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 pdb1alj.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    = 194.760  B   = 167.740  C    =  76.230
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 134.051  B   =  76.230  C    = 134.051
    Alpha=  73.481  Beta=  77.461  Gamma=  73.481

Dimensions of the conventional cell

    A    =  76.230  B   = 167.740  C    = 194.760
    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 : 0.160
CA-only RMS fit for the two chains : 0.072

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.

 899 PO4   ( 453-)  A  -
 900 PO4   ( 453-)  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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   5 GLU   (   8-)  A    High
  89 LYS   (  92-)  A    High
 173 GLU   ( 176-)  A    High
 220 LYS   ( 223-)  A    High
 245 GLU   ( 248-)  A    High
 249 GLN   ( 252-)  A    High
 289 ARG   ( 292-)  A    High
 311 GLU   ( 314-)  A    High
 324 ASP   ( 327-)  A    High
 325 LYS   ( 328-)  A    High
 326 GLN   ( 329-)  A    High
 328 HIS   ( 331-)  A    High
 351 GLU   ( 354-)  A    High
 404 GLU   ( 407-)  A    High
 405 ASP   ( 408-)  A    High
 406 SER   ( 409-)  A    High
 408 GLU   ( 411-)  A    High
 446 LYS   ( 449-)  A    High
 451 GLU   (   8-)  B    High
 486 LYS   (  43-)  B    High
 535 LYS   (  92-)  B    High
 619 GLU   ( 176-)  B    High
 666 LYS   ( 223-)  B    High
 669 ARG   ( 226-)  B    High
 691 GLU   ( 248-)  B    High
 695 GLN   ( 252-)  B    High
 734 GLN   ( 291-)  B    High
 735 ARG   ( 292-)  B    High
 757 GLU   ( 314-)  B    High
 770 ASP   ( 327-)  B    High
 771 LYS   ( 328-)  B    High
 772 GLN   ( 329-)  B    High
 774 HIS   ( 331-)  B    High
 797 GLU   ( 354-)  B    High
 801 LYS   ( 358-)  B    High
 850 GLU   ( 407-)  B    High
 851 ASP   ( 408-)  B    High
 852 SER   ( 409-)  B    High
 892 LYS   ( 449-)  B    High

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 : 17.56

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 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.

  85 ALA   (  88-)  A      CA   CB    1.39   -4.0

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.

  76 PRO   (  79-)  A      N    CA   C   123.80    4.8
  94 ASP   (  97-)  A      N    CA   C    99.21   -4.3
 196 ARG   ( 199-)  A      CB   CG   CD  105.95   -4.1
 273 HIS   ( 276-)  A      CG   ND1  CE1 109.99    4.4
 290 ASN   ( 293-)  A      N    CA   C   122.84    4.2
 308 SER   ( 311-)  A      CA   CB   OG  103.00   -4.1
 320 GLY   ( 323-)  A      N    CA   C    99.14   -4.6
 522 PRO   (  79-)  B      N    CA   C   123.78    4.8
 529 HIS   (  86-)  B      CG   ND1  CE1 110.10    4.5
 736 ASN   ( 293-)  B      N    CA   C   124.60    4.8
 766 GLY   ( 323-)  B      N    CA   C    99.16   -4.6

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.

  62 ALA   (  65-)  A    6.40
 508 ALA   (  65-)  B    6.27
 320 GLY   ( 323-)  A    5.37
 766 GLY   ( 323-)  B    5.36
 520 ALA   (  77-)  B    4.88
 768 SER   ( 325-)  B    4.88
 174 LYS   ( 177-)  A    4.87
 597 ALA   ( 154-)  B    4.76
 321 ALA   ( 324-)  A    4.41
  76 PRO   (  79-)  A    4.29
 522 PRO   (  79-)  B    4.28
 151 ALA   ( 154-)  A    4.24
 736 ASN   ( 293-)  B    4.22
 322 SER   ( 325-)  A    4.07
 643 ALA   ( 200-)  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 : 1.576

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.

 541 TYR   (  98-)  B      OH   4.22
 813 HIS   ( 370-)  B      CB   4.09
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.266

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.

 364 THR   ( 367-)  A    -3.2
 810 THR   ( 367-)  B    -3.1
 112 THR   ( 115-)  A    -2.8
 558 THR   ( 115-)  B    -2.7
 860 LEU   ( 417-)  B    -2.5
 414 LEU   ( 417-)  A    -2.5
 614 PRO   ( 171-)  B    -2.4
 778 PRO   ( 335-)  B    -2.3
 332 PRO   ( 335-)  A    -2.2
 443 LEU   ( 446-)  A    -2.2
 693 ASN   ( 250-)  B    -2.1
 889 LEU   ( 446-)  B    -2.1
 247 ASN   ( 250-)  A    -2.1
 615 SER   ( 172-)  B    -2.1
 815 HIS   ( 372-)  B    -2.1
 369 HIS   ( 372-)  A    -2.1
 168 PRO   ( 171-)  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.

 108 THR   ( 111-)  A  Poor phi/psi
 123 GLU   ( 126-)  A  Poor phi/psi
 146 ALA   ( 149-)  A  Poor phi/psi
 165 CYS   ( 168-)  A  Poor phi/psi
 273 HIS   ( 276-)  A  Poor phi/psi
 290 ASN   ( 293-)  A  Poor phi/psi
 404 GLU   ( 407-)  A  Poor phi/psi
 405 ASP   ( 408-)  A  Poor phi/psi
 422 HIS   ( 425-)  A  Poor phi/psi
 554 THR   ( 111-)  B  Poor phi/psi
 569 GLU   ( 126-)  B  Poor phi/psi
 611 CYS   ( 168-)  B  Poor phi/psi
 719 HIS   ( 276-)  B  Poor phi/psi
 736 ASN   ( 293-)  B  Poor phi/psi
 850 GLU   ( 407-)  B  Poor phi/psi
 851 ASP   ( 408-)  B  Poor phi/psi
 868 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.009

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 : -3.009

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.

 239 SER   ( 242-)  A    0.35

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!

   3 VAL   (   6-)  A      0
   4 LEU   (   7-)  A      0
   6 ASN   (   9-)  A      0
   7 ARG   (  10-)  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
  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
  62 ALA   (  65-)  A      0
  74 ALA   (  77-)  A      0
  83 HIS   (  86-)  A      0
  92 LYS   (  95-)  A      0
 107 SER   ( 110-)  A      0
 113 TYR   ( 116-)  A      0
 114 ASN   ( 117-)  A      0
 116 ALA   ( 119-)  A      0
 117 LEU   ( 120-)  A      0
 121 ILE   ( 124-)  A      0
And so on for a total of 332 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 : 1.995

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]

 176 PRO   ( 179-)  A    0.47 HIGH
 332 PRO   ( 335-)  A    0.50 HIGH
 697 PRO   ( 254-)  B    0.45 HIGH
 778 PRO   ( 335-)  B    0.45 HIGH
 867 PRO   ( 424-)  B    0.45 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.

 494 ASP   (  51-)  B      CB  <->  902 HOH   ( 499 )  B      O      0.35    2.45  INTRA
 706 ASN   ( 263-)  B      ND2 <->  771 LYS   ( 328-)  B      CE     0.30    2.80  INTRA BF
 719 HIS   ( 276-)  B      NE2 <->  825 LYS   ( 382-)  B      NZ     0.29    2.71  INTRA BF
 774 HIS   ( 331-)  B      ND1 <->  853 GLN   ( 410-)  B      O      0.25    2.45  INTRA BF
  20 ARG   (  23-)  A      NE  <->  901 HOH   ( 474 )  A      O      0.25    2.45  INTRA BL
 770 ASP   ( 327-)  B      N   <->  902 HOH   ( 499 )  B      O      0.23    2.47  INTRA BF
 770 ASP   ( 327-)  B      CB  <->  902 HOH   ( 499 )  B      O      0.23    2.57  INTRA BF
 328 HIS   ( 331-)  A      ND1 <->  407 GLN   ( 410-)  A      O      0.21    2.49  INTRA BF
 580 LYS   ( 137-)  B      NZ  <->  641 ALA   ( 198-)  B      O      0.21    2.49  INTRA
 617 THR   ( 174-)  B      O   <->  621 CYS   ( 178-)  B      C      0.19    2.61  INTRA
 171 THR   ( 174-)  A      O   <->  175 CYS   ( 178-)  A      N      0.18    2.52  INTRA
 273 HIS   ( 276-)  A      NE2 <->  379 LYS   ( 382-)  A      NZ     0.18    2.82  INTRA BF
 611 CYS   ( 168-)  B      SG  <->  620 LYS   ( 177-)  B      CB     0.18    3.22  INTRA
 710 ARG   ( 267-)  B      NH1 <->  787 ASP   ( 344-)  B      OD1    0.18    2.52  INTRA
 321 ALA   ( 324-)  A      O   <->  323 ILE   ( 326-)  A      N      0.18    2.52  INTRA BF
 617 THR   ( 174-)  B      O   <->  621 CYS   ( 178-)  B      N      0.17    2.53  INTRA BL
 134 LYS   ( 137-)  A      NZ  <->  195 ALA   ( 198-)  A      O      0.16    2.54  INTRA
 481 SER   (  38-)  B      N   <->  902 HOH   ( 495 )  B      O      0.16    2.54  INTRA BL
 260 ASN   ( 263-)  A      ND2 <->  325 LYS   ( 328-)  A      CE     0.15    2.95  INTRA BF
 264 ARG   ( 267-)  A      NH1 <->  341 ASP   ( 344-)  A      OD1    0.15    2.55  INTRA
  26 GLN   (  29-)  A      N   <->  871 ASN   ( 428-)  B      OD1    0.13    2.57  INTRA BL
 165 CYS   ( 168-)  A      SG  <->  174 LYS   ( 177-)  A      CB     0.13    3.27  INTRA
 802 GLU   ( 359-)  B      OE1 <->  804 ASN   ( 361-)  B      N      0.12    2.58  INTRA
 264 ARG   ( 267-)  A      O   <->  289 ARG   ( 292-)  A      NH2    0.11    2.59  INTRA BF
 469 THR   (  26-)  B      N   <->  902 HOH   ( 537 )  B      O      0.11    2.59  INTRA
And so on for a total of 100 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      -6.96
 272 TYR   ( 275-)  A      -6.71
 695 GLN   ( 252-)  B      -5.97
 249 GLN   ( 252-)  A      -5.90
  89 LYS   (  92-)  A      -5.77
 535 LYS   (  92-)  B      -5.69
 675 ARG   ( 232-)  B      -5.32
 229 ARG   ( 232-)  A      -5.27
 758 LYS   ( 315-)  B      -5.12
 289 ARG   ( 292-)  A      -5.04
 312 LYS   ( 315-)  A      -5.01

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

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.

 321 ALA   ( 324-)  A   -2.74

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 600 ALA   ( 157-)  B     -  603 VAL   ( 160-)  B        -1.61

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.

 901 HOH   ( 455 )  A      O     60.91   41.95   50.98
 901 HOH   ( 483 )  A      O     41.62   39.11   46.53
 902 HOH   ( 498 )  B      O     48.46   50.56   41.11

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.

 902 HOH   ( 481 )  B      O
 902 HOH   ( 483 )  B      O
Metal-coordinating Histidine residue 367 fixed to   1
Metal-coordinating Histidine residue 813 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.

 288 GLN   ( 291-)  A
 568 HIS   ( 125-)  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
  37 LYS   (  40-)  A      NZ
  75 LEU   (  78-)  A      N
  78 THR   (  81-)  A      N
  80 GLN   (  83-)  A      NE2
  99 SER   ( 102-)  A      N
 100 ALA   ( 103-)  A      N
 119 VAL   ( 122-)  A      N
 162 SER   ( 165-)  A      N
 181 GLU   ( 184-)  A      N
 214 ALA   ( 217-)  A      N
 257 ALA   ( 260-)  A      N
 289 ARG   ( 292-)  A      NH2
 293 VAL   ( 296-)  A      N
 323 ILE   ( 326-)  A      N
 325 LYS   ( 328-)  A      N
 335 GLN   ( 338-)  A      NE2
 359 THR   ( 362-)  A      N
 368 ALA   ( 371-)  A      N
 377 ASP   ( 380-)  A      N
 399 TYR   ( 402-)  A      OH
 401 ASN   ( 404-)  A      ND2
 453 ARG   (  10-)  B      N
 487 ASN   (  44-)  B      ND2
 521 LEU   (  78-)  B      N
 524 THR   (  81-)  B      N
 526 GLN   (  83-)  B      NE2
 546 ALA   ( 103-)  B      N
 597 ALA   ( 154-)  B      N
 627 GLU   ( 184-)  B      N
 660 ALA   ( 217-)  B      N
 663 TRP   ( 220-)  B      N
 769 ILE   ( 326-)  B      N
 771 LYS   ( 328-)  B      N
 781 GLN   ( 338-)  B      NE2
 794 ARG   ( 351-)  B      NH1
 814 ALA   ( 371-)  B      N
 821 ALA   ( 378-)  B      N
 825 LYS   ( 382-)  B      N
 828 GLY   ( 385-)  B      N
 845 TYR   ( 402-)  B      OH
 847 ASN   ( 404-)  B      ND2
Only metal coordination for  366 ASP  ( 369-) A      OD2
Only metal coordination for  813 HIS  ( 370-) 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.

 408 GLU   ( 411-)  A      OE1
 409 ASN   ( 412-)  A      OD1
 494 ASP   (  51-)  B      OD1
 765 GLU   ( 322-)  B      OE2
 854 GLU   ( 411-)  B      OE1
 855 ASN   ( 412-)  B      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 895  ZN   ( 451-)  A   -.-  -.-  Low probability ion. Occ=0.24
 896  MG   ( 452-)  A   -.-  -.-  Part of ionic cluster
 896  MG   ( 452-)  A     0.25   0.93 Is perhaps  K
 897  ZN   ( 451-)  B   -.-  -.-  Low probability ion. Occ=0.41
 898  MG   ( 452-)  B   -.-  -.-  Part of ionic cluster
 898  MG   ( 452-)  B   -.-  -.-  Too few ligands (3)

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
 311 GLU   ( 314-)  A   H-bonding suggests Gln
 408 GLU   ( 411-)  A   H-bonding suggests Gln; but Alt-Rotamer
 757 GLU   ( 314-)  B   H-bonding suggests Gln
 854 GLU   ( 411-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :  -0.401
  2nd generation packing quality :  -1.092
  Ramachandran plot appearance   :  -1.266
  chi-1/chi-2 rotamer normality  :  -3.009 (poor)
  Backbone conformation          :  -0.354

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.763
  Bond angles                    :   0.875
  Omega angle restraints         :   0.363 (tight)
  Side chain planarity           :   1.012
  Improper dihedral distribution :   1.257
  Inside/Outside distribution    :   0.931

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.763
  Bond angles                    :   0.875
  Omega angle restraints         :   0.363 (tight)
  Side chain planarity           :   1.012
  Improper dihedral distribution :   1.257
  Inside/Outside distribution    :   0.931
==============

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.