WHAT IF Check report

This file was created 2011-12-15 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 pdb1ew2.ent

Checks that need to be done early-on in validation

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 486 HOH   (1598 )  A      O       3

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.

 485 PO4   (1005-)  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'.

   1 ILE   (   1-)  A      CG1
   1 ILE   (   1-)  A      CG2
   1 ILE   (   1-)  A      CD1
   5 GLU   (   5-)  A      CG
   5 GLU   (   5-)  A      CD
   5 GLU   (   5-)  A      OE1
   5 GLU   (   5-)  A      OE2
  18 GLU   (  18-)  A      CG
  18 GLU   (  18-)  A      CD
  18 GLU   (  18-)  A      OE1
  18 GLU   (  18-)  A      OE2
  30 GLN   (  30-)  A      CG
  30 GLN   (  30-)  A      CD
  30 GLN   (  30-)  A      OE1
  30 GLN   (  30-)  A      NE2
  61 ASP   (  61-)  A      CG
  61 ASP   (  61-)  A      OD1
  61 ASP   (  61-)  A      OD2
  62 LYS   (  62-)  A      CG
  62 LYS   (  62-)  A      CD
  62 LYS   (  62-)  A      CE
  62 LYS   (  62-)  A      NZ
 469 GLU   ( 469-)  A      CG
 469 GLU   ( 469-)  A      CD
 469 GLU   ( 469-)  A      OE1
 469 GLU   ( 469-)  A      OE2

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:

Crystal temperature (K) : 80.000

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.

  14 ARG   (  14-)  A
  53 ARG   (  53-)  A
 150 ARG   ( 150-)  A
 204 ARG   ( 204-)  A
 241 ARG   ( 241-)  A
 280 ARG   ( 280-)  A
 297 ARG   ( 297-)  A
 326 ARG   ( 326-)  A
 385 ARG   ( 385-)  A
 442 ARG   ( 442-)  A

Warning: Tyrosine convention problem

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

 160 TYR   ( 160-)  A
 206 TYR   ( 206-)  A
 276 TYR   ( 276-)  A
 471 TYR   ( 471-)  A

Warning: Phenylalanine convention problem

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

  11 PHE   (  11-)  A
 269 PHE   ( 269-)  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.

  91 ASP   (  91-)  A
 173 ASP   ( 173-)  A
 197 ASP   ( 197-)  A
 214 ASP   ( 214-)  A
 219 ASP   ( 219-)  A
 220 ASP   ( 220-)  A
 259 ASP   ( 259-)  A
 285 ASP   ( 285-)  A
 316 ASP   ( 316-)  A
 349 ASP   ( 349-)  A
 428 ASP   ( 428-)  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.

   6 GLU   (   6-)  A
   7 GLU   (   7-)  A
 181 GLU   ( 181-)  A
 293 GLU   ( 293-)  A
 330 GLU   ( 330-)  A
 339 GLU   ( 339-)  A
 348 GLU   ( 348-)  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.

 358 HIS   ( 358-)  A      ND1  CE1   1.26   -4.8
 479 PRO   ( 479-)  A      CD   N     1.55    5.6

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

 |  0.999953  0.000258 -0.000048|
 |  0.000258  1.002453  0.000369|
 | -0.000048  0.000369  0.989860|
Proposed new scale matrix

 |  0.011261 -0.000003  0.000000|
 | -0.000002  0.008709 -0.000003|
 |  0.000000 -0.000003  0.009446|
With corresponding cell

    A    =  88.806  B   = 114.829  C    = 105.867
    Alpha=  89.958  Beta=  90.001  Gamma=  89.970

The CRYST1 cell dimensions

    A    =  88.810  B   = 114.548  C    = 106.952
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 266.137
(Under-)estimated Z-score: 12.023

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.

   8 ASN   (   8-)  A      CA   CB   CG  117.49    4.9
  10 ASP   (  10-)  A      CA   CB   CG  108.53   -4.1
  29 ALA   (  29-)  A      C    CA   CB  104.05   -4.3
  42 ASP   (  42-)  A      CA   CB   CG  106.86   -5.7
  42 ASP   (  42-)  A      CB   CG   OD2 131.84    5.8
  42 ASP   (  42-)  A      OD2  CG   OD1 112.58   -4.3
  53 ARG   (  53-)  A      CD   NE   CZ  130.18    4.7
  60 LYS   (  60-)  A      CA   C    O   113.45   -4.3
  61 ASP   (  61-)  A     -O   -C    N   113.14   -6.2
  61 ASP   (  61-)  A     -CA  -C    N   133.41    8.6
  61 ASP   (  61-)  A     -C    N    CA  110.79   -6.1
  66 GLU   (  66-)  A      CB   CG   CD  119.99    4.3
  72 ASP   (  72-)  A      CA   CB   CG  120.84    8.2
  82 THR   (  82-)  A      C    CA   CB   89.57  -10.8
  82 THR   (  82-)  A      CA   CB   OG1 125.41   10.5
  90 PRO   (  90-)  A      N    CA   CB   98.48   -4.1
  92 SER   (  92-)  A      C    CA   CB  100.65   -5.0
 107 PHE   ( 107-)  A      CA   CB   CG  123.06    9.3
 120 GLN   ( 120-)  A      CB   CG   CD  119.43    4.0
 120 GLN   ( 120-)  A      NE2  CD   OE1 115.02   -7.6
 125 ARG   ( 125-)  A      CA   CB   CG  104.21   -4.9
 125 ARG   ( 125-)  A      CG   CD   NE  117.52    4.1
 125 ARG   ( 125-)  A      CD   NE   CZ  143.91   12.3
 132 VAL   ( 132-)  A      N    CA   CB  117.38    4.0
 132 VAL   ( 132-)  A      CA   CB   CG2 118.02    4.4
And so on for a total of 125 lines.

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.

   6 GLU   (   6-)  A
   7 GLU   (   7-)  A
  14 ARG   (  14-)  A
  53 ARG   (  53-)  A
  91 ASP   (  91-)  A
 150 ARG   ( 150-)  A
 173 ASP   ( 173-)  A
 181 GLU   ( 181-)  A
 197 ASP   ( 197-)  A
 204 ARG   ( 204-)  A
 214 ASP   ( 214-)  A
 219 ASP   ( 219-)  A
 220 ASP   ( 220-)  A
 241 ARG   ( 241-)  A
 259 ASP   ( 259-)  A
 280 ARG   ( 280-)  A
 285 ASP   ( 285-)  A
 293 GLU   ( 293-)  A
 297 ARG   ( 297-)  A
 316 ASP   ( 316-)  A
 326 ARG   ( 326-)  A
 330 GLU   ( 330-)  A
 339 GLU   ( 339-)  A
 348 GLU   ( 348-)  A
 349 ASP   ( 349-)  A
 385 ARG   ( 385-)  A
 428 ASP   ( 428-)  A
 442 ARG   ( 442-)  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.

  82 THR   (  82-)  A      C     -6.9   -10.06     0.30
 468 LEU   ( 468-)  A      C      8.6    13.75     0.20
 472 THR   ( 472-)  A      CA   -10.6    16.15    33.84
The average deviation= 1.733

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.

 472 THR   ( 472-)  A    5.37
 312 GLY   ( 312-)  A    5.02
 474 CYS   ( 474-)  A    4.65
 154 ALA   ( 154-)  A    4.62
 205 LYS   ( 205-)  A    4.54
 192 SER   ( 192-)  A    4.38
 260 PRO   ( 260-)  A    4.37
 473 ALA   ( 473-)  A    4.21
 239 ALA   ( 239-)  A    4.09

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.

 358 HIS   ( 358-)  A    9.59

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.

 355 THR   ( 355-)  A    -3.0
  90 PRO   (  90-)  A    -2.5
 268 LEU   ( 268-)  A    -2.3
 263 THR   ( 263-)  A    -2.3
 147 THR   ( 147-)  A    -2.2
 163 THR   ( 163-)  A    -2.2
  64 GLY   (  64-)  A    -2.2
 470 PRO   ( 470-)  A    -2.2
  40 LEU   (  40-)  A    -2.1
 358 HIS   ( 358-)  A    -2.1
 245 ARG   ( 245-)  A    -2.0
 267 GLY   ( 267-)  A    -2.0
  82 THR   (  82-)  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.

 108 GLN   ( 108-)  A  Poor phi/psi
 119 ASN   ( 119-)  A  Poor phi/psi
 160 TYR   ( 160-)  A  Poor phi/psi
 261 SER   ( 261-)  A  Poor phi/psi
 262 VAL   ( 262-)  A  Poor phi/psi
 263 THR   ( 263-)  A  Poor phi/psi
 322 SER   ( 322-)  A  Poor phi/psi
 385 ARG   ( 385-)  A  Poor phi/psi
 445 GLN   ( 445-)  A  Poor phi/psi
 467 CYS   ( 467-)  A  Poor phi/psi
 468 LEU   ( 468-)  A  Poor phi/psi
 469 GLU   ( 469-)  A  Poor phi/psi
 473 ALA   ( 473-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.862

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!

   8 ASN   (   8-)  A      0
  30 GLN   (  30-)  A      0
  34 LYS   (  34-)  A      0
  35 ASN   (  35-)  A      0
  42 ASP   (  42-)  A      0
  44 MET   (  44-)  A      0
  61 ASP   (  61-)  A      0
  63 LEU   (  63-)  A      0
  65 PRO   (  65-)  A      0
  74 PHE   (  74-)  A      0
  88 HIS   (  88-)  A      0
 101 CYS   ( 101-)  A      0
 106 ASN   ( 106-)  A      0
 107 PHE   ( 107-)  A      0
 108 GLN   ( 108-)  A      0
 110 ILE   ( 110-)  A      0
 114 ALA   ( 114-)  A      0
 116 ALA   ( 116-)  A      0
 118 PHE   ( 118-)  A      0
 119 ASN   ( 119-)  A      0
 120 GLN   ( 120-)  A      0
 121 CYS   ( 121-)  A      0
 124 THR   ( 124-)  A      0
 125 ARG   ( 125-)  A      0
 127 ASN   ( 127-)  A      0
And so on for a total of 182 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]

  90 PRO   (  90-)  A    0.54 HIGH
 407 PRO   ( 407-)  A    0.18 LOW

Warning: Unusual PRO puckering phases

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

   9 PRO   (   9-)  A   108.2 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.

 480 NAG   (1000-)  A      C7  <->  486 HOH   (1136 )  A      O      2.08    0.72  INTRA
 242 GLN   ( 242-)  A      OE1 <->  486 HOH   (1601 )  A      O      1.87    0.53  INTRA
 242 GLN   ( 242-)  A      CD  <->  486 HOH   (1113 )  A      O      1.79    1.01  INTRA
 242 GLN   ( 242-)  A      NE2 <->  486 HOH   (1113 )  A      O      1.59    1.11  INTRA
 480 NAG   (1000-)  A      N2  <->  486 HOH   (1136 )  A      O      1.57    1.13  INTRA
 486 HOH   (1117 )  A      O   <->  486 HOH   (1353 )  A      O      1.30    0.90  INTRA
 242 GLN   ( 242-)  A      CD  <->  486 HOH   (1601 )  A      O      1.12    1.68  INTRA
 480 NAG   (1000-)  A      O7  <->  486 HOH   (1136 )  A      O      1.07    1.33  INTRA
 242 GLN   ( 242-)  A      CG  <->  486 HOH   (1113 )  A      O      1.02    1.78  INTRA
  26 LEU   (  26-)  A      CD2 <->  486 HOH   (1556 )  A      O      0.80    2.00  INTRA
 480 NAG   (1000-)  A      C8  <->  486 HOH   (1136 )  A      O      0.78    2.02  INTRA
  23 ALA   (  23-)  A      O   <->   26 LEU   (  26-)  A      CD2    0.54    2.26  INTRA
 480 NAG   (1000-)  A      C2  <->  486 HOH   (1136 )  A      O      0.48    2.32  INTRA
 135 ARG   ( 135-)  A      NH1 <->  486 HOH   (1132 )  A      O      0.46    2.24  INTRA
 447 HIS   ( 447-)  A      NE2 <->  486 HOH   (1035 )  A      O      0.45    2.25  INTRA
  92 SER   (  92-)  A      OG  <->  485 PO4   (1005-)  A      P      0.38    2.62  INTRA
 242 GLN   ( 242-)  A      OE1 <->  486 HOH   (1113 )  A      O      0.38    2.02  INTRA
  82 THR   (  82-)  A      CB  <->  486 HOH   (1576 )  A      O      0.36    2.44  INTRA
  82 THR   (  82-)  A      CG2 <->  486 HOH   (1576 )  A      O      0.34    2.46  INTRA
 264 HIS   ( 264-)  A      ND1 <->  486 HOH   (1381 )  A      O      0.33    2.37  INTRA
 472 THR   ( 472-)  A      OG1 <->  473 ALA   ( 473-)  A      N      0.32    2.28  INTRA
 469 GLU   ( 469-)  A      CB  <->  470 PRO   ( 470-)  A      CD     0.30    2.80  INTRA
 122 ASN   ( 122-)  A      ND2 <->  480 NAG   (1000-)  A      N2     0.30    2.30  INTRA B3
 122 ASN   ( 122-)  A      CG  <->  480 NAG   (1000-)  A      N2     0.27    2.83  INTRA
 122 ASN   ( 122-)  A      ND2 <->  480 NAG   (1000-)  A      C2     0.26    1.94  INTRA B2
And so on for a total of 89 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.

 367 TYR   ( 367-)  A      -8.34
 125 ARG   ( 125-)  A      -7.32
 301 ARG   ( 301-)  A      -6.55
 304 ARG   ( 304-)  A      -5.99
 279 HIS   ( 279-)  A      -5.96
  60 LYS   (  60-)  A      -5.89
  73 ARG   (  73-)  A      -5.73
  88 HIS   (  88-)  A      -5.70
 242 GLN   ( 242-)  A      -5.67
 210 MET   ( 210-)  A      -5.66
  63 LEU   (  63-)  A      -5.58
 180 GLN   ( 180-)  A      -5.55
 370 ARG   ( 370-)  A      -5.51
 402 LYS   ( 402-)  A      -5.43
 385 ARG   ( 385-)  A      -5.33
 383 ARG   ( 383-)  A      -5.29
  27 GLN   (  27-)  A      -5.29
 223 GLN   ( 223-)  A      -5.15
 369 LEU   ( 369-)  A      -5.13
   7 GLU   (   7-)  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.

  25 LYS   (  25-)  A        27 - GLN     27- ( A)         -4.58
 240 LYS   ( 240-)  A       242 - GLN    242- ( A)         -4.76

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.

  62 LYS   (  62-)  A   -3.64
 380 GLY   ( 380-)  A   -3.09
 122 ASN   ( 122-)  A   -3.02
 466 ALA   ( 466-)  A   -2.65
 191 ILE   ( 191-)  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.

 467 CYS   ( 467-)  A     -  470 PRO   ( 470-)  A        -1.52

Water, ion, and hydrogenbond related checks

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.

 486 HOH   (1307 )  A      O     55.04   51.40   32.17
 486 HOH   (1391 )  A      O     37.88    2.37   -7.73
 486 HOH   (1409 )  A      O     78.20   41.19   33.61
 486 HOH   (1438 )  A      O     56.63    7.78   38.91
 486 HOH   (1451 )  A      O     54.01  -17.81   21.74
 486 HOH   (1461 )  A      O     52.88  -22.14   23.04
 486 HOH   (1513 )  A      O     50.40  -21.11   21.80
 486 HOH   (1597 )  A      O     77.50   38.14   33.34

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.

 486 HOH   (1389 )  A      O
 486 HOH   (1397 )  A      O
 486 HOH   (1455 )  A      O
 486 HOH   (1497 )  A      O
 486 HOH   (1509 )  A      O
 486 HOH   (1539 )  A      O
 486 HOH   (1584 )  A      O
Bound group on Asn; dont flip  122 ASN  ( 122-) A
Bound to:  480 NAG  (1000-) A
Metal-coordinating Histidine residue 320 fixed to   1
Metal-coordinating Histidine residue 432 fixed to   1
Metal-coordinating Histidine residue 358 fixed to   2

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.

   8 ASN   (   8-)  A
  84 ASN   (  84-)  A
 120 GLN   ( 120-)  A
 134 ASN   ( 134-)  A
 153 HIS   ( 153-)  A
 189 GLN   ( 189-)  A
 193 ASN   ( 193-)  A
 302 ASN   ( 302-)  A
 445 GLN   ( 445-)  A
 455 GLN   ( 455-)  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.

  87 LYS   (  87-)  A      N
  89 VAL   (  89-)  A      N
  92 SER   (  92-)  A      N
 104 LYS   ( 104-)  A      N
 248 TRP   ( 248-)  A      NE1
 292 THR   ( 292-)  A      OG1
 317 HIS   ( 317-)  A      N
 357 ASP   ( 357-)  A      N
 362 PHE   ( 362-)  A      N
 366 GLY   ( 366-)  A      N
 383 ARG   ( 383-)  A      NE
 384 ASP   ( 384-)  A      N
 395 ASN   ( 395-)  A      N
 423 SER   ( 423-)  A      N
 427 LEU   ( 427-)  A      N
 445 GLN   ( 445-)  A      N
 447 HIS   ( 447-)  A      N
 480 NAG   (1000-)  A      N2
Only metal coordination for   42 ASP  (  42-) A      OD1
Only metal coordination for  270 GLU  ( 270-) A      OE2
Only metal coordination for  311 GLU  ( 311-) A      OE2

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.

 106 ASN   ( 106-)  A      OD1
 127 ASN   ( 127-)  A      OD1
 358 HIS   ( 358-)  A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 483  MG   (1003-)  A   -.-  -.-  Part of ionic cluster
 483  MG   (1003-)  A     0.50   1.01 Is perhaps NA
 484  MG   (1004-)  A     0.49   0.98 Is perhaps NA

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.

 486 HOH   (1055 )  A      O  1.03  K  4
 486 HOH   (1063 )  A      O  0.93  K  4
 486 HOH   (1253 )  A      O  0.99  K  5
 486 HOH   (1287 )  A      O  0.86  K  4
 486 HOH   (1370 )  A      O  1.02 NA  4 Ion-B
 486 HOH   (1422 )  A      O  1.10  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.

 259 ASP   ( 259-)  A   H-bonding suggests Asn; but Alt-Rotamer
 349 ASP   ( 349-)  A   H-bonding suggests Asn; but Alt-Rotamer
 430 GLU   ( 430-)  A   H-bonding suggests Gln

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 :  -1.129
  2nd generation packing quality :  -1.929
  Ramachandran plot appearance   :  -0.662
  chi-1/chi-2 rotamer normality  :  -1.862
  Backbone conformation          :  -0.529

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   1.589
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.226
  Improper dihedral distribution :   1.481
  B-factor distribution          :   0.566
  Inside/Outside distribution    :   1.051

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 : 1.82


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   1.589
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.226
  Improper dihedral distribution :   1.481
  B-factor distribution          :   0.566
  Inside/Outside distribution    :   1.051
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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.