WHAT IF Check report

This file was created 2014-04-17 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 pdb2hor.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.

 438 ACT   ( 602-)  A  -
 439 A10   ( 506-)  A  -
 440 MAN   ( 505-)  A  -
 441 BMA   ( 504-)  A  -

Administrative problems that can generate validation failures

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.

  55 GLN   (  55-)  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.

 426 NAG   ( 500-)  A  -   O4  bound to  428 NAG   ( 503-)  A  -   C1
 428 NAG   ( 503-)  A  -   O4  bound to  441 BMA   ( 504-)  A  -   C1

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: Tyrosine convention problem

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

  92 TYR   (  92-)  A
 416 TYR   ( 416-)  A
 417 TYR   ( 417-)  A

Warning: Phenylalanine convention problem

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

 103 PHE   ( 103-)  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.

  49 ASP   (  49-)  A
 123 ASP   ( 123-)  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.

 114 GLU   ( 114-)  A
 209 GLU   ( 209-)  A
 343 GLU   ( 343-)  A
 372 GLU   ( 372-)  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: 0.443
RMS-deviation in bond distances: 0.011

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.

 208 PRO   ( 208-)  A      N    CA   C   122.66    4.3

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: 0.652
RMS-deviation in bond angles: 1.375

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.

  49 ASP   (  49-)  A
 114 GLU   ( 114-)  A
 123 ASP   ( 123-)  A
 209 GLU   ( 209-)  A
 343 GLU   ( 343-)  A
 372 GLU   ( 372-)  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.

  46 THR   (  46-)  A    -2.8
 259 ARG   ( 259-)  A    -2.6
 229 TYR   ( 229-)  A    -2.5
 100 PHE   ( 100-)  A    -2.4
 234 THR   ( 234-)  A    -2.3
 358 PRO   ( 358-)  A    -2.3
 208 PRO   ( 208-)  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
  21 SER   (  21-)  A  Poor phi/psi
  34 GLU   (  34-)  A  Poor phi/psi
  38 LYS   (  38-)  A  omega poor
  40 GLU   (  40-)  A  omega poor
  44 CYS   (  44-)  A  Poor phi/psi
  50 CYS   (  50-)  A  Poor phi/psi
  89 ARG   (  89-)  A  Poor phi/psi
  92 TYR   (  92-)  A  omega poor
  93 PHE   (  93-)  A  omega poor
  95 ASN   (  95-)  A  PRO omega poor
 100 PHE   ( 100-)  A  Poor phi/psi
 121 ALA   ( 121-)  A  Poor phi/psi
 162 ALA   ( 162-)  A  PRO omega poor
 176 ASP   ( 176-)  A  Poor phi/psi
 204 SER   ( 204-)  A  PRO omega poor
 207 ASN   ( 207-)  A  PRO omega poor
 208 PRO   ( 208-)  A  omega poor
 213 ARG   ( 213-)  A  omega poor
 232 HIS   ( 232-)  A  omega poor
 354 ARG   ( 354-)  A  Poor phi/psi
 363 TYR   ( 363-)  A  omega poor
 365 TRP   ( 365-)  A  omega poor
 384 ARG   ( 384-)  A  Poor phi/psi
 387 THR   ( 387-)  A  omega poor
 394 GLU   ( 394-)  A  Poor phi/psi
 406 LYS   ( 406-)  A  Poor phi/psi
 424 ALA   ( 424-)  A  omega poor
 chi-1/chi-2 correlation Z-score : 0.740

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.

 167 VAL   ( 167-)  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!

   3 THR   (   3-)  A      0
   4 TRP   (   4-)  A      0
  18 ILE   (  18-)  A      0
  20 CYS   (  20-)  A      0
  21 SER   (  21-)  A      0
  22 GLU   (  22-)  A      0
  23 HIS   (  23-)  A      0
  29 ASP   (  29-)  A      0
  33 SER   (  33-)  A      0
  41 CYS   (  41-)  A      0
  42 ASN   (  42-)  A      0
  43 THR   (  43-)  A      0
  44 CYS   (  44-)  A      0
  46 THR   (  46-)  A      0
  50 CYS   (  50-)  A      0
  55 GLN   (  55-)  A      0
  57 CYS   (  57-)  A      0
  61 VAL   (  61-)  A      0
  62 ALA   (  62-)  A      0
  87 TRP   (  87-)  A      0
  88 HIS   (  88-)  A      0
  89 ARG   (  89-)  A      0
  90 MET   (  90-)  A      0
  94 PHE   (  94-)  A      0
  95 ASN   (  95-)  A      0
And so on for a total of 174 lines.

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!

  56 GLY   (  56-)  A   1.62   80

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]

  37 PRO   (  37-)  A    0.18 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].

 208 PRO   ( 208-)  A   -58.7 half-chair C-beta/C-alpha (-54 degrees)
 358 PRO   ( 358-)  A   -61.2 half-chair C-beta/C-alpha (-54 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.

 439 A10   ( 506-)  A      O2  <->  441 BMA   ( 504-)  A      C3     1.06    1.34  INTRA BL
 428 NAG   ( 503-)  A      O4  <->  441 BMA   ( 504-)  A      C1     0.96    1.44  INTRA B3
 428 NAG   ( 503-)  A      C4  <->  441 BMA   ( 504-)  A      C1     0.82    2.38  INTRA
 439 A10   ( 506-)  A      C2  <->  441 BMA   ( 504-)  A      C3     0.72    2.48  INTRA BL
  74 LYS   (  74-)  A      NZ  <->  442 HOH   (1138 )  A      O      0.37    2.33  INTRA BF
 178 LYS   ( 178-)  A      NZ  <->  442 HOH   ( 994 )  A      O      0.25    2.45  INTRA BF
 237 LYS   ( 237-)  A      NZ  <->  442 HOH   ( 909 )  A      O      0.22    2.48  INTRA BF
 111 GLU   ( 111-)  A    A OE2 <->  305 LYS   ( 305-)  A      NZ     0.21    2.49  INTRA
  53 LYS   (  53-)  A      NZ  <->  442 HOH   ( 793 )  A      O      0.15    2.55  INTRA BF
  71 GLU   (  71-)  A      OE1 <->  321 LYS   ( 321-)  A    A NZ     0.13    2.57  INTRA
 320 LYS   ( 320-)  A      NZ  <->  442 HOH   ( 825 )  A      O      0.09    2.61  INTRA BF
 295 LYS   ( 295-)  A      NZ  <->  442 HOH   ( 810 )  A      O      0.08    2.62  INTRA BF
 305 LYS   ( 305-)  A      NZ  <->  442 HOH   (1126 )  A      O      0.08    2.62  INTRA BF
 441 BMA   ( 504-)  A      O2  <->  442 HOH   (1201 )  A      O      0.06    2.34  INTRA BF
 266 LYS   ( 266-)  A      NZ  <->  442 HOH   ( 845 )  A      O      0.06    2.64  INTRA
 113 HIS   ( 113-)  A      NE2 <->  262 TRP   ( 262-)  A      NE1    0.06    2.94  INTRA BL
 124 ARG   ( 124-)  A      NH1 <->  442 HOH   ( 859 )  A      O      0.06    2.64  INTRA BF
 124 ARG   ( 124-)  A      NH2 <->  266 LYS   ( 266-)  A      CE     0.05    3.05  INTRA
 298 LYS   ( 298-)  A      NZ  <->  442 HOH   ( 770 )  A      O      0.05    2.65  INTRA BF
  76 HIS   (  76-)  A      ND1 <->  299 GLU   ( 299-)  A      OE2    0.05    2.65  INTRA BL
 111 GLU   ( 111-)  A    A OE2 <->  442 HOH   ( 940 )  A      O      0.04    2.36  INTRA BF
 130 VAL   ( 130-)  A      N   <->  134 GLN   ( 134-)  A      OE1    0.04    2.66  INTRA
 215 ALA   ( 215-)  A      O   <->  218 LYS   ( 218-)  A      NZ     0.04    2.66  INTRA
 191 ASN   ( 191-)  A      ND2 <->  442 HOH   ( 913 )  A      O      0.02    2.68  INTRA BF
 439 A10   ( 506-)  A      C1  <->  441 BMA   ( 504-)  A      C3     0.02    2.78  INTRA BL
 137 HIS   ( 137-)  A      ND1 <->  442 HOH   ( 811 )  A      O      0.02    2.68  INTRA
 253 THR   ( 253-)  A      OG1 <->  255 HIS   ( 255-)  A      ND1    0.02    2.68  INTRA BL
  75 GLN   (  75-)  A      OE1 <->  442 HOH   ( 901 )  A      O      0.01    2.39  INTRA BF
 276 ASN   ( 276-)  A      ND2 <->  442 HOH   (1131 )  A      O      0.01    2.69  INTRA
 267 ASP   ( 267-)  A      OD1 <->  269 SER   ( 269-)  A    A OG     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.

  92 TYR   (  92-)  A      -6.57
  55 GLN   (  55-)  A      -6.18
 346 GLN   ( 346-)  A      -6.17
  90 MET   (  90-)  A      -5.82
 343 GLU   ( 343-)  A      -5.62
 259 ARG   ( 259-)  A      -5.55
  95 ASN   (  95-)  A      -5.52
 354 ARG   ( 354-)  A      -5.52
 213 ARG   ( 213-)  A      -5.44
  22 GLU   (  22-)  A      -5.42
  28 LEU   (  28-)  A      -5.32
 281 ASN   ( 281-)  A      -5.11
  89 ARG   (  89-)  A      -5.04
 197 GLN   ( 197-)  A      -5.04

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.

 212 LEU   ( 212-)  A       214 - HIS    214- ( A)         -4.82

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.

 190 VAL   ( 190-)  A   -2.61
 344 LEU   ( 344-)  A   -2.56

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.

 353 PHE   ( 353-)  A     -  356 MET   ( 356-)  A        -1.80

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.

 442 HOH   (1044 )  A      O     91.26   26.40   52.69

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.

 442 HOH   ( 945 )  A      O
 442 HOH   (1002 )  A      O
 442 HOH   (1004 )  A      O
 442 HOH   (1174 )  A      O
 442 HOH   (1189 )  A      O
 442 HOH   (1192 )  A      O
Bound group on Asn; dont flip  146 ASN  ( 146-) A
Bound to:  426 NAG  ( 500-) A
Bound group on Asn; dont flip  328 ASN  ( 328-) A
Bound to:  429 NAG  ( 555-) A
Marked this atom as acceptor  434  CL  ( 705-) A     CL
Marked this atom as acceptor  435  CL  ( 706-) A     CL

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.

  19 ASN   (  19-)  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.

   2 MET   (   2-)  A      N
  89 ARG   (  89-)  A      N
 118 ASN   ( 118-)  A      ND2
 119 ALA   ( 119-)  A      N
 167 VAL   ( 167-)  A      N
 251 LYS   ( 251-)  A      N
 285 THR   ( 285-)  A      OG1
 315 ASN   ( 315-)  A      ND2

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.

 225 ASP   ( 225-)  A      OD2
 232 HIS   ( 232-)  A      ND1

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.

 442 HOH   ( 710 )  A      O  0.88  K  4
 442 HOH   ( 860 )  A      O  1.12  K  4
 442 HOH   ( 886 )  A      O  0.90  K  4
 442 HOH   ( 971 )  A      O  0.91  K  5
 442 HOH   (1073 )  A      O  0.98  K  4 Ion-B
 442 HOH   (1115 )  A      O  0.87  K  4 Ion-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.

 225 ASP   ( 225-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 334 ASP   ( 334-)  A   H-bonding suggests Asn

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 :  -0.434
  2nd generation packing quality :  -1.437
  Ramachandran plot appearance   :   0.090
  chi-1/chi-2 rotamer normality  :   0.740
  Backbone conformation          :  -0.839

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.443 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   1.109
  Side chain planarity           :   0.723
  Improper dihedral distribution :   0.691
  B-factor distribution          :   0.404
  Inside/Outside distribution    :   1.024

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.443 (tight)
  Bond angles                    :   0.652 (tight)
  Omega angle restraints         :   1.109
  Side chain planarity           :   0.723
  Improper dihedral distribution :   0.691
  B-factor distribution          :   0.404
  Inside/Outside distribution    :   1.024
==============

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.