WHAT IF Check report

This file was created 2011-12-18 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 pdb2waj.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.

 349 SNB   (1401-)  A  -         Fragmented

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

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'.

 169 MET   ( 219-)  A      CG
 169 MET   ( 219-)  A      SD
 169 MET   ( 219-)  A      CE
 173 TYR   ( 223-)  A      CG
 173 TYR   ( 223-)  A      CD1
 173 TYR   ( 223-)  A      CD2
 173 TYR   ( 223-)  A      CE1
 173 TYR   ( 223-)  A      CE2
 173 TYR   ( 223-)  A      CZ
 173 TYR   ( 223-)  A      OH
 324 GLN   ( 374-)  A      CG
 324 GLN   ( 374-)  A      CD
 324 GLN   ( 374-)  A      OE1
 324 GLN   ( 374-)  A      NE2
 330 GLU   ( 382-)  A      CG
 330 GLU   ( 382-)  A      CD
 330 GLU   ( 382-)  A      OE1
 330 GLU   ( 382-)  A      OE2

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.

 166 THR   ( 216-)  A    High
 167 SER   ( 217-)  A    High
 171 THR   ( 221-)  A    High
 172 PRO   ( 222-)  A    High
 321 PRO   ( 371-)  A    High
 322 PRO   ( 372-)  A    High
 323 PRO   ( 373-)  A    High
 324 GLN   ( 374-)  A    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. 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: 2

Crystal temperature (K) :287.000

Note: B-factor plot

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

Chain identifier: A

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.

  41 ARG   (  88-)  A
  50 ARG   (  97-)  A
  60 ARG   ( 107-)  A
  63 ARG   ( 110-)  A
 118 ARG   ( 165-)  A
 177 ARG   ( 227-)  A

Warning: Tyrosine convention problem

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

 190 TYR   ( 240-)  A
 313 TYR   ( 363-)  A

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.

 217 ASP   ( 267-)  A
 284 ASP   ( 334-)  A

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.

  90 GLU   ( 137-)  A
 100 GLU   ( 147-)  A
 227 GLU   ( 277-)  A
 235 GLU   ( 285-)  A
 273 GLU   ( 323-)  A
 340 GLU   ( 392-)  A

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.997107  0.000531  0.000409|
 |  0.000531  0.996972 -0.000095|
 |  0.000409 -0.000095  0.997638|
Proposed new scale matrix

 |  0.019414 -0.000010 -0.000008|
 | -0.000007  0.014061  0.000001|
 | -0.000004  0.000000  0.009321|
With corresponding cell

    A    =  51.509  B   =  71.121  C    = 107.284
    Alpha=  90.006  Beta=  89.953  Gamma=  89.939

The CRYST1 cell dimensions

    A    =  51.659  B   =  71.339  C    = 107.541
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 91.461
(Under-)estimated Z-score: 7.048

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.

 167 SER   ( 217-)  A     -C    N    CA  133.32    6.5

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.

  41 ARG   (  88-)  A
  50 ARG   (  97-)  A
  60 ARG   ( 107-)  A
  63 ARG   ( 110-)  A
  90 GLU   ( 137-)  A
 100 GLU   ( 147-)  A
 118 ARG   ( 165-)  A
 177 ARG   ( 227-)  A
 217 ASP   ( 267-)  A
 227 GLU   ( 277-)  A
 235 GLU   ( 285-)  A
 273 GLU   ( 323-)  A
 284 ASP   ( 334-)  A
 340 GLU   ( 392-)  A

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.

 322 PRO   ( 372-)  A    -3.0
 323 PRO   ( 373-)  A    -2.7
 326 LYS   ( 378-)  A    -2.7
  50 ARG   (  97-)  A    -2.7
 234 PRO   ( 284-)  A    -2.6
 167 SER   ( 217-)  A    -2.6
 172 PRO   ( 222-)  A    -2.5
 210 LYS   ( 260-)  A    -2.2
 332 GLU   ( 384-)  A    -2.2
 154 CYS   ( 201-)  A    -2.2
  23 LYS   (  68-)  A    -2.1
 170 MET   ( 220-)  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.

   8 VAL   (  53-)  A  omega poor
  21 ASN   (  66-)  A  Poor phi/psi
  25 ILE   (  70-)  A  Poor phi/psi
  32 CYS   (  79-)  A  omega poor
  50 ARG   (  97-)  A  Poor phi/psi
  86 GLN   ( 133-)  A  omega poor
 112 MET   ( 159-)  A  omega poor
 139 ILE   ( 186-)  A  omega poor
 141 ARG   ( 188-)  A  Poor phi/psi
 154 CYS   ( 201-)  A  Poor phi/psi
 164 ALA   ( 211-)  A  Poor phi/psi
 167 SER   ( 217-)  A  Poor phi/psi
 177 ARG   ( 227-)  A  omega poor
 188 MET   ( 238-)  A  omega poor
 193 ASN   ( 243-)  A  omega poor
 209 HIS   ( 259-)  A  Poor phi/psi
 312 TRP   ( 362-)  A  omega poor
 323 PRO   ( 373-)  A  omega poor
 326 LYS   ( 378-)  A  Poor phi/psi
 327 GLN   ( 379-)  A  omega poor
 329 ASP   ( 381-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.022

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 : -3.022

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.

  43 VAL   (  90-)  A    0.33
 120 SER   ( 167-)  A    0.36
 150 VAL   ( 197-)  A    0.38
 280 SER   ( 330-)  A    0.38

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!

   8 VAL   (  53-)  A      0
  10 ASP   (  55-)  A      0
  19 TYR   (  64-)  A      0
  20 GLN   (  65-)  A      0
  21 ASN   (  66-)  A      0
  24 PRO   (  69-)  A      0
  25 ILE   (  70-)  A      0
  27 SER   (  72-)  A      0
  28 GLY   (  73-)  A      0
  29 GLY   (  76-)  A      0
  30 ILE   (  77-)  A      0
  42 ASN   (  89-)  A      0
  49 SER   (  96-)  A      0
  50 ARG   (  97-)  A      0
  52 PHE   (  99-)  A      0
  53 GLN   ( 100-)  A      0
  70 CYS   ( 117-)  A      0
  71 VAL   ( 118-)  A      0
  72 ASN   ( 119-)  A      0
  81 ASN   ( 128-)  A      0
  85 PRO   ( 132-)  A      0
  92 PHE   ( 139-)  A      0
  93 GLN   ( 140-)  A      0
  99 MET   ( 146-)  A      0
 103 ASP   ( 150-)  A      0
And so on for a total of 123 lines.

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].

 172 PRO   ( 222-)  A   -19.6 half-chair C-alpha/N (-18 degrees)
 234 PRO   ( 284-)  A   175.7 envelop N (180 degrees)
 315 PRO   ( 365-)  A   103.1 envelop C-beta (108 degrees)
 322 PRO   ( 372-)  A   -12.6 half-chair C-alpha/N (-18 degrees)
 323 PRO   ( 373-)  A    -0.7 envelop N (0 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.

  55 GLN   ( 102-)  A      NE2 <->  333 HIS   ( 385-)  A      O      0.42    2.28  INTRA BF
  50 ARG   (  97-)  A      NH1 <->   93 GLN   ( 140-)  A      OE1    0.39    2.31  INTRA BF
  55 GLN   ( 102-)  A      NE2 <->  338 TRP   ( 390-)  A      NE1    0.35    2.50  INTRA BF
 265 ASP   ( 315-)  A      OD1 <->  283 ARG   ( 333-)  A      NH2    0.32    2.38  INTRA BF
  60 ARG   ( 107-)  A      NH2 <->  160 ASP   ( 207-)  A      OD2    0.23    2.47  INTRA BF
  63 ARG   ( 110-)  A      NH2 <->  350 HOH   (2042 )  A      O      0.22    2.48  INTRA BF
   8 VAL   (  53-)  A      CG1 <->   32 CYS   (  79-)  A    A SG     0.22    3.18  INTRA BF
 177 ARG   ( 227-)  A      N   <->  350 HOH   (2104 )  A      O      0.19    2.51  INTRA BF
  72 ASN   ( 119-)  A      ND2 <->  350 HOH   (2048 )  A      O      0.18    2.52  INTRA BF
  73 HIS   ( 120-)  A      CD2 <->   75 ASN   ( 122-)  A      N      0.18    2.92  INTRA BL
 103 ASP   ( 150-)  A      OD2 <->  152 SER   ( 199-)  A      N      0.17    2.53  INTRA BL
 246 ASN   ( 296-)  A      O   <->  250 ASN   ( 300-)  A      ND2    0.17    2.53  INTRA BL
 141 ARG   ( 188-)  A      NH2 <->  164 ALA   ( 211-)  A      O      0.16    2.54  INTRA BF
  63 ARG   ( 110-)  A      NH2 <->  161 PHE   ( 208-)  A      O      0.14    2.56  INTRA BF
 235 GLU   ( 285-)  A      OE2 <->  296 LYS   ( 346-)  A      NZ     0.13    2.57  INTRA BF
 284 ASP   ( 334-)  A      OD2 <->  306 HIS   ( 356-)  A      NE2    0.12    2.58  INTRA BL
   8 VAL   (  53-)  A      N   <->   11 SER   (  56-)  A      O      0.12    2.58  INTRA BF
  23 LYS   (  68-)  A      O   <->   33 ALA   (  80-)  A      N      0.11    2.59  INTRA BL
   5 SER   (  50-)  A      OG  <->   14 THR   (  59-)  A      OG1    0.11    2.29  INTRA BF
 134 HIS   ( 181-)  A      NE2 <->  195 ASP   ( 245-)  A      OD2    0.11    2.59  INTRA BF
 105 ASN   ( 152-)  A      ND2 <->  350 HOH   (2073 )  A      O      0.10    2.60  INTRA BF
  46 LYS   (  93-)  A      NZ  <->  350 HOH   (2028 )  A      O      0.10    2.60  INTRA BL
 166 THR   ( 216-)  A      CB  <->  167 SER   ( 217-)  A      CB     0.09    2.91  INTRA BF
 208 ARG   ( 258-)  A      NH1 <->  228 GLN   ( 278-)  A      OE1    0.09    2.61  INTRA BF
 110 ILE   ( 157-)  A      O   <->  209 HIS   ( 259-)  A      ND1    0.09    2.61  INTRA BF
And so on for a total of 57 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

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.

 170 MET   ( 220-)  A      -7.36
 216 ARG   ( 266-)  A      -6.86
  87 LYS   ( 134-)  A      -6.01
 332 GLU   ( 384-)  A      -5.79
 190 TYR   ( 240-)  A      -5.68
 208 ARG   ( 258-)  A      -5.45
 168 PHE   ( 218-)  A      -5.31
  72 ASN   ( 119-)  A      -5.24
 312 TRP   ( 362-)  A      -5.23
 253 LYS   ( 303-)  A      -5.12

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.

 166 THR   ( 216-)  A       168 - PHE    218- ( A)         -4.73

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

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.

 173 TYR   ( 223-)  A   -3.22
 324 GLN   ( 374-)  A   -2.90
 320 ALA   ( 370-)  A   -2.70
 169 MET   ( 219-)  A   -2.57

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

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.

 350 HOH   (2019 )  A      O
 350 HOH   (2063 )  A      O
 350 HOH   (2110 )  A      O
 350 HOH   (2174 )  A      O
Marked this atom as acceptor  349 SNB  (1401-) A     CL

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.

  21 ASN   (  66-)  A
  55 GLN   ( 102-)  A
  73 HIS   ( 120-)  A
 305 GLN   ( 355-)  A
 310 ASN   ( 360-)  A
 327 GLN   ( 379-)  A
 333 HIS   ( 385-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   3 PHE   (  48-)  A      N
  16 LEU   (  61-)  A      N
  18 ARG   (  63-)  A      NE
  23 LYS   (  68-)  A      NZ
  52 PHE   (  99-)  A      N
  54 ASN   ( 101-)  A      N
  72 ASN   ( 119-)  A      N
  88 THR   ( 135-)  A      N
 178 TYR   ( 228-)  A      N
 196 ILE   ( 246-)  A      N
 210 LYS   ( 260-)  A      N
 235 GLU   ( 285-)  A      N
 243 THR   ( 293-)  A      N
 244 VAL   ( 294-)  A      N
 301 ASP   ( 351-)  A      N
 311 VAL   ( 361-)  A      N
 327 GLN   ( 379-)  A      N
 331 ARG   ( 383-)  A      N

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.

 132 HIS   ( 179-)  A      ND1

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.

   7 GLU   (  52-)  A   H-bonding suggests Gln
  94 ASP   ( 141-)  A   H-bonding suggests Asn; but Alt-Rotamer
 249 GLU   ( 299-)  A   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 :  -0.764
  2nd generation packing quality :  -0.972
  Ramachandran plot appearance   :  -1.931
  chi-1/chi-2 rotamer normality  :  -3.022 (poor)
  Backbone conformation          :  -0.053

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.548 (tight)
  Bond angles                    :   0.714
  Omega angle restraints         :   1.114
  Side chain planarity           :   0.439 (tight)
  Improper dihedral distribution :   0.735
  B-factor distribution          :   0.580
  Inside/Outside distribution    :   1.034

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.548 (tight)
  Bond angles                    :   0.714
  Omega angle restraints         :   1.114
  Side chain planarity           :   0.439 (tight)
  Improper dihedral distribution :   0.735
  B-factor distribution          :   0.580
  Inside/Outside distribution    :   1.034
==============

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.