WHAT IF Check report

This file was created 2013-12-09 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 pdb3vx1.ent

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Nomenclature related problems

Warning: Tyrosine convention problem

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

  79 TYR   (  79-)  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.

   5 ASP   (   5-)  A
 144 ASP   ( 144-)  A
 270 ASP   ( 270-)  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.

  92 GLU   (  92-)  A
 109 GLU   ( 109-)  A
 294 GLU   ( 294-)  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.

 122 HIS   ( 122-)  A      CG   CD2   1.41    4.5
 216 TRP   ( 216-)  A      NE1  CE2   1.48   10.2
 385 TRP   ( 385-)  A      NE1  CE2   1.48   10.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998922  0.000032 -0.000489|
 |  0.000032  0.998409  0.000340|
 | -0.000489  0.000340  0.998409|
Proposed new scale matrix

 |  0.019875  0.000000  0.000010|
 |  0.000000  0.015021 -0.000005|
 |  0.000004 -0.000003  0.007614|
With corresponding cell

    A    =  50.313  B   =  66.574  C    = 131.335
    Alpha=  89.961  Beta=  90.056  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  50.368  B   =  66.678  C    = 131.551
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 32.812
(Under-)estimated Z-score: 4.222

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.

   5 ASP   (   5-)  A
  92 GLU   (  92-)  A
 109 GLU   ( 109-)  A
 144 ASP   ( 144-)  A
 270 ASP   ( 270-)  A
 294 GLU   ( 294-)  A

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.

  11 ILE   (  11-)  A    4.90

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 THR   ( 207-)  A    -3.3
 334 HIS   ( 334-)  A    -2.9
  14 LEU   (  14-)  A    -2.4
 174 PRO   ( 174-)  A    -2.2
 305 THR   ( 305-)  A    -2.2
 419 TYR   ( 419-)  A    -2.1
 293 VAL   ( 293-)  A    -2.1
  94 TYR   (  94-)  A    -2.1

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.

  70 PRO   (  70-)  A  omega poor
  71 GLN   (  71-)  A  omega poor
 138 LYS   ( 138-)  A  PRO omega poor
 140 PHE   ( 140-)  A  Poor phi/psi
 150 CYS   ( 150-)  A  Poor phi/psi
 168 ASP   ( 168-)  A  Poor phi/psi
 334 HIS   ( 334-)  A  Poor phi/psi
 340 ASP   ( 340-)  A  PRO omega poor
 436 GLU   ( 436-)  A  omega poor
 440 CYS   ( 440-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.897

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.

 104 SER   ( 104-)  A    0.37
 364 SER   ( 364-)  A    0.37
 105 SER   ( 105-)  A    0.38

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 GLN   (   9-)  A      0
  19 PHE   (  19-)  A      0
  29 THR   (  29-)  A      0
  34 ASP   (  34-)  A      0
  36 LYS   (  36-)  A      0
  37 TYR   (  37-)  A      0
  38 CYS   (  38-)  A      0
  42 TRP   (  42-)  A      0
  48 LYS   (  48-)  A      0
  55 MET   (  55-)  A      0
  57 PHE   (  57-)  A      0
  58 THR   (  58-)  A      0
  63 THR   (  63-)  A      0
  65 VAL   (  65-)  A      0
  68 GLN   (  68-)  A      0
  70 PRO   (  70-)  A      0
  75 TYR   (  75-)  A      0
  77 ASP   (  77-)  A      0
  78 ALA   (  78-)  A      0
  82 TYR   (  82-)  A      0
  83 TRP   (  83-)  A      0
  88 TYR   (  88-)  A      0
  91 ASN   (  91-)  A      0
  94 TYR   (  94-)  A      0
  96 THR   (  96-)  A      0
And so on for a total of 187 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.581

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 399 GLY   ( 399-)  A   1.56   20

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]

 341 PRO   ( 341-)  A    0.46 HIGH

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].

  70 PRO   (  70-)  A   -57.5 half-chair C-beta/C-alpha (-54 degrees)
 174 PRO   ( 174-)  A    99.5 envelop C-beta (108 degrees)
 386 PRO   ( 386-)  A    24.3 half-chair N/C-delta (18 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.

 312 LYS   ( 312-)  A      NZ  <->  480 HOH   (1128 )  A      O      0.37    2.33  INTRA BL
 382 TYR   ( 382-)  A      O   <->  398 LYS   ( 398-)  A      NZ     0.35    2.35  INTRA
  21 ARG   (  21-)  A      NH2 <->   23 ASP   (  23-)  A      OD2    0.33    2.37  INTRA BF
 252 TYR   ( 252-)  A      N   <->  253 PRO   ( 253-)  A      CD     0.30    2.70  INTRA BL
 370 ASN   ( 370-)  A      ND2 <->  480 HOH   (1275 )  A      O      0.29    2.41  INTRA BL
 270 ASP   ( 270-)  A      CB  <->  480 HOH   (1245 )  A      O      0.24    2.56  INTRA
 178 THR   ( 178-)  A      OG1 <->  212 GLN   ( 212-)  A      NE2    0.23    2.47  INTRA
 333 GLN   ( 333-)  A      NE2 <->  480 HOH   (1395 )  A      O      0.22    2.48  INTRA
  21 ARG   (  21-)  A      N   <->  480 HOH   (1267 )  A      O      0.20    2.50  INTRA
 204 ARG   ( 204-)  A      NH2 <->  480 HOH   (1270 )  A      O      0.20    2.50  INTRA BL
 217 PRO   ( 217-)  A      CD  <->  245 VAL   ( 245-)  A      CG2    0.20    3.00  INTRA
 121 ASN   ( 121-)  A      ND2 <->  122 HIS   ( 122-)  A      ND1    0.18    2.82  INTRA BL
 322 ASP   ( 322-)  A      OD1 <->  384 ASN   ( 384-)  A      N      0.18    2.52  INTRA
 108 HIS   ( 108-)  A      NE2 <->  201 ASP   ( 201-)  A      OD2    0.18    2.52  INTRA BF
 340 ASP   ( 340-)  A      N   <->  480 HOH   (1111 )  A      O      0.16    2.54  INTRA BL
 397 ARG   ( 397-)  A      NE  <->  480 HOH   (1251 )  A      O      0.14    2.56  INTRA BL
 436 GLU   ( 436-)  A      OE2 <->  462 VAL   ( 462-)  A      N      0.13    2.57  INTRA BL
 322 ASP   ( 322-)  A      CG  <->  384 ASN   ( 384-)  A      N      0.13    2.97  INTRA
 150 CYS   ( 150-)  A      O   <->  165 TRP   ( 165-)  A      N      0.12    2.58  INTRA
 388 TYR   ( 388-)  A      CG  <->  389 LYS   ( 389-)  A      N      0.12    2.88  INTRA BL
 369 ARG   ( 369-)  A      NH1 <->  480 HOH   (1266 )  A      O      0.11    2.59  INTRA BL
 240 CYS   ( 240-)  A      N   <->  241 PRO   ( 241-)  A      CD     0.11    2.89  INTRA
 274 ASN   ( 274-)  A      OD1 <->  480 HOH   (1244 )  A      O      0.11    2.29  INTRA BL
 339 ASN   ( 339-)  A      ND2 <->  480 HOH   (1111 )  A      O      0.11    2.59  INTRA BL
 111 GLY   ( 111-)  A      O   <->  480 HOH   (1294 )  A      O      0.11    2.29  INTRA BF
And so on for a total of 70 lines.

Packing, accessibility and threading

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.

  88 TYR   (  88-)  A      -6.00
 232 LEU   ( 232-)  A      -5.48
 333 GLN   ( 333-)  A      -5.42

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.

 439 GLY   ( 439-)  A   -2.94
 151 PHE   ( 151-)  A   -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 242 TYR   ( 242-)  A     -  245 VAL   ( 245-)  A        -1.71

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.

 480 HOH   (1286 )  A      O     -5.26   49.65   19.43
 480 HOH   (1356 )  A      O      2.56   55.32   -9.99
 480 HOH   (1387 )  A      O     21.02   33.95   27.39
 480 HOH   (1399 )  A      O      6.32   44.84   27.55

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.

 480 HOH   (1197 )  A      O
 480 HOH   (1249 )  A      O
Bound group on Asn; dont flip  197 ASN  ( 197-) A
Bound to:  478 NAG  (1001-) A
Strange metal coordination for HIS 210

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.

   9 GLN   (   9-)  A
  93 ASN   (  93-)  A
 108 HIS   ( 108-)  A
 212 GLN   ( 212-)  A
 296 HIS   ( 296-)  A
 333 GLN   ( 333-)  A
 339 ASN   ( 339-)  A
 370 ASN   ( 370-)  A
 411 ASN   ( 411-)  A
 433 GLN   ( 433-)  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.

  57 PHE   (  57-)  A      N
  58 THR   (  58-)  A      OG1
  79 TYR   (  79-)  A      N
  80 HIS   (  80-)  A      N
 121 ASN   ( 121-)  A      ND2
 122 HIS   ( 122-)  A      N
 140 PHE   ( 140-)  A      N
 142 SER   ( 142-)  A      N
 150 CYS   ( 150-)  A      N
 175 ASP   ( 175-)  A      N
 204 ARG   ( 204-)  A      NE
 209 LYS   ( 209-)  A      N
 249 VAL   ( 249-)  A      N
 264 SER   ( 264-)  A      N
 270 ASP   ( 270-)  A      N
 322 ASP   ( 322-)  A      N
 348 TRP   ( 348-)  A      N
 366 ASN   ( 366-)  A      ND2
 399 GLY   ( 399-)  A      N
 414 ALA   ( 414-)  A      N
 466 THR   ( 466-)  A      OG1
Only metal coordination for  121 ASN  ( 121-) A      OD1

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.

 411 ASN   ( 411-)  A      OD1

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+.

 479  CA   (1002-)  A     0.50   1.47 Scores about as good as  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.

 480 HOH   (1371 )  A      O  0.88  K  4

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.

 163 ASP   ( 163-)  A   H-bonding suggests Asn
 168 ASP   ( 168-)  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 :  -0.524
  2nd generation packing quality :  -2.025
  Ramachandran plot appearance   :  -2.224
  chi-1/chi-2 rotamer normality  :  -2.897
  Backbone conformation          :  -0.864

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   0.469 (tight)
  Side chain planarity           :   0.559 (tight)
  Improper dihedral distribution :   0.661
  B-factor distribution          :   0.514
  Inside/Outside distribution    :   0.963

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   0.469 (tight)
  Side chain planarity           :   0.559 (tight)
  Improper dihedral distribution :   0.661
  B-factor distribution          :   0.514
  Inside/Outside distribution    :   0.963
==============

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.