WHAT IF Check report

This file was created 2011-12-28 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 pdb1g9h.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.

 452 TRS   ( 700-)  A  -
 453 BGC   ( 601-)  A  -
 454 DAF   ( 600-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  49 ARG   (  49-)  A  -
 234 ARG   ( 234-)  A  -
 373 ARG   ( 373-)  A  -
 420 VAL   ( 420-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  49 ARG   (  49-)  A  -
 234 ARG   ( 234-)  A  -
 373 ARG   ( 373-)  A  -
 420 VAL   ( 420-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  49 ARG   (  49-)  A    1.04
  96 THR   (  96-)  A    0.96
 102 SER   ( 102-)  A    0.87
 234 ARG   ( 234-)  A    1.03
 282 ARG   ( 282-)  A    0.97
 373 ARG   ( 373-)  A    1.06

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) :277.000

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 133 ARG   ( 133-)  A
 172 ARG   ( 172-)  A
 338 ARG   ( 338-)  A
 349 ARG   ( 349-)  A

Warning: Tyrosine convention problem

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

  23 TYR   (  23-)  A
  29 TYR   (  29-)  A
  50 TYR   (  50-)  A
  82 TYR   (  82-)  A
 127 TYR   ( 127-)  A
 159 TYR   ( 159-)  A
 214 TYR   ( 214-)  A
 294 TYR   ( 294-)  A
 401 TYR   ( 401-)  A

Warning: Phenylalanine convention problem

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

   5 PHE   (   5-)  A
   9 PHE   (   9-)  A
 103 PHE   ( 103-)  A
 108 PHE   ( 108-)  A
 198 PHE   ( 198-)  A
 223 PHE   ( 223-)  A
 244 PHE   ( 244-)  A
 250 PHE   ( 250-)  A
 278 PHE   ( 278-)  A
 348 PHE   ( 348-)  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.

  15 ASP   (  15-)  A
  80 ASP   (  80-)  A
  84 ASP   (  84-)  A
 115 ASP   ( 115-)  A
 126 ASP   ( 126-)  A
 162 ASP   ( 162-)  A
 174 ASP   ( 174-)  A
 183 ASP   ( 183-)  A
 203 ASP   ( 203-)  A
 280 ASP   ( 280-)  A
 306 ASP   ( 306-)  A
 310 ASP   ( 310-)  A
 312 ASP   ( 312-)  A
 354 ASP   ( 354-)  A
 385 ASP   ( 385-)  A
 395 ASP   ( 395-)  A
 437 ASP   ( 437-)  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.

  10 GLU   (  10-)  A
  39 GLU   (  39-)  A
  56 GLU   (  56-)  A
 213 GLU   ( 213-)  A
 246 GLU   ( 246-)  A
 279 GLU   ( 279-)  A
 384 GLU   ( 384-)  A
 408 GLU   ( 408-)  A
 419 GLU   ( 419-)  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: 0.405
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

 |  0.998132 -0.000715  0.000109|
 | -0.000715  0.996346  0.000085|
 |  0.000109  0.000085  0.998779|
Proposed new scale matrix

 |  0.014045  0.000010 -0.000002|
 |  0.000005  0.007237  0.000000|
 |  0.000000  0.000000  0.008721|
With corresponding cell

    A    =  71.199  B   = 138.170  C    = 114.670
    Alpha=  90.001  Beta=  89.994  Gamma=  90.082

The CRYST1 cell dimensions

    A    =  71.330  B   = 138.680  C    = 114.810
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 82.911
(Under-)estimated Z-score: 6.711

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.

 257 VAL   ( 257-)  A      N    CA   C    98.94   -4.4
 263 HIS   ( 263-)  A      CG   ND1  CE1 109.63    4.0
 403 ASN   ( 403-)  A      N    CA   C    99.75   -4.1

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.

  10 GLU   (  10-)  A
  15 ASP   (  15-)  A
  39 GLU   (  39-)  A
  56 GLU   (  56-)  A
  80 ASP   (  80-)  A
  84 ASP   (  84-)  A
 115 ASP   ( 115-)  A
 126 ASP   ( 126-)  A
 133 ARG   ( 133-)  A
 162 ASP   ( 162-)  A
 172 ARG   ( 172-)  A
 174 ASP   ( 174-)  A
 183 ASP   ( 183-)  A
 203 ASP   ( 203-)  A
 213 GLU   ( 213-)  A
 246 GLU   ( 246-)  A
 279 GLU   ( 279-)  A
 280 ASP   ( 280-)  A
 306 ASP   ( 306-)  A
 310 ASP   ( 310-)  A
 312 ASP   ( 312-)  A
 338 ARG   ( 338-)  A
 349 ARG   ( 349-)  A
 354 ASP   ( 354-)  A
 384 GLU   ( 384-)  A
 385 ASP   ( 385-)  A
 395 ASP   ( 395-)  A
 408 GLU   ( 408-)  A
 419 GLU   ( 419-)  A
 437 ASP   ( 437-)  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.

 129 ASN   ( 129-)  A    5.13
 256 ALA   ( 256-)  A    4.95
 135 GLN   ( 135-)  A    4.56
 257 VAL   ( 257-)  A    4.46
 235 ASN   ( 235-)  A    4.41

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.

 329 PHE   ( 329-)  A    -2.9
 140 VAL   ( 140-)  A    -2.5
  36 PRO   (  36-)  A    -2.2
  37 PRO   (  37-)  A    -2.2
 365 THR   ( 365-)  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.

   3 THR   (   3-)  A  Poor phi/psi
  10 GLU   (  10-)  A  Poor phi/psi
  57 LEU   (  57-)  A  Poor phi/psi
 106 LYS   ( 106-)  A  Poor phi/psi
 295 PRO   ( 295-)  A  Poor phi/psi
 327 GLU   ( 327-)  A  Poor phi/psi
 329 PHE   ( 329-)  A  Poor phi/psi
 330 ALA   ( 330-)  A  Poor phi/psi
 332 ASN   ( 332-)  A  Poor phi/psi
 365 THR   ( 365-)  A  Poor phi/psi
 366 ASN   ( 366-)  A  Poor phi/psi
 413 ALA   ( 413-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.462

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.

 186 SER   ( 186-)  A    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   9 PHE   (   9-)  A      0
  10 GLU   (  10-)  A      0
  11 TRP   (  11-)  A      0
  22 GLN   (  22-)  A      0
  23 TYR   (  23-)  A      0
  30 ALA   (  30-)  A      0
  36 PRO   (  36-)  A      0
  37 PRO   (  37-)  A      0
  38 ASN   (  38-)  A      0
  40 HIS   (  40-)  A      0
  42 THR   (  42-)  A      0
  46 TRP   (  46-)  A      0
  47 TRP   (  47-)  A      0
  50 TYR   (  50-)  A      0
  51 GLN   (  51-)  A      0
  52 PRO   (  52-)  A      0
  55 TYR   (  55-)  A      0
  57 LEU   (  57-)  A      0
  59 SER   (  59-)  A      0
  63 ASN   (  63-)  A      0
  89 HIS   (  89-)  A      0
  90 MET   (  90-)  A      0
  92 ALA   (  92-)  A      0
  94 SER   (  94-)  A      0
 101 ASN   ( 101-)  A      0
And so on for a total of 191 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 : 1.862

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.

 453 BGC   ( 601-)  A      O4  <->  454 DAF   ( 600-)  A      C1     1.00    1.40  INTRA B3
 453 BGC   ( 601-)  A      C4  <->  454 DAF   ( 600-)  A      C1     0.71    2.39  INTRA
 233 PHE   ( 233-)  A      O   <->  383 LYS   ( 383-)  A      NZ     0.12    2.58  INTRA
 354 ASP   ( 354-)  A      OD2 <->  443 LYS   ( 443-)  A      NZ     0.12    2.58  INTRA
  38 ASN   (  38-)  A      ND2 <->  455 HOH   (1016 )  A      O      0.08    2.62  INTRA
 121 THR   ( 121-)  A      O   <->  133 ARG   ( 133-)  A      NH2    0.07    2.63  INTRA
   3 THR   (   3-)  A      OG1 <->  350 ASN   ( 350-)  A      ND2    0.06    2.64  INTRA BL
 318 VAL   ( 318-)  A      CG2 <->  322 ASN   ( 322-)  A      ND2    0.04    3.06  INTRA
 123 ASN   ( 123-)  A      ND2 <->  455 HOH   (1306 )  A      O      0.03    2.67  INTRA
 234 ARG   ( 234-)  A    A NH1 <->  274 ASN   ( 274-)  A      C      0.03    3.07  INTRA
 234 ARG   ( 234-)  A    A NH1 <->  275 VAL   ( 275-)  A      O      0.03    2.67  INTRA
 266 GLN   ( 266-)  A      N   <->  267 ARG   ( 267-)  A      N      0.01    2.59  INTRA BL
 334 LYS   ( 334-)  A      NZ  <->  455 HOH   (1385 )  A      O      0.01    2.69  INTRA BF
 234 ARG   ( 234-)  A    A NH2 <->  280 ASP   ( 280-)  A      OD1    0.01    2.69  INTRA
 177 LYS   ( 177-)  A      NZ  <->  453 BGC   ( 601-)  A      O3     0.01    2.69  INTRA

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.

  60 ARG   (  60-)  A      -6.24
 204 GLN   ( 204-)  A      -5.95
 317 ASN   ( 317-)  A      -5.89
  22 GLN   (  22-)  A      -5.54
 248 TRP   ( 248-)  A      -5.51
 235 ASN   ( 235-)  A      -5.46
 234 ARG   ( 234-)  A      -5.35
 243 ASN   ( 243-)  A      -5.34
 267 ARG   ( 267-)  A      -5.30
 266 GLN   ( 266-)  A      -5.25
 129 ASN   ( 129-)  A      -5.06

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.

 307 PHE   ( 307-)  A   -2.64

Warning: Abnormal packing Z-score for sequential residues

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

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

 276 ILE   ( 276-)  A     -  279 GLU   ( 279-)  A        -1.36

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

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.

 455 HOH   (1392 )  A      O     -0.40   -3.94    4.48

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.

 455 HOH   (1290 )  A      O
 455 HOH   (1357 )  A      O
Marked this atom as acceptor  451  CL  ( 900-) A     CL
Strange metal coordination for HIS 178

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.

 235 ASN   ( 235-)  A
 430 ASN   ( 430-)  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.

   4 THR   (   4-)  A      OG1
  31 ALA   (  31-)  A      N
  47 TRP   (  47-)  A      N
  49 ARG   (  49-)  A    A NH1
  89 HIS   (  89-)  A      N
 110 ILE   ( 110-)  A      N
 111 TYR   ( 111-)  A      N
 172 ARG   ( 172-)  A      NH2
 177 LYS   ( 177-)  A      NZ
 237 SER   ( 237-)  A      N
 245 GLY   ( 245-)  A      N
 263 HIS   ( 263-)  A      NE2
 264 ASP   ( 264-)  A      N
 271 GLY   ( 271-)  A      N
 288 ASN   ( 288-)  A      ND2
 305 TYR   ( 305-)  A      N
 338 ARG   ( 338-)  A      NH2
 377 GLY   ( 377-)  A      N
 386 SER   ( 386-)  A      N
Only metal coordination for   88 ASN  (  88-) 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.

 178 HIS   ( 178-)  A      NE2
 264 ASP   ( 264-)  A      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 450  CA   ( 800-)  A     0.70   0.93 Scores about as good as NA

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.

 455 HOH   (1075 )  A      O  1.05  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 :  -0.480
  2nd generation packing quality :  -1.444
  Ramachandran plot appearance   :  -1.104
  chi-1/chi-2 rotamer normality  :  -1.462
  Backbone conformation          :  -1.192

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.405 (tight)
  Bond angles                    :   0.678
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   0.503 (tight)
  Improper dihedral distribution :   0.830
  B-factor distribution          :   0.685
  Inside/Outside distribution    :   0.982

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.405 (tight)
  Bond angles                    :   0.678
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   0.503 (tight)
  Improper dihedral distribution :   0.830
  B-factor distribution          :   0.685
  Inside/Outside distribution    :   0.982
==============

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.