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 pdb1ist.ent

Checks that need to be done early-on in validation

Warning: Triclinic cell with mixed acute and obtuse angles

The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I).

The CRYST1 cell dimensions

    A    =  44.950  B   =  53.110  C    =  32.018
    Alpha=  84.910  Beta=  95.220  Gamma= 108.560

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  44.950  B   =  53.110  C    =  32.018
    Alpha=  84.910  Beta=  95.220  Gamma= 108.560

Dimensions of a reduced cell

    A    =  32.018  B   =  44.950  C    =  53.110
    Alpha=  71.440  Beta=  84.910  Gamma=  84.780

Dimensions of the conventional cell

    A    =  32.018  B   =  44.950  C    =  53.110
    Alpha=  71.440  Beta=  84.910  Gamma=  84.780

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.623
CA-only RMS fit for the two chains : 0.212

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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

Note: Ramachandran plot

Chain identifier: B

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.

  24 ASP   (  25-)  A    0.50
  58 MET   (  59-)  A    0.50

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) :293.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

   4 TYR   (   5-)  A
  22 TYR   (  23-)  A
 165 TYR   (   5-)  B

Warning: Phenylalanine convention problem

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

   5 PHE   (   6-)  A
  19 PHE   (  20-)  A
  33 PHE   (  34-)  A
  43 PHE   (  44-)  A
  50 PHE   (  51-)  A
  57 PHE   (  58-)  A
  64 PHE   (  65-)  A
  80 PHE   (  81-)  A
 109 PHE   ( 110-)  A
 110 PHE   ( 111-)  A
 126 PHE   ( 127-)  A
 180 PHE   (  20-)  B
 194 PHE   (  34-)  B
 204 PHE   (  44-)  B
 211 PHE   (  51-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 131 ASP   ( 132-)  A
 185 ASP   (  25-)  B
 251 ASP   (  91-)  B
 281 ASP   ( 121-)  B
 292 ASP   ( 132-)  B
 295 ASP   ( 135-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 128 GLU   ( 129-)  A
 192 GLU   (  32-)  B

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.

  25 ILE   (  26-)  A      CA   CB    1.62    4.6
  26 VAL   (  27-)  A      CA   CB    1.63    5.0
  49 PRO   (  50-)  A      CA   CB    1.43   -4.9
 187 VAL   (  27-)  B      CA   CB    1.62    4.6
 279 TRP   ( 119-)  B      CG   CD2   1.36   -4.0

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 SER   (   2-)  A      C    CA   CB  101.04   -4.8
   1 SER   (   2-)  A      CA   CB   OG  102.04   -4.5
   2 GLN   (   3-)  A      NE2  CD   OE1 117.08   -5.5
  12 GLN   (  13-)  A      NE2  CD   OE1 118.38   -4.2
  19 PHE   (  20-)  A      C    CA   CB  101.91   -4.3
  19 PHE   (  20-)  A      CA   CB   CG  118.12    4.3
  23 ASN   (  24-)  A      CB   CG   ND2 123.11    4.5
  23 ASN   (  24-)  A      ND2  CG   OD1 114.91   -7.7
  24 ASP   (  25-)  A      CA   CB   CG  119.01    6.4
  28 LYS   (  29-)  A      N    CA   CB  103.05   -4.4
  32 ASN   (  33-)  A      CB   CG   ND2 122.85    4.3
  41 LYS   (  42-)  A      CG   CD   CE  101.97   -4.1
  48 SER   (  49-)  A      CA   CB   OG  119.35    4.1
  51 HIS   (  52-)  A      CB   CG   ND1 129.12    5.0
  53 VAL   (  54-)  A     -C    N    CA  136.70    8.3
  60 GLN   (  61-)  A      NE2  CD   OE1 116.98   -5.6
  66 ALA   (  67-)  A      C    CA   CB  102.88   -5.1
  79 LYS   (  80-)  A      CB   CG   CD  122.64    4.9
  80 PHE   (  81-)  A      CA   CB   CG  118.28    4.5
  84 ASN   (  85-)  A      CB   CG   ND2 123.06    4.4
  89 HIS   (  90-)  A      CB   CG   ND1 129.06    5.0
  89 HIS   (  90-)  A      CB   CG   CD2 122.53   -5.1
 103 ASN   ( 104-)  A     -C    N    CA  129.40    4.3
 103 ASN   ( 104-)  A      ND2  CG   OD1 117.09   -5.5
 105 ASN   ( 106-)  A      CB   CG   ND2 124.10    5.1
And so on for a total of 74 lines.

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.

 128 GLU   ( 129-)  A
 131 ASP   ( 132-)  A
 185 ASP   (  25-)  B
 192 GLU   (  32-)  B
 251 ASP   (  91-)  B
 281 ASP   ( 121-)  B
 292 ASP   ( 132-)  B
 295 ASP   ( 135-)  B

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

  13 PRO   (  14-)  A    4.52

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.

  52 ARG   (  53-)  A    -2.6
  57 PHE   (  58-)  A    -2.4
 218 PHE   (  58-)  B    -2.4
 252 ARG   (  92-)  B    -2.3
  58 MET   (  59-)  A    -2.3
 128 GLU   ( 129-)  A    -2.3
  20 LYS   (  21-)  A    -2.2
 210 PRO   (  50-)  B    -2.2
 106 GLY   ( 107-)  A    -2.1
 219 MET   (  59-)  B    -2.1
  26 VAL   (  27-)  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.

   5 PHE   (   6-)  A  omega poor
  11 GLY   (  12-)  A  Poor phi/psi
  22 TYR   (  23-)  A  Poor phi/psi
  49 PRO   (  50-)  A  omega poor
  56 ASP   (  57-)  A  Poor phi/psi
  57 PHE   (  58-)  A  Poor phi/psi
 103 ASN   ( 104-)  A  Poor phi/psi
 109 PHE   ( 110-)  A  omega poor
 210 PRO   (  50-)  B  omega poor
 217 ASP   (  57-)  B  Poor phi/psi
 218 PHE   (  58-)  B  Poor phi/psi
 264 ASN   ( 104-)  B  Poor phi/psi
 270 PHE   ( 110-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -2.488

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 ALA   (  10-)  A      0
  13 PRO   (  14-)  A      0
  14 ILE   (  15-)  A      0
  22 TYR   (  23-)  A      0
  23 ASN   (  24-)  A      0
  25 ILE   (  26-)  A      0
  26 VAL   (  27-)  A      0
  40 GLU   (  41-)  A      0
  41 LYS   (  42-)  A      0
  43 PHE   (  44-)  A      0
  45 TYR   (  46-)  A      0
  46 ALA   (  47-)  A      0
  50 PHE   (  51-)  A      0
  51 HIS   (  52-)  A      0
  55 PRO   (  56-)  A      0
  57 PHE   (  58-)  A      0
  58 MET   (  59-)  A      0
  65 THR   (  66-)  A      0
  66 ALA   (  67-)  A      0
  68 ASN   (  69-)  A      0
  70 THR   (  71-)  A      0
  76 TYR   (  77-)  A      0
  83 GLU   (  84-)  A      0
  84 ASN   (  85-)  A      0
  85 PHE   (  86-)  A      0
And so on for a total of 155 lines.

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]

 102 PRO   ( 103-)  A    0.48 HIGH

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].

  13 PRO   (  14-)  A  -112.4 envelop C-gamma (-108 degrees)
 102 PRO   ( 103-)  A  -113.6 envelop C-gamma (-108 degrees)
 216 PRO   (  56-)  B  -128.4 half-chair C-delta/C-gamma (-126 degrees)
 242 PRO   (  82-)  B  -112.2 envelop C-gamma (-108 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.

  91 ARG   (  92-)  A      NH2 <->  279 TRP   ( 119-)  B      CH2    0.29    2.81  INTRA BF
  49 PRO   (  50-)  A      CB  <->  152 ARG   ( 153-)  A      NH2    0.21    2.89  INTRA BF
  52 ARG   (  53-)  A      NH2 <->  325 HOH   ( 205 )  A      O      0.16    2.54  INTRA BF
  97 MET   (  98-)  A      SD  <->  126 PHE   ( 127-)  A      CE1    0.15    3.25  INTRA BL
 240 LYS   (  80-)  B      NZ  <->  265 THR   ( 105-)  B      O      0.10    2.60  INTRA
 258 MET   (  98-)  B      SD  <->  287 PHE   ( 127-)  B      CE1    0.09    3.31  INTRA BL
  20 LYS   (  21-)  A      NZ  <->  128 GLU   ( 129-)  A      CG     0.09    3.01  INTRA
  52 ARG   (  53-)  A      O   <->   60 GLN   (  61-)  A      N      0.09    2.61  INTRA
  91 ARG   (  92-)  A      NE  <->  128 GLU   ( 129-)  A      OE1    0.08    2.62  INTRA BF
 210 PRO   (  50-)  B      CB  <->  313 ARG   ( 153-)  B      NH1    0.07    3.03  INTRA
  28 LYS   (  29-)  A      CE  <->   80 PHE   (  81-)  A      CD2    0.06    3.14  INTRA
  20 LYS   (  21-)  A      CE  <->  128 GLU   ( 129-)  A      CB     0.06    3.14  INTRA
  20 LYS   (  21-)  A      NZ  <->  128 GLU   ( 129-)  A      CB     0.06    3.04  INTRA BL
  97 MET   (  98-)  A      SD  <->  325 HOH   ( 229 )  A      O      0.04    2.96  INTRA
 208 GLY   (  48-)  B      N   <->  316 VAL   ( 156-)  B      O      0.04    2.66  INTRA
 213 ARG   (  53-)  B      O   <->  221 GLN   (  61-)  B      N      0.03    2.67  INTRA
 212 HIS   (  52-)  B      ND1 <->  326 HOH   ( 177 )  B      O      0.03    2.67  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 252 ARG   (  92-)  B      -6.13
 150 LYS   ( 151-)  A      -5.70
  91 ARG   (  92-)  A      -5.53
  79 LYS   (  80-)  A      -5.32
 240 LYS   (  80-)  B      -5.27
 311 LYS   ( 151-)  B      -5.03

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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.

  84 ASN   (  85-)  A   -2.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 325 HOH   ( 176 )  A      O     35.95  -21.98   22.57
 325 HOH   ( 204 )  A      O     18.92  -24.92    3.01
 325 HOH   ( 225 )  A      O     35.19  -24.75   22.22
 326 HOH   ( 166 )  B      O     12.29   15.69   18.01
 326 HOH   ( 168 )  B      O     39.27   26.97   31.02
 326 HOH   ( 197 )  B      O     13.01   25.68   36.05

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.

 326 HOH   ( 195 )  B      O
 326 HOH   ( 212 )  B      O

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.

  34 ARG   (  35-)  A      NE
  43 PHE   (  44-)  A      N
  73 LYS   (  74-)  A      N
  84 ASN   (  85-)  A      N
  85 PHE   (  86-)  A      N
  91 ARG   (  92-)  A      N
 114 VAL   ( 115-)  A      N
 118 TRP   ( 119-)  A      N
 137 LYS   ( 138-)  A      NZ
 151 ALA   ( 152-)  A      N
 158 SER   ( 159-)  A      N
 162 SER   (   2-)  B      OG
 204 PHE   (  44-)  B      N
 235 SER   (  75-)  B      N
 238 GLY   (  78-)  B      N
 245 ASN   (  85-)  B      N
 252 ARG   (  92-)  B      N
 252 ARG   (  92-)  B      NE
 275 VAL   ( 115-)  B      N
 279 TRP   ( 119-)  B      N
 279 TRP   ( 119-)  B      NE1
 312 ALA   ( 152-)  B      N
 319 SER   ( 159-)  B      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 128 GLU   ( 129-)  A      OE2
 184 ASN   (  24-)  B      OD1

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.

 128 GLU   ( 129-)  A   H-bonding suggests Gln

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 :  -0.965
  Ramachandran plot appearance   :  -0.881
  chi-1/chi-2 rotamer normality  :  -2.488
  Backbone conformation          :  -0.309

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.882
  Bond angles                    :   1.545
  Omega angle restraints         :   0.926
  Side chain planarity           :   0.778
  Improper dihedral distribution :   1.355
  B-factor distribution          :   0.912
  Inside/Outside distribution    :   0.910

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.882
  Bond angles                    :   1.545
  Omega angle restraints         :   0.926
  Side chain planarity           :   0.778
  Improper dihedral distribution :   1.355
  B-factor distribution          :   0.912
  Inside/Outside distribution    :   0.910
==============

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.