WHAT IF Check report

This file was created 2012-01-30 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 pdb3irt.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 : 0.415
CA-only RMS fit for the two chains : 0.268

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: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 451 HOH   ( 225 )  A      O
 452 HOH   ( 225 )  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: 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.

   1 MET   (   1-)  A    High
   2 GLN   (   2-)  A    High
   7 GLU   (   7-)  A    High
  11 GLU   (  11-)  A    High
  24 GLY   (  24-)  A    High
  25 GLN   (  25-)  A    High
  27 ARG   (  27-)  A    High
  35 GLU   (  35-)  A    High
  36 GLU   (  36-)  A    High
  37 GLU   (  37-)  A    High
  38 SER   (  38-)  A    High
  39 LEU   (  39-)  A    High
  40 GLY   (  40-)  A    High
  41 SER   (  41-)  A    High
  45 PRO   (  45-)  A    High
  62 PHE   (  62-)  A    High
  65 LYS   (  65-)  A    High
  66 GLN   (  66-)  A    High
  68 GLU   (  68-)  A    High
  69 GLU   (  69-)  A    High
  70 LEU   (  70-)  A    High
  71 LYS   (  71-)  A    High
  72 GLY   (  72-)  A    High
  73 GLN   (  73-)  A    High
  74 GLU   (  74-)  A    High
And so on for a total of 98 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.559 over 2676 bonds
Average difference in B over a bond : 6.10
RMS difference in B over a bond : 8.04

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.

 153 ARG   ( 153-)  A

Warning: Tyrosine convention problem

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

 173 TYR   ( 173-)  A
 396 TYR   ( 173-)  B

Warning: Phenylalanine convention problem

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

  28 PHE   (  28-)  A
 108 PHE   ( 108-)  A
 165 PHE   ( 165-)  A
 181 PHE   ( 181-)  A
 204 PHE   ( 204-)  A
 214 PHE   ( 214-)  A
 251 PHE   (  28-)  B
 331 PHE   ( 108-)  B
 388 PHE   ( 165-)  B
 404 PHE   ( 181-)  B
 427 PHE   ( 204-)  B
 437 PHE   ( 214-)  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.

 110 ASP   ( 110-)  A
 144 ASP   ( 144-)  A
 176 ASP   ( 176-)  A
 196 ASP   ( 196-)  A
 333 ASP   ( 110-)  B
 367 ASP   ( 144-)  B
 399 ASP   ( 176-)  B
 419 ASP   ( 196-)  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.

   7 GLU   (   7-)  A
  36 GLU   (  36-)  A
  37 GLU   (  37-)  A
  60 GLU   (  60-)  A
  69 GLU   (  69-)  A
 120 GLU   ( 120-)  A
 137 GLU   ( 137-)  A
 190 GLU   ( 190-)  A
 203 GLU   ( 203-)  A
 211 GLU   ( 211-)  A
 230 GLU   (   7-)  B
 259 GLU   (  36-)  B
 260 GLU   (  37-)  B
 283 GLU   (  60-)  B
 292 GLU   (  69-)  B
 343 GLU   ( 120-)  B
 360 GLU   ( 137-)  B
 413 GLU   ( 190-)  B
 426 GLU   ( 203-)  B
 434 GLU   ( 211-)  B

Geometric checks

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.

 153 ARG   ( 153-)  A      CD   NE   CZ  131.96    5.7
 376 ARG   ( 153-)  B      CD   NE   CZ  131.62    5.5

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.

   7 GLU   (   7-)  A
  36 GLU   (  36-)  A
  37 GLU   (  37-)  A
  60 GLU   (  60-)  A
  69 GLU   (  69-)  A
 110 ASP   ( 110-)  A
 120 GLU   ( 120-)  A
 137 GLU   ( 137-)  A
 144 ASP   ( 144-)  A
 153 ARG   ( 153-)  A
 176 ASP   ( 176-)  A
 190 GLU   ( 190-)  A
 196 ASP   ( 196-)  A
 203 GLU   ( 203-)  A
 211 GLU   ( 211-)  A
 230 GLU   (   7-)  B
 259 GLU   (  36-)  B
 260 GLU   (  37-)  B
 283 GLU   (  60-)  B
 292 GLU   (  69-)  B
 333 ASP   ( 110-)  B
 343 GLU   ( 120-)  B
 360 GLU   ( 137-)  B
 367 ASP   ( 144-)  B
 399 ASP   ( 176-)  B
 413 GLU   ( 190-)  B
 419 ASP   ( 196-)  B
 426 GLU   ( 203-)  B
 434 GLU   ( 211-)  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.

  62 PHE   (  62-)  A    -2.8
 285 PHE   (  62-)  B    -2.7
 162 PHE   ( 162-)  A    -2.4
 385 PHE   ( 162-)  B    -2.4
 295 GLY   (  72-)  B    -2.3
 123 LYS   ( 123-)  A    -2.2
 346 LYS   ( 123-)  B    -2.2
  35 GLU   (  35-)  A    -2.2
 258 GLU   (  35-)  B    -2.2
 153 ARG   ( 153-)  A    -2.2
  36 GLU   (  36-)  A    -2.1
 259 GLU   (  36-)  B    -2.1

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  38 SER   (  38-)  A  Poor phi/psi
  44 ALA   (  44-)  A  PRO omega poor
  70 LEU   (  70-)  A  Poor phi/psi
  71 LYS   (  71-)  A  omega poor
  72 GLY   (  72-)  A  Poor phi/psi
  88 ASN   (  88-)  A  Poor phi/psi
 152 CYS   ( 152-)  A  Poor phi/psi
 153 ARG   ( 153-)  A  Poor phi/psi
 154 VAL   ( 154-)  A  Poor phi/psi
 157 LYS   ( 157-)  A  Poor phi/psi
 159 ASN   ( 159-)  A  Poor phi/psi
 169 ASP   ( 169-)  A  Poor phi/psi
 191 ASP   ( 191-)  A  Poor phi/psi
 206 GLU   ( 206-)  A  Poor phi/psi
 207 ARG   ( 207-)  A  Poor phi/psi
 209 GLN   ( 209-)  A  Poor phi/psi
 261 SER   (  38-)  B  Poor phi/psi
 267 ALA   (  44-)  B  PRO omega poor
 293 LEU   (  70-)  B  Poor phi/psi
 294 LYS   (  71-)  B  Poor phi/psi, omega poor
 295 GLY   (  72-)  B  Poor phi/psi
 296 GLN   (  73-)  B  omega poor
 297 GLU   (  74-)  B  Poor phi/psi
 311 ASN   (  88-)  B  Poor phi/psi
 375 CYS   ( 152-)  B  Poor phi/psi
 376 ARG   ( 153-)  B  Poor phi/psi
 377 VAL   ( 154-)  B  Poor phi/psi
 380 LYS   ( 157-)  B  Poor phi/psi
 382 ASN   ( 159-)  B  Poor phi/psi
 392 ASP   ( 169-)  B  Poor phi/psi
 414 ASP   ( 191-)  B  Poor phi/psi
 429 GLU   ( 206-)  B  Poor phi/psi
 430 ARG   ( 207-)  B  Poor phi/psi
 432 GLN   ( 209-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.159

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 LEU   (   3-)  A      0
   8 ILE   (   8-)  A      0
   9 ASN   (   9-)  A      0
  20 LEU   (  20-)  A      0
  25 GLN   (  25-)  A      0
  32 LEU   (  32-)  A      0
  34 LEU   (  34-)  A      0
  35 GLU   (  35-)  A      0
  36 GLU   (  36-)  A      0
  37 GLU   (  37-)  A      0
  38 SER   (  38-)  A      0
  43 PRO   (  43-)  A      0
  44 ALA   (  44-)  A      0
  47 CYS   (  47-)  A      0
  70 LEU   (  70-)  A      0
  71 LYS   (  71-)  A      0
  73 GLN   (  73-)  A      0
  74 GLU   (  74-)  A      0
  84 GLN   (  84-)  A      0
  88 ASN   (  88-)  A      0
  90 CYS   (  90-)  A      0
 102 ASN   ( 102-)  A      0
 110 ASP   ( 110-)  A      0
 121 THR   ( 121-)  A      0
 124 MET   ( 124-)  A      0
And so on for a total of 158 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 : 3.936

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!

 295 GLY   (  72-)  B   2.56   80

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].

  45 PRO   (  45-)  A    47.7 half-chair C-delta/C-gamma (54 degrees)
  54 PRO   (  54-)  A    51.4 half-chair C-delta/C-gamma (54 degrees)
  77 PRO   (  77-)  A  -115.4 envelop C-gamma (-108 degrees)
 268 PRO   (  45-)  B    47.8 half-chair C-delta/C-gamma (54 degrees)
 277 PRO   (  54-)  B    51.4 half-chair C-delta/C-gamma (54 degrees)
 300 PRO   (  77-)  B  -115.3 envelop C-gamma (-108 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.

 313 CYS   (  90-)  B      CB  <->  450  CL   ( 224-)  B     CL      0.29    2.91  INTRA BF
  90 CYS   (  90-)  A      CB  <->  449  CL   ( 224-)  A     CL      0.17    3.03  INTRA BF
 294 LYS   (  71-)  B      CB  <->  295 GLY   (  72-)  B      N      0.15    2.55  INTRA BF
 303 TYR   (  80-)  B      CE2 <->  352 ARG   ( 129-)  B      NE     0.14    2.96  INTRA BL
 436 ARG   ( 213-)  B      NH2 <->  452 HOH   ( 225 )  B      O      0.12    2.58  INTRA BF
  80 TYR   (  80-)  A      CE2 <->  129 ARG   ( 129-)  A      NE     0.11    2.99  INTRA BL
  37 GLU   (  37-)  A      C   <->   39 LEU   (  39-)  A      N      0.11    2.79  INTRA BF
 431 GLU   ( 208-)  B      O   <->  433 GLY   ( 210-)  B      N      0.11    2.59  INTRA BF
 260 GLU   (  37-)  B      C   <->  262 LEU   (  39-)  B      N      0.11    2.79  INTRA BF
 208 GLU   ( 208-)  A      O   <->  210 GLY   ( 210-)  A      N      0.09    2.61  INTRA BF
 359 ASN   ( 136-)  B      OD1 <->  362 ILE   ( 139-)  B      N      0.08    2.62  INTRA BL
  71 LYS   (  71-)  A      O   <->   73 GLN   (  73-)  A      N      0.08    2.62  INTRA BF
 136 ASN   ( 136-)  A      OD1 <->  139 ILE   ( 139-)  A      N      0.08    2.62  INTRA BL
 434 GLU   ( 211-)  B      OE2 <->  436 ARG   ( 213-)  B      NH1    0.06    2.64  INTRA BF
 305 MET   (  82-)  B      N   <->  320 HIS   (  97-)  B      NE2    0.06    2.94  INTRA BL
  82 MET   (  82-)  A      N   <->   97 HIS   (  97-)  A      NE2    0.05    2.95  INTRA BL
 211 GLU   ( 211-)  A      OE2 <->  213 ARG   ( 213-)  A      NH1    0.05    2.65  INTRA BF
   1 MET   (   1-)  A      SD  <->  451 HOH   ( 231 )  A      O      0.05    2.95  INTRA BF
 312 SER   (  89-)  B      N   <->  313 CYS   (  90-)  B      N      0.05    2.55  INTRA BL
  63 ARG   (  63-)  A      NH1 <->  204 PHE   ( 204-)  A      CE2    0.05    3.05  INTRA BF
 286 ARG   (  63-)  B      NH1 <->  427 PHE   ( 204-)  B      CE2    0.05    3.05  INTRA BF
  81 PHE   (  81-)  A      O   <->  129 ARG   ( 129-)  A      NH1    0.05    2.65  INTRA BL
  89 SER   (  89-)  A      N   <->   90 CYS   (  90-)  A      N      0.04    2.56  INTRA BL
 288 LYS   (  65-)  B      O   <->  292 GLU   (  69-)  B      N      0.03    2.67  INTRA BF
  65 LYS   (  65-)  A      O   <->   69 GLU   (  69-)  A      N      0.03    2.67  INTRA BF
 376 ARG   ( 153-)  B      CB  <->  377 VAL   ( 154-)  B      N      0.03    2.67  INTRA BF
 388 PHE   ( 165-)  B      CE2 <->  424 CYS   ( 201-)  B      SG     0.03    3.37  INTRA BL
 412 SER   ( 189-)  B      C   <->  414 ASP   ( 191-)  B      N      0.03    2.87  INTRA BF
 189 SER   ( 189-)  A      C   <->  191 ASP   ( 191-)  A      N      0.03    2.87  INTRA BF
 207 ARG   ( 207-)  A      NH1 <->  451 HOH   ( 230 )  A      O      0.03    2.67  INTRA BF
 304 PHE   (  81-)  B      O   <->  352 ARG   ( 129-)  B      NH1    0.02    2.68  INTRA BL
  36 GLU   (  36-)  A      CG  <->   37 GLU   (  37-)  A      N      0.02    2.98  INTRA BF
 165 PHE   ( 165-)  A      CE2 <->  201 CYS   ( 201-)  A      SG     0.02    3.38  INTRA BL
 326 GLN   ( 103-)  B      N   <->  452 HOH   ( 243 )  B      O      0.02    2.68  INTRA BL
  37 GLU   (  37-)  A      CG  <->   38 SER   (  38-)  A      N      0.02    2.98  INTRA BF
 390 ASN   ( 167-)  B      ND2 <->  412 SER   ( 189-)  B      C      0.02    3.08  INTRA BF
 167 ASN   ( 167-)  A      ND2 <->  189 SER   ( 189-)  A      C      0.02    3.08  INTRA BF
 260 GLU   (  37-)  B      CG  <->  261 SER   (  38-)  B      N      0.02    2.98  INTRA BF
 259 GLU   (  36-)  B      CG  <->  260 GLU   (  37-)  B      N      0.01    2.99  INTRA BF
  56 THR   (  56-)  A      OG1 <->   59 HIS   (  59-)  A      ND1    0.01    2.69  INTRA BF
 294 LYS   (  71-)  B      O   <->  295 GLY   (  72-)  B      C      0.01    2.59  INTRA BF
 372 GLU   ( 149-)  B      N   <->  373 GLY   ( 150-)  B      N      0.01    2.59  INTRA BF
 294 LYS   (  71-)  B      C   <->  295 GLY   (  72-)  B      C      0.01    2.79  INTRA BF

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.

 376 ARG   ( 153-)  B      -7.45
 153 ARG   ( 153-)  A      -7.34
 374 GLN   ( 151-)  B      -7.16
 151 GLN   ( 151-)  A      -7.14
 178 ARG   ( 178-)  A      -6.20
  32 LEU   (  32-)  A      -6.19
 401 ARG   ( 178-)  B      -6.18
 255 LEU   (  32-)  B      -6.17
 346 LYS   ( 123-)  B      -5.85
 123 LYS   ( 123-)  A      -5.83
 213 ARG   ( 213-)  A      -5.77
 436 ARG   ( 213-)  B      -5.77
 296 GLN   (  73-)  B      -5.63
 152 CYS   ( 152-)  A      -5.21
 375 CYS   ( 152-)  B      -5.16
  19 ARG   (  19-)  A      -5.04
 209 GLN   ( 209-)  A      -5.00
 242 ARG   (  19-)  B      -5.00

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.

 151 GLN   ( 151-)  A       154 - VAL    154- ( A)         -6.08
 374 GLN   ( 151-)  B       377 - VAL    154- ( B)         -6.10

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: Abnormal packing Z-score for sequential residues

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

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

 377 VAL   ( 154-)  B     -  380 LYS   ( 157-)  B        -1.70

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.

 452 HOH   ( 242 )  B      O
Marked this atom as acceptor  449  CL  ( 224-) A     CL
Marked this atom as acceptor  450  CL  ( 224-) B     CL

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.

   2 GLN   (   2-)  A
 225 GLN   (   2-)  B
 394 HIS   ( 171-)  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.

   8 ILE   (   8-)  A      N
  26 TRP   (  26-)  A      N
  35 GLU   (  35-)  A      N
  38 SER   (  38-)  A      N
  39 LEU   (  39-)  A      N
  58 GLN   (  58-)  A      N
  58 GLN   (  58-)  A      NE2
  75 VAL   (  75-)  A      N
  81 PHE   (  81-)  A      N
  90 CYS   (  90-)  A      N
 123 LYS   ( 123-)  A      NZ
 127 GLU   ( 127-)  A      N
 152 CYS   ( 152-)  A      N
 153 ARG   ( 153-)  A      N
 155 ASP   ( 155-)  A      N
 166 ASN   ( 166-)  A      ND2
 167 ASN   ( 167-)  A      ND2
 181 PHE   ( 181-)  A      N
 190 GLU   ( 190-)  A      N
 191 ASP   ( 191-)  A      N
 193 LEU   ( 193-)  A      N
 225 GLN   (   2-)  B      N
 249 TRP   (  26-)  B      N
 258 GLU   (  35-)  B      N
 261 SER   (  38-)  B      N
 262 LEU   (  39-)  B      N
 267 ALA   (  44-)  B      N
 281 GLN   (  58-)  B      N
 281 GLN   (  58-)  B      NE2
 297 GLU   (  74-)  B      N
 298 VAL   (  75-)  B      N
 309 ILE   (  86-)  B      N
 336 VAL   ( 113-)  B      N
 350 GLU   ( 127-)  B      N
 375 CYS   ( 152-)  B      N
 376 ARG   ( 153-)  B      NE
 377 VAL   ( 154-)  B      N
 389 ASN   ( 166-)  B      ND2
 390 ASN   ( 167-)  B      ND2
 404 PHE   ( 181-)  B      N
 407 ASN   ( 184-)  B      N
 413 GLU   ( 190-)  B      N
 414 ASP   ( 191-)  B      N
 416 LEU   ( 193-)  B      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   7 GLU   (   7-)  A      OE2
  35 GLU   (  35-)  A      OE2
  58 GLN   (  58-)  A      OE1
 166 ASN   ( 166-)  A      OD1
 167 ASN   ( 167-)  A      OD1
 169 ASP   ( 169-)  A      OD1
 171 HIS   ( 171-)  A      ND1
 258 GLU   (  35-)  B      OE2
 281 GLN   (  58-)  B      OE1
 389 ASN   ( 166-)  B      OD1
 390 ASN   ( 167-)  B      OD1

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.

  35 GLU   (  35-)  A   H-bonding suggests Gln
 258 GLU   (  35-)  B   H-bonding suggests Gln

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 :  -0.591
  2nd generation packing quality :  -1.768
  Ramachandran plot appearance   :  -2.006
  chi-1/chi-2 rotamer normality  :  -2.159
  Backbone conformation          :   0.417

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.175 (tight)
  Bond angles                    :   0.437 (tight)
  Omega angle restraints         :   0.716 (tight)
  Side chain planarity           :   0.162 (tight)
  Improper dihedral distribution :   0.373
  B-factor distribution          :   1.559 (loose)
  Inside/Outside distribution    :   0.964

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 :   0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.175 (tight)
  Bond angles                    :   0.437 (tight)
  Omega angle restraints         :   0.716 (tight)
  Side chain planarity           :   0.162 (tight)
  Improper dihedral distribution :   0.373
  B-factor distribution          :   1.559 (loose)
  Inside/Outside distribution    :   0.964
==============

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
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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.