WHAT IF Check report

This file was created 2011-12-28 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 pdb1flj.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.

 263 GTT   (1183-)  A  -
 264 GTT   (1188-)  A  -

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.

   1 ALA   (   2-)  A  -   N   bound to  260 ACE   (   1-)  A  -   C

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: 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) :298.000

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.

 225 ARG   ( 227-)  A
 244 ARG   ( 246-)  A

Warning: Tyrosine convention problem

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

   6 TYR   (   7-)  A
  19 TYR   (  20-)  A
  50 TYR   (  51-)  A
  87 TYR   (  88-)  A
 126 TYR   ( 128-)  A
 192 TYR   ( 194-)  A

Warning: Phenylalanine convention problem

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

  73 PHE   (  74-)  A
  92 PHE   (  93-)  A
 129 PHE   ( 131-)  A
 155 PHE   ( 157-)  A
 177 PHE   ( 179-)  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.

  40 ASP   (  41-)  A
  51 ASP   (  52-)  A
  70 ASP   (  71-)  A
  71 ASP   (  72-)  A
 100 ASP   ( 101-)  A
 101 ASP   ( 102-)  A
 109 ASP   ( 110-)  A
 137 ASP   ( 139-)  A
 163 ASP   ( 165-)  A
 188 ASP   ( 190-)  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.

  17 GLU   (  18-)  A
 131 GLU   ( 133-)  A
 154 GLU   ( 156-)  A
 171 GLU   ( 173-)  A
 212 GLU   ( 214-)  A
 232 GLU   ( 234-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.430
RMS-deviation in bond distances: 0.010

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

 |  0.998947  0.000193  0.000653|
 |  0.000193  0.996251 -0.000285|
 |  0.000653 -0.000285  0.998725|
Proposed new scale matrix

 |  0.024265 -0.000004  0.004146|
 | -0.000004  0.022440  0.000006|
 | -0.000010  0.000004  0.015183|
With corresponding cell

    A    =  41.207  B   =  44.563  C    =  66.809
    Alpha=  90.036  Beta=  99.660  Gamma=  89.978

The CRYST1 cell dimensions

    A    =  41.250  B   =  44.730  C    =  66.910
    Alpha=  90.000  Beta=  99.730  Gamma=  90.000

Variance: 43.969
(Under-)estimated Z-score: 4.887

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.

  94 LEU   (  95-)  A      CA   CB   CG  130.39    4.0
 214 MET   ( 216-)  A      N    CA   C    99.56   -4.2

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.

  17 GLU   (  18-)  A
  40 ASP   (  41-)  A
  51 ASP   (  52-)  A
  70 ASP   (  71-)  A
  71 ASP   (  72-)  A
 100 ASP   ( 101-)  A
 101 ASP   ( 102-)  A
 109 ASP   ( 110-)  A
 131 GLU   ( 133-)  A
 137 ASP   ( 139-)  A
 154 GLU   ( 156-)  A
 163 ASP   ( 165-)  A
 171 GLU   ( 173-)  A
 188 ASP   ( 190-)  A
 212 GLU   ( 214-)  A
 225 ARG   ( 227-)  A
 232 GLU   ( 234-)  A
 244 ARG   ( 246-)  A

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.

 205 ILE   ( 207-)  A    4.47
 214 MET   ( 216-)  A    4.43

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.

  64 THR   (  65-)  A    -3.1
  59 LEU   (  60-)  A    -2.6
  34 THR   (  35-)  A    -2.5
  29 PRO   (  30-)  A    -2.3
  91 GLN   (  92-)  A    -2.2
  12 PRO   (  13-)  A    -2.2
  21 ILE   (  22-)  A    -2.2
 139 ILE   ( 141-)  A    -2.1
  82 PRO   (  83-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

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

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

  28 SER   (  29-)  A  PRO omega poor
  64 THR   (  65-)  A  Poor phi/psi
 127 ASN   ( 129-)  A  Poor phi/psi
 199 PRO   ( 201-)  A  PRO omega poor
 201 CYS   ( 203-)  A  Poor phi/psi
 250 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.193

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 GLU   (   4-)  A      0
   4 TRP   (   5-)  A      0
   6 TYR   (   7-)  A      0
   9 HIS   (  10-)  A      0
  23 LYS   (  24-)  A      0
  26 ASN   (  27-)  A      0
  27 GLN   (  28-)  A      0
  28 SER   (  29-)  A      0
  36 ASP   (  37-)  A      0
  48 VAL   (  49-)  A      0
  56 LYS   (  57-)  A      0
  57 THR   (  58-)  A      0
  61 ASN   (  62-)  A      0
  64 THR   (  65-)  A      0
  65 CYS   (  66-)  A      0
  71 ASP   (  72-)  A      0
  72 THR   (  73-)  A      0
  73 PHE   (  74-)  A      0
  74 ASP   (  75-)  A      0
  75 ARG   (  76-)  A      0
  79 ARG   (  80-)  A      0
  82 PRO   (  83-)  A      0
  84 SER   (  85-)  A      0
  90 ARG   (  91-)  A      0
  91 GLN   (  92-)  A      0
And so on for a total of 111 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 : 1.806

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]

 199 PRO   ( 201-)  A    0.46 HIGH

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.

  49 SER   (  50-)  A      OG  <->   79 ARG   (  80-)  A      NH1    0.17    2.53  INTRA
   4 TRP   (   5-)  A      O   <->   63 LYS   (  64-)  A      NZ     0.13    2.57  INTRA
  50 TYR   (  51-)  A      OH  <->  121 HIS   ( 122-)  A      NE2    0.12    2.58  INTRA BL
  95 HIS   (  96-)  A      ND1 <->  242 ASN   ( 244-)  A      O      0.11    2.59  INTRA BL
   4 TRP   (   5-)  A      CE2 <->   63 LYS   (  64-)  A      NZ     0.11    2.99  INTRA
  71 ASP   (  72-)  A      OD2 <->  122 TRP   ( 123-)  A      NE1    0.10    2.60  INTRA BL
 187 ARG   ( 189-)  A      NH2 <->  263 GTT   (1183-)  A    A C3     0.10    3.00  INTRA BF
  32 LEU   (  33-)  A      N   <->  107 THR   ( 108-)  A      O      0.08    2.62  INTRA BL
  57 THR   (  58-)  A      CG2 <->   58 ILE   (  59-)  A      N      0.08    2.92  INTRA BL
 147 LYS   ( 149-)  A      NZ  <->  265 HOH   ( 434 )  A      O      0.06    2.64  INTRA BF
 143 GLY   ( 145-)  A      N   <->  208 LEU   ( 210-)  A      O      0.06    2.64  INTRA BL
   4 TRP   (   5-)  A      CD2 <->   63 LYS   (  64-)  A      NZ     0.06    3.04  INTRA
 125 LYS   ( 127-)  A      NZ  <->  265 HOH   ( 358 )  A      O      0.05    2.65  INTRA
 164 LYS   ( 166-)  A      NZ  <->  265 HOH   ( 363 )  A      O      0.04    2.66  INTRA
  21 ILE   (  22-)  A      O   <->   24 GLY   (  25-)  A      N      0.04    2.66  INTRA BL
 106 HIS   ( 107-)  A      ND1 <->  116 GLU   ( 117-)  A      OE2    0.03    2.67  INTRA BL
 117 LEU   ( 118-)  A      N   <->  144 ILE   ( 146-)  A      O      0.03    2.67  INTRA BL
  66 ARG   (  67-)  A      NH1 <->  265 HOH   ( 468 )  A      O      0.03    2.67  INTRA
  11 GLY   (  12-)  A      O   <->   14 HIS   (  15-)  A      N      0.03    2.67  INTRA BL
 112 LYS   ( 113-)  A      NZ  <->  265 HOH   ( 272 )  A      O      0.02    2.68  INTRA
  57 THR   (  58-)  A      CG2 <->  171 GLU   ( 173-)  A      CG     0.02    3.18  INTRA
 102 HIS   ( 103-)  A      NE2 <->  265 HOH   ( 321 )  A      O      0.02    2.68  INTRA BL
  91 GLN   (  92-)  A      O   <->  120 VAL   ( 121-)  A      N      0.02    2.68  INTRA BL
 152 LYS   ( 154-)  A      NZ  <->  265 HOH   ( 453 )  A      O      0.02    2.68  INTRA
  54 SER   (  55-)  A      O   <->   70 ASP   (  71-)  A      N      0.02    2.68  INTRA BL
  79 ARG   (  80-)  A      NH2 <->  265 HOH   ( 362 )  A      O      0.01    2.69  INTRA
 139 ILE   ( 141-)  A      CG2 <->  140 ALA   ( 142-)  A      N      0.01    2.99  INTRA BL
 227 LEU   ( 229-)  A      O   <->  239 LEU   ( 241-)  A      N      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.

   9 HIS   (  10-)  A      -5.69
 176 HIS   ( 178-)  A      -5.67
   3 GLU   (   4-)  A      -5.21
  73 PHE   (  74-)  A      -5.13

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.

  85 GLY   (  86-)  A   -3.08

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.

 265 HOH   ( 396 )  A      O     32.60   -9.05   40.57
 265 HOH   ( 397 )  A      O     22.44  -34.15   14.43
 265 HOH   ( 420 )  A      O     33.77   11.46   23.03
 265 HOH   ( 433 )  A      O     49.82   -4.16   31.65
 265 HOH   ( 462 )  A      O     22.54   -8.31   -3.42

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.

  30 ILE   (  31-)  A      N
  73 PHE   (  74-)  A      N
  99 SER   ( 100-)  A      N
 163 ASP   ( 165-)  A      N
 188 ASP   ( 190-)  A      N
 198 THR   ( 200-)  A      N
 243 TRP   ( 245-)  A      N
 252 ARG   ( 254-)  A      N
 258 PHE   ( 260-)  A      N
Only metal coordination for   95 HIS  (  96-) A      NE2

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.

 265 HOH   ( 264 )  A      O  0.96  K  4

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.

  36 ASP   (  37-)  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 :  -0.698
  2nd generation packing quality :  -1.547
  Ramachandran plot appearance   :  -1.205
  chi-1/chi-2 rotamer normality  :  -2.193
  Backbone conformation          :  -1.297

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.430 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.328 (tight)
  Side chain planarity           :   0.468 (tight)
  Improper dihedral distribution :   0.923
  B-factor distribution          :   0.845
  Inside/Outside distribution    :   0.986

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 :  -0.3
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.430 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.328 (tight)
  Side chain planarity           :   0.468 (tight)
  Improper dihedral distribution :   0.923
  B-factor distribution          :   0.845
  Inside/Outside distribution    :   0.986

      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
    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).

    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
      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
    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.