WHAT IF Check report

This file was created 2013-12-10 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb4frc.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.

 261 DMS   ( 304-)  A  -
 262 0VY   ( 303-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

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

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

  31 ASP   (  34-)  A  -
 100 GLN   ( 103-)  A  -
 123 LYS   ( 127-)  A  -
 166 LYS   ( 170-)  A  -
 210 GLU   ( 214-)  A  -
 216 SER   ( 220-)  A  -

Warning: Alternate atom problems quasi solved

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

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

  31 ASP   (  34-)  A  -
 100 GLN   ( 103-)  A  -
 123 LYS   ( 127-)  A  -
 166 LYS   ( 170-)  A  -
 210 GLU   ( 214-)  A  -
 216 SER   ( 220-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: Missing atoms

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

   1 HIS   (   4-)  A      CG
   1 HIS   (   4-)  A      ND1
   1 HIS   (   4-)  A      CD2
   1 HIS   (   4-)  A      CE1
   1 HIS   (   4-)  A      NE2
   6 LYS   (   9-)  A      CG
   6 LYS   (   9-)  A      CD
   6 LYS   (   9-)  A      CE
   6 LYS   (   9-)  A      NZ
  40 SER   (  43-)  A      OG
  42 LYS   (  45-)  A      CG
  42 LYS   (  45-)  A      CD
  42 LYS   (  45-)  A      CE
  42 LYS   (  45-)  A      NZ
  73 LYS   (  76-)  A      CG
  73 LYS   (  76-)  A      CD
  73 LYS   (  76-)  A      CE
  73 LYS   (  76-)  A      NZ
  77 LYS   (  80-)  A      CG
  77 LYS   (  80-)  A      CD
  77 LYS   (  80-)  A      CE
  77 LYS   (  80-)  A      NZ
  82 ASP   (  85-)  A      CG
  82 ASP   (  85-)  A      OD1
  82 ASP   (  85-)  A      OD2
 155 LYS   ( 159-)  A      CG
 155 LYS   ( 159-)  A      CD
 155 LYS   ( 159-)  A      CE
 155 LYS   ( 159-)  A      NZ
 220 LEU   ( 224-)  A      CG
 220 LEU   ( 224-)  A      CD1
 220 LEU   ( 224-)  A      CD2
 257 LYS   ( 261-)  A      CG
 257 LYS   ( 261-)  A      CD
 257 LYS   ( 261-)  A      CE
 257 LYS   ( 261-)  A      NZ

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.

   7 HIS   (  10-)  A    0.66

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

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 12.25

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  24 ARG   (  27-)  A
  55 ARG   (  58-)  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.

  31 ASP   (  34-)  A
  49 ASP   (  52-)  A
  68 ASP   (  71-)  A
 126 ASP   ( 130-)  A
 171 ASP   ( 175-)  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.

 217 GLU   ( 221-)  A
 232 GLU   ( 236-)  A

Geometric checks

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

 |  0.998433 -0.000760  0.001104|
 | -0.000760  0.998267 -0.000171|
 |  0.001104 -0.000171  0.997580|
Proposed new scale matrix

 |  0.023739  0.000019  0.005987|
 |  0.000018  0.024090  0.000004|
 | -0.000016  0.000002  0.014303|
With corresponding cell

    A    =  42.114  B   =  41.511  C    =  72.087
    Alpha=  89.998  Beta= 104.092  Gamma=  90.087

The CRYST1 cell dimensions

    A    =  42.179  B   =  41.584  C    =  72.296
    Alpha=  90.000  Beta= 104.200  Gamma=  90.000

Variance: 36.659
(Under-)estimated Z-score: 4.462

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   (   4-)  A      N    CA   CB  120.25    5.7
   7 HIS   (  10-)  A      CA   CB   CG  108.36   -5.4
   7 HIS   (  10-)  A      CG   ND1  CE1 109.85    4.2
   7 HIS   (  10-)  A      CB   CG   CD2 137.79    6.7
  16 ASP   (  19-)  A      CA   CB   CG  116.78    4.2
  24 ARG   (  27-)  A      CA   CB   CG  128.26    7.1
  24 ARG   (  27-)  A      CG   CD   NE  126.68    9.5
  24 ARG   (  27-)  A      NE   CZ   NH1 130.96    5.8
  24 ARG   (  27-)  A      NE   CZ   NH2 110.70   -4.9
  33 HIS   (  36-)  A      CG   ND1  CE1 111.61    6.0
  33 HIS   (  36-)  A      ND1  CE1  NE2 106.38   -4.1
  49 ASP   (  52-)  A      CA   CB   CG  108.47   -4.1
  50 GLN   (  53-)  A      NE2  CD   OE1 127.34    4.7
  61 HIS   (  64-)  A      CG   ND1  CE1 111.66    6.1
  67 PHE   (  70-)  A      CA   CB   CG  108.79   -5.0
  71 GLN   (  74-)  A      CG   CD   NE2 122.81    4.3
  72 ASP   (  75-)  A      CA   CB   CG  120.64    8.0
  73 LYS   (  76-)  A     -C    N    CA  129.16    4.1
  86 ARG   (  89-)  A      CB   CG   CD  103.84   -5.1
  86 ARG   (  89-)  A      CG   CD   NE   94.14   -9.6
  98 ASP   ( 101-)  A      CA   CB   CG  116.88    4.3
 119 HIS   ( 122-)  A      NE2  CD2  CG  111.60    5.1
 123 LYS   ( 127-)  A     -C    N    CA  114.33   -4.1
 126 ASP   ( 130-)  A      N    CA   CB  117.46    4.1
 126 ASP   ( 130-)  A      CA   CB   CG  123.12   10.5
 158 ASP   ( 162-)  A      CA   CB   CG  106.72   -5.9
 175 PHE   ( 179-)  A      CA   CB   CG  109.45   -4.4
 222 PHE   ( 226-)  A      CB   CG   CD1 128.13    4.4
 226 ASN   ( 230-)  A      CA   CB   CG  117.62    5.0
 227 PHE   ( 231-)  A      CA   CB   CG  118.24    4.4
 249 ASN   ( 253-)  A      ND2  CG   OD1 129.22    6.6

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.

  24 ARG   (  27-)  A
  31 ASP   (  34-)  A
  49 ASP   (  52-)  A
  55 ARG   (  58-)  A
  68 ASP   (  71-)  A
 126 ASP   ( 130-)  A
 171 ASP   ( 175-)  A
 217 GLU   ( 221-)  A
 232 GLU   ( 236-)  A

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  41 LEU   (  44-)  A      C     -9.0   -13.96     0.20
The average deviation= 1.248

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.

 176 ASP   ( 180-)  A    4.72

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.

 159 VAL   ( 163-)  A    -2.1
 198 PRO   ( 202-)  A    -2.1
 172 PHE   ( 176-)  A    -2.1
  24 ARG   (  27-)  A    -2.0
 147 GLY   ( 151-)  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.

  26 SER   (  29-)  A  PRO omega poor
  28 VAL   (  31-)  A  omega poor
  54 LEU   (  57-)  A  omega poor
  62 ALA   (  65-)  A  Poor phi/psi
  83 GLY   (  86-)  A  omega poor
  89 GLN   (  92-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 174 ASN   ( 178-)  A  Poor phi/psi
 187 TYR   ( 191-)  A  omega poor
 193 SER   ( 197-)  A  omega poor
 197 PRO   ( 201-)  A  PRO omega poor
 199 LEU   ( 203-)  A  Poor phi/psi
 202 CYS   ( 206-)  A  omega poor
 203 VAL   ( 207-)  A  omega poor
 211 PRO   ( 215-)  A  omega poor
 239 ASP   ( 243-)  A  Poor phi/psi
 248 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.803

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 TYR   (   7-)  A      0
   7 HIS   (  10-)  A      0
  16 ASP   (  19-)  A      0
  17 PHE   (  20-)  A      0
  21 LYS   (  24-)  A      0
  24 ARG   (  27-)  A      0
  25 GLN   (  28-)  A      0
  26 SER   (  29-)  A      0
  35 ALA   (  38-)  A      0
  42 LYS   (  45-)  A      0
  47 SER   (  50-)  A      0
  49 ASP   (  52-)  A      0
  51 ALA   (  54-)  A      0
  59 ASN   (  62-)  A      0
  61 HIS   (  64-)  A      0
  62 ALA   (  65-)  A      0
  69 ASP   (  72-)  A      0
  70 SER   (  73-)  A      0
  72 ASP   (  75-)  A      0
  73 LYS   (  76-)  A      0
  74 ALA   (  77-)  A      0
  77 LYS   (  80-)  A      0
  80 PRO   (  83-)  A      0
  82 ASP   (  85-)  A      0
  89 GLN   (  92-)  A      0
And so on for a total of 123 lines.

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].

  10 PRO   (  13-)  A   101.1 envelop C-beta (108 degrees)
  18 PRO   (  21-)  A  -117.4 half-chair C-delta/C-gamma (-126 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.

  33 HIS   (  36-)  A      ND1 <->  263 HOH   ( 610 )  A      O      0.24    2.46  INTRA
  12 HIS   (  15-)  A      ND1 <->   15 LYS   (  18-)  A      NZ     0.23    2.77  INTRA BL
  24 ARG   (  27-)  A      NH2 <->  263 HOH   ( 514 )  A      O      0.22    2.48  INTRA
 248 LYS   ( 252-)  A      NZ  <->  263 HOH   ( 461 )  A      O      0.17    2.53  INTRA
 158 ASP   ( 162-)  A      OD2 <->  263 HOH   ( 704 )  A      O      0.15    2.25  INTRA
 232 GLU   ( 236-)  A      OE1 <->  263 HOH   ( 622 )  A      O      0.14    2.26  INTRA
  72 ASP   (  75-)  A      OD1 <->   86 ARG   (  89-)  A      NE     0.13    2.57  INTRA
  43 PRO   (  46-)  A    A O   <->  263 HOH   ( 587 )  A      O      0.12    2.28  INTRA
 161 ASP   ( 165-)  A      OD1 <->  263 HOH   ( 657 )  A      O      0.11    2.29  INTRA BF
 104 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.09    2.61  INTRA BL
  49 ASP   (  52-)  A      OD1 <->  263 HOH   ( 503 )  A      O      0.08    2.32  INTRA BF
 209 LYS   ( 213-)  A      NZ  <->  263 HOH   ( 519 )  A      O      0.08    2.62  INTRA
 110 LYS   ( 113-)  A      NZ  <->  263 HOH   ( 641 )  A      O      0.07    2.63  INTRA
 166 LYS   ( 170-)  A    A NZ  <->  263 HOH   ( 622 )  A      O      0.06    2.64  INTRA
  86 ARG   (  89-)  A      NH1 <->  263 HOH   ( 486 )  A      O      0.05    2.65  INTRA
 150 LYS   ( 154-)  A      NZ  <->  263 HOH   ( 515 )  A      O      0.04    2.66  INTRA
 251 GLN   ( 255-)  A      OE1 <->  263 HOH   ( 550 )  A      O      0.03    2.37  INTRA
 122 THR   ( 125-)  A      OG1 <->  263 HOH   ( 586 )  A      O      0.03    2.37  INTRA
  11 GLU   (  14-)  A      CD  <->  263 HOH   ( 691 )  A      O      0.01    2.79  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Warning: Abnormal packing environment for some residues

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

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

  71 GLN   (  74-)  A      -6.70
   7 HIS   (  10-)  A      -6.58
  97 LEU   ( 100-)  A      -5.36

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

  73 LYS   (  76-)  A   -3.71
  42 LYS   (  45-)  A   -2.95
 243 PRO   ( 247-)  A   -2.70
 251 GLN   ( 255-)  A   -2.66

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.

 263 HOH   ( 493 )  A      O      3.23   21.77   17.54
 263 HOH   ( 606 )  A      O      6.37  -17.03   18.95
 263 HOH   ( 667 )  A      O     23.68   16.29   28.74
 263 HOH   ( 681 )  A      O     16.29  -14.57    1.42
 263 HOH   ( 699 )  A      O     -0.01   20.72   14.14
 263 HOH   ( 707 )  A      O     16.04   22.64   22.01

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.

  28 VAL   (  31-)  A      N
  97 LEU   ( 100-)  A      N
 161 ASP   ( 165-)  A      N
 183 GLU   ( 187-)  A      N
 196 THR   ( 200-)  A      N
 200 LEU   ( 204-)  A      N
 226 ASN   ( 230-)  A      ND2
 240 ASN   ( 244-)  A      ND2
 241 TRP   ( 245-)  A      N
 256 PHE   ( 260-)  A      N
Only metal coordination for   93 HIS  (  96-) A      NE2
Only metal coordination for  116 HIS  ( 119-) 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.

 263 HOH   ( 495 )  A      O  0.95  K  4
 263 HOH   ( 508 )  A      O  0.89  K  4 H2O-B
 263 HOH   ( 553 )  A      O  0.92  K  4 Ion-B
 263 HOH   ( 599 )  A      O  0.91  K  5 Ion-B
 263 HOH   ( 691 )  A      O  0.90  K  5 Ion-B

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 :  -0.071
  2nd generation packing quality :   0.270
  Ramachandran plot appearance   :  -1.168
  chi-1/chi-2 rotamer normality  :   0.803
  Backbone conformation          :  -1.150

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.747
  Bond angles                    :   1.241
  Omega angle restraints         :   1.236
  Side chain planarity           :   1.276
  Improper dihedral distribution :   1.029
  Inside/Outside distribution    :   0.959

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 : 0.98

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.747
  Bond angles                    :   1.241
  Omega angle restraints         :   1.236
  Side chain planarity           :   1.276
  Improper dihedral distribution :   1.029
  Inside/Outside distribution    :   0.959

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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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    Acta Crystallogr. D52, 57--64 (1996).

    W.Kabsch and C.Sander,
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      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
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Ion Checks
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      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
    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.