WHAT IF Check report

This file was created 2011-12-21 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 pdb1dku.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.583
CA-only RMS fit for the two chains : 0.257

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

 591 AP2   (1002-)  A  -
 592 ABM   (1003-)  A  -
 593 ABM   (1004-)  A  -
 594 AP2   (1001-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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) :285.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 590 PHE   ( 315-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.002009  0.000193 -0.000194|
 |  0.000193  1.002650  0.000116|
 | -0.000194  0.000116  0.999295|
Proposed new scale matrix

 |  0.008632  0.004975  0.000001|
 | -0.000002  0.009954 -0.000001|
 |  0.000002 -0.000001  0.009407|
With corresponding cell

    A    = 115.839  B   = 115.946  C    = 106.308
    Alpha=  89.977  Beta=  90.022  Gamma= 119.947

The CRYST1 cell dimensions

    A    = 115.650  B   = 115.650  C    = 106.410
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 46.654
(Under-)estimated Z-score: 5.034

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.

   8 ASN   (  15-)  A      N    CA   C   122.40    4.0
  30 VAL   (  37-)  A      N    CA   C    99.99   -4.0
  79 SER   (  86-)  A      N    CA   C   122.42    4.0
 101 SER   ( 108-)  A      N    CA   C   122.82    4.1
 161 ILE   ( 168-)  A      C    CA   CB  102.25   -4.1
 246 GLU   ( 262-)  A      CA   CB   CG  122.31    4.1
 359 HIS   (  71-)  B      CG   ND1  CE1 109.62    4.0
 456 ILE   ( 168-)  B      C    CA   CB  101.44   -4.6
 457 VAL   ( 169-)  B      N    CA   C    99.93   -4.0
 541 GLU   ( 262-)  B      CA   CB   CG  122.88    4.4

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.

 356 VAL   (  68-)  B    5.90
  61 VAL   (  68-)  A    5.88
 101 SER   ( 108-)  A    4.28
  79 SER   (  86-)  A    4.12
 246 GLU   ( 262-)  A    4.10
  33 PHE   (  40-)  A    4.07
 297 LEU   (   9-)  B    4.03

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 : 1.563

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.

 347 TYR   (  59-)  B      OH   5.37
  52 TYR   (  59-)  A      OH   4.73
 168 HIS   ( 175-)  A      CB   4.09
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.709

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.

 243 PRO   ( 259-)  A    -2.9
 538 PRO   ( 259-)  B    -2.8
  97 ARG   ( 104-)  A    -2.7
 182 LYS   ( 189-)  A    -2.7
 392 ARG   ( 104-)  B    -2.7
 533 PRO   ( 254-)  B    -2.5
 341 ILE   (  53-)  B    -2.5
 187 ILE   ( 194-)  A    -2.4
 482 ILE   ( 194-)  B    -2.4
  46 ILE   (  53-)  A    -2.4
 238 PRO   ( 254-)  A    -2.4
 564 PHE   ( 289-)  B    -2.3
 269 PHE   ( 289-)  A    -2.3
 326 THR   (  38-)  B    -2.3
  27 LYS   (  34-)  A    -2.2
 184 PRO   ( 191-)  A    -2.2
  60 PRO   (  67-)  A    -2.1
 202 THR   ( 218-)  A    -2.1
 497 THR   ( 218-)  B    -2.1
 586 VAL   ( 311-)  B    -2.1
 480 ILE   ( 192-)  B    -2.1
 160 ASP   ( 167-)  A    -2.1
 355 PRO   (  67-)  B    -2.0
 185 ILE   ( 192-)  A    -2.0
 582 GLU   ( 307-)  B    -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.

   7 LEU   (  14-)  A  Poor phi/psi
  59 ASP   (  66-)  A  PRO omega poor
  79 SER   (  86-)  A  Poor phi/psi
  92 TYR   (  99-)  A  Poor phi/psi
  97 ARG   ( 104-)  A  Poor phi/psi
 102 ARG   ( 109-)  A  Poor phi/psi
 145 GLY   ( 152-)  A  Poor phi/psi
 157 ASN   ( 164-)  A  Poor phi/psi
 160 ASP   ( 167-)  A  Poor phi/psi
 211 ASP   ( 227-)  A  Poor phi/psi
 213 ALA   ( 229-)  A  Poor phi/psi
 288 GLN   ( 308-)  A  Poor phi/psi
 302 LEU   (  14-)  B  Poor phi/psi
 323 CYS   (  35-)  B  Poor phi/psi
 326 THR   (  38-)  B  Poor phi/psi
 354 ASP   (  66-)  B  PRO omega poor
 374 SER   (  86-)  B  Poor phi/psi
 387 TYR   (  99-)  B  Poor phi/psi
 392 ARG   ( 104-)  B  Poor phi/psi
 397 ARG   ( 109-)  B  Poor phi/psi
 413 GLY   ( 125-)  B  Poor phi/psi
 455 ASP   ( 167-)  B  Poor phi/psi
 477 LYS   ( 189-)  B  Poor phi/psi
 506 ASP   ( 227-)  B  Poor phi/psi
 508 ALA   ( 229-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.536

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 154 GLU   ( 161-)  A    0.36

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 LEU   (  14-)  A      0
   8 ASN   (  15-)  A      0
   9 SER   (  16-)  A      0
  10 ASN   (  17-)  A      0
  21 VAL   (  28-)  A      0
  27 LYS   (  34-)  A      0
  28 CYS   (  35-)  A      0
  33 PHE   (  40-)  A      0
  43 GLU   (  50-)  A      0
  46 ILE   (  53-)  A      0
  47 ARG   (  54-)  A      0
  55 GLN   (  62-)  A      0
  56 SER   (  63-)  A      0
  57 THR   (  64-)  A      0
  58 SER   (  65-)  A      0
  59 ASP   (  66-)  A      0
  60 PRO   (  67-)  A      0
  61 VAL   (  68-)  A      0
  79 SER   (  86-)  A      0
  82 THR   (  89-)  A      0
  89 TYR   (  96-)  A      0
  92 TYR   (  99-)  A      0
  96 ASP   ( 103-)  A      0
  97 ARG   ( 104-)  A      0
  98 LYS   ( 105-)  A      0
And so on for a total of 227 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.940

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]

 243 PRO   ( 259-)  A    0.45 HIGH
 479 PRO   ( 191-)  B    0.46 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 192 MET   ( 208-)  A      SD  <->  218 LEU   ( 234-)  A      CD2    0.48    2.92  INTRA BF
 487 MET   ( 208-)  B      SD  <->  513 LEU   ( 234-)  B      CD2    0.45    2.95  INTRA BF
  98 LYS   ( 105-)  A      NZ  <->  595 HOH   (1043 )  A      O      0.35    2.35  INTRA
 156 LYS   ( 163-)  A      NZ  <->  255 GLU   ( 271-)  A      OE1    0.31    2.39  INTRA
 455 ASP   ( 167-)  B      OD1 <->  496 LYS   ( 217-)  B      NZ     0.24    2.46  INTRA BF
 310 LYS   (  22-)  B      NZ  <->  314 ASP   (  26-)  B      OD2    0.24    2.46  INTRA
 566 GLN   ( 291-)  B      NE2 <->  596 HOH   (1047 )  B      O      0.22    2.48  INTRA
  42 ILE   (  49-)  A      N   <->  595 HOH   (1047 )  A      O      0.21    2.49  INTRA
 253 ILE   ( 269-)  A      O   <->  268 ARG   ( 288-)  A      NH2    0.21    2.49  INTRA
 127 LEU   ( 134-)  A      N   <->  142 HIS   ( 149-)  A      CE1    0.20    2.90  INTRA BL
 548 ILE   ( 269-)  B      O   <->  563 ARG   ( 288-)  B      NH2    0.19    2.51  INTRA
 271 GLN   ( 291-)  A      NE2 <->  595 HOH   (1073 )  A      O      0.18    2.52  INTRA
 334 GLN   (  46-)  B      OE1 <->  336 ASN   (  48-)  B      ND2    0.17    2.53  INTRA BF
 456 ILE   ( 168-)  B      CG2 <->  457 VAL   ( 169-)  B      N      0.16    2.84  INTRA
 526 VAL   ( 247-)  B      N   <->  596 HOH   (1076 )  B      O      0.15    2.55  INTRA
 310 LYS   (  22-)  B      NZ  <->  314 ASP   (  26-)  B      CG     0.14    2.96  INTRA
 178 ALA   ( 185-)  A      O   <->  182 LYS   ( 189-)  A      N      0.14    2.56  INTRA
 594 AP2   (1001-)  B      N3  <->  596 HOH   (1029 )  B      O      0.14    2.56  INTRA
 336 ASN   (  48-)  B      CA  <->  596 HOH   (1064 )  B      O      0.12    2.68  INTRA
 128 HIS   ( 135-)  A      NE2 <->  592 ABM   (1003-)  A      O3P    0.12    2.58  INTRA
 353 SER   (  65-)  B      O   <->  359 HIS   (  71-)  B      ND1    0.11    2.59  INTRA BL
 173 ARG   ( 180-)  A      NH2 <->  595 HOH   (1051 )  A      O      0.11    2.59  INTRA
 394 ALA   ( 106-)  B      O   <->  395 ARG   ( 107-)  B      NH1    0.11    2.49  INTRA BF
 515 ALA   ( 236-)  B      O   <->  518 LEU   ( 239-)  B      N      0.11    2.59  INTRA
 161 ILE   ( 168-)  A      CG2 <->  162 VAL   ( 169-)  A      N      0.11    2.89  INTRA
And so on for a total of 81 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 102 ARG   ( 109-)  A      -7.38
  24 GLN   (  31-)  A      -7.03
 397 ARG   ( 109-)  B      -6.91
 319 GLN   (  31-)  B      -6.91
 263 LYS   ( 279-)  A      -5.96
 558 LYS   ( 279-)  B      -5.81
 100 ARG   ( 107-)  A      -5.65
 485 LYS   ( 197-)  B      -5.49
 190 LYS   ( 197-)  A      -5.41
 168 HIS   ( 175-)  A      -5.15
 342 ARG   (  54-)  B      -5.11
 463 HIS   ( 175-)  B      -5.09

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 286 HIS   ( 306-)  A       288 - GLN    308- ( A)         -4.47

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 142 HIS   ( 149-)  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.

  44 GLU   (  51-)  A      N
  47 ARG   (  54-)  A      NE
  62 ASN   (  69-)  A      ND2
  94 ARG   ( 101-)  A      NH2
  97 ARG   ( 104-)  A      N
 102 ARG   ( 109-)  A      N
 102 ARG   ( 109-)  A      NE
 103 GLU   ( 110-)  A      N
 129 ALA   ( 136-)  A      N
 133 GLN   ( 140-)  A      NE2
 142 HIS   ( 149-)  A      N
 168 HIS   ( 175-)  A      N
 175 ARG   ( 182-)  A      NE
 255 GLU   ( 271-)  A      N
 262 ILE   ( 278-)  A      N
 269 PHE   ( 289-)  A      N
 291 VAL   ( 311-)  A      N
 307 GLU   (  19-)  B      N
 339 GLU   (  51-)  B      N
 342 ARG   (  54-)  B      NE
 342 ARG   (  54-)  B      NH2
 357 ASN   (  69-)  B      ND2
 389 ARG   ( 101-)  B      NH2
 397 ARG   ( 109-)  B      N
 397 ARG   ( 109-)  B      NE
 424 ALA   ( 136-)  B      N
 428 GLN   ( 140-)  B      NE2
 437 HIS   ( 149-)  B      N
 463 HIS   ( 175-)  B      N
 466 VAL   ( 178-)  B      N
 470 ARG   ( 182-)  B      NE
 550 GLU   ( 271-)  B      N
 557 ILE   ( 278-)  B      N
 564 PHE   ( 289-)  B      N
 586 VAL   ( 311-)  B      N
 587 SER   ( 312-)  B      OG

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.

 432 ASP   ( 144-)  B      OD2

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.

 160 ASP   ( 167-)  A   H-bonding suggests Asn
 455 ASP   ( 167-)  B   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 :   0.021
  2nd generation packing quality :  -1.249
  Ramachandran plot appearance   :  -1.709
  chi-1/chi-2 rotamer normality  :  -2.536
  Backbone conformation          :   0.186

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.702
  Bond angles                    :   0.864
  Omega angle restraints         :   0.353 (tight)
  Side chain planarity           :   0.845
  Improper dihedral distribution :   1.223
  B-factor distribution          :   0.479
  Inside/Outside distribution    :   0.948

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.702
  Bond angles                    :   0.864
  Omega angle restraints         :   0.353 (tight)
  Side chain planarity           :   0.845
  Improper dihedral distribution :   1.223
  B-factor distribution          :   0.479
  Inside/Outside distribution    :   0.948
==============

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.