WHAT IF Check report

This file was created 2013-12-10 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 pdb4bm9.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 311 SO4   (1474-)  A  -
 312 SO4   (1475-)  A  -
 313 SO4   (1476-)  A  -
 314 GOL   (1477-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 182 CYS   ( 323-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 182 CYS   ( 323-)  A  -

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'.

  14 GLN   ( 155-)  A      CG
  14 GLN   ( 155-)  A      CD
  14 GLN   ( 155-)  A      OE1
  14 GLN   ( 155-)  A      NE2
  54 GLU   ( 195-)  A      CG
  54 GLU   ( 195-)  A      CD
  54 GLU   ( 195-)  A      OE1
  54 GLU   ( 195-)  A      OE2
  56 GLN   ( 197-)  A      CG
  56 GLN   ( 197-)  A      CD
  56 GLN   ( 197-)  A      OE1
  56 GLN   ( 197-)  A      NE2
 115 ARG   ( 256-)  A      CG
 115 ARG   ( 256-)  A      CD
 115 ARG   ( 256-)  A      NE
 115 ARG   ( 256-)  A      CZ
 115 ARG   ( 256-)  A      NH1
 115 ARG   ( 256-)  A      NH2
 141 GLN   ( 282-)  A      CG
 141 GLN   ( 282-)  A      CD
 141 GLN   ( 282-)  A      OE1
 141 GLN   ( 282-)  A      NE2
 142 LEU   ( 283-)  A      CG
 142 LEU   ( 283-)  A      CD1
 142 LEU   ( 283-)  A      CD2
And so on for a total of 102 lines.

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.

  59 HIS   ( 200-)  A    High
  93 ARG   ( 234-)  A    High
 201 LEU   ( 342-)  A    High
 204 PRO   ( 345-)  A    High
 205 ASP   ( 346-)  A    High
 206 GLN   ( 347-)  A    High
 211 CYS   ( 352-)  A    High
 213 PHE   ( 362-)  A    High
 225 GLU   ( 374-)  A    High
 227 GLU   ( 376-)  A    High
 233 GLU   ( 382-)  A    High
 248 GLU   ( 404-)  A    High

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: 5

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond 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.

  23 VAL   ( 164-)  A      C    CA   CB  101.23   -4.7

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.

  58 PRO   ( 199-)  A    -3.0
 202 PRO   ( 343-)  A    -2.9
 147 PRO   ( 288-)  A    -2.7
  61 PRO   ( 202-)  A    -2.5
 104 ARG   ( 245-)  A    -2.4
 297 HIS   ( 461-)  A    -2.4
 101 THR   ( 242-)  A    -2.3
 226 GLY   ( 375-)  A    -2.2
 227 GLU   ( 376-)  A    -2.1
  33 LEU   ( 174-)  A    -2.0
  29 ARG   ( 170-)  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.

  11 GLY   ( 152-)  A  PRO omega poor
  14 GLN   ( 155-)  A  Poor phi/psi
  29 ARG   ( 170-)  A  Poor phi/psi
  31 ALA   ( 172-)  A  Poor phi/psi
  49 ASN   ( 190-)  A  Poor phi/psi
  94 ASN   ( 235-)  A  Poor phi/psi
 101 THR   ( 242-)  A  Poor phi/psi
 105 SER   ( 246-)  A  PRO omega poor
 154 ASN   ( 295-)  A  Poor phi/psi
 220 LYS   ( 369-)  A  Poor phi/psi
 258 HIS   ( 422-)  A  Poor phi/psi
 278 ARG   ( 442-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.120

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

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

chi-1/chi-2 correlation Z-score : -3.120

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!

  13 CYS   ( 154-)  A      0
  14 GLN   ( 155-)  A      0
  15 ARG   ( 156-)  A      0
  17 GLN   ( 158-)  A      0
  24 GLN   ( 165-)  A      0
  28 CYS   ( 169-)  A      0
  31 ALA   ( 172-)  A      0
  32 THR   ( 173-)  A      0
  37 GLN   ( 178-)  A      0
  41 CYS   ( 182-)  A      0
  42 TRP   ( 183-)  A      0
  48 PRO   ( 189-)  A      0
  49 ASN   ( 190-)  A      0
  50 ARG   ( 191-)  A      0
  52 SER   ( 193-)  A      0
  56 GLN   ( 197-)  A      0
  58 PRO   ( 199-)  A      0
  59 HIS   ( 200-)  A      0
  61 PRO   ( 202-)  A      0
  73 ALA   ( 214-)  A      0
  75 PRO   ( 216-)  A      0
  80 GLU   ( 221-)  A      0
  86 HIS   ( 227-)  A      0
  97 CYS   ( 238-)  A      0
  98 ILE   ( 239-)  A      0
And so on for a total of 150 lines.

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!

 194 PRO   ( 335-)  A   1.70   10

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].

  48 PRO   ( 189-)  A   110.0 envelop C-beta (108 degrees)
  58 PRO   ( 199-)  A   115.1 envelop C-beta (108 degrees)
  61 PRO   ( 202-)  A   -65.7 envelop C-beta (-72 degrees)
 140 PRO   ( 281-)  A  -120.3 half-chair C-delta/C-gamma (-126 degrees)
 202 PRO   ( 343-)  A   -47.9 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.

 219 CYS   ( 368-)  A      CB  <->  309  ZN   (1472-)  A     ZN      0.89    2.31  INTRA BF
 211 CYS   ( 352-)  A      SG  <->  212 GLU   ( 353-)  A      N      0.51    2.69  INTRA BF
 132 ASN   ( 273-)  A      ND2 <->  315 HOH   (2064 )  A      O      0.34    2.36  INTRA BF
 102 ASP   ( 243-)  A      OD2 <->  104 ARG   ( 245-)  A      NH1    0.32    2.38  INTRA BF
   2 TYR   ( 143-)  A      OH  <->  300 ASP   ( 464-)  A      OD2    0.32    2.08  INTRA BF
 269 HIS   ( 433-)  A      ND1 <->  315 HOH   (2024 )  A      O      0.32    2.38  INTRA BF
  24 GLN   ( 165-)  A      NE2 <->   66 GLU   ( 207-)  A      OE1    0.30    2.40  INTRA BF
 164 ARG   ( 305-)  A      NE  <->  313 SO4   (1476-)  A      O3     0.30    2.40  INTRA BF
  13 CYS   ( 154-)  A      SG  <->   17 GLN   ( 158-)  A      NE2    0.27    3.03  INTRA BL
 112 CYS   ( 253-)  A      SG  <->  116 HIS   ( 257-)  A      ND1    0.25    3.05  INTRA BF
 207 ARG   ( 348-)  A      NH1 <->  315 HOH   (2073 )  A      O      0.18    2.52  INTRA BF
 139 ASP   ( 280-)  A      O   <->  143 GLY   ( 284-)  A      N      0.17    2.53  INTRA BF
 159 GLU   ( 300-)  A      OE2 <->  161 HIS   ( 302-)  A      ND1    0.17    2.53  INTRA BF
 116 HIS   ( 257-)  A      CE1 <->  152 CYS   ( 293-)  A      SG     0.15    3.25  INTRA BF
  13 CYS   ( 154-)  A      SG  <->   74 HIS   ( 215-)  A      CD2    0.12    3.28  INTRA BL
 196 CYS   ( 337-)  A      SG  <->  211 CYS   ( 352-)  A      SG     0.11    3.34  INTRA BF
 148 CYS   ( 289-)  A      O   <->  151 GLY   ( 292-)  A      N      0.10    2.60  INTRA BF
  64 SER   ( 205-)  A      N   <->  315 HOH   (2017 )  A      O      0.10    2.60  INTRA BL
 111 GLN   ( 252-)  A      N   <->  315 HOH   (2059 )  A      O      0.09    2.61  INTRA BF
 191 CYS   ( 332-)  A      SG  <->  211 CYS   ( 352-)  A      SG     0.08    3.37  INTRA BF
 219 CYS   ( 368-)  A      SG  <->  221 GLU   ( 370-)  A      CB     0.08    3.32  INTRA BF
 224 HIS   ( 373-)  A      NE2 <->  228 CYS   ( 377-)  A      SG     0.06    3.24  INTRA BF
 139 ASP   ( 280-)  A      N   <->  143 GLY   ( 284-)  A      O      0.06    2.64  INTRA BF
 116 HIS   ( 257-)  A      ND1 <->  148 CYS   ( 289-)  A      SG     0.05    3.25  INTRA BF
  22 ARG   ( 163-)  A      NH2 <->  311 SO4   (1474-)  A      O3     0.05    2.65  INTRA BF
 124 HIS   ( 265-)  A      ND1 <->  165 ILE   ( 306-)  A      O      0.05    2.65  INTRA BF
 219 CYS   ( 368-)  A      SG  <->  221 GLU   ( 370-)  A      N      0.04    3.26  INTRA BF
 296 ASP   ( 460-)  A      OD2 <->  315 HOH   (2086 )  A      O      0.04    2.36  INTRA BL
  60 CYS   ( 201-)  A      SG  <->   62 GLY   ( 203-)  A      N      0.04    3.26  INTRA BL
  91 ASN   ( 232-)  A      N   <->  105 SER   ( 246-)  A      OG     0.03    2.67  INTRA BL
  27 THR   ( 168-)  A      OG1 <->   60 CYS   ( 201-)  A      SG     0.03    2.97  INTRA BF
 130 ARG   ( 271-)  A      O   <->  135 GLN   ( 276-)  A      N      0.02    2.68  INTRA BL
 270 MET   ( 434-)  A      N   <->  281 TRP   ( 445-)  A      O      0.01    2.69  INTRA BL
 263 LYS   ( 427-)  A      NZ  <->  268 MET   ( 432-)  A      CE     0.01    3.09  INTRA BF
  20 LYS   ( 161-)  A      N   <->   70 LYS   ( 211-)  A      O      0.01    2.69  INTRA BL
 216 CYS   ( 365-)  A      SG  <->  224 HIS   ( 373-)  A      NE2    0.01    3.29  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

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.

 201 LEU   ( 342-)  A      -7.36
  37 GLN   ( 178-)  A      -7.19
 206 GLN   ( 347-)  A      -6.42
  10 LYS   ( 151-)  A      -6.41
  50 ARG   ( 191-)  A      -6.37
  59 HIS   ( 200-)  A      -6.18
 276 GLN   ( 440-)  A      -5.96
 113 ASN   ( 254-)  A      -5.66
 244 GLN   ( 400-)  A      -5.63
 185 GLN   ( 326-)  A      -5.61
 256 ARG   ( 420-)  A      -5.35
 104 ARG   ( 245-)  A      -5.34
  29 ARG   ( 170-)  A      -5.29
 278 ARG   ( 442-)  A      -5.24
 223 TYR   ( 372-)  A      -5.12
 258 HIS   ( 422-)  A      -5.03

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.

 138 HIS   ( 279-)  A       140 - PRO    281- ( A)         -4.50

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 - 301 : -1.530

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.

 193 ARG   ( 334-)  A   -3.53
 115 ARG   ( 256-)  A   -3.20
  14 GLN   ( 155-)  A   -2.91
 141 GLN   ( 282-)  A   -2.89
 169 GLU   ( 310-)  A   -2.84
 236 ARG   ( 392-)  A   -2.77
 248 GLU   ( 404-)  A   -2.77
 235 TYR   ( 391-)  A   -2.74
 246 ARG   ( 402-)  A   -2.72
 224 HIS   ( 373-)  A   -2.58
 230 ALA   ( 379-)  A   -2.58
 142 LEU   ( 283-)  A   -2.50

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.

   1 ILE   ( 142-)  A     -    4 SER   ( 145-)  A        -1.81

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 315 HOH   (2052 )  A      O
 315 HOH   (2060 )  A      O
 315 HOH   (2082 )  A      O
 315 HOH   (2087 )  A      O
Metal-coordinating Histidine residue  74 fixed to   1
Metal-coordinating Histidine residue 116 fixed to   1
Metal-coordinating Histidine residue 297 fixed to   1
Metal-coordinating Histidine residue 224 fixed to   1

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.

   3 ASN   ( 144-)  A
 132 ASN   ( 273-)  A
 185 GLN   ( 326-)  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.

  26 SER   ( 167-)  A      OG
  37 GLN   ( 178-)  A      N
  41 CYS   ( 182-)  A      N
  74 HIS   ( 215-)  A      N
  86 HIS   ( 227-)  A      N
  93 ARG   ( 234-)  A      N
 114 SER   ( 255-)  A      N
 121 ASP   ( 262-)  A      N
 149 VAL   ( 290-)  A      N
 168 GLU   ( 309-)  A      N
 170 GLN   ( 311-)  A      N
 195 GLY   ( 336-)  A      N
 214 ALA   ( 363-)  A      N
 217 ARG   ( 366-)  A      NH1
 224 HIS   ( 373-)  A      N
 231 VAL   ( 380-)  A      N
 234 ALA   ( 383-)  A      N
 281 TRP   ( 445-)  A      NE1
 290 ASN   ( 454-)  A      N
 291 ARG   ( 455-)  A      N
 291 ARG   ( 455-)  A      NE
 299 PHE   ( 463-)  A      N
Only metal coordination for   74 HIS  ( 215-) A      NE2
Only metal coordination for  116 HIS  ( 257-) A      ND1
Only metal coordination for  224 HIS  ( 373-) A      NE2
Only metal coordination for  297 HIS  ( 461-) A      NE2

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.

 133 ASP   ( 274-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.575
  2nd generation packing quality :  -3.499 (poor)
  Ramachandran plot appearance   :  -0.881
  chi-1/chi-2 rotamer normality  :  -3.120 (poor)
  Backbone conformation          :  -1.084

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.287 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.867
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.545
  B-factor distribution          :   1.137
  Inside/Outside distribution    :   1.017

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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.5
  2nd generation packing quality :  -3.6 (poor)
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -1.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.287 (tight)
  Bond angles                    :   0.570 (tight)
  Omega angle restraints         :   0.867
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.545
  B-factor distribution          :   1.137
  Inside/Outside distribution    :   1.017
==============

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.