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 pdb3rye.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 UNR   ( 901-)  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.

 175 ASP   ( 184-)  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.

  35 ARG   (  44-)  A
 132 ARG   ( 141-)  A

Warning: Tyrosine convention problem

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

   3 TYR   (  10-)  A
  42 TYR   (  51-)  A
  49 TYR   (  58-)  A
 110 TYR   ( 119-)  A
 131 TYR   ( 140-)  A
 195 TYR   ( 204-)  A
 206 TYR   ( 215-)  A
 274 TYR   ( 283-)  A
 296 TYR   ( 305-)  A
 308 TYR   ( 317-)  A
 323 TYR   ( 332-)  A
 340 TYR   ( 349-)  A

Warning: Phenylalanine convention problem

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

  90 PHE   (  99-)  A
 179 PHE   ( 188-)  A
 194 PHE   ( 203-)  A
 240 PHE   ( 249-)  A
 332 PHE   ( 341-)  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.

  69 ASP   (  78-)  A
  94 ASP   ( 103-)  A
 242 ASP   ( 251-)  A
 252 ASP   ( 261-)  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.

  25 GLU   (  32-)  A
 181 GLU   ( 190-)  A
 213 GLU   ( 222-)  A
 228 GLU   ( 237-)  A
 279 GLU   ( 288-)  A
 297 GLU   ( 306-)  A
 298 GLU   ( 307-)  A
 321 GLU   ( 330-)  A

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.

  25 GLU   (  32-)  A
  35 ARG   (  44-)  A
  69 ASP   (  78-)  A
  94 ASP   ( 103-)  A
 132 ARG   ( 141-)  A
 181 GLU   ( 190-)  A
 213 GLU   ( 222-)  A
 228 GLU   ( 237-)  A
 242 ASP   ( 251-)  A
 252 ASP   ( 261-)  A
 279 GLU   ( 288-)  A
 297 GLU   ( 306-)  A
 298 GLU   ( 307-)  A
 321 GLU   ( 330-)  A

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.

 326 PRO   ( 335-)  A    -2.9
  22 THR   (  29-)  A    -2.2
  49 TYR   (  58-)  A    -2.1
   5 GLN   (  12-)  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 GLU   (  30-)  A  omega poor
  24 ASP   (  31-)  A  Poor phi/psi, omega poor
  42 TYR   (  51-)  A  omega poor
  49 TYR   (  58-)  A  Poor phi/psi
 117 LEU   ( 126-)  A  omega poor
 137 TYR   ( 146-)  A  omega poor
 174 VAL   ( 183-)  A  Poor phi/psi, omega poor
 192 THR   ( 201-)  A  omega poor
 222 ILE   ( 231-)  A  omega poor
 256 ASN   ( 265-)  A  Poor phi/psi
 268 ARG   ( 277-)  A  omega poor
 269 ALA   ( 278-)  A  omega poor
 300 ASP   ( 309-)  A  Poor phi/psi
 322 GLN   ( 331-)  A  omega poor
 325 ALA   ( 334-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.175

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.

 154 SER   ( 163-)  A    0.37

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!

   6 GLU   (  13-)  A      0
  23 GLU   (  30-)  A      0
  24 ASP   (  31-)  A      0
  25 GLU   (  32-)  A      0
  26 HIS   (  35-)  A      0
  27 PRO   (  36-)  A      0
  43 ASN   (  52-)  A      0
  44 ALA   (  53-)  A      0
  45 ILE   (  54-)  A      0
  48 LYS   (  57-)  A      0
  49 TYR   (  58-)  A      0
  50 ASN   (  59-)  A      0
  62 LEU   (  71-)  A      0
  68 GLN   (  77-)  A      0
  69 ASP   (  78-)  A      0
 101 LEU   ( 110-)  A      0
 102 THR   ( 111-)  A      0
 103 ARG   ( 112-)  A      0
 104 ARG   ( 113-)  A      0
 106 GLN   ( 115-)  A      0
 107 ILE   ( 116-)  A      0
 108 CYS   ( 117-)  A      0
 113 PRO   ( 122-)  A      0
 115 VAL   ( 124-)  A      0
 117 LEU   ( 126-)  A      0
And so on for a total of 78 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.541

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].

  27 PRO   (  36-)  A  -117.1 half-chair C-delta/C-gamma (-126 degrees)
 142 PRO   ( 151-)  A  -115.1 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 175 ASP   ( 184-)  A      OD2 <->  177 VAL   ( 186-)  A      CG1    0.82    1.98  INTRA BF
   6 GLU   (  13-)  A      OE2 <->   60 ARG   (  69-)  A      NH1    0.71    1.99  INTRA BF
 307 GLN   ( 316-)  A      NE2 <->  311 ASP   ( 320-)  A      OD1    0.36    2.34  INTRA BF
  26 HIS   (  35-)  A      N   <->  347 HOH   ( 376 )  A      O      0.33    2.37  INTRA BF
   3 TYR   (  10-)  A      CB  <->  338 LYS   ( 347-)  A      NZ     0.31    2.79  INTRA BF
 301 LEU   ( 310-)  A      N   <->  302 PRO   ( 311-)  A      CD     0.29    2.71  INTRA BF
 185 LYS   ( 194-)  A      NZ  <->  347 HOH   ( 483 )  A      O      0.27    2.43  INTRA BF
   8 GLN   (  15-)  A      CA  <->  347 HOH   ( 438 )  A      O      0.23    2.57  INTRA BF
  24 ASP   (  31-)  A      N   <->  347 HOH   ( 492 )  A      O      0.21    2.49  INTRA BF
  66 ARG   (  75-)  A      NH1 <->  347 HOH   ( 494 )  A      O      0.20    2.50  INTRA BF
 135 LYS   ( 144-)  A      CE  <->  347 HOH   ( 480 )  A      O      0.19    2.61  INTRA BF
 347 HOH   ( 428 )  A      O   <->  347 HOH   ( 478 )  A      O      0.18    2.02  INTRA BF
 103 ARG   ( 112-)  A      NH1 <->  346 UNR   ( 901-)  A      O10    0.16    2.54  INTRA BL
   1 ASP   (   8-)  A      O   <->    5 GLN   (  12-)  A      CG     0.15    2.65  INTRA BF
  64 GLU   (  73-)  A      N   <->  347 HOH   ( 471 )  A      O      0.14    2.56  INTRA BF
 307 GLN   ( 316-)  A      NE2 <->  311 ASP   ( 320-)  A      CG     0.13    2.97  INTRA BF
   6 GLU   (  13-)  A      OE2 <->   60 ARG   (  69-)  A      CD     0.12    2.68  INTRA BF
 191 LYS   ( 200-)  A      NZ  <->  346 UNR   ( 901-)  A      O7     0.12    2.58  INTRA BL
  66 ARG   (  75-)  A      CD  <->  347 HOH   ( 491 )  A      O      0.12    2.68  INTRA BF
 185 LYS   ( 194-)  A      CD  <->  347 HOH   ( 483 )  A      O      0.11    2.69  INTRA BF
  23 GLU   (  30-)  A      N   <->  347 HOH   ( 492 )  A      O      0.09    2.61  INTRA BF
 218 ASN   ( 227-)  A      ND2 <->  347 HOH   ( 424 )  A      O      0.09    2.61  INTRA BF
  64 GLU   (  73-)  A      O   <->   67 LYS   (  76-)  A      N      0.09    2.61  INTRA BF
 283 GLN   ( 292-)  A      OE1 <->  347 HOH   ( 482 )  A      O      0.09    2.31  INTRA BF
 347 HOH   ( 447 )  A      O   <->  347 HOH   ( 468 )  A      O      0.08    2.12  INTRA BF
 174 VAL   ( 183-)  A      CG1 <->  175 ASP   ( 184-)  A      CA     0.07    3.03  INTRA BF
  43 ASN   (  52-)  A      OD1 <->  347 HOH   ( 412 )  A      O      0.07    2.33  INTRA BF
 198 TYR   ( 207-)  A      OH  <->  347 HOH   ( 465 )  A      O      0.06    2.34  INTRA BF
 101 LEU   ( 110-)  A      C   <->  108 CYS   ( 117-)  A      SG     0.04    3.36  INTRA BL
 342  MG   ( 907-)  A     MG   <->  344  MG   ( 909-)  A     MG      0.04    3.16  INTRA BL
 243 PRO   ( 252-)  A      O   <->  247 GLY   ( 256-)  A      N      0.03    2.67  INTRA BF
  75 ARG   (  84-)  A      NE  <->  347 HOH   ( 444 )  A      O      0.03    2.67  INTRA BF
  43 ASN   (  52-)  A      O   <->  104 ARG   ( 113-)  A      NH1    0.03    2.67  INTRA BL
  47 GLY   (  56-)  A      N   <->  347 HOH   ( 389 )  A      O      0.03    2.67  INTRA BF
 220 LYS   ( 229-)  A      NZ  <->  347 HOH   ( 486 )  A      O      0.02    2.68  INTRA BF
 270 THR   ( 279-)  A      N   <->  273 GLN   ( 282-)  A      OE1    0.02    2.68  INTRA BF
 176 LEU   ( 185-)  A      N   <->  177 VAL   ( 186-)  A      N      0.02    2.58  INTRA BF
 273 GLN   ( 282-)  A      NE2 <->  298 GLU   ( 307-)  A      OE2    0.01    2.69  INTRA BF
 181 GLU   ( 190-)  A      OE2 <->  347 HOH   ( 425 )  A      O      0.01    2.39  INTRA BF
 297 GLU   ( 306-)  A      O   <->  347 HOH   ( 441 )  A      O      0.01    2.39  INTRA BF
 242 ASP   ( 251-)  A      O   <->  245 VAL   ( 254-)  A      N      0.01    2.69  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.

 171 GLN   ( 180-)  A      -6.65
 104 ARG   ( 113-)  A      -5.89
 178 ARG   ( 187-)  A      -5.40
 111 GLN   ( 120-)  A      -5.36
 268 ARG   ( 277-)  A      -5.32
 322 GLN   ( 331-)  A      -5.10
  28 GLU   (  37-)  A      -5.01

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.

 245 VAL   ( 254-)  A   -2.62
  47 GLY   (  56-)  A   -2.51

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.

 347 HOH   ( 438 )  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.

 153 GLN   ( 162-)  A
 264 GLN   ( 273-)  A
 275 GLN   ( 284-)  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.

   3 TYR   (  10-)  A      N
  43 ASN   (  52-)  A      ND2
  45 ILE   (  54-)  A      N
  66 ARG   (  75-)  A      NH1
  77 TRP   (  86-)  A      NE1
 107 ILE   ( 116-)  A      N
 143 TYR   ( 152-)  A      N
 162 GLN   ( 171-)  A      NE2
 174 VAL   ( 183-)  A      N
 262 VAL   ( 271-)  A      N
Only metal coordination for   94 ASP  ( 103-) A      OD2
Only metal coordination for   98 ASP  ( 107-) A      OD2

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.

  61 GLU   (  70-)  A      OE1
 159 GLU   ( 168-)  A      OE1

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+.

 342  MG   ( 907-)  A   -.-  -.-  Part of ionic cluster
 343  MG   ( 908-)  A   -.-  -.-  Part of ionic cluster
 344  MG   ( 909-)  A   -.-  -.-  Part of ionic cluster
 344  MG   ( 909-)  A     0.75   1.35 Scores about as good as CA

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   ( 395 )  A      O  0.88 MG  4 *1
 347 HOH   ( 446 )  A      O  1.00  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.

  25 GLU   (  32-)  A   H-bonding suggests Gln
  69 ASP   (  78-)  A   H-bonding suggests Asn
 235 ASP   ( 244-)  A   H-bonding suggests Asn; but Alt-Rotamer
 255 ASP   ( 264-)  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 :   0.399
  2nd generation packing quality :  -0.792
  Ramachandran plot appearance   :  -0.430
  chi-1/chi-2 rotamer normality  :  -2.175
  Backbone conformation          :   0.674

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.246 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   1.371 (loose)
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.761
  Inside/Outside distribution    :   0.993

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 :   0.8
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.246 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   1.371 (loose)
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.761
  Inside/Outside distribution    :   0.993
==============

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.