WHAT IF Check report

This file was created 2012-01-30 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 pdb3cpu.ent

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 498 GLC   ( 500-)  A      O4

Warning: What type of B-factor?

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

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

Crystal temperature (K) :298.000

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 238 GLY   ( 238-)  A      N   -C     1.42    4.5
 241 PRO   ( 241-)  A      N   -C     1.48    7.5
 265 VAL   ( 265-)  A      CA   CB    1.62    4.6

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.

   3 SER   (   3-)  A      C    CA   CB  117.99    4.2
  89 VAL   (  89-)  A      CG1  CB   CG2 122.22    5.2
 101 HIS   ( 101-)  A      CG   ND1  CE1 109.67    4.1
 238 GLY   ( 238-)  A     -O   -C    N   116.48   -4.1
 238 GLY   ( 238-)  A     -CA  -C    N   124.71    4.3
 239 GLY   ( 239-)  A      N    CA   C   126.66    4.9
 334 GLY   ( 334-)  A      N    CA   C   124.22    4.0
 461 ASN   ( 461-)  A      N    CA   CB  117.44    4.1
 461 ASN   ( 461-)  A      CB   CG   ND2 123.51    4.7

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.

  89 VAL   (  89-)  A      CB     7.2   -23.52   -32.96
The average deviation= 0.852

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.

 239 GLY   ( 239-)  A    4.69

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.

 376 THR   ( 376-)  A    -2.7
  45 PRO   (  45-)  A    -2.6
 124 ARG   ( 124-)  A    -2.6
 239 GLY   ( 239-)  A    -2.4
 347 GLN   ( 347-)  A    -2.3
 142 LYS   ( 142-)  A    -2.3
  66 SER   (  66-)  A    -2.3
 243 LYS   ( 243-)  A    -2.2
 414 SER   ( 414-)  A    -2.2
  56 ARG   (  56-)  A    -2.1
  35 LYS   (  35-)  A    -2.1
 273 LYS   ( 273-)  A    -2.1
 459 ASN   ( 459-)  A    -2.1
 440 LEU   ( 440-)  A    -2.1
 458 ILE   ( 458-)  A    -2.0
  13 ILE   (  13-)  A    -2.0
 437 SER   ( 437-)  A    -2.0
 340 SER   ( 340-)  A    -2.0
  89 VAL   (  89-)  A    -2.0
 444 LEU   ( 444-)  A    -2.0
 305 HIS   ( 305-)  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.

   5 ASN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 124 ARG   ( 124-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 149 GLU   ( 149-)  A  Poor phi/psi
 237 LEU   ( 237-)  A  Poor phi/psi
 238 GLY   ( 238-)  A  Poor phi/psi
 239 GLY   ( 239-)  A  Poor phi/psi
 268 LYS   ( 268-)  A  Poor phi/psi
 270 ASN   ( 270-)  A  Poor phi/psi
 301 ASN   ( 301-)  A  Poor phi/psi
 350 ASN   ( 350-)  A  Poor phi/psi
 364 ASN   ( 364-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 384 CYS   ( 384-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 486 PRO   ( 486-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.308

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 : -3.308

Warning: Unusual backbone conformations

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

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

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

   5 ASN   (   5-)  A      0
   8 GLN   (   8-)  A      0
  10 ARG   (  10-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  45 PRO   (  45-)  A      0
  52 TYR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 PHE   (  55-)  A      0
  56 ARG   (  56-)  A      0
  57 PRO   (  57-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
  75 ASN   (  75-)  A      0
And so on for a total of 230 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 : 2.417

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]

 241 PRO   ( 241-)  A    0.19 LOW
 288 PRO   ( 288-)  A    0.07 LOW
 345 PRO   ( 345-)  A    0.18 LOW

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].

  45 PRO   (  45-)  A   -43.5 envelop C-alpha (-36 degrees)
 130 PRO   ( 130-)  A   -41.8 envelop C-alpha (-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.

 497 GLC   ( 499-)  A      C1  <->  500 GLC   ( 499-)  A      O1     1.39    1.41  INTRA
 497 GLC   ( 499-)  A      C1  <->  498 GLC   ( 500-)  A      C4     0.69    2.31  INTRA
 497 GLC   ( 499-)  A      C2  <->  500 GLC   ( 499-)  A      O1     0.34    2.46  INTRA
 390 GLN   ( 390-)  A      CG  <->  504 HOH   ( 618 )  A      O      0.24    2.56  INTRA BF
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      ND1    0.21    2.79  INTRA BL
 448 THR   ( 448-)  A      CG2 <->  466 LYS   ( 466-)  A      NZ     0.21    2.89  INTRA
 485 ASP   ( 485-)  A      OD1 <->  504 HOH   ( 618 )  A      O      0.21    2.19  INTRA BF
 158 ARG   ( 158-)  A      NH2 <->  504 HOH   ( 576 )  A      O      0.20    2.50  INTRA
 408 ASN   ( 408-)  A      ND2 <->  504 HOH   ( 626 )  A      O      0.18    2.52  INTRA
 392 ARG   ( 392-)  A      NH2 <->  504 HOH   ( 644 )  A      O      0.18    2.52  INTRA
 249 GLY   ( 249-)  A      N   <->  504 HOH   ( 566 )  A      O      0.17    2.53  INTRA
 149 GLU   ( 149-)  A      N   <->  156 GLN   ( 156-)  A      OE1    0.17    2.53  INTRA
 373 ASN   ( 373-)  A      N   <->  377 THR   ( 377-)  A      O      0.17    2.53  INTRA
 485 ASP   ( 485-)  A      CG  <->  504 HOH   ( 618 )  A      O      0.16    2.64  INTRA BF
  20 ARG   (  20-)  A      NH1 <->   23 ASP   (  23-)  A      OD2    0.15    2.55  INTRA BL
 268 LYS   ( 268-)  A      NZ  <->  431 ASN   ( 431-)  A      O      0.15    2.55  INTRA
 260 ALA   ( 260-)  A      O   <->  264 THR   ( 264-)  A      CG2    0.14    2.66  INTRA BL
 208 LYS   ( 208-)  A      CE  <->  212 ASP   ( 212-)  A      OD1    0.14    2.66  INTRA
 497 GLC   ( 499-)  A      O5  <->  500 GLC   ( 499-)  A      O1     0.13    2.27  INTRA
  15 HIS   (  15-)  A      CD2 <->  504 HOH   ( 515 )  A      O      0.13    2.67  INTRA BL
  80 ARG   (  80-)  A      NH2 <->  185 HIS   ( 185-)  A      CE1    0.13    2.97  INTRA
 293 LEU   ( 293-)  A      CD2 <->  504 HOH   ( 642 )  A      O      0.12    2.68  INTRA
 322 LYS   ( 322-)  A      NZ  <->  485 ASP   ( 485-)  A      OD1    0.12    2.58  INTRA BL
 170 LEU   ( 170-)  A      CD1 <->  202 MET   ( 202-)  A      SD     0.11    3.29  INTRA BL
  40 VAL   (  40-)  A      N   <->   92 ARG   (  92-)  A      O      0.10    2.60  INTRA BL
And so on for a total of 60 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.

  72 ARG   (  72-)  A      -7.00
   2 TYR   (   2-)  A      -6.29
 343 ARG   ( 343-)  A      -6.01
   8 GLN   (   8-)  A      -6.00
  52 TYR   (  52-)  A      -5.91
 237 LEU   ( 237-)  A      -5.89
 142 LYS   ( 142-)  A      -5.86
   7 GLN   (   7-)  A      -5.78
 284 TRP   ( 284-)  A      -5.43
 279 ASN   ( 279-)  A      -5.34
  88 ASN   (  88-)  A      -5.31
  30 ARG   (  30-)  A      -5.29
  53 ASN   (  53-)  A      -5.18
 349 GLN   ( 349-)  A      -5.11
 118 TYR   ( 118-)  A      -5.09

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.

 300 ASN   ( 300-)  A   -2.57

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.

 355 ASN   ( 355-)  A     -  358 VAL   ( 358-)  A        -1.58

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.

 504 HOH   ( 560 )  A      O     46.68   22.97   30.97
 504 HOH   ( 590 )  A      O     44.95   19.17   31.55
 504 HOH   ( 640 )  A      O     -6.86   15.89   25.74
 504 HOH   ( 647 )  A      O     21.08    6.45  -10.62
 504 HOH   ( 669 )  A      O     -8.49   -8.22   27.42
 504 HOH   ( 683 )  A      O     19.15  -12.07   35.52
 504 HOH   ( 723 )  A      O     -5.54   17.89   26.16

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.

 504 HOH   ( 538 )  A      O
 504 HOH   ( 585 )  A      O
 504 HOH   ( 589 )  A      O
 504 HOH   ( 606 )  A      O
 504 HOH   ( 613 )  A      O
 504 HOH   ( 634 )  A      O
 504 HOH   ( 642 )  A      O
 504 HOH   ( 645 )  A      O
 504 HOH   ( 654 )  A      O
 504 HOH   ( 667 )  A      O
 504 HOH   ( 669 )  A      O
 504 HOH   ( 672 )  A      O
 504 HOH   ( 678 )  A      O
 504 HOH   ( 686 )  A      O
 504 HOH   ( 693 )  A      O
 504 HOH   ( 703 )  A      O
 504 HOH   ( 706 )  A      O
 504 HOH   ( 728 )  A      O
Marked this atom as acceptor  502  CL  ( 498-) A     CL
Strange metal coordination for HIS 201

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.

  15 HIS   (  15-)  A
 105 ASN   ( 105-)  A
 150 ASN   ( 150-)  A
 185 HIS   ( 185-)  A
 218 ASN   ( 218-)  A
 415 ASN   ( 415-)  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.

   2 TYR   (   2-)  A      N
   7 GLN   (   7-)  A      N
  20 ARG   (  20-)  A      N
  30 ARG   (  30-)  A      NH2
  59 TRP   (  59-)  A      N
  80 ARG   (  80-)  A      NH2
  87 ASN   (  87-)  A      ND2
  99 ILE   (  99-)  A      N
 100 ASN   ( 100-)  A      N
 101 HIS   ( 101-)  A      N
 142 LYS   ( 142-)  A      N
 162 LEU   ( 162-)  A      N
 164 GLY   ( 164-)  A      N
 193 GLY   ( 193-)  A      N
 242 ILE   ( 242-)  A      N
 264 THR   ( 264-)  A      OG1
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 298 ASN   ( 298-)  A      ND2
 300 ASN   ( 300-)  A      N
 303 ARG   ( 303-)  A      N
 305 HIS   ( 305-)  A      N
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 344 TRP   ( 344-)  A      N
 352 ASN   ( 352-)  A      N
 355 ASN   ( 355-)  A      ND2
 357 TRP   ( 357-)  A      N
 369 GLU   ( 369-)  A      N
 390 GLN   ( 390-)  A      NE2
 431 ASN   ( 431-)  A      ND2
 434 TRP   ( 434-)  A      N
 487 PHE   ( 487-)  A      N
Only metal coordination for  100 ASN  ( 100-) A      OD1

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.

 215 HIS   ( 215-)  A      NE2
 240 GLU   ( 240-)  A      OE1
 290 ASP   ( 290-)  A      OD1
 300 ASN   ( 300-)  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+.

 501  CA   ( 497-)  A     0.57   0.80 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.

 504 HOH   ( 689 )  A      O  1.03  K  6

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.

 236 ASP   ( 236-)  A   H-bonding suggests Asn; but Alt-Rotamer
 451 ASP   ( 451-)  A   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 :  -0.966
  2nd generation packing quality :  -1.670
  Ramachandran plot appearance   :  -1.520
  chi-1/chi-2 rotamer normality  :  -3.308 (poor)
  Backbone conformation          :  -1.057

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.415 (tight)
  Bond angles                    :   0.702
  Omega angle restraints         :   0.439 (tight)
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.736
  B-factor distribution          :   0.876
  Inside/Outside distribution    :   1.004

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 :  -0.7
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.415 (tight)
  Bond angles                    :   0.702
  Omega angle restraints         :   0.439 (tight)
  Side chain planarity           :   0.279 (tight)
  Improper dihedral distribution :   0.736
  B-factor distribution          :   0.876
  Inside/Outside distribution    :   1.004
==============

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.