WHAT IF Check report

This file was created 2012-01-31 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 pdb2zpx.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    =  49.586  B   = 111.331  C    =  75.382
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  49.586  B   = 111.331  C    =  75.382
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  49.586  B   =  75.382  C    = 111.331
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  49.586  B   =  75.382  C    = 111.331
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

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 : 1.118
CA-only RMS fit for the two chains : 0.447

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 : 1.241
CA-only RMS fit for the two chains : 0.724

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 : 1.144
CA-only RMS fit for the two chains : 0.716

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 PRO   (   8-)  A    High
   2 SER   (   9-)  A    High
   3 ASP   (  10-)  A    High
   4 MET   (  11-)  A    High
  14 GLN   (  21-)  A    High
  16 GLU   (  23-)  A    High
  18 GLN   (  25-)  A    High
  25 ARG   (  32-)  A    High
  35 GLU   (  42-)  A    High
  37 ARG   (  44-)  A    High
  60 GLN   (  67-)  A    High
  61 GLY   (  68-)  A    High
  62 CYS   (  69-)  A    High
  63 PRO   (  70-)  A    High
  64 SER   (  71-)  A    High
  65 THR   (  72-)  A    High
  66 HIS   (  73-)  A    High
  67 VAL   (  74-)  A    High
  82 ARG   (  89-)  A    High
  91 ARG   (  98-)  A    High
  94 CYS   ( 101-)  A    High
  96 ALA   ( 111-)  A    High
  97 ASN   ( 112-)  A    High
 116 ARG   ( 131-)  A    High
 131 GLU   ( 146-)  A    High
And so on for a total of 72 lines.

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: Tyrosine convention problem

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

 104 TYR   ( 119-)  A
 126 TYR   ( 141-)  A
 242 TYR   ( 115-)  B
 246 TYR   ( 119-)  B
 268 TYR   ( 141-)  B
 388 TYR   ( 119-)  C

Warning: Phenylalanine convention problem

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

 413 PHE   ( 144-)  C

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.

 145 ASP   (  10-)  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.

  46 GLU   (  53-)  A
 112 GLU   ( 127-)  A
 188 GLU   (  53-)  B
 254 GLU   ( 127-)  B
 330 GLU   (  53-)  C
 396 GLU   ( 127-)  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.

 166 ARG   (  31-)  B      CA   CB    1.42   -5.5
 167 ARG   (  32-)  B      N    CA    1.27   -9.8
 167 ARG   (  32-)  B      C    O     1.15   -4.1
 168 ALA   (  33-)  B      CA   C     1.43   -4.6
 169 ASN   (  34-)  B      N    CA    1.38   -4.1
 310 ALA   (  33-)  C      N    CA    1.57    5.8
 310 ALA   (  33-)  C      C    O     1.34    5.3
 311 ASN   (  34-)  C      CB   CG    1.26  -10.1

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 HIS   (  15-)  A      CG   ND1  CE1 109.94    4.3
 145 ASP   (  10-)  B      N    CA   C   122.51    4.0
 150 HIS   (  15-)  B      CG   ND1  CE1 109.86    4.3
 166 ARG   (  31-)  B     -C    N    CA  111.29   -5.8
 166 ARG   (  31-)  B      N    CA   CB  119.12    5.1
 167 ARG   (  32-)  B     -O   -C    N   130.66    4.8
 167 ARG   (  32-)  B     -CA  -C    N   102.56   -6.8
 167 ARG   (  32-)  B      N    CA   C   126.79    5.6
 168 ALA   (  33-)  B     -CA  -C    N   107.81   -4.2
 168 ALA   (  33-)  B     -C    N    CA   98.10  -13.1
 168 ALA   (  33-)  B      N    CA   C   152.57   14.8
 168 ALA   (  33-)  B      CA   C    O   130.12    5.5
 168 ALA   (  33-)  B      N    CA   CB  100.05   -6.9
 169 ASN   (  34-)  B     -O   -C    N   133.38    6.5
 169 ASN   (  34-)  B     -CA  -C    N    93.83  -11.2
 169 ASN   (  34-)  B      N    CA   CB  126.20    9.2
 169 ASN   (  34-)  B      C    CA   CB  125.53    8.1
 169 ASN   (  34-)  B      CA   CB   CG  117.27    4.7
 309 ARG   (  32-)  C     -C    N    CA  100.73  -11.6
 309 ARG   (  32-)  C      N    CA   CB   99.43   -6.5
 309 ARG   (  32-)  C      CA   CB   CG  122.48    4.2
 310 ALA   (  33-)  C     -C    N    CA  104.83   -9.4
 311 ASN   (  34-)  C     -C    N    CA  101.69  -11.1
 311 ASN   (  34-)  C      N    CA   C    89.10   -7.9
 311 ASN   (  34-)  C      N    CA   CB  141.94   18.5
 311 ASN   (  34-)  C      C    CA   CB  101.09   -4.7
 311 ASN   (  34-)  C      CA   CB   CG  118.99    6.4
 312 ALA   (  35-)  C      N    CA   C    79.02  -11.5

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.

  46 GLU   (  53-)  A
 112 GLU   ( 127-)  A
 145 ASP   (  10-)  B
 188 GLU   (  53-)  B
 254 GLU   ( 127-)  B
 330 GLU   (  53-)  C
 396 GLU   ( 127-)  C

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.

 167 ARG   (  32-)  B      C      7.2    11.05     0.13
 168 ALA   (  33-)  B      CA   -14.6    15.60    34.09
 168 ALA   (  33-)  B      C      8.1    12.46     0.08
 169 ASN   (  34-)  B      CA   -17.2     0.97    33.59
 309 ARG   (  32-)  C      CA     6.1    43.83    33.91
 310 ALA   (  33-)  C      C    -11.3   -17.15     0.08
The average deviation= 0.968

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.

 168 ALA   (  33-)  B   17.09
 312 ALA   (  35-)  C   13.43
 311 ASN   (  34-)  C    7.41
 167 ARG   (  32-)  B    5.80
 166 ARG   (  31-)  B    4.13

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 : 1.584

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.

 169 ASN   (  34-)  B    5.62

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.722

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.

 413 PHE   ( 144-)  C    -3.6
 349 THR   (  72-)  C    -3.0
 207 THR   (  72-)  B    -3.0
  65 THR   (  72-)  A    -3.0
 129 PHE   ( 144-)  A    -2.9
 140 ILE   ( 155-)  A    -2.6
 424 ILE   ( 155-)  C    -2.6
 282 ILE   ( 155-)  B    -2.5
 423 ILE   ( 154-)  C    -2.5
 281 ILE   ( 154-)  B    -2.5
 139 ILE   ( 154-)  A    -2.5
 364 ILE   (  87-)  C    -2.4
 411 LEU   ( 142-)  C    -2.4
 271 PHE   ( 144-)  B    -2.3
 366 ARG   (  89-)  C    -2.2
 415 GLU   ( 146-)  C    -2.2
  78 PRO   (  85-)  A    -2.2
  44 PRO   (  51-)  A    -2.2
 186 PRO   (  51-)  B    -2.2
 328 PRO   (  51-)  C    -2.2
 148 VAL   (  13-)  B    -2.2
 290 VAL   (  13-)  C    -2.2
  64 SER   (  71-)  A    -2.2
   6 VAL   (  13-)  A    -2.2
 206 SER   (  71-)  B    -2.2
 348 SER   (  71-)  C    -2.2
 226 VAL   (  91-)  B    -2.1
 247 LEU   ( 120-)  B    -2.1
 389 LEU   ( 120-)  C    -2.1
 105 LEU   ( 120-)  A    -2.1
  16 GLU   (  23-)  A    -2.1
 300 GLU   (  23-)  C    -2.1
  75 ARG   (  82-)  A    -2.1
 151 VAL   (  16-)  B    -2.1
 311 ASN   (  34-)  C    -2.0
 308 ARG   (  31-)  C    -2.0
   9 VAL   (  16-)  A    -2.0
 158 GLU   (  23-)  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.

  26 ALA   (  33-)  A  Poor phi/psi
  30 LEU   (  37-)  A  Poor phi/psi
  32 ASN   (  39-)  A  Poor phi/psi
  38 ASP   (  45-)  A  Poor phi/psi
  39 ASN   (  46-)  A  Poor phi/psi
  44 PRO   (  51-)  A  Poor phi/psi
  53 SER   (  60-)  A  Poor phi/psi
  64 SER   (  71-)  A  Poor phi/psi
  65 THR   (  72-)  A  Poor phi/psi
  79 ALA   (  86-)  A  Poor phi/psi
  97 ASN   ( 112-)  A  Poor phi/psi
 167 ARG   (  32-)  B  Poor phi/psi, omega poor
 168 ALA   (  33-)  B  omega poor
 169 ASN   (  34-)  B  Poor phi/psi
 172 LEU   (  37-)  B  Poor phi/psi
 174 ASN   (  39-)  B  Poor phi/psi
 180 ASP   (  45-)  B  Poor phi/psi
 181 ASN   (  46-)  B  Poor phi/psi
 206 SER   (  71-)  B  Poor phi/psi
 207 THR   (  72-)  B  Poor phi/psi
 221 ALA   (  86-)  B  Poor phi/psi
 286 SER   (   9-)  C  Poor phi/psi
 287 ASP   (  10-)  C  Poor phi/psi
 308 ARG   (  31-)  C  Poor phi/psi
 309 ARG   (  32-)  C  omega poor
 310 ALA   (  33-)  C  omega poor
 314 LEU   (  37-)  C  Poor phi/psi
 316 ASN   (  39-)  C  Poor phi/psi
 322 ASP   (  45-)  C  Poor phi/psi
 323 ASN   (  46-)  C  Poor phi/psi
 337 SER   (  60-)  C  Poor phi/psi
 348 SER   (  71-)  C  Poor phi/psi
 349 THR   (  72-)  C  Poor phi/psi
 378 CYS   ( 101-)  C  Poor phi/psi
 413 PHE   ( 144-)  C  Poor phi/psi
 414 ALA   ( 145-)  C  Poor phi/psi
 415 GLU   ( 146-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.150

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.150

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   (  10-)  A      0
   5 PRO   (  12-)  A      0
   8 HIS   (  15-)  A      0
  15 ALA   (  22-)  A      0
  16 GLU   (  23-)  A      0
  23 ASN   (  30-)  A      0
  24 ARG   (  31-)  A      0
  25 ARG   (  32-)  A      0
  26 ALA   (  33-)  A      0
  27 ASN   (  34-)  A      0
  29 LEU   (  36-)  A      0
  30 LEU   (  37-)  A      0
  31 ALA   (  38-)  A      0
  32 ASN   (  39-)  A      0
  37 ARG   (  44-)  A      0
  39 ASN   (  46-)  A      0
  44 PRO   (  51-)  A      0
  46 GLU   (  53-)  A      0
  48 LEU   (  55-)  A      0
  52 TYR   (  59-)  A      0
  60 GLN   (  67-)  A      0
  62 CYS   (  69-)  A      0
  64 SER   (  71-)  A      0
  65 THR   (  72-)  A      0
  66 HIS   (  73-)  A      0
And so on for a total of 219 lines.

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...

 287 ASP   (  10-)  C   1.80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 408 PRO   ( 139-)  C    0.45 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.

 252 GLN   ( 125-)  B      CB  <->  311 ASN   (  34-)  C      ND2    0.72    2.38  INTRA BL
 169 ASN   (  34-)  B      CB  <->  430 HOH   ( 162 )  A      O      0.54    2.26  INTRA BF
 311 ASN   (  34-)  C      CB  <->  313 LEU   (  36-)  C      CD2    0.44    2.76  INTRA BL
 165 ASN   (  30-)  B      OD1 <->  172 LEU   (  37-)  B      CD2    0.43    2.37  INTRA BF
 167 ARG   (  32-)  B      CB  <->  168 ALA   (  33-)  B      N      0.35    2.35  INTRA BF
  23 ASN   (  30-)  A      O   <->   25 ARG   (  32-)  A      N      0.30    2.40  INTRA BF
  91 ARG   (  98-)  A      CZ  <->  233 ARG   (  98-)  B      NH2    0.29    2.81  INTRA BF
 252 GLN   ( 125-)  B      CA  <->  311 ASN   (  34-)  C      ND2    0.27    2.83  INTRA BL
 167 ARG   (  32-)  B      C   <->  168 ALA   (  33-)  B      CA     0.27    2.03  INTRA BF
  91 ARG   (  98-)  A      NH2 <->  375 ARG   (  98-)  C      CZ     0.26    2.84  INTRA BF
 265 ARG   ( 138-)  B      NH2 <->  268 TYR   ( 141-)  B      OH     0.25    2.45  INTRA BF
 252 GLN   ( 125-)  B      N   <->  311 ASN   (  34-)  C      CG     0.23    2.87  INTRA BL
 157 ALA   (  22-)  B      O   <->  159 GLY   (  24-)  B      N      0.22    2.48  INTRA BF
 299 ALA   (  22-)  C      O   <->  301 GLY   (  24-)  C      N      0.21    2.49  INTRA BF
 252 GLN   ( 125-)  B      N   <->  311 ASN   (  34-)  C      OD1    0.21    2.49  INTRA BL
 308 ARG   (  31-)  C      C   <->  309 ARG   (  32-)  C      CA     0.20    2.10  INTRA BF
 308 ARG   (  31-)  C      O   <->  309 ARG   (  32-)  C      CA     0.20    2.20  INTRA BF
 287 ASP   (  10-)  C      CB  <->  288 MET   (  11-)  C      N      0.20    2.50  INTRA BF
 127 LEU   ( 142-)  A      CD2 <->  128 ASP   ( 143-)  A      N      0.20    2.80  INTRA BL
 410 TYR   ( 141-)  C      N   <->  411 LEU   ( 142-)  C      N      0.19    2.41  INTRA BF
 168 ALA   (  33-)  B      O   <->  169 ASN   (  34-)  B      ND2    0.19    2.41  INTRA BF
 168 ALA   (  33-)  B      CA  <->  169 ASN   (  34-)  B      N      0.19    2.01  INTRA BF
 150 HIS   (  15-)  B      O   <->  170 ALA   (  35-)  B      CB     0.19    2.61  INTRA BL
 270 ASP   ( 143-)  B      OD1 <->  276 GLN   ( 149-)  B      NE2    0.19    2.51  INTRA BL
 233 ARG   (  98-)  B      CZ  <->  375 ARG   (  98-)  C      NH2    0.18    2.92  INTRA BF
And so on for a total of 124 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.

  24 ARG   (  31-)  A      -7.52
 344 GLN   (  67-)  C      -7.32
  60 GLN   (  67-)  A      -7.07
 167 ARG   (  32-)  B      -6.66
 202 GLN   (  67-)  B      -6.29
 300 GLU   (  23-)  C      -5.18
 166 ARG   (  31-)  B      -5.13

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.

 311 ASN   (  34-)  C   -2.78

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: 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.

  71 HIS   (  78-)  A
 213 HIS   (  78-)  B
 316 ASN   (  39-)  C
 355 HIS   (  78-)  C
 394 GLN   ( 125-)  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.

   3 ASP   (  10-)  A      N
  14 GLN   (  21-)  A      NE2
  20 GLN   (  27-)  A      N
  56 LEU   (  63-)  A      N
  64 SER   (  71-)  A      N
  90 ILE   (  97-)  A      N
  94 CYS   ( 101-)  A      N
  99 TRP   ( 114-)  A      NE1
 110 GLN   ( 125-)  A      NE2
 127 LEU   ( 142-)  A      N
 131 GLU   ( 146-)  A      N
 134 GLN   ( 149-)  A      NE2
 158 GLU   (  23-)  B      N
 161 LEU   (  26-)  B      N
 162 GLN   (  27-)  B      N
 167 ARG   (  32-)  B      N
 198 LEU   (  63-)  B      N
 206 SER   (  71-)  B      N
 209 VAL   (  74-)  B      N
 212 THR   (  77-)  B      OG1
 217 ARG   (  82-)  B      NE
 219 THR   (  84-)  B      N
 222 ILE   (  87-)  B      N
 224 ARG   (  89-)  B      N
 232 ILE   (  97-)  B      N
And so on for a total of 51 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.

 254 GLU   ( 127-)  B      OE1
 257 ASP   ( 130-)  B      OD1
 311 ASN   (  34-)  C      OD1
 381 ASN   ( 112-)  C      OD1
 399 ASP   ( 130-)  C      OD1

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.

   3 ASP   (  10-)  A   H-bonding suggests Asn; but Alt-Rotamer
 131 GLU   ( 146-)  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 :  -0.581
  2nd generation packing quality :  -1.750
  Ramachandran plot appearance   :  -3.722 (poor)
  chi-1/chi-2 rotamer normality  :  -3.150 (poor)
  Backbone conformation          :   0.277

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.534 (tight)
  Bond angles                    :   0.791
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.613 (tight)
  Improper dihedral distribution :   1.133
  B-factor distribution          :   0.438
  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 : 2.83


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.534 (tight)
  Bond angles                    :   0.791
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.613 (tight)
  Improper dihedral distribution :   1.133
  B-factor distribution          :   0.438
  Inside/Outside distribution    :   0.964
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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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.