WHAT IF Check report

This file was created 2011-12-16 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 pdb1ivb.ent

Checks that need to be done early-on in validation

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.

 395 ST1   ( 471-)  A  -

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

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

 |  0.997073  0.000219 -0.000230|
 |  0.000219  0.996722  0.000519|
 | -0.000230  0.000519  0.998182|
Proposed new scale matrix

 |  0.008054 -0.000002  0.000002|
 | -0.000002  0.008056 -0.000004|
 |  0.000003 -0.000007  0.013949|
With corresponding cell

    A    = 124.169  B   = 124.125  C    =  71.688
    Alpha=  89.940  Beta=  90.026  Gamma=  89.975

The CRYST1 cell dimensions

    A    = 124.540  B   = 124.540  C    =  71.820
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 95.037
(Under-)estimated Z-score: 7.185

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.

  38 ILE   ( 114-)  A      N    CA   C    99.96   -4.0
  53 HIS   ( 129-)  A      CG   ND1  CE1 109.69    4.1
 113 THR   ( 189-)  A      N    CA   C    97.31   -5.0
 118 ASP   ( 194-)  A      C    CA   CB  117.84    4.1
 139 HIS   ( 215-)  A      CG   ND1  CE1 109.65    4.1
 149 GLN   ( 225-)  A      N    CA   C   123.55    4.4
 197 HIS   ( 273-)  A      CG   ND1  CE1 109.82    4.2
 214 ALA   ( 290-)  A      N    CA   C    93.83   -6.2
 220 TYR   ( 296-)  A     -C    N    CA  130.61    5.0
 220 TYR   ( 296-)  A      N    CA   C   127.61    5.9
 279 GLN   ( 355-)  A      N    CA   C    98.38   -4.6
 303 LEU   ( 379-)  A      CA   CB   CG  138.12    6.2
 355 HIS   ( 431-)  A      CG   ND1  CE1 109.66    4.1
 359 LYS   ( 435-)  A      N    CA   C   125.14    5.0

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.

 214 ALA   ( 290-)  A    6.65
 220 TYR   ( 296-)  A    6.24
  26 ARG   ( 102-)  A    5.36
 359 LYS   ( 435-)  A    5.32
 113 THR   ( 189-)  A    5.12
 139 HIS   ( 215-)  A    4.79
 149 GLN   ( 225-)  A    4.78
 103 GLY   ( 179-)  A    4.55
 133 ALA   ( 209-)  A    4.53
 279 GLN   ( 355-)  A    4.47
 379 LEU   ( 455-)  A    4.38
  20 LEU   (  96-)  A    4.06

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 : 1.908

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 289 TYR   ( 365-)  A      OH   4.35
  97 HIS   ( 173-)  A      CB   4.04
 161 TYR   ( 237-)  A      CB   4.02
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.291

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.291

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.

 361 THR   ( 437-)  A    -3.3
 165 THR   ( 241-)  A    -3.1
 252 PRO   ( 328-)  A    -3.0
 306 ARG   ( 382-)  A    -2.8
 220 TYR   ( 296-)  A    -2.8
  39 ILE   ( 115-)  A    -2.6
  59 TYR   ( 135-)  A    -2.5
 284 LYS   ( 360-)  A    -2.5
  20 LEU   (  96-)  A    -2.5
 182 GLU   ( 258-)  A    -2.4
 144 ASN   ( 220-)  A    -2.4
  40 ARG   ( 116-)  A    -2.4
 202 THR   ( 278-)  A    -2.4
 291 ARG   ( 367-)  A    -2.4
 305 VAL   ( 381-)  A    -2.4
 327 ILE   ( 403-)  A    -2.3
   3 GLU   (  79-)  A    -2.3
 173 SER   ( 249-)  A    -2.2
 245 THR   ( 321-)  A    -2.2
 239 ARG   ( 315-)  A    -2.2
 219 SER   ( 295-)  A    -2.2
 331 GLY   ( 407-)  A    -2.2
 237 GLU   ( 313-)  A    -2.1
 148 THR   ( 224-)  A    -2.1
  41 GLU   ( 117-)  A    -2.1
 303 LEU   ( 379-)  A    -2.1
 318 LEU   ( 394-)  A    -2.1
 157 GLY   ( 233-)  A    -2.1
 210 THR   ( 286-)  A    -2.1
  65 GLY   ( 141-)  A    -2.1
 111 GLU   ( 187-)  A    -2.1
  15 THR   (  91-)  A    -2.1
 269 LEU   ( 345-)  A    -2.1
 207 SER   ( 283-)  A    -2.1
 221 THR   ( 297-)  A    -2.1
  23 SER   (  99-)  A    -2.0
 328 GLU   ( 404-)  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.

  14 SER   (  90-)  A  Poor phi/psi
  41 GLU   ( 117-)  A  Poor phi/psi
  55 ALA   ( 131-)  A  Poor phi/psi
  62 GLN   ( 138-)  A  PRO omega poor
 109 GLY   ( 185-)  A  Poor phi/psi
 145 ILE   ( 221-)  A  Poor phi/psi
 150 GLU   ( 226-)  A  Poor phi/psi
 166 ASP   ( 242-)  A  Poor phi/psi
 182 GLU   ( 258-)  A  Poor phi/psi
 187 LYS   ( 263-)  A  Poor phi/psi
 207 SER   ( 283-)  A  Poor phi/psi
 215 CYS   ( 291-)  A  Poor phi/psi
 219 SER   ( 295-)  A  Poor phi/psi
 220 TYR   ( 296-)  A  Poor phi/psi
 234 ASP   ( 310-)  A  Poor phi/psi
 249 THR   ( 325-)  A  PRO omega poor
 252 PRO   ( 328-)  A  Poor phi/psi
 306 ARG   ( 382-)  A  Poor phi/psi
 308 ASP   ( 384-)  A  Poor phi/psi
 332 TRP   ( 408-)  A  Poor phi/psi
 361 THR   ( 437-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.691

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 : -4.691

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 TRP   (  80-)  A      0
   8 ARG   (  84-)  A      0
   9 LEU   (  85-)  A      0
  12 GLN   (  88-)  A      0
  15 THR   (  91-)  A      0
  18 LYS   (  94-)  A      0
  19 ALA   (  95-)  A      0
  20 LEU   (  96-)  A      0
  25 HIS   ( 101-)  A      0
  27 PHE   ( 103-)  A      0
  34 SER   ( 110-)  A      0
  39 ILE   ( 115-)  A      0
  41 GLU   ( 117-)  A      0
  42 PRO   ( 118-)  A      0
  49 LYS   ( 125-)  A      0
  50 GLU   ( 126-)  A      0
  54 PHE   ( 130-)  A      0
  58 HIS   ( 134-)  A      0
  59 TYR   ( 135-)  A      0
  60 ALA   ( 136-)  A      0
  62 GLN   ( 138-)  A      0
  63 PRO   ( 139-)  A      0
  66 TYR   ( 142-)  A      0
  67 TYR   ( 143-)  A      0
  68 ASN   ( 144-)  A      0
And so on for a total of 218 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 : 2.067

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 270 GLY   ( 346-)  A   1.61   23

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]

  89 PRO   ( 165-)  A    0.47 HIGH

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].

   2 PRO   (  78-)  A  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 311 PRO   ( 387-)  A   115.6 envelop C-beta (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.

 194 ARG   ( 270-)  A      NH2 <->  217 ASP   ( 293-)  A      OD2    0.31    2.39  INTRA BL
  14 SER   (  90-)  A      N   <->  374 GLY   ( 450-)  A      O      0.30    2.40  INTRA BL
  41 GLU   ( 117-)  A      N   <->   42 PRO   ( 118-)  A      CD     0.26    2.74  INTRA BL
   7 PRO   (  83-)  A      O   <->  391 NAG   ( 467-)  A      N2     0.25    2.45  INTRA BL
 298 ARG   ( 374-)  A      NH1 <->  332 TRP   ( 408-)  A      CE3    0.24    2.86  INTRA BL
 246 TYR   ( 322-)  A      O   <->  291 ARG   ( 367-)  A      NH2    0.24    2.46  INTRA BL
  25 HIS   ( 101-)  A      NE2 <->  364 SER   ( 440-)  A      CB     0.23    2.87  INTRA BL
  47 GLY   ( 123-)  A      N   <->   50 GLU   ( 126-)  A      O      0.22    2.48  INTRA BL
 223 LYS   ( 299-)  A      NZ  <->  261 CYS   ( 337-)  A      O      0.18    2.52  INTRA BL
 216 ARG   ( 292-)  A      NH1 <->  272 ILE   ( 348-)  A      CA     0.18    2.92  INTRA BL
  26 ARG   ( 102-)  A      N   <->   27 PHE   ( 103-)  A      N      0.17    2.43  INTRA BL
 289 TYR   ( 365-)  A      O   <->  304 TYR   ( 380-)  A      N      0.17    2.53  INTRA BL
  25 HIS   ( 101-)  A      NE2 <->  364 SER   ( 440-)  A      OG     0.16    2.54  INTRA BL
 216 ARG   ( 292-)  A      CD  <->  272 ILE   ( 348-)  A      N      0.16    2.94  INTRA BL
  52 ARG   ( 128-)  A      CG  <->  112 TRP   ( 188-)  A      CZ2    0.15    3.05  INTRA BL
 157 GLY   ( 233-)  A      O   <->  181 ARG   ( 257-)  A      NH2    0.15    2.55  INTRA BL
  58 HIS   ( 134-)  A      CE1 <->   70 THR   ( 146-)  A      O      0.14    2.66  INTRA BL
 218 ASN   ( 294-)  A      O   <->  270 GLY   ( 346-)  A      N      0.14    2.56  INTRA BL
 281 MET   ( 357-)  A      CE  <->  284 LYS   ( 360-)  A      CD     0.14    3.06  INTRA BL
 302 GLU   ( 378-)  A      CG  <->  304 TYR   ( 380-)  A      CE1    0.13    3.07  INTRA BL
 177 PHE   ( 253-)  A      N   <->  189 ILE   ( 265-)  A      O      0.13    2.57  INTRA BL
 107 HIS   ( 183-)  A      CE1 <->  109 GLY   ( 185-)  A      C      0.13    3.07  INTRA BL
 163 MET   ( 239-)  A      SD  <->  201 CYS   ( 277-)  A      SG     0.13    3.32  INTRA BL
 108 ASP   ( 184-)  A      OD1 <->  111 GLU   ( 187-)  A      N      0.13    2.57  INTRA BL
 141 TYR   ( 217-)  A      CE1 <->  166 ASP   ( 242-)  A      CB     0.12    3.08  INTRA BL
And so on for a total of 95 lines.

Packing, accessibility and threading

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.

  12 GLN   (  88-)  A      -7.13
  49 LYS   ( 125-)  A      -6.73
 298 ARG   ( 374-)  A      -5.93
 110 ARG   ( 186-)  A      -5.91
  66 TYR   ( 142-)  A      -5.80
  33 ASN   ( 109-)  A      -5.54
  26 ARG   ( 102-)  A      -5.53
 379 LEU   ( 455-)  A      -5.44
  30 ILE   ( 106-)  A      -5.36
  59 TYR   ( 135-)  A      -5.27
 181 ARG   ( 257-)  A      -5.23
  71 ARG   ( 147-)  A      -5.18
 343 LYS   ( 419-)  A      -5.16

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.

  66 TYR   ( 142-)  A        68 - ASN    144- ( A)         -5.10

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.

  12 GLN   (  88-)  A   -2.64

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.

  17 GLN   (  93-)  A
  58 HIS   ( 134-)  A
  93 ASN   ( 169-)  A
 218 ASN   ( 294-)  A
 264 ASN   ( 340-)  A
 355 HIS   ( 431-)  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.

  16 PHE   (  92-)  A      N
  17 GLN   (  93-)  A      NE2
  25 HIS   ( 101-)  A      N
  31 LYS   ( 107-)  A      N
  34 SER   ( 110-)  A      N
  40 ARG   ( 116-)  A      NE
  40 ARG   ( 116-)  A      NH2
  44 VAL   ( 120-)  A      N
  51 CYS   ( 127-)  A      N
  52 ARG   ( 128-)  A      NE
  75 ASN   ( 151-)  A      N
  78 ARG   ( 154-)  A      NE
  78 ARG   ( 154-)  A      NH1
  86 GLY   ( 162-)  A      N
  88 ILE   ( 164-)  A      N
  93 ASN   ( 169-)  A      ND2
  98 MET   ( 174-)  A      N
 102 SER   ( 178-)  A      N
 119 GLY   ( 195-)  A      N
 124 ALA   ( 200-)  A      N
 134 TYR   ( 210-)  A      N
 137 THR   ( 213-)  A      N
 146 LEU   ( 222-)  A      N
 147 ARG   ( 223-)  A      NE
 147 ARG   ( 223-)  A      NH1
And so on for a total of 51 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  41 GLU   ( 117-)  A      OE1
 154 ASN   ( 230-)  A      OD1
 197 HIS   ( 273-)  A      NE2
 200 GLU   ( 276-)  A      OE1
 208 ASN   ( 284-)  A      OD1
 237 GLU   ( 313-)  A      OE1
 355 HIS   ( 431-)  A      NE2

Warning: Unusual ion packing

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

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

 394  CA   ( 501-)  A     0.80   1.04 Scores about as good as NA (Few ligands (4) ) *S
Since there are no waters, the water check has been skipped.

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.

   1 GLU   (  77-)  A   H-bonding suggests Gln
  29 GLU   ( 105-)  A   H-bonding suggests Gln
 108 ASP   ( 184-)  A   H-bonding suggests Asn; but Alt-Rotamer
 166 ASP   ( 242-)  A   H-bonding suggests Asn
 360 ASP   ( 436-)  A   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 :  -1.419
  2nd generation packing quality :  -1.666
  Ramachandran plot appearance   :  -3.291 (poor)
  chi-1/chi-2 rotamer normality  :  -4.691 (bad)
  Backbone conformation          :  -0.990

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.688
  Bond angles                    :   0.973
  Omega angle restraints         :   0.376 (tight)
  Side chain planarity           :   0.716
  Improper dihedral distribution :   1.259
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.083

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 :  -0.7
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.688
  Bond angles                    :   0.973
  Omega angle restraints         :   0.376 (tight)
  Side chain planarity           :   0.716
  Improper dihedral distribution :   1.259
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.083
==============

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.