WHAT IF Check report

This file was created 2011-12-17 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 pdb1q39.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: 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'.

   2 GLU   (   5-)  A      CG
   2 GLU   (   5-)  A      CD
   2 GLU   (   5-)  A      OE1
   2 GLU   (   5-)  A      OE2
   3 ILE   (   6-)  A      CG1
   3 ILE   (   6-)  A      CG2
   3 ILE   (   6-)  A      CD1
   5 ARG   (   8-)  A      CG
   5 ARG   (   8-)  A      CD
   5 ARG   (   8-)  A      NE
   5 ARG   (   8-)  A      CZ
   5 ARG   (   8-)  A      NH1
   5 ARG   (   8-)  A      NH2
  34 SER   (  37-)  A      OG
  58 ASP   (  61-)  A      CG
  58 ASP   (  61-)  A      OD1
  58 ASP   (  61-)  A      OD2
  78 GLU   (  81-)  A      CG
  78 GLU   (  81-)  A      CD
  78 GLU   (  81-)  A      OE1
  78 GLU   (  81-)  A      OE2
 119 ARG   ( 124-)  A      CG
 119 ARG   ( 124-)  A      CD
 119 ARG   ( 124-)  A      NE
 119 ARG   ( 124-)  A      CZ
 119 ARG   ( 124-)  A      NH1
 119 ARG   ( 124-)  A      NH2
 132 GLU   ( 137-)  A      CG
 132 GLU   ( 137-)  A      CD
 132 GLU   ( 137-)  A      OE1
 132 GLU   ( 137-)  A      OE2
 135 LYS   ( 140-)  A      CG
 135 LYS   ( 140-)  A      CD
 135 LYS   ( 140-)  A      CE
 135 LYS   ( 140-)  A      NZ
 230 GLU   ( 235-)  A      CG
 230 GLU   ( 235-)  A      CD
 230 GLU   ( 235-)  A      OE1
 230 GLU   ( 235-)  A      OE2
 244 LEU   ( 249-)  A      CG
 244 LEU   ( 249-)  A      CD1
 244 LEU   ( 249-)  A      CD2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   2 GLU   (   5-)  A    High
   3 ILE   (   6-)  A    High
  78 GLU   (  81-)  A    High
  79 GLU   (  82-)  A    High
  80 THR   (  85-)  A    High
 112 THR   ( 117-)  A    High
 161 LEU   ( 166-)  A    High
 233 GLU   ( 238-)  A    High

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 PRO   (   4-)  A    0.40
 207 ARG   ( 212-)  A    0.50
 208 GLY   ( 213-)  A    0.50
 209 GLN   ( 214-)  A    0.50
 210 VAL   ( 215-)  A    0.50
 211 ASP   ( 216-)  A    0.50
 243 THR   ( 248-)  A    0.50
 244 LEU   ( 249-)  A    0.50
 245 SER   ( 250-)  A    0.50
 246 SER   ( 251-)  A    0.50
 247 ARG   ( 252-)  A    0.50
 248 PRO   ( 253-)  A    0.50

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

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.

 244 LEU   ( 249-)  A      N   -C     1.41    4.0

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.

  99 SER   ( 104-)  A      N    CA   C   122.45    4.0
 244 LEU   ( 249-)  A     -CA  -C    N    91.02  -12.6
 244 LEU   ( 249-)  A     -C    N    CA  134.99    7.4
 244 LEU   ( 249-)  A      N    CA   C    97.14   -5.0
 245 SER   ( 250-)  A     -C    N    CA  106.99   -8.2
 245 SER   ( 250-)  A      N    CA   C   125.00    4.9

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.

 244 LEU   ( 249-)  A    5.73
 245 SER   ( 250-)  A    5.11
  14 ILE   (  17-)  A    4.64
  48 GLY   (  51-)  A    4.30
  99 SER   ( 104-)  A    4.13

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.796

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.

 115 PRO   ( 120-)  A    -2.7
 248 PRO   ( 253-)  A    -2.7
 234 ARG   ( 239-)  A    -2.5
 153 LEU   ( 158-)  A    -2.2
  87 LYS   (  92-)  A    -2.2
   4 ARG   (   7-)  A    -2.1
  43 HIS   (  46-)  A    -2.0
 199 ILE   ( 204-)  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.

   5 ARG   (   8-)  A  Poor phi/psi
  16 GLY   (  19-)  A  Poor phi/psi
  58 ASP   (  61-)  A  Poor phi/psi
  66 GLN   (  69-)  A  Poor phi/psi
  69 GLY   (  72-)  A  Poor phi/psi
  81 THR   (  86-)  A  Poor phi/psi
  99 SER   ( 104-)  A  Poor phi/psi
 211 ASP   ( 216-)  A  Poor phi/psi
 224 VAL   ( 229-)  A  Poor phi/psi
 226 HIS   ( 231-)  A  Poor phi/psi
 243 THR   ( 248-)  A  Poor phi/psi
 244 LEU   ( 249-)  A  omega poor
 246 SER   ( 251-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.202

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.202

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 ILE   (   6-)  A      0
   5 ARG   (   8-)  A      0
  14 ILE   (  17-)  A      0
  15 LYS   (  18-)  A      0
  21 ASP   (  24-)  A      0
  23 TRP   (  26-)  A      0
  25 ALA   (  28-)  A      0
  26 PHE   (  29-)  A      0
  37 ILE   (  40-)  A      0
  42 THR   (  45-)  A      0
  43 HIS   (  46-)  A      0
  47 ARG   (  50-)  A      0
  49 LYS   (  52-)  A      0
  58 ASP   (  61-)  A      0
  65 ASN   (  68-)  A      0
  66 GLN   (  69-)  A      0
  67 LEU   (  70-)  A      0
  76 THR   (  79-)  A      0
  78 GLU   (  81-)  A      0
  79 GLU   (  82-)  A      0
  80 THR   (  85-)  A      0
  81 THR   (  86-)  A      0
  98 TYR   ( 103-)  A      0
  99 SER   ( 104-)  A      0
 101 SER   ( 106-)  A      0
And so on for a total of 104 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 : 1.881

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.

 137 ARG   ( 142-)  A      NE  <->  157 PHE   ( 162-)  A      O      0.25    2.45  INTRA BF
 143 PHE   ( 148-)  A      O   <->  145 ASN   ( 150-)  A      N      0.24    2.46  INTRA BF
  75 ASP   (  78-)  A      O   <->   77 GLY   (  80-)  A      N      0.24    2.46  INTRA BF
 232 CYS   ( 237-)  A      O   <->  234 ARG   ( 239-)  A      N      0.23    2.47  INTRA BF
 185 ASN   ( 190-)  A      OD1 <->  188 GLN   ( 193-)  A      N      0.22    2.48  INTRA BF
 199 ILE   ( 204-)  A      N   <->  200 PRO   ( 205-)  A      CD     0.21    2.79  INTRA BL
 118 GLN   ( 123-)  A      O   <->  142 ARG   ( 147-)  A      NH2    0.20    2.50  INTRA BF
 163 ASN   ( 168-)  A      OD1 <->  166 ARG   ( 171-)  A      NH2    0.20    2.50  INTRA BL
 218 ALA   ( 223-)  A      O   <->  221 ARG   ( 226-)  A      NE     0.20    2.50  INTRA BF
 171 TRP   ( 176-)  A      CE3 <->  261  CA   ( 304-)  A     CA      0.18    3.02  INTRA BF
 234 ARG   ( 239-)  A      NH1 <->  255 CYS   ( 260-)  A      CB     0.18    2.92  INTRA BF
 199 ILE   ( 204-)  A      CG1 <->  200 PRO   ( 205-)  A      CD     0.15    3.05  INTRA BF
 232 CYS   ( 237-)  A      C   <->  234 ARG   ( 239-)  A      N      0.14    2.76  INTRA BF
  19 LEU   (  22-)  A      N   <->   39 GLN   (  42-)  A      O      0.12    2.58  INTRA BL
  14 ILE   (  17-)  A      CD1 <->   95 ILE   ( 100-)  A      CD1    0.11    3.09  INTRA BL
 232 CYS   ( 237-)  A      SG  <->  234 ARG   ( 239-)  A      CB     0.11    3.29  INTRA BF
 165 LEU   ( 170-)  A      O   <->  169 ILE   ( 174-)  A      CG1    0.10    2.70  INTRA BL
 252 CYS   ( 257-)  A      C   <->  254 GLY   ( 259-)  A      N      0.10    2.80  INTRA BF
 234 ARG   ( 239-)  A      NH1 <->  255 CYS   ( 260-)  A      SG     0.09    3.21  INTRA BF
  64 HIS   (  67-)  A      CD2 <->   66 GLN   (  69-)  A      NE2    0.09    3.01  INTRA BL
 180 LYS   ( 185-)  A      C   <->  182 LYS   ( 187-)  A      N      0.09    2.81  INTRA BF
 223 LYS   ( 228-)  A      O   <->  227 ARG   ( 232-)  A      NH1    0.08    2.62  INTRA BF
  90 THR   (  95-)  A      N   <->   93 LYS   (  98-)  A      O      0.08    2.62  INTRA BF
  64 HIS   (  67-)  A      CD2 <->   66 GLN   (  69-)  A      N      0.08    3.02  INTRA BF
 235 CYS   ( 240-)  A      SG  <->  237 SER   ( 242-)  A      OG     0.08    2.92  INTRA BF
 171 TRP   ( 176-)  A      CZ3 <->  223 LYS   ( 228-)  A      CG     0.08    3.12  INTRA BF
 143 PHE   ( 148-)  A      C   <->  145 ASN   ( 150-)  A      N      0.08    2.82  INTRA BF
 149 ALA   ( 154-)  A      O   <->  166 ARG   ( 171-)  A      NH1    0.07    2.63  INTRA BF
 107 ARG   ( 112-)  A      NE  <->  109 GLU   ( 114-)  A      OE2    0.06    2.64  INTRA BF
   8 ASP   (  11-)  A      O   <->   12 ALA   (  15-)  A      N      0.05    2.65  INTRA BF
 252 CYS   ( 257-)  A      SG  <->  254 GLY   ( 259-)  A      N      0.05    3.25  INTRA BF
  66 GLN   (  69-)  A      CB  <->   67 LEU   (  70-)  A      N      0.05    2.65  INTRA BL
 196 LEU   ( 201-)  A      O   <->  200 PRO   ( 205-)  A      CG     0.05    2.75  INTRA BL
 169 ILE   ( 174-)  A      CG1 <->  199 ILE   ( 204-)  A      CG1    0.04    3.16  INTRA BF
 185 ASN   ( 190-)  A      OD1 <->  187 ALA   ( 192-)  A      N      0.04    2.66  INTRA BF
  80 THR   (  85-)  A      O   <->   82 ARG   (  87-)  A      N      0.03    2.67  INTRA BF
 123 ASP   ( 128-)  A      O   <->  126 ASP   ( 131-)  A      N      0.02    2.68  INTRA BF
 146 ARG   ( 151-)  A      NH1 <->  154 ASP   ( 159-)  A      OD2    0.02    2.68  INTRA BF
  77 GLY   (  80-)  A      C   <->   78 GLU   (  81-)  A      C      0.02    2.78  INTRA BF
 176 THR   ( 181-)  A      CG2 <->  257 HIS   ( 262-)  A      CA     0.02    3.18  INTRA BF
   2 GLU   (   5-)  A      N   <->    3 ILE   (   6-)  A      N      0.01    2.59  INTRA BF
 153 LEU   ( 158-)  A      N   <->  154 ASP   ( 159-)  A      N      0.01    2.59  INTRA BF
 116 PHE   ( 121-)  A      O   <->  119 ARG   ( 124-)  A      N      0.01    2.69  INTRA BF
  76 THR   (  79-)  A      OG1 <->   90 THR   (  95-)  A      O      0.01    2.39  INTRA BL

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.

 234 ARG   ( 239-)  A      -6.96
  67 LEU   (  70-)  A      -5.99
  68 TYR   (  71-)  A      -5.92
 207 ARG   ( 212-)  A      -5.78
   4 ARG   (   7-)  A      -5.60
 247 ARG   ( 252-)  A      -5.21
 172 GLN   ( 177-)  A      -5.20
 210 VAL   ( 215-)  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

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.

 244 LEU   ( 249-)  A   -2.59

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  35 GLN   (  38-)  A
 216 HIS   ( 221-)  A
 257 HIS   ( 262-)  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.

   4 ARG   (   7-)  A      NE
  22 VAL   (  25-)  A      N
  47 ARG   (  50-)  A      NE
  57 ASN   (  60-)  A      ND2
  71 TRP   (  74-)  A      NE1
  75 ASP   (  78-)  A      N
 100 ALA   ( 105-)  A      N
 107 ARG   ( 112-)  A      N
 130 THR   ( 135-)  A      N
 163 ASN   ( 168-)  A      N
 168 GLU   ( 173-)  A      N
 172 GLN   ( 177-)  A      NE2
 174 GLY   ( 179-)  A      N
 219 LEU   ( 224-)  A      N
 220 PHE   ( 225-)  A      N
 226 HIS   ( 231-)  A      N
 233 GLU   ( 238-)  A      N
 234 ARG   ( 239-)  A      NE
 234 ARG   ( 239-)  A      NH1
 234 ARG   ( 239-)  A      NH2
 244 LEU   ( 249-)  A      N
 250 TYR   ( 255-)  A      N
 256 GLN   ( 261-)  A      NE2

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+.

 259  CA   ( 302-)  A   -.-  -.-  Part of ionic cluster
 259  CA   ( 302-)  A   -.-  -.-  Too few ligands (1)
 260  CA   ( 303-)  A   -.-  -.-  Too few ligands (2)
 261  CA   ( 304-)  A   -.-  -.-  Low probability ion. B= 87.4

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.

 136 GLU   ( 141-)  A   H-bonding suggests Gln
 211 ASP   ( 216-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.299
  2nd generation packing quality :  -0.791
  Ramachandran plot appearance   :  -3.796 (poor)
  chi-1/chi-2 rotamer normality  :  -3.202 (poor)
  Backbone conformation          :  -0.355

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.371 (tight)
  Bond angles                    :   0.729
  Omega angle restraints         :   0.342 (tight)
  Side chain planarity           :   0.208 (tight)
  Improper dihedral distribution :   0.552
  B-factor distribution          :   1.172
  Inside/Outside distribution    :   1.016

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.371 (tight)
  Bond angles                    :   0.729
  Omega angle restraints         :   0.342 (tight)
  Side chain planarity           :   0.208 (tight)
  Improper dihedral distribution :   0.552
  B-factor distribution          :   1.172
  Inside/Outside distribution    :   1.016
==============

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.