WHAT IF Check report

This file was created 2011-12-21 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 pdb1byc.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.

 496 BGC   ( 499-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 493 GLC   ( 497-)  A  -   O4  bound to  492 GLC   ( 496-)  A  -   C1
 494 GLC   ( 498-)  A  -   O4  bound to  493 GLC   ( 497-)  A  -   C1

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

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 491 GLY   ( 495-)  A

Warning: What type of B-factor?

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

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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Nomenclature related problems

Error: Threonine nomenclature problem

The threonine residues listed in the table below have their O-gamma-1 and C-gamma-2 swapped.

 252 THR   ( 256-)  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.

  17 GLY   (  21-)  A      N   -C     1.24   -4.4
  22 ASP   (  26-)  A      CG   OD1   1.33    4.3
  27 ASP   (  31-)  A      CG   OD2   1.33    4.0
  29 ASP   (  33-)  A      CG   OD1   1.33    4.3
  33 GLU   (  37-)  A      CD   OE2   1.36    5.7
  56 GLU   (  60-)  A      CD   OE2   1.33    4.2
 109 ASP   ( 113-)  A      CG   OD2   1.37    6.5
 112 GLU   ( 116-)  A      CD   OE2   1.33    4.1
 159 GLU   ( 163-)  A      CD   OE1   1.33    4.4
 166 GLU   ( 170-)  A      CD   OE1   1.36    5.8
 194 TRP   ( 198-)  A      NE1  CE2   1.31   -5.5
 224 GLU   ( 228-)  A      CD   OE2   1.34    4.7
 230 ASP   ( 234-)  A      CG   OD2   1.33    4.3
 252 THR   ( 256-)  A      CB   OG1   1.50    4.3
 253 GLU   ( 257-)  A      CD   OE2   1.36    5.8
 302 GLU   ( 306-)  A      CD   OE2   1.37    6.4
 309 THR   ( 313-)  A      N   -C     1.21   -5.9
 319 ASP   ( 323-)  A      CG   OD1   1.17   -4.0
 343 ARG   ( 347-)  A      NE   CZ    1.43    7.2
 346 GLU   ( 350-)  A      CD   OE1   1.33    4.4
 370 ASP   ( 374-)  A      CG   OD1   1.33    4.0
 440 ASP   ( 444-)  A      CG   OD1   1.33    4.1
 467 GLU   ( 471-)  A      CD   OE2   1.33    4.1
 471 GLU   ( 475-)  A      CD   OE1   1.34    4.7
 484 GLU   ( 488-)  A      CD   OE2   1.33    4.0
 486 ASP   ( 490-)  A      CG   OD2   1.33    4.3

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.

   2 ASN   (   6-)  A      N    CA   C   124.00    4.6
   2 ASN   (   6-)  A      N    CA   CB  120.06    5.6
  17 GLY   (  21-)  A     -C    N    CA  109.53   -6.5
  21 VAL   (  25-)  A      N    CA   CB  117.53    4.1
  25 PHE   (  29-)  A      CA   CB   CG  117.81    4.0
  27 ASP   (  31-)  A     -C    N    CA  113.33   -4.7
  29 ASP   (  33-)  A      CA   CB   CG  106.89   -5.7
  37 GLN   (  41-)  A      CB   CG   CD  104.97   -4.5
  48 VAL   (  52-)  A      CG1  CB   CG2 101.42   -4.3
  55 ILE   (  59-)  A      CA   CB   CG1 118.10    4.5
 113 SER   ( 117-)  A     -C    N    CA  112.45   -5.1
 115 HIS   ( 119-)  A      CA   CB   CG  107.75   -6.1
 126 ARG   ( 130-)  A      N    CA   CB  118.16    4.5
 126 ARG   ( 130-)  A      CG   CD   NE  119.36    5.2
 141 PHE   ( 145-)  A      CA   CB   CG  109.64   -4.2
 142 HIS   ( 146-)  A      CA   CB   CG  108.86   -4.9
 162 SER   ( 166-)  A      CA   CB   OG  102.69   -4.2
 198 ARG   ( 202-)  A      C    CA   CB  120.81    5.6
 213 PHE   ( 217-)  A      CA   CB   CG  109.42   -4.4
 228 PRO   ( 232-)  A      N    CA   CB  108.40    4.9
 229 ASP   ( 233-)  A      CB   CG   OD2 108.89   -4.1
 245 LYS   ( 249-)  A     -C    N    CA  112.02   -5.4
 253 GLU   ( 257-)  A      C    CA   CB  100.87   -4.9
 253 GLU   ( 257-)  A      CB   CG   CD  104.90   -4.5
 257 PHE   ( 261-)  A      CA   CB   CG  109.56   -4.2
 258 PHE   ( 262-)  A      CA   CB   CG  108.91   -4.9
 309 THR   ( 313-)  A     -O   -C    N   114.15   -5.5
 309 THR   ( 313-)  A     -C    N    CA  112.37   -5.2
 309 THR   ( 313-)  A      N    CA   CB  132.95   13.2
 309 THR   ( 313-)  A      CA   CB   CG2 119.26    5.2
 323 PRO   ( 327-)  A      N    CA   CB  109.03    5.5
 332 HIS   ( 336-)  A      CA   CB   CG  109.14   -4.7
 343 ARG   ( 347-)  A      CD   NE   CZ  130.57    4.9
 350 ASP   ( 354-)  A      CA   CB   CG  107.68   -4.9
 406 LYS   ( 410-)  A      N    CA   CB  117.40    4.1
 412 VAL   ( 416-)  A      C    CA   CB  102.33   -4.1
 426 ASN   ( 430-)  A      CA   CB   CG  107.63   -5.0
 452 HIS   ( 456-)  A      C    CA   CB  102.35   -4.1
 454 ILE   ( 458-)  A      N    CA   CB  119.69    5.4
 455 THR   ( 459-)  A      N    CA   CB  102.12   -4.9

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.

 252 THR   ( 256-)  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.

   2 ASN   (   6-)  A      CA   -16.3     2.59    33.59
  21 VAL   (  25-)  A      C     -6.2    -8.31     0.15
  51 TRP   (  55-)  A      C      6.6     9.87     0.23
  55 ILE   (  59-)  A      CB    -6.5    23.83    32.31
 253 GLU   ( 257-)  A      C     -6.4    -9.31    -0.03
 309 THR   ( 313-)  A      CA   -14.4     9.79    33.84
 339 CYS   ( 343-)  A      C     -6.9    -9.96     0.22
 488 LYS   ( 492-)  A      C      6.3     9.59     0.11
The average deviation= 2.341

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.

 308 LEU   ( 312-)  A    5.94
 207 LYS   ( 211-)  A    5.19
   2 ASN   (   6-)  A    4.02
 112 GLU   ( 116-)  A    4.02

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  37 GLN   (  41-)  A    8.70
  62 GLN   (  66-)  A    7.44
  90 GLN   (  94-)  A    6.98
 307 GLU   ( 311-)  A    6.84
  22 ASP   (  26-)  A    6.46
  49 ASP   (  53-)  A    5.94
 253 GLU   ( 257-)  A    5.74
 319 ASP   ( 323-)  A    5.38
 347 GLN   ( 351-)  A    5.36
 361 GLN   ( 365-)  A    5.26
  29 ASP   (  33-)  A    4.96
 142 HIS   ( 146-)  A    4.91
 203 GLN   ( 207-)  A    4.84
 304 HIS   ( 308-)  A    4.82
 230 ASP   ( 234-)  A    4.56
 262 TYR   ( 266-)  A    4.29
 452 HIS   ( 456-)  A    4.29
 296 HIS   ( 300-)  A    4.22
 331 HIS   ( 335-)  A    4.12
 433 PHE   ( 437-)  A    4.09
 119 TYR   ( 123-)  A    4.01

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

   7 TYR   (  11-)  A      CB   4.46
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.398

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.

 309 THR   ( 313-)  A    -3.4
 196 PHE   ( 200-)  A    -2.8
 139 PRO   ( 143-)  A    -2.6
 416 ARG   ( 420-)  A    -2.6
 417 LEU   ( 421-)  A    -2.4
 102 PRO   ( 106-)  A    -2.4
 285 LYS   ( 289-)  A    -2.4
 452 HIS   ( 456-)  A    -2.3
 466 ILE   ( 470-)  A    -2.3
  98 ILE   ( 102-)  A    -2.3
 352 LYS   ( 356-)  A    -2.3
 126 ARG   ( 130-)  A    -2.3
 488 LYS   ( 492-)  A    -2.2
 313 TYR   ( 317-)  A    -2.2
 290 ILE   ( 294-)  A    -2.1
 198 ARG   ( 202-)  A    -2.1
 300 LYS   ( 304-)  A    -2.1
 332 HIS   ( 336-)  A    -2.1
 354 GLY   ( 358-)  A    -2.0
 233 LYS   ( 237-)  A    -2.0
 402 ASN   ( 406-)  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.

  23 ASN   (  27-)  A  Poor phi/psi
  61 LYS   (  65-)  A  Poor phi/psi
 142 HIS   ( 146-)  A  Poor phi/psi
 180 ALA   ( 184-)  A  Poor phi/psi
 186 PRO   ( 190-)  A  Poor phi/psi
 194 TRP   ( 198-)  A  Poor phi/psi
 195 GLU   ( 199-)  A  omega poor
 196 PHE   ( 200-)  A  Poor phi/psi, PRO omega poor
 197 PRO   ( 201-)  A  Poor phi/psi
 198 ARG   ( 202-)  A  omega poor
 247 ASN   ( 251-)  A  Poor phi/psi
 298 TRP   ( 302-)  A  Poor phi/psi
 309 THR   ( 313-)  A  Poor phi/psi
 332 HIS   ( 336-)  A  Poor phi/psi
 340 LEU   ( 344-)  A  Poor phi/psi
 370 ASP   ( 374-)  A  Poor phi/psi
 416 ARG   ( 420-)  A  Poor phi/psi
 439 ALA   ( 443-)  A  Poor phi/psi
 440 ASP   ( 444-)  A  Poor phi/psi
 451 ASN   ( 455-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.890

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!

  16 LEU   (  20-)  A      0
  18 VAL   (  22-)  A      0
  23 ASN   (  27-)  A      0
  26 GLU   (  30-)  A      0
  44 ASP   (  48-)  A      0
  51 TRP   (  55-)  A      0
  52 TRP   (  56-)  A      0
  60 PRO   (  64-)  A      0
  61 LYS   (  65-)  A      0
  63 TYR   (  67-)  A      0
  65 TRP   (  69-)  A      0
  78 CYS   (  82-)  A      0
  86 MET   (  90-)  A      0
  87 SER   (  91-)  A      0
  88 PHE   (  92-)  A      0
  89 HIS   (  93-)  A      0
  91 CYS   (  95-)  A      0
  94 ASN   (  98-)  A      0
  95 VAL   (  99-)  A      0
  98 ILE   ( 102-)  A      0
 103 ILE   ( 107-)  A      0
 113 SER   ( 117-)  A      0
 115 HIS   ( 119-)  A      0
 116 ASP   ( 120-)  A      0
 117 ILE   ( 121-)  A      0
And so on for a total of 172 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!

 308 LEU   ( 312-)  A   3.06   12
 193 GLY   ( 197-)  A   1.74   80

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]

  15 PRO   (  19-)  A    0.10 LOW
  28 PRO   (  32-)  A    0.10 LOW
  60 PRO   (  64-)  A    0.16 LOW
 102 PRO   ( 106-)  A    0.13 LOW
 179 PRO   ( 183-)  A    0.03 LOW
 197 PRO   ( 201-)  A    0.07 LOW
 223 PRO   ( 227-)  A    0.09 LOW
 228 PRO   ( 232-)  A    0.08 LOW
 238 PRO   ( 242-)  A    0.09 LOW
 323 PRO   ( 327-)  A    0.17 LOW
 348 PRO   ( 352-)  A    0.12 LOW
 355 PRO   ( 359-)  A    0.19 LOW
 380 PRO   ( 384-)  A    0.13 LOW
 404 PRO   ( 408-)  A    0.15 LOW
 405 PRO   ( 409-)  A    0.19 LOW
 447 PRO   ( 451-)  A    0.07 LOW
 459 PRO   ( 463-)  A    0.18 LOW
 462 PRO   ( 466-)  A    0.13 LOW
 465 PRO   ( 469-)  A    0.05 LOW
 475 PRO   ( 479-)  A    0.17 LOW
 478 PRO   ( 482-)  A    0.19 LOW
 480 PRO   ( 484-)  A    0.11 LOW
 483 PRO   ( 487-)  A    0.20 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].

 104 PRO   ( 108-)  A   121.0 half-chair C-beta/C-alpha (126 degrees)
 139 PRO   ( 143-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 189 PRO   ( 193-)  A   -46.0 half-chair C-beta/C-alpha (-54 degrees)
 456 PRO   ( 460-)  A   116.2 envelop C-beta (108 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.

 198 ARG   ( 202-)  A      CG  <->  235 ASN   ( 239-)  A      CA     0.92    2.28  INTRA
 198 ARG   ( 202-)  A      CG  <->  235 ASN   ( 239-)  A      C      0.78    2.42  INTRA
 198 ARG   ( 202-)  A      NE  <->  235 ASN   ( 239-)  A      O      0.70    2.00  INTRA BF
 196 PHE   ( 200-)  A      CB  <->  197 PRO   ( 201-)  A      CD     0.69    2.41  INTRA
 198 ARG   ( 202-)  A      CG  <->  235 ASN   ( 239-)  A      CB     0.60    2.60  INTRA
 198 ARG   ( 202-)  A      CG  <->  235 ASN   ( 239-)  A      O      0.60    2.20  INTRA
 198 ARG   ( 202-)  A      CB  <->  235 ASN   ( 239-)  A      ND2    0.53    2.57  INTRA
 198 ARG   ( 202-)  A      CB  <->  235 ASN   ( 239-)  A      CA     0.49    2.71  INTRA
 196 PHE   ( 200-)  A      O   <->  198 ARG   ( 202-)  A      N      0.49    2.21  INTRA
 309 THR   ( 313-)  A      N   <->  496 HOH   ( 566 )  A      O      0.47    2.23  INTRA
 452 HIS   ( 456-)  A      ND1 <->  496 HOH   ( 599 )  A      O      0.43    2.27  INTRA
 406 LYS   ( 410-)  A      NZ  <->  496 HOH   ( 797 )  A      O      0.43    2.27  INTRA BF
 406 LYS   ( 410-)  A      N   <->  496 HOH   ( 659 )  A      O      0.41    2.29  INTRA
 198 ARG   ( 202-)  A      CD  <->  235 ASN   ( 239-)  A      O      0.36    2.44  INTRA BF
 377 ASN   ( 381-)  A      ND2 <->  415 LEU   ( 419-)  A      CB     0.36    2.74  INTRA BL
 198 ARG   ( 202-)  A      CG  <->  496 HOH   ( 778 )  A      O      0.35    2.45  INTRA BF
 285 LYS   ( 289-)  A      NZ  <->  456 PRO   ( 460-)  A      CD     0.35    2.75  INTRA
 485 THR   ( 489-)  A      N   <->  496 HOH   ( 526 )  A      O      0.33    2.37  INTRA
 344 ASP   ( 348-)  A      N   <->  356 GLN   ( 360-)  A      OE1    0.33    2.37  INTRA
 285 LYS   ( 289-)  A      NZ  <->  456 PRO   ( 460-)  A      N      0.33    2.67  INTRA
 196 PHE   ( 200-)  A      CG  <->  197 PRO   ( 201-)  A      CD     0.32    2.88  INTRA
 455 THR   ( 459-)  A      CG2 <->  458 LYS   ( 462-)  A      NZ     0.28    2.82  INTRA BF
 158 ARG   ( 162-)  A      NE  <->  496 HOH   ( 582 )  A      O      0.28    2.42  INTRA
 423 GLN   ( 427-)  A      OE1 <->  425 SER   ( 429-)  A      N      0.28    2.42  INTRA
 343 ARG   ( 347-)  A      NH1 <->  385 THR   ( 389-)  A      O      0.26    2.44  INTRA
And so on for a total of 149 lines.

Packing, accessibility and threading

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.

 122 ARG   ( 126-)  A      -7.11
 463 LYS   ( 467-)  A      -6.30
 382 TYR   ( 386-)  A      -5.73
 219 ARG   ( 223-)  A      -5.72
 192 GLN   ( 196-)  A      -5.63
  58 LYS   (  62-)  A      -5.51
 179 PRO   ( 183-)  A      -5.33
 477 LEU   ( 481-)  A      -5.28
 188 TYR   ( 192-)  A      -5.25
 196 PHE   ( 200-)  A      -5.17
 397 GLN   ( 401-)  A      -5.08
  98 ILE   ( 102-)  A      -5.03
 415 LEU   ( 419-)  A      -5.02
   6 ASN   (  10-)  A      -5.02

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.

   5 LEU   (   9-)  A   -2.95
 351 ALA   ( 355-)  A   -2.54
 415 LEU   ( 419-)  A   -2.50

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 496 HOH   ( 729 )  A      O

Warning: Water molecules need moving

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

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

 496 HOH   ( 517 )  A      O     13.10   42.13   49.47
 496 HOH   ( 520 )  A      O     10.36   58.06   39.62
 496 HOH   ( 591 )  A      O     13.79   35.87   -2.75
 496 HOH   ( 695 )  A      O     -6.89   43.59   42.80
 496 HOH   ( 750 )  A      O    -19.90   39.42   25.58
 496 HOH   ( 760 )  A      O      7.93   37.82   52.52
 496 HOH   ( 762 )  A      O     28.99   26.03   31.30
 496 HOH   ( 763 )  A      O     -8.42   55.34    6.03
 496 HOH   ( 771 )  A      O    -24.42   40.10   10.96
 496 HOH   ( 801 )  A      O    -21.44   44.47   22.56
 496 HOH   ( 827 )  A      O      8.10   32.15   57.73

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.

 496 HOH   ( 568 )  A      O
 496 HOH   ( 586 )  A      O
 496 HOH   ( 672 )  A      O
 496 HOH   ( 691 )  A      O
 496 HOH   ( 709 )  A      O
 496 HOH   ( 727 )  A      O
 496 HOH   ( 729 )  A      O
 496 HOH   ( 733 )  A      O
 496 HOH   ( 739 )  A      O
 496 HOH   ( 776 )  A      O
 496 HOH   ( 785 )  A      O
 496 HOH   ( 791 )  A      O
 496 HOH   ( 811 )  A      O
 496 HOH   ( 829 )  A      O
 496 HOH   ( 848 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  23 ASN   (  27-)  A
  37 GLN   (  41-)  A
  62 GLN   (  66-)  A
 100 ASN   ( 104-)  A
 127 ASN   ( 131-)  A
 303 ASN   ( 307-)  A
 316 ASN   ( 320-)  A
 336 ASN   ( 340-)  A
 389 GLN   ( 393-)  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.

   2 ASN   (   6-)  A      ND2
   4 LEU   (   8-)  A      N
  63 TYR   (  67-)  A      N
  83 GLN   (  87-)  A      NE2
  89 HIS   (  93-)  A      N
  93 GLY   (  97-)  A      N
  99 VAL   ( 103-)  A      N
 130 TYR   ( 134-)  A      N
 178 GLY   ( 182-)  A      N
 194 TRP   ( 198-)  A      N
 195 GLU   ( 199-)  A      N
 219 ARG   ( 223-)  A      NH2
 235 ASN   ( 239-)  A      N
 278 ASN   ( 282-)  A      ND2
 285 LYS   ( 289-)  A      NZ
 297 TRP   ( 301-)  A      N
 303 ASN   ( 307-)  A      N
 306 ALA   ( 310-)  A      N
 339 CYS   ( 343-)  A      N
 353 SER   ( 357-)  A      OG
 372 ARG   ( 376-)  A      NH1
 377 ASN   ( 381-)  A      ND2
 381 ARG   ( 385-)  A      N
 385 THR   ( 389-)  A      N
 401 ASN   ( 405-)  A      N
 411 GLY   ( 415-)  A      N
 420 ASP   ( 424-)  A      N
 455 THR   ( 459-)  A      N
 467 GLU   ( 471-)  A      N
 484 GLU   ( 488-)  A      N
 490 ASP   ( 494-)  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.

 172 ASP   ( 176-)  A      OD1
 296 HIS   ( 300-)  A      NE2
 336 ASN   ( 340-)  A      OD1
 357 GLU   ( 361-)  A      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 496 HOH   ( 866 )  A      O  1.02  K  4

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.

  97 ASP   ( 101-)  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 :  -0.874
  2nd generation packing quality :  -0.234
  Ramachandran plot appearance   :  -1.398
  chi-1/chi-2 rotamer normality  :  -2.890
  Backbone conformation          :  -0.341

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.108
  Bond angles                    :   1.204
  Omega angle restraints         :   0.881
  Side chain planarity           :   2.601 (loose)
  Improper dihedral distribution :   1.999 (loose)
  B-factor distribution          :   0.742
  Inside/Outside distribution    :   0.975

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 : 2.20


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.108
  Bond angles                    :   1.204
  Omega angle restraints         :   0.881
  Side chain planarity           :   2.601 (loose)
  Improper dihedral distribution :   1.999 (loose)
  B-factor distribution          :   0.742
  Inside/Outside distribution    :   0.975
==============

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.