WHAT IF Check report

This file was created 2013-07-12 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 pdb3s3e.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 : 0.981
CA-only RMS fit for the two chains : 0.653

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.

 573 1BO   ( 309-)  A  -
 575 1BO   ( 311-)  A  -
 576 1BO   ( 309-)  B  -
 577 1BO   ( 310-)  B  -
 578 1BO   ( 311-)  B  -
 579 1BO   ( 312-)  B  -
 582 1BO   ( 314-)  B  -
 583 BU1   ( 308-)  B  -

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: Missing atoms

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

  11 LYS   (  29-)  A      CD
  11 LYS   (  29-)  A      CE
  11 LYS   (  29-)  A      NZ
  76 ASP   (  94-)  A      CG
  76 ASP   (  94-)  A      OD1
  76 ASP   (  94-)  A      OD2
  78 GLU   (  96-)  A      CB
  78 GLU   (  96-)  A      CG
  78 GLU   (  96-)  A      CD
  78 GLU   (  96-)  A      OE1
  78 GLU   (  96-)  A      OE2
 106 SER   ( 124-)  A      OG
 134 ARG   ( 152-)  A      CZ
 134 ARG   ( 152-)  A      NH1
 134 ARG   ( 152-)  A      NH2
 177 SER   ( 195-)  A      CB
 177 SER   ( 195-)  A      OG
 249 TYR   ( 267-)  A      CG
 249 TYR   ( 267-)  A      CD1
 249 TYR   ( 267-)  A      CD2
 249 TYR   ( 267-)  A      CE1
 249 TYR   ( 267-)  A      CE2
 249 TYR   ( 267-)  A      CZ
 249 TYR   ( 267-)  A      OH
 296 LYS   (  29-)  B      CG
 296 LYS   (  29-)  B      CD
 296 LYS   (  29-)  B      CE
 296 LYS   (  29-)  B      NZ
 315 GLU   (  48-)  B      CG
 315 GLU   (  48-)  B      CD
 315 GLU   (  48-)  B      OE1
 315 GLU   (  48-)  B      OE2
 321 LYS   (  54-)  B      CE
 321 LYS   (  54-)  B      NZ
 478 PHE   ( 211-)  B      CG
 478 PHE   ( 211-)  B      CD1
 478 PHE   ( 211-)  B      CD2
 478 PHE   ( 211-)  B      CE1
 478 PHE   ( 211-)  B      CE2
 478 PHE   ( 211-)  B      CZ
 502 GLN   ( 235-)  B      CG
 502 GLN   ( 235-)  B      CD
 502 GLN   ( 235-)  B      OE1
 502 GLN   ( 235-)  B      NE2

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 2

Crystal temperature (K) :100.000

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: Arginine nomenclature problem

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

 180 ARG   ( 198-)  A
 230 ARG   ( 248-)  A
 465 ARG   ( 198-)  B
 515 ARG   ( 248-)  B

Warning: Tyrosine convention problem

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

 150 TYR   ( 168-)  A
 163 TYR   ( 181-)  A
 257 TYR   ( 275-)  A
 448 TYR   ( 181-)  B
 534 TYR   ( 267-)  B
 542 TYR   ( 275-)  B

Warning: Phenylalanine convention problem

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

  69 PHE   (  87-)  A
 130 PHE   ( 148-)  A
 149 PHE   ( 167-)  A
 185 PHE   ( 203-)  A
 193 PHE   ( 211-)  A
 311 PHE   (  44-)  B
 415 PHE   ( 148-)  B
 470 PHE   ( 203-)  B
 494 PHE   ( 227-)  B
 538 PHE   ( 271-)  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.

  23 ASP   (  41-)  A
 211 ASP   ( 229-)  A
 326 ASP   (  59-)  B
 360 ASP   (  93-)  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.

  33 GLU   (  51-)  A
 216 GLU   ( 234-)  A
 300 GLU   (  33-)  B
 319 GLU   (  52-)  B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  86 ASN   ( 104-)  A      N   -C     1.23   -5.2

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

 |  0.998577 -0.000035  0.000134|
 | -0.000035  0.998725  0.000051|
 |  0.000134  0.000051  0.998009|
Proposed new scale matrix

 |  0.009774  0.005643 -0.000002|
 |  0.000000  0.011284  0.000000|
 |  0.000000  0.000000  0.005831|
With corresponding cell

    A    = 102.312  B   = 102.325  C    = 171.509
    Alpha=  90.006  Beta=  89.991  Gamma= 119.998

The CRYST1 cell dimensions

    A    = 102.460  B   = 102.460  C    = 171.842
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 50.309
(Under-)estimated Z-score: 5.227

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.

  86 ASN   ( 104-)  A     -C    N    CA  130.45    4.9
 267 VAL   ( 285-)  A     -O   -C    N   116.01   -4.4
 267 VAL   ( 285-)  A     -CA  -C    N   125.47    4.6
 267 VAL   ( 285-)  A     -C    N    CA  107.55   -7.9
 503 ARG   ( 236-)  B     -C    N    CA  130.42    4.8
 552 VAL   ( 285-)  B     -CA  -C    N   124.24    4.0
 552 VAL   ( 285-)  B     -C    N    CA  109.37   -6.8

Error: Nomenclature error(s)

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

  23 ASP   (  41-)  A
  33 GLU   (  51-)  A
 180 ARG   ( 198-)  A
 211 ASP   ( 229-)  A
 216 GLU   ( 234-)  A
 230 ARG   ( 248-)  A
 300 GLU   (  33-)  B
 319 GLU   (  52-)  B
 326 ASP   (  59-)  B
 360 ASP   (  93-)  B
 465 ARG   ( 198-)  B
 515 ARG   ( 248-)  B

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.

 483 PRO   ( 216-)  B    -3.0
 213 ILE   ( 231-)  A    -2.5
  24 SER   (  42-)  A    -2.4
 175 ARG   ( 193-)  A    -2.4
 498 ILE   ( 231-)  B    -2.3
 121 ARG   ( 139-)  A    -2.3
 291 ARG   (  24-)  B    -2.2
 176 GLY   ( 194-)  A    -2.1
 474 THR   ( 207-)  B    -2.0
 144 ASP   ( 162-)  A    -2.0
 225 SER   ( 243-)  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.

   2 HIS   (  20-)  A  Poor phi/psi
  23 ASP   (  41-)  A  Poor phi/psi
  25 ASP   (  43-)  A  Poor phi/psi
  35 LEU   (  53-)  A  omega poor
  66 HIS   (  84-)  A  omega poor
  67 SER   (  85-)  A  Poor phi/psi
  74 VAL   (  92-)  A  omega poor
  97 PHE   ( 115-)  A  omega poor
 103 PRO   ( 121-)  A  omega poor
 119 ASN   ( 137-)  A  Poor phi/psi
 127 THR   ( 145-)  A  omega poor
 144 ASP   ( 162-)  A  Poor phi/psi
 171 PHE   ( 189-)  A  omega poor
 177 SER   ( 195-)  A  Poor phi/psi
 197 ASN   ( 215-)  A  PRO omega poor
 224 CYS   ( 242-)  A  Poor phi/psi
 245 ASN   ( 263-)  A  omega poor
 267 VAL   ( 285-)  A  omega poor
 308 ASP   (  41-)  B  Poor phi/psi
 310 ASP   (  43-)  B  Poor phi/psi
 352 SER   (  85-)  B  omega poor
 358 PRO   (  91-)  B  omega poor
 361 ASP   (  94-)  B  Poor phi/psi
 366 ASP   (  99-)  B  omega poor
 371 ASN   ( 104-)  B  omega poor
 404 ASN   ( 137-)  B  Poor phi/psi
 412 THR   ( 145-)  B  omega poor
 417 LYS   ( 150-)  B  Poor phi/psi
 444 ASN   ( 177-)  B  Poor phi/psi
 456 PHE   ( 189-)  B  omega poor
 461 GLY   ( 194-)  B  omega poor
 473 THR   ( 206-)  B  omega poor
 481 PRO   ( 214-)  B  omega poor
 482 ASN   ( 215-)  B  PRO omega poor
 503 ARG   ( 236-)  B  Poor phi/psi
 509 CYS   ( 242-)  B  Poor phi/psi
 531 THR   ( 264-)  B  Poor phi/psi
 550 TRP   ( 283-)  B  Poor phi/psi
 552 VAL   ( 285-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -1.433

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.

 516 SER   ( 249-)  B    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 MET   (  21-)  A      0
   4 ALA   (  22-)  A      0
   5 SER   (  23-)  A      0
  23 ASP   (  41-)  A      0
  24 SER   (  42-)  A      0
  25 ASP   (  43-)  A      0
  38 VAL   (  56-)  A      0
  61 ILE   (  79-)  A      0
  67 SER   (  85-)  A      0
  78 GLU   (  96-)  A      0
  80 SER   (  98-)  A      0
  83 ILE   ( 101-)  A      0
  84 ASN   ( 102-)  A      0
  87 TYR   ( 105-)  A      0
  91 HIS   ( 109-)  A      0
  92 ASN   ( 110-)  A      0
  93 SER   ( 111-)  A      0
  95 ARG   ( 113-)  A      0
 105 HIS   ( 123-)  A      0
 118 SER   ( 136-)  A      0
 119 ASN   ( 137-)  A      0
 120 SER   ( 138-)  A      0
 126 LEU   ( 144-)  A      0
 129 CYS   ( 147-)  A      0
 130 PHE   ( 148-)  A      0
And so on for a total of 226 lines.

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!

 176 GLY   ( 194-)  A   3.04   14
 461 GLY   ( 194-)  B   2.18   13

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]

 504 PRO   ( 237-)  B    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

   7 PRO   (  25-)  A    52.4 half-chair C-delta/C-gamma (54 degrees)
 199 PRO   ( 217-)  A  -133.7 half-chair C-delta/C-gamma (-126 degrees)
 358 PRO   (  91-)  B   -36.9 envelop C-alpha (-36 degrees)
 483 PRO   ( 216-)  B     1.7 envelop N (0 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 580 IPA   ( 310-)  A      O2  <->  584 HOH   ( 384 )  A      O      0.64    1.76  INTRA BF
 503 ARG   ( 236-)  B      CB  <->  504 PRO   ( 237-)  B      CD     0.46    2.64  INTRA
 228 VAL   ( 246-)  A      O   <->  266 MET   ( 284-)  A      O      0.28    1.97  INTRA BL
 513 VAL   ( 246-)  B      O   <->  551 MET   ( 284-)  B      O      0.26    1.99  INTRA BL
 291 ARG   (  24-)  B      NH1 <->  319 GLU   (  52-)  B      OE1    0.18    2.52  INTRA BF
 545 ARG   ( 278-)  B      NH2 <->  552 VAL   ( 285-)  B      O      0.18    2.52  INTRA BL
 457 MET   ( 190-)  B      SD  <->  464 GLN   ( 197-)  B      NE2    0.16    3.14  INTRA BF
  17 TYR   (  35-)  A      OH  <->  278 GLN   ( 296-)  A      NE2    0.14    2.56  INTRA
 287 LYS   ( 305-)  A      NZ  <->  584 HOH   ( 319 )  A      O      0.14    2.56  INTRA
 482 ASN   ( 215-)  B      ND2 <->  483 PRO   ( 216-)  B      CD     0.13    2.97  INTRA BF
  77 ASP   (  95-)  A      OD1 <->   78 GLU   (  96-)  A      N      0.13    2.47  INTRA BF
 266 MET   ( 284-)  A      O   <->  267 VAL   ( 285-)  A      CA     0.10    2.30  INTRA BL
 340 LYS   (  73-)  B      NZ  <->  585 HOH   ( 356 )  B      O      0.09    2.61  INTRA BL
 338 ARG   (  71-)  B      N   <->  339 PRO   (  72-)  B      CD     0.09    2.91  INTRA BL
 119 ASN   ( 137-)  A      OD1 <->  121 ARG   ( 139-)  A      NH1    0.09    2.61  INTRA
  92 ASN   ( 110-)  A      N   <->   96 GLU   ( 114-)  A      OE1    0.08    2.62  INTRA BL
 502 GLN   ( 235-)  B      C   <->  503 ARG   ( 236-)  B      O      0.08    2.52  INTRA
 412 THR   ( 145-)  B      O   <->  471 HIS   ( 204-)  B      NE2    0.08    2.62  INTRA BL
 288 MET   (  21-)  B      CB  <->  289 ALA   (  22-)  B      N      0.07    2.63  INTRA BF
 462 SER   ( 195-)  B      N   <->  463 GLU   ( 196-)  B      N      0.07    2.53  INTRA B3
 448 TYR   ( 181-)  B      OH  <->  497 ARG   ( 230-)  B      NH2    0.07    2.63  INTRA
 224 CYS   ( 242-)  A      SG  <->  225 SER   ( 243-)  A      N      0.06    3.14  INTRA BL
 282 ALA   ( 300-)  A      O   <->  287 LYS   ( 305-)  A      N      0.06    2.64  INTRA BF
  53 ARG   (  71-)  A      N   <->   54 PRO   (  72-)  A      CD     0.06    2.94  INTRA
  33 GLU   (  51-)  A      OE2 <->   36 LYS   (  54-)  A      NZ     0.05    2.65  INTRA
 495 ARG   ( 228-)  B      NH2 <->  523 ASP   ( 256-)  B      OD2    0.05    2.65  INTRA BL
 266 MET   ( 284-)  A      C   <->  267 VAL   ( 285-)  A      CA     0.05    2.25  INTRA BL
 401 TRP   ( 134-)  B      O   <->  465 ARG   ( 198-)  B      NH1    0.04    2.66  INTRA BL
 551 MET   ( 284-)  B      O   <->  552 VAL   ( 285-)  B      CA     0.04    2.36  INTRA BL
 551 MET   ( 284-)  B      C   <->  552 VAL   ( 285-)  B      CA     0.03    2.27  INTRA BL
  39 GLY   (  57-)  A      N   <->  584 HOH   ( 342 )  A      O      0.03    2.67  INTRA
 228 VAL   ( 246-)  A      CG2 <->  229 GLY   ( 247-)  A      N      0.03    2.97  INTRA BL
 443 LEU   ( 176-)  B      N   <->  455 GLU   ( 188-)  B      O      0.02    2.68  INTRA
  70 LYS   (  88-)  A      N   <->  584 HOH   ( 329 )  A      O      0.02    2.68  INTRA BL
 408 ILE   ( 141-)  B      O   <->  470 PHE   ( 203-)  B      N      0.02    2.68  INTRA BL
 503 ARG   ( 236-)  B      CB  <->  504 PRO   ( 237-)  B      N      0.02    2.68  INTRA B3
   8 ILE   (  26-)  A      N   <->  250 VAL   ( 268-)  A      O      0.01    2.69  INTRA
 140 TYR   ( 158-)  A      OH  <->  223 HIS   ( 241-)  A      NE2    0.01    2.69  INTRA BL
 410 MET   ( 143-)  B      N   <->  470 PHE   ( 203-)  B      O      0.01    2.69  INTRA BL
 186 HIS   ( 204-)  A      ND1 <->  584 HOH   ( 385 )  A      O      0.01    2.69  INTRA BL
 333 ASP   (  66-)  B      O   <->  338 ARG   (  71-)  B      NE     0.01    2.69  INTRA BL
 174 CYS   ( 192-)  A      SG  <->  179 GLN   ( 197-)  A      CG     0.01    3.39  INTRA

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.

 193 PHE   ( 211-)  A      -7.31
 217 GLN   ( 235-)  A      -6.53
 132 LYS   ( 150-)  A      -6.25
 175 ARG   ( 193-)  A      -6.11
 197 ASN   ( 215-)  A      -5.94
   3 MET   (  21-)  A      -5.69
 497 ARG   ( 230-)  B      -5.69
 428 ASN   ( 161-)  B      -5.65
 482 ASN   ( 215-)  B      -5.64
 212 ARG   ( 230-)  A      -5.63
 503 ARG   ( 236-)  B      -5.54
 143 ASN   ( 161-)  A      -5.47
  66 HIS   (  84-)  A      -5.43
 218 ARG   ( 236-)  A      -5.30
 357 GLN   (  90-)  B      -5.18
 130 PHE   ( 148-)  A      -5.03

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.

 478 PHE   ( 211-)  B   -2.82
 502 GLN   ( 235-)  B   -2.81
 106 SER   ( 124-)  A   -2.75
  78 GLU   (  96-)  A   -2.54
 296 LYS   (  29-)  B   -2.51
  11 LYS   (  29-)  A   -2.50

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: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 584 HOH   ( 357 )  A      O
 584 HOH   ( 363 )  A      O

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.

  66 HIS   (  84-)  A
 105 HIS   ( 123-)  A
 357 GLN   (  90-)  B
 371 ASN   ( 104-)  B
 390 HIS   ( 123-)  B
 447 HIS   ( 180-)  B
 530 ASN   ( 263-)  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 SER   (  23-)  A      N
  62 LEU   (  80-)  A      N
 121 ARG   ( 139-)  A      NE
 127 THR   ( 145-)  A      N
 141 TRP   ( 159-)  A      N
 144 ASP   ( 162-)  A      N
 162 HIS   ( 180-)  A      N
 165 ASP   ( 183-)  A      N
 166 TRP   ( 184-)  A      N
 175 ARG   ( 193-)  A      NE
 189 THR   ( 207-)  A      N
 193 PHE   ( 211-)  A      N
 217 GLN   ( 235-)  A      N
 226 ALA   ( 244-)  A      N
 239 ARG   ( 257-)  A      NE
 260 ARG   ( 278-)  A      NE
 267 VAL   ( 285-)  A      N
 312 ARG   (  45-)  B      N
 344 THR   (  77-)  B      OG1
 371 ASN   ( 104-)  B      ND2
 412 THR   ( 145-)  B      N
 426 TRP   ( 159-)  B      N
 429 ASP   ( 162-)  B      N
 445 ASP   ( 178-)  B      N
 451 TRP   ( 184-)  B      N
 474 THR   ( 207-)  B      N
 511 ALA   ( 244-)  B      N
 515 ARG   ( 248-)  B      N
 534 TYR   ( 267-)  B      N
 536 ASP   ( 269-)  B      N
 545 ARG   ( 278-)  B      NE
 545 ARG   ( 278-)  B      NH2
 552 VAL   ( 285-)  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.

 301 HIS   (  34-)  B      ND1
 333 ASP   (  66-)  B      OD1
 423 ASP   ( 156-)  B      OD2

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.

 423 ASP   ( 156-)  B   H-bonding suggests Asn
 536 ASP   ( 269-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.219
  2nd generation packing quality :  -1.261
  Ramachandran plot appearance   :  -0.113
  chi-1/chi-2 rotamer normality  :  -1.433
  Backbone conformation          :  -0.752

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.476 (tight)
  Bond angles                    :   0.662 (tight)
  Omega angle restraints         :   1.168
  Side chain planarity           :   0.311 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   0.433
  Inside/Outside distribution    :   1.061

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 :  -0.2
  Ramachandran plot appearance   :   1.3
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.476 (tight)
  Bond angles                    :   0.662 (tight)
  Omega angle restraints         :   1.168
  Side chain planarity           :   0.311 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   0.433
  Inside/Outside distribution    :   1.061
==============

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.