WHAT IF Check report

This file was created 2011-12-16 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 pdb1inf.ent

Checks that need to be done early-on in validation

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 394  CA   ( 501-)  A  -  CA

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 394  CA   ( 501-)  A  -  CA       4

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.

 395 ST4   ( 471-)  A  -

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

Error: Weights outside the 0.0 -- 1.0 range

The atoms listed in the table below have their weight/occupancy outside the 0.0-1.0 range. This problem is not hampering proper WHAT IF functioning, but it is indicative of problems with the X-ray refinement.

 396 HOH   ( 582 )  A      O   1.27
 396 HOH   ( 532 )  A      O   1.23
 396 HOH   ( 535 )  A      O   1.20
 396 HOH   ( 524 )  A      O   1.18
 396 HOH   ( 556 )  A      O   1.18
 396 HOH   ( 596 )  A      O   1.16
 396 HOH   ( 525 )  A      O   1.15
 396 HOH   ( 542 )  A      O   1.15
 396 HOH   ( 567 )  A      O   1.14
 396 HOH   ( 534 )  A      O   1.14
 396 HOH   ( 552 )  A      O   1.12
 396 HOH   ( 611 )  A      O   1.12
 396 HOH   ( 577 )  A      O   1.12
 396 HOH   ( 587 )  A      O   1.12
 396 HOH   ( 583 )  A      O   1.11
 396 HOH   ( 530 )  A      O   1.11
 396 HOH   ( 619 )  A      O   1.11
 396 HOH   ( 507 )  A      O   1.11
 396 HOH   ( 575 )  A      O   1.09
 396 HOH   ( 624 )  A      O   1.09
 396 HOH   ( 563 )  A      O   1.09
 396 HOH   ( 519 )  A      O   1.09
 396 HOH   ( 581 )  A      O   1.08
 396 HOH   ( 613 )  A      O   1.08
 396 HOH   ( 547 )  A      O   1.08
And so on for a total of 51 lines.

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 11.36

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.

  53 HIS   ( 129-)  A      CG   ND1  CE1 109.80    4.2
 135 THR   ( 211-)  A      N    CA   C   122.64    4.1
 214 ALA   ( 290-)  A      N    CA   C    97.13   -5.0
 217 ASP   ( 293-)  A      N    CA   C    97.25   -5.0
 220 TYR   ( 296-)  A      N    CA   C   122.81    4.1

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.

  26 ARG   ( 102-)  A    5.95
 135 THR   ( 211-)  A    5.57
 214 ALA   ( 290-)  A    5.25
 217 ASP   ( 293-)  A    4.75
 354 VAL   ( 430-)  A    4.70
 139 HIS   ( 215-)  A    4.64
 195 VAL   ( 271-)  A    4.44
 220 TYR   ( 296-)  A    4.42
 203 CYS   ( 279-)  A    4.05

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.770

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  25 HIS   ( 101-)  A      CB   4.01
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.961

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.

 361 THR   ( 437-)  A    -3.1
 252 PRO   ( 328-)  A    -3.0
  40 ARG   ( 116-)  A    -2.7
  59 TYR   ( 135-)  A    -2.6
 182 GLU   ( 258-)  A    -2.6
 111 GLU   ( 187-)  A    -2.6
 130 TYR   ( 206-)  A    -2.5
 198 THR   ( 274-)  A    -2.5
 180 ILE   ( 256-)  A    -2.5
 298 ARG   ( 374-)  A    -2.4
 245 THR   ( 321-)  A    -2.4
 165 THR   ( 241-)  A    -2.4
 343 LYS   ( 419-)  A    -2.4
 194 ARG   ( 270-)  A    -2.4
  39 ILE   ( 115-)  A    -2.3
   3 GLU   (  79-)  A    -2.2
 197 HIS   ( 273-)  A    -2.2
 162 LEU   ( 238-)  A    -2.2
 243 THR   ( 319-)  A    -2.2
  56 LEU   ( 132-)  A    -2.2
 239 ARG   ( 315-)  A    -2.2
 277 VAL   ( 353-)  A    -2.1
 331 GLY   ( 407-)  A    -2.1
 305 VAL   ( 381-)  A    -2.1
   8 ARG   (  84-)  A    -2.1
 179 LYS   ( 255-)  A    -2.1
 276 PHE   ( 352-)  A    -2.1
 195 VAL   ( 271-)  A    -2.0
 148 THR   ( 224-)  A    -2.0
 364 SER   ( 440-)  A    -2.0
  58 HIS   ( 134-)  A    -2.0
  21 LEU   (  97-)  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.

  14 SER   (  90-)  A  Poor phi/psi
  62 GLN   ( 138-)  A  PRO omega poor
  98 MET   ( 174-)  A  Poor phi/psi
 150 GLU   ( 226-)  A  Poor phi/psi
 182 GLU   ( 258-)  A  Poor phi/psi
 187 LYS   ( 263-)  A  Poor phi/psi
 249 THR   ( 325-)  A  PRO omega poor
 268 TRP   ( 344-)  A  Poor phi/psi
 308 ASP   ( 384-)  A  Poor phi/psi
 332 TRP   ( 408-)  A  Poor phi/psi
 374 GLY   ( 450-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.671

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.671

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!

   4 TRP   (  80-)  A      0
   8 ARG   (  84-)  A      0
  12 GLN   (  88-)  A      0
  14 SER   (  90-)  A      0
  17 GLN   (  93-)  A      0
  18 LYS   (  94-)  A      0
  19 ALA   (  95-)  A      0
  20 LEU   (  96-)  A      0
  25 HIS   ( 101-)  A      0
  27 PHE   ( 103-)  A      0
  34 SER   ( 110-)  A      0
  39 ILE   ( 115-)  A      0
  40 ARG   ( 116-)  A      0
  41 GLU   ( 117-)  A      0
  42 PRO   ( 118-)  A      0
  49 LYS   ( 125-)  A      0
  58 HIS   ( 134-)  A      0
  59 TYR   ( 135-)  A      0
  60 ALA   ( 136-)  A      0
  62 GLN   ( 138-)  A      0
  63 PRO   ( 139-)  A      0
  66 TYR   ( 142-)  A      0
  67 TYR   ( 143-)  A      0
  68 ASN   ( 144-)  A      0
  73 ASP   ( 149-)  A      0
And so on for a total of 208 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.877

Warning: Backbone oxygen evaluation

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

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

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

 270 GLY   ( 346-)  A   1.99   16

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]

  89 PRO   ( 165-)  A    0.48 HIGH
 191 PRO   ( 267-)  A    0.45 HIGH
 260 PRO   ( 336-)  A    0.46 HIGH

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.

 163 MET   ( 239-)  A      SD  <->  201 CYS   ( 277-)  A      SG     0.32    3.13  INTRA BL
  52 ARG   ( 128-)  A      NH1 <->   82 SER   ( 158-)  A      OG     0.27    2.43  INTRA
   8 ARG   (  84-)  A      O   <->  280 ARG   ( 356-)  A      NH1    0.23    2.47  INTRA
   7 PRO   (  83-)  A      O   <->  391 NAG   ( 467-)  A      N2     0.22    2.48  INTRA
 216 ARG   ( 292-)  A      NH2 <->  333 TYR   ( 409-)  A      OH     0.21    2.49  INTRA
 223 LYS   ( 299-)  A      NZ  <->  261 CYS   ( 337-)  A      O      0.17    2.53  INTRA BL
 106 CYS   ( 182-)  A      SG  <->  155 CYS   ( 231-)  A      SG     0.16    3.29  INTRA
 194 ARG   ( 270-)  A      NH2 <->  217 ASP   ( 293-)  A      OD2    0.16    2.54  INTRA BL
  26 ARG   ( 102-)  A      N   <->   27 PHE   ( 103-)  A      N      0.15    2.45  INTRA BL
 139 HIS   ( 215-)  A      CD2 <->  396 HOH   ( 546 )  A      O      0.15    2.65  INTRA BL
 276 PHE   ( 352-)  A      CZ  <->  278 HIS   ( 354-)  A      NE2    0.14    2.96  INTRA BL
  40 ARG   ( 116-)  A      NH2 <->  395 ST4   ( 471-)  A      O1'    0.13    2.57  INTRA
 209 LYS   ( 285-)  A      CE  <->  230 ASN   ( 306-)  A      ND2    0.13    2.97  INTRA
  97 HIS   ( 173-)  A      CE1 <->  114 TYR   ( 190-)  A      CE1    0.12    3.08  INTRA BL
 172 ILE   ( 248-)  A      CG2 <->  174 LYS   ( 250-)  A      NZ     0.11    2.99  INTRA
 209 LYS   ( 285-)  A      NZ  <->  230 ASN   ( 306-)  A      ND2    0.11    2.74  INTRA
  71 ARG   ( 147-)  A      NH2 <->  356 ASP   ( 432-)  A      OD2    0.11    2.59  INTRA
   8 ARG   (  84-)  A      NH2 <->  341 ASP   ( 417-)  A      O      0.11    2.59  INTRA
 254 ASP   ( 330-)  A      OD1 <->  291 ARG   ( 367-)  A      NH2    0.10    2.60  INTRA
  11 CYS   (  87-)  A      SG  <->  344 CYS   ( 420-)  A      C      0.10    3.30  INTRA BL
 132 GLU   ( 208-)  A      O   <->  396 HOH   ( 552 )  A      O      0.09    2.31  INTRA
 206 ALA   ( 282-)  A      N   <->  207 SER   ( 283-)  A      N      0.09    2.51  INTRA BL
 139 HIS   ( 215-)  A      NE2 <->  396 HOH   ( 554 )  A      O      0.09    2.61  INTRA
 145 ILE   ( 221-)  A      O   <->  147 ARG   ( 223-)  A      NH1    0.09    2.61  INTRA BL
 275 GLY   ( 351-)  A      N   <->  334 SER   ( 410-)  A      OG     0.08    2.62  INTRA BL
And so on for a total of 70 lines.

Packing, accessibility and threading

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.

  12 GLN   (  88-)  A      -7.33
  49 LYS   ( 125-)  A      -6.63
  71 ARG   ( 147-)  A      -6.22
  66 TYR   ( 142-)  A      -6.03
  74 ARG   ( 150-)  A      -5.94
 298 ARG   ( 374-)  A      -5.70
 110 ARG   ( 186-)  A      -5.64
  33 ASN   ( 109-)  A      -5.53
  26 ARG   ( 102-)  A      -5.52
  30 ILE   ( 106-)  A      -5.40
  67 TYR   ( 143-)  A      -5.35
 181 ARG   ( 257-)  A      -5.29
 379 LEU   ( 455-)  A      -5.27
 343 LYS   ( 419-)  A      -5.09
  59 TYR   ( 135-)  A      -5.08

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.

  25 HIS   ( 101-)  A        27 - PHE    103- ( A)         -4.54
  66 TYR   ( 142-)  A        68 - ASN    144- ( A)         -5.14

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.

  12 GLN   (  88-)  A   -2.69

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.

 396 HOH   ( 527 )  A      O     58.59  -21.15   73.40

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.

 396 HOH   ( 503 )  A      O
 396 HOH   ( 556 )  A      O
Bound group on Asn; dont flip  208 ASN  ( 284-) A
Bound to:  391 NAG  ( 467-) A

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.

  12 GLN   (  88-)  A
  17 GLN   (  93-)  A
  58 HIS   ( 134-)  A
  93 ASN   ( 169-)  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.

  40 ARG   ( 116-)  A      NH1
  44 VAL   ( 120-)  A      N
  51 CYS   ( 127-)  A      N
  60 ALA   ( 136-)  A      N
  74 ARG   ( 150-)  A      NE
  75 ASN   ( 151-)  A      N
  78 ARG   ( 154-)  A      NE
  90 THR   ( 166-)  A      OG1
  92 GLU   ( 168-)  A      N
 102 SER   ( 178-)  A      N
 119 GLY   ( 195-)  A      N
 134 TYR   ( 210-)  A      N
 151 SER   ( 227-)  A      N
 183 GLY   ( 259-)  A      N
 194 ARG   ( 270-)  A      NH1
 197 HIS   ( 273-)  A      N
 218 ASN   ( 294-)  A      N
 221 THR   ( 297-)  A      N
 249 THR   ( 325-)  A      N
 253 ASP   ( 329-)  A      N
 273 LYS   ( 349-)  A      N
 276 PHE   ( 352-)  A      N
 290 SER   ( 366-)  A      OG
 299 MET   ( 375-)  A      N
 322 GLY   ( 398-)  A      N
 336 GLY   ( 412-)  A      N
 354 VAL   ( 430-)  A      N
 360 ASP   ( 436-)  A      N
 363 HIS   ( 439-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 197 HIS   ( 273-)  A      NE2
 199 GLU   ( 275-)  A      OE2
 208 ASN   ( 284-)  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+.

 393  CA   ( 500-)  A     1.90   0.95 Is perhaps MG
 394  CA   ( 501-)  A     1.26   1.17 Scores about as good as NA *S

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.

  29 GLU   ( 105-)  A   H-bonding suggests Gln; but Alt-Rotamer
 108 ASP   ( 184-)  A   H-bonding suggests Asn; but Alt-Rotamer
 136 ASP   ( 212-)  A   H-bonding suggests Asn
 150 GLU   ( 226-)  A   H-bonding suggests Gln
 166 ASP   ( 242-)  A   H-bonding suggests Asn; but Alt-Rotamer
 314 ASP   ( 390-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.429
  2nd generation packing quality :  -1.725
  Ramachandran plot appearance   :  -2.961
  chi-1/chi-2 rotamer normality  :  -3.671 (poor)
  Backbone conformation          :  -0.999

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.505 (tight)
  Bond angles                    :   0.859
  Omega angle restraints         :   0.341 (tight)
  Side chain planarity           :   0.521 (tight)
  Improper dihedral distribution :   1.062
  Inside/Outside distribution    :   1.080

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.505 (tight)
  Bond angles                    :   0.859
  Omega angle restraints         :   0.341 (tight)
  Side chain planarity           :   0.521 (tight)
  Improper dihedral distribution :   1.062
  Inside/Outside distribution    :   1.080
==============

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.