ( 100-)  E      N
 354 GLU   ( 102-)  E      N
 355 HIS   ( 103-)  E      N
 382 SER   ( 130-)  E      N
 389 LYS   ( 137-)  E      NZ
 410 GLN   ( 158-)  E      NE2
 440 SER   ( 188-)  E      N
 452 HIS   ( 200-)  E      N
 456 TYR   ( 204-)  E      N
 473 GLU   ( 221-)  E      N
 484 ASN   ( 232-)  E      ND2
 496 ASN   ( 244-)  E      ND2
 498 ARG   ( 246-)  E      NE
 512 PHE   ( 260-)  E      N
Only metal coordination for   90 HIS  (  94-) A      NE2
Only metal coordination for   92 HIS  (  96-) A      NE2
Only metal coordination for  115 HIS  ( 119-) A      ND1
Only metal coordination for  346 HIS  (  94-) E      NE2
Only metal coordination for  348 HIS  (  96-) E      NE2
Only metal coordination for  371 HIS  ( 119-) E      ND1

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.

 102 GLU   ( 106-)  A      OE1
 358 GLU   ( 106-)  E      OE1

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.

 518 HOH   ( 403 )  A      O  1.11  K  4 Ion-B
 519 HOH   ( 407 )  E      O  0.91  K  5

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.

  28 ASP   (  32-)  A   H-bonding suggests Asn
 158 ASP   ( 162-)  A   H-bonding suggests Asn
 284 ASP   (  32-)  E   H-bonding suggests Asn
 414 ASP   ( 162-)  E   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.609
  2nd generation packing quality :  -0.448
  Ramachandran plot appearance   :  -1.719
  chi-1/chi-2 rotamer normality  :  -0.793
  Backbone conformation          :  -1.543

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.197 (tight)
  Bond angles                    :   0.477 (tight)
  Omega angle restraints         :   0.736
  Side chain planarity           :   0.151 (tight)
  Improper dihedral distribution :   0.495
  B-factor distribution          :   0.742
  Inside/Outside distribution    :   0.953

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 : 2.69


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.9
  2nd generation packing quality :   1.1
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :   1.4
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.197 (tight)
  Bond angles                    :   0.477 (tight)
  Omega angle restraints         :   0.736
  Side chain planarity           :   0.151 (tight)
  Improper dihedral distribution :   0.495
  B-factor distribution          :   0.742
  Inside/Outside distribution    :   0.953
==============

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.