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 pdb2anh.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 194.770  B   = 166.960  C    =  76.330
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 133.826  B   =  76.330  C    = 133.826
    Alpha=  73.430  Beta=  77.188  Gamma=  73.430

Dimensions of the conventional cell

    A    =  76.330  B   = 166.960  C    = 194.770
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000  1.000000|
 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|

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 : 0.167
CA-only RMS fit for the two chains : 0.074

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.

 898 PO4   ( 453-)  A  -
 902 PO4   ( 458-)  A  -
 903 PO4   ( 453-)  B  -

Administrative problems that can generate validation failures

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.

 405 ASP   ( 408-)  A  -   OD1
 405 ASP   ( 408-)  A  -   OD2

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:

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 : 13.69

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

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.

  94 ASP   (  97-)  A      N    CA   C    99.21   -4.3
 150 HIS   ( 153-)  A      CG   ND1  CE1 109.74    4.1
 159 HIS   ( 162-)  A      CG   ND1  CE1 109.71    4.1
 264 ARG   ( 267-)  A      CB   CG   CD  105.96   -4.1
 273 HIS   ( 276-)  A      CG   ND1  CE1 109.80    4.2
 290 ASN   ( 293-)  A      N    CA   C   126.44    5.4
 320 GLY   ( 323-)  A      N    CA   C    99.84   -4.4
 321 ALA   ( 324-)  A      N    CA   C   122.86    4.2
 493 GLY   (  50-)  B      N    CA   C    99.62   -4.4
 529 HIS   (  86-)  B      CG   ND1  CE1 109.60    4.0
 719 HIS   ( 276-)  B      CG   ND1  CE1 109.67    4.1
 736 ASN   ( 293-)  B      N    CA   C   127.92    6.0
 766 GLY   ( 323-)  B      N    CA   C    98.67   -4.8

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.

 508 ALA   (  65-)  B    5.92
 766 GLY   ( 323-)  B    5.58
 768 SER   ( 325-)  B    5.32
 736 ASN   ( 293-)  B    5.31
 493 GLY   (  50-)  B    5.16
  62 ALA   (  65-)  A    5.15
 320 GLY   ( 323-)  A    5.06
 290 ASN   ( 293-)  A    4.83
 321 ALA   ( 324-)  A    4.76
 151 ALA   ( 154-)  A    4.61
 767 ALA   ( 324-)  B    4.52
 861 ARG   ( 418-)  B    4.49
 597 ALA   ( 154-)  B    4.46
 322 SER   ( 325-)  A    4.42
  47 GLY   (  50-)  A    4.34
 327 ASP   ( 330-)  A    4.16
 415 ARG   ( 418-)  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 : 1.530

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.

 810 THR   ( 367-)  B    -3.1
 364 THR   ( 367-)  A    -3.1
 112 THR   ( 115-)  A    -3.0
 558 THR   ( 115-)  B    -2.9
 614 PRO   ( 171-)  B    -2.8
 414 LEU   ( 417-)  A    -2.6
 860 LEU   ( 417-)  B    -2.6
 168 PRO   ( 171-)  A    -2.5
 369 HIS   ( 372-)  A    -2.3
 229 ARG   ( 232-)  A    -2.3
 825 LYS   ( 382-)  B    -2.2
 129 ILE   ( 132-)  A    -2.2
 152 THR   ( 155-)  A    -2.2
 247 ASN   ( 250-)  A    -2.2
 612 TYR   ( 169-)  B    -2.1
 443 LEU   ( 446-)  A    -2.1
 245 GLU   ( 248-)  A    -2.1
 889 LEU   ( 446-)  B    -2.1
 691 GLU   ( 248-)  B    -2.1
 379 LYS   ( 382-)  A    -2.0
  81 TYR   (  84-)  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.

  85 ALA   (  88-)  A  Poor phi/psi
 123 GLU   ( 126-)  A  Poor phi/psi
 165 CYS   ( 168-)  A  Poor phi/psi
 219 GLY   ( 222-)  A  Poor phi/psi
 273 HIS   ( 276-)  A  Poor phi/psi
 290 ASN   ( 293-)  A  Poor phi/psi
 330 ALA   ( 333-)  A  Poor phi/psi
 422 HIS   ( 425-)  A  Poor phi/psi
 531 ALA   (  88-)  B  Poor phi/psi
 569 GLU   ( 126-)  B  Poor phi/psi
 611 CYS   ( 168-)  B  Poor phi/psi
 665 GLY   ( 222-)  B  Poor phi/psi
 719 HIS   ( 276-)  B  Poor phi/psi
 736 ASN   ( 293-)  B  Poor phi/psi
 776 ALA   ( 333-)  B  Poor phi/psi
 868 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.845

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!

   6 ASN   (   9-)  A      0
   7 ARG   (  10-)  A      0
   9 ALA   (  12-)  A      0
  10 GLN   (  13-)  A      0
  12 ASP   (  15-)  A      0
  15 ALA   (  18-)  A      0
  16 PRO   (  19-)  A      0
  20 ARG   (  23-)  A      0
  25 ASP   (  28-)  A      0
  35 SER   (  38-)  A      0
  36 ASP   (  39-)  A      0
  40 LYS   (  43-)  A      0
  41 ASN   (  44-)  A      0
  48 ASP   (  51-)  A      0
  50 MET   (  53-)  A      0
  74 ALA   (  77-)  A      0
  83 HIS   (  86-)  A      0
  95 TYR   (  98-)  A      0
 107 SER   ( 110-)  A      0
 111 LYS   ( 114-)  A      0
 113 TYR   ( 116-)  A      0
 114 ASN   ( 117-)  A      0
 117 LEU   ( 120-)  A      0
 121 ILE   ( 124-)  A      0
 123 GLU   ( 126-)  A      0
And so on for a total of 344 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 : 1.736

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]

 251 PRO   ( 254-)  A    0.45 HIGH
 285 PRO   ( 288-)  A    0.45 HIGH
 332 PRO   ( 335-)  A    0.46 HIGH
 381 PRO   ( 384-)  A    0.46 HIGH
 539 PRO   (  96-)  B    0.46 HIGH
 731 PRO   ( 288-)  B    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].

 268 PRO   ( 271-)  A    52.3 half-chair C-delta/C-gamma (54 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.

 166 TYR   ( 169-)  A      OH  <->  902 PO4   ( 458-)  A      P      0.37    2.63  INTRA BF
 580 LYS   ( 137-)  B      NZ  <->  641 ALA   ( 198-)  B      O      0.27    2.43  INTRA
 902 PO4   ( 458-)  A      P   <->  904 HOH   ( 563 )  A      O      0.26    2.74  INTRA BF
 545 SER   ( 102-)  B      CB  <->  903 PO4   ( 453-)  B      P      0.22    3.18  INTRA
 545 SER   ( 102-)  B      CB  <->  900  ZN   ( 451-)  B     ZN      0.21    2.99  INTRA BL
 163 ARG   ( 166-)  A      NH2 <->  902 PO4   ( 458-)  A      O3     0.20    2.50  INTRA BF
 134 LYS   ( 137-)  A      NZ  <->  195 ALA   ( 198-)  A      O      0.20    2.50  INTRA
 642 ARG   ( 199-)  B      NH2 <->  675 ARG   ( 232-)  B      O      0.19    2.51  INTRA
 689 VAL   ( 246-)  B      O   <->  748 LYS   ( 305-)  B      NZ     0.18    2.52  INTRA
 611 CYS   ( 168-)  B      SG  <->  620 LYS   ( 177-)  B      CB     0.18    3.22  INTRA
 617 THR   ( 174-)  B      O   <->  621 CYS   ( 178-)  B      C      0.16    2.64  INTRA
 617 THR   ( 174-)  B      O   <->  621 CYS   ( 178-)  B      N      0.15    2.55  INTRA
 483 LYS   (  40-)  B      NZ  <->  804 ASN   ( 361-)  B      OD1    0.14    2.56  INTRA BF
  20 ARG   (  23-)  A      NE  <->  904 HOH   ( 515 )  A      O      0.14    2.56  INTRA
 225 GLN   ( 228-)  A      OE1 <->  229 ARG   ( 232-)  A      NH1    0.14    2.56  INTRA
 243 VAL   ( 246-)  A      O   <->  302 LYS   ( 305-)  A      NZ     0.14    2.56  INTRA
 742 LEU   ( 299-)  B      N   <->  905 HOH   ( 490 )  B      O      0.13    2.57  INTRA
 367 HIS   ( 370-)  A      NE2 <->  409 HIS   ( 412-)  A      CE1    0.13    2.97  INTRA BL
 286 ASN   ( 289-)  A      O   <->  289 ARG   ( 292-)  A      CG     0.13    2.67  INTRA
 671 GLN   ( 228-)  B      OE1 <->  675 ARG   ( 232-)  B      NH1    0.13    2.57  INTRA
 611 CYS   ( 168-)  B      SG  <->  621 CYS   ( 178-)  B      N      0.11    3.19  INTRA
 642 ARG   ( 199-)  B      NH1 <->  694 GLN   ( 251-)  B      O      0.10    2.60  INTRA
 454 ALA   (  11-)  B      O   <->  456 GLN   (  13-)  B      NE2    0.10    2.60  INTRA
 165 CYS   ( 168-)  A      SG  <->  175 CYS   ( 178-)  A      N      0.10    3.20  INTRA
  99 SER   ( 102-)  A      CB  <->  898 PO4   ( 453-)  A      P      0.10    3.30  INTRA
And so on for a total of 80 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.

 718 TYR   ( 275-)  B      -6.82
 272 TYR   ( 275-)  A      -6.64
 695 GLN   ( 252-)  B      -5.79
 249 GLN   ( 252-)  A      -5.74
  89 LYS   (  92-)  A      -5.70
 535 LYS   (  92-)  B      -5.69
 675 ARG   ( 232-)  B      -5.49
 735 ARG   ( 292-)  B      -5.43

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

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.

 904 HOH   ( 465 )  A      O     95.85   33.68   31.13
 904 HOH   ( 498 )  A      O     43.22   44.95   40.20
 904 HOH   ( 513 )  A      O     97.43   59.29   39.25
 904 HOH   ( 531 )  A      O     33.29   23.17   14.66

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 904 HOH   ( 518 )  A      O
Metal-coordinating Histidine residue 328 fixed to   1
Metal-coordinating Histidine residue 409 fixed to   1
Metal-coordinating Histidine residue 367 fixed to   1
Metal-coordinating Histidine residue 150 fixed to   1
Metal-coordinating Histidine residue 774 fixed to   1
Metal-coordinating Histidine residue 855 fixed to   1
Metal-coordinating Histidine residue 813 fixed to   1
Metal-coordinating Histidine residue 596 fixed to   1

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.

 122 HIS   ( 125-)  A
 178 ASN   ( 181-)  A
 273 HIS   ( 276-)  A
 335 GLN   ( 338-)  A
 624 ASN   ( 181-)  B
 719 HIS   ( 276-)  B
 781 GLN   ( 338-)  B

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.

   7 ARG   (  10-)  A      N
  24 GLY   (  27-)  A      N
  28 ALA   (  31-)  A      N
  75 LEU   (  78-)  A      N
  78 THR   (  81-)  A      N
  96 VAL   (  99-)  A      N
  99 SER   ( 102-)  A      N
 100 ALA   ( 103-)  A      N
 119 VAL   ( 122-)  A      N
 140 THR   ( 143-)  A      OG1
 151 ALA   ( 154-)  A      N
 185 LYS   ( 188-)  A      N
 207 THR   ( 210-)  A      N
 214 ALA   ( 217-)  A      N
 264 ARG   ( 267-)  A      NE
 273 HIS   ( 276-)  A      N
 293 VAL   ( 296-)  A      N
 297 ALA   ( 300-)  A      N
 323 ILE   ( 326-)  A      N
 379 LYS   ( 382-)  A      N
 401 ASN   ( 404-)  A      ND2
 402 SER   ( 405-)  A      N
 406 SER   ( 409-)  A      N
 412 SER   ( 415-)  A      N
 453 ARG   (  10-)  B      N
 466 ARG   (  23-)  B      NE
 470 GLY   (  27-)  B      N
 472 GLN   (  29-)  B      NE2
 521 LEU   (  78-)  B      N
 524 THR   (  81-)  B      N
 545 SER   ( 102-)  B      N
 546 ALA   ( 103-)  B      N
 561 GLY   ( 118-)  B      N
 565 VAL   ( 122-)  B      N
 608 SER   ( 165-)  B      N
 631 LYS   ( 188-)  B      N
 653 THR   ( 210-)  B      N
 660 ALA   ( 217-)  B      N
 743 ALA   ( 300-)  B      N
 769 ILE   ( 326-)  B      N
 779 CYS   ( 336-)  B      N
 805 THR   ( 362-)  B      N
 825 LYS   ( 382-)  B      N
 826 ALA   ( 383-)  B      N
 847 ASN   ( 404-)  B      ND2
 852 SER   ( 409-)  B      N
 858 SER   ( 415-)  B      N
Only metal coordination for   48 ASP  (  51-) A      OD1
Only metal coordination for  150 HIS  ( 153-) A      NE2
Only metal coordination for  319 GLU  ( 322-) A      OE2
Only metal coordination for  324 ASP  ( 327-) A      OD2
Only metal coordination for  367 HIS  ( 370-) A      NE2
Only metal coordination for  494 ASP  (  51-) B      OD1
Only metal coordination for  596 HIS  ( 153-) B      NE2
Only metal coordination for  765 GLU  ( 322-) B      OE2
Only metal coordination for  774 HIS  ( 331-) B      NE2
Only metal coordination for  812 ASP  ( 369-) B      OD2
Only metal coordination for  813 HIS  ( 370-) B      NE2
Only metal coordination for  855 HIS  ( 412-) B      NE2

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.

 831 GLN   ( 388-)  B      OE1

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.

  54 GLU   (  57-)  A   H-bonding suggests Gln

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 :  -0.366
  2nd generation packing quality :  -1.047
  Ramachandran plot appearance   :  -0.871
  chi-1/chi-2 rotamer normality  :  -2.845
  Backbone conformation          :  -0.143

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.528 (tight)
  Bond angles                    :   0.776
  Omega angle restraints         :   0.316 (tight)
  Side chain planarity           :   0.686
  Improper dihedral distribution :   1.031
  Inside/Outside distribution    :   0.933

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.528 (tight)
  Bond angles                    :   0.776
  Omega angle restraints         :   0.316 (tight)
  Side chain planarity           :   0.686
  Improper dihedral distribution :   1.031
  Inside/Outside distribution    :   0.933
==============

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.