WHAT IF Check report

This file was created 2011-12-17 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 pdb2okk.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.

 484 ABU   ( 585-)  A  -
 486 ABU   ( 586-)  A  -

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 486 ABU   ( 586-)  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: 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'.

   4 PHE   (  91-)  A      CG
   4 PHE   (  91-)  A      CD1
   4 PHE   (  91-)  A      CD2
   4 PHE   (  91-)  A      CE1
   4 PHE   (  91-)  A      CE2
   4 PHE   (  91-)  A      CZ
  15 ASP   ( 102-)  A      CG
  15 ASP   ( 102-)  A      OD1
  15 ASP   ( 102-)  A      OD2
  18 ARG   ( 105-)  A      CG
  18 ARG   ( 105-)  A      CD
  18 ARG   ( 105-)  A      NE
  18 ARG   ( 105-)  A      CZ
  18 ARG   ( 105-)  A      NH1
  18 ARG   ( 105-)  A      NH2
  33 GLN   ( 120-)  A      OE1
  33 GLN   ( 120-)  A      NE2
  37 LYS   ( 124-)  A      CD
  37 LYS   ( 124-)  A      CE
  37 LYS   ( 124-)  A      NZ
  52 ASN   ( 139-)  A      CG
  52 ASN   ( 139-)  A      OD1
  52 ASN   ( 139-)  A      ND2
  64 ASP   ( 151-)  A      OD1
  64 ASP   ( 151-)  A      OD2
And so on for a total of 87 lines.

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: 0

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

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.

 231 ARG   ( 318-)  A
 416 ARG   ( 514-)  A
 457 ARG   ( 558-)  A

Warning: Tyrosine convention problem

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

   2 TYR   (  89-)  A
  34 TYR   ( 121-)  A
 131 TYR   ( 218-)  A
 254 TYR   ( 341-)  A
 382 TYR   ( 480-)  A
 384 TYR   ( 482-)  A
 393 TYR   ( 491-)  A
 410 TYR   ( 508-)  A
 439 TYR   ( 540-)  A
 446 TYR   ( 547-)  A

Warning: Phenylalanine convention problem

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

  92 PHE   ( 179-)  A
 118 PHE   ( 205-)  A
 152 PHE   ( 239-)  A
 196 PHE   ( 283-)  A
 240 PHE   ( 327-)  A
 243 PHE   ( 330-)  A
 369 PHE   ( 467-)  A
 472 PHE   ( 573-)  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.

  26 ASP   ( 113-)  A
 107 ASP   ( 194-)  A
 374 ASP   ( 472-)  A
 451 ASP   ( 552-)  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.

  61 GLU   ( 148-)  A
 121 GLU   ( 208-)  A
 130 GLU   ( 217-)  A
 139 GLU   ( 226-)  A
 229 GLU   ( 316-)  A
 234 GLU   ( 321-)  A
 298 GLU   ( 385-)  A
 324 GLU   ( 411-)  A
 325 GLU   ( 412-)  A
 381 GLU   ( 479-)  A
 394 GLU   ( 492-)  A
 475 GLU   ( 576-)  A
 476 GLU   ( 577-)  A
 478 GLU   ( 579-)  A

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.996014  0.000187  0.000300|
 |  0.000187  0.997834 -0.000021|
 |  0.000300 -0.000021  0.996993|
Proposed new scale matrix

 |  0.012830 -0.000002 -0.000004|
 | -0.000002  0.010117  0.000000|
 | -0.000003  0.000000  0.008358|
With corresponding cell

    A    =  77.941  B   =  98.844  C    = 119.644
    Alpha=  90.001  Beta=  89.966  Gamma=  89.978

The CRYST1 cell dimensions

    A    =  78.251  B   =  99.057  C    = 120.009
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 149.086
(Under-)estimated Z-score: 8.999

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.

 316 GLN   ( 403-)  A     -C    N    CA  129.62    4.4
 341 THR   ( 439-)  A     -C    N    CA  132.29    5.9
 402 GLN   ( 500-)  A      N    CA   C   127.05    5.7
 403 HIS   ( 501-)  A     -CA  -C    N   127.29    5.5
 403 HIS   ( 501-)  A     -C    N    CA  135.11    7.5
 403 HIS   ( 501-)  A      N    CA   C   125.70    5.2
 403 HIS   ( 501-)  A      CG   ND1  CE1 109.66    4.1

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.

  26 ASP   ( 113-)  A
  61 GLU   ( 148-)  A
 107 ASP   ( 194-)  A
 121 GLU   ( 208-)  A
 130 GLU   ( 217-)  A
 139 GLU   ( 226-)  A
 229 GLU   ( 316-)  A
 231 ARG   ( 318-)  A
 234 GLU   ( 321-)  A
 298 GLU   ( 385-)  A
 324 GLU   ( 411-)  A
 325 GLU   ( 412-)  A
 374 ASP   ( 472-)  A
 381 GLU   ( 479-)  A
 394 GLU   ( 492-)  A
 416 ARG   ( 514-)  A
 451 ASP   ( 552-)  A
 457 ARG   ( 558-)  A
 475 GLU   ( 576-)  A
 476 GLU   ( 577-)  A
 478 GLU   ( 579-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 403 HIS   ( 501-)  A      CA   -14.0     8.30    34.11
The average deviation= 0.748

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.

 402 GLN   ( 500-)  A    6.16
 403 HIS   ( 501-)  A    4.69

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.

 151 ILE   ( 238-)  A    -2.6
 442 THR   ( 543-)  A    -2.6
 482 GLN   ( 583-)  A    -2.4
 403 HIS   ( 501-)  A    -2.4
 122 ILE   ( 209-)  A    -2.4
 315 LEU   ( 402-)  A    -2.3
  12 PRO   (  99-)  A    -2.2
 154 PRO   ( 241-)  A    -2.2
 190 THR   ( 277-)  A    -2.2
 299 ARG   ( 386-)  A    -2.1
 236 LYS   ( 323-)  A    -2.1
 457 ARG   ( 558-)  A    -2.1
 447 GLN   ( 548-)  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.

  11 LEU   (  98-)  A  PRO omega poor
  16 GLY   ( 103-)  A  Poor phi/psi
  46 ILE   ( 133-)  A  omega poor
 117 MET   ( 204-)  A  omega poor
 154 PRO   ( 241-)  A  Poor phi/psi
 244 LEU   ( 331-)  A  omega poor
 271 LYS   ( 358-)  A  Poor phi/psi
 316 GLN   ( 403-)  A  Poor phi/psi, omega poor
 319 ALA   ( 406-)  A  omega poor
 340 ASP   ( 438-)  A  omega poor
 341 THR   ( 439-)  A  Poor phi/psi
 348 CYS   ( 446-)  A  Poor phi/psi
 402 GLN   ( 500-)  A  omega poor
 403 HIS   ( 501-)  A  Poor phi/psi
 409 TRP   ( 507-)  A  omega poor
 415 LEU   ( 513-)  A  Poor phi/psi
 461 SER   ( 562-)  A  Poor phi/psi
 482 GLN   ( 583-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -3.189

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.189

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.

 111 SER   ( 198-)  A    0.34
 423 SER   ( 524-)  A    0.37

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 PHE   (  91-)  A      0
   6 HIS   (  93-)  A      0
  10 LEU   (  97-)  A      0
  11 LEU   (  98-)  A      0
  12 PRO   (  99-)  A      0
  13 ALA   ( 100-)  A      0
  14 CYS   ( 101-)  A      0
  15 ASP   ( 102-)  A      0
  41 ARG   ( 128-)  A      0
  45 VAL   ( 132-)  A      0
  46 ILE   ( 133-)  A      0
  47 ASP   ( 134-)  A      0
  50 TYR   ( 137-)  A      0
  57 GLU   ( 144-)  A      0
  58 TYR   ( 145-)  A      0
  60 TRP   ( 147-)  A      0
  85 LYS   ( 172-)  A      0
  90 ARG   ( 177-)  A      0
  92 PHE   ( 179-)  A      0
  93 ASN   ( 180-)  A      0
  94 GLN   ( 181-)  A      0
  95 LEU   ( 182-)  A      0
  96 SER   ( 183-)  A      0
  97 THR   ( 184-)  A      0
 113 ALA   ( 200-)  A      0
And so on for a total of 175 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!

 399 GLY   ( 497-)  A   1.59   17

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].

 154 PRO   ( 241-)  A   -66.0 envelop C-beta (-72 degrees)
 259 PRO   ( 346-)  A   -47.3 half-chair C-beta/C-alpha (-54 degrees)
 448 PRO   ( 549-)  A   -54.2 half-chair C-beta/C-alpha (-54 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.

 356 LYS   ( 454-)  A      NZ  <->  486 HOH   ( 664 )  A      O      0.49    2.21  INTRA BF
 176 LYS   ( 263-)  A      NZ  <->  333 GLN   ( 420-)  A      O      0.30    2.40  INTRA BF
 340 ASP   ( 438-)  A      CA  <->  341 THR   ( 439-)  A      OG1    0.26    2.44  INTRA BF
 277 ASP   ( 364-)  A      OD2 <->  309 LLP   ( 396-)  A      N1     0.24    2.46  INTRA BL
 372 HIS   ( 470-)  A      CE1 <->  376 CYS   ( 474-)  A      SG     0.23    3.17  INTRA BF
 351 HIS   ( 449-)  A      CE1 <->  486 HOH   ( 649 )  A      O      0.23    2.57  INTRA BF
 245 VAL   ( 332-)  A      CG1 <->  267 CYS   ( 354-)  A      SG     0.22    3.18  INTRA BL
 476 GLU   ( 577-)  A      OE1 <->  479 ARG   ( 580-)  A      NH1    0.19    2.51  INTRA BF
 458 MET   ( 559-)  A      SD  <->  473 LEU   ( 574-)  A      CD2    0.17    3.23  INTRA BF
 351 HIS   ( 449-)  A      CD2 <->  353 ASP   ( 451-)  A      OD1    0.14    2.66  INTRA BF
 100 ASP   ( 187-)  A      OD2 <->  364 LYS   ( 462-)  A      NZ     0.13    2.57  INTRA BF
 288 ARG   ( 375-)  A      NH1 <->  370 GLU   ( 468-)  A      OE1    0.13    2.57  INTRA BF
 392 GLY   ( 490-)  A      O   <->  411 ILE   ( 509-)  A      N      0.13    2.57  INTRA BF
 462 ASN   ( 563-)  A      ND2 <->  463 PRO   ( 564-)  A      CD     0.10    3.00  INTRA BF
  41 ARG   ( 128-)  A      NE  <->  469 ASP   ( 570-)  A      OD1    0.08    2.62  INTRA BF
 390 ARG   ( 488-)  A      NE  <->  478 GLU   ( 579-)  A      OE2    0.08    2.62  INTRA BF
 421 ARG   ( 522-)  A      N   <->  422 MET   ( 523-)  A      N      0.08    2.52  INTRA BF
 467 HIS   ( 568-)  A      ND1 <->  486 HOH   ( 672 )  A      O      0.07    2.63  INTRA BF
 290 HIS   ( 377-)  A      ND1 <->  293 LYS   ( 380-)  A      NZ     0.07    2.93  INTRA BF
 403 HIS   ( 501-)  A      ND1 <->  404 THR   ( 502-)  A      N      0.06    2.84  INTRA BF
 265 ASP   ( 352-)  A      OD1 <->  299 ARG   ( 386-)  A      NH2    0.05    2.65  INTRA BF
 160 ASN   ( 247-)  A      ND2 <->  275 HIS   ( 362-)  A      NE2    0.04    2.96  INTRA BL
 411 ILE   ( 509-)  A      O   <->  416 ARG   ( 514-)  A      NE     0.04    2.66  INTRA BF
 176 LYS   ( 263-)  A      NZ  <->  330 ASN   ( 417-)  A      O      0.03    2.67  INTRA BF
 436 MET   ( 537-)  A      O   <->  440 GLY   ( 541-)  A      N      0.03    2.67  INTRA BF
 422 MET   ( 523-)  A      O   <->  426 SER   ( 527-)  A      N      0.02    2.68  INTRA BF
 153 SER   ( 240-)  A      OG  <->  159 SER   ( 246-)  A      OG     0.02    2.38  INTRA BF
   1 ASN   (  88-)  A      CB  <->    2 TYR   (  89-)  A      N      0.02    2.68  INTRA BF
 116 ASN   ( 203-)  A      OD1 <->  350 ARG   ( 448-)  A      N      0.02    2.68  INTRA BF
 309 LLP   ( 396-)  A      C4' <->  485 ABU   ( 586-)  A      CA     0.02    3.18  INTRA BL
 149 ASP   ( 236-)  A      N   <->  322 VAL   ( 409-)  A      O      0.01    2.69  INTRA BL
  88 HIS   ( 175-)  A      ND1 <->   90 ARG   ( 177-)  A      N      0.01    2.99  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.

 334 MET   ( 421-)  A      -7.27
 482 GLN   ( 583-)  A      -7.26
  62 LEU   ( 149-)  A      -7.00
 400 LYS   ( 498-)  A      -6.26
 315 LEU   ( 402-)  A      -6.24
  14 CYS   ( 101-)  A      -6.09
 347 GLN   ( 445-)  A      -6.08
 418 LEU   ( 516-)  A      -5.77
 144 PRO   ( 231-)  A      -5.59
 397 PHE   ( 495-)  A      -5.56
 237 GLN   ( 324-)  A      -5.50
 299 ARG   ( 386-)  A      -5.42
 479 ARG   ( 580-)  A      -5.39
  11 LEU   (  98-)  A      -5.26
  50 TYR   ( 137-)  A      -5.19
 288 ARG   ( 375-)  A      -5.05
 177 GLU   ( 264-)  A      -5.03
 346 LEU   ( 444-)  A      -5.03
  57 GLU   ( 144-)  A      -5.02
 332 ASN   ( 419-)  A      -5.00

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.

 144 PRO   ( 231-)  A       146 - GLY    233- ( A)         -4.64
 332 ASN   ( 419-)  A       334 - MET    421- ( A)         -5.75
 346 LEU   ( 444-)  A       348 - CYS    446- ( A)         -5.11

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.

 335 HIS   ( 422-)  A   -2.94
 339 TYR   ( 437-)  A   -2.90
 337 LEU   ( 435-)  A   -2.60

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: 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.

  49 HIS   ( 136-)  A
  68 ASN   ( 155-)  A
  75 HIS   ( 162-)  A
 114 ASN   ( 201-)  A
 160 ASN   ( 247-)  A
 193 HIS   ( 280-)  A
 306 ASN   ( 393-)  A
 330 ASN   ( 417-)  A
 333 GLN   ( 420-)  A
 347 GLN   ( 445-)  A
 351 HIS   ( 449-)  A
 389 ASN   ( 487-)  A
 402 GLN   ( 500-)  A
 454 ASN   ( 555-)  A
 462 ASN   ( 563-)  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.

  46 ILE   ( 133-)  A      N
  93 ASN   ( 180-)  A      N
  94 GLN   ( 181-)  A      N
  96 SER   ( 183-)  A      N
  96 SER   ( 183-)  A      OG
 118 PHE   ( 205-)  A      N
 119 THR   ( 206-)  A      N
 152 PHE   ( 239-)  A      N
 156 GLY   ( 243-)  A      N
 157 ALA   ( 244-)  A      N
 196 PHE   ( 283-)  A      N
 200 LYS   ( 287-)  A      NZ
 239 GLY   ( 326-)  A      N
 252 THR   ( 339-)  A      OG1
 306 ASN   ( 393-)  A      ND2
 316 GLN   ( 403-)  A      N
 345 ALA   ( 443-)  A      N
 346 LEU   ( 444-)  A      N
 347 GLN   ( 445-)  A      N
 397 PHE   ( 495-)  A      N
 416 ARG   ( 514-)  A      N
 424 ARG   ( 525-)  A      N
 442 THR   ( 543-)  A      N
 444 VAL   ( 545-)  A      N
 459 VAL   ( 560-)  A      N
 469 ASP   ( 570-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

  75 HIS   ( 162-)  A      ND1
 306 ASN   ( 393-)  A      OD1
 447 GLN   ( 548-)  A      OE1

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.

 218 ASP   ( 305-)  A   H-bonding suggests Asn; but Alt-Rotamer
 265 ASP   ( 352-)  A   H-bonding suggests Asn
 340 ASP   ( 438-)  A   H-bonding suggests Asn; but Alt-Rotamer
 374 ASP   ( 472-)  A   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 :  -0.893
  2nd generation packing quality :  -1.769
  Ramachandran plot appearance   :  -1.274
  chi-1/chi-2 rotamer normality  :  -3.189 (poor)
  Backbone conformation          :  -0.258

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   0.983
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.787
  B-factor distribution          :   0.509
  Inside/Outside distribution    :   1.072

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.447 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   0.983
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.787
  B-factor distribution          :   0.509
  Inside/Outside distribution    :   1.072
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.