WHAT IF Check report

This file was created 2012-01-13 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 pdb1uvq.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.

 391 ACY   (1197-)  B  -
 392 BMA   (1196-)  B  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

 387 NAG   (1193-)  B  -   O4  bound to  389 NAG   (1195-)  B  -   C1
 389 NAG   (1195-)  B  -   O4  bound to  392 BMA   (1196-)  B  -   C1

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

 390  ZN   (1192-)  A  -

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: Missing atoms

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

 182 PRO   ( 183-)  A      CG
 182 PRO   ( 183-)  A      CD
 365 MET   (   1-)  C      CG
 365 MET   (   1-)  C      SD
 365 MET   (   1-)  C      CE

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) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

 322 ARG   ( 149-)  B

Warning: Tyrosine convention problem

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

  24 TYR   (  25-)  A
  35 TYR   (  36-)  A
  79 TYR   (  80-)  A
 163 TYR   ( 164-)  A
 218 TYR   (  37-)  B

Warning: Phenylalanine convention problem

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

  53 PHE   (  54-)  A
  94 PHE   (  95-)  A
 148 PHE   ( 149-)  A
 268 PHE   (  87-)  B
 305 PHE   ( 132-)  B
 328 PHE   ( 155-)  B

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.

 187 ASP   (   6-)  B

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.

  90 GLU   (  91-)  A
 132 GLU   ( 133-)  A
 136 GLU   ( 137-)  A
 161 GLU   ( 162-)  A
 168 GLU   ( 169-)  A
 186 GLU   (   5-)  B

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: 0.255
RMS-deviation in bond distances: 0.006

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.

 182 PRO   ( 183-)  A      N    CA   CB  109.71    6.1

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: 0.621
RMS-deviation in bond angles: 1.421

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.

  90 GLU   (  91-)  A
 132 GLU   ( 133-)  A
 136 GLU   ( 137-)  A
 161 GLU   ( 162-)  A
 168 GLU   ( 169-)  A
 186 GLU   (   5-)  B
 187 ASP   (   6-)  B
 322 ARG   ( 149-)  B

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.

 146 SER   ( 147-)  A    4.40
 293 THR   ( 120-)  B    4.03

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.

  19 GLY   (  20-)  A    -2.2
 119 VAL   ( 120-)  A    -2.2

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.

  10 CYS   (  11-)  A  omega poor
  19 GLY   (  20-)  A  PRO omega poor
  41 LYS   (  42-)  A  Poor phi/psi
  81 SER   (  82-)  A  Poor phi/psi
 113 ASN   ( 114-)  A  Poor phi/psi
 115 PHE   ( 116-)  A  PRO omega poor
 145 HIS   ( 146-)  A  Poor phi/psi
 160 ASP   ( 161-)  A  Poor phi/psi
 200 ASN   (  19-)  B  Poor phi/psi
 214 ASN   (  33-)  B  Poor phi/psi
 296 TYR   ( 123-)  B  PRO omega poor
 308 ASP   ( 135-)  B  Poor phi/psi
 326 TRP   ( 153-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.336

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!

   4 ALA   (   5-)  A      0
   5 ASP   (   6-)  A      0
   9 SER   (  10-)  A      0
  10 CYS   (  11-)  A      0
  12 VAL   (  13-)  A      0
  17 PHE   (  18-)  A      0
  18 TYR   (  19-)  A      0
  20 PRO   (  21-)  A      0
  21 SER   (  22-)  A      0
  28 PHE   (  29-)  A      0
  33 GLN   (  34-)  A      0
  34 PHE   (  35-)  A      0
  40 ARG   (  41-)  A      0
  46 ARG   (  47-)  A      0
  53 PHE   (  54-)  A      0
  79 TYR   (  80-)  A      0
  81 SER   (  82-)  A      0
 101 LEU   ( 102-)  A      0
 112 ASP   ( 113-)  A      0
 115 PHE   ( 116-)  A      0
 116 PRO   ( 117-)  A      0
 117 PRO   ( 118-)  A      0
 118 VAL   ( 119-)  A      0
 125 SER   ( 126-)  A      0
 132 GLU   ( 133-)  A      0
And so on for a total of 153 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 : 1.567

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!

 378 GLY   (  14-)  C   2.28   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]

 182 PRO   ( 183-)  A    0.00 LOW

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 389 NAG   (1195-)  B      O4   <->   392 BMA   (1196-)  B      C1   1.02    1.38  INTRA B3
 389 NAG   (1195-)  B      C4   <->   392 BMA   (1196-)  B      C1   0.80    2.40  INTRA
  80 ASN   (  81-)  A      ND2  <->   386 NAG   (1185-)  A      C7   0.44    2.66  INTRA BF
 169 HIS   ( 170-)  A      ND1  <->   171 GLY   ( 172-)  A      N    0.24    2.76  INTRA BL
  46 ARG   (  47-)  A      NH1  <->   393 HOH   (2071 )  A      O    0.19    2.51  INTRA
 149 LYS   ( 150-)  A      NZ   <->   393 HOH   (2157 )  A      O    0.15    2.55  INTRA
 379 GLY   (  15-)  C      N    <->   395 HOH   (2013 )  C      O    0.14    2.56  INTRA
  49 GLU   (  50-)  A      CD   <->   274 ARG   (  93-)  B      NH1  0.11    2.99  INTRA
  40 ARG   (  41-)  A      NH1  <->   393 HOH   (2056 )  A      O    0.10    2.60  INTRA
 145 HIS   ( 146-)  A      ND1  <->   193 LYS   (  12-)  B      NZ   0.10    2.90  INTRA BL
 236 ARG   (  55-)  B      NE   <->   394 HOH   (2065 )  B      O    0.10    2.60  INTRA
 261 ARG   (  80-)  B      NH1  <->   394 HOH   (2094 )  B      O    0.09    2.61  INTRA BL
 206 ARG   (  25-)  B      NH2  <->   222 ASP   (  41-)  B      OD2  0.09    2.61  INTRA BL
 236 ARG   (  55-)  B      N    <->   237 PRO   (  56-)  B      CD   0.07    2.93  INTRA BL
 189 VAL   (   8-)  B      O    <->   214 ASN   (  33-)  B      N    0.07    2.63  INTRA BL
  50 PHE   (  51-)  A      CZ   <->   326 TRP   ( 153-)  B      CD2  0.07    3.13  INTRA BL
  73 ASN   (  74-)  A      ND2  <->   393 HOH   (2096 )  A      O    0.07    2.63  INTRA
  63 ARG   (  64-)  A      NE   <->   393 HOH   (2088 )  A      O    0.05    2.65  INTRA
 378 GLY   (  14-)  C      C    <->   395 HOH   (2013 )  C      O    0.04    2.76  INTRA
  69 LYS   (  70-)  A      NZ   <->   393 HOH   (2093 )  A      O    0.04    2.66  INTRA
  96 LYS   (  97-)  A      NZ   <->   294 ASP   ( 121-)  B      OD1  0.03    2.67  INTRA
 309 GLN   ( 136-)  B      NE2  <->   394 HOH   (2129 )  B      O    0.03    2.67  INTRA BF
 347 HIS   ( 174-)  B      ND1  <->   394 HOH   (2149 )  B      O    0.03    2.67  INTRA
  46 ARG   (  47-)  A      N    <->    47 TRP   (  48-)  A      N    0.02    2.58  INTRA BL
  94 PHE   (  95-)  A      O    <->   108 ILE   ( 109-)  A      N    0.02    2.68  INTRA BL
  10 CYS   (  11-)  A      CA   <->    11 GLY   (  12-)  A      CA   0.02    2.78  INTRA BL
  49 GLU   (  50-)  A      OE2  <->   274 ARG   (  93-)  B      NH1  0.01    2.69  INTRA
 350 HIS   ( 177-)  B      CD2  <->   352 SER   ( 179-)  B      OG   0.01    2.79  INTRA BL
 144 ASP   ( 145-)  A      N    <->   145 HIS   ( 146-)  A      N    0.01    2.59  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 354 GLN   ( 181-)  B      -7.07
 299 GLN   ( 126-)  B      -6.38
  46 ARG   (  47-)  A      -5.75
 181 GLU   ( 182-)  A      -5.60
 377 VAL   (  13-)  C      -5.43
 322 ARG   ( 149-)  B      -5.42
 339 GLN   ( 166-)  B      -5.27
  40 ARG   (  41-)  A      -5.07
   3 VAL   (   4-)  A      -5.06
  18 TYR   (  19-)  A      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 377 VAL   (  13-)  C       379 - GLY     15- ( C)         -4.72

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

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: B

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: C

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

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 394 HOH   (2059 )  B      O     79.44   52.10   22.20

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.

 393 HOH   (2012 )  A      O
 393 HOH   (2023 )  A      O
 393 HOH   (2062 )  A      O
 394 HOH   (2055 )  B      O
Bound group on Asn; dont flip   80 ASN  (  81-) A
Bound to:  386 NAG  (1185-) A
Bound group on Asn; dont flip  120 ASN  ( 121-) A
Bound to:  385 NAG  (1184-) A
Bound group on Asn; dont flip  200 ASN  (  19-) B
Bound to:  387 NAG  (1193-) B
Metal-coordinating Histidine residue 262 fixed to   1
Metal-coordinating Histidine residue 179 fixed to   1

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.

  59 GLN   (  60-)  A
  70 HIS   (  71-)  A
 309 GLN   ( 136-)  B
 350 HIS   ( 177-)  B

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.

   3 VAL   (   4-)  A      N
  33 GLN   (  34-)  A      NE2
  71 ASN   (  72-)  A      ND2
  78 ARG   (  79-)  A      NH1
 227 VAL   (  46-)  B      N
 307 ASN   ( 134-)  B      ND2
Only metal coordination for  164 ASP  ( 165-) A      OD1
Only metal coordination for  179 HIS  ( 180-) A      ND1
Only metal coordination for  257 ASP  (  76-) B      OD2
Only metal coordination for  262 HIS  (  81-) B      NE2

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.

  16 GLN   (  17-)  A      OE1
 187 ASP   (   6-)  B      OD2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 393 HOH   (2032 )  A      O  0.98  K  4
 393 HOH   (2036 )  A      O  0.85  K  4
 393 HOH   (2053 )  A      O  0.87  K  4
 393 HOH   (2127 )  A      O  0.96  K  4 Ion-B
 393 HOH   (2170 )  A      O  1.09  K  4
 394 HOH   (2053 )  B      O  1.13  K  4
 394 HOH   (2063 )  B      O  1.05  K  4
 394 HOH   (2087 )  B      O  1.10  K  4
 394 HOH   (2090 )  B      O  0.88  K  4
 394 HOH   (2121 )  B      O  0.95  K  5
 394 HOH   (2127 )  B      O  0.90  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 :   0.315
  2nd generation packing quality :  -0.631
  Ramachandran plot appearance   :   0.249
  chi-1/chi-2 rotamer normality  :   0.336
  Backbone conformation          :  -0.049

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.255 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.285 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.625
  B-factor distribution          :   0.590
  Inside/Outside distribution    :   1.036

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 :   0.7
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.255 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.285 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.625
  B-factor distribution          :   0.590
  Inside/Outside distribution    :   1.036
==============

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.