WHAT IF Check report

This file was created 2011-12-18 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 pdb1xc8.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 41 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
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: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 8

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 39793.297
Volume of the Unit Cell V= 1222731.1
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.682
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.520 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 8
which would result in the much more normal Vm= 3.841
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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.

 302 FOX   (   7-)  B  -

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: 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'.

  42 LYS   (  15-)  A      CD
  42 LYS   (  15-)  A      CE
  42 LYS   (  15-)  A      NZ
  58 ARG   (  31-)  A      CZ
  58 ARG   (  31-)  A      NH1
  58 ARG   (  31-)  A      NH2
  69 LYS   (  42-)  A      CD
  69 LYS   (  42-)  A      CE
  69 LYS   (  42-)  A      NZ
  92 ASP   (  65-)  A      CG
  92 ASP   (  65-)  A      OD1
  92 ASP   (  65-)  A      OD2
  93 ASP   (  66-)  A      CG
  93 ASP   (  66-)  A      OD1
  93 ASP   (  66-)  A      OD2
 105 LYS   (  78-)  A      CD
 105 LYS   (  78-)  A      CE
 105 LYS   (  78-)  A      NZ
 115 ARG   (  88-)  A      CG
 115 ARG   (  88-)  A      CD
 115 ARG   (  88-)  A      NE
 115 ARG   (  88-)  A      CZ
 115 ARG   (  88-)  A      NH1
 115 ARG   (  88-)  A      NH2
 127 ASP   ( 100-)  A      CG
And so on for a total of 59 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: 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.

   1 DCYT  (   1-)  B      C1'  N1    1.53    4.7
   6 DTHY  (   6-)  B      C3'  C2'   1.56    4.1
   7 DTHY  (   8-)  B      C5'  C4'   1.55    4.9
   7 DTHY  (   8-)  B      N1   C6    1.41    4.1
   7 DTHY  (   8-)  B      C5   C7    1.53    6.4
   8 DTHY  (   9-)  B      N1   C6    1.41    4.3
   9 DTHY  (  10-)  B      C5   C7    1.52    4.8
  12 DCYT  (  13-)  B      C1'  N1    1.52    4.0
  15 DCYT  (  16-)  C      C1'  N1    1.52    4.2

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

 |  0.997066  0.001166 -0.000452|
 |  0.001166  0.996429 -0.001492|
 | -0.000452 -0.001492  0.993659|
Proposed new scale matrix

 |  0.010841 -0.000013  0.000005|
 | -0.000013  0.010848  0.000016|
 |  0.000003  0.000011  0.007045|
With corresponding cell

    A    =  92.244  B   =  92.185  C    = 141.951
    Alpha=  90.172  Beta=  90.052  Gamma=  89.866

The CRYST1 cell dimensions

    A    =  92.513  B   =  92.513  C    = 142.867
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 393.360
(Under-)estimated Z-score: 14.617

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.

   4 DTHY  (   4-)  B      N3   C2   O2  119.85   -4.1
   6 DTHY  (   6-)  B      C6   C5   C7  119.69   -5.3
   6 DTHY  (   6-)  B      C4   C5   C7  123.27    7.1
   7 DTHY  (   8-)  B      P    O5'  C5' 113.32   -4.7
   7 DTHY  (   8-)  B      O4'  C1'  N1  103.64   -5.2
   8 DTHY  (   9-)  B      N3   C2   O2  119.44   -4.8
   9 DTHY  (  10-)  B      C4   C5   C7  121.82    4.7
  10 DCYT  (  11-)  B      N3   C2   O2  118.79   -4.4
  11 DTHY  (  12-)  B      C5   C4   O4  120.38   -6.5
  11 DTHY  (  12-)  B      C4   C5   C7  122.04    5.1
  11 DTHY  (  12-)  B      O4   C4   N3  122.37    4.1
  12 DCYT  (  13-)  B      O4'  C1'  C2' 100.74   -4.9
  12 DCYT  (  13-)  B      O4'  C1'  N1  103.33   -5.6
  13 DGUA  (  14-)  B      C5   C6   O6  125.90   -4.5
  14 DGUA  (  15-)  C      O4'  C1'  N9  112.23    5.5
  14 DGUA  (  15-)  C      N9   C8   N7  114.35    6.5
  14 DGUA  (  15-)  C      N9   C4   C5  107.16    4.4
  14 DGUA  (  15-)  C      C8   N9   C4  104.55   -4.6
  16 DGUA  (  17-)  C      P   -C3* -O3* 126.81    5.9
  16 DGUA  (  17-)  C      O5'  C5'  C4' 103.36   -4.9
  17 DADE  (  18-)  C      O4'  C1'  N9  103.40   -5.5
  17 DADE  (  18-)  C      C2   N3   C4  108.54   -4.1
  18 DGUA  (  19-)  C      N9   C8   N7  113.33    4.5
  19 DADE  (  20-)  C      O4'  C1'  N9  112.89    6.4
  19 DADE  (  20-)  C      N6   C6   N1  121.54    4.9
  22 DCYT  (  23-)  C      OP1  P    OP2 126.09    4.3
  22 DCYT  (  23-)  C      C4'  O4'  C1' 103.72   -4.3
  22 DCYT  (  23-)  C      O4'  C1'  N1  103.92   -4.8
  22 DCYT  (  23-)  C      N1   C2   O2  121.97    5.1
  26 DGUA  (  27-)  C      O4'  C1'  N9  112.50    5.9
  26 DGUA  (  27-)  C      N9   C8   N7  113.77    5.3
  27 DADE  (  28-)  C      O4'  C1'  N9  112.84    6.3
  67 LEU   (  40-)  A      CA   CB   CG  133.68    5.0
  95 ARG   (  68-)  A      CG   CD   NE  118.54    4.7
 225 HIS   ( 198-)  A      CG   ND1  CE1 109.61    4.0
 236 GLN   ( 209-)  A      CB   CG   CD  119.72    4.2

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.

  43 ARG   (  16-)  A    5.21

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.

 193 VAL   ( 166-)  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.

  60 VAL   (  33-)  A  omega poor
  90 ILE   (  63-)  A  omega poor
  91 GLY   (  64-)  A  Poor phi/psi
 101 ARG   (  74-)  A  Poor phi/psi
 137 LYS   ( 110-)  A  Poor phi/psi
 157 LYS   ( 130-)  A  Poor phi/psi
 162 PRO   ( 135-)  A  Poor phi/psi
 190 GLN   ( 163-)  A  Poor phi/psi
 194 ALA   ( 167-)  A  omega poor
 209 LYS   ( 182-)  A  Poor phi/psi
 247 ARG   ( 220-)  A  omega poor
 248 THR   ( 221-)  A  Poor phi/psi
 249 TYR   ( 222-)  A  omega poor
 288 GLY   ( 261-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.347

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  (   3-)  B      0
   4 DTHY  (   4-)  B      0
   5 DTHY  (   5-)  B      0
   6 DTHY  (   6-)  B      0
   7 DTHY  (   8-)  B      0
   8 DTHY  (   9-)  B      0
   9 DTHY  (  10-)  B      0
  10 DCYT  (  11-)  B      0
  11 DTHY  (  12-)  B      0
  12 DCYT  (  13-)  B      0
  13 DGUA  (  14-)  B      0
  14 DGUA  (  15-)  C      0
  15 DCYT  (  16-)  C      0
  16 DGUA  (  17-)  C      0
  17 DADE  (  18-)  C      0
  18 DGUA  (  19-)  C      0
  19 DADE  (  20-)  C      0
  20 DADE  (  21-)  C      0
  21 DADE  (  22-)  C      0
  22 DCYT  (  23-)  C      0
  23 DADE  (  24-)  C      0
  24 DADE  (  25-)  C      0
  25 DADE  (  26-)  C      0
  26 DGUA  (  27-)  C      0
  27 DADE  (  28-)  C      0
And so on for a total of 123 lines.

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]

  28 PRO   (   1-)  A    0.46 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

   6 DTHY  (   6-)  B      O3' <->  302 FOX   (   7-)  B      P      1.00    1.60  INTRA BL
   6 DTHY  (   6-)  B      C3' <->  302 FOX   (   7-)  B      P      0.81    2.59  INTRA BL
  13 DGUA  (  14-)  B      N1  <->   15 DCYT  (  16-)  C      N3     0.26    2.74  INTRA BF
   2 DTHY  (   2-)  B      N3  <->   27 DADE  (  28-)  C      N1     0.25    2.75  INTRA BF
   5 DTHY  (   5-)  B      N3  <->   24 DADE  (  25-)  C      N1     0.25    2.75  INTRA
 162 PRO   ( 135-)  A      O   <->  236 GLN   ( 209-)  A      NE2    0.24    2.46  INTRA
   4 DTHY  (   4-)  B      N3  <->   25 DADE  (  26-)  C      N1     0.24    2.76  INTRA BF
  20 DADE  (  21-)  C      N7  <->  304 HOH   ( 196 )  C      O      0.22    2.48  INTRA BF
 271 LYS   ( 244-)  A      NZ  <->  278 GLU   ( 251-)  A      OE2    0.21    2.49  INTRA BF
  21 DADE  (  22-)  C      OP2 <->  304 HOH   ( 372 )  C      O      0.21    2.19  INTRA BF
  92 ASP   (  65-)  A      CB  <->  305 HOH   (5269 )  A      O      0.20    2.60  INTRA BF
 175 LYS   ( 148-)  A      NZ  <->  305 HOH   (5113 )  A      O      0.19    2.51  INTRA
 180 THR   ( 153-)  A      N   <->  305 HOH   (5297 )  A      O      0.19    2.51  INTRA BF
  11 DTHY  (  12-)  B      N3  <->   17 DADE  (  18-)  C      N1     0.18    2.82  INTRA BF
  53 GLU   (  26-)  A      OE2 <->  305 HOH   (5181 )  A      O      0.18    2.22  INTRA BF
 275 CYS   ( 248-)  A      SG  <->  292 CYS   ( 265-)  A      SG     0.18    3.27  INTRA
   6 DTHY  (   6-)  B      N3  <->   23 DADE  (  24-)  C      N1     0.16    2.84  INTRA BL
  15 DCYT  (  16-)  C      C2' <->   16 DGUA  (  17-)  C      C8     0.16    3.04  INTRA BF
   9 DTHY  (  10-)  B      N3  <->   19 DADE  (  20-)  C      N1     0.15    2.85  INTRA
  24 DADE  (  25-)  C      N7  <->  304 HOH   ( 178 )  C      O      0.15    2.55  INTRA BF
  12 DCYT  (  13-)  B      N3  <->   16 DGUA  (  17-)  C      N1     0.12    2.88  INTRA BF
  10 DCYT  (  11-)  B      N3  <->   18 DGUA  (  19-)  C      N1     0.12    2.88  INTRA
 272 CYS   ( 245-)  A      N   <->  277 ALA   ( 250-)  A      O      0.12    2.58  INTRA
  94 PHE   (  67-)  A      CD1 <->  305 HOH   (5218 )  A      O      0.11    2.69  INTRA BF
  76 ILE   (  49-)  A      CD1 <->  123 MET   (  96-)  A      CE     0.11    3.09  INTRA
And so on for a total of 54 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.

 102 MET   (  75-)  A      -6.70
 274 ARG   ( 247-)  A      -6.56
 297 GLN   ( 270-)  A      -6.47

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

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.

 247 ARG   ( 220-)  A   -2.91
 100 LEU   (  73-)  A   -2.89
 136 ARG   ( 109-)  A   -2.73
 298 LYS   ( 271-)  A   -2.65
 103 GLU   (  76-)  A   -2.52

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.

  99 HIS   (  72-)  A     -  103 GLU   (  76-)  A        -1.90

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

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.

 305 HOH   (5278 )  A      O     23.49   71.73    7.29

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.

 305 HOH   (5242 )  A      O
 305 HOH   (5318 )  A      O
 305 HOH   (5323 )  A      O
 305 HOH   (5325 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 280 GLN   ( 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.

  28 PRO   (   1-)  A      N
  45 VAL   (  18-)  A      N
  95 ARG   (  68-)  A      NH1
 127 ASP   ( 100-)  A      N
 138 PHE   ( 111-)  A      N
 198 ASN   ( 171-)  A      ND2
 246 ILE   ( 219-)  A      N
 247 ARG   ( 220-)  A      N
 266 GLY   ( 239-)  A      N
 287 ARG   ( 260-)  A      NH2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 305 HOH   (5015 )  A      O  0.98  K  4
 305 HOH   (5046 )  A      O  1.06  K  4
 305 HOH   (5155 )  A      O  0.86 NA  4 *2 ION-B
 305 HOH   (5199 )  A      O  0.97  K  5 Ion-B
 305 HOH   (5270 )  A      O  1.03  K  5

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.

  29 GLU   (   2-)  A   H-bonding suggests Gln
  32 GLU   (   5-)  A   H-bonding suggests Gln
  39 GLU   (  12-)  A   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.

Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.485
  2nd generation packing quality :  -1.441
  Ramachandran plot appearance   :   0.031
  chi-1/chi-2 rotamer normality  :  -0.347
  Backbone conformation          :  -0.281

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.983
  Bond angles                    :   1.110
  Omega angle restraints         :   1.088
  Side chain planarity           :   0.904
  Improper dihedral distribution :   0.943
  B-factor distribution          :   0.504
  Inside/Outside distribution    :   1.003

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 : 1.95

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.983
  Bond angles                    :   1.110
  Omega angle restraints         :   1.088
  Side chain planarity           :   0.904
  Improper dihedral distribution :   0.943
  B-factor distribution          :   0.504
  Inside/Outside distribution    :   1.003

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Protein side chain planarity
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Quality Control
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Ramachandran plot
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Symmetry Checks
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    M.Nayal and E.Di Cera,
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      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
    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
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