WHAT IF Check report

This file was created 2012-01-25 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 pdb2hfw.ent

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

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

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) :293.000

Note: B-factor plot

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

Chain identifier: A

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.

 242 ARG   ( 246-)  A

Warning: Tyrosine convention problem

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

  48 TYR   (  51-)  A
  71 TYR   (  74-)  A
  85 TYR   (  88-)  A
 124 TYR   ( 128-)  A
 187 TYR   ( 191-)  A
 190 TYR   ( 194-)  A

Warning: Phenylalanine convention problem

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

  17 PHE   (  20-)  A
  90 PHE   (  93-)  A
 127 PHE   ( 131-)  A
 153 PHE   ( 157-)  A
 156 PHE   ( 160-)  A
 194 PHE   ( 198-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  34 ASP   (  37-)  A
  38 ASP   (  41-)  A
  49 ASP   (  52-)  A
  68 ASP   (  71-)  A
  69 ASP   (  72-)  A
  98 ASP   ( 101-)  A
  99 ASP   ( 102-)  A
 107 ASP   ( 110-)  A
 135 ASP   ( 139-)  A
 161 ASP   ( 165-)  A
 186 ASP   ( 190-)  A
 217 ASP   ( 221-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  23 GLU   (  26-)  A
 149 GLU   ( 153-)  A
 152 GLU   ( 156-)  A
 169 GLU   ( 173-)  A
 232 GLU   ( 236-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  22 GLY   (  25-)  A      C    O     1.14   -4.3
  27 PRO   (  30-)  A      C    O     1.15   -4.0
  28 ILE   (  31-)  A      CG1  CD1   1.34   -4.3
  30 LEU   (  33-)  A      CG   CD2   1.38   -4.2
  35 ILE   (  38-)  A      CG1  CD1   1.35   -4.3
  36 ARG   (  39-)  A      NE   CZ    1.27   -4.4
  37 HIS   (  40-)  A      C    O     1.15   -4.1
  41 LEU   (  44-)  A      CG   CD2   1.37   -4.6
  43 PRO   (  46-)  A      CB   CG    1.29   -4.1
  48 TYR   (  51-)  A      N    CA    1.38   -4.1
  66 VAL   (  69-)  A      CB   CG1   1.38   -4.1
  69 ASP   (  72-)  A      CB   CG    1.41   -4.2
  70 THR   (  73-)  A      CA   C     1.43   -4.7
  73 ARG   (  76-)  A      CB   CG    1.39   -4.2
  73 ARG   (  76-)  A      CG   CD    1.39   -4.2
  81 LEU   (  84-)  A      CG   CD2   1.37   -4.7
  87 LEU   (  90-)  A      CA   C     1.44   -4.1
  87 LEU   (  90-)  A      C    O     1.15   -4.2
  92 LEU   (  95-)  A      CG   CD2   1.37   -4.5
  98 ASP   ( 101-)  A      N    CA    1.37   -4.6
 111 TYR   ( 114-)  A      C    O     1.15   -4.0
 114 GLU   ( 117-)  A      CD   OE1   1.17   -4.3
 118 VAL   ( 121-)  A      C    O     1.15   -4.2
 119 HIS   ( 122-)  A      C    O     1.13   -5.1
 126 THR   ( 130-)  A      N    CA    1.55    5.0
And so on for a total of 57 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.898
RMS-deviation in bond distances: 0.047

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.020851 -0.000685 -0.001075|
 | -0.000685  1.018406 -0.000411|
 | -0.001075 -0.000411  1.017605|
Proposed new scale matrix

 |  0.023118  0.000016  0.000024|
 |  0.000013  0.019002  0.000008|
 |  0.000009  0.000003  0.008352|
With corresponding cell

    A    =  43.256  B   =  52.625  C    = 119.732
    Alpha=  90.046  Beta=  90.121  Gamma=  90.077

The CRYST1 cell dimensions

    A    =  42.373  B   =  51.674  C    = 117.659
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 3238.813
(Under-)estimated Z-score: 41.943

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.

  49 ASP   (  52-)  A      CB   CG   OD1 127.79    4.1
  55 THR   (  58-)  A      CG2  CB   OG1 100.83   -4.2
  78 GLY   (  81-)  A     -C    N    CA  128.38    4.6
  82 PRO   (  85-)  A     -C    N    CD  106.01   -4.6
  88 ARG   (  91-)  A      CG   CD   NE  118.94    5.0
  93 HIS   (  96-)  A      N    CA   C    99.62   -4.1
 104 HIS   ( 107-)  A      CG   ND1  CE1 109.75    4.1
 119 HIS   ( 122-)  A      CG   ND1  CE1 109.85    4.2
 126 THR   ( 130-)  A      N    CA   CB  124.08    8.0
 137 ILE   ( 141-)  A      C    CA   CB  118.67    4.5
 151 GLY   ( 155-)  A      N    CA   C   125.82    4.6
 173 THR   ( 177-)  A      CG2  CB   OG1 100.43   -4.4
 187 TYR   ( 191-)  A      CA   CB   CG  121.35    4.1
 189 THR   ( 193-)  A      CG2  CB   OG1 100.62   -4.3
 202 CYS   ( 206-)  A      CA   CB   SG  124.00    4.2
 249 ASN   ( 253-)  A      N    CA   C   122.99    4.2
 249 ASN   ( 253-)  A      N    CA   CB  101.98   -5.0

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.

  23 GLU   (  26-)  A
  34 ASP   (  37-)  A
  38 ASP   (  41-)  A
  49 ASP   (  52-)  A
  68 ASP   (  71-)  A
  69 ASP   (  72-)  A
  98 ASP   ( 101-)  A
  99 ASP   ( 102-)  A
 107 ASP   ( 110-)  A
 135 ASP   ( 139-)  A
 149 GLU   ( 153-)  A
 152 GLU   ( 156-)  A
 161 ASP   ( 165-)  A
 169 GLU   ( 173-)  A
 186 ASP   ( 190-)  A
 217 ASP   ( 221-)  A
 232 GLU   ( 236-)  A
 242 ARG   ( 246-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  10 PRO   (  13-)  A      N     -8.0   -28.80    -2.48
  18 PRO   (  21-)  A      N     -7.4   -26.67    -2.48
  52 SER   (  55-)  A      CA    -6.1    22.94    34.32
  82 PRO   (  85-)  A      N     -9.4   -33.39    -2.48
  84 PRO   (  87-)  A      N     -6.4   -23.53    -2.48
 149 GLU   ( 153-)  A      CA    -8.2    20.49    33.96
 171 PRO   ( 175-)  A      N     -8.7   -31.13    -2.48
 234 PRO   ( 238-)  A      N      9.6    29.08    -2.48
 246 PRO   ( 250-)  A      N     -6.7   -24.44    -2.48
The average deviation= 1.806

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.

 151 GLY   ( 155-)  A    7.21
 178 SER   ( 182-)  A    6.50
  11 ASP   (  14-)  A    6.17
  52 SER   (  55-)  A    5.72
 203 ILE   ( 207-)  A    5.08
 161 ASP   ( 165-)  A    4.95
  47 SER   (  50-)  A    4.83
 192 GLY   ( 196-)  A    4.73
 118 VAL   ( 121-)  A    4.62
  45 SER   (  48-)  A    4.43
  93 HIS   (  96-)  A    4.32
 191 GLN   ( 195-)  A    4.29
  77 ARG   (  80-)  A    4.23
 179 SER   ( 183-)  A    4.15

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 : 2.023

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 : -3.612

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.

  82 PRO   (  85-)  A    -3.0
 198 PRO   ( 202-)  A    -2.8
  27 PRO   (  30-)  A    -2.8
  91 HIS   (  94-)  A    -2.8
  77 ARG   (  80-)  A    -2.7
 185 ARG   ( 189-)  A    -2.7
  18 PRO   (  21-)  A    -2.6
  62 THR   (  65-)  A    -2.6
 182 PRO   ( 186-)  A    -2.6
 163 ILE   ( 167-)  A    -2.5
 248 ASN   ( 252-)  A    -2.4
 214 VAL   ( 218-)  A    -2.4
 243 PRO   ( 247-)  A    -2.3
 145 LYS   ( 149-)  A    -2.3
   6 SER   (   9-)  A    -2.2
  57 LEU   (  60-)  A    -2.2
   2 TRP   (   5-)  A    -2.2
  36 ARG   (  39-)  A    -2.2
 172 PHE   ( 176-)  A    -2.1
  92 LEU   (  95-)  A    -2.1
 177 PRO   ( 181-)  A    -2.1
  33 LYS   (  36-)  A    -2.1
 168 LYS   ( 172-)  A    -2.1

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.

   2 TRP   (   5-)  A  omega poor
   5 ALA   (   8-)  A  Poor phi/psi
   6 SER   (   9-)  A  Poor phi/psi
   7 HIS   (  10-)  A  Poor phi/psi
   9 GLY   (  12-)  A  Poor phi/psi
  10 PRO   (  13-)  A  omega poor
  11 ASP   (  14-)  A  Poor phi/psi
  12 HIS   (  15-)  A  omega poor
  16 LEU   (  19-)  A  Poor phi/psi
  18 PRO   (  21-)  A  omega poor
  26 SER   (  29-)  A  PRO omega poor
  28 ILE   (  31-)  A  omega poor
  31 HIS   (  34-)  A  omega poor
  46 VAL   (  49-)  A  omega poor
  51 GLY   (  54-)  A  omega poor
  57 LEU   (  60-)  A  omega poor
  64 ASN   (  67-)  A  omega poor
  73 ARG   (  76-)  A  Poor phi/psi
  74 SER   (  77-)  A  omega poor
  75 MET   (  78-)  A  omega poor
  77 ARG   (  80-)  A  omega poor
  81 LEU   (  84-)  A  PRO omega poor
  82 PRO   (  85-)  A  omega poor
  84 PRO   (  87-)  A  omega poor
  91 HIS   (  94-)  A  Poor phi/psi
And so on for a total of 59 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 : -4.766

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!

   4 TYR   (   7-)  A      0
   5 ALA   (   8-)  A      0
   6 SER   (   9-)  A      0
   7 HIS   (  10-)  A      0
  12 HIS   (  15-)  A      0
  13 TRP   (  16-)  A      0
  16 LEU   (  19-)  A      0
  21 LYS   (  24-)  A      0
  24 ASN   (  27-)  A      0
  25 GLN   (  28-)  A      0
  26 SER   (  29-)  A      0
  53 ALA   (  56-)  A      0
  54 LYS   (  57-)  A      0
  55 THR   (  58-)  A      0
  59 ASN   (  62-)  A      0
  61 HIS   (  64-)  A      0
  62 THR   (  65-)  A      0
  69 ASP   (  72-)  A      0
  70 THR   (  73-)  A      0
  71 TYR   (  74-)  A      0
  72 ASP   (  75-)  A      0
  73 ARG   (  76-)  A      0
  74 SER   (  77-)  A      0
  77 ARG   (  80-)  A      0
  80 PRO   (  83-)  A      0
And so on for a total of 110 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 11.898

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].

  10 PRO   (  13-)  A   116.3 envelop C-beta (108 degrees)
  39 PRO   (  42-)  A  -121.2 half-chair C-delta/C-gamma (-126 degrees)
  80 PRO   (  83-)  A   -63.1 envelop C-beta (-72 degrees)
  82 PRO   (  85-)  A  -133.3 half-chair C-delta/C-gamma (-126 degrees)
  84 PRO   (  87-)  A  -116.7 envelop C-gamma (-108 degrees)
 171 PRO   ( 175-)  A   106.8 envelop C-beta (108 degrees)
 177 PRO   ( 181-)  A    19.2 half-chair N/C-delta (18 degrees)
 233 PRO   ( 237-)  A   102.2 envelop C-beta (108 degrees)
 246 PRO   ( 250-)  A  -138.0 envelop C-delta (-144 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.

   2 TRP   (   5-)  A      CH2 <->   61 HIS   (  64-)  A      CD2    0.86    2.34  INTRA BF
  91 HIS   (  94-)  A      CE1 <->  258  ZN   ( 262-)  A     ZN      0.57    2.63  INTRA BL
   2 TRP   (   5-)  A      CZ2 <->   61 HIS   (  64-)  A      CD2    0.55    2.65  INTRA BF
  32 THR   (  35-)  A      OG1 <->  107 ASP   ( 110-)  A      OD2    0.54    1.86  INTRA BF
 162 LYS   ( 166-)  A      NZ  <->  259 HOH   ( 328 )  A      O      0.47    2.23  INTRA BF
 146 ILE   ( 150-)  A      CG2 <->  147 GLY   ( 151-)  A      N      0.46    2.54  INTRA BF
 234 PRO   ( 238-)  A      O   <->  235 VAL   ( 239-)  A      CG2    0.46    2.24  INTRA BF
   3 GLY   (   6-)  A      CA  <->    8 ASN   (  11-)  A      ND2    0.44    2.66  INTRA BF
  19 ASN   (  22-)  A      O   <->   21 LYS   (  24-)  A      N      0.40    2.30  INTRA BF
  81 LEU   (  84-)  A      CA  <->   82 PRO   (  85-)  A      CD     0.40    2.40  INTRA BL
 163 ILE   ( 167-)  A      O   <->  165 THR   ( 169-)  A      N      0.39    2.31  INTRA
  12 HIS   (  15-)  A      ND1 <->   15 GLU   (  18-)  A      OE2    0.35    2.35  INTRA BF
 165 THR   ( 169-)  A      CG2 <->  166 LYS   ( 170-)  A      O      0.32    2.38  INTRA BF
 134 ARG   ( 138-)  A      NH2 <->  191 GLN   ( 195-)  A      OE1    0.32    2.38  INTRA
 162 LYS   ( 166-)  A      O   <->  168 LYS   ( 172-)  A      CD     0.31    2.49  INTRA BF
   2 TRP   (   5-)  A      CZ3 <->   61 HIS   (  64-)  A      CD2    0.31    2.89  INTRA BF
 224 SER   ( 228-)  A      O   <->  225 LEU   ( 229-)  A      C      0.29    2.31  INTRA BF
 194 PHE   ( 198-)  A      CE2 <->  202 CYS   ( 206-)  A      SG     0.28    3.12  INTRA BL
  12 HIS   (  15-)  A      ND1 <->   15 GLU   (  18-)  A      CD     0.28    2.82  INTRA BF
 215 SER   ( 219-)  A      OG  <->  218 GLN   ( 222-)  A      N      0.27    2.43  INTRA BF
   2 TRP   (   5-)  A      CZ2 <->   61 HIS   (  64-)  A      NE2    0.27    2.83  INTRA BF
  19 ASN   (  22-)  A      C   <->   21 LYS   (  24-)  A      N      0.26    2.64  INTRA BF
 125 ASN   ( 129-)  A      C   <->  126 THR   ( 130-)  A      CG2    0.26    2.84  INTRA BL
 224 SER   ( 228-)  A      C   <->  225 LEU   ( 229-)  A      O      0.26    2.34  INTRA BF
  32 THR   (  35-)  A      O   <->  259 HOH   ( 403 )  A      O      0.24    2.16  INTRA BF
And so on for a total of 90 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

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.

   7 HIS   (  10-)  A      -6.03
 134 ARG   ( 138-)  A      -5.89
  71 TYR   (  74-)  A      -5.64

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: 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

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.

  31 HIS   (  34-)  A
 248 ASN   ( 252-)  A
 249 ASN   ( 253-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   3 GLY   (   6-)  A      N
   9 GLY   (  12-)  A      N
  14 HIS   (  17-)  A      N
  20 ALA   (  23-)  A      N
  28 ILE   (  31-)  A      N
  29 GLU   (  32-)  A      N
  35 ILE   (  38-)  A      N
  42 GLN   (  45-)  A      N
  46 VAL   (  49-)  A      N
  95 GLY   (  98-)  A      N
  97 SER   ( 100-)  A      N
 100 HIS   ( 103-)  A      ND1
 101 GLY   ( 104-)  A      N
 126 THR   ( 130-)  A      N
 132 LYS   ( 136-)  A      N
 156 PHE   ( 160-)  A      N
 165 THR   ( 169-)  A      N
 228 SER   ( 232-)  A      N
 231 ASN   ( 235-)  A      N
 232 GLU   ( 236-)  A      N
 241 TRP   ( 245-)  A      N
 242 ARG   ( 246-)  A      NE
 242 ARG   ( 246-)  A      NH2
 256 PHE   ( 260-)  A      N
Only metal coordination for   93 HIS  (  96-) A      NE2

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.

  15 GLU   (  18-)  A      OE1
  23 GLU   (  26-)  A      OE2
  37 HIS   (  40-)  A      ND1
  64 ASN   (  67-)  A      OD1
  89 GLN   (  92-)  A      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.

  34 ASP   (  37-)  A   H-bonding suggests Asn

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 :  -1.415
  2nd generation packing quality :  -2.202
  Ramachandran plot appearance   :  -3.612 (poor)
  chi-1/chi-2 rotamer normality  :  -4.766 (bad)
  Backbone conformation          :  -1.074

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.898 (loose)
  Bond angles                    :   1.132
  Omega angle restraints         :   2.163 (loose)
  Side chain planarity           :   0.787
  Improper dihedral distribution :   1.583 (loose)
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   0.957

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.898 (loose)
  Bond angles                    :   1.132
  Omega angle restraints         :   2.163 (loose)
  Side chain planarity           :   0.787
  Improper dihedral distribution :   1.583 (loose)
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   0.957
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.