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 pdb1jwu.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: 71056.555
Volume of the Unit Cell V= 3078127.5
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.813
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.720

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'.

 381 GLU   (   1-)  D      CG
 381 GLU   (   1-)  D      CD
 381 GLU   (   1-)  D      OE1
 381 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.

  48 ARG   (  50-)  A
 203 ARG   (  23-)  B
 251 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

  77 TYR   (  79-)  A
 148 TYR   ( 150-)  A
 282 TYR   ( 102-)  B
 457 TYR   (  77-)  D
 465 TYR   (  85-)  D
 547 TYR   ( 174-)  D
 554 TYR   ( 181-)  D
 571 TYR   ( 198-)  D
 590 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.

 106 PHE   ( 108-)  A
 424 PHE   (  44-)  D
 425 PHE   (  45-)  D
 496 PHE   ( 123-)  D
 569 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
 385 ASP   (   5-)  D
 390 ASP   (  10-)  D
 409 ASP   (  29-)  D
 422 ASP   (  42-)  D
 435 ASP   (  55-)  D
 442 ASP   (  62-)  D
 533 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
 139 GLU   ( 141-)  A
 156 GLU   ( 158-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 249 GLU   (  69-)  B
 447 GLU   (  67-)  D
 492 GLU   ( 119-)  D
 531 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.

  86 GLU   (  88-)  A      N    CA   C    98.81   -4.4
 341 VAL   ( 164-)  B      N    CA   C    99.74   -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.

  28 GLU   (  30-)  A
  48 ARG   (  50-)  A
 139 GLU   ( 141-)  A
 156 GLU   ( 158-)  A
 169 ASP   ( 171-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 203 ARG   (  23-)  B
 249 GLU   (  69-)  B
 251 ARG   (  71-)  B
 385 ASP   (   5-)  D
 390 ASP   (  10-)  D
 409 ASP   (  29-)  D
 422 ASP   (  42-)  D
 435 ASP   (  55-)  D
 442 ASP   (  62-)  D
 447 GLU   (  67-)  D
 492 GLU   ( 119-)  D
 531 GLU   ( 158-)  D
 533 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    4.58

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.

  14 PRO   (  16-)  A    -2.8
 516 ILE   ( 143-)  D    -2.7
 111 THR   ( 113-)  A    -2.6
  94 PRO   (  96-)  A    -2.5
 518 PHE   ( 145-)  D    -2.4
 151 PHE   ( 153-)  A    -2.3
 334 THR   ( 157-)  B    -2.3
 498 ASN   ( 125-)  D    -2.3
 591 ASN   ( 218-)  D    -2.2
 209 ARG   (  29-)  B    -2.2
 201 THR   (  21-)  B    -2.1
 115 VAL   ( 117-)  A    -2.1
 331 THR   ( 154-)  B    -2.1
 218 VAL   (  38-)  B    -2.1
 551 SER   ( 178-)  D    -2.1
  21 MET   (  23-)  A    -2.1
  96 GLU   (  98-)  A    -2.0
 477 SER   (  97-)  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
  37 LYS   (  39-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 113 PRO   ( 115-)  A  Poor phi/psi
 122 ASN   ( 124-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 199 ASN   (  19-)  B  Poor phi/psi
 212 TYR   (  32-)  B  Poor phi/psi
 213 ASN   (  33-)  B  Poor phi/psi
 270 THR   (  90-)  B  Poor phi/psi
 286 THR   ( 106-)  B  Poor phi/psi
 300 TYR   ( 123-)  B  PRO omega poor
 311 ASN   ( 134-)  B  Poor phi/psi
 318 GLY   ( 141-)  B  Poor phi/psi
 330 TRP   ( 153-)  B  Poor phi/psi
 412 TYR   (  32-)  D  Poor phi/psi
 417 LYS   (  37-)  D  Poor phi/psi
 437 LYS   (  57-)  D  Poor phi/psi
 439 LYS   (  59-)  D  Poor phi/psi
 441 TYR   (  61-)  D  Poor phi/psi
 472 ASN   (  92-)  D  Poor phi/psi
 475 PHE   (  95-)  D  Poor phi/psi
 477 SER   (  97-)  D  Poor phi/psi
 486 GLY   ( 113-)  D  Poor phi/psi
 497 ASP   ( 124-)  D  Poor phi/psi
 498 ASN   ( 125-)  D  Poor phi/psi
 511 ASN   ( 138-)  D  Poor phi/psi
 512 LYS   ( 139-)  D  Poor phi/psi
 551 SER   ( 178-)  D  Poor phi/psi
 593 ASN   ( 220-)  D  Poor phi/psi
 600 SER   ( 227-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.833

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.

 232 GLU   (  52-)  B    0.36

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 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  17 SER   (  19-)  A      0
  20 PHE   (  22-)  A      0
  24 PHE   (  26-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  37 LYS   (  39-)  A      0
  42 ARG   (  44-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  94 PRO   (  96-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 100 PRO   ( 102-)  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 269 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 : 1.429

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]

  85 PRO   (  87-)  A    0.45 HIGH
 137 PRO   ( 139-)  A    0.45 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].

  94 PRO   (  96-)  A  -112.7 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.

 201 THR   (  21-)  B      O   <->  260 ARG   (  80-)  B      NH1    0.45    2.25  INTRA BF
  55 GLN   (  57-)  A      CG  <->  472 ASN   (  92-)  D      CG     0.35    2.85  INTRA
 327 ASN   ( 150-)  B      ND2 <->  331 THR   ( 154-)  B      CG2    0.34    2.76  INTRA
 191 LEU   (  11-)  B      CD2 <->  375 THR   ( 313-)  C      CG2    0.29    2.91  INTRA
 182 ASP   (   2-)  B      CG  <->  186 ARG   (   6-)  B      NH2    0.27    2.83  INTRA BF
 288 HIS   ( 111-)  B      ND1 <->  289 HIS   ( 112-)  B      N      0.27    2.63  INTRA BF
 182 ASP   (   2-)  B      OD1 <->  186 ARG   (   6-)  B      NH2    0.26    2.44  INTRA
   1 GLU   (   3-)  A      OE2 <->  196 HIS   (  16-)  B      ND1    0.26    2.44  INTRA BF
 205 ARG   (  25-)  B      NH2 <->  221 ASP   (  41-)  B      OD2    0.25    2.45  INTRA
 591 ASN   ( 218-)  D      ND2 <->  620 HOH   ( 247 )  D      O      0.23    2.47  INTRA
 473 CYS   (  93-)  D      SG  <->  483 CYS   ( 110-)  D      N      0.23    3.07  INTRA BL
 305 GLU   ( 128-)  B      CD  <->  307 ARG   ( 130-)  B      NH2    0.23    2.87  INTRA BF
 402 GLY   (  22-)  D      N   <->  549 PHE   ( 176-)  D      O      0.23    2.47  INTRA
 288 HIS   ( 111-)  B      CG  <->  289 HIS   ( 112-)  B      N      0.22    2.78  INTRA BF
  74 ARG   (  76-)  A      NH2 <->  237 ASP   (  57-)  B      OD2    0.22    2.48  INTRA
  74 ARG   (  76-)  A      NH2 <->  237 ASP   (  57-)  B      CG     0.22    2.88  INTRA
 203 ARG   (  23-)  B      NH2 <->  223 ASP   (  43-)  B      OD2    0.18    2.52  INTRA BF
 343 ARG   ( 166-)  B      N   <->  346 GLU   ( 169-)  B      OE1    0.18    2.52  INTRA BF
 226 GLU   (  46-)  B      OE2 <->  228 ARG   (  48-)  B      NE     0.18    2.52  INTRA BL
 273 ARG   (  93-)  B      NE  <->  618 HOH   ( 235 )  B      O      0.17    2.53  INTRA BF
 182 ASP   (   2-)  B      OD1 <->  184 ARG   (   4-)  B      CD     0.16    2.64  INTRA
 448 LEU   (  68-)  D      C   <->  591 ASN   ( 218-)  D      ND2    0.15    2.95  INTRA
 139 GLU   ( 141-)  A      CD  <->  618 HOH   ( 223 )  B      O      0.15    2.65  INTRA BF
  28 GLU   (  30-)  A      OE2 <->   31 HIS   (  33-)  A      ND1    0.14    2.56  INTRA BL
 307 ARG   ( 130-)  B      NH1 <->  351 GLN   ( 174-)  B      NE2    0.14    2.71  INTRA BF
And so on for a total of 104 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.

  98 ARG   ( 100-)  A      -6.27
 285 LYS   ( 105-)  B      -5.78
 610 LYS   ( 237-)  D      -5.72
 343 ARG   ( 166-)  B      -5.56
 366 ARG   ( 189-)  B      -5.38
 449 LEU   (  69-)  D      -5.31
 611 ASN   ( 238-)  D      -5.21
 316 LYS   ( 139-)  B      -5.20

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

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.

 576 ALA   ( 203-)  D   -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

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.

 617 HOH   ( 236 )  A      O
 619 HOH   ( 139 )  C      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.

 141 HIS   ( 143-)  A
 190 GLN   (  10-)  B
 287 GLN   ( 107-)  B
 351 GLN   ( 174-)  B
 468 ASN   (  88-)  D
 491 HIS   ( 118-)  D
 514 ASN   ( 141-)  D
 530 GLN   ( 157-)  D
 606 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.

  43 LEU   (  45-)  A      N
  45 GLU   (  47-)  A      N
  74 ARG   (  76-)  A      NH2
 119 TRP   ( 121-)  A      NE1
 138 ARG   ( 140-)  A      NE
 201 THR   (  21-)  B      OG1
 209 ARG   (  29-)  B      NE
 213 ASN   (  33-)  B      N
 215 GLU   (  35-)  B      N
 226 GLU   (  46-)  B      N
 287 GLN   ( 107-)  B      N
 289 HIS   ( 112-)  B      N
 319 VAL   ( 142-)  B      N
 327 ASN   ( 150-)  B      ND2
 427 TRP   (  47-)  D      N
 438 LEU   (  58-)  D      N
 450 ASN   (  70-)  D      N
 475 PHE   (  95-)  D      N
 476 SER   (  96-)  D      N
 492 GLU   ( 119-)  D      N
 500 ASN   ( 127-)  D      N
 547 TYR   ( 174-)  D      N
 557 GLY   ( 184-)  D      N
 565 ASN   ( 192-)  D      N
 568 THR   ( 195-)  D      N
 599 LYS   ( 226-)  D      N
 609 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      OE1
  64 ASP   (  66-)  A      OD2
 147 HIS   ( 149-)  A      ND1
 606 HIS   ( 233-)  D      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.

 617 HOH   ( 205 )  A      O  0.97  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; but Alt-Rotamer
 160 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 179 ASP   ( 181-)  A   H-bonding suggests Asn
 422 ASP   (  42-)  D   H-bonding suggests Asn
 442 ASP   (  62-)  D   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 :  -0.059
  2nd generation packing quality :  -1.269
  Ramachandran plot appearance   :  -1.369
  chi-1/chi-2 rotamer normality  :  -1.833
  Backbone conformation          :  -0.432

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.302 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.236 (tight)
  Improper dihedral distribution :   0.606
  B-factor distribution          :   1.194
  Inside/Outside distribution    :   1.042

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   :   0.1
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.302 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.236 (tight)
  Improper dihedral distribution :   0.606
  B-factor distribution          :   1.194
  Inside/Outside distribution    :   1.042
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
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      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      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,
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    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.