WHAT IF Check report

This file was created 2013-12-10 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 pdb4aa2.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: 70464.328
Volume of the Unit Cell V= 2673968.3
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= 4.216
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.300

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.

 611 BMA   (1619-)  A  -
 612 MAN   (1620-)  A  -
 613 BMA   (1624-)  A  -
 614 MAN   (1623-)  A  -

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.

 605 NAG   (1617-)  A  -   O4  bound to  606 NAG   (1618-)  A  -   C1
 606 NAG   (1618-)  A  -   O4  bound to  611 BMA   (1619-)  A  -   C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: 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'.

   4 LYS   (  20-)  A      CG
   4 LYS   (  20-)  A      CD
   4 LYS   (  20-)  A      CE
   4 LYS   (  20-)  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.

  52 GLU   (  68-)  A    0.50
  59 GLU   (  75-)  A    0.50
  94 GLU   ( 110-)  A    0.50
 135 GLU   ( 151-)  A    0.50
 195 ASP   ( 211-)  A    0.50
 213 GLN   ( 229-)  A    0.50
 263 GLU   ( 279-)  A    0.50
 607 NAG   (1621-)  A    0.80
 608 NAG   (1622-)  A    0.80

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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: 0.367
RMS-deviation in bond distances: 0.009

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

 |  0.996640  0.000237 -0.000120|
 |  0.000237  0.998078 -0.000178|
 | -0.000120 -0.000178  0.995776|
Proposed new scale matrix

 |  0.005792  0.003338  0.000001|
 | -0.000002  0.006679  0.000001|
 |  0.000001  0.000002  0.009759|
With corresponding cell

    A    = 172.638  B   = 172.791  C    = 102.467
    Alpha=  90.011  Beta=  90.014  Gamma= 119.944

The CRYST1 cell dimensions

    A    = 173.214  B   = 173.214  C    = 102.898
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 213.371
(Under-)estimated Z-score: 10.765

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: 0.524
RMS-deviation in bond angles: 1.102

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.

 371 THR   ( 387-)  A    -2.7
 131 PRO   ( 147-)  A    -2.7
 318 LEU   ( 334-)  A    -2.6
 141 ARG   ( 157-)  A    -2.2
 362 TYR   ( 378-)  A    -2.2
 208 ILE   ( 224-)  A    -2.1
 463 ILE   ( 479-)  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.

  68 GLN   (  84-)  A  Poor phi/psi
 130 ASP   ( 146-)  A  PRO omega poor
 180 ASN   ( 196-)  A  Poor phi/psi
 295 ASN   ( 311-)  A  Poor phi/psi
 315 GLY   ( 331-)  A  omega poor
 328 TYR   ( 344-)  A  Poor phi/psi
 329 LEU   ( 345-)  A  Poor phi/psi
 331 ASP   ( 347-)  A  Poor phi/psi
 338 CYS   ( 354-)  A  omega poor
 370 ARG   ( 386-)  A  Poor phi/psi
 373 ALA   ( 389-)  A  omega poor
 403 ASP   ( 419-)  A  Poor phi/psi
 421 ASP   ( 437-)  A  omega poor
 474 PHE   ( 490-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.452

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.

 483 SER   ( 499-)  A    0.38
 163 SER   ( 179-)  A    0.40

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!

  36 SER   (  52-)  A      0
  37 ASN   (  53-)  A      0
  68 GLN   (  84-)  A      0
  69 TRP   (  85-)  A      0
  72 TYR   (  88-)  A      0
  73 GLN   (  89-)  A      0
  87 LEU   ( 103-)  A      0
  89 TYR   ( 105-)  A      0
 124 LYS   ( 140-)  A      0
 125 CYS   ( 141-)  A      0
 126 ASP   ( 142-)  A      0
 132 GLU   ( 148-)  A      0
 139 LYS   ( 155-)  A      0
 141 ARG   ( 157-)  A      0
 143 HIS   ( 159-)  A      0
 159 THR   ( 175-)  A      0
 180 ASN   ( 196-)  A      0
 226 HIS   ( 242-)  A      0
 227 TYR   ( 243-)  A      0
 231 VAL   ( 247-)  A      0
 235 THR   ( 251-)  A      0
 240 MET   ( 256-)  A      0
 245 ASN   ( 261-)  A      0
 247 TRP   ( 263-)  A      0
 249 GLN   ( 265-)  A      0
And so on for a total of 171 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].

 131 PRO   ( 147-)  A   -41.5 envelop C-alpha (-36 degrees)
 366 PRO   ( 382-)  A   108.4 envelop C-beta (108 degrees)
 600 PRO   (   7-)  P  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 603 PRO   (  10-)  P    51.3 half-chair C-delta/C-gamma (54 degrees)
 604 PRO   (  11-)  P  -114.7 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 611 BMA   (1619-)  A      O3  <->  614 MAN   (1623-)  A      C1     0.95    1.45  INTRA BF
 611 BMA   (1619-)  A      C3  <->  614 MAN   (1623-)  A      C1     0.83    2.37  INTRA
 141 ARG   ( 157-)  A      NH2 <->  256 ASP   ( 272-)  A      OD1    0.31    2.39  INTRA BF
  29 GLU   (  45-)  A      OE2 <->  334 ARG   ( 350-)  A      NH2    0.12    2.58  INTRA BF
  96 ASP   ( 112-)  A      OD2 <->  174 LYS   ( 190-)  A      NZ     0.12    2.58  INTRA
 338 CYS   ( 354-)  A      N   <->  615 HOH   (2267 )  A      O      0.12    2.58  INTRA
 469 ARG   ( 485-)  A      NH2 <->  475 ASP   ( 491-)  A      OD1    0.12    2.58  INTRA BL
 599 ARG   (   6-)  P      NH1 <->  615 HOH   (2356 )  A      O      0.12    2.58  INTRA BF
 550 ASP   ( 566-)  A      OD1 <->  559 ARG   ( 575-)  A      NH1    0.12    2.58  INTRA
 485 ASP   ( 501-)  A      O   <->  599 ARG   (   6-)  P      NH2    0.10    2.60  INTRA BF
 220 ARG   ( 236-)  A      NH2 <->  589 GLY   ( 605-)  A      O      0.08    2.62  INTRA BL
 599 ARG   (   6-)  P      CG  <->  600 PRO   (   7-)  P      CD     0.08    3.12  INTRA BF
 355 HIS   ( 371-)  A      ND1 <->  378 HIS   ( 394-)  A      ND1    0.07    2.93  INTRA BL
  20 LEU   (  36-)  A      CD2 <->   57 MET   (  73-)  A      SD     0.06    3.34  INTRA BF
 548 TRP   ( 564-)  A      N   <->  549 PRO   ( 565-)  A      CD     0.06    2.94  INTRA BL
 222 ARG   ( 238-)  A      NH1 <->  259 SER   ( 275-)  A      O      0.06    2.64  INTRA
 278 TYR   ( 294-)  A      CE2 <->  286 MET   ( 302-)  A      SD     0.06    3.34  INTRA BF
 184 GLY   ( 200-)  A      N   <->  615 HOH   (2138 )  A      O      0.06    2.64  INTRA BL
  58 LYS   (  74-)  A      NZ  <->  615 HOH   (2027 )  A      O      0.06    2.64  INTRA BF
 351 HIS   ( 367-)  A      ND1 <->  383 ASP   ( 399-)  A      OD1    0.06    2.64  INTRA BL
 422 LYS   ( 438-)  A      NZ  <->  615 HOH   (2224 )  A      O      0.05    2.65  INTRA BL
 411 ARG   ( 427-)  A      NH2 <->  615 HOH   (2321 )  A      O      0.05    2.65  INTRA BF
 209 ARG   ( 225-)  A      NE  <->  615 HOH   (2187 )  A      O      0.04    2.66  INTRA BL
 177 LYS   ( 193-)  A      O   <->  615 HOH   (2143 )  A      O      0.04    2.36  INTRA BL
 118 ASP   ( 134-)  A      OD1 <->  120 LYS   ( 136-)  A      N      0.03    2.67  INTRA BF
 587 HIS   ( 603-)  A      NE2 <->  615 HOH   (2217 )  A      O      0.02    2.68  INTRA BL
 241 HIS   ( 257-)  A      NE2 <->  615 HOH   (2116 )  A      O      0.02    2.68  INTRA
 209 ARG   ( 225-)  A      N   <->  210 PRO   ( 226-)  A      CD     0.02    2.98  INTRA BL
 433 ASP   ( 449-)  A      O   <->  437 TRP   ( 453-)  A      N      0.02    2.68  INTRA BL
 320 CYS   ( 336-)  A      O   <->  615 HOH   (2267 )  A      O      0.02    2.38  INTRA
 202 GLU   ( 218-)  A      OE2 <->  434 LYS   ( 450-)  A      NZ     0.01    2.69  INTRA BL
 462 GLY   ( 478-)  A      CA  <->  590 TRP   ( 606-)  A      CE2    0.01    3.19  INTRA BL
 479 LYS   ( 495-)  A      NZ  <->  604 PRO   (  11-)  P      O      0.01    2.69  INTRA BL
 269 VAL   ( 285-)  A      N   <->  343 GLN   ( 359-)  A      OE1    0.01    2.69  INTRA BF
 422 LYS   ( 438-)  A      NZ  <->  615 HOH   (2302 )  A      O      0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 226 HIS   ( 242-)  A      -5.84
 119 TYR   ( 135-)  A      -5.25
 406 ARG   ( 422-)  A      -5.16
 556 ASN   ( 572-)  A      -5.14
 588 ILE   ( 604-)  A      -5.14
 298 LYS   ( 314-)  A      -5.10
 263 GLU   ( 279-)  A      -5.06
  86 LYS   ( 102-)  A      -5.01

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.

 459 GLU   ( 475-)  A       461 - SER    477- ( A)         -4.25

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 484 ALA   ( 500-)  A   -2.94
 257 ILE   ( 273-)  A   -2.61

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: 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.

 250 GLN   ( 266-)  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.

  39 THR   (  55-)  A      N
  39 THR   (  55-)  A      OG1
 143 HIS   ( 159-)  A      N
 150 TRP   ( 166-)  A      NE1
 224 ARG   ( 240-)  A      NE
 245 ASN   ( 261-)  A      N
 250 GLN   ( 266-)  A      N
 330 THR   ( 346-)  A      N
 337 GLN   ( 353-)  A      NE2
 340 ARG   ( 356-)  A      NH2
 374 ASN   ( 390-)  A      N
 383 ASP   ( 399-)  A      N
 404 TYR   ( 420-)  A      N
 428 PHE   ( 444-)  A      N
 444 VAL   ( 460-)  A      N
 467 VAL   ( 483-)  A      N
Only metal coordination for  351 HIS  ( 367-) A      NE2
Only metal coordination for  355 HIS  ( 371-) A      NE2
Only metal coordination for  379 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.

 337 GLN   ( 353-)  A      OE1
 352 GLU   ( 368-)  A      OE2
 581 ASN   ( 597-)  A      OD1

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.

 615 HOH   (2093 )  A      O  0.99  K  4
 615 HOH   (2099 )  A      O  0.88  K  5
 615 HOH   (2176 )  A      O  1.03  K  4
 615 HOH   (2177 )  A      O  0.99  K  4 H2O-B

Warning: Possible wrong residue type

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

 352 GLU   ( 368-)  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 :  -0.014
  2nd generation packing quality :  -0.768
  Ramachandran plot appearance   :   0.150
  chi-1/chi-2 rotamer normality  :  -0.452
  Backbone conformation          :  -0.019

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.524 (tight)
  Omega angle restraints         :   0.893
  Side chain planarity           :   0.313 (tight)
  Improper dihedral distribution :   0.526
  B-factor distribution          :   0.340
  Inside/Outside distribution    :   1.002

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 : 1.99


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.367 (tight)
  Bond angles                    :   0.524 (tight)
  Omega angle restraints         :   0.893
  Side chain planarity           :   0.313 (tight)
  Improper dihedral distribution :   0.526
  B-factor distribution          :   0.340
  Inside/Outside distribution    :   1.002
==============

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.