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 pdb1a8m.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.948
CA-only RMS fit for the two chains : 1.187

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.714
CA-only RMS fit for the two chains : 0.976

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 1.744
CA-only RMS fit for the two chains : 1.031

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

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: 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.

   1 ARG   (   6-)  A    High
  29 ASN   (  34-)  A    High
  99 GLU   ( 104-)  A    High
 153 ARG   (   6-)  B    High
 154 THR   (   7-)  B    High
 251 GLU   ( 104-)  B    High
 257 GLU   ( 110-)  B    High
 330 ASP   (  31-)  C    High
 403 GLU   ( 104-)  C    High
 443 PHE   ( 144-)  C    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) :290.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 2.300 over 3151 bonds
Average difference in B over a bond : 5.89
RMS difference in B over a bond : 7.45

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

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.

 216 CYS   (  69-)  B      SG  -SG*   2.39    8.9
 248 CYS   ( 101-)  B      SG  -SG*   2.39    8.9
 368 CYS   (  69-)  C      SG  -SG*   2.36    8.0
 400 CYS   ( 101-)  C      SG  -SG*   2.36    8.0

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 HIS   (  15-)  A      CG   ND1  CE1 109.71    4.1
  34 ASN   (  39-)  A      N    CA   C   123.45    4.4
  97 GLN   ( 102-)  A      N    CA   C    96.23   -5.3
 152 LEU   ( 157-)  A      CA   CB   CG  133.08    4.8
 162 HIS   (  15-)  B      CG   ND1  CE1 109.62    4.0
 177 ASN   (  30-)  B      N    CA   C    96.57   -5.2
 204 LEU   (  57-)  B      N    CA   C    97.77   -4.8
 214 GLN   (  67-)  B      N    CA   C    99.21   -4.3
 220 HIS   (  73-)  B      CG   ND1  CE1 109.70    4.1
 244 ILE   (  97-)  B      C    CA   CB  101.86   -4.3
 291 PHE   ( 144-)  B      N    CA   C   132.86    7.7
 292 ALA   ( 145-)  B      N    CA   C    95.80   -5.5
 293 GLU   ( 146-)  B      N    CA   C   122.73    4.1
 294 SER   ( 147-)  B      N    CA   C    93.30   -6.4
 333 ASN   (  34-)  C      N    CA   C    98.33   -4.6
 336 LEU   (  37-)  C      N    CA   C    93.46   -6.3
 339 GLY   (  40-)  C      N    CA   C   126.03    4.7
 347 LEU   (  48-)  C      N    CA   C    98.03   -4.7
 411 LYS   ( 112-)  C     -C    N    CA  130.43    4.9
 411 LYS   ( 112-)  C      N    CA   C    99.05   -4.3
 446 SER   ( 147-)  C      N    CA   C    98.27   -4.6

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.

 291 PHE   ( 144-)  B      CA    -7.8    21.55    33.98
The average deviation= 1.597

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.

 291 PHE   ( 144-)  B    8.33
 294 SER   ( 147-)  B    6.98
 336 LEU   (  37-)  C    6.93
 292 ALA   ( 145-)  B    6.47
  97 GLN   ( 102-)  A    5.95
 446 SER   ( 147-)  C    5.09
 204 LEU   (  57-)  B    5.04
 177 ASN   (  30-)  B    4.96
 347 LEU   (  48-)  C    4.93
 411 LYS   ( 112-)  C    4.72
 444 ALA   ( 145-)  C    4.62
 339 GLY   (  40-)  C    4.47
 333 ASN   (  34-)  C    4.38
 259 LYS   ( 112-)  B    4.29
 222 LEU   (  75-)  B    4.22
 214 GLN   (  67-)  B    4.13
 185 ALA   (  38-)  B    4.12
   6 LYS   (  11-)  A    4.01
 250 ARG   ( 103-)  B    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 2.029

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.

 177 ASN   (  30-)  B    4.14

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.619

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.

 100 THR   ( 105-)  A    -3.4
 252 THR   ( 105-)  B    -3.2
 404 THR   ( 105-)  C    -3.2
 350 PRO   (  51-)  C    -3.1
 147 PHE   ( 152-)  A    -3.0
 219 THR   (  72-)  B    -2.9
 372 HIS   (  73-)  C    -2.8
 453 ILE   ( 154-)  C    -2.8
  32 LEU   (  37-)  A    -2.8
 291 PHE   ( 144-)  B    -2.8
 184 LEU   (  37-)  B    -2.8
 371 THR   (  72-)  C    -2.8
  67 THR   (  72-)  A    -2.7
  65 PRO   (  70-)  A    -2.7
 294 SER   ( 147-)  B    -2.7
 427 LYS   ( 128-)  C    -2.7
 156 SER   (   9-)  B    -2.6
  84 THR   (  89-)  A    -2.6
 112 PRO   ( 117-)  A    -2.5
 454 ILE   ( 155-)  C    -2.4
 308 SER   (   9-)  C    -2.4
 378 THR   (  79-)  C    -2.4
 254 GLU   ( 107-)  B    -2.4
  77 ARG   (  82-)  A    -2.4
  78 ILE   (  83-)  A    -2.4
And so on for a total of 58 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   4 SER   (   9-)  A  Poor phi/psi
  16 GLN   (  21-)  A  Poor phi/psi
  28 ALA   (  33-)  A  Poor phi/psi
  30 ALA   (  35-)  A  Poor phi/psi
  33 ALA   (  38-)  A  Poor phi/psi
  34 ASN   (  39-)  A  Poor phi/psi
  39 ARG   (  44-)  A  Poor phi/psi
  41 ASN   (  46-)  A  Poor phi/psi
  65 PRO   (  70-)  A  Poor phi/psi
  67 THR   (  72-)  A  Poor phi/psi
  70 LEU   (  75-)  A  Poor phi/psi
  96 CYS   ( 101-)  A  Poor phi/psi
  98 ARG   ( 103-)  A  Poor phi/psi
  99 GLU   ( 104-)  A  Poor phi/psi
 100 THR   ( 105-)  A  Poor phi/psi
 106 ALA   ( 111-)  A  Poor phi/psi
 115 LEU   ( 120-)  A  Poor phi/psi
 142 SER   ( 147-)  A  Poor phi/psi
 144 GLN   ( 149-)  A  Poor phi/psi
 147 PHE   ( 152-)  A  Poor phi/psi
 156 SER   (   9-)  B  Poor phi/psi
 161 ALA   (  14-)  B  Poor phi/psi
 178 ASP   (  31-)  B  Poor phi/psi
 181 ASN   (  34-)  B  Poor phi/psi
 191 ARG   (  44-)  B  Poor phi/psi
And so on for a total of 62 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -6.070

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 PRO   (   8-)  A      0
   4 SER   (   9-)  A      0
   6 LYS   (  11-)  A      0
  10 HIS   (  15-)  A      0
  18 GLU   (  23-)  A      0
  25 ASN   (  30-)  A      0
  26 ASP   (  31-)  A      0
  27 ARG   (  32-)  A      0
  28 ALA   (  33-)  A      0
  29 ASN   (  34-)  A      0
  30 ALA   (  35-)  A      0
  31 LEU   (  36-)  A      0
  32 LEU   (  37-)  A      0
  33 ALA   (  38-)  A      0
  34 ASN   (  39-)  A      0
  39 ARG   (  44-)  A      0
  40 ASP   (  45-)  A      0
  41 ASN   (  46-)  A      0
  46 PRO   (  51-)  A      0
  48 GLU   (  53-)  A      0
  50 LEU   (  55-)  A      0
  60 LYS   (  65-)  A      0
  62 GLN   (  67-)  A      0
  65 PRO   (  70-)  A      0
  67 THR   (  72-)  A      0
And so on for a total of 254 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 : 1.921

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!

 143 GLY   ( 148-)  A   2.00   67
 187 GLY   (  40-)  B   1.84   19

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  33 ALA   (  38-)  A   1.76
  68 HIS   (  73-)  A   1.90
 185 ALA   (  38-)  B   1.87

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]

   3 PRO   (   8-)  A    0.46 HIGH
 108 PRO   ( 113-)  A    0.46 HIGH
 112 PRO   ( 117-)  A    0.45 HIGH
 311 PRO   (  12-)  C    0.48 HIGH
 412 PRO   ( 113-)  C    0.45 HIGH

Warning: Unusual PRO puckering phases

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

 198 PRO   (  51-)  B  -112.5 envelop C-gamma (-108 degrees)
 253 PRO   ( 106-)  B   122.7 half-chair C-beta/C-alpha (126 degrees)
 264 PRO   ( 117-)  B   -60.0 half-chair C-beta/C-alpha (-54 degrees)
 350 PRO   (  51-)  C   -45.6 half-chair C-beta/C-alpha (-54 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.

  64 CYS   (  69-)  A      SG  <->   96 CYS   ( 101-)  A      SG     0.89    2.56  INTRA BF
  64 CYS   (  69-)  A      SG  <->   96 CYS   ( 101-)  A      CB     0.57    2.83  INTRA BF
  64 CYS   (  69-)  A      CB  <->   96 CYS   ( 101-)  A      SG     0.47    2.93  INTRA BF
  66 SER   (  71-)  A      O   <->   68 HIS   (  73-)  A      N      0.36    2.34  INTRA BF
 314 HIS   (  15-)  C      ND1 <->  358 TYR   (  59-)  C      OH     0.34    2.36  INTRA BL
 350 PRO   (  51-)  C      C   <->  427 LYS   ( 128-)  C      NZ     0.34    2.76  INTRA
 133 ARG   ( 138-)  A      NH1 <->  136 TYR   ( 141-)  A      CE2    0.33    2.77  INTRA BF
 160 VAL   (  13-)  B      CG2 <->  161 ALA   (  14-)  B      N      0.33    2.67  INTRA BL
 319 PRO   (  20-)  C      CD  <->  331 ARG   (  32-)  C      NH1    0.29    2.81  INTRA BF
  56 GLN   (  61-)  A      CD  <->  460 HOH   ( 236 )  A      O      0.27    2.53  INTRA BL
 351 SER   (  52-)  C      N   <->  427 LYS   ( 128-)  C      NZ     0.27    2.58  INTRA BL
 229 ARG   (  82-)  B      NH2 <->  277 ASP   ( 130-)  B      OD2    0.27    2.43  INTRA BL
 310 LYS   (  11-)  C      CB  <->  462 HOH   ( 266 )  C      O      0.25    2.55  INTRA BL
  77 ARG   (  82-)  A      NH1 <->   79 ALA   (  84-)  A      CB     0.25    2.85  INTRA BL
 437 ARG   ( 138-)  C      NH2 <->  439 ASP   ( 140-)  C      OD2    0.24    2.46  INTRA BL
 138 ASP   ( 143-)  A      C   <->  144 GLN   ( 149-)  A      OE1    0.24    2.56  INTRA
 319 PRO   (  20-)  C      O   <->  321 ALA   (  22-)  C      N      0.23    2.47  INTRA BF
 362 LEU   (  63-)  C      CD2 <->  448 GLN   ( 149-)  C      NE2    0.22    2.88  INTRA
 291 PHE   ( 144-)  B      C   <->  293 GLU   ( 146-)  B      N      0.22    2.68  INTRA BL
  97 GLN   ( 102-)  A      O   <->   99 GLU   ( 104-)  A      N      0.21    2.49  INTRA BF
 254 GLU   ( 107-)  B      O   <->  256 ALA   ( 109-)  B      N      0.21    2.49  INTRA BF
 377 HIS   (  78-)  C      ND1 <->  419 LEU   ( 120-)  C      CD1    0.21    2.89  INTRA BL
 245 LYS   (  98-)  B      NZ  <->  264 PRO   ( 117-)  B      O      0.20    2.50  INTRA BL
 343 ARG   (  44-)  C      N   <->  346 GLN   (  47-)  C      O      0.20    2.50  INTRA
 381 ARG   (  82-)  C      NH1 <->  462 HOH   ( 257 )  C      O      0.20    2.50  INTRA
And so on for a total of 143 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.

 320 GLN   (  21-)  C      -7.12
 366 GLN   (  67-)  C      -6.49
 402 ARG   ( 103-)  C      -6.44
 249 GLN   ( 102-)  B      -6.33
 386 TYR   (  87-)  C      -6.31
 409 GLU   ( 110-)  C      -6.16
 251 GLU   ( 104-)  B      -5.76
 403 GLU   ( 104-)  C      -5.72
 214 GLN   (  67-)  B      -5.63
  97 GLN   ( 102-)  A      -5.48
  98 ARG   ( 103-)  A      -5.33
 406 GLU   ( 107-)  C      -5.32
 324 GLN   (  25-)  C      -5.17
 257 GLU   ( 110-)  B      -5.16
 411 LYS   ( 112-)  C      -5.14
 234 TYR   (  87-)  B      -5.06
 443 PHE   ( 144-)  C      -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.

 249 GLN   ( 102-)  B       251 - GLU    104- ( B)         -5.58
 401 GLN   ( 102-)  C       403 - GLU    104- ( C)         -5.55

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.

 220 HIS   (  73-)  B   -2.95
 172 GLN   (  25-)  B   -2.78
  68 HIS   (  73-)  A   -2.64

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

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.

 460 HOH   ( 212 )  A      O     19.03   28.70   25.03
 461 HOH   ( 221 )  B      O     14.87   77.57   44.36
 461 HOH   ( 227 )  B      O     -1.10   63.05   42.15
 462 HOH   ( 229 )  C      O     -0.29   43.61   33.50

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.

 460 HOH   ( 203 )  A      O
 460 HOH   ( 205 )  A      O
 461 HOH   ( 215 )  B      O
 461 HOH   ( 216 )  B      O
 461 HOH   ( 218 )  B      O
 461 HOH   ( 251 )  B      O
 461 HOH   ( 252 )  B      O
 462 HOH   ( 230 )  C      O
 462 HOH   ( 231 )  C      O
 462 HOH   ( 234 )  C      O
 462 HOH   ( 235 )  C      O
 462 HOH   ( 241 )  C      O
 462 HOH   ( 259 )  C      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.

  41 ASN   (  46-)  A
  73 HIS   (  78-)  A
 249 GLN   ( 102-)  B
 272 GLN   ( 125-)  B
 360 GLN   (  61-)  C
 377 HIS   (  78-)  C

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.

   1 ARG   (   6-)  A      NH2
   8 VAL   (  13-)  A      N
  16 GLN   (  21-)  A      N
  26 ASP   (  31-)  A      N
  27 ARG   (  32-)  A      N
  27 ARG   (  32-)  A      NE
  40 ASP   (  45-)  A      N
  42 GLN   (  47-)  A      N
  47 SER   (  52-)  A      N
  56 GLN   (  61-)  A      NE2
  58 LEU   (  63-)  A      N
  69 VAL   (  74-)  A      N
  77 ARG   (  82-)  A      NH1
  79 ALA   (  84-)  A      N
  81 SER   (  86-)  A      N
  82 TYR   (  87-)  A      N
  83 GLN   (  88-)  A      N
  92 ILE   (  97-)  A      N
  98 ARG   ( 103-)  A      NE
 133 ARG   ( 138-)  A      N
 141 GLU   ( 146-)  A      N
 147 PHE   ( 152-)  A      N
 172 GLN   (  25-)  B      N
 173 LEU   (  26-)  B      N
 174 GLN   (  27-)  B      N
And so on for a total of 78 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

  73 HIS   (  78-)  A      ND1
  97 GLN   ( 102-)  A      OE1
 144 GLN   ( 149-)  A      OE1
 194 GLN   (  47-)  B      OE1
 251 GLU   ( 104-)  B      OE1
 377 HIS   (  78-)  C      ND1
 424 GLN   ( 125-)  C      OE1
 445 GLU   ( 146-)  C      OE1

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.

  37 GLU   (  42-)  A   H-bonding suggests Gln
 200 GLU   (  53-)  B   H-bonding suggests Gln
 251 GLU   ( 104-)  B   H-bonding suggests Gln
 263 GLU   ( 116-)  B   H-bonding suggests Gln
 293 GLU   ( 146-)  B   H-bonding suggests Gln
 330 ASP   (  31-)  C   H-bonding suggests Asn
 403 GLU   ( 104-)  C   H-bonding suggests Gln
 415 GLU   ( 116-)  C   H-bonding suggests Gln
 429 ASP   ( 130-)  C   H-bonding suggests Asn; but Alt-Rotamer
 445 GLU   ( 146-)  C   H-bonding suggests Gln; 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 :  -1.532
  2nd generation packing quality :  -2.823
  Ramachandran plot appearance   :  -4.619 (bad)
  chi-1/chi-2 rotamer normality  :  -6.070 (bad)
  Backbone conformation          :  -0.760

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.673
  Bond angles                    :   0.991
  Omega angle restraints         :   0.349 (tight)
  Side chain planarity           :   0.684
  Improper dihedral distribution :   1.318
  B-factor distribution          :   2.300 (loose)
  Inside/Outside distribution    :   0.964

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.0
  2nd generation packing quality :  -1.7
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -4.0 (poor)
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.673
  Bond angles                    :   0.991
  Omega angle restraints         :   0.349 (tight)
  Side chain planarity           :   0.684
  Improper dihedral distribution :   1.318
  B-factor distribution          :   2.300 (loose)
  Inside/Outside distribution    :   0.964
==============

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.