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 pdb4dgr.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.

 398 BMA   ( 471-)  A  -
 399 MAN   ( 472-)  A  -
 400 MAN   ( 473-)  A  -
 401 MAN   ( 474-)  A  -
 402 MAN   ( 475-)  A  -
 403 MAN   ( 476-)  A  -
 404 BGC   ( 484-)  A  -
 405 BGC   ( 486-)  A  -
 411 3LV   ( 488-)  A  -
 412 BGC   ( 487-)  A  -
 413 BMA   ( 483-)  A  -
 414 MAN   ( 477-)  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.

  60 ILE   ( 140-)  A  -
  85 SER   ( 165-)  A  -
 290 SER   ( 370-)  A  -
 340 ARG   ( 419-)  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.

  60 ILE   ( 140-)  A  -
  85 SER   ( 165-)  A  -
 290 SER   ( 370-)  A  -
 340 ARG   ( 419-)  A  -

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.

 390 NAG   ( 469-)  A  -   O4  bound to  391 NAG   ( 470-)  A  -   C1
 391 NAG   ( 470-)  A  -   O4  bound to  398 BMA   ( 471-)  A  -   C1
 392 NAG   ( 478-)  A  -   O4  bound to  393 NAG   ( 479-)  A  -   C1
 394 NAG   ( 481-)  A  -   O4  bound to  395 NAG   ( 482-)  A  -   C1
 395 NAG   ( 482-)  A  -   O4  bound to  413 BMA   ( 483-)  A  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 182 LYS   ( 261-)  A  -   CE
 182 LYS   ( 261-)  A  -   NZ
 307 LYS   ( 387-)  A  -   NZ

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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 ILE   (  81-)  A      CG1
   1 ILE   (  81-)  A      CG2
   1 ILE   (  81-)  A      CD1

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.

   2 ARG   (  82-)  A    0.67
 335 GLU   ( 414-)  A    0.57
 353 LYS   ( 432-)  A    0.46
 356 LYS   ( 435-)  A    0.69
 396 GLC   ( 485-)  A    0.78

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

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.

 340 ARG   ( 419-)  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.

 187 GLU   ( 266-)  A
 204 GLU   ( 283-)  A
 207 GLU   ( 286-)  A
 386 GLU   ( 465-)  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: 0.392
RMS-deviation in bond distances: 0.010

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: 0.644
RMS-deviation in bond angles: 1.384

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.

 187 GLU   ( 266-)  A
 204 GLU   ( 283-)  A
 207 GLU   ( 286-)  A
 340 ARG   ( 419-)  A
 386 GLU   ( 465-)  A

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.

 109 THR   ( 188-)  A    -2.9
 146 THR   ( 225-)  A    -2.5
  38 ARG   ( 118-)  A    -2.4
  58 THR   ( 138-)  A    -2.4
 252 PRO   ( 331-)  A    -2.3
 102 THR   ( 181-)  A    -2.2
 352 PRO   ( 431-)  A    -2.1
 138 THR   ( 217-)  A    -2.1
 269 VAL   ( 349-)  A    -2.1
  41 TYR   ( 121-)  A    -2.1
 148 GLU   ( 227-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  37 THR   ( 117-)  A  omega poor
  44 CYS   ( 124-)  A  omega poor
  68 THR   ( 148-)  A  omega poor
  84 SER   ( 164-)  A  Poor phi/psi
 101 SER   ( 180-)  A  omega poor
 129 ASN   ( 208-)  A  Poor phi/psi
 130 ARG   ( 209-)  A  Poor phi/psi
 141 ARG   ( 220-)  A  Poor phi/psi
 143 ILE   ( 222-)  A  Poor phi/psi
 146 THR   ( 225-)  A  Poor phi/psi, omega poor
 148 GLU   ( 227-)  A  Poor phi/psi, omega poor
 185 LYS   ( 264-)  A  omega poor
 197 GLU   ( 276-)  A  omega poor
 206 ALA   ( 285-)  A  Poor phi/psi
 217 GLN   ( 296-)  A  omega poor
 219 SER   ( 298-)  A  omega poor
 231 MET   ( 310-)  A  Poor phi/psi
 236 GLN   ( 315-)  A  Poor phi/psi
 246 ASN   ( 325-)  A  PRO omega poor
 266 ASN   ( 346-)  A  Poor phi/psi
 279 ASN   ( 359-)  A  Poor phi/psi
 301 ASN   ( 381-)  A  Poor phi/psi
 323 SER   ( 404-)  A  Poor phi/psi
 351 ARG   ( 430-)  A  PRO omega poor
 361 SER   ( 440-)  A  Poor phi/psi
 362 ASN   ( 441-)  A  omega poor
 364 ILE   ( 443-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.463

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!

   8 THR   (  88-)  A      0
  13 THR   (  93-)  A      0
  15 ASN   (  95-)  A      0
  23 ASP   ( 103-)  A      0
  31 ASP   ( 111-)  A      0
  32 SER   ( 112-)  A      0
  33 ASP   ( 113-)  A      0
  38 ARG   ( 118-)  A      0
  39 GLU   ( 119-)  A      0
  40 PRO   ( 120-)  A      0
  47 ASP   ( 127-)  A      0
  56 GLN   ( 136-)  A      0
  64 HIS   ( 144-)  A      0
  66 ASN   ( 146-)  A      0
  68 THR   ( 148-)  A      0
  69 ILE   ( 149-)  A      0
  72 ARG   ( 152-)  A      0
  73 SER   ( 153-)  A      0
  81 TRP   ( 161-)  A      0
  83 LEU   ( 163-)  A      0
  84 SER   ( 164-)  A      0
  95 GLU   ( 174-)  A      0
  96 CYS   ( 175-)  A      0
  97 ILE   ( 176-)  A      0
  99 TRP   ( 178-)  A      0
And so on for a total of 227 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.051

Warning: Backbone oxygen evaluation

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

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

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

  21 GLY   ( 101-)  A   1.55   11

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 222 PRO   ( 301-)  A    0.20 LOW

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].

  86 PRO   ( 166-)  A   -13.3 half-chair C-alpha/N (-18 degrees)
 380 PRO   ( 459-)  A    18.0 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 395 NAG   ( 482-)  A      O4  <->  413 BMA   ( 483-)  A      C1     0.97    1.43  INTRA BF
 402 MAN   ( 475-)  A      O6  <->  414 MAN   ( 477-)  A      C1     0.96    1.44  INTRA B3
 395 NAG   ( 482-)  A      C4  <->  413 BMA   ( 483-)  A      C1     0.89    2.31  INTRA
 402 MAN   ( 475-)  A      C6  <->  414 MAN   ( 477-)  A      C1     0.72    2.48  INTRA
  95 GLU   ( 174-)  A      OE1 <->  130 ARG   ( 209-)  A      NH1    0.20    2.50  INTRA
  72 ARG   ( 152-)  A      NH1 <->  411 3LV   ( 488-)  A      O15    0.16    2.54  INTRA
 309 LYS   ( 389-)  A      NZ  <->  415 HOH   ( 785 )  A      O      0.16    2.54  INTRA
 340 ARG   ( 419-)  A    A CD  <->  415 HOH   ( 875 )  A      O      0.11    2.69  INTRA
 180 GLU   ( 259-)  A      OE2 <->  415 HOH   ( 711 )  A      O      0.09    2.31  INTRA
 207 GLU   ( 286-)  A      OE1 <->  415 HOH   ( 850 )  A      O      0.09    2.31  INTRA
  96 CYS   ( 175-)  A      C   <->  114 CYS   ( 193-)  A      SG     0.08    3.32  INTRA BL
 172 GLU   ( 251-)  A      OE1 <->  415 HOH   ( 861 )  A      O      0.07    2.33  INTRA
 190 ALA   ( 269-)  A      N   <->  233 HIS   ( 312-)  A      NE2    0.06    2.94  INTRA BL
 105 HIS   ( 184-)  A      ND1 <->  107 GLY   ( 186-)  A      N      0.06    2.94  INTRA BL
   7 LEU   (  87-)  A      N   <->  154 HIS   ( 233-)  A      ND1    0.05    2.95  INTRA BL
 410 PO4   ( 489-)  A      O1  <->  415 HOH   ( 949 )  A      O      0.05    2.35  INTRA BF
 103 SER   ( 182-)  A      C   <->  151 CYS   ( 230-)  A      SG     0.03    3.37  INTRA BL
  39 GLU   ( 119-)  A      N   <->   40 PRO   ( 120-)  A      CD     0.03    2.97  INTRA BL
  12 CYS   (  92-)  A      SG  <->  338 CYS   ( 417-)  A      C      0.02    3.38  INTRA BL
  45 ASP   ( 125-)  A      N   <->   48 GLU   ( 128-)  A      O      0.02    2.68  INTRA BL
 109 THR   ( 188-)  A      CG2 <->  128 TYR   ( 207-)  A      CZ     0.02    3.18  INTRA BL
 204 GLU   ( 283-)  A      OE2 <->  415 HOH   ( 943 )  A      O      0.01    2.39  INTRA

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.

   2 ARG   (  82-)  A      -6.99
 335 GLU   ( 414-)  A      -6.15
 376 GLN   ( 455-)  A      -5.80
  75 TYR   ( 155-)  A      -5.49
  72 ARG   ( 152-)  A      -5.48
 261 TYR   ( 341-)  A      -5.45
 373 PHE   ( 452-)  A      -5.44
  90 TYR   ( 169-)  A      -5.36
 250 ASN   ( 329-)  A      -5.08

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.

  66 ASN   ( 146-)  A   -2.74
   6 ASN   (  86-)  A   -2.54

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.

 373 PHE   ( 452-)  A     -  376 GLN   ( 455-)  A        -1.85

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.

 415 HOH   ( 823 )  A      O     -0.32    8.21   76.46
 415 HOH   ( 826 )  A      O     23.21   47.42   62.95
 415 HOH   ( 829 )  A      O     37.39   -4.25   65.08

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.

 415 HOH   ( 853 )  A      O
 415 HOH   ( 860 )  A      O
 415 HOH   ( 865 )  A      O
Bound group on Asn; dont flip    6 ASN  (  86-) A
Bound to:  392 NAG  ( 478-) A
Bound group on Asn; dont flip   66 ASN  ( 146-) A
Bound to:  394 NAG  ( 481-) A
Bound group on Asn; dont flip  121 ASN  ( 200-) A
Bound to:  390 NAG  ( 469-) A

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.

 142 ASN   ( 221-)  A
 301 ASN   ( 381-)  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.

  17 TRP   (  97-)  A      NE1
  38 ARG   ( 118-)  A      NH2
  41 TYR   ( 121-)  A      OH
  42 VAL   ( 122-)  A      N
  58 THR   ( 138-)  A      N
  73 SER   ( 153-)  A      N
  84 SER   ( 164-)  A      N
  88 THR   ( 168-)  A      OG1
 117 GLY   ( 196-)  A      N
 130 ARG   ( 209-)  A      NH1
 149 SER   ( 228-)  A      N
 169 GLY   ( 248-)  A      N
 195 HIS   ( 274-)  A      N
 213 ARG   ( 292-)  A      NH2
 218 GLY   ( 297-)  A      N
 248 ARG   ( 327-)  A      NH2
 251 ASP   ( 330-)  A      N
 270 LYS   ( 350-)  A      N
 284 ARG   ( 364-)  A      NH1
 284 ARG   ( 364-)  A      NH2
 359 TRP   ( 438-)  A      N
 359 TRP   ( 438-)  A      NE1

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+.

 407  CA   ( 490-)  A     0.58   0.80 Scores about as good as NA
 408  CA   ( 491-)  A   -.-  -.-  Low probability ion. Occ=0.19
 409   K   ( 492-)  A   -.-  -.-  Low probability ion. Occ=0.65

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.

 415 HOH   ( 495 )  A      O  1.11  K  4 *1
 415 HOH   ( 542 )  A      O  1.10  K  5 *1
 415 HOH   ( 545 )  A      O  0.90  K  4 *1
 415 HOH   ( 566 )  A      O  0.93  K  5 *1
 415 HOH   ( 612 )  A      O  0.96  K  4 *1
 415 HOH   ( 674 )  A      O  0.93  K  5 *1
 415 HOH   ( 723 )  A      O  0.89  K  4 *1 Ion-B
 415 HOH   ( 906 )  A      O  0.94  K  4 *1

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.

 106 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 164 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.644
  2nd generation packing quality :  -2.267
  Ramachandran plot appearance   :  -1.593
  chi-1/chi-2 rotamer normality  :  -0.463
  Backbone conformation          :  -1.522

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.392 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   1.282 (loose)
  Side chain planarity           :   0.555 (tight)
  Improper dihedral distribution :   0.706
  B-factor distribution          :   0.505
  Inside/Outside distribution    :   1.079

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 : 1.55


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -2.1
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -2.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.392 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   1.282 (loose)
  Side chain planarity           :   0.555 (tight)
  Improper dihedral distribution :   0.706
  B-factor distribution          :   0.505
  Inside/Outside distribution    :   1.079
==============

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Quality Control
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Ion Checks
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    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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