WHAT IF Check report

This file was created 2012-01-25 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 pdb2ipk.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 71184.719
Volume of the Unit Cell V= 3102410.8
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.843
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.730

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.

 616 ACE   ( 305-)  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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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.

   1 GLU   (   3-)  A    High
   2 GLU   (   4-)  A    High
  44 GLU   (  46-)  A    High
  45 GLU   (  47-)  A    High
  53 GLU   (  55-)  A    High
  96 GLU   (  98-)  A    High
  99 GLU   ( 101-)  A    High
 106 PHE   ( 108-)  A    High
 124 LYS   ( 126-)  A    High
 139 GLU   ( 141-)  A    High
 156 GLU   ( 158-)  A    High
 179 ASP   ( 181-)  A    High
 180 GLY   (   1-)  B    High
 198 ASN   (  19-)  B    High
 214 GLU   (  35-)  B    High
 245 ASP   (  66-)  B    High
 249 GLN   (  70-)  B    High
 266 GLU   (  87-)  B    High
 287 PRO   ( 108-)  B    High
 288 LEU   ( 109-)  B    High
 289 GLN   ( 110-)  B    High
 290 HIS   ( 111-)  B    High
 291 HIS   ( 112-)  B    High
 307 GLU   ( 128-)  B    High
 309 ARG   ( 130-)  B    High
 315 GLN   ( 136-)  B    High
 317 GLU   ( 138-)  B    High
 318 LYS   ( 139-)  B    High
 341 GLU   ( 162-)  B    High
 343 VAL   ( 164-)  B    High
 345 ARG   ( 166-)  B    High
 346 SER   ( 167-)  B    High
 379 LYS   ( 315-)  C    High
 383 GLU   (   1-)  D    High
 389 MET   (   7-)  D    High
 391 ASP   (   9-)  D    High
 392 ASP   (  10-)  D    High
 438 LYS   (  56-)  D    High
 441 LYS   (  59-)  D    High
 475 CYS   (  93-)  D    High
 480 LYS   (  98-)  D    High
 485 CYS   ( 110-)  D    High
 494 GLU   ( 119-)  D    High
 499 ASP   ( 124-)  D    High
 500 ASN   ( 125-)  D    High
 501 GLY   ( 126-)  D    High
 502 ASN   ( 127-)  D    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) : 95.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

  48 ARG   (  50-)  A
 250 ARG   (  71-)  B
 515 ARG   ( 140-)  D

Warning: Tyrosine convention problem

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

  11 TYR   (  13-)  A
 148 TYR   ( 150-)  A
 410 TYR   (  28-)  D
 414 TYR   (  32-)  D
 459 TYR   (  77-)  D
 467 TYR   (  85-)  D
 472 TYR   (  90-)  D
 487 TYR   ( 112-)  D
 549 TYR   ( 174-)  D
 556 TYR   ( 181-)  D
 560 TYR   ( 185-)  D
 573 TYR   ( 198-)  D
 592 TYR   ( 217-)  D

Warning: Phenylalanine convention problem

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

 110 PHE   ( 112-)  A
 192 PHE   (  13-)  B
 426 PHE   (  44-)  D
 427 PHE   (  45-)  D
 498 PHE   ( 123-)  D
 571 PHE   ( 196-)  D

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.

 169 ASP   ( 171-)  A
 387 ASP   (   5-)  D
 391 ASP   (   9-)  D
 392 ASP   (  10-)  D
 411 ASP   (  29-)  D
 424 ASP   (  42-)  D
 437 ASP   (  55-)  D
 499 ASP   ( 124-)  D
 535 ASP   ( 160-)  D

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.

  28 GLU   (  30-)  A
  69 GLU   (  71-)  A
  96 GLU   (  98-)  A
 164 GLU   ( 166-)  A
 177 GLU   ( 179-)  A
 449 GLU   (  67-)  D
 494 GLU   ( 119-)  D
 533 GLU   ( 158-)  D

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.

   7 GLN   (   9-)  A      N    CA   C    99.74   -4.1
  86 GLU   (  88-)  A      N    CA   C    97.42   -4.9
 343 VAL   ( 164-)  B      N    CA   C    98.69   -4.5

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.

  28 GLU   (  30-)  A
  48 ARG   (  50-)  A
  69 GLU   (  71-)  A
  96 GLU   (  98-)  A
 164 GLU   ( 166-)  A
 169 ASP   ( 171-)  A
 177 GLU   ( 179-)  A
 250 ARG   (  71-)  B
 387 ASP   (   5-)  D
 391 ASP   (   9-)  D
 392 ASP   (  10-)  D
 411 ASP   (  29-)  D
 424 ASP   (  42-)  D
 437 ASP   (  55-)  D
 449 GLU   (  67-)  D
 494 GLU   ( 119-)  D
 499 ASP   ( 124-)  D
 515 ARG   ( 140-)  D
 533 GLU   ( 158-)  D
 535 ASP   ( 160-)  D

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.

  86 GLU   (  88-)  A    5.19
 265 GLY   (  86-)  B    4.41
 343 VAL   ( 164-)  B    4.38

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.

 268 PHE   (  89-)  B    -2.7
 111 THR   ( 113-)  A    -2.7
  14 PRO   (  16-)  A    -2.6
 390 PRO   (   8-)  D    -2.6
 336 THR   ( 157-)  B    -2.4
 287 PRO   ( 108-)  B    -2.4
 151 PHE   ( 153-)  A    -2.3
 217 VAL   (  38-)  B    -2.1
 115 VAL   ( 117-)  A    -2.1
 520 PHE   ( 145-)  D    -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.

  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  37 LYS   (  39-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  93 SER   (  95-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 122 ASN   ( 124-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 302 TYR   ( 123-)  B  PRO omega poor
 313 ASN   ( 134-)  B  Poor phi/psi
 332 TRP   ( 153-)  B  Poor phi/psi
 414 TYR   (  32-)  D  Poor phi/psi
 439 LYS   (  57-)  D  Poor phi/psi
 474 ASN   (  92-)  D  Poor phi/psi
 477 PHE   (  95-)  D  Poor phi/psi
 513 ASN   ( 138-)  D  Poor phi/psi
 514 LYS   ( 139-)  D  Poor phi/psi
 553 SER   ( 178-)  D  Poor phi/psi
 595 ASN   ( 220-)  D  Poor phi/psi
 613 ASN   ( 238-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.747

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.

 586 SER   ( 211-)  D    0.38

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 HIS   (   5-)  A      0
   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  16 GLN   (  18-)  A      0
  17 SER   (  19-)  A      0
  24 PHE   (  26-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  37 LYS   (  39-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  92 ASN   (  94-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 101 ASN   ( 103-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 113 PRO   ( 115-)  A      0
 114 VAL   ( 116-)  A      0
 121 ARG   ( 123-)  A      0
And so on for a total of 255 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 : 1.581

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 304 GLY   ( 125-)  B   1.51   32

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.

 497 HIS   ( 122-)  D      NE2 <->  622 HOH   ( 407 )  D      O      0.49    2.21  INTRA BF
 268 PHE   (  89-)  B      CE2 <->  372 4DP   ( 308-)  C      CAC    0.48    2.72  INTRA BF
 421 LYS   (  39-)  D      NZ  <->  461 ASP   (  79-)  D      C      0.37    2.73  INTRA BF
 190 LEU   (  11-)  B      CD2 <->  377 THR   ( 313-)  C      CG2    0.34    2.86  INTRA BF
 200 THR   (  21-)  B      O   <->  259 ARG   (  80-)  B      NH1    0.32    2.38  INTRA BF
 493 HIS   ( 118-)  D      CD2 <->  622 HOH   ( 407 )  D      O      0.31    2.49  INTRA BF
 421 LYS   (  39-)  D      NZ  <->  461 ASP   (  79-)  D      CA     0.28    2.82  INTRA BF
 162 ARG   ( 164-)  A      NH1 <->  164 GLU   ( 166-)  A      OE2    0.20    2.50  INTRA BF
 504 GLN   ( 129-)  D      NE2 <->  601 LYS   ( 226-)  D      CB     0.20    2.90  INTRA BF
 269 THR   (  90-)  B      CG2 <->  372 4DP   ( 308-)  C      CAD    0.20    3.00  INTRA BF
 179 ASP   ( 181-)  A      O   <->  284 LYS   ( 105-)  B      NZ     0.19    2.51  INTRA BF
 475 CYS   (  93-)  D      SG  <->  485 CYS   ( 110-)  D      N      0.19    3.11  INTRA BF
 204 ARG   (  25-)  B      NH2 <->  220 ASP   (  41-)  B      OD2    0.18    2.52  INTRA BF
 612 LYS   ( 237-)  D      C   <->  613 ASN   ( 238-)  D      ND2    0.17    2.83  INTRA BF
 421 LYS   (  39-)  D      NZ  <->  461 ASP   (  79-)  D      O      0.17    2.53  INTRA BF
 389 MET   (   7-)  D      O   <->  392 ASP   (  10-)  D      N      0.17    2.53  INTRA BF
   1 GLU   (   3-)  A      OE2 <->  195 HIS   (  16-)  B      ND1    0.17    2.53  INTRA BF
 207 GLU   (  28-)  B      OE1 <->  250 ARG   (  71-)  B      NE     0.16    2.54  INTRA BF
  60 ASN   (  62-)  A      ND2 <->  377 THR   ( 313-)  C      CG2    0.16    2.94  INTRA BF
 356 HIS   ( 177-)  B      ND1 <->  358 SER   ( 179-)  B      N      0.15    2.85  INTRA BL
 141 HIS   ( 143-)  A      CD2 <->  191 LYS   (  12-)  B      NZ     0.15    2.95  INTRA BL
 475 CYS   (  93-)  D      SG  <->  484 THR   ( 109-)  D      C      0.15    3.25  INTRA BF
  90 LEU   (  92-)  A      O   <->  104 ILE   ( 106-)  A      N      0.15    2.55  INTRA BL
 283 SER   ( 104-)  B      O   <->  286 GLN   ( 107-)  B      NE2    0.14    2.56  INTRA BF
 225 GLU   (  46-)  B      OE2 <->  227 ARG   (  48-)  B      NE     0.13    2.57  INTRA BF
And so on for a total of 86 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 289 GLN   ( 110-)  B      -6.35
  98 ARG   ( 100-)  A      -6.12
 612 LYS   ( 237-)  D      -5.86
 345 ARG   ( 166-)  B      -5.82
 368 ARG   ( 189-)  B      -5.65
 613 ASN   ( 238-)  D      -5.49
 451 LEU   (  69-)  D      -5.33
 476 TYR   (  94-)  D      -5.18
 318 LYS   ( 139-)  B      -5.11
 273 ARG   (  94-)  B      -5.11

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.

 612 LYS   ( 237-)  D       614 - GLY    239- ( D)         -5.15

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: 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: C

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: D

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 147 HIS   ( 149-)  A
 175 HIS   ( 177-)  A
 189 GLN   (  10-)  B
 375 GLN   ( 311-)  C
 376 ASN   ( 312-)  C
 470 ASN   (  88-)  D
 474 ASN   (  92-)  D
 493 HIS   ( 118-)  D
 496 ASN   ( 121-)  D
 504 GLN   ( 129-)  D
 516 ASN   ( 141-)  D
 532 GLN   ( 157-)  D
 608 HIS   ( 233-)  D

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.

  17 SER   (  19-)  A      OG
  43 LEU   (  45-)  A      N
  93 SER   (  95-)  A      N
 119 TRP   ( 121-)  A      NE1
 128 THR   ( 130-)  A      N
 185 ARG   (   6-)  B      NH2
 208 ARG   (  29-)  B      NE
 225 GLU   (  46-)  B      N
 231 GLU   (  52-)  B      N
 254 VAL   (  75-)  B      N
 272 ARG   (  93-)  B      NH1
 333 THR   ( 154-)  B      N
 361 SER   ( 182-)  B      N
 375 GLN   ( 311-)  C      NE2
 401 GLY   (  19-)  D      N
 429 TRP   (  47-)  D      N
 440 LEU   (  58-)  D      N
 452 ASN   (  70-)  D      N
 487 TYR   ( 112-)  D      OH
 549 TYR   ( 174-)  D      N
 570 THR   ( 195-)  D      N
 594 ASP   ( 219-)  D      N
 611 THR   ( 236-)  D      OG1

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.

   9 GLU   (  11-)  A      OE2
  64 ASP   (  66-)  A      OD2
 141 HIS   ( 143-)  A      NE2
 291 HIS   ( 112-)  B      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 619 HOH   ( 207 )  A      O  0.89  K  4
 619 HOH   ( 212 )  A      O  1.02  K  5
 619 HOH   ( 227 )  A      O  0.91  K  4
 619 HOH   ( 314 )  A      O  1.00  K  4
 622 HOH   ( 256 )  D      O  0.90  K  5
 622 HOH   ( 282 )  D      O  0.85  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.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn
 160 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 170 GLU   ( 172-)  A   H-bonding suggests Gln
 179 ASP   ( 181-)  A   H-bonding suggests Asn
 424 ASP   (  42-)  D   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 :  -0.050
  2nd generation packing quality :  -1.358
  Ramachandran plot appearance   :  -0.752
  chi-1/chi-2 rotamer normality  :  -0.747
  Backbone conformation          :  -0.365

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.315 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   0.287 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   0.937
  Inside/Outside distribution    :   1.047

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.315 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   0.287 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.614
  B-factor distribution          :   0.937
  Inside/Outside distribution    :   1.047
==============

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Quality Control
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    M.Nayal and E.Di Cera,
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      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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