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 pdb1gwz.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'.

   1 PHE   ( 250-)  A      CG
   1 PHE   ( 250-)  A      CD1
   1 PHE   ( 250-)  A      CD2
   1 PHE   ( 250-)  A      CE1
   1 PHE   ( 250-)  A      CE2
   1 PHE   ( 250-)  A      CZ
   9 VAL   ( 258-)  A      CG1
   9 VAL   ( 258-)  A      CG2
  12 LEU   ( 261-)  A      CG
  12 LEU   ( 261-)  A      CD1
  12 LEU   ( 261-)  A      CD2
  65 LEU   ( 314-)  A      CG
  65 LEU   ( 314-)  A      CD1
  65 LEU   ( 314-)  A      CD2
  68 ASP   ( 317-)  A      CG
  68 ASP   ( 317-)  A      OD1
  68 ASP   ( 317-)  A      OD2
 113 LYS   ( 362-)  A      CG
 113 LYS   ( 362-)  A      CD
 113 LYS   ( 362-)  A      CE
 113 LYS   ( 362-)  A      NZ
 184 ASP   ( 436-)  A      CG
 184 ASP   ( 436-)  A      OD1
 184 ASP   ( 436-)  A      OD2
 229 ASP   ( 481-)  A      CG
 229 ASP   ( 481-)  A      OD1
 229 ASP   ( 481-)  A      OD2
 252 GLU   ( 504-)  A      CG
 252 GLU   ( 504-)  A      CD
 252 GLU   ( 504-)  A      OE1
 252 GLU   ( 504-)  A      OE2
 256 LYS   ( 508-)  A      CG
 256 LYS   ( 508-)  A      CD
 256 LYS   ( 508-)  A      CE
 256 LYS   ( 508-)  A      NZ
 267 GLU   ( 519-)  A      CG
 267 GLU   ( 519-)  A      CD
 267 GLU   ( 519-)  A      OE1
 267 GLU   ( 519-)  A      OE2
 277 GLN   ( 529-)  A      CG
 277 GLN   ( 529-)  A      CD
 277 GLN   ( 529-)  A      OE1
 277 GLN   ( 529-)  A      NE2

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) : 85.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 12.67

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 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.

  54 TYR   ( 303-)  A      N    CA   C   123.93    4.5
  69 GLU   ( 318-)  A      N    CA   C    95.89   -5.5
  88 PHE   ( 337-)  A      N    CA   C    99.57   -4.2
 157 ARG   ( 409-)  A      N    CA   C    99.74   -4.1
 195 HIS   ( 447-)  A      CG   ND1  CE1 109.65    4.0
 202 HIS   ( 454-)  A      CG   ND1  CE1 109.67    4.1
 250 GLN   ( 502-)  A      N    CA   C   124.12    4.6
 274 GLU   ( 526-)  A      N    CA   C    95.82   -5.5

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.

 274 GLU   ( 526-)  A   10.52
  88 PHE   ( 337-)  A    6.65
  69 GLU   ( 318-)  A    5.31
 250 GLN   ( 502-)  A    5.01
 180 LEU   ( 432-)  A    4.86
 271 LYS   ( 523-)  A    4.85
  54 TYR   ( 303-)  A    4.84
  19 GLN   ( 268-)  A    4.82
  94 GLN   ( 343-)  A    4.75
  77 SER   ( 326-)  A    4.45
 209 ARG   ( 461-)  A    4.43
 157 ARG   ( 409-)  A    4.33
   3 SER   ( 252-)  A    4.17
  81 LEU   ( 330-)  A    4.16
  82 GLU   ( 331-)  A    4.08
  92 ALA   ( 341-)  A    4.03
 125 ARG   ( 374-)  A    4.03

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 2.171

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.437

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.

  50 PRO   ( 299-)  A    -3.1
 141 THR   ( 390-)  A    -3.1
 268 THR   ( 520-)  A    -3.0
 207 ILE   ( 459-)  A    -2.8
 193 LEU   ( 445-)  A    -2.8
 278 SER   ( 530-)  A    -2.6
  62 ASN   ( 311-)  A    -2.6
 129 PRO   ( 378-)  A    -2.6
 117 TYR   ( 366-)  A    -2.6
 103 THR   ( 352-)  A    -2.6
 155 LEU   ( 407-)  A    -2.6
 276 LEU   ( 528-)  A    -2.6
  84 THR   ( 333-)  A    -2.5
   2 GLU   ( 251-)  A    -2.5
  60 ILE   ( 309-)  A    -2.5
 176 PRO   ( 428-)  A    -2.5
 144 LYS   ( 393-)  A    -2.4
 156 ILE   ( 408-)  A    -2.4
 271 LYS   ( 523-)  A    -2.4
 138 HIS   ( 387-)  A    -2.3
  55 ILE   ( 304-)  A    -2.3
 102 MET   ( 351-)  A    -2.3
 225 THR   ( 477-)  A    -2.3
 213 ILE   ( 465-)  A    -2.3
 165 LEU   ( 417-)  A    -2.2
And so on for a total of 51 lines.

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.

   2 GLU   ( 251-)  A  Poor phi/psi
  18 GLY   ( 267-)  A  Poor phi/psi
  50 PRO   ( 299-)  A  Poor phi/psi
  62 ASN   ( 311-)  A  Poor phi/psi
  67 PRO   ( 316-)  A  Poor phi/psi
  68 ASP   ( 317-)  A  Poor phi/psi
  71 ALA   ( 320-)  A  Poor phi/psi
  79 GLY   ( 328-)  A  Poor phi/psi
 106 GLU   ( 355-)  A  Poor phi/psi
 109 LYS   ( 358-)  A  Poor phi/psi
 110 GLY   ( 359-)  A  Poor phi/psi
 174 SER   ( 426-)  A  Poor phi/psi
 177 GLY   ( 429-)  A  Poor phi/psi
 203 CYS   ( 455-)  A  Poor phi/psi
 210 THR   ( 462-)  A  Poor phi/psi
 211 GLY   ( 463-)  A  Poor phi/psi
 226 LYS   ( 478-)  A  Poor phi/psi
 248 MET   ( 500-)  A  Poor phi/psi
 269 THR   ( 521-)  A  Poor phi/psi
 273 LEU   ( 525-)  A  Poor phi/psi
 278 SER   ( 530-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -7.004

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -7.004

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 SER   ( 252-)  A      0
   4 LEU   ( 253-)  A      0
   5 GLN   ( 254-)  A      0
   7 GLN   ( 256-)  A      0
   9 VAL   ( 258-)  A      0
  10 LYS   ( 259-)  A      0
  11 ASN   ( 260-)  A      0
  12 LEU   ( 261-)  A      0
  13 HIS   ( 262-)  A      0
  14 GLN   ( 263-)  A      0
  15 ARG   ( 264-)  A      0
  26 LYS   ( 275-)  A      0
  32 ILE   ( 281-)  A      0
  43 GLN   ( 292-)  A      0
  55 ILE   ( 304-)  A      0
  56 ASN   ( 305-)  A      0
  60 ILE   ( 309-)  A      0
  61 LYS   ( 310-)  A      0
  62 ASN   ( 311-)  A      0
  63 GLN   ( 312-)  A      0
  64 LEU   ( 313-)  A      0
  65 LEU   ( 314-)  A      0
  67 PRO   ( 316-)  A      0
  68 ASP   ( 317-)  A      0
  69 GLU   ( 318-)  A      0
And so on for a total of 126 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 : 1.652

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!

 136 GLY   ( 385-)  A   1.98   40

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 251 THR   ( 503-)  A   1.65

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].

  50 PRO   ( 299-)  A   171.7 envelop N (180 degrees)
  67 PRO   ( 316-)  A   108.8 envelop C-beta (108 degrees)
 119 PRO   ( 368-)  A    31.7 envelop C-delta (36 degrees)
 129 PRO   ( 378-)  A   -30.7 envelop C-alpha (-36 degrees)
 152 PRO   ( 401-)  A  -153.8 half-chair N/C-delta (-162 degrees)
 168 PRO   ( 420-)  A    49.4 half-chair C-delta/C-gamma (54 degrees)
 176 PRO   ( 428-)  A   -53.3 half-chair C-beta/C-alpha (-54 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.

  12 LEU   ( 261-)  A      CB  <->   37 HIS   ( 286-)  A      ND1    0.72    2.38  INTRA
  98 ARG   ( 347-)  A      NH2 <->  157 ARG   ( 409-)  A      CG     0.68    2.42  INTRA
  62 ASN   ( 311-)  A      O   <->  240 MET   ( 492-)  A      SD     0.64    2.21  INTRA
  12 LEU   ( 261-)  A      CB  <->   37 HIS   ( 286-)  A      CG     0.55    2.65  INTRA
 174 SER   ( 426-)  A      C   <->  176 PRO   ( 428-)  A      CD     0.52    2.68  INTRA
 211 GLY   ( 463-)  A      CA  <->  248 MET   ( 500-)  A      CE     0.48    2.72  INTRA BL
 118 TRP   ( 367-)  A      CZ2 <->  146 ARG   ( 395-)  A      NH1    0.47    2.63  INTRA BL
 272 LYS   ( 524-)  A      CD  <->  273 LEU   ( 525-)  A      CD1    0.47    2.73  INTRA
 135 CYS   ( 384-)  A      SG  <->  149 GLN   ( 398-)  A      CG     0.46    2.94  INTRA
 174 SER   ( 426-)  A      O   <->  176 PRO   ( 428-)  A      CD     0.45    2.35  INTRA
 233 ASP   ( 485-)  A      OD2 <->  236 LYS   ( 488-)  A      CB     0.45    2.35  INTRA
 104 THR   ( 353-)  A      CG2 <->  209 ARG   ( 461-)  A      NH1    0.44    2.66  INTRA BL
  45 ARG   ( 294-)  A      NH2 <->   87 ASP   ( 336-)  A      CB     0.44    2.66  INTRA BL
  45 ARG   ( 294-)  A      NH1 <->   52 SER   ( 301-)  A      O      0.43    2.27  INTRA
 104 THR   ( 353-)  A      CG2 <->  209 ARG   ( 461-)  A      CZ     0.43    2.77  INTRA BL
 104 THR   ( 353-)  A      CG2 <->  209 ARG   ( 461-)  A      NH2    0.42    2.68  INTRA
 172 VAL   ( 424-)  A      CG1 <->  257 PHE   ( 509-)  A      CD1    0.42    2.78  INTRA
 102 MET   ( 351-)  A      CE  <->  163 GLN   ( 415-)  A      OE1    0.42    2.38  INTRA BL
  12 LEU   ( 261-)  A      CB  <->   14 GLN   ( 263-)  A      OE1    0.41    2.39  INTRA
  43 GLN   ( 292-)  A      NE2 <->   94 GLN   ( 343-)  A      CD     0.40    2.70  INTRA
  79 GLY   ( 328-)  A      N   <->  204 SER   ( 456-)  A      O      0.40    2.30  INTRA BL
 272 LYS   ( 524-)  A      C   <->  274 GLU   ( 526-)  A      OE2    0.40    2.40  INTRA
  39 ARG   ( 288-)  A      NH2 <->   53 ASP   ( 302-)  A      OD2    0.40    2.30  INTRA BL
  98 ARG   ( 347-)  A      NH2 <->  158 GLU   ( 410-)  A      C      0.39    2.71  INTRA
 203 CYS   ( 455-)  A      SG  <->  206 GLY   ( 458-)  A      N      0.39    2.91  INTRA BL
And so on for a total of 222 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  64 LEU   ( 313-)  A      -7.06
 279 GLN   ( 531-)  A      -7.05
  63 GLN   ( 312-)  A      -6.87
   7 GLN   ( 256-)  A      -6.51
 170 HIS   ( 422-)  A      -6.44
  10 LYS   ( 259-)  A      -6.32
  28 ARG   ( 277-)  A      -6.23
 175 GLU   ( 427-)  A      -5.82
 250 GLN   ( 502-)  A      -5.75
  19 GLN   ( 268-)  A      -5.58
   4 LEU   ( 253-)  A      -5.46
 195 HIS   ( 447-)  A      -5.43
 111 ARG   ( 360-)  A      -5.33
 109 LYS   ( 358-)  A      -5.31
  43 GLN   ( 292-)  A      -5.09

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.

  62 ASN   ( 311-)  A        64 - LEU    313- ( A)         -6.08

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 280 : -1.499

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.

  12 LEU   ( 261-)  A   -3.54
 113 LYS   ( 362-)  A   -2.96
 277 GLN   ( 529-)  A   -2.88
   1 PHE   ( 250-)  A   -2.64
  65 LEU   ( 314-)  A   -2.58

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.

  19 GLN   ( 268-)  A
  23 ASN   ( 272-)  A
  90 GLN   ( 339-)  A
 161 HIS   ( 413-)  A
 163 GLN   ( 415-)  A
 264 GLN   ( 516-)  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.

   1 PHE   ( 250-)  A      N
   4 LEU   ( 253-)  A      N
  13 HIS   ( 262-)  A      N
  14 GLN   ( 263-)  A      N
  15 ARG   ( 264-)  A      N
  17 GLU   ( 266-)  A      N
  22 GLU   ( 271-)  A      N
  28 ARG   ( 277-)  A      NH1
  29 TYR   ( 278-)  A      N
  37 HIS   ( 286-)  A      N
  39 ARG   ( 288-)  A      NE
  39 ARG   ( 288-)  A      NH2
  48 ASN   ( 297-)  A      N
  63 GLN   ( 312-)  A      N
  65 LEU   ( 314-)  A      N
  79 GLY   ( 328-)  A      N
  87 ASP   ( 336-)  A      N
  88 PHE   ( 337-)  A      N
  90 GLN   ( 339-)  A      N
  98 ARG   ( 347-)  A      N
  98 ARG   ( 347-)  A      NE
  98 ARG   ( 347-)  A      NH2
  99 VAL   ( 348-)  A      N
 104 THR   ( 353-)  A      N
 106 GLU   ( 355-)  A      N
And so on for a total of 51 lines.

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.

  36 ASP   ( 285-)  A      OD1
  37 HIS   ( 286-)  A      ND1
 106 GLU   ( 355-)  A      OE1
 138 HIS   ( 387-)  A      NE2
 190 GLN   ( 442-)  A      OE1
 254 GLN   ( 506-)  A      OE1

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.

  87 ASP   ( 336-)  A   H-bonding suggests Asn
 274 GLU   ( 526-)  A   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 :  -2.496
  2nd generation packing quality :  -3.645 (poor)
  Ramachandran plot appearance   :  -5.437 (bad)
  chi-1/chi-2 rotamer normality  :  -7.004 (bad)
  Backbone conformation          :  -1.165

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.534 (tight)
  Bond angles                    :   0.871
  Omega angle restraints         :   0.300 (tight)
  Side chain planarity           :   0.234 (tight)
  Improper dihedral distribution :   0.745
  Inside/Outside distribution    :   1.069

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.7
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -2.7
  chi-1/chi-2 rotamer normality  :  -4.7 (bad)
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.534 (tight)
  Bond angles                    :   0.871
  Omega angle restraints         :   0.300 (tight)
  Side chain planarity           :   0.234 (tight)
  Improper dihedral distribution :   0.745
  Inside/Outside distribution    :   1.069
==============

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.