WHAT IF Check report

This file was created 2014-03-19 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 pdb4jnl.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 247 PZH   ( 301-)  U  -         Fragmented
 248 SO4   ( 302-)  U  -         OK

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: U

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.

  23 ARG   (  37-)  U    High
  24 GLY   (  37-)  U    High
  51 TYR   (  60-)  U    High
  85 LYS   (  92-)  U    High
  90 ASP   (  97-)  U    High
  91 THR   (  97-)  U    High
 107 GLU   ( 110-)  U    High
 128 ASP   ( 129-)  U    High
 130 GLN   ( 131-)  U    High
 131 PHE   ( 132-)  U    High
 165 ARG   ( 166-)  U    High
 171 HIS   ( 170-)  U    High
 176 GLU   ( 175-)  U    High
 207 GLN   ( 204-)  U    High
 209 ARG   ( 206-)  U    High
 220 ARG   ( 217-)  U    High
 246 LYS   ( 243-)  U    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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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: U

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.

  21 ARG   (  36-)  U

Warning: Tyrosine convention problem

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

  51 TYR   (  60-)  U

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.

   5 GLU   (  20-)  U
  77 GLU   (  84-)  U
  79 GLU   (  86-)  U
 143 GLU   ( 144-)  U
 176 GLU   ( 175-)  U

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.

  46 HIS   (  57-)  U      CG   CD2   1.42    5.7
  52 PRO   (  60-)  U      CD   N     1.54    4.5
  55 GLU   (  62-)  U      N   -C     1.45    6.1
 170 PRO   ( 170-)  U      CD   N     1.55    5.3
 187 PRO   ( 185-)  U      CD   N     1.54    5.0
 189 TRP   ( 186-)  U      NE1  CE2   1.32   -4.3
 226 ASP   ( 223-)  U      N   -C     1.49    8.1

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

 |  1.000241  0.002204 -0.000905|
 |  0.002204  0.996895 -0.000972|
 | -0.000905 -0.000972  0.999567|
Proposed new scale matrix

 |  0.008213  0.004746  0.000012|
 | -0.000021  0.009528  0.000009|
 |  0.000021  0.000023  0.023700|
With corresponding cell

    A    = 121.610  B   = 121.067  C    =  42.194
    Alpha=  90.045  Beta=  90.104  Gamma= 119.895

The CRYST1 cell dimensions

    A    = 121.575  B   = 121.575  C    =  42.212
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 30.769
(Under-)estimated Z-score: 4.088

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.

  52 PRO   (  60-)  U      CD   N    CA  105.34   -4.8
  55 GLU   (  62-)  U     -O   -C    N   116.21   -4.2
  55 GLU   (  62-)  U     -C    N    CA  129.47    4.3
  93 ALA   (  98-)  U      C    CA   CB  130.57   13.4
  94 HIS   (  99-)  U     -C    N    CA  130.41    4.8
  94 HIS   (  99-)  U      CG   ND1  CE1 109.65    4.1
 170 PRO   ( 170-)  U      CD   N    CA  106.28   -4.1
 172 TYR   ( 171-)  U      N    CA   C   129.89    6.7
 172 TYR   ( 171-)  U      C    CA   CB  100.07   -5.3
 187 PRO   ( 185-)  U      CD   N    CA  105.83   -4.4
 226 ASP   ( 223-)  U     -O   -C    N   144.39   13.4
 226 ASP   ( 223-)  U     -CA  -C    N    98.31   -8.9
 226 ASP   ( 223-)  U     -C    N    CA  104.43   -9.6

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.

   5 GLU   (  20-)  U
  21 ARG   (  36-)  U
  77 GLU   (  84-)  U
  79 GLU   (  86-)  U
 143 GLU   ( 144-)  U
 176 GLU   ( 175-)  U

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.

  93 ALA   (  98-)  U      CA   -10.8    20.40    34.09
The average deviation= 1.333

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.

 172 TYR   ( 171-)  U    7.11

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 157 THR   ( 158-)  U    -2.7
  52 PRO   (  60-)  U    -2.4
   9 ILE   (  24-)  U    -2.4
 206 LEU   ( 203-)  U    -2.3
   7 THR   (  22-)  U    -2.3
 126 TYR   ( 127-)  U    -2.2
 104 ARG   ( 109-)  U    -2.2
  12 GLN   (  27-)  U    -2.1
 218 TRP   ( 215-)  U    -2.1
 245 THR   ( 242-)  U    -2.1
 125 MET   ( 126-)  U    -2.1
  45 THR   (  56-)  U    -2.1
 120 ILE   ( 121-)  U    -2.1
 220 ARG   ( 217-)  U    -2.0
  92 LEU   (  97-)  U    -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.

  13 PRO   (  28-)  U  omega poor
  43 SER   (  54-)  U  Poor phi/psi
  90 ASP   (  97-)  U  Poor phi/psi, omega poor
  93 ALA   (  98-)  U  omega poor
 110 CYS   ( 111-)  U  Poor phi/psi
 126 TYR   ( 127-)  U  Poor phi/psi
 172 TYR   ( 171-)  U  omega poor
 173 TYR   ( 172-)  U  Poor phi/psi
 181 MET   ( 180-)  U  omega poor
 189 TRP   ( 186-)  U  Poor phi/psi
 202 LEU   ( 199-)  U  omega poor
 223 ALA   ( 221-)  U  Poor phi/psi
 226 ASP   ( 223-)  U  Poor phi/psi
 230 VAL   ( 227-)  U  omega poor
 chi-1/chi-2 correlation Z-score : -3.353

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 : -3.353

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!

   5 GLU   (  20-)  U      0
   6 PHE   (  21-)  U      0
  13 PRO   (  28-)  U      0
  14 TRP   (  29-)  U      0
  23 ARG   (  37-)  U      0
  30 VAL   (  41-)  U      0
  31 CYS   (  42-)  U      0
  39 CYS   (  50-)  U      0
  51 TYR   (  60-)  U      0
  52 PRO   (  60-)  U      0
  56 ASP   (  63-)  U      0
  61 LEU   (  68-)  U      0
  63 ARG   (  70-)  U      0
  67 ASN   (  74-)  U      0
  68 SER   (  75-)  U      0
  71 GLN   (  78-)  U      0
  87 TYR   (  94-)  U      0
  90 ASP   (  97-)  U      0
  91 THR   (  97-)  U      0
  92 LEU   (  97-)  U      0
  93 ALA   (  98-)  U      0
  95 HIS   ( 100-)  U      0
  97 ASP   ( 102-)  U      0
  98 ILE   ( 103-)  U      0
 104 ARG   ( 109-)  U      0
And so on for a total of 112 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 : 7.039

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]

  13 PRO   (  28-)  U    0.45 HIGH
 123 PRO   ( 124-)  U    0.18 LOW
 187 PRO   ( 185-)  U    0.46 HIGH
 228 PRO   ( 225-)  U    0.19 LOW

Warning: Unusual PRO puckering phases

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

  52 PRO   (  60-)  U    41.2 envelop C-delta (36 degrees)
 113 PRO   ( 114-)  U   127.3 half-chair C-beta/C-alpha (126 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.

  21 ARG   (  36-)  U      NH1 <->  249 HOH   ( 438 )  U      O      0.76    1.94  INTRA BF
  79 GLU   (  86-)  U      CG  <->  104 ARG   ( 109-)  U      NH1    0.66    2.44  INTRA BF
  79 GLU   (  86-)  U      CD  <->  104 ARG   ( 109-)  U      NH1    0.39    2.71  INTRA BF
  10 GLU   (  25-)  U      OE2 <->  115 ARG   ( 116-)  U      NH1    0.37    2.33  INTRA BF
 196 GLY   ( 193-)  U      N   <->  248 SO4   ( 302-)  U      O3     0.36    2.34  INTRA BF
 225 LYS   ( 223-)  U      C   <->  227 LYS   ( 224-)  U      N      0.31    2.59  INTRA BF
  67 ASN   (  74-)  U      N   <->  152 GLU   ( 153-)  U      OE2    0.27    2.43  INTRA BF
  65 ARG   (  72-)  U      NH2 <->  152 GLU   ( 153-)  U      CG     0.24    2.86  INTRA BF
  79 GLU   (  86-)  U      OE2 <->  104 ARG   ( 109-)  U      NH1    0.24    2.46  INTRA BF
  79 GLU   (  86-)  U      CB  <->  104 ARG   ( 109-)  U      NH1    0.19    2.91  INTRA BF
  72 GLY   (  79-)  U      C   <->  249 HOH   ( 425 )  U      O      0.19    2.61  INTRA BF
  46 HIS   (  57-)  U      ND1 <->   97 ASP   ( 102-)  U      OD2    0.17    2.53  INTRA BL
  63 ARG   (  70-)  U      CG  <->  249 HOH   ( 431 )  U      O      0.16    2.64  INTRA BL
 132 GLY   ( 133-)  U      N   <->  161 LEU   ( 162-)  U      O      0.16    2.54  INTRA BF
  74 MET   (  81-)  U      CE  <->  112 GLN   ( 113-)  U      N      0.14    2.96  INTRA BF
 225 LYS   ( 223-)  U      C   <->  226 ASP   ( 223-)  U      C      0.13    2.67  INTRA BF
 210 MET   ( 207-)  U      O   <->  249 HOH   ( 410 )  U      O      0.13    2.27  INTRA BF
 142 LYS   ( 143-)  U      NZ  <->  195 GLN   ( 192-)  U      OE1    0.12    2.58  INTRA BF
  87 TYR   (  94-)  U      OH  <->   94 HIS   (  99-)  U      ND1    0.12    2.58  INTRA BF
 198 SER   ( 195-)  U      CB  <->  248 SO4   ( 302-)  U      O2     0.12    2.68  INTRA BF
  90 ASP   (  97-)  U      OD1 <->   95 HIS   ( 100-)  U      NE2    0.12    2.58  INTRA BF
  53 LYS   (  61-)  U      CB  <->  249 HOH   ( 433 )  U      O      0.11    2.69  INTRA BF
 206 LEU   ( 203-)  U      N   <->  209 ARG   ( 206-)  U      O      0.10    2.60  INTRA BF
  22 HIS   (  37-)  U      CB  <->   26 SER   (  37-)  U      O      0.10    2.70  INTRA BF
 238 LEU   ( 235-)  U      N   <->  239 PRO   ( 236-)  U      CD     0.09    2.91  INTRA BF
And so on for a total of 60 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: U

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.

  23 ARG   (  37-)  U      -8.78
 148 TYR   ( 149-)  U      -7.31
  71 GLN   (  78-)  U      -6.37
 149 LEU   ( 150-)  U      -6.06
 207 GLN   ( 204-)  U      -5.98
 220 ARG   ( 217-)  U      -5.97
 106 LYS   ( 110-)  U      -5.77
 125 MET   ( 126-)  U      -5.75
  11 ASN   (  26-)  U      -5.40
 188 GLN   ( 185-)  U      -5.22

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: U

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.

 176 GLU   ( 175-)  U   -2.53

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: U

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.

  69 ASN   (  76-)  U
 168 GLN   ( 169-)  U

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  14 TRP   (  29-)  U      N
  65 ARG   (  72-)  U      NE
  65 ARG   (  72-)  U      NH2
  68 SER   (  75-)  U      N
  90 ASP   (  97-)  U      N
  92 LEU   (  97-)  U      N
  93 ALA   (  98-)  U      N
  94 HIS   (  99-)  U      N
 112 GLN   ( 113-)  U      N
 138 THR   ( 139-)  U      N
 145 SER   ( 146-)  U      N
 153 GLN   ( 154-)  U      N
 163 SER   ( 164-)  U      N
 188 GLN   ( 185-)  U      N
 191 THR   ( 188-)  U      N
 195 GLN   ( 192-)  U      N
 196 GLY   ( 193-)  U      N
 213 THR   ( 210-)  U      OG1
 219 GLY   ( 216-)  U      N
 224 LEU   ( 222-)  U      N
 226 ASP   ( 223-)  U      N
 235 SER   ( 232-)  U      N
 238 LEU   ( 235-)  U      N

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

  46 HIS   (  57-)  U      NE2
 128 ASP   ( 129-)  U      OD1

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 :  -0.625
  2nd generation packing quality :   0.390
  Ramachandran plot appearance   :  -1.862
  chi-1/chi-2 rotamer normality  :  -3.353 (poor)
  Backbone conformation          :  -0.637

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.011
  Bond angles                    :   0.997
  Omega angle restraints         :   1.280 (loose)
  Side chain planarity           :   0.903
  Improper dihedral distribution :   1.162
  B-factor distribution          :   1.200
  Inside/Outside distribution    :   0.999

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.011
  Bond angles                    :   0.997
  Omega angle restraints         :   1.280 (loose)
  Side chain planarity           :   0.903
  Improper dihedral distribution :   1.162
  B-factor distribution          :   1.200
  Inside/Outside distribution    :   0.999
==============

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.