WHAT IF Check report

This file was created 2012-01-04 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 pdb1n1t.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.

 631 DAN   ( 700-)  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'.

  26 SER   (  26-)  A      OG
 126 GLN   ( 126-)  A      CG
 126 GLN   ( 126-)  A      CD
 126 GLN   ( 126-)  A      OE1
 126 GLN   ( 126-)  A      NE2
 128 ARG   ( 128-)  A      CG
 128 ARG   ( 128-)  A      CD
 128 ARG   ( 128-)  A      NE
 128 ARG   ( 128-)  A      CZ
 128 ARG   ( 128-)  A      NH1
 128 ARG   ( 128-)  A      NH2
 170 GLU   ( 170-)  A      CG
 170 GLU   ( 170-)  A      CD
 170 GLU   ( 170-)  A      OE1
 170 GLU   ( 170-)  A      OE2
 628 ASP   ( 634-)  A      CG
 628 ASP   ( 634-)  A      OD1
 628 ASP   ( 634-)  A      OD2

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.

  39 ARG   (  39-)  A
  91 ARG   (  91-)  A
 254 ARG   ( 254-)  A
 255 ARG   ( 255-)  A
 387 ARG   ( 387-)  A
 435 ARG   ( 441-)  A
 472 ARG   ( 478-)  A
 552 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

  58 TYR   (  58-)  A
  73 TYR   (  73-)  A
 111 TYR   ( 111-)  A
 196 TYR   ( 196-)  A
 357 TYR   ( 357-)  A
 473 TYR   ( 479-)  A
 516 TYR   ( 522-)  A
 526 TYR   ( 532-)  A
 543 TYR   ( 549-)  A
 583 TYR   ( 589-)  A

Warning: Phenylalanine convention problem

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

  14 PHE   (  14-)  A
  38 PHE   (  38-)  A
  62 PHE   (  62-)  A
 117 PHE   ( 117-)  A
 171 PHE   ( 171-)  A
 179 PHE   ( 179-)  A
 208 PHE   ( 208-)  A
 230 PHE   ( 230-)  A
 420 PHE   ( 426-)  A
 453 PHE   ( 459-)  A
 475 PHE   ( 481-)  A
 582 PHE   ( 588-)  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.

  63 ASP   (  63-)  A
  77 ASP   (  77-)  A
 172 ASP   ( 172-)  A
 216 ASP   ( 216-)  A
 217 ASP   ( 217-)  A
 251 ASP   ( 251-)  A
 262 ASP   ( 262-)  A
 319 ASP   ( 319-)  A
 327 ASP   ( 327-)  A
 354 ASP   ( 354-)  A
 508 ASP   ( 514-)  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.

  12 GLU   (  12-)  A
  32 GLU   (  32-)  A
 259 GLU   ( 259-)  A
 299 GLU   ( 299-)  A
 342 GLU   ( 342-)  A
 361 GLU   ( 361-)  A
 431 GLU   ( 437-)  A
 445 GLU   ( 451-)  A
 490 GLU   ( 496-)  A
 504 GLU   ( 510-)  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: 0.557
RMS-deviation in bond distances: 0.014

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

 |  0.997508  0.000278 -0.000211|
 |  0.000278  0.998096 -0.000279|
 | -0.000211 -0.000279  0.998682|
Proposed new scale matrix

 |  0.013558 -0.000004  0.000003|
 | -0.000003  0.010409  0.000003|
 |  0.000002  0.000003  0.009401|
With corresponding cell

    A    =  73.758  B   =  96.072  C    = 106.367
    Alpha=  90.032  Beta=  90.024  Gamma=  89.968

The CRYST1 cell dimensions

    A    =  73.945  B   =  96.258  C    = 106.513
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 77.248
(Under-)estimated Z-score: 6.478

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.

  29 THR   (  29-)  A      CG2  CB   OG1 101.28   -4.0
  55 ASP   (  55-)  A      C    CA   CB  102.01   -4.3
  60 THR   (  60-)  A      CG2  CB   OG1  99.08   -5.1
 464 VAL   ( 470-)  A      C    CA   CB  118.06    4.2
 533 PRO   ( 539-)  A      CG   CD   N    96.42   -4.5
 628 ASP   ( 634-)  A      N    CA   C   126.30    5.4

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.

  12 GLU   (  12-)  A
  32 GLU   (  32-)  A
  39 ARG   (  39-)  A
  63 ASP   (  63-)  A
  77 ASP   (  77-)  A
  91 ARG   (  91-)  A
 172 ASP   ( 172-)  A
 216 ASP   ( 216-)  A
 217 ASP   ( 217-)  A
 251 ASP   ( 251-)  A
 254 ARG   ( 254-)  A
 255 ARG   ( 255-)  A
 259 GLU   ( 259-)  A
 262 ASP   ( 262-)  A
 299 GLU   ( 299-)  A
 319 ASP   ( 319-)  A
 327 ASP   ( 327-)  A
 342 GLU   ( 342-)  A
 354 ASP   ( 354-)  A
 361 GLU   ( 361-)  A
 387 ARG   ( 387-)  A
 431 GLU   ( 437-)  A
 435 ARG   ( 441-)  A
 445 GLU   ( 451-)  A
 472 ARG   ( 478-)  A
 490 GLU   ( 496-)  A
 504 GLU   ( 510-)  A
 508 ASP   ( 514-)  A
 552 ARG   ( 558-)  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.

 628 ASP   ( 634-)  A      CA    -8.3    17.29    33.73
The average deviation= 1.230

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.

 628 ASP   ( 634-)  A    5.09

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.

 279 THR   ( 279-)  A    -2.9
  40 ILE   (  40-)  A    -2.7
 135 PRO   ( 135-)  A    -2.6
  60 THR   (  60-)  A    -2.5
 238 LEU   ( 238-)  A    -2.5
 588 ARG   ( 594-)  A    -2.4
 263 MET   ( 263-)  A    -2.3
 148 ASN   ( 148-)  A    -2.2
 293 PHE   ( 293-)  A    -2.2
 172 ASP   ( 172-)  A    -2.2
 534 THR   ( 540-)  A    -2.2
 299 GLU   ( 299-)  A    -2.2
 494 GLY   ( 500-)  A    -2.2
 150 LYS   ( 150-)  A    -2.2
 121 ARG   ( 121-)  A    -2.1
 253 ASN   ( 253-)  A    -2.1
 222 LYS   ( 222-)  A    -2.1
 593 PRO   ( 599-)  A    -2.1
 586 GLY   ( 592-)  A    -2.0
 540 HIS   ( 546-)  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.

   4 LEU   (   4-)  A  omega poor
  40 ILE   (  40-)  A  Poor phi/psi
  84 GLN   (  84-)  A  omega poor
  91 ARG   (  91-)  A  Poor phi/psi
 100 ASP   ( 100-)  A  Poor phi/psi
 148 ASN   ( 148-)  A  Poor phi/psi
 172 ASP   ( 172-)  A  Poor phi/psi
 183 VAL   ( 183-)  A  Poor phi/psi
 186 ALA   ( 186-)  A  Poor phi/psi
 187 ILE   ( 187-)  A  omega poor
 217 ASP   ( 217-)  A  Poor phi/psi
 228 SER   ( 228-)  A  omega poor
 234 GLU   ( 234-)  A  Poor phi/psi
 270 ALA   ( 270-)  A  Poor phi/psi
 273 THR   ( 273-)  A  Poor phi/psi
 276 HIS   ( 276-)  A  Poor phi/psi
 281 SER   ( 281-)  A  Poor phi/psi
 284 SER   ( 284-)  A  Poor phi/psi
 311 ASN   ( 311-)  A  Poor phi/psi
 315 ARG   ( 315-)  A  Poor phi/psi
 318 ARG   ( 318-)  A  Poor phi/psi
 320 ARG   ( 320-)  A  Poor phi/psi
 328 ASN   ( 328-)  A  Poor phi/psi
 344 SER   ( 344-)  A  Poor phi/psi
 354 ASP   ( 354-)  A  Poor phi/psi
 361 GLU   ( 361-)  A  omega poor
 365 ASN   ( 365-)  A  Poor phi/psi
 366 ASP   ( 366-)  A  Poor phi/psi
 422 SER   ( 428-)  A  Poor phi/psi
 426 ASN   ( 432-)  A  Poor phi/psi
 435 ARG   ( 441-)  A  Poor phi/psi
 449 ASN   ( 455-)  A  Poor phi/psi
 464 VAL   ( 470-)  A  Poor phi/psi
 480 PHE   ( 486-)  A  omega poor
 520 ARG   ( 526-)  A  Poor phi/psi
 540 HIS   ( 546-)  A  Poor phi/psi
 552 ARG   ( 558-)  A  Poor phi/psi
 581 HIS   ( 587-)  A  omega poor
 593 PRO   ( 599-)  A  Poor phi/psi
 627 THR   ( 633-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.442

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 SER   (   3-)  A      0
   4 LEU   (   4-)  A      0
   6 PRO   (   6-)  A      0
   8 SER   (   8-)  A      0
   9 SER   (   9-)  A      0
  16 ARG   (  16-)  A      0
  17 LYS   (  17-)  A      0
  18 ASN   (  18-)  A      0
  36 HIS   (  36-)  A      0
  39 ARG   (  39-)  A      0
  40 ILE   (  40-)  A      0
  41 PRO   (  41-)  A      0
  58 TYR   (  58-)  A      0
  59 GLU   (  59-)  A      0
  60 THR   (  60-)  A      0
  62 PHE   (  62-)  A      0
  64 ASN   (  64-)  A      0
  66 PHE   (  66-)  A      0
  77 ASP   (  77-)  A      0
  80 THR   (  80-)  A      0
  86 ALA   (  86-)  A      0
  90 SER   (  90-)  A      0
  92 ALA   (  92-)  A      0
  96 SER   (  96-)  A      0
  99 MET   (  99-)  A      0
And so on for a total of 285 lines.

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]

 413 PRO   ( 419-)  A    0.09 LOW
 497 PRO   ( 503-)  A    0.19 LOW
 533 PRO   ( 539-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

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

 135 PRO   ( 135-)  A   -38.8 envelop C-alpha (-36 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.

 109 LYS   ( 109-)  A      CE  <->  632 HOH   (1214 )  A      O      0.58    2.22  INTRA
 394 ASN   ( 394-)  A      CB  <->  632 HOH   (1407 )  A      O      0.57    2.23  INTRA
  27 ASN   (  27-)  A      OD1 <->   29 THR   (  29-)  A      CG2    0.56    2.24  INTRA
 317 MET   ( 317-)  A      CE  <->  343 ASN   ( 343-)  A      ND2    0.53    2.57  INTRA
 243 LYS   ( 243-)  A      NZ  <->  259 GLU   ( 259-)  A      CB     0.41    2.69  INTRA
 525 LEU   ( 531-)  A      CD2 <->  531 ALA   ( 537-)  A      CB     0.38    2.82  INTRA
  82 ASN   (  82-)  A      ND2 <->  632 HOH   (1378 )  A      O      0.33    2.37  INTRA
   1 ALA   (   1-)  A      N   <->  632 HOH   (1081 )  A      O      0.32    2.38  INTRA
 301 LYS   ( 301-)  A      NZ  <->  632 HOH   (1116 )  A      O      0.31    2.39  INTRA
 121 ARG   ( 121-)  A      NH2 <->  632 HOH   (1219 )  A      O      0.26    2.44  INTRA
 227 ARG   ( 227-)  A      NH1 <->  630 SO4   ( 802-)  A      O1     0.26    2.44  INTRA
 591 GLY   ( 597-)  A      N   <->  632 HOH   (1211 )  A      O      0.23    2.47  INTRA
 171 PHE   ( 171-)  A      O   <->  174 ILE   ( 174-)  A      N      0.23    2.47  INTRA
 171 PHE   ( 171-)  A      O   <->  172 ASP   ( 172-)  A      C      0.18    2.42  INTRA
 171 PHE   ( 171-)  A      O   <->  173 GLY   ( 173-)  A      N      0.16    2.54  INTRA
 523 ARG   ( 529-)  A      CZ  <->  533 PRO   ( 539-)  A      CG     0.16    3.04  INTRA
 121 ARG   ( 121-)  A      NE  <->  632 HOH   (1219 )  A      O      0.15    2.55  INTRA
 243 LYS   ( 243-)  A      CE  <->  259 GLU   ( 259-)  A      CB     0.14    3.06  INTRA
  77 ASP   (  77-)  A      OD1 <->  352 LYS   ( 352-)  A      NZ     0.14    2.56  INTRA
  15 LYS   (  15-)  A      NZ  <->  632 HOH   (1210 )  A      O      0.10    2.60  INTRA
 164 LYS   ( 164-)  A      N   <->  165 PRO   ( 165-)  A      CD     0.09    2.91  INTRA BL
 616 ARG   ( 622-)  A      NH1 <->  632 HOH   (1385 )  A      O      0.09    2.61  INTRA
 423 HIS   ( 429-)  A      ND1 <->  449 ASN   ( 455-)  A      N      0.08    2.92  INTRA BL
 518 LYS   ( 524-)  A      NZ  <->  632 HOH   (1239 )  A      O      0.08    2.62  INTRA
 313 LYS   ( 313-)  A      NZ  <->  341 ASP   ( 341-)  A      O      0.06    2.64  INTRA
 352 LYS   ( 352-)  A      NZ  <->  353 ASP   ( 353-)  A      OD2    0.05    2.65  INTRA
 394 ASN   ( 394-)  A      OD1 <->  632 HOH   (1309 )  A      O      0.05    2.35  INTRA
 288 ASP   ( 288-)  A      OD1 <->  308 HIS   ( 308-)  A      NE2    0.05    2.65  INTRA BL
 540 HIS   ( 546-)  A      CD2 <->  632 HOH   (1043 )  A      O      0.05    2.75  INTRA BL
 363 ASN   ( 363-)  A      ND2 <->  366 ASP   ( 366-)  A      N      0.05    2.80  INTRA BL
 574 ALA   ( 580-)  A      N   <->  575 THR   ( 581-)  A      N      0.04    2.56  INTRA B3
 127 HIS   ( 127-)  A      CD2 <->  178 GLU   ( 178-)  A      OE2    0.03    2.77  INTRA BL
 580 SER   ( 586-)  A      OG  <->  581 HIS   ( 587-)  A      ND1    0.03    2.67  INTRA BL
  27 ASN   (  27-)  A      CG  <->   29 THR   (  29-)  A      CG2    0.03    3.17  INTRA
 422 SER   ( 428-)  A      OG  <->  602 ASN   ( 608-)  A      ND2    0.03    2.67  INTRA BL
 302 ARG   ( 302-)  A      NH2 <->  632 HOH   (1016 )  A      O      0.02    2.68  INTRA BL
  40 ILE   (  40-)  A      N   <->   41 PRO   (  41-)  A      CD     0.02    2.98  INTRA BL
 147 ALA   ( 147-)  A      O   <->  148 ASN   ( 148-)  A      C      0.02    2.58  INTRA BF
 171 PHE   ( 171-)  A      C   <->  172 ASP   ( 172-)  A      C      0.02    2.78  INTRA B3
 100 ASP   ( 100-)  A      OD2 <->  631 DAN   ( 700-)  A      N5     0.02    2.68  INTRA
  89 ASN   (  89-)  A      ND2 <->   91 ARG   (  91-)  A      N      0.02    2.83  INTRA BL
 589 SER   ( 595-)  A      N   <->  590 LYS   ( 596-)  A      N      0.01    2.59  INTRA BL
 322 HIS   ( 322-)  A      NE2 <->  632 HOH   ( 921 )  A      O      0.01    2.69  INTRA BL
 269 GLU   ( 269-)  A      OE2 <->  276 HIS   ( 276-)  A      CE1    0.01    2.79  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

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.

 572 ARG   ( 578-)  A      -8.01
 446 ARG   ( 452-)  A      -6.52
 588 ARG   ( 594-)  A      -6.18
 590 LYS   ( 596-)  A      -6.08
 493 LYS   ( 499-)  A      -6.00
 121 ARG   ( 121-)  A      -5.76
 203 MET   ( 203-)  A      -5.64
 466 ARG   ( 472-)  A      -5.56
 467 GLN   ( 473-)  A      -5.41

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.

 588 ARG   ( 594-)  A       590 - LYS    596- ( A)         -5.64

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.

 128 ARG   ( 128-)  A   -3.42
 126 GLN   ( 126-)  A   -2.53

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.

 314 GLY   ( 314-)  A     -  317 MET   ( 317-)  A        -1.65

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: 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.

 632 HOH   (1434 )  A      O
ERROR. No convergence in HB2STD
Old,New value: 1133.424 1133.447

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.

  89 ASN   (  89-)  A
 127 HIS   ( 127-)  A
 199 GLN   ( 199-)  A
 276 HIS   ( 276-)  A
 280 ASN   ( 280-)  A
 363 ASN   ( 363-)  A
 540 HIS   ( 546-)  A
 544 HIS   ( 550-)  A
 602 ASN   ( 608-)  A
 622 GLN   ( 628-)  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.

  39 ARG   (  39-)  A      NH1
  39 ARG   (  39-)  A      NH2
  57 ARG   (  57-)  A      NH2
  64 ASN   (  64-)  A      N
  89 ASN   (  89-)  A      ND2
 125 THR   ( 125-)  A      OG1
 175 LEU   ( 175-)  A      N
 179 PHE   ( 179-)  A      N
 215 GLU   ( 215-)  A      N
 243 LYS   ( 243-)  A      NZ
 247 ASN   ( 247-)  A      ND2
 248 ASN   ( 248-)  A      ND2
 254 ARG   ( 254-)  A      N
 256 LEU   ( 256-)  A      N
 278 TRP   ( 278-)  A      NE1
 279 THR   ( 279-)  A      OG1
 289 CYS   ( 289-)  A      N
 290 GLN   ( 290-)  A      N
 316 TRP   ( 316-)  A      N
 318 ARG   ( 318-)  A      NH2
 328 ASN   ( 328-)  A      ND2
 467 GLN   ( 473-)  A      NE2
 543 TYR   ( 549-)  A      OH
 608 ARG   ( 614-)  A      N
 625 ILE   ( 631-)  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.

 100 ASP   ( 100-)  A      OD1
 178 GLU   ( 178-)  A      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 632 HOH   ( 830 )  A      O  0.98  K  4
 632 HOH   ( 854 )  A      O  1.06  K  4
 632 HOH   ( 861 )  A      O  1.07  K  4
 632 HOH   ( 875 )  A      O  1.01  K  4
 632 HOH   ( 926 )  A      O  0.96  K  4
 632 HOH   ( 929 )  A      O  1.08  K  4
 632 HOH   (1098 )  A      O  0.89  K  4
 632 HOH   (1141 )  A      O  0.96  K  5 Ion-B
 632 HOH   (1232 )  A      O  0.91  K  4 Ion-B

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.

  76 ASP   (  76-)  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 :   0.449
  2nd generation packing quality :  -0.794
  Ramachandran plot appearance   :   0.122
  chi-1/chi-2 rotamer normality  :  -0.442
  Backbone conformation          :  -0.268

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.815
  Omega angle restraints         :   0.961
  Side chain planarity           :   0.816
  Improper dihedral distribution :   1.020
  B-factor distribution          :   0.608
  Inside/Outside distribution    :   0.983

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.815
  Omega angle restraints         :   0.961
  Side chain planarity           :   0.816
  Improper dihedral distribution :   1.020
  B-factor distribution          :   0.608
  Inside/Outside distribution    :   0.983
==============

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.