WHAT IF Check report

This file was created 2011-12-13 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 pdb3bax.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.

 500 AZI   ( 500-)  A  -
 504 AZI   ( 501-)  A  -

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

 151 TYR   ( 151-)  A

Warning: Phenylalanine convention problem

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

 406 PHE   ( 406-)  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.

  77 ASP   (  77-)  A
 375 ASP   ( 375-)  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.

  78 GLU   (  78-)  A
 369 GLU   ( 369-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.314
RMS-deviation in bond distances: 0.008

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

 |  0.998115 -0.000019 -0.000215|
 | -0.000019  0.998009  0.000230|
 | -0.000215  0.000230  0.998713|
Proposed new scale matrix

 |  0.019241  0.000000  0.000004|
 |  0.000000  0.014770 -0.000003|
 |  0.000002 -0.000002  0.007695|
With corresponding cell

    A    =  51.972  B   =  67.703  C    = 129.956
    Alpha=  89.974  Beta=  90.025  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  52.070  B   =  67.840  C    = 130.120
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 50.904
(Under-)estimated Z-score: 5.258

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.

   2 TYR   (   2-)  A     -C    N    CA  129.54    4.4
  11 THR   (  11-)  A      N    CA   C   122.60    4.1
 190 GLY   ( 190-)  A      N    CA   C   124.92    4.3
 195 ARG   ( 195-)  A      N    CA   C    97.88   -4.8
 238 GLY   ( 238-)  A      N    CA   C   125.79    4.6
 293 LEU   ( 293-)  A      N    CA   C    96.83   -5.1
 308 GLY   ( 308-)  A      N    CA   C   100.51   -4.1

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.661
RMS-deviation in bond angles: 1.492

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.

  77 ASP   (  77-)  A
  78 GLU   (  78-)  A
 369 GLU   ( 369-)  A
 375 ASP   ( 375-)  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.

 293 LEU   ( 293-)  A    5.45
 195 ARG   ( 195-)  A    5.35
 318 ALA   ( 318-)  A    5.29
 336 THR   ( 336-)  A    5.15
 308 GLY   ( 308-)  A    4.69
 238 GLY   ( 238-)  A    4.38
 190 GLY   ( 190-)  A    4.07

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.546

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.

 407 THR   ( 407-)  A    -2.9
 376 THR   ( 376-)  A    -2.7
  10 ARG   (  10-)  A    -2.4
  45 PRO   (  45-)  A    -2.3
 343 ARG   ( 343-)  A    -2.3
  44 PRO   (  44-)  A    -2.2
 440 LEU   ( 440-)  A    -2.1
  56 ARG   (  56-)  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.

   5 ASN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 124 ARG   ( 124-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 268 LYS   ( 268-)  A  Poor phi/psi
 345 PRO   ( 345-)  A  Poor phi/psi
 350 ASN   ( 350-)  A  Poor phi/psi
 364 ASN   ( 364-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 486 PRO   ( 486-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.096

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!

   5 ASN   (   5-)  A      0
   8 GLN   (   8-)  A      0
  10 ARG   (  10-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  37 PHE   (  37-)  A      0
  52 TYR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 PHE   (  55-)  A      0
  56 ARG   (  56-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  66 SER   (  66-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
  75 ASN   (  75-)  A      0
  89 VAL   (  89-)  A      0
And so on for a total of 230 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 : 1.609

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!

 110 GLY   ( 110-)  A   1.53   19

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.

 268 LYS   ( 268-)  A      NZ  <->  505 HOH   ( 631 )  A      O      0.28    2.42  INTRA
 504 AZI   ( 501-)  A      N3  <->  505 HOH   ( 989 )  A      O      0.24    2.36  INTRA
 308 GLY   ( 308-)  A      N   <->  309 GLY   ( 309-)  A      N      0.23    2.37  INTRA BF
 466 LYS   ( 466-)  A      NZ  <->  505 HOH   ( 911 )  A      O      0.18    2.52  INTRA BF
 316 TRP   ( 316-)  A      CZ3 <->  343 ARG   ( 343-)  A      NH1    0.17    2.93  INTRA
 235 ILE   ( 235-)  A      CG2 <->  307 ALA   ( 307-)  A      CB     0.16    3.04  INTRA
 201 HIS   ( 201-)  A      NE2 <->  505 HOH   ( 674 )  A      O      0.16    2.54  INTRA
 283 GLY   ( 283-)  A      N   <->  505 HOH   ( 816 )  A      O      0.15    2.55  INTRA
 235 ILE   ( 235-)  A      N   <->  500 AZI   ( 500-)  A      N3     0.14    2.86  INTRA
 331 HIS   ( 331-)  A      O   <->  398 ARG   ( 398-)  A      NH1    0.14    2.56  INTRA BL
 208 LYS   ( 208-)  A      NZ  <->  212 ASP   ( 212-)  A      OD2    0.13    2.57  INTRA
 185 HIS   ( 185-)  A      ND1 <->  505 HOH   (1035 )  A      O      0.13    2.57  INTRA
 227 LYS   ( 227-)  A      CD  <->  503  NA   ( 504-)  A     NA      0.12    3.08  INTRA BF
 275 SER   ( 275-)  A      O   <->  278 LYS   ( 278-)  A      NZ     0.12    2.58  INTRA
 137 ASN   ( 137-)  A      OD1 <->  140 LYS   ( 140-)  A      NZ     0.10    2.60  INTRA
 431 ASN   ( 431-)  A      ND2 <->  505 HOH   ( 893 )  A      O      0.10    2.60  INTRA BL
 307 ALA   ( 307-)  A      N   <->  505 HOH   ( 835 )  A      O      0.10    2.60  INTRA BF
  80 ARG   (  80-)  A      NH1 <->  505 HOH   ( 569 )  A      O      0.10    2.60  INTRA
 352 ASN   ( 352-)  A      ND2 <->  505 HOH   ( 710 )  A      O      0.10    2.60  INTRA
   8 GLN   (   8-)  A      N   <->  505 HOH   (1026 )  A      O      0.09    2.61  INTRA
 470 SER   ( 470-)  A      OG  <->  472 ASP   ( 472-)  A      OD1    0.09    2.31  INTRA
 505 HOH   ( 572 )  A      O   <->  505 HOH   (1018 )  A      O      0.07    2.13  INTRA BF
 497 NAG   ( 497-)  A      N2  <->  505 HOH   ( 522 )  A      O      0.07    2.63  INTRA BF
 140 LYS   ( 140-)  A      N   <->  504 AZI   ( 501-)  A      N1     0.07    2.93  INTRA
 249 GLY   ( 249-)  A      C   <->  505 HOH   (1018 )  A      O      0.07    2.73  INTRA BF
 267 ARG   ( 267-)  A      N   <->  268 LYS   ( 268-)  A      N      0.06    2.54  INTRA BL
 273 LYS   ( 273-)  A      NZ  <->  505 HOH   (1091 )  A      O      0.05    2.65  INTRA
  10 ARG   (  10-)  A      CZ  <->  505 HOH   (1103 )  A      O      0.05    2.75  INTRA BF
 243 LYS   ( 243-)  A      NZ  <->  505 HOH   ( 854 )  A      O      0.04    2.66  INTRA
 436 PHE   ( 436-)  A      O   <->  479 ILE   ( 479-)  A      N      0.04    2.66  INTRA
 302 GLN   ( 302-)  A      N   <->  303 ARG   ( 303-)  A      N      0.04    2.56  INTRA B3
  10 ARG   (  10-)  A      NH1 <->   36 GLY   (  36-)  A      CA     0.04    3.06  INTRA
  68 LYS   (  68-)  A      NZ  <->  117 SER   ( 117-)  A      OG     0.04    2.66  INTRA BL
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      ND1    0.04    2.96  INTRA BL
 410 TYR   ( 410-)  A      CG  <->  411 ASP   ( 411-)  A      N      0.03    2.97  INTRA BL
 265 VAL   ( 265-)  A      CG2 <->  266 ILE   ( 266-)  A      N      0.03    2.97  INTRA BL
 344 TRP   ( 344-)  A      O   <->  346 ARG   ( 346-)  A      N      0.03    2.67  INTRA
 200 LYS   ( 200-)  A      NZ  <->  235 ILE   ( 235-)  A      O      0.02    2.68  INTRA BL
 152 ASN   ( 152-)  A      N   <->  153 ASP   ( 153-)  A      N      0.02    2.58  INTRA BL
 219 SER   ( 219-)  A      O   <->  505 HOH   ( 953 )  A      O      0.02    2.38  INTRA BL
 345 PRO   ( 345-)  A      O   <->  355 ASN   ( 355-)  A      ND2    0.02    2.68  INTRA
 476 HIS   ( 476-)  A      N   <->  505 HOH   ( 639 )  A      O      0.02    2.68  INTRA
 147 ASP   ( 147-)  A      OD1 <->  161 ARG   ( 161-)  A      NE     0.02    2.68  INTRA BL
  13 ILE   (  13-)  A      CG2 <->   14 VAL   (  14-)  A      N      0.01    2.99  INTRA BL
 180 ALA   ( 180-)  A      O   <->  184 ASN   ( 184-)  A      N      0.01    2.69  INTRA BL
 480 SER   ( 480-)  A      C   <->  482 SER   ( 482-)  A      N      0.01    2.89  INTRA
 294 VAL   ( 294-)  A      C   <->  295 PHE   ( 295-)  A      CD1    0.01    3.09  INTRA BL
 306 GLY   ( 306-)  A      CA  <->  505 HOH   ( 835 )  A      O      0.01    2.79  INTRA BF

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.

  72 ARG   (  72-)  A      -6.92
 142 LYS   ( 142-)  A      -6.56
 343 ARG   ( 343-)  A      -6.02
   2 TYR   (   2-)  A      -5.94
   8 GLN   (   8-)  A      -5.92
  52 TYR   (  52-)  A      -5.86
 237 LEU   ( 237-)  A      -5.46
   7 GLN   (   7-)  A      -5.43
 269 TRP   ( 269-)  A      -5.39
 284 TRP   ( 284-)  A      -5.38
 279 ASN   ( 279-)  A      -5.34
  88 ASN   (  88-)  A      -5.30
 270 ASN   ( 270-)  A      -5.30
  30 ARG   (  30-)  A      -5.29
 302 GLN   ( 302-)  A      -5.26
 303 ARG   ( 303-)  A      -5.23
  53 ASN   (  53-)  A      -5.20
 118 TYR   ( 118-)  A      -5.07

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 269 TRP   ( 269-)  A       271 - GLY    271- ( A)         -4.96

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.

 505 HOH   ( 512 )  A      O      1.26   25.82    1.98
 505 HOH   ( 725 )  A      O    -13.17   -7.75  -22.33
 505 HOH   ( 757 )  A      O      5.28    9.85   -1.18
 505 HOH   ( 792 )  A      O    -14.86   -5.03  -23.26
 505 HOH   (1105 )  A      O      3.39   -5.45    3.15

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.

 105 ASN   ( 105-)  A
 270 ASN   ( 270-)  A
 350 ASN   ( 350-)  A
 364 ASN   ( 364-)  A
 415 ASN   ( 415-)  A
 476 HIS   ( 476-)  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.

  10 ARG   (  10-)  A      NE
  10 ARG   (  10-)  A      NH1
  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 140 LYS   ( 140-)  A      N
 156 GLN   ( 156-)  A      N
 175 VAL   ( 175-)  A      N
 182 TYR   ( 182-)  A      OH
 193 GLY   ( 193-)  A      N
 235 ILE   ( 235-)  A      N
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 305 HIS   ( 305-)  A      NE2
 306 GLY   ( 306-)  A      N
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 342 TYR   ( 342-)  A      N
 344 TRP   ( 344-)  A      N
 357 TRP   ( 357-)  A      N
 370 VAL   ( 370-)  A      N
 434 TRP   ( 434-)  A      N
 487 PHE   ( 487-)  A      N
 491 HIS   ( 491-)  A      ND1
 493 GLU   ( 493-)  A      N
Only metal coordination for  100 ASN  ( 100-) 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.

  15 HIS   (  15-)  A      NE2
 272 GLU   ( 272-)  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+.

 498  CA   ( 498-)  A     0.56   0.78 Scores about as good as NA *1
 501  NA   ( 502-)  A     0.64   1.13 Is perhaps  K
 502  NA   ( 503-)  A   -.-  -.-  Too few ligands (0)
 503  NA   ( 504-)  A   -.-  -.-  Too few ligands (2)

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.

 505 HOH   ( 537 )  A      O  0.88  K  6 Ion-B
 505 HOH   ( 541 )  A      O  1.02  K  5 ION-B
 505 HOH   ( 566 )  A      O  1.09  K  4
 505 HOH   ( 592 )  A      O  0.93  K  6
 505 HOH   ( 595 )  A      O  1.07  K  4
 505 HOH   ( 613 )  A      O  1.11  K  5
 505 HOH   ( 623 )  A      O  0.95  K  5
 505 HOH   ( 703 )  A      O  1.03  K  4
 505 HOH   ( 769 )  A      O  0.88  K  4 Ion-B
 505 HOH   ( 910 )  A      O  0.96  K  4 ION-B H2O-B
 505 HOH   ( 959 )  A      O  0.89 NA  5 *1
 505 HOH   (1008 )  A      O  0.93  K  4
 505 HOH   (1011 )  A      O  1.15  K  4

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 :  -0.798
  2nd generation packing quality :  -1.666
  Ramachandran plot appearance   :  -1.521
  chi-1/chi-2 rotamer normality  :  -1.096
  Backbone conformation          :  -1.295

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.314 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   0.293 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.602
  B-factor distribution          :   0.412
  Inside/Outside distribution    :   1.006

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -1.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.314 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   0.293 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.602
  B-factor distribution          :   0.412
  Inside/Outside distribution    :   1.006
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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      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
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      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.