WHAT IF Check report

This file was created 2012-01-05 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 pdb1ohe.ent

Checks that need to be done early-on in validation

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.

 343 ACE   (   0-)  B  -

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.

 340 ALA   (   1-)  B  -   N   bound to  343 ACE   (   0-)  B  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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'.

   1 ARG   (  42-)  A      CG
   1 ARG   (  42-)  A      CD
   1 ARG   (  42-)  A      NE
   1 ARG   (  42-)  A      CZ
   1 ARG   (  42-)  A      NH1
   1 ARG   (  42-)  A      NH2
   2 ASP   (  43-)  A      CG
   2 ASP   (  43-)  A      OD1
   2 ASP   (  43-)  A      OD2
 332 TYR   ( 373-)  A      CG
 332 TYR   ( 373-)  A      CD1
 332 TYR   ( 373-)  A      CD2
 332 TYR   ( 373-)  A      CE1
 332 TYR   ( 373-)  A      CE2
 332 TYR   ( 373-)  A      CZ
 332 TYR   ( 373-)  A      OH
 336 LYS   ( 377-)  A      CG
 336 LYS   ( 377-)  A      CD
 336 LYS   ( 377-)  A      CE
 336 LYS   ( 377-)  A      NZ
 338 LYS   ( 379-)  A      CG
 338 LYS   ( 379-)  A      CD
 338 LYS   ( 379-)  A      CE
 338 LYS   ( 379-)  A      NZ

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 339 GLY   ( 380-)  A

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Tyrosine convention problem

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

 121 TYR   ( 162-)  A
 129 TYR   ( 170-)  A
 151 TYR   ( 192-)  A
 164 TYR   ( 205-)  A
 167 TYR   ( 208-)  A
 227 TYR   ( 268-)  A
 287 TYR   ( 328-)  A

Warning: Phenylalanine convention problem

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

  33 PHE   (  74-)  A
  44 PHE   (  85-)  A
  48 PHE   (  89-)  A
  80 PHE   ( 121-)  A
 124 PHE   ( 165-)  A
 142 PHE   ( 183-)  A
 153 PHE   ( 194-)  A
 156 PHE   ( 197-)  A
 183 PHE   ( 224-)  A
 186 PHE   ( 227-)  A
 244 PHE   ( 285-)  A

Warning: Aspartic acid convention problem

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

 238 ASP   ( 279-)  A
 241 ASP   ( 282-)  A
 260 ASP   ( 301-)  A

Warning: Glutamic acid convention problem

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

  42 GLU   (  83-)  A
 168 GLU   ( 209-)  A
 205 GLU   ( 246-)  A

Geometric checks

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

 |  0.995141 -0.000612 -0.000448|
 | -0.000612  0.996497 -0.000255|
 | -0.000448 -0.000255  0.997085|
Proposed new scale matrix

 |  0.008759  0.000007  0.004549|
 |  0.000012  0.018881  0.000005|
 |  0.000008  0.000005  0.017616|
With corresponding cell

    A    = 114.200  B   =  52.963  C    =  63.981
    Alpha=  89.994  Beta= 117.473  Gamma=  90.070

The CRYST1 cell dimensions

    A    = 114.760  B   =  53.150  C    =  64.170
    Alpha=  90.000  Beta= 117.480  Gamma=  90.000

Variance: 166.559
(Under-)estimated Z-score: 9.512

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.

 103 LEU   ( 144-)  A      N    CA   C    99.41   -4.2
 175 LEU   ( 216-)  A      CA   CB   CG  133.77    5.0
 191 SER   ( 232-)  A      N    CA   C    99.80   -4.1

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.

  42 GLU   (  83-)  A
 168 GLU   ( 209-)  A
 205 GLU   ( 246-)  A
 238 ASP   ( 279-)  A
 241 ASP   ( 282-)  A
 260 ASP   ( 301-)  A

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.

 103 LEU   ( 144-)  A    4.80
 205 GLU   ( 246-)  A    4.59
 167 TYR   ( 208-)  A    4.52
 191 SER   ( 232-)  A    4.50
 291 HIS   ( 332-)  A    4.43
 102 TYR   ( 143-)  A    4.33
 101 ILE   ( 142-)  A    4.30
 183 PHE   ( 224-)  A    4.07
 322 LYS   ( 363-)  A    4.06

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.

 118 GLU   ( 159-)  A    -2.4
  35 ILE   (  76-)  A    -2.4
 125 ARG   ( 166-)  A    -2.3
 197 SER   ( 238-)  A    -2.2
 103 LEU   ( 144-)  A    -2.2
 313 GLY   ( 354-)  A    -2.1
 273 SER   ( 314-)  A    -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.

  45 TYR   (  86-)  A  Poor phi/psi
  49 GLY   (  90-)  A  PRO omega poor
 181 ASP   ( 222-)  A  Poor phi/psi
 192 ARG   ( 233-)  A  Poor phi/psi
 198 GLY   ( 239-)  A  Poor phi/psi
 273 SER   ( 314-)  A  Poor phi/psi
 311 VAL   ( 352-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.543

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!

  12 THR   (  53-)  A      0
  14 ARG   (  55-)  A      0
  20 LEU   (  61-)  A      0
  21 TYR   (  62-)  A      0
  22 SER   (  63-)  A      0
  35 ILE   (  76-)  A      0
  39 LEU   (  80-)  A      0
  44 PHE   (  85-)  A      0
  45 TYR   (  86-)  A      0
  46 ALA   (  87-)  A      0
  48 PHE   (  89-)  A      0
  50 PRO   (  91-)  A      0
  72 MET   ( 113-)  A      0
  73 LEU   ( 114-)  A      0
  74 ARG   ( 115-)  A      0
  83 SER   ( 124-)  A      0
 102 TYR   ( 143-)  A      0
 118 GLU   ( 159-)  A      0
 129 TYR   ( 170-)  A      0
 134 PHE   ( 175-)  A      0
 151 TYR   ( 192-)  A      0
 153 PHE   ( 194-)  A      0
 154 LEU   ( 195-)  A      0
 156 PHE   ( 197-)  A      0
 158 SER   ( 199-)  A      0
And so on for a total of 109 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.536

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 313 GLY   ( 354-)  A   1.65   17

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].

   3 PRO   (  44-)  A  -119.1 half-chair C-delta/C-gamma (-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.

 176 ASN   ( 217-)  A      ND2 <->  344 HOH   (2086 )  A      O      0.17    2.53  INTRA BL
 304 ARG   ( 345-)  A      NH2 <->  316 GLN   ( 357-)  A      NE2    0.15    2.70  INTRA BL
  14 ARG   (  55-)  A      NH2 <->   72 MET   ( 113-)  A      O      0.11    2.59  INTRA
 221 ARG   ( 262-)  A      NE  <->  241 ASP   ( 282-)  A      OD1    0.10    2.60  INTRA
  88 GLN   ( 129-)  A      NE2 <->  344 HOH   (2049 )  A      O      0.08    2.62  INTRA BL
  52 ASN   (  93-)  A      ND2 <->  344 HOH   (2022 )  A      O      0.07    2.63  INTRA BL
 146 LYS   ( 187-)  A      NZ  <->  344 HOH   (2037 )  A      O      0.06    2.64  INTRA
  31 HIS   (  72-)  A      O   <->   78 VAL   ( 119-)  A      N      0.06    2.64  INTRA BL
 148 ALA   ( 189-)  A      O   <->  153 PHE   ( 194-)  A      N      0.05    2.65  INTRA
 304 ARG   ( 345-)  A      NE  <->  310 SER   ( 351-)  A      O      0.05    2.65  INTRA BL
 176 ASN   ( 217-)  A      ND2 <->  307 ARG   ( 348-)  A      NH1    0.04    2.81  INTRA BL
  48 PHE   (  89-)  A      O   <->   90 ASN   ( 131-)  A      ND2    0.04    2.66  INTRA BL
 222 LEU   ( 263-)  A      N   <->  223 ASN   ( 264-)  A      N      0.03    2.57  INTRA B3
 194 ARG   ( 235-)  A      NH1 <->  344 HOH   (2094 )  A      O      0.03    2.67  INTRA BF
 302 TRP   ( 343-)  A      CZ2 <->  306 CYS   ( 347-)  A      SG     0.03    3.37  INTRA BL
 104 GLY   ( 145-)  A      N   <->  344 HOH   (2040 )  A      O      0.02    2.68  INTRA BF
 167 TYR   ( 208-)  A      O   <->  175 LEU   ( 216-)  A      N      0.02    2.68  INTRA BL
 302 TRP   ( 343-)  A      CE2 <->  306 CYS   ( 347-)  A      SG     0.02    3.38  INTRA BL
  93 PHE   ( 134-)  A      CE1 <->   97 CYS   ( 138-)  A      SG     0.01    3.39  INTRA BL
 238 ASP   ( 279-)  A      OD2 <->  240 HIS   ( 281-)  A      NE2    0.01    2.69  INTRA
  58 ARG   (  99-)  A      NE  <->  165 GLU   ( 206-)  A      OE2    0.01    2.69  INTRA
 279 ARG   ( 320-)  A      N   <->  340 SEP   (   2-)  B      O3P    0.01    2.69  INTRA

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.

 129 TYR   ( 170-)  A      -8.08
 225 ARG   ( 266-)  A      -6.24
  23 ARG   (  64-)  A      -5.93
 192 ARG   ( 233-)  A      -5.71
  44 PHE   (  85-)  A      -5.69
 266 GLU   ( 307-)  A      -5.66
 150 GLN   ( 191-)  A      -5.51
  74 ARG   ( 115-)  A      -5.48
  25 LYS   (  66-)  A      -5.40
 172 ASN   ( 213-)  A      -5.28
 291 HIS   ( 332-)  A      -5.14
 274 LYS   ( 315-)  A      -5.13

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 224 LYS   ( 265-)  A       226 - MET    267- ( A)         -5.19

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: 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.

 344 HOH   (2007 )  A      O
 344 HOH   (2017 )  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.

   4 GLN   (  45-)  A
  37 ASN   (  78-)  A
  43 ASN   (  84-)  A
  85 GLN   ( 126-)  A
  88 GLN   ( 129-)  A
 157 ASN   ( 198-)  A
 160 ASN   ( 201-)  A
 176 ASN   ( 217-)  A
 214 HIS   ( 255-)  A
 316 GLN   ( 357-)  A
 317 GLN   ( 358-)  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.

   2 ASP   (  43-)  A      N
   4 GLN   (  45-)  A      N
   6 ASP   (  47-)  A      N
  22 SER   (  63-)  A      N
  23 ARG   (  64-)  A      NE
  23 ARG   (  64-)  A      NH2
  27 ALA   (  68-)  A      N
  49 GLY   (  90-)  A      N
 119 THR   ( 160-)  A      OG1
 125 ARG   ( 166-)  A      NH2
 128 ALA   ( 169-)  A      N
 133 ASN   ( 174-)  A      ND2
 192 ARG   ( 233-)  A      N
 215 ASN   ( 256-)  A      N
 223 ASN   ( 264-)  A      N
 273 SER   ( 314-)  A      N
 280 THR   ( 321-)  A      N
 294 MET   ( 335-)  A      N
 317 GLN   ( 358-)  A      N

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.

   5 ASP   (  46-)  A   H-bonding suggests Asn
  40 GLU   (  81-)  A   H-bonding suggests Gln
  42 GLU   (  83-)  A   H-bonding suggests Gln
 234 ASP   ( 275-)  A   H-bonding suggests Asn; 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 :  -0.389
  2nd generation packing quality :  -1.125
  Ramachandran plot appearance   :  -0.897
  chi-1/chi-2 rotamer normality  :  -0.543
  Backbone conformation          :  -0.471

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.554 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.279 (tight)
  Side chain planarity           :   0.359 (tight)
  Improper dihedral distribution :   0.945
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.025

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :   0.6
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.554 (tight)
  Bond angles                    :   0.751
  Omega angle restraints         :   0.279 (tight)
  Side chain planarity           :   0.359 (tight)
  Improper dihedral distribution :   0.945
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.025
==============

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.