WHAT IF Check report

This file was created 2011-12-13 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 pdb1bji.ent

Checks that need to be done early-on in validation

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   ( 472-)  A  -
 395 MAN   ( 473-)  A  -
 396 MAN   ( 474-)  A  -
 398 DPC   ( 479-)  A  -
 399 MAN   ( 475-)  A  -
 400 BMA   ( 471-)  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  400 BMA   ( 471-)  A  -   C1

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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) :300.000

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.

  17 HIS   (  98-)  A      CG   ND1  CE1 109.65    4.1
  44 ASP   ( 125-)  A      N    CA   C    99.41   -4.2
  63 HIS   ( 144-)  A      CG   ND1  CE1 109.74    4.1
 104 HIS   ( 184-)  A      CG   ND1  CE1 109.62    4.0
 146 GLN   ( 226-)  A      N    CA   C   124.23    4.7
 219 ASN   ( 299-)  A      N    CA   C    97.65   -4.8
 232 HIS   ( 312-)  A      CG   ND1  CE1 109.97    4.4
 389 NAG   ( 469-)  A      N2   C2   C1  101.49   -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.

 146 GLN   ( 226-)  A    5.05
  24 ALA   ( 105-)  A    4.73
 219 ASN   ( 299-)  A    4.61
  44 ASP   ( 125-)  A    4.02

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 : 1.527

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    -2.6
 283 ARG   ( 364-)  A    -2.6
  37 ARG   ( 118-)  A    -2.5
  57 THR   ( 138-)  A    -2.3
 145 THR   ( 225-)  A    -2.3
 101 THR   ( 181-)  A    -2.2
 271 PHE   ( 352-)  A    -2.2
 140 ARG   ( 220-)  A    -2.2
 366 MET   ( 446-)  A    -2.2
 251 PRO   ( 331-)  A    -2.2
 384 ILE   ( 464-)  A    -2.2
  60 ARG   ( 141-)  A    -2.2
 262 GLY   ( 343-)  A    -2.1
 268 VAL   ( 349-)  A    -2.1
 233 THR   ( 313-)  A    -2.1
  68 ILE   ( 149-)  A    -2.1
 224 ARG   ( 304-)  A    -2.1
 137 THR   ( 217-)  A    -2.0
 203 GLU   ( 283-)  A    -2.0
  39 PRO   ( 120-)  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
 186 GLU   ( 266-)  A  PRO omega poor
 205 ALA   ( 285-)  A  Poor phi/psi
 211 CYS   ( 291-)  A  Poor phi/psi
 230 MET   ( 310-)  A  Poor phi/psi
 245 ASN   ( 325-)  A  PRO omega poor
 278 ASN   ( 359-)  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 : -1.944

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 224 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 : 3.093

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   1.69   10

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]

  39 PRO   ( 120-)  A    0.47 HIGH
  45 PRO   ( 126-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 117 PRO   ( 197-)  A    23.4 half-chair N/C-delta (18 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.

 390 NAG   ( 470-)  A      O4  <->  400 BMA   ( 471-)  A      C1     1.04    1.36  INTRA B3
 390 NAG   ( 470-)  A      C4  <->  400 BMA   ( 471-)  A      C1     0.77    2.43  INTRA
  17 HIS   (  98-)  A      CE1 <->  339 ARG   ( 419-)  A      NH1    0.31    2.79  INTRA BL
   1 ARG   (  82-)  A      N   <->  401 HOH   ( 658 )  A      O      0.23    2.47  INTRA BF
  87 THR   ( 168-)  A      OG1 <->   90 ASN   ( 170-)  A      ND2    0.21    2.49  INTRA
 108 THR   ( 188-)  A      CG2 <->  127 TYR   ( 207-)  A      CZ     0.15    3.05  INTRA BL
 313 GLN   ( 395-)  A      NE2 <->  401 HOH   ( 559 )  A      O      0.14    2.56  INTRA BL
   4 ASN   (  85-)  A      ND2 <->  401 HOH   ( 537 )  A      O      0.13    2.57  INTRA
 297 LYS   ( 378-)  A      NZ  <->  401 HOH   ( 643 )  A      O      0.12    2.58  INTRA
 291 SER   ( 372-)  A      OG  <->  318 ASN   ( 400-)  A      ND2    0.12    2.58  INTRA
  44 ASP   ( 125-)  A      OD1 <->  109 ARG   ( 189-)  A      NH2    0.11    2.59  INTRA BL
 212 ARG   ( 292-)  A      NH2 <->  214 ASN   ( 294-)  A      ND2    0.10    2.75  INTRA
  92 ARG   ( 172-)  A      NH1 <->  401 HOH   ( 491 )  A      O      0.09    2.61  INTRA
 104 HIS   ( 184-)  A      ND1 <->  106 GLY   ( 186-)  A      N      0.08    2.92  INTRA BL
   8 LYS   (  89-)  A      NZ  <->  335 GLY   ( 415-)  A      O      0.08    2.62  INTRA
   6 LEU   (  87-)  A      N   <->  153 HIS   ( 233-)  A      CD2    0.07    3.03  INTRA
 189 ALA   ( 269-)  A      N   <->  232 HIS   ( 312-)  A      NE2    0.07    2.93  INTRA
 238 CYS   ( 318-)  A      SG  <->  302 LEU   ( 383-)  A      O      0.06    2.79  INTRA
 186 GLU   ( 266-)  A      OE1 <->  232 HIS   ( 312-)  A      ND1    0.05    2.65  INTRA
  21 LYS   ( 102-)  A      NZ  <->  401 HOH   ( 563 )  A      O      0.05    2.65  INTRA BL
  11 CYS   (  92-)  A      SG  <->  337 CYS   ( 417-)  A      C      0.05    3.35  INTRA
 348 ARG   ( 428-)  A      NH1 <->  380 ASP   ( 460-)  A      OD2    0.04    2.66  INTRA BL
 291 SER   ( 372-)  A      C   <->  318 ASN   ( 400-)  A      ND2    0.04    3.06  INTRA
  87 THR   ( 168-)  A      N   <->   90 ASN   ( 170-)  A      ND2    0.04    2.81  INTRA
 381 GLY   ( 461-)  A      N   <->  401 HOH   ( 612 )  A      O      0.03    2.67  INTRA BL
 194 HIS   ( 274-)  A      CE1 <->  196 GLU   ( 276-)  A      OE2    0.03    2.77  INTRA
 207 ILE   ( 287-)  A      O   <->  225 ILE   ( 305-)  A      N      0.03    2.67  INTRA
  38 GLU   ( 119-)  A      N   <->   39 PRO   ( 120-)  A      CD     0.02    2.98  INTRA BL
 226 ASP   ( 306-)  A      O   <->  230 MET   ( 310-)  A      N      0.02    2.68  INTRA
 218 SER   ( 298-)  A      N   <->  219 ASN   ( 299-)  A      N      0.02    2.58  INTRA B3
  29 GLU   ( 110-)  A      OE2 <->   60 ARG   ( 141-)  A      NH1    0.02    2.68  INTRA
 168 GLY   ( 248-)  A      O   <->  194 HIS   ( 274-)  A      CD2    0.02    2.78  INTRA
 214 ASN   ( 294-)  A      ND2 <->  266 ASN   ( 347-)  A      C      0.02    3.08  INTRA
 245 ASN   ( 325-)  A      O   <->  267 GLY   ( 348-)  A      CA     0.02    2.78  INTRA
  64 SER   ( 145-)  A      N   <->   65 ASN   ( 146-)  A      N      0.02    2.58  INTRA B3
 370 THR   ( 450-)  A      N   <->  371 GLU   ( 451-)  A      N      0.02    2.58  INTRA B3
  70 ASP   ( 151-)  A      OD1 <->  398 DPC   ( 479-)  A      NE     0.02    2.68  INTRA
  95 CYS   ( 175-)  A      C   <->  113 CYS   ( 193-)  A      SG     0.01    3.39  INTRA BL
 116 GLY   ( 196-)  A      CA  <->  117 PRO   ( 197-)  A      CD     0.01    2.79  INTRA BL
  50 PHE   ( 131-)  A      CE1 <->   82 LEU   ( 163-)  A      CD1    0.01    3.19  INTRA BL
  66 GLY   ( 147-)  A      O   <->   68 ILE   ( 149-)  A      N      0.01    2.69  INTRA
  68 ILE   ( 149-)  A      N   <->   69 HIS   ( 150-)  A      N      0.01    2.59  INTRA B3

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      -6.27
 375 GLN   ( 455-)  A      -6.13
 129 ARG   ( 209-)  A      -5.91
  71 ARG   ( 152-)  A      -5.75
 336 GLU   ( 416-)  A      -5.57
  74 TYR   ( 155-)  A      -5.42
 260 TYR   ( 341-)  A      -5.36
 372 PHE   ( 452-)  A      -5.32
 204 ARG   ( 284-)  A      -5.32
 249 ASN   ( 329-)  A      -5.13
  89 TYR   ( 169-)  A      -5.11
 193 LYS   ( 273-)  A      -5.00

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.

 313 GLN   ( 395-)  A   -2.52

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.

 401 HOH   ( 510 )  A      O     -0.64   16.96   60.20
 401 HOH   ( 526 )  A      O      0.92   30.84   57.96
 401 HOH   ( 528 )  A      O      0.74   32.01   55.50
 401 HOH   ( 654 )  A      O     24.27   -1.48   41.31
 401 HOH   ( 660 )  A      O     23.14   47.93   63.53

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
 318 ASN   ( 400-)  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
  25 VAL   ( 106-)  A      N
  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
 146 GLN   ( 226-)  A      NE2
 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
 247 ARG   ( 327-)  A      NH2
 250 ASP   ( 330-)  A      N
 253 VAL   ( 333-)  A      N
 260 TYR   ( 341-)  A      OH
 265 ASN   ( 346-)  A      ND2
 269 LYS   ( 350-)  A      N
 283 ARG   ( 364-)  A      NH1
 337 CYS   ( 417-)  A      N
 358 TRP   ( 438-)  A      N
 365 SER   ( 445-)  A      OG
 392 NAG   ( 477-)  A      N2

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+.

 397  CA   ( 478-)  A     0.66   0.89 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.

 401 HOH   ( 562 )  A      O  1.14  K  4
 401 HOH   ( 593 )  A      O  0.91  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
 258 ASP   ( 339-)  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 :  -0.834
  2nd generation packing quality :  -1.935
  Ramachandran plot appearance   :  -2.040
  chi-1/chi-2 rotamer normality  :  -1.944
  Backbone conformation          :  -1.422

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.571 (tight)
  Bond angles                    :   0.826
  Omega angle restraints         :   0.562 (tight)
  Side chain planarity           :   0.703
  Improper dihedral distribution :   1.113
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   1.076

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   :  -1.4
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.571 (tight)
  Bond angles                    :   0.826
  Omega angle restraints         :   0.562 (tight)
  Side chain planarity           :   0.703
  Improper dihedral distribution :   1.113
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   1.076
==============

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.