WHAT IF Check report

This file was created 2012-01-12 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 pdb1rrp.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    = 121.339  B   = 139.463  C    =  91.654
    Alpha=  90.000  Beta= 135.780  Gamma=  90.000

Dimensions of a reduced cell

    A    =  84.754  B   =  91.654  C    =  92.430
    Alpha= 118.061  Beta= 115.532  Gamma=  93.175

Dimensions of the conventional cell

    A    = 121.339  B   = 139.463  C    =  84.754
    Alpha=  90.000  Beta= 131.045  Gamma=  90.000

Transformation to conventional cell

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

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 C

All-atom RMS fit for the two chains : 0.205
CA-only RMS fit for the two chains : 0.078

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 C

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: B and D

All-atom RMS fit for the two chains : 0.913
CA-only RMS fit for the two chains : 0.885

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: B and D

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 657 GNP   ( 250-)  A  -
 659 GNP   ( 250-)  C  -

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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.

   1 GLN   (   8-)  A    High
  39 GLU   (  46-)  A    High
  63 GLU   (  70-)  A    High
  64 LYS   (  71-)  A    High
  75 GLN   (  82-)  A    High
  88 ARG   (  95-)  A    High
  92 LYS   (  99-)  A    High
  96 ASN   ( 103-)  A    High
  99 ARG   ( 106-)  A    High
 100 ASP   ( 107-)  A    High
 103 ARG   ( 110-)  A    High
 106 GLU   ( 113-)  A    High
 107 ASN   ( 114-)  A    High
 121 ASP   ( 128-)  A    High
 125 LYS   ( 132-)  A    High
 127 LYS   ( 134-)  A    High
 132 HIS   ( 139-)  A    High
 133 ARG   ( 140-)  A    High
 134 LYS   ( 141-)  A    High
 135 LYS   ( 142-)  A    High
 136 ASN   ( 143-)  A    High
 168 GLU   ( 175-)  A    High
 181 VAL   ( 188-)  A    High
 182 MET   ( 189-)  A    High
 183 ASP   ( 190-)  A    High
And so on for a total of 94 lines.

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) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 3.085 over 4446 bonds
Average difference in B over a bond : 9.29
RMS difference in B over a bond : 12.04

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Geometric checks

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 184 PRO   ( 191-)  A      N      6.2    17.87    -2.48
The average deviation= 0.796

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.

 185 ALA   ( 192-)  A    4.72
 629 LEU   ( 127-)  D    4.26
 623 LEU   ( 121-)  D    4.03

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.409

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.

 184 PRO   ( 191-)  A    -3.1
 192 HIS   ( 199-)  A    -3.0
 534 THR   (  32-)  D    -2.7
 220 THR   (  32-)  B    -2.7
 216 ILE   (  28-)  B    -2.7
 441 ARG   ( 110-)  C    -2.4
 103 ARG   ( 110-)  A    -2.4
 291 ASN   ( 103-)  B    -2.4
 605 ASN   ( 103-)  D    -2.4
  85 VAL   (  92-)  A    -2.4
 423 VAL   (  92-)  C    -2.4
 537 GLU   (  35-)  D    -2.4
 223 GLU   (  35-)  B    -2.4
 218 VAL   (  30-)  B    -2.4
 308 GLU   ( 120-)  B    -2.3
 622 GLU   ( 120-)  D    -2.3
 508 VAL   ( 177-)  C    -2.3
 173 PRO   ( 180-)  A    -2.3
 170 VAL   ( 177-)  A    -2.3
 524 VAL   (  22-)  D    -2.3
 511 PRO   ( 180-)  C    -2.3
 544 CYS   (  42-)  D    -2.2
 230 CYS   (  42-)  B    -2.2
 424 THR   (  93-)  C    -2.2
  86 THR   (  93-)  A    -2.2
 517 GLU   ( 186-)  C    -2.2
 376 VAL   (  45-)  C    -2.2
  36 LEU   (  43-)  A    -2.2
 374 LEU   (  43-)  C    -2.2
  38 VAL   (  45-)  A    -2.2
  37 GLY   (  44-)  A    -2.1
 150 PHE   ( 157-)  A    -2.1
  52 ILE   (  59-)  A    -2.1
 107 ASN   ( 114-)  A    -2.1
 390 ILE   (  59-)  C    -2.1
 272 GLN   (  84-)  B    -2.1
 445 ASN   ( 114-)  C    -2.1
 586 GLN   (  84-)  D    -2.1
 375 GLY   (  44-)  C    -2.1
 619 TYR   ( 117-)  D    -2.0
 312 PRO   ( 124-)  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.

  38 VAL   (  45-)  A  Poor phi/psi
  61 GLY   (  68-)  A  Poor phi/psi
  66 GLY   (  73-)  A  Poor phi/psi
  69 ARG   (  76-)  A  Poor phi/psi
  70 ASP   (  77-)  A  Poor phi/psi
  78 CYS   (  85-)  A  Poor phi/psi
  85 VAL   (  92-)  A  Poor phi/psi
 102 VAL   ( 109-)  A  Poor phi/psi
 107 ASN   ( 114-)  A  Poor phi/psi
 108 ILE   ( 115-)  A  Poor phi/psi
 116 LYS   ( 123-)  A  Poor phi/psi
 117 VAL   ( 124-)  A  Poor phi/psi
 121 ASP   ( 128-)  A  Poor phi/psi
 136 ASN   ( 143-)  A  Poor phi/psi
 147 ASN   ( 154-)  A  Poor phi/psi
 149 ASN   ( 156-)  A  Poor phi/psi
 171 ALA   ( 178-)  A  Poor phi/psi
 182 MET   ( 189-)  A  Poor phi/psi
 184 PRO   ( 191-)  A  Poor phi/psi
 186 LEU   ( 193-)  A  Poor phi/psi
 197 ALA   ( 204-)  A  Poor phi/psi
 217 GLU   (  29-)  B  Poor phi/psi
 219 LYS   (  31-)  B  Poor phi/psi
 220 THR   (  32-)  B  Poor phi/psi
 221 GLY   (  33-)  B  Poor phi/psi
And so on for a total of 80 lines.

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 : -3.973

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!

   9 VAL   (  16-)  A      0
  11 ASP   (  18-)  A      0
  14 THR   (  21-)  A      0
  30 LYS   (  37-)  A      0
  33 VAL   (  40-)  A      0
  36 LEU   (  43-)  A      0
  38 VAL   (  45-)  A      0
  41 HIS   (  48-)  A      0
  49 ARG   (  56-)  A      0
  51 PRO   (  58-)  A      0
  58 ASP   (  65-)  A      0
  62 GLN   (  69-)  A      0
  69 ARG   (  76-)  A      0
  74 ILE   (  81-)  A      0
  75 GLN   (  82-)  A      0
  77 GLN   (  84-)  A      0
  78 CYS   (  85-)  A      0
  84 ASP   (  91-)  A      0
  85 VAL   (  92-)  A      0
 104 VAL   ( 111-)  A      0
 105 CYS   ( 112-)  A      0
 106 GLU   ( 113-)  A      0
 107 ASN   ( 114-)  A      0
 108 ILE   ( 115-)  A      0
 109 PRO   ( 116-)  A      0
And so on for a total of 292 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 : 1.223

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].

 184 PRO   ( 191-)  A   123.0 half-chair C-beta/C-alpha (126 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.

 223 GLU   (  35-)  B      O   <->  225 GLU   (  37-)  B      N      0.56    2.14  INTRA BF
 537 GLU   (  35-)  D      O   <->  539 GLU   (  37-)  D      N      0.55    2.15  INTRA BF
  22 ARG   (  29-)  A      NH2 <->  247 GLU   (  59-)  B      OE2    0.43    2.27  INTRA BF
  49 ARG   (  56-)  A      NE  <->  212 LEU   (  24-)  B      CD1    0.42    2.68  INTRA BL
 344 LEU   (  13-)  C      CD1 <->  416 CYS   (  85-)  C      SG     0.40    3.00  INTRA BL
 387 ARG   (  56-)  C      NE  <->  526 LEU   (  24-)  D      CD1    0.37    2.73  INTRA BL
 183 ASP   ( 190-)  A      N   <->  184 PRO   ( 191-)  A      CD     0.36    2.64  INTRA BF
 453 ASN   ( 122-)  C      CG  <->  454 LYS   ( 123-)  C      N      0.35    2.65  INTRA BL
 115 ASN   ( 122-)  A      CG  <->  116 LYS   ( 123-)  A      N      0.34    2.66  INTRA BF
   6 LEU   (  13-)  A      CD1 <->   78 CYS   (  85-)  A      SG     0.34    3.06  INTRA BF
 220 THR   (  32-)  B      O   <->  222 GLU   (  34-)  B      N      0.34    2.36  INTRA BF
 567 VAL   (  65-)  D      CG1 <->  582 MET   (  80-)  D      SD     0.32    3.08  INTRA BL
 239 ASP   (  51-)  B      O   <->  241 GLU   (  53-)  B      N      0.32    2.38  INTRA BF
 223 GLU   (  35-)  B      C   <->  225 GLU   (  37-)  B      N      0.32    2.58  INTRA BF
 534 THR   (  32-)  D      O   <->  536 GLU   (  34-)  D      N      0.31    2.39  INTRA BF
 179 GLU   ( 186-)  A      CD  <->  263 LYS   (  75-)  B      NZ     0.31    2.79  INTRA BF
 216 ILE   (  28-)  B      O   <->  218 VAL   (  30-)  B      N      0.30    2.40  INTRA BL
 618 ASP   ( 116-)  D      OD2 <->  620 ALA   ( 118-)  D      N      0.30    2.40  INTRA BL
 537 GLU   (  35-)  D      C   <->  539 GLU   (  37-)  D      N      0.30    2.60  INTRA BF
 151 GLU   ( 158-)  A      C   <->  153 PRO   ( 160-)  A      CD     0.30    2.90  INTRA BL
 489 GLU   ( 158-)  C      C   <->  491 PRO   ( 160-)  C      CD     0.30    2.90  INTRA BL
 553 ASP   (  51-)  D      O   <->  555 GLU   (  53-)  D      N      0.29    2.41  INTRA BF
 401 GLU   (  70-)  C      C   <->  403 PHE   (  72-)  C      N      0.28    2.62  INTRA
 304 ASP   ( 116-)  B      OD2 <->  306 ALA   ( 118-)  B      N      0.27    2.43  INTRA BL
 143 SER   ( 150-)  A      O   <->  145 LYS   ( 152-)  A      N      0.27    2.43  INTRA BL
And so on for a total of 364 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 219 LYS   (  31-)  B      -6.37
 533 LYS   (  31-)  D      -6.29
 370 TYR   (  39-)  C      -6.16
 175 LEU   ( 182-)  A      -6.15
  32 TYR   (  39-)  A      -6.14
 513 LEU   ( 182-)  C      -5.74
 546 ARG   (  44-)  D      -5.68
 232 ARG   (  44-)  B      -5.66
 520 PHE   (  18-)  D      -5.57
 517 GLU   ( 186-)  C      -5.54
 374 LEU   (  43-)  C      -5.52
  36 LEU   (  43-)  A      -5.49
 182 MET   ( 189-)  A      -5.42
 320 LYS   ( 132-)  B      -5.20
 634 LYS   ( 132-)  D      -5.15
 181 VAL   ( 188-)  A      -5.14

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.

 180 VAL   ( 187-)  A       182 - MET    189- ( A)         -5.07

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: 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: C

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: D

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.

 372 ALA   (  41-)  C   -2.77
 186 LEU   ( 193-)  A   -2.69

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 660 HOH   ( 455 )  A      O
 661 HOH   ( 460 )  B      O
 661 HOH   ( 461 )  B      O
 662 HOH   ( 470 )  C      O
 662 HOH   ( 475 )  C      O
 662 HOH   ( 479 )  C      O
 663 HOH   ( 458 )  D      O
 663 HOH   ( 466 )  D      O
 663 HOH   ( 474 )  D      O
 663 HOH   ( 478 )  D      O

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.

   3 GLN   (  10-)  A
 192 HIS   ( 199-)  A
 280 HIS   (  92-)  B
 341 GLN   (  10-)  C
 379 HIS   (  48-)  C
 586 GLN   (  84-)  D
 594 HIS   (  92-)  D

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.

  10 GLY   (  17-)  A      N
  13 GLY   (  20-)  A      N
  14 THR   (  21-)  A      OG1
  15 GLY   (  22-)  A      N
  16 LYS   (  23-)  A      N
  16 LYS   (  23-)  A      NZ
  17 THR   (  24-)  A      N
  27 GLU   (  34-)  A      N
  35 THR   (  42-)  A      N
  36 LEU   (  43-)  A      N
  38 VAL   (  45-)  A      N
  60 ALA   (  67-)  A      N
  61 GLY   (  68-)  A      N
  63 GLU   (  70-)  A      N
  68 LEU   (  75-)  A      N
  69 ARG   (  76-)  A      NE
  73 TYR   (  80-)  A      N
  87 SER   (  94-)  A      N
  88 ARG   (  95-)  A      N
  98 HIS   ( 105-)  A      ND1
 108 ILE   ( 115-)  A      N
 110 ILE   ( 117-)  A      N
 115 ASN   ( 122-)  A      ND2
 116 LYS   ( 123-)  A      N
 143 SER   ( 150-)  A      OG
And so on for a total of 87 lines.

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.

  58 ASP   (  65-)  A      OD1
 314 GLN   ( 126-)  B      OE1
 361 HIS   (  30-)  C      ND1
 379 HIS   (  48-)  C      ND1
 396 ASP   (  65-)  C      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+.

 656  MG   ( 251-)  A     0.24   0.77 Could be  K
 658  MG   ( 251-)  C     0.27   0.91 Could be  K

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 118 ASP   ( 125-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 183 ASP   ( 190-)  A   H-bonding suggests Asn
 456 ASP   ( 125-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.259
  2nd generation packing quality :  -2.486
  Ramachandran plot appearance   :  -4.409 (bad)
  chi-1/chi-2 rotamer normality  :  -3.973 (poor)
  Backbone conformation          :  -0.562

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.689
  Omega angle restraints         :   0.222 (tight)
  Side chain planarity           :   0.221 (tight)
  Improper dihedral distribution :   0.676
  B-factor distribution          :   3.085 (loose)
  Inside/Outside distribution    :   1.042

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 : 2.96


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.365 (tight)
  Bond angles                    :   0.689
  Omega angle restraints         :   0.222 (tight)
  Side chain planarity           :   0.221 (tight)
  Improper dihedral distribution :   0.676
  B-factor distribution          :   3.085 (loose)
  Inside/Outside distribution    :   1.042
==============

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.