WHAT IF Check report

This file was created 2011-12-17 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 pdb3rfc.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.

 346 ADP   ( 368-)  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: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 304 ARG   ( 324-)  A    0.50

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

Note: B-factor plot

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

Chain identifier: A

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.

 160 ARG   ( 163-)  A

Warning: Tyrosine convention problem

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

 211 TYR   ( 214-)  A

Warning: Phenylalanine convention problem

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

   9 PHE   (  10-)  A
  35 PHE   (  36-)  A
 124 PHE   ( 127-)  A
 155 PHE   ( 158-)  A
 302 PHE   ( 322-)  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.

  43 ASP   (  44-)  A
 110 ASP   ( 113-)  A
 159 ASP   ( 162-)  A
 255 ASP   ( 275-)  A
 337 ASP   ( 357-)  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.

 218 GLU   ( 221-)  A
 225 GLU   ( 228-)  A
 227 GLU   ( 230-)  A
 295 GLU   ( 315-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 292 VAL   ( 312-)  A      CA   CB    1.63    5.1
 305 ILE   ( 325-)  A      CA   CB    1.61    4.1

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.

  24 ARG   (  25-)  A      CB   CG   CD  103.25   -5.4
  49 HIS   (  50-)  A      CG   ND1  CE1 109.65    4.1
 149 ARG   ( 152-)  A      CB   CG   CD  105.51   -4.3
 271 GLN   ( 291-)  A      CA   CB   CG  105.61   -4.2
 290 ARG   ( 310-)  A      N    CA   C    98.82   -4.4
 292 VAL   ( 312-)  A      C    CA   CB  119.92    5.2
 292 VAL   ( 312-)  A      CA   CB   CG2 118.16    4.5

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.

  43 ASP   (  44-)  A
 110 ASP   ( 113-)  A
 159 ASP   ( 162-)  A
 160 ARG   ( 163-)  A
 218 GLU   ( 221-)  A
 225 GLU   ( 228-)  A
 227 GLU   ( 230-)  A
 255 ASP   ( 275-)  A
 295 GLU   ( 315-)  A
 337 ASP   ( 357-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 292 VAL   ( 312-)  A      CA    -6.4    23.95    33.23
 292 VAL   ( 312-)  A      CB     7.7   -22.93   -32.96
The average deviation= 1.370

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.

  10 GLY   (  11-)  A    4.90
 290 ARG   ( 310-)  A    4.68

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.

 189 SER   ( 192-)  A    -2.4
  59 HIS   (  60-)  A    -2.3
 342 SER   ( 362-)  A    -2.2
  30 LEU   (  31-)  A    -2.1
 101 PRO   ( 104-)  A    -2.1
 322 LEU   ( 342-)  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.

   8 ILE   (   9-)  A  omega poor
  35 PHE   (  36-)  A  omega poor
  37 PRO   (  38-)  A  omega poor
  88 PRO   (  89-)  A  omega poor
 106 THR   ( 109-)  A  omega poor
 117 LEU   ( 120-)  A  omega poor
 121 ASN   ( 124-)  A  Poor phi/psi
 149 ARG   ( 152-)  A  Poor phi/psi
 177 LEU   ( 180-)  A  PRO omega poor
 187 GLY   ( 190-)  A  omega poor
 189 SER   ( 192-)  A  Poor phi/psi
 233 ASN   ( 236-)  A  Poor phi/psi
 236 PRO   ( 239-)  A  omega poor
 239 SER   ( 242-)  A  omega poor
 250 ILE   ( 270-)  A  PRO omega poor
 253 ASP   ( 273-)  A  Poor phi/psi
 278 MET   ( 298-)  A  omega poor
 279 ALA   ( 299-)  A  omega poor
 288 ASP   ( 308-)  A  omega poor
 295 GLU   ( 315-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -3.519

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 : -3.519

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!

   9 PHE   (  10-)  A      0
  12 LYS   (  13-)  A      0
  13 SER   (  14-)  A      0
  34 ARG   (  35-)  A      0
  45 GLN   (  46-)  A      0
  55 SER   (  56-)  A      0
  56 PHE   (  57-)  A      0
  58 LEU   (  59-)  A      0
  65 ARG   (  66-)  A      0
  66 ILE   (  67-)  A      0
  70 ARG   (  71-)  A      0
  71 SER   (  72-)  A      0
  79 PRO   (  80-)  A      0
  82 GLN   (  83-)  A      0
  83 GLN   (  84-)  A      0
  84 GLN   (  85-)  A      0
  85 GLN   (  86-)  A      0
  86 LEU   (  87-)  A      0
  89 ILE   (  90-)  A      0
  90 GLN   (  91-)  A      0
  91 GLN   (  94-)  A      0
  92 ALA   (  95-)  A      0
 101 PRO   ( 104-)  A      0
 102 ILE   ( 105-)  A      0
 104 HIS   ( 107-)  A      0
And so on for a total of 118 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

 183 PRO   ( 186-)  A    0.19 LOW

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].

  53 PRO   (  54-)  A  -173.1 envelop N (180 degrees)
  63 PRO   (  64-)  A   102.3 envelop C-beta (108 degrees)
 101 PRO   ( 104-)  A   -36.6 envelop C-alpha (-36 degrees)
 178 PRO   ( 181-)  A   -24.4 half-chair C-alpha/N (-18 degrees)
 236 PRO   ( 239-)  A    49.3 half-chair C-delta/C-gamma (54 degrees)
 300 PRO   ( 320-)  A   -51.2 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.

 341 ARG   ( 361-)  A      NH1 <->  347 HOH   ( 445 )  A      O      0.49    2.21  INTRA
 186 GLN   ( 189-)  A      NE2 <->  295 GLU   ( 315-)  A      OE2    0.38    2.32  INTRA BF
  91 GLN   (  94-)  A      N   <->  347 HOH   ( 393 )  A      O      0.36    2.34  INTRA BF
 224 ARG   ( 227-)  A      NH1 <->  243 GLU   ( 246-)  A      OE1    0.33    2.37  INTRA BF
 186 GLN   ( 189-)  A      NE2 <->  295 GLU   ( 315-)  A      CD     0.32    2.78  INTRA BF
 136 MET   ( 139-)  A      CE  <->  185 ASN   ( 188-)  A      ND2    0.31    2.79  INTRA BF
  25 ASN   (  26-)  A      OD1 <->  304 ARG   ( 324-)  A      N      0.29    2.41  INTRA
  29 ALA   (  30-)  A      O   <->  320 ARG   ( 340-)  A      NH1    0.29    2.41  INTRA BF
 185 ASN   ( 188-)  A      OD1 <->  187 GLY   ( 190-)  A      N      0.26    2.44  INTRA BF
  49 HIS   (  50-)  A      ND1 <->   72 GLY   (  73-)  A      N      0.24    2.76  INTRA
 340 LEU   ( 360-)  A      O   <->  342 SER   ( 362-)  A      N      0.23    2.47  INTRA BF
  11 GLY   (  12-)  A      O   <->   16 HIS   (  17-)  A      ND1    0.22    2.48  INTRA BL
 310 LYS   ( 330-)  A      CG  <->  347 HOH   ( 425 )  A      O      0.20    2.60  INTRA BF
 182 LYS   ( 185-)  A      NZ  <->  347 HOH   ( 454 )  A      O      0.16    2.54  INTRA
 221 VAL   ( 224-)  A      N   <->  346 ADP   ( 368-)  A      N1     0.16    2.84  INTRA BL
 196 ARG   ( 199-)  A      N   <->  347 HOH   ( 411 )  A      O      0.16    2.54  INTRA BF
  34 ARG   (  35-)  A      NH2 <->  328 GLU   ( 348-)  A      OE2    0.15    2.55  INTRA BF
 105 GLY   ( 108-)  A      N   <->  109 GLU   ( 112-)  A      OE2    0.15    2.55  INTRA
  65 ARG   (  66-)  A      CD  <->  347 HOH   ( 467 )  A      O      0.15    2.65  INTRA BF
  76 ALA   (  77-)  A      N   <->   87 ARG   (  88-)  A      O      0.14    2.56  INTRA
  58 LEU   (  59-)  A      N   <->   67 ALA   (  68-)  A      O      0.11    2.59  INTRA
 308 TYR   ( 328-)  A      N   <->  309 PRO   ( 329-)  A      CD     0.11    2.89  INTRA BL
  24 ARG   (  25-)  A      NH2 <->   61 ASP   (  62-)  A      OD1    0.11    2.59  INTRA BF
  76 ALA   (  77-)  A      O   <->   87 ARG   (  88-)  A      N      0.11    2.59  INTRA
  12 LYS   (  13-)  A      CG  <->   44 LYS   (  45-)  A      O      0.10    2.70  INTRA
  29 ALA   (  30-)  A      O   <->  320 ARG   ( 340-)  A      CG     0.10    2.70  INTRA
 182 LYS   ( 185-)  A      O   <->  216 LEU   ( 219-)  A      N      0.10    2.60  INTRA BL
 341 ARG   ( 361-)  A      NH1 <->  347 HOH   ( 438 )  A      O      0.09    2.61  INTRA
   3 ILE   (   4-)  A      N   <->   34 ARG   (  35-)  A      O      0.09    2.61  INTRA
 171 LEU   ( 174-)  A      O   <->  175 LEU   ( 178-)  A      N      0.09    2.61  INTRA
 245 VAL   ( 248-)  A      N   <->  247 GLU   ( 267-)  A      O      0.08    2.62  INTRA BF
 182 LYS   ( 185-)  A      NZ  <->  346 ADP   ( 368-)  A      N7     0.07    2.93  INTRA BL
  21 GLN   (  22-)  A      OE1 <->  347 HOH   ( 499 )  A      O      0.06    2.34  INTRA
  86 LEU   (  87-)  A      CD1 <->  122 LEU   ( 125-)  A      CD1    0.06    3.14  INTRA
 231 LEU   ( 234-)  A      O   <->  237 HIS   ( 240-)  A      N      0.06    2.64  INTRA BL
 158 PHE   ( 161-)  A      O   <->  215 VAL   ( 218-)  A      N      0.05    2.65  INTRA
  17 GLU   (  18-)  A      OE2 <->  347 HOH   ( 493 )  A      O      0.05    2.35  INTRA
 137 ASP   ( 140-)  A      OD2 <->  347 HOH   ( 498 )  A      O      0.04    2.36  INTRA
 284 PHE   ( 304-)  A      N   <->  292 VAL   ( 312-)  A      O      0.03    2.67  INTRA BL
 261 ARG   ( 281-)  A      NH2 <->  289 GLY   ( 309-)  A      O      0.03    2.67  INTRA BF
 156 VAL   ( 159-)  A      CG1 <->  157 CYS   ( 160-)  A      N      0.03    2.97  INTRA BL
 340 LEU   ( 360-)  A      C   <->  342 SER   ( 362-)  A      N      0.03    2.87  INTRA BF
 318 ASP   ( 338-)  A      O   <->  322 LEU   ( 342-)  A      N      0.02    2.68  INTRA BL
  84 GLN   (  85-)  A      N   <->   95 GLN   (  98-)  A      OE1    0.02    2.68  INTRA
 346 ADP   ( 368-)  A      N3  <->  347 HOH   ( 489 )  A      O      0.02    2.68  INTRA
 302 PHE   ( 322-)  A      O   <->  319 TYR   ( 339-)  A      OH     0.01    2.39  INTRA
  52 ASP   (  53-)  A      CA  <->   53 PRO   (  54-)  A      CD     0.01    2.79  INTRA B3
 225 GLU   ( 228-)  A      O   <->  244 VAL   ( 247-)  A      N      0.01    2.69  INTRA
 187 GLY   ( 190-)  A      CA  <->  188 SER   ( 191-)  A      CA     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

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.

 196 ARG   ( 199-)  A      -6.76
  70 ARG   (  71-)  A      -6.75
  82 GLN   (  83-)  A      -6.32
  83 GLN   (  84-)  A      -5.70
  12 LYS   (  13-)  A      -5.60
 174 GLN   ( 177-)  A      -5.59
  89 ILE   (  90-)  A      -5.47
 161 HIS   ( 164-)  A      -5.42

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.

 299 LEU   ( 319-)  A   -2.72

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 347 HOH   ( 479 )  A      O     14.15  -14.39   20.98

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.

 347 HOH   ( 449 )  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.

  69 HIS   (  70-)  A
 165 HIS   ( 168-)  A
 186 GLN   ( 189-)  A
 259 GLN   ( 279-)  A
 297 ASN   ( 317-)  A
 334 HIS   ( 354-)  A
 338 GLN   ( 358-)  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.

  51 ASN   (  52-)  A      ND2
  52 ASP   (  53-)  A      N
  54 ASP   (  55-)  A      N
  70 ARG   (  71-)  A      NE
  93 LEU   (  96-)  A      N
 160 ARG   ( 163-)  A      N
 164 ALA   ( 167-)  A      N
 168 VAL   ( 171-)  A      N
 169 ASP   ( 172-)  A      N
 182 LYS   ( 185-)  A      NZ
 214 LYS   ( 217-)  A      N
 221 VAL   ( 224-)  A      N
 258 THR   ( 278-)  A      N
 303 THR   ( 323-)  A      OG1
 312 TRP   ( 332-)  A      NE1
 338 GLN   ( 358-)  A      NE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 345  MG   ( 369-)  A     0.27   0.99 Could be  K

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 347 HOH   ( 430 )  A      O  1.08  K  4
 347 HOH   ( 486 )  A      O  0.96  K  4 ION-B

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.

 110 ASP   ( 113-)  A   H-bonding suggests Asn; but Alt-Rotamer
 336 ASP   ( 356-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :   0.307
  2nd generation packing quality :  -0.420
  Ramachandran plot appearance   :  -0.458
  chi-1/chi-2 rotamer normality  :  -3.519 (poor)
  Backbone conformation          :   0.600

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.960
  Bond angles                    :   0.944
  Omega angle restraints         :   1.192
  Side chain planarity           :   0.909
  Improper dihedral distribution :   1.185
  B-factor distribution          :   0.519
  Inside/Outside distribution    :   1.026

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.960
  Bond angles                    :   0.944
  Omega angle restraints         :   1.192
  Side chain planarity           :   0.909
  Improper dihedral distribution :   1.185
  B-factor distribution          :   0.519
  Inside/Outside distribution    :   1.026
==============

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