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 pdb6nn9.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   ( 557 )  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.

 129 ARG   ( 209-)  A  -   CB
 129 ARG   ( 209-)  A  -   CG
 129 ARG   ( 209-)  A  -   CD
 129 ARG   ( 209-)  A  -   NE
 129 ARG   ( 209-)  A  -   CZ
 129 ARG   ( 209-)  A  -   NH1
 129 ARG   ( 209-)  A  -   NH2
 181 LYS   ( 261-)  A  -   CB
 181 LYS   ( 261-)  A  -   CG
 181 LYS   ( 261-)  A  -   CD
 181 LYS   ( 261-)  A  -   CE
 181 LYS   ( 261-)  A  -   NZ
 193 LYS   ( 273-)  A  -   CB
 193 LYS   ( 273-)  A  -   CG
 193 LYS   ( 273-)  A  -   CD
 193 LYS   ( 273-)  A  -   CE
 193 LYS   ( 273-)  A  -   NZ
 224 ARG   ( 304-)  A  -   CB
 224 ARG   ( 304-)  A  -   CG
 224 ARG   ( 304-)  A  -   CD
 224 ARG   ( 304-)  A  -   NE
 224 ARG   ( 304-)  A  -   CZ
 224 ARG   ( 304-)  A  -   NH1
 224 ARG   ( 304-)  A  -   NH2
 263 ASN   ( 344-)  A  -   CB
And so on for a total of 51 lines.

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:

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

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

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

Percentage of buried atoms with B less than 5 : 10.29

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.

 104 HIS   ( 184-)  A      CD2  NE2   1.29   -4.1
 108 THR   ( 188-)  A      CA   CB    1.63    4.8
 124 VAL   ( 204-)  A      CA   CB    1.65    5.8
 145 THR   ( 225-)  A      CA   CB    1.64    5.4
 151 VAL   ( 231-)  A      CA   CB    1.62    4.3
 378 TRP   ( 458-)  A      CG   CD2   1.35   -4.4

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 PHE   (  84-)  A      CA   CB   CG  118.06    4.3
   7 THR   (  88-)  A      N    CA   CB   98.96   -6.8
   7 THR   (  88-)  A      CA   CB   CG2 118.41    4.7
   7 THR   (  88-)  A      CA   CB   OG1  99.63   -6.6
  14 ASN   (  95-)  A      ND2  CG   OD1 116.52   -6.1
  16 TRP   (  97-)  A     -O   -C    N   115.76   -4.5
  17 HIS   (  98-)  A      CB   CG   ND1 128.02    4.3
  18 ILE   (  99-)  A     -O   -C    N   116.14   -4.3
  18 ILE   (  99-)  A     -CA  -C    N   125.45    4.6
  18 ILE   (  99-)  A      N    CA   CB  122.34    7.0
  18 ILE   (  99-)  A      C    CA   CB  100.04   -5.3
  22 ASP   ( 103-)  A     -CA  -C    N   107.16   -4.5
  22 ASP   ( 103-)  A     -C    N    CA  131.30    5.3
  22 ASP   ( 103-)  A      CA   CB   CG  118.34    5.7
  23 ASN   ( 104-)  A      ND2  CG   OD1 115.75   -6.8
  37 ARG   ( 118-)  A      CD   NE   CZ  129.43    4.3
  40 TYR   ( 121-)  A      CA   CB   CG  124.54    5.8
  45 PRO   ( 126-)  A     -O   -C    N   116.19   -4.2
  45 PRO   ( 126-)  A     -CA  -C    N   125.29    5.6
  47 GLU   ( 128-)  A     -CA  -C    N   125.71    4.8
  50 PHE   ( 131-)  A      CA   CB   CG  120.98    7.2
  55 GLN   ( 136-)  A      NE2  CD   OE1 117.97   -4.6
  57 THR   ( 138-)  A      N    CA   CB  119.93    5.5
  57 THR   ( 138-)  A      C    CA   CB   99.36   -5.7
  63 HIS   ( 144-)  A      CB   CG   ND1 132.01    6.9
And so on for a total of 152 lines.

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.

  36 THR   ( 117-)  A      C     -6.2    -9.07     0.30
The average deviation= 1.640

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    6.61
 197 GLU   ( 277-)  A    4.62
 146 GLN   ( 226-)  A    4.59
 144 ARG   ( 224-)  A    4.34
 210 THR   ( 290-)  A    4.26
 200 CYS   ( 280-)  A    4.17
  70 ASP   ( 151-)  A    4.16
 298 VAL   ( 379-)  A    4.15
 376 TRP   ( 456-)  A    4.07

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 : 1.758

Error: Connections to aromatic rings out of plane

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

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

 343 TYR   ( 423-)  A      OH   4.11
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.267

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.

 167 THR   ( 247-)  A    -3.2
 108 THR   ( 188-)  A    -2.9
 351 PRO   ( 431-)  A    -2.7
 251 PRO   ( 331-)  A    -2.6
  57 THR   ( 138-)  A    -2.4
 144 ARG   ( 224-)  A    -2.4
 145 THR   ( 225-)  A    -2.4
 283 ARG   ( 364-)  A    -2.3
 271 PHE   ( 352-)  A    -2.3
  37 ARG   ( 118-)  A    -2.3
 268 VAL   ( 349-)  A    -2.3
  83 SER   ( 164-)  A    -2.2
 203 GLU   ( 283-)  A    -2.2
  53 LEU   ( 134-)  A    -2.2
 262 GLY   ( 343-)  A    -2.2
 101 THR   ( 181-)  A    -2.1
  60 ARG   ( 141-)  A    -2.1
 384 ILE   ( 464-)  A    -2.1
 199 SER   ( 279-)  A    -2.1
 376 TRP   ( 456-)  A    -2.1
 206 GLU   ( 286-)  A    -2.1
   7 THR   (  88-)  A    -2.1
  68 ILE   ( 149-)  A    -2.1
 137 THR   ( 217-)  A    -2.1
  40 TYR   ( 121-)  A    -2.1
 360 SER   ( 440-)  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.

  36 THR   ( 117-)  A  omega poor
  40 TYR   ( 121-)  A  Poor phi/psi
  83 SER   ( 164-)  A  Poor phi/psi
 116 GLY   ( 196-)  A  PRO omega poor
 129 ARG   ( 209-)  A  Poor phi/psi
 145 THR   ( 225-)  A  Poor phi/psi
 147 GLU   ( 227-)  A  Poor phi/psi
 179 GLU   ( 259-)  A  Poor phi/psi
 204 ARG   ( 284-)  A  Poor phi/psi
 205 ALA   ( 285-)  A  Poor phi/psi
 230 MET   ( 310-)  A  Poor phi/psi
 235 GLN   ( 315-)  A  omega poor
 245 ASN   ( 325-)  A  PRO omega poor
 251 PRO   ( 331-)  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 : -3.102

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 : -3.102

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!

  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
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  40 TYR   ( 121-)  A      0
  46 ASP   ( 127-)  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
  75 ARG   ( 156-)  A      0
  80 TRP   ( 161-)  A      0
  82 LEU   ( 163-)  A      0
  83 SER   ( 164-)  A      0
  87 THR   ( 168-)  A      0
  91 SER   ( 171-)  A      0
  94 GLU   ( 174-)  A      0
  95 CYS   ( 175-)  A      0
  96 ILE   ( 176-)  A      0
  98 TRP   ( 178-)  A      0
And so on for a total of 229 lines.

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 204 ARG   ( 284-)  A   1.82

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
  86 PRO   ( 167-)  A    0.17 LOW
 259 PRO   ( 340-)  A    0.47 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   -59.7 half-chair C-beta/C-alpha (-54 degrees)
 221 PRO   ( 301-)  A    49.8 half-chair C-delta/C-gamma (54 degrees)
 351 PRO   ( 431-)  A   -42.7 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.

 394 MAN   ( 471-)  A      O6  <->  399 MAN   ( 475-)  A      C1     0.93    1.47  INTRA B3
 386 TYR   ( 466-)  A      OH  <->  400 HOH   ( 484 )  A      O      0.82    1.58  INTRA
 394 MAN   ( 471-)  A      C6  <->  399 MAN   ( 475-)  A      C1     0.66    2.54  INTRA
 380 ASP   ( 460-)  A      N   <->  400 HOH   ( 560 )  A      O      0.22    2.48  INTRA
  29 GLU   ( 110-)  A      CG  <->   60 ARG   ( 141-)  A      NH1    0.13    2.97  INTRA
 386 TYR   ( 466-)  A      CZ  <->  400 HOH   ( 484 )  A      O      0.11    2.69  INTRA
 241 VAL   ( 321-)  A      CG1 <->  283 ARG   ( 364-)  A      NH2    0.10    3.00  INTRA BL
 245 ASN   ( 325-)  A      ND2 <->  289 SER   ( 370-)  A      O      0.08    2.62  INTRA BL
 214 ASN   ( 294-)  A      ND2 <->  266 ASN   ( 347-)  A      C      0.06    3.04  INTRA
  17 HIS   (  98-)  A      CE1 <->  339 ARG   ( 419-)  A      NH2    0.04    3.06  INTRA BL
 108 THR   ( 188-)  A      CG2 <->  127 TYR   ( 207-)  A      CZ     0.04    3.16  INTRA BL
   3 PHE   (  84-)  A      O   <->  392 NAG   ( 477-)  A      N2     0.02    2.68  INTRA
 189 ALA   ( 269-)  A      N   <->  232 HIS   ( 312-)  A      NE2    0.02    2.98  INTRA BL
 386 TYR   ( 466-)  A      OH  <->  400 HOH   ( 564 )  A      O      0.02    2.38  INTRA
   5 ASN   (  86-)  A      O   <->    7 THR   (  88-)  A      N      0.01    2.69  INTRA BL

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.

 375 GLN   ( 455-)  A      -6.49
 334 GLU   ( 414-)  A      -6.26
  71 ARG   ( 152-)  A      -6.14
  74 TYR   ( 155-)  A      -5.87
 260 TYR   ( 341-)  A      -5.86
 129 ARG   ( 209-)  A      -5.55
 372 PHE   ( 452-)  A      -5.30
 204 ARG   ( 284-)  A      -5.29
 336 GLU   ( 416-)  A      -5.27
 249 ASN   ( 329-)  A      -5.15
 193 LYS   ( 273-)  A      -5.08

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   -2.53

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   ( 512 )  A      O     -0.50   17.09   61.05
 400 HOH   ( 530 )  A      O      0.80   31.18   58.81
 400 HOH   ( 533 )  A      O      0.80   32.49   56.37

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
 136 ASN   ( 216-)  A
 214 ASN   ( 294-)  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
  24 ALA   ( 105-)  A      N
  25 VAL   ( 106-)  A      N
  26 ARG   ( 107-)  A      N
  37 ARG   ( 118-)  A      NH2
  41 VAL   ( 122-)  A      N
  43 CYS   ( 124-)  A      N
  46 ASP   ( 127-)  A      N
  57 THR   ( 138-)  A      N
  57 THR   ( 138-)  A      OG1
  72 SER   ( 153-)  A      N
  83 SER   ( 164-)  A      N
  87 THR   ( 168-)  A      N
  89 TYR   ( 169-)  A      N
  99 SER   ( 179-)  A      N
 116 GLY   ( 196-)  A      N
 139 ALA   ( 219-)  A      N
 143 LEU   ( 223-)  A      N
 148 SER   ( 228-)  A      N
 155 GLY   ( 235-)  A      N
 168 GLY   ( 248-)  A      N
 194 HIS   ( 274-)  A      N
 200 CYS   ( 280-)  A      N
 217 GLY   ( 297-)  A      N
 224 ARG   ( 304-)  A      NE
 234 SER   ( 314-)  A      N
 247 ARG   ( 327-)  A      NH2
 253 VAL   ( 333-)  A      N
 258 ASP   ( 339-)  A      N
 263 ASN   ( 344-)  A      N
 269 LYS   ( 350-)  A      N
 270 GLY   ( 351-)  A      N
 337 CYS   ( 417-)  A      N
 355 LYS   ( 435-)  A      N
 358 TRP   ( 438-)  A      N
 363 ILE   ( 443-)  A      N
 389 NAG   ( 469-)  A      O6
 391 NAG   ( 476-)  A      N2

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.

  23 ASN   ( 104-)  A      OD1
 206 GLU   ( 286-)  A      OE2

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   (  18-)  A     0.33   0.73 Is perhaps  K

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.

  22 ASP   ( 103-)  A   H-bonding suggests Asn
 105 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 163 ASP   ( 243-)  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 :  -1.579
  2nd generation packing quality :  -2.218
  Ramachandran plot appearance   :  -2.267
  chi-1/chi-2 rotamer normality  :  -3.102 (poor)
  Backbone conformation          :  -1.604

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.886
  Bond angles                    :   1.765
  Omega angle restraints         :   1.067
  Side chain planarity           :   0.858
  Improper dihedral distribution :   1.391
  Inside/Outside distribution    :   1.083

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.886
  Bond angles                    :   1.765
  Omega angle restraints         :   1.067
  Side chain planarity           :   0.858
  Improper dihedral distribution :   1.391
  Inside/Outside distribution    :   1.083
==============

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.