WHAT IF Check report

This file was created 2011-12-21 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 pdb1cal.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

   1 HIS   (   3-)  A    0.50
  12 GLU   (  14-)  A    0.80
 133 GLN   ( 136-)  A    0.60

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 190 THR   ( 193-)  A      CA   CB    1.62    4.6

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998728  0.000330  0.000467|
 |  0.000330  0.991474 -0.000635|
 |  0.000467 -0.000635  0.988407|
Proposed new scale matrix

 |  0.023446 -0.000004  0.006160|
 | -0.000008  0.024187  0.000016|
 | -0.000007  0.000009  0.014322|
With corresponding cell

    A    =  42.646  B   =  41.344  C    =  72.184
    Alpha=  90.081  Beta= 104.695  Gamma=  89.962

The CRYST1 cell dimensions

    A    =  42.700  B   =  41.700  C    =  73.000
    Alpha=  90.000  Beta= 104.600  Gamma=  90.000

Variance: 518.959
(Under-)estimated Z-score: 16.789

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.

   1 HIS   (   3-)  A      CG   ND1  CE1 109.83    4.2
   2 HIS   (   4-)  A      CA   C    O   127.92    4.2
   2 HIS   (   4-)  A      CA   CB   CG  124.21   10.4
   2 HIS   (   4-)  A      CG   ND1  CE1 110.21    4.6
   3 TRP   (   5-)  A     -C    N    CA  135.49    7.7
   8 HIS   (  10-)  A      CG   ND1  CE1 109.78    4.2
  12 GLU   (  14-)  A      CB   CG   CD  123.12    6.2
  15 HIS   (  17-)  A      CG   ND1  CE1 110.50    4.9
  15 HIS   (  17-)  A      ND1  CE1  NE2 106.46   -4.0
  17 ASP   (  19-)  A      CA   CB   CG  117.56    5.0
  25 ARG   (  27-)  A      CA   CB   CG  123.18    4.5
  25 ARG   (  27-)  A      CB   CG   CD  124.10    5.0
  25 ARG   (  27-)  A      CG   CD   NE  133.48   13.5
  30 ASP   (  32-)  A      CA   CB   CG  108.49   -4.1
  32 ASP   (  34-)  A      C    CA   CB  120.24    5.3
  34 HIS   (  36-)  A      CG   ND1  CE1 110.51    4.9
  35 THR   (  37-)  A     -C    N    CA  129.15    4.1
  35 THR   (  37-)  A      CA   CB   CG2 121.88    6.7
  35 THR   (  37-)  A      CA   CB   OG1 101.48   -5.4
  39 ASP   (  41-)  A      C    CA   CB  119.91    5.2
  43 LYS   (  45-)  A     -O   -C    N   130.41    4.6
  51 GLN   (  53-)  A      NE2  CD   OE1 117.95   -4.6
  56 ARG   (  58-)  A      N    CA   CB   98.75   -6.9
  57 ILE   (  59-)  A      N    CA   CB  117.56    4.2
  58 LEU   (  60-)  A      N    CA   CB  103.21   -4.3
And so on for a total of 98 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

  56 ARG   (  58-)  A      CA     6.4    44.42    33.91
The average deviation= 1.913

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.

  56 ARG   (  58-)  A    4.32
 130 LYS   ( 133-)  A    4.22
 219 GLN   ( 222-)  A    4.17
 204 VAL   ( 207-)  A    4.08

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.552

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 120 HIS   ( 122-)  A    4.58
  92 HIS   (  94-)  A    4.26
  30 ASP   (  32-)  A    4.26

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.

  81 PRO   (  83-)  A    -2.5
 236 GLU   ( 239-)  A    -2.2
  48 SER   (  50-)  A    -2.2
 160 VAL   ( 163-)  A    -2.2
 249 LYS   ( 252-)  A    -2.2
  98 LEU   ( 100-)  A    -2.1
  90 GLN   (  92-)  A    -2.1
 164 ILE   ( 167-)  A    -2.1
  35 THR   (  37-)  A    -2.0
 200 LEU   ( 203-)  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.

  27 SER   (  29-)  A  PRO omega poor
  62 HIS   (  64-)  A  Poor phi/psi
  73 ASP   (  75-)  A  Poor phi/psi
 109 LYS   ( 111-)  A  Poor phi/psi
 126 GLY   ( 129-)  A  Poor phi/psi
 175 ASN   ( 178-)  A  Poor phi/psi
 198 PRO   ( 201-)  A  PRO omega poor
 249 LYS   ( 252-)  A  Poor phi/psi
 250 ASN   ( 253-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.276

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.276

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 TRP   (   5-)  A      0
   5 TYR   (   7-)  A      0
   8 HIS   (  10-)  A      0
  18 PHE   (  20-)  A      0
  22 LYS   (  24-)  A      0
  25 ARG   (  27-)  A      0
  26 GLN   (  28-)  A      0
  27 SER   (  29-)  A      0
  48 SER   (  50-)  A      0
  50 ASP   (  52-)  A      0
  52 ALA   (  54-)  A      0
  60 ASN   (  62-)  A      0
  62 HIS   (  64-)  A      0
  70 ASP   (  72-)  A      0
  71 SER   (  73-)  A      0
  73 ASP   (  75-)  A      0
  74 LYS   (  76-)  A      0
  75 ALA   (  77-)  A      0
  78 LYS   (  80-)  A      0
  81 PRO   (  83-)  A      0
  83 ASP   (  85-)  A      0
  90 GLN   (  92-)  A      0
 101 GLN   ( 103-)  A      0
 104 GLU   ( 106-)  A      0
 105 HIS   ( 107-)  A      0
And so on for a total of 123 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 : 3.081

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  55 LEU   (  57-)  A   1.70

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]

  19 PRO   (  21-)  A    0.47 HIGH
  44 PRO   (  46-)  A    0.07 LOW
 135 PRO   ( 138-)  A    0.20 LOW
 192 PRO   ( 195-)  A    0.19 LOW
 212 PRO   ( 215-)  A    0.48 HIGH
 244 PRO   ( 247-)  A    0.16 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].

  40 PRO   (  42-)  A    -5.7 envelop N (0 degrees)
  81 PRO   (  83-)  A   -64.9 envelop C-beta (-72 degrees)
 212 PRO   ( 215-)  A    51.5 half-chair C-delta/C-gamma (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.

  13 HIS   (  15-)  A      ND1 <->   16 LYS   (  18-)  A      NZ     0.21    2.79  INTRA BL
  94 HIS   (  96-)  A      ND1 <->  241 ASN   ( 244-)  A      O      0.12    2.58  INTRA BL
  90 GLN   (  92-)  A      O   <->  119 VAL   ( 121-)  A      N      0.11    2.59  INTRA BL
  70 ASP   (  72-)  A      OD2 <->  121 TRP   ( 123-)  A      NE1    0.11    2.59  INTRA BL
 226 LEU   ( 229-)  A      O   <->  238 MET   ( 241-)  A      N      0.10    2.60  INTRA BL
 186 LEU   ( 189-)  A      N   <->  261 HOH   ( 428 )  A      O      0.09    2.61  INTRA
  27 SER   (  29-)  A      O   <->  243 ARG   ( 246-)  A      NH1    0.09    2.61  INTRA BL
  62 HIS   (  64-)  A      ND1 <->  261 HOH   ( 332 )  A      O      0.08    2.62  INTRA
  73 ASP   (  75-)  A      OD1 <->   87 ARG   (  89-)  A      NE     0.08    2.62  INTRA
 142 GLY   ( 145-)  A      N   <->  207 ILE   ( 210-)  A      O      0.08    2.62  INTRA BL
  22 LYS   (  24-)  A      NZ  <->  261 HOH   ( 429 )  A      O      0.08    2.62  INTRA
 148 GLY   ( 151-)  A      N   <->  215 VAL   ( 218-)  A      O      0.08    2.62  INTRA BL
 193 GLY   ( 196-)  A      N   <->  204 VAL   ( 207-)  A      O      0.07    2.63  INTRA BL
  32 ASP   (  34-)  A      N   <->  261 HOH   ( 427 )  A      O      0.04    2.66  INTRA
 244 PRO   ( 247-)  A      O   <->  246 GLN   ( 249-)  A      NE2    0.04    2.66  INTRA BL
  31 ILE   (  33-)  A      N   <->  106 THR   ( 108-)  A      O      0.04    2.66  INTRA BL
 115 GLU   ( 117-)  A      OE2 <->  117 HIS   ( 119-)  A      NE2    0.04    2.66  INTRA BL
  41 SER   (  43-)  A      N   <->   42 LEU   (  44-)  A      N      0.03    2.57  INTRA B3
  90 GLN   (  92-)  A      OE1 <->   92 HIS   (  94-)  A      ND1    0.03    2.67  INTRA BL
 249 LYS   ( 252-)  A      NZ  <->  261 HOH   ( 363 )  A      O      0.03    2.67  INTRA
  31 ILE   (  33-)  A      O   <->  108 ASP   ( 110-)  A      N      0.03    2.67  INTRA BL
 177 ASP   ( 180-)  A      OD2 <->  179 ARG   ( 182-)  A      NH2    0.01    2.69  INTRA
 105 HIS   ( 107-)  A      NE2 <->  191 TYR   ( 194-)  A      OH     0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Warning: Abnormal packing environment for some residues

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

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

   2 HIS   (   4-)  A      -5.91
   8 HIS   (  10-)  A      -5.89
  98 LEU   ( 100-)  A      -5.28
 133 GLN   ( 136-)  A      -5.10

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: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 261 HOH   ( 315 )  A      O    -14.28  -18.95   18.86
 261 HOH   ( 317 )  A      O    -13.56  -18.61   15.53
 261 HOH   ( 349 )  A      O     -2.96  -17.77    5.09
 261 HOH   ( 382 )  A      O    -18.75   -2.85   -2.25
 261 HOH   ( 443 )  A      O    -18.57  -10.21   37.76
 261 HOH   ( 445 )  A      O     -0.14   -7.01   35.25
 261 HOH   ( 447 )  A      O     -1.50   -8.88   33.33

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.

 261 HOH   ( 345 )  A      O
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue  94 fixed to   1
Metal-coordinating Histidine residue 117 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.

   1 HIS   (   3-)  A
  51 GLN   (  53-)  A
 134 GLN   ( 137-)  A
 175 ASN   ( 178-)  A
 250 ASN   ( 253-)  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.

  29 VAL   (  31-)  A      N
  72 GLN   (  74-)  A      N
  98 LEU   ( 100-)  A      N
 122 ASN   ( 124-)  A      ND2
 201 LEU   ( 204-)  A      N
 229 ASN   ( 232-)  A      N
 241 ASN   ( 244-)  A      ND2
 242 TRP   ( 245-)  A      N
 257 PHE   ( 260-)  A      N
Only metal coordination for   94 HIS  (  96-) A      NE2
Only metal coordination for  117 HIS  ( 119-) A      ND1

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.

 261 HOH   ( 470 )  A      O  1.03  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.

  30 ASP   (  32-)  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 :  -0.166
  2nd generation packing quality :   0.121
  Ramachandran plot appearance   :  -1.646
  chi-1/chi-2 rotamer normality  :  -3.276 (poor)
  Backbone conformation          :  -0.776

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.053
  Bond angles                    :   1.774
  Omega angle restraints         :   0.560 (tight)
  Side chain planarity           :   1.460
  Improper dihedral distribution :   1.583 (loose)
  B-factor distribution          :   0.530
  Inside/Outside distribution    :   0.948

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.053
  Bond angles                    :   1.774
  Omega angle restraints         :   0.560 (tight)
  Side chain planarity           :   1.460
  Improper dihedral distribution :   1.583 (loose)
  B-factor distribution          :   0.530
  Inside/Outside distribution    :   0.948
==============

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.