WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb7nn9.ent

Checks that need to be done early-on in validation

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.

 400 HOH   ( 785 )  A      O      44

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.

 394 MAN   ( 471-)  A  -
 395 MAN   ( 472-)  A  -
 396 MAN   ( 473-)  A  -
 397 MAN   ( 474-)  A  -
 399 MAN   ( 475-)  A  -

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.

 389 NAG   ( 469A)  A  -   O4  bound to  390 NAG   ( 470B)  A  -   C1
 390 NAG   ( 470B)  A  -   O4  bound to  394 MAN   ( 471-)  A  -   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.

   1 ARG   (  82-)  A  -   CB
   1 ARG   (  82-)  A  -   CG
   1 ARG   (  82-)  A  -   CD
   1 ARG   (  82-)  A  -   NE
   1 ARG   (  82-)  A  -   CZ
   1 ARG   (  82-)  A  -   NH1
   1 ARG   (  82-)  A  -   NH2
 129 ARG   ( 209-)  A  -   NE
 129 ARG   ( 209-)  A  -   CZ
 129 ARG   ( 209-)  A  -   NH1
 129 ARG   ( 209-)  A  -   NH2
 181 LYS   ( 261-)  A  -   CE
 181 LYS   ( 261-)  A  -   NZ
 193 LYS   ( 273-)  A  -   CE
 193 LYS   ( 273-)  A  -   NZ
 334 GLU   ( 414-)  A  -   CG
 334 GLU   ( 414-)  A  -   CD
 334 GLU   ( 414-)  A  -   OE1
 334 GLU   ( 414-)  A  -   OE2
 336 GLU   ( 416-)  A  -   CG
 336 GLU   ( 416-)  A  -   CD
 336 GLU   ( 416-)  A  -   OE1
 336 GLU   ( 416-)  A  -   OE2
 355 LYS   ( 435-)  A  -   CG
 355 LYS   ( 435-)  A  -   CD
 355 LYS   ( 435-)  A  -   CE
 355 LYS   ( 435-)  A  -   NZ
 383 LYS   ( 463-)  A  -   CD
 383 LYS   ( 463-)  A  -   CE
 383 LYS   ( 463-)  A  -   NZ

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone 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. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

   1 ARG   (  82-)  A  -   N

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 215 TRP   ( 295-)  A
 239 SER   ( 319-)  A

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.

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   ( 144-)  A      CG   ND1  CE1 109.68    4.1
 124 VAL   ( 204-)  A      N    CA   CB  117.55    4.1
 146 GLN   ( 226-)  A      N    CA   C   122.84    4.2
 219 ASN   ( 299-)  A      N    CA   C    99.69   -4.1
 389 NAG   ( 469-)  A      N2   C2   C1  100.52   -4.3

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.

  24 ALA   ( 105-)  A    4.52
 146 GLN   ( 226-)  A    4.50

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.

 108 THR   ( 188-)  A    -2.7
  37 ARG   ( 118-)  A    -2.5
 283 ARG   ( 364-)  A    -2.5
  57 THR   ( 138-)  A    -2.4
 251 PRO   ( 331-)  A    -2.4
  60 ARG   ( 141-)  A    -2.3
 140 ARG   ( 220-)  A    -2.3
 101 THR   ( 181-)  A    -2.2
 145 THR   ( 225-)  A    -2.2
 224 ARG   ( 304-)  A    -2.1
 271 PHE   ( 352-)  A    -2.1
 203 GLU   ( 283-)  A    -2.1
 233 THR   ( 313-)  A    -2.0
  68 ILE   ( 149-)  A    -2.0
 147 GLU   ( 227-)  A    -2.0
 366 MET   ( 446-)  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.

  38 GLU   ( 119-)  A  Poor phi/psi
  83 SER   ( 164-)  A  Poor phi/psi
 128 ASN   ( 208-)  A  Poor phi/psi
 129 ARG   ( 209-)  A  Poor phi/psi
 140 ARG   ( 220-)  A  Poor phi/psi
 145 THR   ( 225-)  A  Poor phi/psi
 147 GLU   ( 227-)  A  Poor phi/psi
 184 LYS   ( 264-)  A  Poor phi/psi
 211 CYS   ( 291-)  A  Poor phi/psi
 216 GLN   ( 296-)  A  Poor phi/psi
 230 MET   ( 310-)  A  Poor phi/psi
 245 ASN   ( 325-)  A  PRO omega poor
 266 ASN   ( 347-)  A  Poor phi/psi
 300 ASN   ( 381-)  A  Poor phi/psi
 322 SER   ( 404-)  A  Poor phi/psi
 350 ARG   ( 430-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -1.746

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!

   7 THR   (  88-)  A      0
  14 ASN   (  95-)  A      0
  22 ASP   ( 103-)  A      0
  30 ASP   ( 111-)  A      0
  31 SER   ( 112-)  A      0
  32 ASP   ( 113-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  40 TYR   ( 121-)  A      0
  46 ASP   ( 127-)  A      0
  47 GLU   ( 128-)  A      0
  55 GLN   ( 136-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  67 THR   ( 148-)  A      0
  68 ILE   ( 149-)  A      0
  71 ARG   ( 152-)  A      0
  72 SER   ( 153-)  A      0
  80 TRP   ( 161-)  A      0
  82 LEU   ( 163-)  A      0
  83 SER   ( 164-)  A      0
  94 GLU   ( 174-)  A      0
  95 CYS   ( 175-)  A      0
  96 ILE   ( 176-)  A      0
And so on for a total of 220 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 : 3.039

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!

  20 GLY   ( 101-)  A   1.63   11

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].

 117 PRO   ( 197-)  A    38.5 envelop C-delta (36 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.

 394 MAN   ( 471-)  A      O6  <->  399 MAN   ( 475-)  A      C1     1.02    1.38  INTRA B3
 394 MAN   ( 471-)  A      C6  <->  399 MAN   ( 475-)  A      C1     0.86    2.34  INTRA
   1 ARG   (  82-)  A      N   <->  400 HOH   ( 784 )  A      O      0.36    2.34  INTRA
  17 HIS   (  98-)  A      CE1 <->  339 ARG   ( 419-)  A      NH1    0.32    2.78  INTRA BL
 394 MAN   ( 471-)  A      C6  <->  399 MAN   ( 475-)  A      O5     0.25    2.55  INTRA
 212 ARG   ( 292-)  A      NH2 <->  214 ASN   ( 294-)  A      ND2    0.21    2.64  INTRA
 214 ASN   ( 294-)  A      ND2 <->  266 ASN   ( 347-)  A      C      0.13    2.97  INTRA
 189 ALA   ( 269-)  A      N   <->  232 HIS   ( 312-)  A      NE2    0.12    2.88  INTRA
 108 THR   ( 188-)  A      CG2 <->  127 TYR   ( 207-)  A      CZ     0.10    3.10  INTRA BL
 104 HIS   ( 184-)  A      ND1 <->  106 GLY   ( 186-)  A      N      0.09    2.91  INTRA BL
   6 LEU   (  87-)  A      N   <->  153 HIS   ( 233-)  A      CD2    0.09    3.01  INTRA BL
  71 ARG   ( 152-)  A      NH2 <->  400 HOH   ( 795 )  A      O      0.09    2.61  INTRA BF
   4 ASN   (  85-)  A      ND2 <->  400 HOH   ( 658 )  A      O      0.09    2.61  INTRA
  87 THR   ( 168-)  A      OG1 <->   90 ASN   ( 170-)  A      ND2    0.08    2.62  INTRA
 238 CYS   ( 318-)  A      SG  <->  302 LEU   ( 383-)  A      O      0.07    2.78  INTRA
 313 GLN   ( 395-)  A      NE2 <->  400 HOH   ( 680 )  A      O      0.07    2.63  INTRA BL
  44 ASP   ( 125-)  A      OD1 <->  109 ARG   ( 189-)  A      NH2    0.07    2.63  INTRA
   8 LYS   (  89-)  A      NZ  <->  335 GLY   ( 415-)  A      O      0.06    2.64  INTRA
  63 HIS   ( 144-)  A      CD2 <->  400 HOH   ( 637 )  A      O      0.06    2.74  INTRA BL
  92 ARG   ( 172-)  A      NH1 <->  129 ARG   ( 209-)  A      NH2    0.05    2.80  INTRA
 334 GLU   ( 414-)  A      N   <->  400 HOH   ( 735 )  A      O      0.05    2.65  INTRA
 381 GLY   ( 461-)  A      N   <->  400 HOH   ( 734 )  A      O      0.05    2.65  INTRA
 184 LYS   ( 264-)  A      NZ  <->  230 MET   ( 310-)  A      O      0.05    2.65  INTRA
  38 GLU   ( 119-)  A      N   <->   39 PRO   ( 120-)  A      CD     0.04    2.96  INTRA BL
  29 GLU   ( 110-)  A      OE2 <->   60 ARG   ( 141-)  A      NH1    0.02    2.68  INTRA
 218 SER   ( 298-)  A      N   <->  219 ASN   ( 299-)  A      N      0.02    2.58  INTRA B3
  95 CYS   ( 175-)  A      C   <->  113 CYS   ( 193-)  A      SG     0.01    3.39  INTRA BL
 145 THR   ( 225-)  A      OG1 <->  146 GLN   ( 226-)  A      N      0.01    2.59  INTRA BL
 370 THR   ( 450-)  A      N   <->  371 GLU   ( 451-)  A      N      0.01    2.59  INTRA BL
 289 SER   ( 370-)  A      O   <->  291 SER   ( 372-)  A      N      0.01    2.69  INTRA
   3 PHE   (  84-)  A      CE1 <->  107 LYS   ( 187-)  A      CD     0.01    3.19  INTRA

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.

 334 GLU   ( 414-)  A      -6.26
  71 ARG   ( 152-)  A      -6.11
 375 GLN   ( 455-)  A      -5.82
 129 ARG   ( 209-)  A      -5.77
  74 TYR   ( 155-)  A      -5.60
 372 PHE   ( 452-)  A      -5.53
 336 GLU   ( 416-)  A      -5.41
 260 TYR   ( 341-)  A      -5.38
 204 ARG   ( 284-)  A      -5.35
  89 TYR   ( 169-)  A      -5.10

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.

   5 ASN   (  86-)  A   -2.69
 313 GLN   ( 395-)  A   -2.54

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 372 PHE   ( 452-)  A     -  375 GLN   ( 455-)  A        -1.94

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.

 400 HOH   ( 631 )  A      O     -0.78   16.77   60.39
 400 HOH   ( 647 )  A      O      0.88   31.14   57.92
 400 HOH   ( 649 )  A      O      0.52   32.09   55.44
 400 HOH   ( 775 )  A      O     26.31   40.83   69.45
 400 HOH   ( 779 )  A      O     24.28   -1.49   41.37
 400 HOH   ( 787 )  A      O     23.33   47.98   63.71

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.

 400 HOH   ( 810 )  A      O
Bound group on Asn; dont flip    5 ASN  (  86-) A
Bound to:  391 NAG  ( 476-) A
Bound group on Asn; dont flip   65 ASN  ( 146-) A
Bound to:  392 NAG  ( 477-) A
Bound group on Asn; dont flip  120 ASN  ( 200-) A
Bound to:  389 NAG  ( 469-) 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.

  14 ASN   (  95-)  A
  17 HIS   (  98-)  A
  63 HIS   ( 144-)  A
  90 ASN   ( 170-)  A
 136 ASN   ( 216-)  A
 214 ASN   ( 294-)  A
 264 ASN   ( 345-)  A
 311 GLN   ( 392-)  A
 313 GLN   ( 395-)  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.

   6 LEU   (  87-)  A      N
  16 TRP   (  97-)  A      NE1
  37 ARG   ( 118-)  A      NH2
  41 VAL   ( 122-)  A      N
  57 THR   ( 138-)  A      N
  72 SER   ( 153-)  A      N
  83 SER   ( 164-)  A      N
  87 THR   ( 168-)  A      OG1
  99 SER   ( 179-)  A      N
 116 GLY   ( 196-)  A      N
 148 SER   ( 228-)  A      N
 168 GLY   ( 248-)  A      N
 194 HIS   ( 274-)  A      N
 217 GLY   ( 297-)  A      N
 224 ARG   ( 304-)  A      NH1
 245 ASN   ( 325-)  A      ND2
 247 ARG   ( 327-)  A      NH2
 253 VAL   ( 333-)  A      N
 258 ASP   ( 339-)  A      N
 269 LYS   ( 350-)  A      N
 279 THR   ( 360-)  A      N
 283 ARG   ( 364-)  A      NH1
 308 LYS   ( 389-)  A      NZ
 318 ASN   ( 400-)  A      ND2
 337 CYS   ( 417-)  A      N
 355 LYS   ( 435-)  A      N
 358 TRP   ( 438-)  A      N
 365 SER   ( 445-)  A      OG
 385 GLU   ( 465-)  A      N
 392 NAG   ( 477-)  A      N2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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+.

 398  CA   ( 600-)  A     0.66   0.88 Scores about as good as NA

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.

 400 HOH   ( 715 )  A      O  1.09  K  4

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.

 105 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 163 ASP   ( 243-)  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 :  -0.791
  2nd generation packing quality :  -2.028
  Ramachandran plot appearance   :  -1.819
  chi-1/chi-2 rotamer normality  :  -1.746
  Backbone conformation          :  -1.420

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.514 (tight)
  Bond angles                    :   0.797
  Omega angle restraints         :   0.553 (tight)
  Side chain planarity           :   0.592 (tight)
  Improper dihedral distribution :   1.104
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.078

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.514 (tight)
  Bond angles                    :   0.797
  Omega angle restraints         :   0.553 (tight)
  Side chain planarity           :   0.592 (tight)
  Improper dihedral distribution :   1.104
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.078
==============

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.