WHAT IF Check report

This file was created 2012-01-04 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 pdb1mtc.ent

Checks that need to be done early-on in validation

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 : 0.887
CA-only RMS fit for the two chains : 0.435

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

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.

 435 GPR   (5218-)  A  -
 436 GPR   (6218-)  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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   2 MET   (   2-)  A    High
  34 MET   (  34-)  A    High
 108 MET   ( 108-)  A    High
 112 MET   ( 112-)  A    High
 325 MET   ( 108-)  B    High
 329 MET   ( 112-)  B    High

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) :143.000

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: Phenylalanine convention problem

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

  56 PHE   (  56-)  A
 169 PHE   ( 169-)  A
 273 PHE   (  56-)  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.

 342 GLU   ( 125-)  B

Geometric checks

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.

  10 ARG   (  10-)  A      N    CA   CB  103.28   -4.2
  11 GLY   (  11-)  A     -O   -C    N   115.73   -4.5
  17 ARG   (  17-)  A      CG   CD   NE  102.35   -4.8
  26 SER   (  26-)  A      CA   C    O   113.86   -4.1
  26 SER   (  26-)  A      N    CA   CB  121.78    6.6
  27 TYR   (  27-)  A     -O   -C    N   129.89    4.3
  30 LYS   (  30-)  A     -C    N    CA  129.57    4.4
  30 LYS   (  30-)  A      CA   CB   CG  105.39   -4.4
  31 ARG   (  31-)  A      CD   NE   CZ  132.65    6.1
  36 ASP   (  36-)  A      CA   CB   CG  120.52    7.9
  37 ALA   (  37-)  A     -O   -C    N   130.07    4.4
  37 ALA   (  37-)  A     -C    N    CA  130.15    4.7
  39 ASP   (  39-)  A      CA   CB   CG  105.74   -6.9
  42 ARG   (  42-)  A      CD   NE   CZ  132.94    6.2
  44 GLN   (  44-)  A      CA   C    O   128.86    4.7
  44 GLN   (  44-)  A      CG   CD   NE2 123.64    4.8
  44 GLN   (  44-)  A      NE2  CD   OE1 115.27   -7.3
  45 TRP   (  45-)  A     -O   -C    N   115.70   -4.6
  45 TRP   (  45-)  A      CA   C    O   132.28    6.8
  48 GLU   (  48-)  A      CB   CG   CD  104.61   -4.7
  49 LYS   (  49-)  A      CA   C    O   111.49   -5.5
  50 PHE   (  50-)  A      CA   CB   CG  101.96  -11.8
  55 ASP   (  55-)  A      CA   CB   CG  108.09   -4.5
  56 PHE   (  56-)  A     -C    N    CA  129.57    4.4
  56 PHE   (  56-)  A      CA   CB   CG  118.07    4.3
And so on for a total of 179 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.

 342 GLU   ( 125-)  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.

 347 ILE   ( 130-)  B    4.23

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.

 257 TYR   (  40-)  B    -3.1
  38 PRO   (  38-)  A    -2.8
 191 LYS   ( 191-)  A    -2.6
 215 SER   ( 215-)  A    -2.6
 432 SER   ( 215-)  B    -2.6
 170 GLU   ( 170-)  A    -2.5
  30 LYS   (  30-)  A    -2.3
 368 LYS   ( 151-)  B    -2.2
 391 LEU   ( 174-)  B    -2.2
  14 HIS   (  14-)  A    -2.2
  57 PRO   (  57-)  A    -2.2
 387 GLU   ( 170-)  B    -2.2
 174 LEU   ( 174-)  A    -2.2
 228 GLY   (  11-)  B    -2.1
 247 LYS   (  30-)  B    -2.1
 330 LEU   ( 113-)  B    -2.1
 256 ASP   (  39-)  B    -2.1
 366 GLY   ( 149-)  B    -2.1
 251 MET   (  34-)  B    -2.1
 149 GLY   ( 149-)  A    -2.1
  11 GLY   (  11-)  A    -2.0
  42 ARG   (  42-)  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.

  24 ASP   (  24-)  A  Poor phi/psi
  37 ALA   (  37-)  A  PRO omega poor
  59 LEU   (  59-)  A  PRO omega poor
  71 GLN   (  71-)  A  Poor phi/psi
 205 THR   ( 205-)  A  PRO omega poor
 215 SER   ( 215-)  A  Poor phi/psi
 228 GLY   (  11-)  B  Poor phi/psi
 241 ASP   (  24-)  B  Poor phi/psi
 254 ALA   (  37-)  B  PRO omega poor
 257 TYR   (  40-)  B  Poor phi/psi
 276 LEU   (  59-)  B  PRO omega poor
 288 GLN   (  71-)  B  Poor phi/psi
 301 HIS   (  84-)  B  Poor phi/psi
 422 THR   ( 205-)  B  PRO omega poor
 426 SER   ( 209-)  B  Poor phi/psi
 428 LEU   ( 211-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.327

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

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

chi-1/chi-2 correlation Z-score : -3.327

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!

   6 TYR   (   6-)  A      0
   7 TRP   (   7-)  A      0
   8 ASN   (   8-)  A      0
   9 VAL   (   9-)  A      0
  10 ARG   (  10-)  A      0
  12 LEU   (  12-)  A      0
  13 THR   (  13-)  A      0
  23 THR   (  23-)  A      0
  36 ASP   (  36-)  A      0
  37 ALA   (  37-)  A      0
  39 ASP   (  39-)  A      0
  40 TYR   (  40-)  A      0
  41 ASP   (  41-)  A      0
  42 ARG   (  42-)  A      0
  55 ASP   (  55-)  A      0
  57 PRO   (  57-)  A      0
  58 ASN   (  58-)  A      0
  59 LEU   (  59-)  A      0
  64 ASP   (  64-)  A      0
  66 SER   (  66-)  A      0
  70 THR   (  70-)  A      0
  71 GLN   (  71-)  A      0
  84 HIS   (  84-)  A      0
  85 LEU   (  85-)  A      0
  88 GLU   (  88-)  A      0
And so on for a total of 148 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 3.332

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]

  57 PRO   (  57-)  A    0.49 HIGH
 124 PRO   ( 124-)  A    0.15 LOW
 131 PRO   ( 131-)  A    0.45 HIGH
 178 PRO   ( 178-)  A    0.49 HIGH
 232 PRO   (  15-)  B    0.48 HIGH
 348 PRO   ( 131-)  B    0.20 LOW
 362 PRO   ( 145-)  B    0.16 LOW
 395 PRO   ( 178-)  B    0.49 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].

   1 PRO   (   1-)  A  -116.6 envelop C-gamma (-108 degrees)
  38 PRO   (  38-)  A   -58.9 half-chair C-beta/C-alpha (-54 degrees)
 255 PRO   (  38-)  B    23.8 half-chair N/C-delta (18 degrees)
 274 PRO   (  57-)  B   104.3 envelop C-beta (108 degrees)
 423 PRO   ( 206-)  B   -53.0 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  45 TRP   (  45-)  A      NE1 <->  435 GPR   (5218-)  A      O32    0.22    2.48  INTRA BL
  35 GLY   (  35-)  A      N   <->   41 ASP   (  41-)  A      O      0.22    2.48  INTRA
 186 ARG   ( 186-)  A      NH1 <->  437 HOH   ( 435 )  A      O      0.21    2.49  INTRA
 305 GLU   (  88-)  B      N   <->  309 GLU   (  92-)  B      OE1    0.21    2.49  INTRA
 253 ASP   (  36-)  B      O   <->  257 TYR   (  40-)  B      N      0.21    2.49  INTRA BF
 331 CYS   ( 114-)  B      SG  <->  431 TRP   ( 214-)  B      CB     0.21    3.19  INTRA BF
 294 ARG   (  77-)  B      NE  <->  317 GLU   ( 100-)  B      OE1    0.21    2.49  INTRA BL
  71 GLN   (  71-)  A      NE2 <->  322 ASP   ( 105-)  B      OD2    0.20    2.50  INTRA BL
 174 LEU   ( 174-)  A      O   <->  181 LYS   ( 181-)  A      NZ     0.20    2.50  INTRA BF
   2 MET   (   2-)  A      O   <->   28 GLU   (  28-)  A      N      0.20    2.50  INTRA BL
 324 ARG   ( 107-)  B      NE  <->  438 HOH   ( 362 )  B      O      0.20    2.50  INTRA
 251 MET   (  34-)  B      O   <->  427 LYS   ( 210-)  B      NZ     0.20    2.50  INTRA BF
 148 ALA   ( 148-)  A      N   <->  437 HOH   ( 428 )  A      O      0.20    2.50  INTRA
 389 LYS   ( 172-)  B      NZ  <->  392 ASP   ( 175-)  B      OD2    0.20    2.50  INTRA BF
  95 ARG   (  95-)  A      NH2 <->  147 PHE   ( 147-)  A      O      0.20    2.50  INTRA BL
 325 MET   ( 108-)  B      O   <->  329 MET   ( 112-)  B      N      0.20    2.50  INTRA
 276 LEU   (  59-)  B      O   <->  436 GPR   (6218-)  B      N2     0.20    2.50  INTRA BL
 424 ILE   ( 207-)  B      N   <->  432 SER   ( 215-)  B      OG     0.20    2.50  INTRA BF
  36 ASP   (  36-)  A      O   <->   40 TYR   (  40-)  A      N      0.20    2.50  INTRA
 125 GLU   ( 125-)  A      OE1 <->  128 LYS   ( 128-)  A      NZ     0.19    2.51  INTRA BF
 132 GLU   ( 132-)  A      N   <->  437 HOH   ( 438 )  A      O      0.19    2.51  INTRA
  24 ASP   (  24-)  A      OD2 <->  192 LYS   ( 192-)  A      NZ     0.19    2.51  INTRA BF
 252 GLY   (  35-)  B      N   <->  258 ASP   (  41-)  B      O      0.19    2.51  INTRA BF
 297 ALA   (  80-)  B      O   <->  302 LEU   (  85-)  B      N      0.17    2.53  INTRA BL
 219 MET   (   2-)  B      O   <->  245 GLU   (  28-)  B      N      0.17    2.53  INTRA BL
And so on for a total of 146 lines.

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.

 360 LYS   ( 143-)  B      -5.88
 143 LYS   ( 143-)  A      -5.57
 144 ARG   ( 144-)  A      -5.11
 267 PHE   (  50-)  B      -5.05

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

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

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.

 437 HOH   ( 340 )  A      O
 437 HOH   ( 430 )  A      O
 437 HOH   ( 446 )  A      O
 437 HOH   ( 471 )  A      O
 438 HOH   ( 334 )  B      O
 438 HOH   ( 354 )  B      O
 438 HOH   ( 483 )  B      O

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.

 122 GLN   ( 122-)  A
 225 ASN   (   8-)  B
 300 HIS   (  83-)  B

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.

   6 TYR   (   6-)  A      OH
   7 TRP   (   7-)  A      N
   9 VAL   (   9-)  A      N
  13 THR   (  13-)  A      OG1
  14 HIS   (  14-)  A      NE2
  33 ALA   (  33-)  A      N
  45 TRP   (  45-)  A      NE1
  58 ASN   (  58-)  A      N
  70 THR   (  70-)  A      N
  72 SER   (  72-)  A      N
  77 ARG   (  77-)  A      NH2
  81 ARG   (  81-)  A      NH2
 120 GLU   ( 120-)  A      N
 151 LYS   ( 151-)  A      N
 203 LEU   ( 203-)  A      N
 209 SER   ( 209-)  A      N
 214 TRP   ( 214-)  A      N
 217 LYS   ( 217-)  A      N
 223 TYR   (   6-)  B      OH
 224 TRP   (   7-)  B      N
 224 TRP   (   7-)  B      NE1
 226 VAL   (   9-)  B      N
 230 THR   (  13-)  B      OG1
 231 HIS   (  14-)  B      N
 254 ALA   (  37-)  B      N
 258 ASP   (  41-)  B      N
 262 TRP   (  45-)  B      NE1
 275 ASN   (  58-)  B      N
 282 GLY   (  65-)  B      N
 289 SER   (  72-)  B      N
 299 LYS   (  82-)  B      NZ
 303 CYS   (  86-)  B      N
 333 ASN   ( 116-)  B      N
 335 ASP   ( 118-)  B      N
 337 GLU   ( 120-)  B      N
 369 VAL   ( 152-)  B      N
 384 HIS   ( 167-)  B      ND1
 389 LYS   ( 172-)  B      N
 426 SER   ( 209-)  B      OG
 427 LYS   ( 210-)  B      N
 428 LEU   ( 211-)  B      N
 429 ALA   ( 212-)  B      N

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.

  39 ASP   (  39-)  A   H-bonding suggests Asn; but Alt-Rotamer
 182 ASP   ( 182-)  A   H-bonding suggests Asn
 256 ASP   (  39-)  B   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.218
  2nd generation packing quality :  -1.350
  Ramachandran plot appearance   :  -2.317
  chi-1/chi-2 rotamer normality  :  -3.327 (poor)
  Backbone conformation          :  -0.383

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.538 (tight)
  Bond angles                    :   1.742
  Omega angle restraints         :   0.606 (tight)
  Side chain planarity           :   0.190 (tight)
  Improper dihedral distribution :   0.691
  B-factor distribution          :   1.137
  Inside/Outside distribution    :   0.987

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.538 (tight)
  Bond angles                    :   1.742
  Omega angle restraints         :   0.606 (tight)
  Side chain planarity           :   0.190 (tight)
  Improper dihedral distribution :   0.691
  B-factor distribution          :   1.137
  Inside/Outside distribution    :   0.987
==============

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.