WHAT IF Check report

This file was created 2011-12-28 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 pdb1g3x.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 11
Highest polymer chain multiplicity according to SEQRES: 12
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 48
Polymer chain multiplicity and SEQRES multiplicity disagree 11 12
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 155 9AC   ( 700-)  M  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 144 ARG   ( 701-)  M  -   N   bound to  155 9AC   ( 700-)  M  -   C15

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 144 ARG   ( 701-)  M  -   NE
 144 ARG   ( 701-)  M  -   CZ
 144 ARG   ( 701-)  M  -   NH1
 144 ARG   ( 701-)  M  -   NH2
 145 ARG   ( 702-)  M  -   NE
 145 ARG   ( 702-)  M  -   CZ
 145 ARG   ( 702-)  M  -   NH1
 145 ARG   ( 702-)  M  -   NH2
 147 ARG   ( 704-)  M  -   NE
 147 ARG   ( 704-)  M  -   CZ
 147 ARG   ( 704-)  M  -   NH1
 147 ARG   ( 704-)  M  -   NH2

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: 6

Crystal temperature (K) :110.000

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.

   5 DADE  ( 105-)  A  -   C5'  C4'   1.54    4.2
   7 DTHY  ( 107-)  A  -   C3'  O3'   1.38   -4.1
   8 DTHY  ( 108-)  A  -   C3'  O3'   1.37   -4.7
   8 DTHY  ( 108-)  A  -   O5'  C5'   1.37   -4.1
  15 DCYT  ( 115-)  B  -   O5'  C5'   1.37   -4.3
  38 DGUA  ( 214-)  D  -   N7   C5    1.36   -4.9
  45 DCYT  ( 221-)  D  -   O5'  C5'   1.37   -4.6
  51 DCYT  ( 303-)  E  -   C3'  O3'   1.38   -4.3
  57 DCYT  ( 309-)  E  -   C3'  O3'   1.38   -4.0
  74 DCYT  ( 403-)  G  -   N1   C6    1.33   -5.8
  81 DGUA  ( 410-)  G  -   C3'  O3'   1.37   -4.8
  83 DGUA  ( 412-)  G  -   O5'  C5'   1.38   -4.0
  83 DGUA  ( 412-)  G  -   C6   N1    1.36   -4.0
  84 DCYT  ( 413-)  H  -   C1'  N1    1.53    5.1
  85 DGUA  ( 414-)  H  -   N7   C5    1.36   -4.3
  90 DTHY  ( 419-)  H  -   C3'  O3'   1.37   -4.3
  98 DCYT  ( 503-)  I  -   N1   C6    1.34   -4.6
 104 DCYT  ( 509-)  I  -   C1'  N1    1.52    4.2
 108 DCYT  ( 513-)  J  -   C1'  N1    1.52    4.5
 119 DGUA  ( 524-)  J  -   N9   C8    1.34   -4.2
 122 DCYT  ( 603-)  K  -   N1   C6    1.34   -4.9
 122 DCYT  ( 603-)  K  -   C4   N3    1.31   -4.0
 124 DADE  ( 605-)  K  -   O5'  C5'   1.37   -4.3
 124 DADE  ( 605-)  K  -   N3   C4    1.32   -4.0
 134 DCYT  ( 615-)  L  -   O5'  C5'   1.36   -4.8
 136 DADE  ( 617-)  L  -   O5'  C5'   1.38   -4.0

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

 |  1.003513 -0.000228  0.000004|
 | -0.000228  1.003820  0.000387|
 |  0.000004  0.000387  1.003120|
Proposed new scale matrix

 |  0.014991  0.000003  0.000000|
 |  0.000003  0.014571 -0.000006|
 |  0.000000 -0.000005  0.012886|
With corresponding cell

    A    =  66.705  B   =  68.628  C    =  77.605
    Alpha=  89.956  Beta=  90.001  Gamma=  90.026

The CRYST1 cell dimensions

    A    =  66.471  B   =  68.365  C    =  77.362
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 874.345
(Under-)estimated Z-score: 21.793

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.

   2 DGUA  ( 102-)  A  -   P   -C3* -O3* 124.53    4.0
   2 DGUA  ( 102-)  A  -   O4'  C1'  C2'  99.76   -5.8
   2 DGUA  ( 102-)  A  -   N9   C8   N7  113.75    5.3
   4 DGUA  ( 104-)  A  -   O5'  C5'  C4' 104.10   -4.4
   5 DADE  ( 105-)  A  -   C3'  C4'  C5' 120.89    4.1
   5 DADE  ( 105-)  A  -   O5'  C5'  C4' 116.77    4.7
   5 DADE  ( 105-)  A  -   O4'  C1'  N9  111.22    4.3
   6 DADE  ( 106-)  A  -   N1   C2   N3  127.22   -4.2
   7 DTHY  ( 107-)  A  -   P    O5'  C5' 113.57   -4.6
   7 DTHY  ( 107-)  A  -   O4'  C1'  C2' 100.35   -5.2
   7 DTHY  ( 107-)  A  -   O4   C4   N3  123.45    5.9
   8 DTHY  ( 108-)  A  -   O4'  C1'  C2' 101.11   -4.5
   8 DTHY  ( 108-)  A  -   C6   C5   C7  119.67   -5.4
   8 DTHY  ( 108-)  A  -   C4   C5   C7  122.60    6.0
  10 DGUA  ( 110-)  A  -   N9   C8   N7  113.52    4.8
  11 DCYT  ( 111-)  A  -   P    O5'  C5' 113.30   -4.8
  11 DCYT  ( 111-)  A  -   O3'  C3'  C4' 100.58   -4.4
  12 DGUA  ( 112-)  A  -   O5'  C5'  C4' 104.13   -4.3
  12 DGUA  ( 112-)  A  -   O4'  C1'  N9  112.80    6.3
  12 DGUA  ( 112-)  A  -   C2'  C1'  N9  107.32   -4.3
  12 DGUA  ( 112-)  A  -   N9   C8   N7  113.44    4.7
  12 DGUA  ( 112-)  A  -   C5   C6   O6  125.35   -5.4
  13 DCYT  ( 113-)  B  -   O4'  C1'  N1  103.55   -5.3
  14 DGUA  ( 114-)  B  -   P    O5'  C5' 113.93   -4.4
  14 DGUA  ( 114-)  B  -   O4'  C1'  N9  103.36   -5.5
And so on for a total of 340 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.081
RMS-deviation in bond angles: 2.440

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

 102 DTHY  ( 507-)  I  -   0.13
  67 DTHY  ( 319-)  F  -   0.13
  56 DTHY  ( 308-)  E  -   0.12
 115 DTHY  ( 520-)  J  -   0.11
 139 DTHY  ( 620-)  L  -   0.10
 Ramachandran Z-score : -11.177

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -11.177

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.

 146 ARG   ( 703-)  M  -   -2.2

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.

 145 ARG   ( 702-)  M  - Poor phi/psi
 146 ARG   ( 703-)  M  - Poor phi/psi
 chi-1/chi-2 correlation Z-score : -8.312

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 : -8.312

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 DCYT  ( 103-)  A  -     0
   4 DGUA  ( 104-)  A  -     0
   5 DADE  ( 105-)  A  -     0
   6 DADE  ( 106-)  A  -     0
   7 DTHY  ( 107-)  A  -     0
   8 DTHY  ( 108-)  A  -     0
   9 DCYT  ( 109-)  A  -     0
  10 DGUA  ( 110-)  A  -     0
  11 DCYT  ( 111-)  A  -     0
  12 DGUA  ( 112-)  A  -     0
  13 DCYT  ( 113-)  B  -     0
  14 DGUA  ( 114-)  B  -     0
  15 DCYT  ( 115-)  B  -     0
  16 DGUA  ( 116-)  B  -     0
  17 DADE  ( 117-)  B  -     0
  18 DADE  ( 118-)  B  -     0
  19 DTHY  ( 119-)  B  -     0
  20 DTHY  ( 120-)  B  -     0
  21 DCYT  ( 121-)  B  -     0
  22 DGUA  ( 122-)  B  -     0
  23 DCYT  ( 123-)  B  -     0
  24 DGUA  ( 124-)  B  -     0
  25 DCYT  ( 201-)  C  -     0
  26 DGUA  ( 202-)  C  -     0
  27 DCYT  ( 203-)  C  -     0
And so on for a total of 143 lines.

Error: Backbone conformation Z-score very low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual.

Backbone conformation Z-score : -6818.788

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.

 144 ARG   ( 701-)  M  -   N   <->  155 9AC   ( 700-)  M  -   C15    1.38    1.32  INTRA BL
 144 ARG   ( 701-)  M  -   CA  <->  155 9AC   ( 700-)  M  -   C15    0.74    2.46  INTRA BL
 124 DADE  ( 605-)  K  -   N1  <->  139 DTHY  ( 620-)  L  -   N3     0.30    2.70  INTRA BL
   7 DTHY  ( 107-)  A  -   N3  <->   18 DADE  ( 118-)  B  -   N1     0.29    2.71  INTRA
  77 DADE  ( 406-)  G  -   N1  <->   90 DTHY  ( 419-)  H  -   N3     0.29    2.71  INTRA BL
  74 DCYT  ( 403-)  G  -   N3  <->   93 DGUA  ( 422-)  H  -   N1     0.28    2.72  INTRA
  54 DADE  ( 306-)  E  -   N1  <->   67 DTHY  ( 319-)  F  -   N3     0.26    2.74  INTRA
  35 DCYT  ( 211-)  C  -   N3  <->   38 DGUA  ( 214-)  D  -   N1     0.26    2.74  INTRA BL
  29 DADE  ( 205-)  C  -   N1  <->   44 DTHY  ( 220-)  D  -   N3     0.25    2.75  INTRA
 128 DCYT  ( 609-)  K  -   N3  <->  135 DGUA  ( 616-)  L  -   N1     0.23    2.77  INTRA BL
  60 DGUA  ( 312-)  E  -   N1  <->   61 DCYT  ( 313-)  F  -   N3     0.22    2.78  INTRA BL
  79 DTHY  ( 408-)  G  -   N3  <->   88 DADE  ( 417-)  H  -   N1     0.22    2.78  INTRA BL
 103 DTHY  ( 508-)  I  -   N3  <->  112 DADE  ( 517-)  J  -   N1     0.21    2.79  INTRA BF
 126 DTHY  ( 607-)  K  -   N3  <->  137 DADE  ( 618-)  L  -   N1     0.21    2.79  INTRA
  55 DTHY  ( 307-)  E  -   N3  <->   66 DADE  ( 318-)  F  -   N1     0.21    2.79  INTRA
 121 DGUA  ( 602-)  K  -   P   <->  166 HOH   ( 893 )  K      O      0.19    2.81  INTRA BF
 123 DGUA  ( 604-)  K  -   N1  <->  140 DCYT  ( 621-)  L  -   N3     0.19    2.81  INTRA BL
  11 DCYT  ( 111-)  A  -   N3  <->   14 DGUA  ( 114-)  B  -   N1     0.18    2.82  INTRA
 121 DGUA  ( 602-)  K  -   N1  <->  142 DCYT  ( 623-)  L  -   N3     0.18    2.82  INTRA
  52 DGUA  ( 304-)  E  -   N1  <->   69 DCYT  ( 321-)  F  -   N3     0.18    2.82  INTRA
  78 DTHY  ( 407-)  G  -   N3  <->   89 DADE  ( 418-)  H  -   N1     0.17    2.83  INTRA
  53 DADE  ( 305-)  E  -   N1  <->   68 DTHY  ( 320-)  F  -   N3     0.17    2.83  INTRA
  26 DGUA  ( 202-)  C  -   N1  <->   47 DCYT  ( 223-)  D  -   N3     0.17    2.83  INTRA BL
  32 DTHY  ( 208-)  C  -   N3  <->   41 DADE  ( 217-)  D  -   N1     0.16    2.84  INTRA
  56 DTHY  ( 308-)  E  -   N3  <->   65 DADE  ( 317-)  F  -   N1     0.16    2.84  INTRA
And so on for a total of 72 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.668

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.

 145 ARG   ( 702-)  M  -  -3.75
 147 ARG   ( 704-)  M  -  -3.23
 144 ARG   ( 701-)  M  -  -3.21

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 144 ARG   ( 701-)  M  -  -  147 ARG   ( 704-)  M  -     -3.12

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 157 HOH   ( 883 )  B      O
 166 HOH   ( 897 )  K      O
 167 HOH   ( 891 )  L      O
ERROR. No atoms within 50 A?
ERROR. No atoms within 50 A?
ERROR. No atoms within 50 A?

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 159 HOH   ( 817 )  D      O     26.01   44.58   43.51
 162 HOH   ( 807 )  G      O     -2.99   62.56   21.87
 165 HOH   ( 839 )  J      O     -0.23   63.73   54.96
 165 HOH   ( 840 )  J      O     67.19   62.97   57.49
 167 HOH   ( 828 )  L      O     13.13   63.47   68.05
 167 HOH   ( 844 )  L      O     11.53   69.08   24.85

Error: Water molecules without hydrogen bonds

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

 156 HOH   ( 819 )  A      O
 156 HOH   ( 849 )  A      O
 157 HOH   ( 883 )  B      O
 159 HOH   ( 812 )  D      O
 159 HOH   ( 823 )  D      O
 159 HOH   ( 833 )  D      O
 160 HOH   ( 852 )  E      O
 164 HOH   ( 822 )  I      O
 165 HOH   ( 821 )  J      O
 166 HOH   ( 897 )  K      O
 167 HOH   ( 846 )  L      O
 167 HOH   ( 891 )  L      O
Since there are no HIS GLN or ASN residues in the soup, no hydrogen-bond
flip check will be performed.

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 DCYT  ( 103-)  A  -   N4
  95 DGUA  ( 424-)  H  -   N2
 143 DGUA  ( 624-)  L  -   N2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 151  MG   ( 801-)  J  -  -.-  -.-  Low probability ion. Occ=0.50

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:

  2nd generation packing quality : -17.272 (bad)
  Ramachandran plot appearance   : -11.177 (bad)
  chi-1/chi-2 rotamer normality  :  -8.312 (bad)

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.329
  Bond angles                    :   2.081 (loose)
  Omega angle restraints         :   0.754
  Side chain planarity           :   0.083 (tight)
  Improper dihedral distribution :   0.881
  B-factor distribution          :   0.385
  Inside/Outside distribution    :   1.668 (unusual)

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 : 2.70


Structure Z-scores, positive is better than average:

  2nd generation packing quality : -14.2 (bad)
  Ramachandran plot appearance   :  -7.2 (bad)
  chi-1/chi-2 rotamer normality  :  -5.6 (bad)

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.329
  Bond angles                    :   2.081 (loose)
  Omega angle restraints         :   0.754
  Side chain planarity           :   0.083 (tight)
  Improper dihedral distribution :   0.881
  B-factor distribution          :   0.385
  Inside/Outside distribution    :   1.668 (unusual)
==============

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.