WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3ryj.ent

Checks that need to be done early-on in validation

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.

 259 RYJ   (   1-)  B  -         Atom types

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: B

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 HIS   (   4-)  B      CG
   1 HIS   (   4-)  B      ND1
   1 HIS   (   4-)  B      CD2
   1 HIS   (   4-)  B      CE1
   1 HIS   (   4-)  B      NE2
 257 LYS   ( 261-)  B      CG
 257 LYS   ( 261-)  B      CD
 257 LYS   ( 261-)  B      CE
 257 LYS   ( 261-)  B      NZ

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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.

Note: B-factor plot

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

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  55 ARG   (  58-)  B

Warning: Tyrosine convention problem

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

   4 TYR   (   7-)  B
 111 TYR   ( 114-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  72 ASP   (  75-)  B
 171 ASP   ( 175-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  23 GLU   (  26-)  B
  66 GLU   (  69-)  B
 235 GLU   ( 239-)  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.

   5 GLY   (   8-)  B      N    CA    1.52    4.5
  11 GLU   (  14-)  B      CD   OE2   1.33    4.5
 129 LYS   ( 133-)  B      CE   NZ    1.64    5.1
 157 VAL   ( 161-)  B      CB   CG2   1.31   -6.3
 158 ASP   ( 162-)  B      CG   OD2   1.16   -4.7
 183 GLU   ( 187-)  B      CB   CG    1.40   -4.1
 210 GLU   ( 214-)  B      CG   CD    1.62    4.0

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.995786  0.000407 -0.000805|
 |  0.000407  0.995347 -0.001069|
 | -0.000805 -0.001069  0.992357|
Proposed new scale matrix

 |  0.023604 -0.000003  0.006011|
 | -0.000010  0.024082  0.000026|
 |  0.000012  0.000015  0.014370|
With corresponding cell

    A    =  42.374  B   =  41.525  C    =  71.826
    Alpha=  90.131  Beta= 104.333  Gamma=  89.953

The CRYST1 cell dimensions

    A    =  42.554  B   =  41.718  C    =  72.338
    Alpha=  90.000  Beta= 104.200  Gamma=  90.000

Variance: 280.950
(Under-)estimated Z-score: 12.353

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.

   7 HIS   (  10-)  B     -C    N    CA  114.04   -4.3
  86 ARG   (  89-)  B      CG   CD   NE  102.30   -4.8
 137 LEU   ( 141-)  B      CB   CG   CD2 125.27    4.9

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  23 GLU   (  26-)  B
  55 ARG   (  58-)  B
  66 GLU   (  69-)  B
  72 ASP   (  75-)  B
 171 ASP   ( 175-)  B
 235 GLU   ( 239-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 137 LEU   ( 141-)  B      CG    18.5    -0.42   -33.01
The average deviation= 1.674

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.

 172 PHE   ( 176-)  B    -2.4
 198 PRO   ( 202-)  B    -2.2
  19 ILE   (  22-)  B    -2.2
 159 VAL   ( 163-)  B    -2.1
 147 GLY   ( 151-)  B    -2.1
  89 GLN   (  92-)  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.

  26 SER   (  29-)  B  PRO omega poor
  54 LEU   (  57-)  B  omega poor
  72 ASP   (  75-)  B  Poor phi/psi
  73 LYS   (  76-)  B  Poor phi/psi
  80 PRO   (  83-)  B  omega poor
  83 GLY   (  86-)  B  omega poor
  89 GLN   (  92-)  B  omega poor
 108 LYS   ( 111-)  B  Poor phi/psi
 174 ASN   ( 178-)  B  Poor phi/psi
 187 TYR   ( 191-)  B  omega poor
 193 SER   ( 197-)  B  omega poor
 197 PRO   ( 201-)  B  PRO omega poor
 199 LEU   ( 203-)  B  Poor phi/psi
 201 GLU   ( 205-)  B  omega poor
 203 VAL   ( 207-)  B  omega poor
 239 ASP   ( 243-)  B  Poor phi/psi
 248 LYS   ( 252-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.783

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!

   4 TYR   (   7-)  B      0
   7 HIS   (  10-)  B      0
  17 PHE   (  20-)  B      0
  21 LYS   (  24-)  B      0
  24 ARG   (  27-)  B      0
  25 GLN   (  28-)  B      0
  26 SER   (  29-)  B      0
  35 ALA   (  38-)  B      0
  47 SER   (  50-)  B      0
  51 ALA   (  54-)  B      0
  59 ASN   (  62-)  B      0
  61 HIS   (  64-)  B      0
  69 ASP   (  72-)  B      0
  70 SER   (  73-)  B      0
  72 ASP   (  75-)  B      0
  74 ALA   (  77-)  B      0
  77 LYS   (  80-)  B      0
  80 PRO   (  83-)  B      0
  82 ASP   (  85-)  B      0
  89 GLN   (  92-)  B      0
  96 SER   (  99-)  B      0
 100 GLN   ( 103-)  B      0
 104 HIS   ( 107-)  B      0
 108 LYS   ( 111-)  B      0
 111 TYR   ( 114-)  B      0
And so on for a total of 115 lines.

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]

  18 PRO   (  21-)  B    0.19 LOW
 211 PRO   ( 215-)  B    0.12 LOW
 243 PRO   ( 247-)  B    0.13 LOW

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].

  10 PRO   (  13-)  B   101.7 envelop C-beta (108 degrees)
 134 PRO   ( 138-)  B  -116.6 envelop C-gamma (-108 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.

 183 GLU   ( 187-)  B      OE1 <->  260 HOH   ( 563 )  B      O      0.40    2.00  INTRA
 209 LYS   ( 213-)  B      NZ  <->  260 HOH   ( 270 )  B      O      0.40    2.30  INTRA BF
 141 GLY   ( 145-)  B      N   <->  260 HOH   ( 291 )  B      O      0.39    2.31  INTRA BF
 253 LYS   ( 257-)  B      NZ  <->  260 HOH   ( 364 )  B      O      0.35    2.35  INTRA BF
  24 ARG   (  27-)  B      CB  <->  260 HOH   ( 586 )  B      O      0.34    2.46  INTRA BF
  33 HIS   (  36-)  B      ND1 <->  260 HOH   ( 539 )  B      O      0.32    2.38  INTRA
 118 VAL   ( 121-)  B      CG2 <->  260 HOH   ( 335 )  B      O      0.30    2.50  INTRA BF
 248 LYS   ( 252-)  B      NZ  <->  260 HOH   ( 461 )  B      O      0.30    2.40  INTRA
 120 TRP   ( 123-)  B      O   <->  260 HOH   ( 312 )  B      O      0.28    2.12  INTRA BF
  23 GLU   (  26-)  B      OE2 <->  260 HOH   ( 397 )  B      O      0.28    2.12  INTRA BF
 144 LEU   ( 148-)  B      CD1 <->  260 HOH   ( 398 )  B      O      0.25    2.55  INTRA BF
  17 PHE   (  20-)  B      CB  <->  260 HOH   ( 378 )  B      O      0.24    2.56  INTRA BF
 198 PRO   ( 202-)  B      CD  <->  259 RYJ   (   1-)  B     F2'1    0.22    2.98  INTRA
  13 TRP   (  16-)  B      CB  <->  260 HOH   ( 391 )  B      O      0.21    2.59  INTRA BF
  17 PHE   (  20-)  B      CG  <->  260 HOH   ( 378 )  B      O      0.16    2.64  INTRA BF
 116 HIS   ( 119-)  B      O   <->  260 HOH   ( 335 )  B      O      0.16    2.24  INTRA BF
  72 ASP   (  75-)  B      OD1 <->   86 ARG   (  89-)  B      NE     0.15    2.55  INTRA
 158 ASP   ( 162-)  B      OD2 <->  260 HOH   ( 486 )  B      O      0.14    2.26  INTRA
  23 GLU   (  26-)  B      OE2 <->  260 HOH   ( 366 )  B      O      0.14    2.26  INTRA BF
 122 THR   ( 125-)  B      CG2 <->  260 HOH   ( 312 )  B      O      0.14    2.66  INTRA BF
 133 GLN   ( 137-)  B      NE2 <->  260 HOH   ( 281 )  B      O      0.12    2.58  INTRA
 171 ASP   ( 175-)  B      CB  <->  260 HOH   ( 523 )  B      O      0.11    2.69  INTRA
  31 ASP   (  34-)  B      OD1 <->  260 HOH   ( 539 )  B      O      0.11    2.29  INTRA
 209 LYS   ( 213-)  B      CE  <->  260 HOH   ( 270 )  B      O      0.11    2.69  INTRA
  86 ARG   (  89-)  B      NH1 <->  260 HOH   ( 356 )  B      O      0.10    2.60  INTRA
 237 MET   ( 241-)  B      O   <->  260 HOH   ( 396 )  B      O      0.10    2.30  INTRA BF
  42 LYS   (  45-)  B      NZ  <->  260 HOH   ( 526 )  B      O      0.09    2.61  INTRA BF
  49 ASP   (  52-)  B      CB  <->  260 HOH   ( 322 )  B      O      0.08    2.72  INTRA BF
 205 TRP   ( 209-)  B      CE3 <->  260 HOH   ( 291 )  B      O      0.08    2.72  INTRA BF
  48 TYR   (  51-)  B      CE2 <->  260 HOH   ( 388 )  B      O      0.08    2.72  INTRA BF
 234 GLU   ( 238-)  B      OE1 <->  260 HOH   ( 565 )  B      O      0.08    2.32  INTRA BF
 104 HIS   ( 107-)  B      NE2 <->  190 TYR   ( 194-)  B      OH     0.07    2.63  INTRA BL
  12 HIS   (  15-)  B      ND1 <->   15 LYS   (  18-)  B      NZ     0.07    2.93  INTRA
 260 HOH   ( 331 )  B      O   <->  260 HOH   ( 454 )  B      O      0.06    2.14  INTRA BF
 183 GLU   ( 187-)  B      C   <->  260 HOH   ( 351 )  B      O      0.05    2.75  INTRA BF
  24 ARG   (  27-)  B      CG  <->  201 GLU   ( 205-)  B      CD     0.05    3.15  INTRA
  72 ASP   (  75-)  B      OD1 <->   86 ARG   (  89-)  B      NH2    0.05    2.65  INTRA
  42 LYS   (  45-)  B      CE  <->  260 HOH   ( 346 )  B      O      0.04    2.76  INTRA BF
 132 GLN   ( 136-)  B      CG  <->  260 HOH   ( 544 )  B      O      0.04    2.76  INTRA BF
 154 GLN   ( 158-)  B      CD  <->  157 VAL   ( 161-)  B      CG2    0.04    3.16  INTRA
 226 ASN   ( 230-)  B      OD1 <->  260 HOH   ( 387 )  B      O      0.04    2.36  INTRA
 114 GLU   ( 117-)  B      OE2 <->  116 HIS   ( 119-)  B      NE2    0.03    2.67  INTRA BL
 260 HOH   ( 459 )  B      O   <->  260 HOH   ( 523 )  B      O      0.03    2.17  INTRA
 166 LYS   ( 170-)  B      NZ  <->  260 HOH   ( 404 )  B      O      0.02    2.68  INTRA BF
 183 GLU   ( 187-)  B      O   <->  260 HOH   ( 351 )  B      O      0.01    2.39  INTRA BF
  16 ASP   (  19-)  B      OD1 <->  260 HOH   ( 583 )  B      O      0.01    2.39  INTRA BF
  98 ASP   ( 101-)  B      OD2 <->  260 HOH   ( 558 )  B      O      0.01    2.39  INTRA BF

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: 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.

   7 HIS   (  10-)  B      -6.21
  97 LEU   ( 100-)  B      -5.21
 132 GLN   ( 136-)  B      -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: 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: B

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.

 260 HOH   ( 341 )  B      O
 260 HOH   ( 370 )  B      O
 260 HOH   ( 418 )  B      O
Marked this atom as acceptor  259 RYJ  (   1-) B     F2'1
Marked this atom as acceptor  259 RYJ  (   1-) B     F2'2
Marked this atom as acceptor  259 RYJ  (   1-) B     F2'3
Metal-coordinating Histidine residue  91 fixed to   1
Metal-coordinating Histidine residue  93 fixed to   1
Metal-coordinating Histidine residue 116 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.

  33 HIS   (  36-)  B
  50 GLN   (  53-)  B
 174 ASN   ( 178-)  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.

  28 VAL   (  31-)  B      N
  71 GLN   (  74-)  B      N
  97 LEU   ( 100-)  B      N
 196 THR   ( 200-)  B      N
 200 LEU   ( 204-)  B      N
 226 ASN   ( 230-)  B      ND2
 228 ASN   ( 232-)  B      N
 241 TRP   ( 245-)  B      N
 256 PHE   ( 260-)  B      N
Only metal coordination for   93 HIS  (  96-) B      NE2
Only metal coordination for  116 HIS  ( 119-) B      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 260 HOH   ( 379 )  B      O  0.86  K  4
 260 HOH   ( 462 )  B      O  1.01  K  4

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 :   0.152
  2nd generation packing quality :   0.749
  Ramachandran plot appearance   :  -1.257
  chi-1/chi-2 rotamer normality  :   0.783
  Backbone conformation          :  -0.817

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.088
  Bond angles                    :   1.037
  Omega angle restraints         :   1.158
  Side chain planarity           :   1.542
  Improper dihedral distribution :   1.516 (loose)
  B-factor distribution          :   0.726
  Inside/Outside distribution    :   0.952

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 : 1.39


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.088
  Bond angles                    :   1.037
  Omega angle restraints         :   1.158
  Side chain planarity           :   1.542
  Improper dihedral distribution :   1.516 (loose)
  B-factor distribution          :   0.726
  Inside/Outside distribution    :   0.952
==============

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.