WHAT IF Check report

This file was created 2012-01-19 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 pdb1zcl.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.084
CA-only RMS fit for the two chains : 0.683

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 B

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 306 SO4   (4397-)  B  -
 307 SO4   (4398-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :200.000

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 : 1.699 over 2202 bonds
Average difference in B over a bond : 2.34
RMS difference in B over a bond : 7.76

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

   6 TYR   (  14-)  A
  45 TYR   (  53-)  A
 158 TYR   (  14-)  B
 197 TYR   (  53-)  B
 270 TYR   ( 126-)  B

Warning: Phenylalanine convention problem

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

  11 PHE   (  19-)  A
  84 PHE   (  92-)  A
 152 PHE   ( 160-)  A
 163 PHE   (  19-)  B
 236 PHE   (  92-)  B
 304 PHE   ( 160-)  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.

  46 ASP   (  54-)  A
  59 ASP   (  67-)  A
 215 ASP   (  71-)  B
 216 ASP   (  72-)  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.

   3 GLU   (  11-)  A
  27 GLU   (  35-)  A
  42 GLU   (  50-)  A
  51 GLU   (  59-)  A
 194 GLU   (  50-)  B
 203 GLU   (  59-)  B
 205 GLU   (  61-)  B

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

 |  1.002206 -0.000073  0.000168|
 | -0.000073  1.001073  0.000164|
 |  0.000168  0.000164  1.001883|
Proposed new scale matrix

 |  0.006803  0.000000 -0.000001|
 |  0.000000  0.006811 -0.000001|
 | -0.000001 -0.000001  0.006805|
With corresponding cell

    A    = 146.994  B   = 146.828  C    = 146.947
    Alpha=  89.981  Beta=  89.981  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 146.681  B   = 146.681  C    = 146.681
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 31.449
(Under-)estimated Z-score: 4.133

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.

   3 GLU   (  11-)  A
  27 GLU   (  35-)  A
  42 GLU   (  50-)  A
  46 ASP   (  54-)  A
  51 GLU   (  59-)  A
  59 ASP   (  67-)  A
 194 GLU   (  50-)  B
 203 GLU   (  59-)  B
 205 GLU   (  61-)  B
 215 ASP   (  71-)  B
 216 ASP   (  72-)  B

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.

  82 ILE   (  90-)  A    6.13
 202 VAL   (  58-)  B    5.02
  83 LYS   (  91-)  A    4.31
 178 ILE   (  34-)  B    4.16
  27 GLU   (  35-)  A    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.639

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 : -5.332

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.

 282 ARG   ( 138-)  B    -3.1
 235 LYS   (  91-)  B    -2.6
 200 THR   (  56-)  B    -2.6
 106 LEU   ( 114-)  A    -2.5
 229 LEU   (  85-)  B    -2.5
 100 LEU   ( 108-)  A    -2.5
 138 LEU   ( 146-)  A    -2.4
 252 LEU   ( 108-)  B    -2.4
  26 ILE   (  34-)  A    -2.4
 129 ARG   ( 137-)  A    -2.4
  32 TYR   (  40-)  A    -2.3
  47 THR   (  55-)  A    -2.3
  77 LEU   (  85-)  A    -2.3
  60 TRP   (  68-)  A    -2.3
 168 ASN   (  24-)  B    -2.2
  69 SER   (  77-)  A    -2.2
 270 TYR   ( 126-)  B    -2.1
  53 GLU   (  61-)  A    -2.1
 302 LEU   ( 158-)  B    -2.1
 101 GLY   ( 109-)  A    -2.1
  45 TYR   (  53-)  A    -2.0
 151 ARG   ( 159-)  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.

   7 LYS   (  15-)  A  Poor phi/psi
  18 THR   (  26-)  A  Poor phi/psi
  19 ASN   (  27-)  A  Poor phi/psi
  22 LEU   (  30-)  A  Poor phi/psi
  32 TYR   (  40-)  A  Poor phi/psi
  45 TYR   (  53-)  A  Poor phi/psi
  52 LYS   (  60-)  A  Poor phi/psi
  69 SER   (  77-)  A  Poor phi/psi
  82 ILE   (  90-)  A  Poor phi/psi
  83 LYS   (  91-)  A  Poor phi/psi
  90 CYS   (  98-)  A  Poor phi/psi
  91 CYS   (  99-)  A  Poor phi/psi
 116 MET   ( 124-)  A  Poor phi/psi
 133 PHE   ( 141-)  A  Poor phi/psi
 148 MET   ( 156-)  A  Poor phi/psi
 159 LYS   (  15-)  B  Poor phi/psi
 174 LEU   (  30-)  B  Poor phi/psi
 193 CYS   (  49-)  B  Poor phi/psi
 206 GLY   (  62-)  B  Poor phi/psi
 214 PHE   (  70-)  B  Poor phi/psi
 221 SER   (  77-)  B  Poor phi/psi
 234 ILE   (  90-)  B  Poor phi/psi
 235 LYS   (  91-)  B  Poor phi/psi
 248 SER   ( 104-)  B  Poor phi/psi
 267 GLY   ( 123-)  B  Poor phi/psi
 284 ALA   ( 140-)  B  Poor phi/psi
 285 PHE   ( 141-)  B  Poor phi/psi
 287 SER   ( 143-)  B  Poor phi/psi
 300 MET   ( 156-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.208

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.208

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.

  78 SER   (  86-)  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!

   6 TYR   (  14-)  A      0
   7 LYS   (  15-)  A      0
   8 ASN   (  16-)  A      0
   9 MET   (  17-)  A      0
  18 THR   (  26-)  A      0
  19 ASN   (  27-)  A      0
  22 LEU   (  30-)  A      0
  31 LYS   (  39-)  A      0
  32 TYR   (  40-)  A      0
  36 THR   (  44-)  A      0
  39 ARG   (  47-)  A      0
  41 CYS   (  49-)  A      0
  44 THR   (  52-)  A      0
  45 TYR   (  53-)  A      0
  47 THR   (  55-)  A      0
  48 THR   (  56-)  A      0
  53 GLU   (  61-)  A      0
  59 ASP   (  67-)  A      0
  60 TRP   (  68-)  A      0
  61 PRO   (  69-)  A      0
  62 PHE   (  70-)  A      0
  64 ASP   (  72-)  A      0
  68 PRO   (  76-)  A      0
  69 SER   (  77-)  A      0
  87 GLU   (  95-)  A      0
And so on for a total of 105 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 : 1.078

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]

  68 PRO   (  76-)  A    0.46 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 205 GLU   (  61-)  B      O   <->  207 ILE   (  63-)  B      N      0.50    2.20  INTRA BF
  22 LEU   (  30-)  A      O   <->   25 PHE   (  33-)  A      N      0.39    2.31  INTRA BF
   3 GLU   (  11-)  A      O   <->  128 LYS   ( 136-)  A      NZ     0.33    2.37  INTRA BF
 202 VAL   (  58-)  B      O   <->  204 LYS   (  60-)  B      N      0.32    2.38  INTRA BL
  69 SER   (  77-)  A      OG  <->   70 ASN   (  78-)  A      N      0.32    2.28  INTRA BF
  90 CYS   (  98-)  A      SG  <->   91 CYS   (  99-)  A      N      0.31    2.89  INTRA BF
 190 VAL   (  46-)  B      N   <->  245 ALA   ( 101-)  B      O      0.29    2.41  INTRA BL
 199 THR   (  55-)  B      O   <->  202 VAL   (  58-)  B      N      0.29    2.41  INTRA BL
 248 SER   ( 104-)  B      OG  <->  251 GLY   ( 107-)  B      N      0.29    2.41  INTRA BL
 162 ARG   (  18-)  B      NH1 <->  243 CYS   (  99-)  B      SG     0.28    3.02  INTRA BL
 104 PRO   ( 112-)  A      O   <->  108 ALA   ( 116-)  A      N      0.28    2.42  INTRA BF
 109 LEU   ( 117-)  A      O   <->  112 ILE   ( 120-)  A      N      0.27    2.43  INTRA BL
 112 ILE   ( 120-)  A      O   <->  115 GLY   ( 123-)  A      N      0.26    2.44  INTRA BF
  82 ILE   (  90-)  A      O   <->   85 ARG   (  93-)  A      N      0.26    2.44  INTRA BL
  50 VAL   (  58-)  A      O   <->   53 GLU   (  61-)  A      N      0.26    2.44  INTRA BF
 176 LYS   (  32-)  B      O   <->  180 GLU   (  36-)  B      N      0.25    2.45  INTRA BF
 249 VAL   ( 105-)  B      CG2 <->  250 ALA   ( 106-)  B      N      0.25    2.75  INTRA BF
 162 ARG   (  18-)  B      NH2 <->  184 TYR   (  40-)  B      O      0.25    2.45  INTRA BL
  29 LEU   (  37-)  A      O   <->   31 LYS   (  39-)  A      N      0.24    2.46  INTRA BF
 168 ASN   (  24-)  B      ND2 <->  196 THR   (  52-)  B      CG2    0.23    2.87  INTRA BF
 171 ASN   (  27-)  B      ND2 <->  196 THR   (  52-)  B      O      0.23    2.47  INTRA BF
 259 VAL   ( 115-)  B      O   <->  262 ALA   ( 118-)  B      N      0.23    2.47  INTRA BL
 202 VAL   (  58-)  B      C   <->  204 LYS   (  60-)  B      N      0.22    2.68  INTRA BL
  16 ASN   (  24-)  A      OD1 <->   95 HIS   ( 103-)  A      CE1    0.22    2.58  INTRA BF
 265 GLU   ( 121-)  B      OE2 <->  299 LYS   ( 155-)  B      N      0.21    2.49  INTRA BF
And so on for a total of 188 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 303 ARG   ( 159-)  B      -7.15
 151 ARG   ( 159-)  A      -7.01
  15 HIS   (  23-)  A      -6.56
 130 ARG   ( 138-)  A      -6.51
 282 ARG   ( 138-)  B      -6.19
 301 ARG   ( 157-)  B      -5.87
 149 ARG   ( 157-)  A      -5.18
  86 GLU   (  94-)  A      -5.01

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 302 LEU   ( 158-)  B   -2.71
 301 ARG   ( 157-)  B   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 300 MET   ( 156-)  B     -  303 ARG   ( 159-)  B        -2.22

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 127 GLN   ( 135-)  A
 289 GLN   ( 145-)  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.

   5 THR   (  13-)  A      N
  10 ARG   (  18-)  A      N
  11 PHE   (  19-)  A      N
  14 THR   (  22-)  A      OG1
  22 LEU   (  30-)  A      N
  39 ARG   (  47-)  A      NH1
  44 THR   (  52-)  A      N
  50 VAL   (  58-)  A      N
  55 ILE   (  63-)  A      N
  73 VAL   (  81-)  A      N
  84 PHE   (  92-)  A      N
  89 GLY   (  97-)  A      N
  96 SER   ( 104-)  A      N
  96 SER   ( 104-)  A      OG
  97 VAL   ( 105-)  A      N
 100 LEU   ( 108-)  A      N
 101 GLY   ( 109-)  A      N
 102 ARG   ( 110-)  A      N
 102 ARG   ( 110-)  A      NE
 120 ASP   ( 128-)  A      N
 150 LEU   ( 158-)  A      N
 151 ARG   ( 159-)  A      NE
 157 THR   (  13-)  B      N
 162 ARG   (  18-)  B      N
 175 ASN   (  31-)  B      N
 188 THR   (  44-)  B      N
 191 ARG   (  47-)  B      NH1
 195 ALA   (  51-)  B      N
 196 THR   (  52-)  B      N
 207 ILE   (  63-)  B      N
 214 PHE   (  70-)  B      N
 248 SER   ( 104-)  B      OG
 249 VAL   ( 105-)  B      N
 251 GLY   ( 107-)  B      N
 252 LEU   ( 108-)  B      N
 253 GLY   ( 109-)  B      N
 254 ARG   ( 110-)  B      N
 254 ARG   ( 110-)  B      NE
 255 ALA   ( 111-)  B      N
 266 GLY   ( 122-)  B      N
 304 PHE   ( 160-)  B      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.

  16 ASN   (  24-)  A      OD1
  95 HIS   ( 103-)  A      ND1
 155 GLU   (  11-)  B      OE2
 167 HIS   (  23-)  B      ND1
 168 ASN   (  24-)  B      OD1
 211 ASP   (  67-)  B      OD1

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.

  51 GLU   (  59-)  A   H-bonding suggests Gln
  53 GLU   (  61-)  A   H-bonding suggests Gln; but Alt-Rotamer
  74 ASP   (  82-)  A   H-bonding suggests Asn
 203 GLU   (  59-)  B   H-bonding suggests Gln
 205 GLU   (  61-)  B   H-bonding suggests Gln
 272 ASP   ( 128-)  B   H-bonding suggests Asn

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 :  -1.410
  2nd generation packing quality :  -2.374
  Ramachandran plot appearance   :  -5.332 (bad)
  chi-1/chi-2 rotamer normality  :  -5.208 (bad)
  Backbone conformation          :  -0.087

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.386 (tight)
  Bond angles                    :   0.692
  Omega angle restraints         :   0.196 (tight)
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.716
  B-factor distribution          :   1.699 (loose)
  Inside/Outside distribution    :   0.935

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -2.7
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.386 (tight)
  Bond angles                    :   0.692
  Omega angle restraints         :   0.196 (tight)
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.716
  B-factor distribution          :   1.699 (loose)
  Inside/Outside distribution    :   0.935
==============

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.