WHAT IF Check report

This file was created 2012-01-12 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 pdb3qcg.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 287 NX1   (2001-)  A  -         Fragmented
 288 ACY   (2051-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  68 LYS   ( 892-)  A  -   NZ

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'.

   2 GLU   ( 826-)  A      CG
   2 GLU   ( 826-)  A      CD
   2 GLU   ( 826-)  A      OE1
   2 GLU   ( 826-)  A      OE2
   7 LYS   ( 831-)  A      CG
   7 LYS   ( 831-)  A      CD
   7 LYS   ( 831-)  A      CE
   7 LYS   ( 831-)  A      NZ
  74 SER   ( 901-)  A      OG
  75 LYS   ( 902-)  A      CG
  75 LYS   ( 902-)  A      CD
  75 LYS   ( 902-)  A      CE
  75 LYS   ( 902-)  A      NZ
 129 LYS   ( 956-)  A      CG
 129 LYS   ( 956-)  A      CD
 129 LYS   ( 956-)  A      CE
 129 LYS   ( 956-)  A      NZ
 131 ARG   ( 958-)  A      CG
 131 ARG   ( 958-)  A      CD
 131 ARG   ( 958-)  A      NE
 131 ARG   ( 958-)  A      CZ
 131 ARG   ( 958-)  A      NH1
 131 ARG   ( 958-)  A      NH2
 175 LYS   (1002-)  A      CG
 175 LYS   (1002-)  A      CD
 175 LYS   (1002-)  A      CE
 175 LYS   (1002-)  A      NZ
 176 GLN   (1013-)  A      CG
 176 GLN   (1013-)  A      CD
 176 GLN   (1013-)  A      OE1
 176 GLN   (1013-)  A      NE2
 244 LYS   (1081-)  A      CG
 244 LYS   (1081-)  A      CD
 244 LYS   (1081-)  A      CE
 244 LYS   (1081-)  A      NZ
 286 LYS   (1123-)  A      CG
 286 LYS   (1123-)  A      CD
 286 LYS   (1123-)  A      CE
 286 LYS   (1123-)  A      NZ

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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.

  33 ARG   ( 857-)  A
  70 ARG   ( 894-)  A
 170 ARG   ( 997-)  A
 206 ARG   (1043-)  A
 207 ARG   (1044-)  A

Warning: Tyrosine convention problem

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

  17 TYR   ( 841-)  A
  94 TYR   ( 921-)  A
 146 TYR   ( 973-)  A
 197 TYR   (1034-)  A
 264 TYR   (1101-)  A

Warning: Phenylalanine convention problem

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

 167 PHE   ( 994-)  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.

  30 GLU   ( 854-)  A
  43 GLU   ( 867-)  A
 128 GLU   ( 955-)  A
 144 GLU   ( 971-)  A
 269 GLU   (1106-)  A

Geometric checks

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.

  30 GLU   ( 854-)  A
  33 ARG   ( 857-)  A
  43 GLU   ( 867-)  A
  70 ARG   ( 894-)  A
 128 GLU   ( 955-)  A
 144 GLU   ( 971-)  A
 170 ARG   ( 997-)  A
 206 ARG   (1043-)  A
 207 ARG   (1044-)  A
 269 GLU   (1106-)  A

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 124 THR   ( 951-)  A    -2.2

Warning: Backbone evaluation reveals unusual conformations

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

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

  19 ASN   ( 843-)  A  Poor phi/psi
  21 GLN   ( 845-)  A  Poor phi/psi
  89 ASN   ( 916-)  A  Poor phi/psi
  94 TYR   ( 921-)  A  omega poor
 116 ASN   ( 943-)  A  Poor phi/psi
 124 THR   ( 951-)  A  omega poor
 142 ASN   ( 969-)  A  Poor phi/psi
 167 PHE   ( 994-)  A  omega poor
 188 GLN   (1025-)  A  omega poor
 214 PRO   (1051-)  A  omega poor
 215 GLU   (1052-)  A  omega poor
 222 HIS   (1059-)  A  omega poor
 223 CYS   (1060-)  A  Poor phi/psi
 247 SER   (1084-)  A  Poor phi/psi
 261 GLN   (1098-)  A  omega poor
 264 TYR   (1101-)  A  Poor phi/psi
 266 VAL   (1103-)  A  Poor phi/psi, omega poor
 chi-1/chi-2 correlation Z-score : -0.179

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

  45 SER   ( 869-)  A    0.39

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!

   9 PHE   ( 833-)  A      0
  19 ASN   ( 843-)  A      0
  20 ASN   ( 844-)  A      0
  21 GLN   ( 845-)  A      0
  34 CYS   ( 858-)  A      0
  42 ALA   ( 866-)  A      0
  43 GLU   ( 867-)  A      0
  56 TYR   ( 880-)  A      0
  72 LEU   ( 896-)  A      0
  73 PRO   ( 897-)  A      0
  74 SER   ( 901-)  A      0
  75 LYS   ( 902-)  A      0
  77 SER   ( 904-)  A      0
  81 ASN   ( 908-)  A      0
  88 TYR   ( 915-)  A      0
  89 ASN   ( 916-)  A      0
  91 ALA   ( 918-)  A      0
  92 LYS   ( 919-)  A      0
  93 ALA   ( 920-)  A      0
  96 ALA   ( 923-)  A      0
 100 PRO   ( 927-)  A      0
 115 GLN   ( 942-)  A      0
 116 ASN   ( 943-)  A      0
 117 THR   ( 944-)  A      0
 123 ILE   ( 950-)  A      0
And so on for a total of 115 lines.

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.

 206 ARG   (1043-)  A    A NH2 <->  289 HOH   (2197 )  A      O      0.27    2.43  INTRA
   1 MET   ( 825-)  A      SD  <->  256 LYS   (1093-)  A      NZ     0.24    3.06  INTRA BF
 189 TRP   (1026-)  A    A CD1 <->  229 ARG   (1066-)  A      NH2    0.16    2.94  INTRA
 199 LEU   (1036-)  A      N   <->  200 PRO   (1037-)  A      CD     0.16    2.84  INTRA BL
  70 ARG   ( 894-)  A      O   <->  110 ARG   ( 937-)  A      NH1    0.15    2.55  INTRA
  20 ASN   ( 844-)  A      ND2 <->  289 HOH   (2217 )  A      O      0.15    2.55  INTRA
 161 CYS   ( 988-)  A      CA  <->  188 GLN   (1025-)  A    A CG     0.14    3.06  INTRA
 223 CYS   (1060-)  A      SG  <->  226 GLY   (1063-)  A      N      0.10    3.20  INTRA BL
  33 ARG   ( 857-)  A      O   <->   36 ALA   ( 860-)  A      N      0.10    2.60  INTRA BF
 124 THR   ( 951-)  A      O   <->  185 HIS   (1022-)  A      CE1    0.10    2.70  INTRA BL
 125 ASN   ( 952-)  A      ND2 <->  289 HOH   (2218 )  A      O      0.09    2.61  INTRA
 129 LYS   ( 956-)  A      CB  <->  191 ASP   (1028-)  A    A CG     0.09    3.11  INTRA BF
  53 LYS   ( 877-)  A      NZ  <->  289 HOH   (2116 )  A      O      0.08    2.62  INTRA
 189 TRP   (1026-)  A    A CD1 <->  229 ARG   (1066-)  A      CZ     0.07    3.13  INTRA
  33 ARG   ( 857-)  A      C   <->   35 THR   ( 859-)  A      N      0.07    2.83  INTRA BF
 121 VAL   ( 948-)  A      N   <->  220 LEU   (1057-)  A      O      0.06    2.64  INTRA BL
 165 ARG   ( 992-)  A      NH1 <->  185 HIS   (1022-)  A      CD2    0.05    3.05  INTRA BL
  35 THR   ( 859-)  A      O   <->   38 MET   ( 862-)  A      N      0.05    2.65  INTRA BF
 228 GLY   (1065-)  A      N   <->  289 HOH   (2102 )  A      O      0.05    2.65  INTRA BL
 120 ILE   ( 947-)  A      O   <->  184 TYR   (1021-)  A      N      0.04    2.66  INTRA BL
  89 ASN   ( 916-)  A      N   <->  289 HOH   (2190 )  A      O      0.04    2.66  INTRA
 110 ARG   ( 937-)  A      NE  <->  289 HOH   (2161 )  A      O      0.02    2.68  INTRA
  33 ARG   ( 857-)  A      O   <->   35 THR   ( 859-)  A      N      0.02    2.68  INTRA BF
 212 ARG   (1049-)  A      NH1 <->  289 HOH   (2173 )  A      O      0.02    2.68  INTRA BF
 159 HIS   ( 986-)  A      ND1 <->  289 HOH   (2141 )  A      O      0.02    2.68  INTRA
 122 MET   ( 949-)  A      N   <->  184 TYR   (1021-)  A      O      0.02    2.68  INTRA BL
 206 ARG   (1043-)  A    A NH1 <->  289 HOH   (2179 )  A      O      0.01    2.69  INTRA
 214 PRO   (1051-)  A      CA  <->  215 GLU   (1052-)  A      CA     0.01    2.79  INTRA BF
  30 GLU   ( 854-)  A      OE2 <->  256 LYS   (1093-)  A      NZ     0.01    2.69  INTRA
 142 ASN   ( 969-)  A      CB  <->  143 SER   ( 970-)  A      N      0.01    2.69  INTRA B3

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.

 192 MET   (1029-)  A      -7.72
  72 LEU   ( 896-)  A      -6.18
 197 TYR   (1034-)  A      -5.85
 215 GLU   (1052-)  A      -5.82
 188 GLN   (1025-)  A      -5.38
 173 LYS   (1000-)  A      -5.36
  20 ASN   ( 844-)  A      -5.19
  19 ASN   ( 843-)  A      -5.18
 132 ARG   ( 959-)  A      -5.13
  46 ASN   ( 870-)  A      -5.12
 212 ARG   (1049-)  A      -5.04

Warning: Abnormal packing environment for sequential residues

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

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

 191 ASP   (1028-)  A       193 - GLY   1030- ( A)         -5.33

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.

 147 GLY   ( 974-)  A   -3.24
 131 ARG   ( 958-)  A   -2.71
   7 LYS   ( 831-)  A   -2.71
 129 LYS   ( 956-)  A   -2.63

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

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.

 289 HOH   (2204 )  A      O
Marked this atom as acceptor  287 NX1  (2001-) A    BCL18

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.

  20 ASN   ( 844-)  A
  89 ASN   ( 916-)  A
 136 GLN   ( 963-)  A
 177 ASN   (1014-)  A
 185 HIS   (1022-)  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.

  35 THR   ( 859-)  A      N
  66 ARG   ( 890-)  A      NH1
  76 HIS   ( 903-)  A      N
 124 THR   ( 951-)  A      N
 137 TYR   ( 964-)  A      N
 138 TRP   ( 965-)  A      N
 162 TYR   ( 989-)  A      N
 178 GLU   (1015-)  A      N
 183 GLN   (1020-)  A      NE2
 248 THR   (1085-)  A      N

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.

 289 HOH   (2201 )  A      O  0.90  K  5

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.

  63 ASP   ( 887-)  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 :   0.066
  2nd generation packing quality :  -0.889
  Ramachandran plot appearance   :   0.184
  chi-1/chi-2 rotamer normality  :  -0.179
  Backbone conformation          :  -0.639

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.256 (tight)
  Bond angles                    :   0.515 (tight)
  Omega angle restraints         :   1.081
  Side chain planarity           :   0.132 (tight)
  Improper dihedral distribution :   0.572
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   1.012

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.256 (tight)
  Bond angles                    :   0.515 (tight)
  Omega angle restraints         :   1.081
  Side chain planarity           :   0.132 (tight)
  Improper dihedral distribution :   0.572
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   1.012
==============

WHAT IF
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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.