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 pdb3o9k.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 388 ETT   (   1-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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.

  25 ARG   ( 107-)  A
  36 ARG   ( 118-)  A
  48 ARG   ( 130-)  A
  70 ARG   ( 152-)  A
  74 ARG   ( 156-)  A
  91 ARG   ( 174-)  A
 143 ARG   ( 226-)  A
 211 ARG   ( 294-)  A
 219 ARG   ( 302-)  A
 245 ARG   ( 329-)  A
 281 ARG   ( 369-)  A
 288 ARG   ( 376-)  A
 348 ARG   ( 438-)  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   (  84-)  A
  88 TYR   ( 170-)  A
 126 TYR   ( 209-)  A
 171 TYR   ( 254-)  A
 174 TYR   ( 257-)  A
 230 TYR   ( 314-)  A
 370 TYR   ( 461-)  A

Warning: Phenylalanine convention problem

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

  15 PHE   (  97-)  A
  33 PHE   ( 115-)  A
  73 PHE   ( 155-)  A
  92 PHE   ( 175-)  A
 271 PHE   ( 359-)  A
 291 PHE   ( 379-)  A
 326 PHE   ( 415-)  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.

  11 ASP   (  93-)  A
  21 ASP   ( 103-)  A
 162 ASP   ( 245-)  A
 212 ASP   ( 295-)  A
 242 ASP   ( 326-)  A
 336 ASP   ( 426-)  A
 379 ASP   ( 470-)  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.

  93 GLU   ( 176-)  A
 195 GLU   ( 278-)  A
 207 GLU   ( 290-)  A
 306 GLU   ( 394-)  A
 352 GLU   ( 442-)  A
 371 GLU   ( 462-)  A

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.

  88 TYR   ( 170-)  A      CA   C     1.65    6.0
  88 TYR   ( 170-)  A      CB   CG    2.10   26.7
  89 GLN   ( 172-)  A      N    CA    1.59    7.1
  89 GLN   ( 172-)  A      C    O     1.34    5.5
  89 GLN   ( 172-)  A      CA   CB    1.43   -5.0
  89 GLN   ( 172-)  A      CB   CG    1.77    8.2
  89 GLN   ( 172-)  A      N   -C     1.22   -5.4
 225 SER   ( 308-)  A      CA   CB    1.62    4.6
 226 PRO   ( 310-)  A      CD   N     1.63   11.4
 249 THR   ( 333-)  A      CB   OG1   1.37   -4.1
 249 THR   ( 333-)  A      CB   CG2   1.93   12.3
 251 PHE   ( 337-)  A      CB   CG    2.20   30.5
 251 PHE   ( 337-)  A      N   -C     1.45    6.1
 255 CYS   ( 342-)  A      N   -C     1.49    8.3
 259 MET   ( 346-)  A      N   -C     1.59   13.0
 309 ARG   ( 397-)  A      C    O     1.14   -4.5
 309 ARG   ( 397-)  A      CB   CG    1.90   12.7
 309 ARG   ( 397-)  A      N   -C     1.54   10.7
 310 LYS   ( 399-)  A      N    CA    1.56    5.6
 310 LYS   ( 399-)  A      CB   CG    2.11   19.7
 332 LEU   ( 421-)  A      CB   CG    1.27  -13.0
 332 LEU   ( 421-)  A      N   -C     1.22   -5.5
 333 SER   ( 423-)  A      N    CA    1.54    4.3
 334 GLY   ( 424-)  A      N   -C     1.24   -4.3
 353 GLU   ( 443-)  A      CA   CB    1.68    7.4
 354 LYS   ( 445-)  A      CB   CG    2.25   24.4
 355 THR   ( 446-)  A      N   -C     1.08  -12.5

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.

  88 TYR   ( 170-)  A      CA   C    O   128.21    4.4
  88 TYR   ( 170-)  A      CA   CB   CG   91.55  -11.6
  88 TYR   ( 170-)  A      CB   CG   CD1 129.45    5.8
  88 TYR   ( 170-)  A      CB   CG   CD2 111.56   -6.2
  89 GLN   ( 172-)  A     -O   -C    N   115.94   -4.4
  89 GLN   ( 172-)  A      CA   CB   CG  103.33   -5.4
 225 SER   ( 308-)  A      C    CA   CB  135.53   13.4
 226 PRO   ( 310-)  A      N    CA   CB  112.00    8.2
 226 PRO   ( 310-)  A      CG   CD   N   115.64    8.3
 226 PRO   ( 310-)  A      CD   N    CA   97.61  -10.3
 249 THR   ( 333-)  A      CA   CB   CG2  91.07  -11.4
 249 THR   ( 333-)  A      CG2  CB   OG1  92.51   -8.4
 250 GLN   ( 334-)  A      CA   CB   CG  127.98    6.9
 251 PHE   ( 337-)  A     -O   -C    N   112.20   -6.7
 251 PHE   ( 337-)  A      CA   CB   CG   90.27  -23.5
 251 PHE   ( 337-)  A      CB   CG   CD1 132.74    7.1
 251 PHE   ( 337-)  A      CB   CG   CD2 108.56   -7.1
 255 CYS   ( 342-)  A     -CA  -C    N   124.92    4.4
 309 ARG   ( 397-)  A      N    CA   CB  125.91    9.1
 309 ARG   ( 397-)  A      CB   CG   CD  122.77    4.3
 310 LYS   ( 399-)  A      N    CA   C    99.89   -4.0
 310 LYS   ( 399-)  A      CA   CB   CG   98.93   -7.6
 311 GLN   ( 400-)  A     -CA  -C    N   124.44    4.1
 332 LEU   ( 421-)  A     -O   -C    N   109.98   -8.1
 332 LEU   ( 421-)  A     -CA  -C    N   128.16    6.0
 332 LEU   ( 421-)  A     -C    N    CA  138.14    9.1
 332 LEU   ( 421-)  A      CB   CG   CD2  93.51   -5.7
 353 GLU   ( 443-)  A     -O   -C    N   112.81   -6.4
 353 GLU   ( 443-)  A      C    CA   CB  124.91    7.8
 354 LYS   ( 445-)  A      CA   C    O   113.93   -4.0
 354 LYS   ( 445-)  A      CA   CB   CG   97.65   -8.2
 355 THR   ( 446-)  A     -O   -C    N   107.90   -9.4
 355 THR   ( 446-)  A     -CA  -C    N   133.18    8.5
 355 THR   ( 446-)  A     -C    N    CA  141.91   11.2

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.

  11 ASP   (  93-)  A
  21 ASP   ( 103-)  A
  25 ARG   ( 107-)  A
  36 ARG   ( 118-)  A
  48 ARG   ( 130-)  A
  70 ARG   ( 152-)  A
  74 ARG   ( 156-)  A
  91 ARG   ( 174-)  A
  93 GLU   ( 176-)  A
 143 ARG   ( 226-)  A
 162 ASP   ( 245-)  A
 195 GLU   ( 278-)  A
 207 GLU   ( 290-)  A
 211 ARG   ( 294-)  A
 212 ASP   ( 295-)  A
 219 ARG   ( 302-)  A
 242 ASP   ( 326-)  A
 245 ARG   ( 329-)  A
 281 ARG   ( 369-)  A
 288 ARG   ( 376-)  A
 306 GLU   ( 394-)  A
 336 ASP   ( 426-)  A
 348 ARG   ( 438-)  A
 352 GLU   ( 442-)  A
 371 GLU   ( 462-)  A
 379 ASP   ( 470-)  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.

  89 GLN   ( 172-)  A      C      7.3    11.55     0.15
 225 SER   ( 308-)  A      CA    -8.0    19.53    34.32
 248 ASP   ( 332-)  A      C     -6.9   -10.56    -0.01
 249 THR   ( 333-)  A      CB    13.5    64.27    34.09
 250 GLN   ( 334-)  A      C      8.5    13.41     0.15
 309 ARG   ( 397-)  A      CA    -6.5    23.22    33.91
 331 GLU   ( 420-)  A      C     -6.1    -8.88    -0.03
 332 LEU   ( 421-)  A      CG    -6.9   -45.19   -33.01
 352 GLU   ( 442-)  A      C     10.0    14.43    -0.03
 353 GLU   ( 443-)  A      CA   -10.2    17.28    33.96
 354 LYS   ( 445-)  A      C      8.1    12.38     0.11
The average deviation= 0.969

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.

 310 LYS   ( 399-)  A    4.38
 332 LEU   ( 421-)  A    4.15

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.

 189 PHE   ( 272-)  A    -3.5
 249 THR   ( 333-)  A    -3.0
 144 THR   ( 227-)  A    -2.9
 114 THR   ( 197-)  A    -2.9
 228 LEU   ( 312-)  A    -2.6
 363 ILE   ( 454-)  A    -2.5
 303 THR   ( 391-)  A    -2.5
 375 TRP   ( 466-)  A    -2.4
 119 LYS   ( 202-)  A    -2.4
 367 GLY   ( 458-)  A    -2.3
 384 PRO   ( 475-)  A    -2.3
 266 VAL   ( 354-)  A    -2.2
 232 VAL   ( 316-)  A    -2.2
  29 ARG   ( 111-)  A    -2.2
 136 SER   ( 219-)  A    -2.1
 215 THR   ( 298-)  A    -2.1
 146 GLU   ( 229-)  A    -2.1
 250 GLN   ( 334-)  A    -2.1
 129 VAL   ( 212-)  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.

  22 ASN   ( 104-)  A  Poor phi/psi
  29 ARG   ( 111-)  A  Poor phi/psi
  45 ILE   ( 127-)  A  Poor phi/psi
  59 ASN   ( 141-)  A  Poor phi/psi
  64 ASN   ( 146-)  A  omega poor
  85 PRO   ( 167-)  A  Poor phi/psi
  96 ALA   ( 179-)  A  omega poor
  99 ALA   ( 182-)  A  omega poor
 131 THR   ( 214-)  A  Poor phi/psi
 144 THR   ( 227-)  A  Poor phi/psi, omega poor
 146 GLU   ( 229-)  A  Poor phi/psi
 149 CYS   ( 232-)  A  omega poor
 166 ASN   ( 249-)  A  Poor phi/psi
 167 ARG   ( 250-)  A  Poor phi/psi
 169 ALA   ( 252-)  A  Poor phi/psi
 209 VAL   ( 292-)  A  omega poor
 210 CYS   ( 293-)  A  Poor phi/psi
 214 TRP   ( 297-)  A  omega poor
 215 THR   ( 298-)  A  Poor phi/psi
 217 THR   ( 300-)  A  omega poor
 228 LEU   ( 312-)  A  Poor phi/psi, omega poor
 230 TYR   ( 314-)  A  omega poor
 235 LEU   ( 319-)  A  omega poor
 238 GLY   ( 322-)  A  Poor phi/psi
 243 THR   ( 327-)  A  PRO omega poor
 250 GLN   ( 334-)  A  Poor phi/psi, omega poor
 255 CYS   ( 342-)  A  omega poor
 256 THR   ( 343-)  A  omega poor
 258 PRO   ( 345-)  A  omega poor
 264 TYR   ( 352-)  A  Poor phi/psi
 277 VAL   ( 365-)  A  omega poor
 298 ASN   ( 386-)  A  Poor phi/psi
 313 VAL   ( 402-)  A  Poor phi/psi
 320 SER   ( 409-)  A  Poor phi/psi
 331 GLU   ( 420-)  A  omega poor
 334 GLY   ( 424-)  A  Poor phi/psi
 350 LYS   ( 440-)  A  PRO omega poor
 354 LYS   ( 445-)  A  omega poor
 356 ILE   ( 447-)  A  omega poor
 366 CYS   ( 457-)  A  omega poor
 367 GLY   ( 458-)  A  Poor phi/psi
 368 VAL   ( 459-)  A  Poor phi/psi
 383 LEU   ( 474-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -3.502

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 : -3.502

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!

   5 ASN   (  87-)  A      0
   6 THR   (  88-)  A      0
  19 SER   ( 101-)  A      0
  28 SER   ( 110-)  A      0
  29 ARG   ( 111-)  A      0
  33 PHE   ( 115-)  A      0
  36 ARG   ( 118-)  A      0
  37 GLU   ( 119-)  A      0
  38 PRO   ( 120-)  A      0
  45 ILE   ( 127-)  A      0
  46 GLU   ( 128-)  A      0
  54 GLN   ( 136-)  A      0
  58 LEU   ( 140-)  A      0
  59 ASN   ( 141-)  A      0
  63 SER   ( 145-)  A      0
  66 THR   ( 148-)  A      0
  67 VAL   ( 149-)  A      0
  70 ARG   ( 152-)  A      0
  74 ARG   ( 156-)  A      0
  81 VAL   ( 163-)  A      0
  85 PRO   ( 167-)  A      0
  86 ASN   ( 168-)  A      0
  90 ALA   ( 173-)  A      0
  92 PHE   ( 175-)  A      0
  93 GLU   ( 176-)  A      0
And so on for a total of 199 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.330

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!

 331 GLU   ( 420-)  A   1.81   15

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]

 226 PRO   ( 310-)  A    0.09 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].

  17 PRO   (  99-)  A  -112.3 envelop C-gamma (-108 degrees)
  72 PRO   ( 154-)  A  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 201 PRO   ( 284-)  A     4.1 envelop N (0 degrees)
 329 PRO   ( 418-)  A    99.5 envelop C-beta (108 degrees)
 351 PRO   ( 441-)  A    17.6 half-chair N/C-delta (18 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.

 254 SER   ( 341-)  A      CB  <->  259 MET   ( 346-)  A      CE     0.97    2.23  INTRA
 254 SER   ( 341-)  A      N   <->  259 MET   ( 346-)  A      CE     0.64    2.46  INTRA
 249 THR   ( 333-)  A      O   <->  251 PHE   ( 337-)  A      N      0.54    2.16  INTRA BF
 251 PHE   ( 337-)  A      CE2 <->  252 THR   ( 338-)  A      O      0.53    2.17  INTRA
 254 SER   ( 341-)  A      CA  <->  259 MET   ( 346-)  A      CE     0.40    2.80  INTRA
 254 SER   ( 341-)  A      OG  <->  259 MET   ( 346-)  A      CE     0.33    2.47  INTRA
 253 GLY   ( 340-)  A      C   <->  259 MET   ( 346-)  A      CE     0.30    2.90  INTRA
 249 THR   ( 333-)  A      C   <->  251 PHE   ( 337-)  A      N      0.29    2.61  INTRA BF
  20 LYS   ( 102-)  A      NZ  <->   22 ASN   ( 104-)  A      ND2    0.28    2.57  INTRA BL
 103 HIS   ( 186-)  A      CD2 <->  105 GLY   ( 188-)  A      N      0.25    2.85  INTRA
 252 THR   ( 338-)  A      CB  <->  259 MET   ( 346-)  A      SD     0.24    3.16  INTRA
  18 PHE   ( 100-)  A      N   <->  364 VAL   ( 455-)  A      O      0.24    2.46  INTRA BL
 277 VAL   ( 365-)  A      CG1 <->  300 TRP   ( 388-)  A      CE3    0.23    2.97  INTRA BL
 102 CYS   ( 185-)  A      N   <->  149 CYS   ( 232-)  A      SG     0.21    3.09  INTRA BL
 248 ASP   ( 332-)  A      O   <->  251 PHE   ( 337-)  A      CB     0.21    2.59  INTRA
 385 PHE   ( 476-)  A      O   <->  387 ILE   ( 478-)  A      N      0.19    2.51  INTRA BF
 133 VAL   ( 216-)  A      CG1 <->  134 VAL   ( 217-)  A      N      0.18    2.82  INTRA BL
 101 ALA   ( 184-)  A      C   <->  149 CYS   ( 232-)  A      SG     0.18    3.22  INTRA BL
 251 PHE   ( 337-)  A      CG  <->  252 THR   ( 338-)  A      N      0.17    2.83  INTRA
 251 PHE   ( 337-)  A      CD2 <->  252 THR   ( 338-)  A      O      0.17    2.53  INTRA
 196 GLU   ( 279-)  A      OE2 <->  322 TYR   ( 411-)  A      OH     0.17    2.23  INTRA
  36 ARG   ( 118-)  A      NE  <->  345 GLU   ( 435-)  A      OE2    0.16    2.54  INTRA
 251 PHE   ( 337-)  A      CE1 <->  259 MET   ( 346-)  A      CG     0.15    3.05  INTRA
 385 PHE   ( 476-)  A      C   <->  387 ILE   ( 478-)  A      N      0.15    2.75  INTRA BF
 141 ILE   ( 224-)  A      O   <->  143 ARG   ( 226-)  A      NH1    0.15    2.55  INTRA BL
And so on for a total of 80 lines.

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.

 264 TYR   ( 352-)  A      -7.86
  29 ARG   ( 111-)  A      -6.85
 354 LYS   ( 445-)  A      -5.83
 190 ASN   ( 273-)  A      -5.63
 168 GLN   ( 251-)  A      -5.51
 317 LEU   ( 406-)  A      -5.37
 382 ILE   ( 473-)  A      -5.36
 261 ASN   ( 349-)  A      -5.27
 285 ARG   ( 373-)  A      -5.16
 167 ARG   ( 250-)  A      -5.16
  88 TYR   ( 170-)  A      -5.03

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.

 331 GLU   ( 420-)  A       333 - SER    423- ( A)         -4.31

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: 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.

  22 ASN   ( 104-)  A
  62 HIS   ( 144-)  A
 125 HIS   ( 208-)  A
 145 GLN   ( 228-)  A
 168 GLN   ( 251-)  A
 311 GLN   ( 400-)  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.

   5 ASN   (  87-)  A      N
  20 LYS   ( 102-)  A      N
  22 ASN   ( 104-)  A      N
  24 ILE   ( 106-)  A      N
  25 ARG   ( 107-)  A      N
  32 ILE   ( 114-)  A      N
  36 ARG   ( 118-)  A      NH2
  40 VAL   ( 122-)  A      N
  57 LEU   ( 139-)  A      N
  60 ASP   ( 142-)  A      N
  66 THR   ( 148-)  A      N
  70 ARG   ( 152-)  A      N
  71 SER   ( 153-)  A      N
  74 ARG   ( 156-)  A      NE
  88 TYR   ( 170-)  A      N
  95 VAL   ( 178-)  A      N
 105 GLY   ( 188-)  A      N
 120 ALA   ( 203-)  A      N
 129 VAL   ( 212-)  A      N
 142 LEU   ( 225-)  A      N
 147 SER   ( 230-)  A      N
 148 SER   ( 231-)  A      N
 154 GLY   ( 237-)  A      N
 167 ARG   ( 250-)  A      NE
 194 ILE   ( 277-)  A      N
And so on for a total of 57 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

  37 GLU   ( 119-)  A      OE1
  37 GLU   ( 119-)  A      OE2
 103 HIS   ( 186-)  A      ND1
 125 HIS   ( 208-)  A      ND1
 195 GLU   ( 278-)  A      OE1
 242 ASP   ( 326-)  A      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.

   7 GLU   (  89-)  A   H-bonding suggests Gln; but Alt-Rotamer
  21 ASP   ( 103-)  A   H-bonding suggests Asn; but Alt-Rotamer
 104 ASP   ( 187-)  A   H-bonding suggests Asn; but Alt-Rotamer
 162 ASP   ( 245-)  A   H-bonding suggests Asn; but Alt-Rotamer
 242 ASP   ( 326-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.041
  2nd generation packing quality :  -1.476
  Ramachandran plot appearance   :  -2.759
  chi-1/chi-2 rotamer normality  :  -3.502 (poor)
  Backbone conformation          :  -0.912

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.588 (tight)
  Bond angles                    :   0.866
  Omega angle restraints         :   1.333 (loose)
  Side chain planarity           :   0.343 (tight)
  Improper dihedral distribution :   1.181
  B-factor distribution          :   1.136
  Inside/Outside distribution    :   1.069

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 : 2.49


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.588 (tight)
  Bond angles                    :   0.866
  Omega angle restraints         :   1.333 (loose)
  Side chain planarity           :   0.343 (tight)
  Improper dihedral distribution :   1.181
  B-factor distribution          :   1.136
  Inside/Outside distribution    :   1.069
==============

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.