WHAT IF Check report

This file was created 2011-12-29 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 pdb1klg.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: 70661.148
Volume of the Unit Cell V= 3146894.5
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.948
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.860

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: 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'.

 380 GLU   (   1-)  D      CG
 380 GLU   (   1-)  D      CD
 380 GLU   (   1-)  D      OE1
 380 GLU   (   1-)  D      OE2

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

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.

  47 ARG   (  50-)  A
 200 ARG   (  23-)  B
 248 ARG   (  71-)  B

Warning: Tyrosine convention problem

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

  10 TYR   (  13-)  A
 147 TYR   ( 150-)  A
 279 TYR   ( 102-)  B
 407 TYR   (  28-)  D
 464 TYR   (  85-)  D
 469 TYR   (  90-)  D
 545 TYR   ( 174-)  D
 552 TYR   ( 181-)  D
 569 TYR   ( 198-)  D
 588 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.

 105 PHE   ( 108-)  A
 109 PHE   ( 112-)  A
 190 PHE   (  13-)  B
 423 PHE   (  44-)  D
 424 PHE   (  45-)  D
 494 PHE   ( 123-)  D
 567 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.

 168 ASP   ( 171-)  A
 384 ASP   (   5-)  D
 389 ASP   (  10-)  D
 408 ASP   (  29-)  D
 421 ASP   (  42-)  D
 434 ASP   (  55-)  D
 441 ASP   (  62-)  D
 531 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.

  27 GLU   (  30-)  A
  95 GLU   (  98-)  A
 155 GLU   ( 158-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 246 GLU   (  69-)  B
 366 GLU   (  24-)  C
 446 GLU   (  67-)  D
 490 GLU   ( 119-)  D
 529 GLU   ( 158-)  D

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.

 370 ILE   (  28-)  C      N   -C     1.56   11.3
 371 LEU   (  29-)  C      N   -C     1.16   -8.7

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.

  73 ARG   (  76-)  A      CB   CG   CD  105.67   -4.2
  85 GLU   (  88-)  A      N    CA   C    99.33   -4.2
 160 CYS   ( 163-)  A      N    CA   C    98.48   -4.5
 338 VAL   ( 164-)  B      N    CA   C    99.79   -4.1
 371 LEU   (  29-)  C     -O   -C    N   106.66  -10.2
 371 LEU   (  29-)  C     -CA  -C    N   132.24    8.0
 371 LEU   (  29-)  C     -C    N    CA  133.96    6.8
 460 VAL   (  81-)  D      N    CA   C    99.69   -4.1

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.

  27 GLU   (  30-)  A
  47 ARG   (  50-)  A
  95 GLU   (  98-)  A
 155 GLU   ( 158-)  A
 168 ASP   ( 171-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 200 ARG   (  23-)  B
 246 GLU   (  69-)  B
 248 ARG   (  71-)  B
 366 GLU   (  24-)  C
 384 ASP   (   5-)  D
 389 ASP   (  10-)  D
 408 ASP   (  29-)  D
 421 ASP   (  42-)  D
 434 ASP   (  55-)  D
 441 ASP   (  62-)  D
 446 GLU   (  67-)  D
 490 GLU   ( 119-)  D
 529 GLU   ( 158-)  D
 531 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.

 160 CYS   ( 163-)  A    4.69
 141 LEU   ( 144-)  A    4.43
 527 ALA   ( 156-)  D    4.41
  85 GLU   (  88-)  A    4.36

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.

  13 PRO   (  16-)  A    -2.8
 110 THR   ( 113-)  A    -2.6
 301 ILE   ( 127-)  B    -2.5
   2 HIS   (   5-)  A    -2.4
 331 THR   ( 157-)  B    -2.3
 516 PHE   ( 145-)  D    -2.3
 549 SER   ( 178-)  D    -2.3
 496 ASN   ( 125-)  D    -2.3
 200 ARG   (  23-)  B    -2.2
  99 PRO   ( 102-)  A    -2.2
  79 ILE   (  82-)  A    -2.2
 114 VAL   ( 117-)  A    -2.2
 206 ARG   (  29-)  B    -2.2
 480 THR   ( 109-)  D    -2.1
 277 THR   ( 100-)  B    -2.1
  20 MET   (  23-)  A    -2.1
 520 THR   ( 149-)  D    -2.0
 150 PHE   ( 153-)  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.

   2 HIS   (   5-)  A  Poor phi/psi
  12 ASN   (  15-)  A  PRO omega poor
  29 PHE   (  32-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  97 ARG   ( 100-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 112 PRO   ( 115-)  A  Poor phi/psi
 121 ASN   ( 124-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 196 ASN   (  19-)  B  Poor phi/psi
 209 TYR   (  32-)  B  Poor phi/psi
 210 ASN   (  33-)  B  Poor phi/psi
 297 TYR   ( 123-)  B  PRO omega poor
 308 ASN   ( 134-)  B  Poor phi/psi
 315 GLY   ( 141-)  B  Poor phi/psi
 327 TRP   ( 153-)  B  Poor phi/psi
 411 TYR   (  32-)  D  Poor phi/psi
 436 LYS   (  57-)  D  Poor phi/psi
 440 TYR   (  61-)  D  Poor phi/psi
 471 ASN   (  92-)  D  Poor phi/psi
 474 PHE   (  95-)  D  Poor phi/psi
 476 SER   (  97-)  D  Poor phi/psi
 495 ASP   ( 124-)  D  Poor phi/psi
 496 ASN   ( 125-)  D  Poor phi/psi
 509 ASN   ( 138-)  D  Poor phi/psi
 510 LYS   ( 139-)  D  Poor phi/psi
 549 SER   ( 178-)  D  Poor phi/psi
 591 ASN   ( 220-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.314

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.

 265 SER   (  88-)  B    0.37
 582 SER   ( 211-)  D    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!

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  16 SER   (  19-)  A      0
  23 PHE   (  26-)  A      0
  28 ILE   (  31-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  36 LYS   (  39-)  A      0
  48 PHE   (  51-)  A      0
  74 SER   (  77-)  A      0
  75 ASN   (  78-)  A      0
  76 TYR   (  79-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
  99 PRO   ( 102-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 120 ARG   ( 123-)  A      0
 126 THR   ( 129-)  A      0
 127 THR   ( 130-)  A      0
 130 SER   ( 133-)  A      0
And so on for a total of 252 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 : 1.467

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]

  84 PRO   (  87-)  A    0.45 HIGH

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 198 THR   (  21-)  B      O   <->  257 ARG   (  80-)  B      NH1    0.52    2.18  INTRA
 179 ASP   (   2-)  B      CG  <->  183 ARG   (   6-)  B      NH2    0.37    2.73  INTRA BL
 164 HIS   ( 167-)  A      ND1 <->  166 GLY   ( 169-)  A      N      0.31    2.69  INTRA BL
 301 ILE   ( 127-)  B      CD1 <->  302 GLU   ( 128-)  B      N      0.31    2.69  INTRA
 208 ILE   (  31-)  B      CD1 <->  213 GLU   (  36-)  B      CA     0.31    2.89  INTRA
 206 ARG   (  29-)  B      NH2 <->  213 GLU   (  36-)  B      OE1    0.30    2.40  INTRA BL
 465 GLY   (  86-)  D      CA  <->  528 GLN   ( 157-)  D      NE2    0.28    2.82  INTRA BL
 324 ASN   ( 150-)  B      ND2 <->  328 THR   ( 154-)  B      CG2    0.27    2.83  INTRA BL
 340 ARG   ( 166-)  B      N   <->  343 GLU   ( 169-)  B      OE1    0.26    2.44  INTRA BF
 285 HIS   ( 111-)  B      ND1 <->  286 HIS   ( 112-)  B      N      0.26    2.64  INTRA BF
 421 ASP   (  42-)  D      OD2 <->  477 LYS   (  98-)  D      N      0.25    2.45  INTRA BF
  19 PHE   (  22-)  A      CZ  <->  370 ILE   (  28-)  C      CD1    0.25    2.95  INTRA
 386 MET   (   7-)  D      O   <->  389 ASP   (  10-)  D      N      0.24    2.46  INTRA BF
 208 ILE   (  31-)  B      CD1 <->  213 GLU   (  36-)  B      CB     0.24    2.96  INTRA
 472 CYS   (  93-)  D      SG  <->  480 THR   ( 109-)  D      C      0.23    3.17  INTRA BL
  73 ARG   (  76-)  A      NH2 <->  234 ASP   (  57-)  B      CG     0.23    2.87  INTRA BL
  91 ASN   (  94-)  A      ND2 <->  101 VAL   ( 104-)  A      CB     0.22    2.88  INTRA BF
 214 SER   (  37-)  B      O   <->  227 VAL   (  50-)  B      N      0.22    2.48  INTRA BL
 301 ILE   ( 127-)  B      CD1 <->  349 VAL   ( 175-)  B      CG1    0.20    3.00  INTRA
  73 ARG   (  76-)  A      NH2 <->  234 ASP   (  57-)  B      OD2    0.20    2.50  INTRA BL
 138 GLU   ( 141-)  A      N   <->  615 HOH   ( 234 )  A      O      0.20    2.50  INTRA
 466 SER   (  87-)  D      N   <->  528 GLN   ( 157-)  D      NE2    0.18    2.67  INTRA BL
 179 ASP   (   2-)  B      OD1 <->  183 ARG   (   6-)  B      NH2    0.17    2.53  INTRA BL
 450 GLU   (  71-)  D      N   <->  618 HOH   ( 316 )  D      O      0.16    2.54  INTRA
 104 CYS   ( 107-)  A      SG  <->  106 ILE   ( 109-)  A      CD1    0.16    3.24  INTRA
And so on for a total of 124 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.

  97 ARG   ( 100-)  A      -6.04
 282 LYS   ( 105-)  B      -5.89
 363 ARG   ( 189-)  B      -5.79
 608 LYS   ( 237-)  D      -5.76
 340 ARG   ( 166-)  B      -5.73
 448 LEU   (  69-)  D      -5.33
 313 LYS   ( 139-)  B      -5.22
 609 ASN   ( 238-)  D      -5.14
 375 LYS   (  33-)  C      -5.06
 271 ARG   (  94-)  B      -5.01

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: 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.

 618 HOH   ( 300 )  D      O
 618 HOH   ( 320 )  D      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.

 140 HIS   ( 143-)  A
 187 GLN   (  10-)  B
 284 GLN   ( 107-)  B
 348 GLN   ( 174-)  B
 372 ASN   (  30-)  C
 402 ASN   (  23-)  D
 431 ASN   (  52-)  D
 467 ASN   (  88-)  D
 500 GLN   ( 129-)  D
 512 ASN   ( 141-)  D
 528 GLN   ( 157-)  D
 604 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.

  42 LEU   (  45-)  A      N
  73 ARG   (  76-)  A      NH2
 118 TRP   ( 121-)  A      NE1
 127 THR   ( 130-)  A      N
 155 GLU   ( 158-)  A      N
 158 TYR   ( 161-)  A      OH
 183 ARG   (   6-)  B      NH2
 223 GLU   (  46-)  B      N
 252 VAL   (  75-)  B      N
 283 THR   ( 106-)  B      N
 284 GLN   ( 107-)  B      N
 286 HIS   ( 112-)  B      N
 316 VAL   ( 142-)  B      N
 325 GLY   ( 151-)  B      N
 426 TRP   (  47-)  D      N
 449 ASN   (  70-)  D      N
 451 ASP   (  72-)  D      N
 474 PHE   (  95-)  D      N
 475 SER   (  96-)  D      N
 490 GLU   ( 119-)  D      N
 498 ASN   ( 127-)  D      N
 520 THR   ( 149-)  D      OG1
 545 TYR   ( 174-)  D      N
 563 ASN   ( 192-)  D      N
 566 THR   ( 195-)  D      N
 607 THR   ( 236-)  D      OG1
 609 ASN   ( 238-)  D      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.

   8 GLU   (  11-)  A      OE1
  63 ASP   (  66-)  A      OD2
 146 HIS   ( 149-)  A      ND1
 493 HIS   ( 122-)  D      NE2

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.

  18 GLU   (  21-)  A   H-bonding suggests Gln
 236 GLU   (  59-)  B   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 :  -0.114
  2nd generation packing quality :  -1.462
  Ramachandran plot appearance   :  -1.803
  chi-1/chi-2 rotamer normality  :  -2.314
  Backbone conformation          :  -0.263

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.678
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.242 (tight)
  Improper dihedral distribution :   0.635
  B-factor distribution          :   0.540
  Inside/Outside distribution    :   1.040

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.678
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.242 (tight)
  Improper dihedral distribution :   0.635
  B-factor distribution          :   0.540
  Inside/Outside distribution    :   1.040
==============

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.