WHAT IF Check report

This file was created 2011-12-28 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1itv.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.168
CA-only RMS fit for the two chains : 0.662

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

 393 SO4   ( 196-)  A  -
 394 SO4   ( 198-)  A  -
 395 SO4   ( 196-)  B  -
 396 SO4   ( 197-)  B  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  17 ASN   (  17-)  A  -   CB
  17 ASN   (  17-)  A  -   CG
  17 ASN   (  17-)  A  -   OD1
  17 ASN   (  17-)  A  -   ND2
  34 ARG   (  34-)  A  -   CB
  34 ARG   (  34-)  A  -   CG
  34 ARG   (  34-)  A  -   CD
  34 ARG   (  34-)  A  -   NE
  34 ARG   (  34-)  A  -   CZ
  34 ARG   (  34-)  A  -   NH1
  34 ARG   (  34-)  A  -   NH2
  37 ARG   (  37-)  A  -   CG
  37 ARG   (  37-)  A  -   CD
  37 ARG   (  37-)  A  -   NE
  37 ARG   (  37-)  A  -   CZ
  37 ARG   (  37-)  A  -   NH1
  37 ARG   (  37-)  A  -   NH2
  47 LYS   (  47-)  A  -   CE
  47 LYS   (  47-)  A  -   NZ
 140 ARG   ( 140-)  A  -   CD
 140 ARG   ( 140-)  A  -   NE
 140 ARG   ( 140-)  A  -   CZ
 140 ARG   ( 140-)  A  -   NH1
 140 ARG   ( 140-)  A  -   NH2
 172 SER   ( 172-)  A  -   CB
And so on for a total of 66 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 195 ASP   ( 195-)  A  -   O
 390 ASP   ( 195-)  B  -   N
 390 ASP   ( 195-)  B  -   CA
 390 ASP   ( 195-)  B  -   C
 390 ASP   ( 195-)  B  -   O

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

Note: Ramachandran plot

Chain identifier: B

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

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  29 ARG   (  29-)  A
  34 ARG   (  34-)  A
  37 ARG   (  37-)  A
  53 ARG   (  53-)  A
  73 ARG   (  73-)  A
  87 ARG   (  87-)  A
  88 ARG   (  88-)  A
 106 ARG   ( 106-)  A
 109 ARG   ( 109-)  A
 118 ARG   ( 118-)  A
 122 ARG   ( 122-)  A
 140 ARG   ( 140-)  A
 156 ARG   ( 156-)  A
 165 ARG   ( 165-)  A
 173 ARG   ( 173-)  A
 224 ARG   (  29-)  B
 229 ARG   (  34-)  B
 248 ARG   (  53-)  B
 268 ARG   (  73-)  B
 282 ARG   (  87-)  B
 283 ARG   (  88-)  B
 301 ARG   ( 106-)  B
 304 ARG   ( 109-)  B
 313 ARG   ( 118-)  B
 317 ARG   ( 122-)  B
 335 ARG   ( 140-)  B
 351 ARG   ( 156-)  B
 368 ARG   ( 173-)  B

Warning: Tyrosine convention problem

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

  20 TYR   (  20-)  A
  78 TYR   (  78-)  A
 187 TYR   ( 187-)  A
 215 TYR   (  20-)  B
 222 TYR   (  27-)  B
 273 TYR   (  78-)  B
 382 TYR   ( 187-)  B

Warning: Phenylalanine convention problem

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

  30 PHE   (  30-)  A
  42 PHE   (  42-)  A
  68 PHE   (  68-)  A
  70 PHE   (  70-)  A
 166 PHE   ( 166-)  A
 225 PHE   (  30-)  B
 237 PHE   (  42-)  B
 263 PHE   (  68-)  B

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.

   1 ASP   (   1-)  A
   2 ASP   (   2-)  A
  56 ASP   (  56-)  A
  97 ASP   (  97-)  A
 151 ASP   ( 151-)  A
 180 ASP   ( 180-)  A
 188 ASP   ( 188-)  A
 196 ASP   (   1-)  B
 197 ASP   (   2-)  B
 251 ASP   (  56-)  B
 292 ASP   (  97-)  B
 346 ASP   ( 151-)  B
 375 ASP   ( 180-)  B
 383 ASP   ( 188-)  B
 390 ASP   ( 195-)  B

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.

 157 GLU   ( 157-)  A
 175 GLU   ( 175-)  A
 194 GLU   ( 194-)  A
 352 GLU   ( 157-)  B
 389 GLU   ( 194-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.288
RMS-deviation in bond distances: 0.007

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.569
RMS-deviation in bond angles: 1.294

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.

   1 ASP   (   1-)  A
   2 ASP   (   2-)  A
  29 ARG   (  29-)  A
  34 ARG   (  34-)  A
  37 ARG   (  37-)  A
  53 ARG   (  53-)  A
  56 ASP   (  56-)  A
  73 ARG   (  73-)  A
  87 ARG   (  87-)  A
  88 ARG   (  88-)  A
  97 ASP   (  97-)  A
 106 ARG   ( 106-)  A
 109 ARG   ( 109-)  A
 118 ARG   ( 118-)  A
 122 ARG   ( 122-)  A
 140 ARG   ( 140-)  A
 151 ASP   ( 151-)  A
 156 ARG   ( 156-)  A
 157 GLU   ( 157-)  A
 165 ARG   ( 165-)  A
 173 ARG   ( 173-)  A
 175 GLU   ( 175-)  A
 180 ASP   ( 180-)  A
 188 ASP   ( 188-)  A
 194 GLU   ( 194-)  A
 196 ASP   (   1-)  B
 197 ASP   (   2-)  B
 224 ARG   (  29-)  B
 229 ARG   (  34-)  B
 248 ARG   (  53-)  B
 251 ASP   (  56-)  B
 268 ARG   (  73-)  B
 282 ARG   (  87-)  B
 283 ARG   (  88-)  B
 292 ASP   (  97-)  B
 301 ARG   ( 106-)  B
 304 ARG   ( 109-)  B
 313 ARG   ( 118-)  B
 317 ARG   ( 122-)  B
 335 ARG   ( 140-)  B
 346 ASP   ( 151-)  B
 351 ARG   ( 156-)  B
 352 GLU   ( 157-)  B
 368 ARG   ( 173-)  B
 375 ASP   ( 180-)  B
 383 ASP   ( 188-)  B
 389 GLU   ( 194-)  B
 390 ASP   ( 195-)  B

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.

 120 LEU   ( 120-)  A    -2.6
 315 LEU   ( 120-)  B    -2.4
 370 GLU   ( 175-)  B    -2.3
 253 VAL   (  58-)  B    -2.2
  58 VAL   (  58-)  A    -2.2
  92 LEU   (  92-)  A    -2.2
 190 LEU   ( 190-)  A    -2.2
  34 ARG   (  34-)  A    -2.1
 165 ARG   ( 165-)  A    -2.1
 287 LEU   (  92-)  B    -2.1
 157 GLU   ( 157-)  A    -2.1
  37 ARG   (  37-)  A    -2.0
 100 GLN   ( 100-)  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.

  40 GLY   (  40-)  A  PRO omega poor
  65 LYS   (  65-)  A  Poor phi/psi
  85 GLY   (  85-)  A  PRO omega poor
 107 SER   ( 107-)  A  Poor phi/psi
 128 GLN   ( 128-)  A  Poor phi/psi
 156 ARG   ( 156-)  A  Poor phi/psi
 157 GLU   ( 157-)  A  Poor phi/psi
 164 ASP   ( 164-)  A  Poor phi/psi
 175 GLU   ( 175-)  A  Poor phi/psi
 190 LEU   ( 190-)  A  Poor phi/psi
 191 GLN   ( 191-)  A  Poor phi/psi
 235 GLY   (  40-)  B  PRO omega poor
 252 SER   (  57-)  B  Poor phi/psi
 260 LYS   (  65-)  B  Poor phi/psi
 280 GLY   (  85-)  B  PRO omega poor
 302 SER   ( 107-)  B  Poor phi/psi
 323 GLN   ( 128-)  B  Poor phi/psi
 352 GLU   ( 157-)  B  Poor phi/psi
 359 ASP   ( 164-)  B  Poor phi/psi
 370 GLU   ( 175-)  B  Poor phi/psi
 385 LEU   ( 190-)  B  Poor phi/psi
 389 GLU   ( 194-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.862

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!

  15 ILE   (  15-)  A      0
  17 ASN   (  17-)  A      0
  23 LYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  32 GLU   (  32-)  A      0
  34 ARG   (  34-)  A      0
  36 SER   (  36-)  A      0
  39 GLN   (  39-)  A      0
  41 PRO   (  41-)  A      0
  47 LYS   (  47-)  A      0
  48 TRP   (  48-)  A      0
  64 SER   (  64-)  A      0
  65 LYS   (  65-)  A      0
  71 SER   (  71-)  A      0
  73 ARG   (  73-)  A      0
  79 THR   (  79-)  A      0
  81 ALA   (  81-)  A      0
  84 LEU   (  84-)  A      0
  86 PRO   (  86-)  A      0
  87 ARG   (  87-)  A      0
  92 LEU   (  92-)  A      0
  94 LEU   (  94-)  A      0
  99 ALA   (  99-)  A      0
 100 GLN   ( 100-)  A      0
 102 THR   ( 102-)  A      0
And so on for a total of 183 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 : 1.109

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!

 303 GLY   ( 108-)  B   1.73   10
 108 GLY   ( 108-)  A   1.57   13

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.

 196 ASP   (   1-)  B      N   <->  398 HOH   ( 214 )  B      O      0.28    2.42  INTRA
 368 ARG   ( 173-)  B      NH1 <->  373 GLN   ( 178-)  B      CD     0.26    2.84  INTRA BF
  66 LYS   (  66-)  A      NZ  <->   79 THR   (  79-)  A      CG2    0.22    2.88  INTRA BL
 368 ARG   ( 173-)  B      NH1 <->  373 GLN   ( 178-)  B      NE2    0.21    2.64  INTRA BF
 368 ARG   ( 173-)  B      CZ  <->  373 GLN   ( 178-)  B      NE2    0.21    2.89  INTRA BF
 368 ARG   ( 173-)  B      NH2 <->  373 GLN   ( 178-)  B      NE2    0.19    2.66  INTRA BF
  32 GLU   (  32-)  A      CB  <->  156 ARG   ( 156-)  A      NH2    0.17    2.93  INTRA BF
 173 ARG   ( 173-)  A      NH2 <->  178 GLN   ( 178-)  A      NE2    0.16    2.69  INTRA
 257 PRO   (  62-)  B      O   <->  260 LYS   (  65-)  B      NZ     0.16    2.54  INTRA
 248 ARG   (  53-)  B      CD  <->  249 LYS   (  54-)  B      N      0.11    2.89  INTRA
 239 ILE   (  44-)  B      O   <->  243 TRP   (  48-)  B      N      0.11    2.59  INTRA BL
 300 LEU   ( 105-)  B      O   <->  308 LEU   ( 113-)  B      N      0.10    2.60  INTRA
 248 ARG   (  53-)  B      NH2 <->  266 SER   (  71-)  B      OG     0.10    2.60  INTRA
 257 PRO   (  62-)  B      CG  <->  301 ARG   ( 106-)  B      NE     0.09    3.01  INTRA
  61 GLU   (  61-)  A      OE1 <->   64 SER   (  64-)  A      N      0.09    2.61  INTRA BL
 118 ARG   ( 118-)  A      CZ  <->  148 ASP   ( 148-)  A      OD1    0.07    2.73  INTRA
 174 SER   ( 174-)  A      C   <->  176 LEU   ( 176-)  A      N      0.07    2.83  INTRA BF
 359 ASP   ( 164-)  B      CG  <->  360 ARG   ( 165-)  B      N      0.06    2.94  INTRA
 125 VAL   ( 125-)  A      CG1 <->  126 LYS   ( 126-)  A      N      0.06    2.94  INTRA
 353 LYS   ( 158-)  B      NZ  <->  366 SER   ( 171-)  B      OG     0.05    2.65  INTRA
 106 ARG   ( 106-)  A      N   <->  154 GLN   ( 154-)  A      NE2    0.04    2.81  INTRA
 150 HIS   ( 150-)  A      O   <->  397 HOH   ( 238 )  A      O      0.04    2.36  INTRA
 384 ILE   ( 189-)  B      C   <->  386 GLN   ( 191-)  B      N      0.04    2.86  INTRA
 301 ARG   ( 106-)  B      CG  <->  349 GLN   ( 154-)  B      NE2    0.03    3.07  INTRA
  32 GLU   (  32-)  A      CD  <->  156 ARG   ( 156-)  A      NH2    0.03    3.07  INTRA BF
 145 VAL   ( 145-)  A      CG1 <->  146 PRO   ( 146-)  A      CD     0.03    3.17  INTRA
 340 VAL   ( 145-)  B      CG1 <->  356 PHE   ( 161-)  B      CD2    0.03    3.17  INTRA
  61 GLU   (  61-)  A      O   <->   65 LYS   (  65-)  A      N      0.03    2.67  INTRA BL
 301 ARG   ( 106-)  B      N   <->  349 GLN   ( 154-)  B      NE2    0.02    2.83  INTRA
 276 ALA   (  81-)  B      N   <->  398 HOH   ( 236 )  B      O      0.02    2.68  INTRA
 287 LEU   (  92-)  B      N   <->  288 GLY   (  93-)  B      N      0.02    2.58  INTRA BL
 253 VAL   (  58-)  B      CG2 <->  254 PHE   (  59-)  B      N      0.02    2.98  INTRA BL
  29 ARG   (  29-)  A      NH2 <->   42 PHE   (  42-)  A      CZ     0.02    3.08  INTRA
  32 GLU   (  32-)  A      CG  <->   33 GLY   (  33-)  A      N      0.02    2.98  INTRA BF
 335 ARG   ( 140-)  B      CB  <->  398 HOH   ( 279 )  B      O      0.02    2.78  INTRA
  62 PRO   (  62-)  A      O   <->   65 LYS   (  65-)  A      NZ     0.02    2.68  INTRA
  58 VAL   (  58-)  A      CG2 <->   59 PHE   (  59-)  A      N      0.02    2.98  INTRA BL
  87 ARG   (  87-)  A      NE  <->  397 HOH   ( 210 )  A      O      0.01    2.69  INTRA BL
 112 MET   ( 112-)  A      O   <->  123 PHE   ( 123-)  A      N      0.01    2.69  INTRA BL
 302 SER   ( 107-)  B      CB  <->  303 GLY   ( 108-)  B      N      0.01    2.69  INTRA BF
 302 SER   ( 107-)  B      OG  <->  303 GLY   ( 108-)  B      N      0.01    2.59  INTRA BF
 227 GLU   (  32-)  B      CD  <->  351 ARG   ( 156-)  B      NH1    0.01    3.09  INTRA BF
 306 LYS   ( 111-)  B      NZ  <->  319 ASP   ( 124-)  B      OD1    0.01    2.69  INTRA
 333 VAL   ( 138-)  B      O   <->  337 PHE   ( 142-)  B      N      0.01    2.69  INTRA
 282 ARG   (  87-)  B      NH2 <->  398 HOH   ( 232 )  B      O      0.01    2.69  INTRA BL
 196 ASP   (   1-)  B      CB  <->  197 ASP   (   2-)  B      N      0.01    2.69  INTRA B3

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

  34 ARG   (  34-)  A      -8.36
 229 ARG   (  34-)  B      -7.50
 328 ARG   ( 133-)  B      -7.46
 109 ARG   ( 109-)  A      -7.17
 106 ARG   ( 106-)  A      -7.04
 304 ARG   ( 109-)  B      -7.00
 301 ARG   ( 106-)  B      -6.37
 156 ARG   ( 156-)  A      -6.01
 351 ARG   ( 156-)  B      -5.90
 248 ARG   (  53-)  B      -5.84
 389 GLU   ( 194-)  B      -5.65
  32 GLU   (  32-)  A      -5.40
   5 ASN   (   5-)  A      -5.19
 212 ASN   (  17-)  B      -5.16
 227 GLU   (  32-)  B      -5.15
  53 ARG   (  53-)  A      -5.10

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: 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: B

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.

  91 LYS   (  91-)  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

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 397 HOH   ( 261 )  A      O
 397 HOH   ( 270 )  A      O
 398 HOH   ( 294 )  B      O
 398 HOH   ( 295 )  B      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.

  18 GLN   (  18-)  A
 163 GLN   ( 163-)  A
 177 ASN   ( 177-)  A
 178 GLN   ( 178-)  A
 345 HIS   ( 150-)  B
 349 GLN   ( 154-)  B
 372 ASN   ( 177-)  B

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.

   7 ASN   (   7-)  A      N
   8 ILE   (   8-)  A      N
  16 GLY   (  16-)  A      N
  31 SER   (  31-)  A      N
  33 GLY   (  33-)  A      N
 100 GLN   ( 100-)  A      N
 106 ARG   ( 106-)  A      N
 118 ARG   ( 118-)  A      N
 178 GLN   ( 178-)  A      N
 181 GLN   ( 181-)  A      N
 190 LEU   ( 190-)  A      N
 191 GLN   ( 191-)  A      N
 202 ASN   (   7-)  B      N
 203 ILE   (   8-)  B      N
 224 ARG   (  29-)  B      NE
 248 ARG   (  53-)  B      N
 249 LYS   (  54-)  B      N
 258 LEU   (  63-)  B      N
 278 VAL   (  83-)  B      N
 295 GLN   ( 100-)  B      N
 298 GLY   ( 103-)  B      N
 330 ALA   ( 135-)  B      N
 360 ARG   ( 165-)  B      N
 377 VAL   ( 182-)  B      N
 379 TYR   ( 184-)  B      N
 385 LEU   ( 190-)  B      N
 386 GLN   ( 191-)  B      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.

 251 ASP   (  56-)  B   H-bonding suggests Asn
 346 ASP   ( 151-)  B   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 :  -0.182
  2nd generation packing quality :  -1.642
  Ramachandran plot appearance   :  -1.422
  chi-1/chi-2 rotamer normality  :  -1.862
  Backbone conformation          :  -1.044

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.288 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.205 (tight)
  Improper dihedral distribution :   0.606
  B-factor distribution          :   1.023
  Inside/Outside distribution    :   0.906

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 :   0.3
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -2.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.288 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.205 (tight)
  Improper dihedral distribution :   0.606
  B-factor distribution          :   1.023
  Inside/Outside distribution    :   0.906
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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,
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      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.