WHAT IF Check report

This file was created 2012-10-25 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 pdb2xs0.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  62.530  B   = 106.550  C    = 130.910
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  61.772  B   =  61.772  C    = 130.910
    Alpha=  90.000  Beta=  90.000  Gamma=  60.814

Dimensions of the conventional cell

    A    =  61.772  B   =  62.530  C    = 130.910
    Alpha=  90.000  Beta=  90.000  Gamma= 120.407

Transformation to conventional cell

 |  0.500000 -0.500000  0.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: HEXAGONAL

Space group name: C 2 2 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 360 ANP   (1367-)  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

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 ARG   (   6-)  A    High
   2 ASP   (   7-)  A    High
   3 ASN   (   8-)  A    High
 123 MET   ( 128-)  A    High
 169 THR   ( 188-)  A    High
 170 ARG   ( 189-)  A    High
 181 MET   ( 200-)  A    High
 209 THR   ( 228-)  A    High
 210 ASP   ( 229-)  A    High
 211 HIS   ( 230-)  A    High
 212 ILE   ( 231-)  A    High
 215 TRP   ( 234-)  A    High
 220 GLU   ( 239-)  A    High
 224 THR   ( 243-)  A    High
 225 PRO   ( 244-)  A    High
 226 CYS   ( 245-)  A    High
 227 PRO   ( 246-)  A    High
 228 GLU   ( 247-)  A    High
 229 PHE   ( 248-)  A    High
 230 MET   ( 249-)  A    High
 231 LYS   ( 250-)  A    High
 233 LEU   ( 252-)  A    High
 234 GLN   ( 253-)  A    High
 235 PRO   ( 254-)  A    High
 236 THR   ( 255-)  A    High
 237 VAL   ( 256-)  A    High
 238 ARG   ( 257-)  A    High
 239 THR   ( 258-)  A    High
 240 TYR   ( 259-)  A    High
 241 VAL   ( 260-)  A    High
 242 GLU   ( 261-)  A    High
 243 ASN   ( 262-)  A    High
 244 ARG   ( 263-)  A    High
 245 PRO   ( 264-)  A    High
 246 LYS   ( 265-)  A    High
 247 TYR   ( 266-)  A    High
 248 ALA   ( 267-)  A    High
 258 ASP   ( 277-)  A    High
 262 PRO   ( 281-)  A    High
 263 ALA   ( 282-)  A    High
 264 ASP   ( 283-)  A    High
 265 SER   ( 284-)  A    High
 266 GLU   ( 285-)  A    High
 269 LYS   ( 288-)  A    High
 282 MET   ( 301-)  A    High
 289 LYS   ( 308-)  A    High
 322 GLN   ( 341-)  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: 13

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

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.

  67 ARG   (  72-)  A

Warning: Tyrosine convention problem

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

 172 TYR   ( 191-)  A
 183 TYR   ( 202-)  A
 240 TYR   ( 259-)  A

Warning: Phenylalanine convention problem

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

 165 PHE   ( 170-)  A
 229 PHE   ( 248-)  A

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.

 320 ASP   ( 339-)  A

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.

  95 GLU   ( 100-)  A
 104 GLU   ( 109-)  A
 117 GLU   ( 122-)  A
 220 GLU   ( 239-)  A
 228 GLU   ( 247-)  A
 310 GLU   ( 329-)  A
 325 GLU   ( 344-)  A
 327 GLU   ( 346-)  A
 346 GLU   ( 365-)  A
 358 GLU   ( 154-)  B

Geometric checks

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.

  67 ARG   (  72-)  A
  95 GLU   ( 100-)  A
 104 GLU   ( 109-)  A
 117 GLU   ( 122-)  A
 220 GLU   ( 239-)  A
 228 GLU   ( 247-)  A
 310 GLU   ( 329-)  A
 320 ASP   ( 339-)  A
 325 GLU   ( 344-)  A
 327 GLU   ( 346-)  A
 346 GLU   ( 365-)  A
 358 GLU   ( 154-)  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.

 207 PRO   ( 226-)  A    -2.9
 319 PRO   ( 338-)  A    -2.8
 235 PRO   ( 254-)  A    -2.7
 350 ARG   ( 146-)  B    -2.5
 323 LEU   ( 342-)  A    -2.4
 158 CYS   ( 163-)  A    -2.2
 326 ARG   ( 345-)  A    -2.2
 206 PHE   ( 225-)  A    -2.2
  58 ASN   (  63-)  A    -2.2
 325 GLU   ( 344-)  A    -2.1
 327 GLU   ( 346-)  A    -2.0
 180 GLY   ( 199-)  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.

  23 ASN   (  28-)  A  Poor phi/psi
  32 GLN   (  37-)  A  Poor phi/psi
  36 CYS   (  41-)  A  omega poor
  44 GLU   (  49-)  A  Poor phi/psi
  58 ASN   (  63-)  A  Poor phi/psi
  90 GLN   (  95-)  A  omega poor
 143 ILE   ( 148-)  A  omega poor
 145 ARG   ( 150-)  A  Poor phi/psi
 158 CYS   ( 163-)  A  Poor phi/psi
 197 GLY   ( 216-)  A  Poor phi/psi
 264 ASP   ( 283-)  A  Poor phi/psi
 283 LEU   ( 302-)  A  Poor phi/psi
 287 ALA   ( 306-)  A  Poor phi/psi
 302 ILE   ( 321-)  A  omega poor
 321 LYS   ( 340-)  A  Poor phi/psi
 325 GLU   ( 344-)  A  Poor phi/psi
 356 PRO   ( 152-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.793

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 191 SER   ( 210-)  A    0.36

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!

  10 ILE   (  15-)  A      0
  12 ASP   (  17-)  A      0
  21 TYR   (  26-)  A      0
  22 GLN   (  27-)  A      0
  23 ASN   (  28-)  A      0
  29 SER   (  34-)  A      0
  31 ALA   (  36-)  A      0
  32 GLN   (  37-)  A      0
  46 ASN   (  51-)  A      0
  53 SER   (  58-)  A      0
  54 ARG   (  59-)  A      0
  56 PHE   (  61-)  A      0
  57 GLN   (  62-)  A      0
  58 ASN   (  63-)  A      0
  74 CYS   (  79-)  A      0
  76 ASN   (  81-)  A      0
  85 ASN   (  90-)  A      0
  89 PRO   (  94-)  A      0
  90 GLN   (  95-)  A      0
  91 LYS   (  96-)  A      0
  96 PHE   ( 101-)  A      0
  97 GLN   ( 102-)  A      0
 103 MET   ( 108-)  A      0
 107 ASP   ( 112-)  A      0
 115 GLN   ( 120-)  A      0
And so on for a total of 122 lines.

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].

 175 PRO   ( 194-)  A  -115.8 envelop C-gamma (-108 degrees)
 207 PRO   ( 226-)  A   -61.3 half-chair C-beta/C-alpha (-54 degrees)
 235 PRO   ( 254-)  A  -161.0 half-chair N/C-delta (-162 degrees)
 245 PRO   ( 264-)  A  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 319 PRO   ( 338-)  A   -65.8 envelop C-beta (-72 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.

 326 ARG   ( 345-)  A      NH1 <->  328 HIS   ( 347-)  A      NE2    0.37    2.63  INTRA BF
 320 ASP   ( 339-)  A      O   <->  322 GLN   ( 341-)  A      N      0.26    2.44  INTRA BF
  54 ARG   (  59-)  A      O   <->   57 GLN   (  62-)  A      CG     0.23    2.57  INTRA BL
 179 LEU   ( 198-)  A      CB  <->  181 MET   ( 200-)  A      SD     0.21    3.19  INTRA BF
 299 HIS   ( 318-)  A      ND1 <->  300 PRO   ( 319-)  A      CD     0.20    2.90  INTRA BF
 148 LYS   ( 153-)  A      CE  <->  170 ARG   ( 189-)  A      NH1    0.19    2.91  INTRA BF
  54 ARG   (  59-)  A      NH1 <->   97 GLN   ( 102-)  A      OE1    0.17    2.53  INTRA BF
 181 MET   ( 200-)  A      SD  <->  233 LEU   ( 252-)  A      CD2    0.15    3.25  INTRA BF
  54 ARG   (  59-)  A      NH1 <->   97 GLN   ( 102-)  A      CD     0.14    2.96  INTRA BF
 329 THR   ( 348-)  A      N   <->  332 GLU   ( 351-)  A      OE1    0.14    2.56  INTRA BF
 360 ANP   (1367-)  A      O3A <->  361 HOH   (2018 )  A      O      0.13    2.27  INTRA BF
 240 TYR   ( 259-)  A      CD2 <->  244 ARG   ( 263-)  A      NH1    0.12    2.98  INTRA BF
  20 ARG   (  25-)  A      NH1 <->  346 GLU   ( 365-)  A      OE2    0.11    2.59  INTRA BF
 134 ILE   ( 139-)  A      CG2 <->  138 HIS   ( 143-)  A      CE1    0.11    3.09  INTRA BL
 321 LYS   ( 340-)  A      C   <->  323 LEU   ( 342-)  A      N      0.11    2.79  INTRA BF
 145 ARG   ( 150-)  A      N   <->  188 ASP   ( 207-)  A      OD1    0.09    2.61  INTRA BL
  77 HIS   (  82-)  A      ND1 <->   79 ASN   (  84-)  A      N      0.07    2.93  INTRA BL
 232 LYS   ( 251-)  A      N   <->  233 LEU   ( 252-)  A      N      0.07    2.53  INTRA BF
  82 GLY   (  87-)  A      N   <->  104 GLU   ( 109-)  A      OE2    0.07    2.63  INTRA BF
 145 ARG   ( 150-)  A      NH2 <->  168 ALA   ( 173-)  A      C      0.06    3.04  INTRA BF
 292 SER   ( 311-)  A      N   <->  295 GLU   ( 314-)  A      OE1    0.06    2.64  INTRA BF
  84 LEU   (  89-)  A      N   <->  102 VAL   ( 107-)  A      O      0.06    2.64  INTRA BL
 237 VAL   ( 256-)  A      C   <->  239 THR   ( 258-)  A      N      0.05    2.85  INTRA BF
 171 TYR   ( 190-)  A      CA  <->  214 GLN   ( 233-)  A      NE2    0.05    3.05  INTRA BF
 226 CYS   ( 245-)  A      SG  <->  228 GLU   ( 247-)  A      OE1    0.05    2.95  INTRA BF
  57 GLN   (  62-)  A      O   <->   58 ASN   (  63-)  A      CG     0.05    2.65  INTRA BF
  54 ARG   (  59-)  A      C   <->   56 PHE   (  61-)  A      N      0.04    2.86  INTRA BL
 360 ANP   (1367-)  A      O1G <->  361 HOH   (2018 )  A      O      0.03    2.27  INTRA BF
 124 SER   ( 129-)  A      OG  <->  305 TRP   ( 324-)  A      NE1    0.02    2.68  INTRA BL
 156 SER   ( 161-)  A      O   <->  355 LEU   ( 151-)  B      N      0.02    2.68  INTRA BL
 138 HIS   ( 143-)  A      O   <->  141 GLY   ( 146-)  A      N      0.01    2.69  INTRA BL
 106 MET   ( 111-)  A      N   <->  360 ANP   (1367-)  A      N1     0.01    2.99  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Warning: Abnormal packing environment for some residues

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

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

 317 LYS   ( 336-)  A      -6.11
 244 ARG   ( 263-)  A      -6.01
 117 GLU   ( 122-)  A      -5.68
 183 TYR   ( 202-)  A      -5.68
 247 TYR   ( 266-)  A      -5.56
  57 GLN   (  62-)  A      -5.53
  91 LYS   (  96-)  A      -5.33
 327 GLU   ( 346-)  A      -5.21
 298 GLN   ( 317-)  A      -5.07
  76 ASN   (  81-)  A      -5.06

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: 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.

 361 HOH   (2005 )  A      O

Error: HIS, ASN, GLN side chain flips

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

  59 GLN   (  64-)  A
 216 ASN   ( 235-)  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.

  18 LEU   (  23-)  A      N
  43 LEU   (  48-)  A      N
  56 PHE   (  61-)  A      N
  91 LYS   (  96-)  A      N
  92 SER   (  97-)  A      N
 106 MET   ( 111-)  A      N
 119 ASP   ( 124-)  A      N
 120 HIS   ( 125-)  A      NE2
 157 ASP   ( 162-)  A      N
 164 ASP   ( 169-)  A      N
 173 ARG   ( 192-)  A      N
 184 LYS   ( 203-)  A      N
 189 ILE   ( 208-)  A      N
 210 ASP   ( 229-)  A      N
 228 GLU   ( 247-)  A      N
 233 LEU   ( 252-)  A      N
 238 ARG   ( 257-)  A      NE
 242 GLU   ( 261-)  A      N
 244 ARG   ( 263-)  A      N
 284 VAL   ( 303-)  A      N
 290 ARG   ( 309-)  A      N
 292 SER   ( 311-)  A      OG
 304 VAL   ( 323-)  A      N
 320 ASP   ( 339-)  A      N
 326 ARG   ( 345-)  A      N
 331 GLU   ( 350-)  A      N
 353 LEU   ( 149-)  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.

 186 ASN   ( 205-)  A      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.

  98 ASP   ( 103-)  A   H-bonding suggests Asn; but Alt-Rotamer
 242 GLU   ( 261-)  A   H-bonding suggests Gln; but Alt-Rotamer
 324 ASP   ( 343-)  A   H-bonding suggests Asn
 343 ASP   ( 362-)  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 :  -0.963
  2nd generation packing quality :  -0.971
  Ramachandran plot appearance   :  -2.424
  chi-1/chi-2 rotamer normality  :  -2.793
  Backbone conformation          :  -0.446

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.220 (tight)
  Bond angles                    :   0.477 (tight)
  Omega angle restraints         :   0.909
  Side chain planarity           :   0.204 (tight)
  Improper dihedral distribution :   0.450
  B-factor distribution          :   1.147
  Inside/Outside distribution    :   0.983

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.220 (tight)
  Bond angles                    :   0.477 (tight)
  Omega angle restraints         :   0.909
  Side chain planarity           :   0.204 (tight)
  Improper dihedral distribution :   0.450
  B-factor distribution          :   1.147
  Inside/Outside distribution    :   0.983
==============

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.