WHAT IF Check report

This file was created 2011-12-18 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 pdb3zqz.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 69824.266
Volume of the Unit Cell V= 2636605.0
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.196
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.250

Warning: Topology could not be determined for some ligands

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

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

 602 BMA   (1619-)  A  -         OK
 603 MAN   (1620-)  A  -         OK
 604 SLC   (1626-)  A  -         Atom types
 605 BMA   (1624-)  A  -         OK
 606 MAN   (1623-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 597 NAG   (1617-)  A  -   O4  bound to  598 NAG   (1618-)  A  -   C1
 598 NAG   (1618-)  A  -   O4  bound to  602 BMA   (1619-)  A  -   C1

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 VAL   (  19-)  A      CG1
   1 VAL   (  19-)  A      CG2
   2 LYS   (  20-)  A      CG
   2 LYS   (  20-)  A      CD
   2 LYS   (  20-)  A      CE
   2 LYS   (  20-)  A      NZ
   6 GLN   (  24-)  A      CG
   6 GLN   (  24-)  A      CD
   6 GLN   (  24-)  A      OE1
   6 GLN   (  24-)  A      NE2
 470 LYS   ( 488-)  A      CD
 470 LYS   ( 488-)  A      CE
 470 LYS   ( 488-)  A      NZ

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.

  50 GLU   (  68-)  A    0.50
  57 GLU   (  75-)  A    0.50
  92 GLU   ( 110-)  A    0.50
 133 GLU   ( 151-)  A    0.50
 193 ASP   ( 211-)  A    0.50
 211 GLN   ( 229-)  A    0.50
 261 GLU   ( 279-)  A    0.50
 599 NAG   (1621-)  A    0.40
 600 NAG   (1622-)  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: 1

Crystal temperature (K) :100.000

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.

 597 NAG   (1617-)  A      C1   O5    1.24   -4.6

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

 |  0.997260 -0.000067 -0.000238|
 | -0.000067  0.998380 -0.000053|
 | -0.000238 -0.000053  0.995671|
Proposed new scale matrix

 |  0.005770  0.003328  0.000002|
 |  0.000000  0.006655  0.000000|
 |  0.000002  0.000000  0.009964|
With corresponding cell

    A    = 173.311  B   = 173.470  C    = 100.360
    Alpha=  89.987  Beta=  90.029  Gamma= 119.974

The CRYST1 cell dimensions

    A    = 173.797  B   = 173.797  C    = 100.795
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 182.321
(Under-)estimated Z-score: 9.951

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.

 129 PRO   ( 147-)  A    -2.9
 369 THR   ( 387-)  A    -2.8
 316 LEU   ( 334-)  A    -2.6
 360 TYR   ( 378-)  A    -2.2
 544 LYS   ( 562-)  A    -2.1
 461 ILE   ( 479-)  A    -2.1
 267 VAL   ( 285-)  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.

  66 GLN   (  84-)  A  Poor phi/psi, omega poor
 128 ASP   ( 146-)  A  PRO omega poor
 137 LYS   ( 155-)  A  Poor phi/psi
 178 ASN   ( 196-)  A  Poor phi/psi, omega poor
 237 PRO   ( 255-)  A  omega poor
 246 ALA   ( 264-)  A  Poor phi/psi
 293 ASN   ( 311-)  A  Poor phi/psi
 294 LEU   ( 312-)  A  omega poor
 303 ASP   ( 321-)  A  omega poor
 311 THR   ( 329-)  A  omega poor
 326 TYR   ( 344-)  A  Poor phi/psi
 327 LEU   ( 345-)  A  Poor phi/psi
 329 ASP   ( 347-)  A  Poor phi/psi
 336 CYS   ( 354-)  A  omega poor
 371 ALA   ( 389-)  A  omega poor
 378 ALA   ( 396-)  A  omega poor
 401 ASP   ( 419-)  A  Poor phi/psi
 419 ASP   ( 437-)  A  omega poor
 446 ASN   ( 464-)  A  omega poor
 472 PHE   ( 490-)  A  omega poor
 483 ASP   ( 501-)  A  Poor phi/psi
 592 ASN   ( 610-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -2.130

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.

 481 SER   ( 499-)  A    0.38
 161 SER   ( 179-)  A    0.39

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!

  34 SER   (  52-)  A      0
  35 ASN   (  53-)  A      0
  66 GLN   (  84-)  A      0
  67 TRP   (  85-)  A      0
  70 TYR   (  88-)  A      0
  71 GLN   (  89-)  A      0
  84 LYS   ( 102-)  A      0
  87 TYR   ( 105-)  A      0
 122 LYS   ( 140-)  A      0
 123 CYS   ( 141-)  A      0
 124 ASP   ( 142-)  A      0
 136 SER   ( 154-)  A      0
 137 LYS   ( 155-)  A      0
 138 SER   ( 156-)  A      0
 139 ARG   ( 157-)  A      0
 141 HIS   ( 159-)  A      0
 157 THR   ( 175-)  A      0
 224 HIS   ( 242-)  A      0
 225 TYR   ( 243-)  A      0
 229 VAL   ( 247-)  A      0
 233 THR   ( 251-)  A      0
 238 MET   ( 256-)  A      0
 243 ASN   ( 261-)  A      0
 245 TRP   ( 263-)  A      0
 247 GLN   ( 265-)  A      0
And so on for a total of 168 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 129 PRO   ( 147-)  A   -34.8 envelop C-alpha (-36 degrees)
 258 PRO   ( 276-)  A   100.6 envelop C-beta (108 degrees)
 278 PRO   ( 296-)  A   109.3 envelop C-beta (108 degrees)
 364 PRO   ( 382-)  A   107.9 envelop C-beta (108 degrees)
 425 PRO   ( 443-)  A  -115.4 envelop C-gamma (-108 degrees)
 518 PRO   ( 536-)  A   -42.3 envelop C-alpha (-36 degrees)
 547 PRO   ( 565-)  A   104.4 envelop C-beta (108 degrees)
 570 PRO   ( 588-)  A  -123.6 half-chair C-delta/C-gamma (-126 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.

 602 BMA   (1619-)  A      O3  <->  606 MAN   (1623-)  A      C1     0.95    1.45  INTRA BF
 602 BMA   (1619-)  A      C3  <->  606 MAN   (1623-)  A      C1     0.83    2.37  INTRA BF
 601  ZN   (1001-)  A     ZN   <->  604 SLC   (1626-)  A     SE      0.47    2.73  INTRA BF
 601  ZN   (1001-)  A     ZN   <->  604 SLC   (1626-)  A      C1     0.44    2.76  INTRA BF
 455 ARG   ( 473-)  A      NH1 <->  607 HOH   (2147 )  A      O      0.33    2.37  INTRA BL
 431 ASP   ( 449-)  A      OD1 <->  434 ARG   ( 452-)  A      NH2    0.29    2.41  INTRA BL
 139 ARG   ( 157-)  A      NH2 <->  254 ASP   ( 272-)  A      OD1    0.24    2.46  INTRA BF
 467 ARG   ( 485-)  A      NH2 <->  473 ASP   ( 491-)  A      OD1    0.23    2.47  INTRA BL
 319 HIS   ( 337-)  A      NE2 <->  604 SLC   (1626-)  A      O1     0.23    2.47  INTRA BF
 293 ASN   ( 311-)  A      ND2 <->  599 NAG   (1621-)  A      C2     0.22    1.98  INTRA BF
 474 ALA   ( 492-)  A      N   <->  475 PRO   ( 493-)  A      CD     0.16    2.84  INTRA BL
 431 ASP   ( 449-)  A      O   <->  435 TRP   ( 453-)  A      N      0.15    2.55  INTRA BL
 598 NAG   (1618-)  A      N2  <->  607 HOH   (2199 )  A      O      0.14    2.56  INTRA BF
 200 GLU   ( 218-)  A      OE2 <->  432 LYS   ( 450-)  A      NZ     0.14    2.56  INTRA BL
 319 HIS   ( 337-)  A      ND1 <->  607 HOH   (2120 )  A      O      0.14    2.56  INTRA BL
 207 ARG   ( 225-)  A      N   <->  208 PRO   ( 226-)  A      CD     0.14    2.86  INTRA BL
 492 SER   ( 510-)  A      O   <->  496 GLN   ( 514-)  A      N      0.13    2.57  INTRA BL
 349 HIS   ( 367-)  A      NE2 <->  604 SLC   (1626-)  A      C1     0.13    2.97  INTRA BF
 207 ARG   ( 225-)  A      NE  <->  607 HOH   (2085 )  A      O      0.12    2.58  INTRA BL
 431 ASP   ( 449-)  A      OD2 <->  487 LEU   ( 505-)  A      N      0.12    2.58  INTRA BL
 455 ARG   ( 473-)  A      CZ  <->  607 HOH   (2147 )  A      O      0.11    2.69  INTRA BL
 353 HIS   ( 371-)  A      ND1 <->  376 HIS   ( 394-)  A      ND1    0.11    2.89  INTRA BL
 546 TRP   ( 564-)  A      CG  <->  547 PRO   ( 565-)  A      CD     0.10    3.10  INTRA BL
 546 TRP   ( 564-)  A      N   <->  547 PRO   ( 565-)  A      CD     0.10    2.90  INTRA BL
 467 ARG   ( 485-)  A      N   <->  593 LYS   ( 611-)  A      O      0.09    2.61  INTRA BL
And so on for a total of 60 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.

 224 HIS   ( 242-)  A      -5.90
 404 ARG   ( 422-)  A      -5.29
 296 LYS   ( 314-)  A      -5.24
 554 ASN   ( 572-)  A      -5.16
 117 TYR   ( 135-)  A      -5.13
 586 ILE   ( 604-)  A      -5.12
 261 GLU   ( 279-)  A      -5.10

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.

 457 GLU   ( 475-)  A       459 - SER    477- ( A)         -4.17

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.

 482 ALA   ( 500-)  A   -3.10
   1 VAL   (  19-)  A   -3.08

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.

 607 HOH   (2022 )  A      O
 607 HOH   (2097 )  A      O
 607 HOH   (2200 )  A      O
 607 HOH   (2201 )  A      O
Bound group on Asn; dont flip   35 ASN  (  53-) A
Bound to:  600 NAG  (1622-) A
Bound group on Asn; dont flip  178 ASN  ( 196-) A
Bound to:  597 NAG  (1617-) A
Bound group on Asn; dont flip  293 ASN  ( 311-) A
Bound to:  599 NAG  (1621-) A
Metal-coordinating Histidine residue 349 fixed to   1
Metal-coordinating Histidine residue 353 fixed to   1

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.

  37 THR   (  55-)  A      N
 122 LYS   ( 140-)  A      N
 243 ASN   ( 261-)  A      N
 248 GLN   ( 266-)  A      N
 277 THR   ( 295-)  A      N
 319 HIS   ( 337-)  A      NE2
 328 THR   ( 346-)  A      N
 372 ASN   ( 390-)  A      N
 384 SER   ( 402-)  A      OG
 397 GLY   ( 415-)  A      N
 404 ARG   ( 422-)  A      NH1
 442 VAL   ( 460-)  A      N
 448 ASN   ( 466-)  A      ND2
 455 ARG   ( 473-)  A      NH1
 465 VAL   ( 483-)  A      N
 483 ASP   ( 501-)  A      N
 486 TYR   ( 504-)  A      OH
 587 GLY   ( 605-)  A      N
Only metal coordination for  349 HIS  ( 367-) A      NE2
Only metal coordination for  377 GLU  ( 395-) A      OE1

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.

 214 HIS   ( 232-)  A      ND1
 335 GLN   ( 353-)  A      OE1
 350 GLU   ( 368-)  A      OE1
 350 GLU   ( 368-)  A      OE2
 412 GLN   ( 430-)  A      OE1
 579 ASN   ( 597-)  A      OD1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

   4 GLU   (  22-)  A   H-bonding suggests Gln; but Alt-Rotamer
 100 ASP   ( 118-)  A   H-bonding suggests Asn
 184 GLU   ( 202-)  A   H-bonding suggests Gln
 205 ASP   ( 223-)  A   H-bonding suggests Asn
 350 GLU   ( 368-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 469 GLU   ( 487-)  A   H-bonding suggests Gln

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 :  -0.255
  2nd generation packing quality :  -1.193
  Ramachandran plot appearance   :  -1.584
  chi-1/chi-2 rotamer normality  :  -2.130
  Backbone conformation          :  -0.125

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.455 (tight)
  Bond angles                    :   0.425 (tight)
  Omega angle restraints         :   1.062
  Side chain planarity           :   0.354 (tight)
  Improper dihedral distribution :   0.504
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.000

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 : 2.35

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.455 (tight)
  Bond angles                    :   0.425 (tight)
  Omega angle restraints         :   1.062
  Side chain planarity           :   0.354 (tight)
  Improper dihedral distribution :   0.504
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.000

      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
    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).

    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
      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
    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.