WHAT IF Check report

This file was created 2011-12-13 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 pdb2dga.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 56559.039
Volume of the Unit Cell V= 7376856.5
Space group multiplicity: 24
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.434
Vm by authors and this calculated Vm agree only marginally
Matthews coefficient read from REMARK 280 Vm= 4.790

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.

 492 SO4   (1001-)  A  -
 493 GOL   (1314-)  A  -
 494 GOL   (1315-)  A  -
 495 GOL   (1316-)  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

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) : 95.000

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: Tyrosine convention problem

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

 420 TYR   ( 431-)  A

Warning: Phenylalanine convention problem

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

   4 PHE   (  15-)  A
 160 PHE   ( 171-)  A
 176 PHE   ( 187-)  A
 290 PHE   ( 301-)  A
 327 PHE   ( 338-)  A
 482 PHE   ( 493-)  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.

  16 ASP   (  27-)  A
 156 ASP   ( 167-)  A
 243 ASP   ( 254-)  A
 316 ASP   ( 327-)  A
 356 ASP   ( 367-)  A
 405 ASP   ( 416-)  A
 410 ASP   ( 421-)  A
 413 ASP   ( 424-)  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.

  75 GLU   (  86-)  A
  76 GLU   (  87-)  A
 191 GLU   ( 202-)  A
 269 GLU   ( 280-)  A
 306 GLU   ( 317-)  A
 406 GLU   ( 417-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.258
RMS-deviation in bond distances: 0.006

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

 |  0.998787 -0.000223  0.000034|
 | -0.000223  0.998652  0.000080|
 |  0.000034  0.000080  0.998159|
Proposed new scale matrix

 |  0.005143  0.000001  0.000000|
 |  0.000001  0.005144  0.000000|
 |  0.000000  0.000000  0.005146|
With corresponding cell

    A    = 194.430  B   = 194.404  C    = 194.308
    Alpha=  90.002  Beta=  90.002  Gamma=  90.026

The CRYST1 cell dimensions

    A    = 194.650  B   = 194.650  C    = 194.650
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 36.981
(Under-)estimated Z-score: 4.482

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.

 136 ASP   ( 147-)  A     -C    N    CA  130.29    4.8
 394 ILE   ( 405-)  A      N    CA   C    99.69   -4.1
 401 ASP   ( 412-)  A      N    CA   C    97.35   -4.9
 446 LEU   ( 457-)  A      N    CA   C    99.91   -4.0

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.620
RMS-deviation in bond angles: 1.376

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.

  16 ASP   (  27-)  A
  75 GLU   (  86-)  A
  76 GLU   (  87-)  A
 156 ASP   ( 167-)  A
 191 GLU   ( 202-)  A
 243 ASP   ( 254-)  A
 269 GLU   ( 280-)  A
 306 GLU   ( 317-)  A
 316 ASP   ( 327-)  A
 356 ASP   ( 367-)  A
 405 ASP   ( 416-)  A
 406 GLU   ( 417-)  A
 410 ASP   ( 421-)  A
 413 ASP   ( 424-)  A

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.

  33 ILE   (  44-)  A    5.20
 130 VAL   ( 141-)  A    4.79
 446 LEU   ( 457-)  A    4.61
 237 ARG   ( 248-)  A    4.41
 401 ASP   ( 412-)  A    4.36
 385 GLU   ( 396-)  A    4.30
  30 ALA   (  41-)  A    4.26
 265 ASP   ( 276-)  A    4.14
 439 ARG   ( 450-)  A    4.07

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.

 324 THR   ( 335-)  A    -2.9
 365 GLY   ( 376-)  A    -2.2
  61 MET   (  72-)  A    -2.1

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.

  33 ILE   (  44-)  A  Poor phi/psi
  61 MET   (  72-)  A  Poor phi/psi
  67 ALA   (  78-)  A  Poor phi/psi
 125 ASP   ( 136-)  A  Poor phi/psi
 135 TRP   ( 146-)  A  Poor phi/psi
 136 ASP   ( 147-)  A  Poor phi/psi
 195 ALA   ( 206-)  A  PRO omega poor
 208 PRO   ( 219-)  A  Poor phi/psi
 313 SER   ( 324-)  A  Poor phi/psi
 340 THR   ( 351-)  A  Poor phi/psi
 389 ASN   ( 400-)  A  Poor phi/psi
 452 TRP   ( 463-)  A  Poor phi/psi
 471 ASN   ( 482-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.766

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.

 294 SER   ( 305-)  A    0.38
 483 SER   ( 494-)  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!

   3 VAL   (  14-)  A      0
  17 TRP   (  28-)  A      0
  22 PHE   (  33-)  A      0
  33 ILE   (  44-)  A      0
  34 GLU   (  45-)  A      0
  36 ALA   (  47-)  A      0
  37 TRP   (  48-)  A      0
  39 GLU   (  50-)  A      0
  40 ASP   (  51-)  A      0
  42 LYS   (  53-)  A      0
  53 THR   (  64-)  A      0
  55 PRO   (  66-)  A      0
  61 MET   (  72-)  A      0
  65 ASP   (  76-)  A      0
  67 ALA   (  78-)  A      0
  68 ALA   (  79-)  A      0
  70 SER   (  81-)  A      0
  72 HIS   (  83-)  A      0
  84 MET   (  95-)  A      0
  86 MET   (  97-)  A      0
  95 TRP   ( 106-)  A      0
  98 ILE   ( 109-)  A      0
 103 THR   ( 114-)  A      0
 105 LYS   ( 116-)  A      0
 132 ILE   ( 143-)  A      0
And so on for a total of 187 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 : 1.523

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!

 210 GLY   ( 221-)  A   1.75   10

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.

  87 LYS   (  98-)  A      NZ  <->  496 HOH   (1631 )  A      O      0.22    2.48  INTRA
 194 HIS   ( 205-)  A      NE2 <->  495 GOL   (1316-)  A      O1     0.21    2.49  INTRA
 115 ASN   ( 126-)  A      ND2 <->  171 ARG   ( 182-)  A      NH2    0.20    2.65  INTRA
  46 THR   (  57-)  A      CG2 <->  142 GLU   ( 153-)  A      CG     0.17    3.03  INTRA
 462 LEU   ( 473-)  A      N   <->  463 VAL   ( 474-)  A      N      0.16    2.44  INTRA BL
 239 ASN   ( 250-)  A      ND2 <->  496 HOH   (1602 )  A      O      0.15    2.55  INTRA BF
 170 ASP   ( 181-)  A      OD2 <->  171 ARG   ( 182-)  A      CD     0.15    2.65  INTRA
 134 HIS   ( 145-)  A      CE1 <->  179 ASN   ( 190-)  A      ND2    0.13    2.97  INTRA BL
  88 VAL   (  99-)  A      CG1 <->   89 TYR   ( 100-)  A      N      0.12    2.88  INTRA BL
 481 TRP   ( 492-)  A      CD1 <->  484 LYS   ( 495-)  A      NZ     0.12    2.98  INTRA
 194 HIS   ( 205-)  A      O   <->  197 GLY   ( 208-)  A      N      0.10    2.60  INTRA BL
 215 GLU   ( 226-)  A      N   <->  216 PRO   ( 227-)  A      CD     0.10    2.90  INTRA BL
  38 ASN   (  49-)  A      ND2 <->  496 HOH   (1593 )  A      O      0.10    2.60  INTRA
  46 THR   (  57-)  A      N   <->  137 THR   ( 148-)  A      O      0.10    2.60  INTRA BL
 259 GLN   ( 270-)  A      CG  <->  492 SO4   (1001-)  A      S      0.09    3.31  INTRA
   4 PHE   (  15-)  A      N   <->  496 HOH   (1884 )  A      O      0.09    2.61  INTRA
 437 ASP   ( 448-)  A      OD1 <->  439 ARG   ( 450-)  A      NE     0.08    2.62  INTRA
 197 GLY   ( 208-)  A      O   <->  207 VAL   ( 218-)  A      CG1    0.08    2.72  INTRA
 330 HIS   ( 341-)  A      CE1 <->  332 ASP   ( 343-)  A      CG     0.07    3.13  INTRA
 281 GLU   ( 292-)  A      N   <->  282 PRO   ( 293-)  A      CD     0.07    2.93  INTRA BL
 144 LYS   ( 155-)  A      NZ  <->  496 HOH   (1717 )  A      O      0.07    2.63  INTRA BF
 434 GLN   ( 445-)  A      NE2 <->  496 HOH   (1445 )  A      O      0.06    2.64  INTRA
  93 ILE   ( 104-)  A      CG2 <->   98 ILE   ( 109-)  A      CD1    0.06    3.14  INTRA
  66 VAL   (  77-)  A      CG1 <->  496 HOH   (1370 )  A      O      0.05    2.75  INTRA
 446 LEU   ( 457-)  A      N   <->  447 ILE   ( 458-)  A      N      0.05    2.55  INTRA BL
 245 LYS   ( 256-)  A      NZ  <->  496 HOH   (1594 )  A      O      0.05    2.65  INTRA
 270 ARG   ( 281-)  A      NH2 <->  330 HIS   ( 341-)  A      CD2    0.05    3.05  INTRA BL
 416 LYS   ( 427-)  A      NZ  <->  496 HOH   (1558 )  A      O      0.04    2.66  INTRA
 389 ASN   ( 400-)  A      N   <->  390 PRO   ( 401-)  A      CD     0.04    2.96  INTRA BL
  90 ARG   ( 101-)  A      NH2 <->  179 ASN   ( 190-)  A      OD1    0.04    2.66  INTRA
 259 GLN   ( 270-)  A      CG  <->  492 SO4   (1001-)  A      O3     0.04    2.76  INTRA
 408 MET   ( 419-)  A      N   <->  409 PRO   ( 420-)  A      CD     0.04    2.96  INTRA
 198 ARG   ( 209-)  A      CG  <->  207 VAL   ( 218-)  A      CG1    0.04    3.16  INTRA
 417 ARG   ( 428-)  A      NH2 <->  459 ARG   ( 470-)  A      O      0.03    2.67  INTRA BL
 199 CYS   ( 210-)  A      N   <->  205 CYS   ( 216-)  A      SG     0.03    3.27  INTRA
 142 GLU   ( 153-)  A      OE2 <->  496 HOH   (1337 )  A      O      0.03    2.37  INTRA
  14 LYS   (  25-)  A      C   <->  485 PHE   ( 496-)  A      CE1    0.02    3.18  INTRA BL
 182 HIS   ( 193-)  A      ND1 <->  251 ASP   ( 262-)  A      OD2    0.02    2.68  INTRA BL
  66 VAL   (  77-)  A      O   <->   69 ASN   (  80-)  A      N      0.02    2.68  INTRA BL
 136 ASP   ( 147-)  A      CG  <->  496 HOH   (1436 )  A      O      0.02    2.78  INTRA
 221 HIS   ( 232-)  A      CD2 <->  288 TYR   ( 299-)  A      OH     0.02    2.78  INTRA BL
 207 VAL   ( 218-)  A      CG2 <->  209 GLU   ( 220-)  A      CG     0.01    3.19  INTRA
 200 SER   ( 211-)  A      OG  <->  212 SER   ( 223-)  A      N      0.01    2.69  INTRA BL
 237 ARG   ( 248-)  A      NH1 <->  496 HOH   (1696 )  A      O      0.01    2.69  INTRA BF
 445 GLY   ( 456-)  A      C   <->  446 LEU   ( 457-)  A      C      0.01    2.79  INTRA BL
 250 PHE   ( 261-)  A      N   <->  319 GLY   ( 330-)  A      O      0.01    2.69  INTRA BL
 248 MET   ( 259-)  A      CG  <->  250 PHE   ( 261-)  A      CZ     0.01    3.19  INTRA
 401 ASP   ( 412-)  A      OD2 <->  417 ARG   ( 428-)  A      NH1    0.01    2.69  INTRA BL
 255 TYR   ( 266-)  A      OH  <->  275 ASN   ( 286-)  A      ND2    0.01    2.69  INTRA BL

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.

 490 LYS   ( 501-)  A      -7.25
 333 MET   ( 344-)  A      -7.07
 367 TYR   ( 378-)  A      -6.48
 240 MET   ( 251-)  A      -6.20
  17 TRP   (  28-)  A      -5.68
  11 GLN   (  22-)  A      -5.48
 371 MET   ( 382-)  A      -5.28
 302 MET   ( 313-)  A      -5.26
 275 ASN   ( 286-)  A      -5.13
 167 ASN   ( 178-)  A      -5.08
 299 ARG   ( 310-)  A      -5.08
  61 MET   (  72-)  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

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.

 346 ALA   ( 357-)  A   -2.85
 468 ASN   ( 479-)  A   -2.83
  38 ASN   (  49-)  A   -2.82

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.

 387 TYR   ( 398-)  A     -  390 PRO   ( 401-)  A        -1.46

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 496 HOH   (1589 )  A      O    -52.10  -22.35   14.30
 496 HOH   (1789 )  A      O    -56.68    2.62  -25.47
 496 HOH   (1810 )  A      O    -53.37  -22.01   23.18
 496 HOH   (1841 )  A      O    -74.22  -23.99  -10.06
 496 HOH   (1849 )  A      O    -48.56    3.84  -21.95

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.

  63 ASN   (  74-)  A
  69 ASN   (  80-)  A
  72 HIS   (  83-)  A
 134 HIS   ( 145-)  A
 150 ASN   ( 161-)  A
 167 ASN   ( 178-)  A
 221 HIS   ( 232-)  A
 222 HIS   ( 233-)  A
 330 HIS   ( 341-)  A
 358 ASN   ( 369-)  A
 486 ASN   ( 497-)  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.

  10 TRP   (  21-)  A      N
  14 LYS   (  25-)  A      N
  29 SER   (  40-)  A      N
  32 GLN   (  43-)  A      NE2
 103 THR   ( 114-)  A      N
 115 ASN   ( 126-)  A      ND2
 135 TRP   ( 146-)  A      N
 136 ASP   ( 147-)  A      N
 171 ARG   ( 182-)  A      NH2
 179 ASN   ( 190-)  A      ND2
 195 ALA   ( 206-)  A      N
 239 ASN   ( 250-)  A      N
 248 MET   ( 259-)  A      N
 259 GLN   ( 270-)  A      NE2
 261 SER   ( 272-)  A      OG
 287 ASP   ( 298-)  A      N
 303 PHE   ( 314-)  A      N
 304 THR   ( 315-)  A      OG1
 361 GLY   ( 372-)  A      N
 368 TRP   ( 379-)  A      N
 374 LYS   ( 385-)  A      NZ
 397 ASN   ( 408-)  A      N
 398 GLY   ( 409-)  A      N
 415 TRP   ( 426-)  A      N
 440 GLY   ( 451-)  A      N
 447 ILE   ( 458-)  A      N
 449 ASN   ( 460-)  A      ND2
 453 SER   ( 464-)  A      N
 458 SER   ( 469-)  A      N
 486 ASN   ( 497-)  A      ND2

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.

 194 HIS   ( 205-)  A      NE2
 275 ASN   ( 286-)  A      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.

 112 ASP   ( 123-)  A   H-bonding suggests Asn; but Alt-Rotamer
 123 ASP   ( 134-)  A   H-bonding suggests Asn
 142 GLU   ( 153-)  A   H-bonding suggests Gln
 143 ASP   ( 154-)  A   H-bonding suggests Asn
 180 GLU   ( 191-)  A   H-bonding suggests Gln; Ligand-contact
 451 GLU   ( 462-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.573
  2nd generation packing quality :  -1.494
  Ramachandran plot appearance   :  -0.474
  chi-1/chi-2 rotamer normality  :  -0.766
  Backbone conformation          :  -1.334

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.258 (tight)
  Bond angles                    :   0.620 (tight)
  Omega angle restraints         :   0.277 (tight)
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.015

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.258 (tight)
  Bond angles                    :   0.620 (tight)
  Omega angle restraints         :   0.277 (tight)
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.015
==============

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.