WHAT IF Check report

This file was created 2011-12-16 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 pdb1jk8.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 284 ARG   ( 105-)  B  -   CB
 285 THR   ( 106-)  B  -   CB
 286 GLU   ( 107-)  B  -   CB
 287 ALA   ( 108-)  B  -   CB
 288 LEU   ( 109-)  B  -   CB
 289 ASN   ( 110-)  B  -   CB
 290 HIS   ( 111-)  B  -   CB
 291 HIS   ( 112-)  B  -   CB

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 284 ARG   ( 105-)  B  -   N
 284 ARG   ( 105-)  B  -   CA
 284 ARG   ( 105-)  B  -   C
 284 ARG   ( 105-)  B  -   O
 285 THR   ( 106-)  B  -   N
 285 THR   ( 106-)  B  -   CA
 285 THR   ( 106-)  B  -   C
 285 THR   ( 106-)  B  -   O
 286 GLU   ( 107-)  B  -   N
 286 GLU   ( 107-)  B  -   CA
 286 GLU   ( 107-)  B  -   C
 286 GLU   ( 107-)  B  -   O
 287 ALA   ( 108-)  B  -   N
 287 ALA   ( 108-)  B  -   CA
 287 ALA   ( 108-)  B  -   C
 287 ALA   ( 108-)  B  -   O
 288 LEU   ( 109-)  B  -   N
 288 LEU   ( 109-)  B  -   CA
 288 LEU   ( 109-)  B  -   C
 288 LEU   ( 109-)  B  -   O
 289 ASN   ( 110-)  B  -   N
 289 ASN   ( 110-)  B  -   CA
 289 ASN   ( 110-)  B  -   C
 289 ASN   ( 110-)  B  -   O
 290 HIS   ( 111-)  B  -   N
 290 HIS   ( 111-)  B  -   CA
 290 HIS   ( 111-)  B  -   C
 290 HIS   ( 111-)  B  -   O
 291 HIS   ( 112-)  B  -   N
 291 HIS   ( 112-)  B  -   CA
 291 HIS   ( 112-)  B  -   C
 291 HIS   ( 112-)  B  -   O

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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'.

 284 ARG   ( 105-)  B      CG
 284 ARG   ( 105-)  B      CD
 284 ARG   ( 105-)  B      NE
 284 ARG   ( 105-)  B      CZ
 284 ARG   ( 105-)  B      NH1
 284 ARG   ( 105-)  B      NH2
 285 THR   ( 106-)  B      OG1
 285 THR   ( 106-)  B      CG2
 286 GLU   ( 107-)  B      CG
 286 GLU   ( 107-)  B      CD
 286 GLU   ( 107-)  B      OE1
 286 GLU   ( 107-)  B      OE2
 288 LEU   ( 109-)  B      CG
 288 LEU   ( 109-)  B      CD1
 288 LEU   ( 109-)  B      CD2
 289 ASN   ( 110-)  B      CG
 289 ASN   ( 110-)  B      OD1
 289 ASN   ( 110-)  B      ND2
 290 HIS   ( 111-)  B      CG
 290 HIS   ( 111-)  B      ND1
 290 HIS   ( 111-)  B      CD2
 290 HIS   ( 111-)  B      CE1
 290 HIS   ( 111-)  B      NE2
 291 HIS   ( 112-)  B      CG
 291 HIS   ( 112-)  B      ND1
 291 HIS   ( 112-)  B      CD2
 291 HIS   ( 112-)  B      CE1
 291 HIS   ( 112-)  B      NE2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 181 GLU   ( 181-)  A    High

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) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

  50 ARG   (  50-)  A
 328 ARG   ( 149-)  B

Warning: Tyrosine convention problem

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

 188 TYR   (   9-)  B
 216 TYR   (  37-)  B
 350 TYR   ( 171-)  B

Warning: Phenylalanine convention problem

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

 219 PHE   (  40-)  B
 334 PHE   ( 155-)  B

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.

 157 ASP   ( 157-)  A
 185 ASP   (   6-)  B

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.

 134 GLU   ( 134-)  A
 159 GLU   ( 159-)  A
 201 GLU   (  22-)  B
 275 GLU   (  96-)  B

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.

  37 GLU   (  37-)  A      CG   CD    1.17  -13.7
  88 GLU   (  88-)  A      CG   CD    1.77   10.0
 101 GLN   ( 101-)  A      CG   CD    1.37   -6.0
 157 ASP   ( 157-)  A      CG   OD1   1.03  -11.6
 157 ASP   ( 157-)  A      CG   OD2   1.42    9.2
 171 ASP   ( 171-)  A      CG   OD1   1.70   23.9
 181 GLU   ( 181-)  A      N   -C     1.12  -10.5

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.

  10 VAL   (  10-)  A      N    CA   C    99.67   -4.1
  37 GLU   (  37-)  A      CB   CG   CD  122.74    6.0
  88 GLU   (  88-)  A      CB   CG   CD   93.94  -11.0
  88 GLU   (  88-)  A      CG   CD   OE2 129.66    4.9
  88 GLU   (  88-)  A      CG   CD   OE1 106.53   -5.2
 101 GLN   ( 101-)  A      CG   CD   OE1 131.44    5.3
 101 GLN   ( 101-)  A      NE2  CD   OE1 113.12   -9.5
 157 ASP   ( 157-)  A      CB   CG   OD2 102.39   -7.0
 171 ASP   ( 171-)  A      CB   CG   OD2 142.96   10.7
 171 ASP   ( 171-)  A      OD2  CG   OD1  94.28  -11.9
 181 GLU   ( 181-)  A     -O   -C    N   112.53   -6.5
 181 GLU   ( 181-)  A     -CA  -C    N   126.34    5.1
 284 ARG   ( 105-)  B     -O   -C    N   104.16  -11.8
 284 ARG   ( 105-)  B     -CA  -C    N   130.09    6.9
 284 ARG   ( 105-)  B     -C    N    CA  138.10    9.1
 360 GLN   ( 181-)  B      CG   CD   NE2 126.23    6.6
 360 GLN   ( 181-)  B      NE2  CD   OE1 112.17  -10.4

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  50 ARG   (  50-)  A
 134 GLU   ( 134-)  A
 157 ASP   ( 157-)  A
 159 GLU   ( 159-)  A
 185 ASP   (   6-)  B
 201 GLU   (  22-)  B
 275 GLU   (  96-)  B
 328 ARG   ( 149-)  B

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.

 283 SER   ( 104-)  B      C     -9.3   -15.00     0.37
The average deviation= 0.803

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.

  51 PHE   (  51-)  A    4.64
 299 THR   ( 120-)  B    4.26
  10 VAL   (  10-)  A    4.13

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.

 171 ASP   ( 171-)  A   17.28
 157 ASP   ( 157-)  A   10.41
  88 GLU   (  88-)  A    4.89

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.

 200 THR   (  21-)  B    -2.3
  79 SER   (  79-)  A    -2.3
   9 GLY   (   9-)  A    -2.2
 368 ARG   ( 189-)  B    -2.2
  52 ARG   (  52-)  A    -2.2
 273 ARG   (  94-)  B    -2.2
  17 GLY   (  17-)  A    -2.2
 117 VAL   ( 117-)  A    -2.2
 306 ILE   ( 127-)  B    -2.1
 359 LEU   ( 180-)  B    -2.1
 376 LEU   (   5-)  C    -2.1
 229 VAL   (  50-)  B    -2.1
 225 VAL   (  46-)  B    -2.1
  53 ARG   (  53-)  A    -2.1
 370 GLN   ( 191-)  B    -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.

  17 GLY   (  17-)  A  PRO omega poor
  27 ASP   (  27-)  A  Poor phi/psi
  78 ASN   (  78-)  A  Poor phi/psi
  79 SER   (  79-)  A  Poor phi/psi
 113 PHE   ( 113-)  A  Poor phi/psi, PRO omega poor
 115 PRO   ( 115-)  A  Poor phi/psi
 143 HIS   ( 143-)  A  Poor phi/psi
 180 PRO   ( 180-)  A  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 268 THR   (  89-)  B  Poor phi/psi
 284 ARG   ( 105-)  B  Poor phi/psi
 285 THR   ( 106-)  B  Poor phi/psi
 286 GLU   ( 107-)  B  Poor phi/psi
 287 ALA   ( 108-)  B  Poor phi/psi
 289 ASN   ( 110-)  B  Poor phi/psi
 290 HIS   ( 111-)  B  Poor phi/psi
 292 ASN   ( 113-)  B  Poor phi/psi
 302 TYR   ( 123-)  B  PRO omega poor
 313 ASN   ( 134-)  B  Poor phi/psi
 332 TRP   ( 153-)  B  Poor phi/psi
 370 GLN   ( 191-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.285

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 ASP   (   4-)  A      0
   8 TYR   (   9-)  A      0
  16 TYR   (  16-)  A      0
  18 PRO   (  18-)  A      0
  19 SER   (  19-)  A      0
  26 PHE   (  26-)  A      0
  31 GLU   (  31-)  A      0
  32 PHE   (  32-)  A      0
  44 GLN   (  44-)  A      0
  51 PHE   (  51-)  A      0
  78 ASN   (  78-)  A      0
  79 SER   (  79-)  A      0
  99 LEU   (  99-)  A      0
 110 ASP   ( 110-)  A      0
 113 PHE   ( 113-)  A      0
 114 PRO   ( 114-)  A      0
 115 PRO   ( 115-)  A      0
 116 VAL   ( 116-)  A      0
 123 SER   ( 123-)  A      0
 130 GLU   ( 130-)  A      0
 132 VAL   ( 132-)  A      0
 133 SER   ( 133-)  A      0
 134 GLU   ( 134-)  A      0
 137 PHE   ( 137-)  A      0
 143 HIS   ( 143-)  A      0
And so on for a total of 148 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.452

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]

  96 PRO   (  96-)  A    0.45 HIGH
 183 PRO   (   4-)  B    0.47 HIGH

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.

   9 GLY   (   9-)  A      C   <->   11 ASN   (  11-)  A      ND2    0.30    2.80  INTRA BL
  94 LYS   (  94-)  A      NZ  <->  300 ASP   ( 121-)  B      OD1    0.28    2.42  INTRA BL
 353 HIS   ( 174-)  B      ND1 <->  391 HOH   ( 222 )  B      O      0.28    2.42  INTRA
 258 CYS   (  79-)  B      SG  <->  377 TYR   (   6-)  C      OH     0.27    2.73  INTRA BL
 177 HIS   ( 177-)  A      NE2 <->  179 GLU   ( 179-)  A      OE1    0.26    2.44  INTRA
  39 LYS   (  39-)  A      NZ  <->   57 GLN   (  57-)  A      OE1    0.18    2.52  INTRA
  14 GLN   (  14-)  A      NE2 <->  185 ASP   (   6-)  B      OD2    0.18    2.52  INTRA
 289 ASN   ( 110-)  B      C   <->  291 HIS   ( 112-)  B      N      0.16    2.74  INTRA BL
  78 ASN   (  78-)  A      ND2 <->  386 NAG   ( 401-)  A      C7     0.15    2.95  INTRA BF
 305 GLN   ( 126-)  B      CG  <->  391 HOH   ( 207 )  B      O      0.15    2.65  INTRA
 187 VAL   (   8-)  B      O   <->  212 ASN   (  33-)  B      N      0.14    2.56  INTRA BL
 216 TYR   (  37-)  B      C   <->  229 VAL   (  50-)  B      CG1    0.13    3.07  INTRA BL
 294 LEU   ( 115-)  B      CD1 <->  342 MET   ( 163-)  B      SD     0.13    3.27  INTRA
 233 GLY   (  54-)  B      N   <->  234 PRO   (  55-)  B      CD     0.12    2.88  INTRA BL
 179 GLU   ( 179-)  A      O   <->  181 GLU   ( 181-)  A      N      0.11    2.59  INTRA BF
  43 TRP   (  43-)  A      O   <->   49 ARG   (  49-)  A      NH1    0.11    2.59  INTRA
 123 SER   ( 123-)  A      CB  <->  128 VAL   ( 128-)  A      CG2    0.11    3.09  INTRA
 283 SER   ( 104-)  B      N   <->  293 LEU   ( 114-)  B      O      0.11    2.59  INTRA
  94 LYS   (  94-)  A      NZ  <->  331 ASP   ( 152-)  B      OD2    0.11    2.59  INTRA BL
  52 ARG   (  52-)  A      NH1 <->  265 GLU   (  86-)  B      OE2    0.10    2.60  INTRA
   3 ASP   (   4-)  A      OD2 <->  198 ASN   (  19-)  B      N      0.10    2.60  INTRA
 313 ASN   ( 134-)  B      N   <->  349 VAL   ( 170-)  B      O      0.10    2.60  INTRA BL
 215 GLU   (  36-)  B      OE2 <->  218 ARG   (  39-)  B      NE     0.09    2.61  INTRA
 180 PRO   ( 180-)  A      O   <->  181 GLU   ( 181-)  A      C      0.09    2.51  INTRA BF
 205 LEU   (  26-)  B      N   <->  221 SER   (  42-)  B      OG     0.08    2.62  INTRA BL
And so on for a total of 69 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 383 ARG   (  12-)  C      -7.29
 360 GLN   ( 181-)  B      -7.03
 305 GLN   ( 126-)  B      -6.32
 370 GLN   ( 191-)  B      -6.17
 346 ARG   ( 167-)  B      -5.76
 328 ARG   ( 149-)  B      -5.35
  50 ARG   (  50-)  A      -5.22
 271 GLN   (  92-)  B      -5.17
  16 TYR   (  16-)  A      -5.15

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.

 383 ARG   (  12-)  C       385 - GLY     14- ( C)         -5.47

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: 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: B

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: C

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.

 291 HIS   ( 112-)  B   -3.03
 288 LEU   ( 109-)  B   -2.84
 289 ASN   ( 110-)  B   -2.62
 284 ARG   ( 105-)  B   -2.53

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

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 390 HOH   ( 433 )  A      O
 391 HOH   ( 215 )  B      O
Bound group on Asn; dont flip   78 ASN  (  78-) A
Bound to:  386 NAG  ( 401-) A

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.

 101 GLN   ( 101-)  A
 271 GLN   (  92-)  B

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.

  14 GLN   (  14-)  A      NE2
  45 LEU   (  45-)  A      N
  52 ARG   (  52-)  A      NH1
  53 ARG   (  53-)  A      N
 130 GLU   ( 130-)  A      N
 169 GLY   ( 169-)  A      N
 179 GLU   ( 179-)  A      N
 225 VAL   (  46-)  B      N
 245 GLU   (  66-)  B      N
 261 ASN   (  82-)  B      ND2
 329 ASN   ( 150-)  B      ND2
 345 GLN   ( 166-)  B      N
 351 THR   ( 172-)  B      OG1
 368 ARG   ( 189-)  B      N
 373 VAL   (   2-)  C      N
 379 VAL   (   8-)  C      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.

 370 GLN   ( 191-)  B      OE1

Warning: Unusual water packing

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

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

 390 HOH   ( 422 )  A      O  0.86  K  5

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.

 162 ASP   ( 162-)  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 :   0.104
  2nd generation packing quality :  -0.917
  Ramachandran plot appearance   :  -1.428
  chi-1/chi-2 rotamer normality  :  -2.285
  Backbone conformation          :  -0.243

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.264 (tight)
  Side chain planarity           :   1.626
  Improper dihedral distribution :   0.804
  B-factor distribution          :   0.677
  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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.264 (tight)
  Side chain planarity           :   1.626
  Improper dihedral distribution :   0.804
  B-factor distribution          :   0.677
  Inside/Outside distribution    :   1.069
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
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      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
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      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.