WHAT IF Check report

This file was created 2011-12-16 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 pdb3lwb.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

 622 NO3   ( 374-)  A  -
 623 NO3   ( 374-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: 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'.

   1 ARG   (   7-)  A      CG
   1 ARG   (   7-)  A      CD
   1 ARG   (   7-)  A      NE
   1 ARG   (   7-)  A      CZ
   1 ARG   (   7-)  A      NH1
   1 ARG   (   7-)  A      NH2
   2 ASP   (   8-)  A      CG
   2 ASP   (   8-)  A      OD1
   2 ASP   (   8-)  A      OD2
   3 ARG   (   9-)  A      CG
   3 ARG   (   9-)  A      CD
   3 ARG   (   9-)  A      NE
   3 ARG   (   9-)  A      CZ
   3 ARG   (   9-)  A      NH1
   3 ARG   (   9-)  A      NH2
  15 ILE   (  26-)  A      CG1
  15 ILE   (  26-)  A      CG2
  15 ILE   (  26-)  A      CD1
  52 VAL   (  97-)  A      CB
  52 VAL   (  97-)  A      CG1
  52 VAL   (  97-)  A      CG2
  53 SER   (  98-)  A      CB
  53 SER   (  98-)  A      OG
  54 LEU   (  99-)  A      CG
  54 LEU   (  99-)  A      CD1
And so on for a total of 156 lines.

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 ARG   (   7-)  A    High
   2 ASP   (   8-)  A    High
  13 GLY   (  19-)  A    High
  51 ASN   (  62-)  A    High
 217 GLY   ( 262-)  A    High
 218 VAL   ( 263-)  A    High
 246 ASP   ( 291-)  A    High
 248 GLN   ( 293-)  A    High
 324 ARG   (  10-)  B    High
 331 PHE   (  17-)  B    High
 332 HIS   (  24-)  B    High
 333 ALA   (  25-)  B    High
 334 ILE   (  26-)  B    High
 335 SER   (  27-)  B    High
 336 CYS   (  28-)  B    High
 343 LEU   (  35-)  B    High
 348 SER   (  40-)  B    High
 352 ASP   (  44-)  B    High
 354 ILE   (  46-)  B    High
 355 ALA   (  47-)  B    High
 356 VAL   (  48-)  B    High
 357 GLY   (  49-)  B    High
 358 ILE   (  50-)  B    High
 359 THR   (  51-)  B    High
 360 PRO   (  52-)  B    High
 361 VAL   ( 106-)  B    High
 362 LEU   ( 107-)  B    High
 363 GLU   ( 108-)  B    High
 364 SER   ( 109-)  B    High
 365 VAL   ( 110-)  B    High
 373 HIS   ( 118-)  B    High
 398 MET   ( 150-)  B    High
 429 ARG   ( 181-)  B    High
 510 GLY   ( 262-)  B    High
 511 VAL   ( 263-)  B    High
 512 ARG   ( 264-)  B    High
 572 ASP   ( 324-)  B    High
 582 MET   ( 334-)  B    High
 609 MET   ( 361-)  B    High
 617 GLY   ( 369-)  B    High
 618 VAL   ( 370-)  B    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 4

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

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.

 323 ARG   ( 368-)  A
 467 ARG   ( 219-)  B

Warning: Tyrosine convention problem

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

  76 TYR   ( 121-)  A
  93 TYR   ( 138-)  A
 226 TYR   ( 271-)  A
 386 TYR   ( 138-)  B
 519 TYR   ( 271-)  B
 591 TYR   ( 343-)  B
 602 TYR   ( 354-)  B

Warning: Phenylalanine convention problem

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

  69 PHE   ( 114-)  A
 147 PHE   ( 192-)  A
 225 PHE   ( 270-)  A
 261 PHE   ( 306-)  A
 369 PHE   ( 114-)  B
 440 PHE   ( 192-)  B
 518 PHE   ( 270-)  B
 521 PHE   ( 273-)  B
 554 PHE   ( 306-)  B
 585 PHE   ( 337-)  B

Warning: Aspartic acid convention problem

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

  28 ASP   (  39-)  A
  33 ASP   (  44-)  A
  79 ASP   ( 124-)  A
 166 ASP   ( 211-)  A
 235 ASP   ( 280-)  A
 265 ASP   ( 310-)  A
 273 ASP   ( 318-)  A
 278 ASP   ( 323-)  A
 279 ASP   ( 324-)  A
 347 ASP   (  39-)  B
 410 ASP   ( 162-)  B
 520 ASP   ( 272-)  B
 558 ASP   ( 310-)  B
 566 ASP   ( 318-)  B
 572 ASP   ( 324-)  B

Warning: Glutamic acid convention problem

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

  60 GLU   ( 105-)  A
  78 GLU   ( 123-)  A
 138 GLU   ( 183-)  A
 185 GLU   ( 230-)  A
 194 GLU   ( 239-)  A
 212 GLU   ( 257-)  A
 222 GLU   ( 267-)  A
 238 GLU   ( 283-)  A
 285 GLU   ( 330-)  A
 478 GLU   ( 230-)  B
 487 GLU   ( 239-)  B
 505 GLU   ( 257-)  B
 515 GLU   ( 267-)  B
 578 GLU   ( 330-)  B

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  51 ASN   (  62-)  A      N    CA   C    90.06   -7.5
 357 GLY   (  49-)  B      N    CA   C   100.88   -4.0
 360 PRO   (  52-)  B      N    CA   C    90.58   -8.5
 360 PRO   (  52-)  B      N    CA   CB  113.09    9.2

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 ASP   (  39-)  A
  33 ASP   (  44-)  A
  60 GLU   ( 105-)  A
  78 GLU   ( 123-)  A
  79 ASP   ( 124-)  A
 138 GLU   ( 183-)  A
 166 ASP   ( 211-)  A
 185 GLU   ( 230-)  A
 194 GLU   ( 239-)  A
 212 GLU   ( 257-)  A
 222 GLU   ( 267-)  A
 235 ASP   ( 280-)  A
 238 GLU   ( 283-)  A
 265 ASP   ( 310-)  A
 273 ASP   ( 318-)  A
 278 ASP   ( 323-)  A
 279 ASP   ( 324-)  A
 285 GLU   ( 330-)  A
 323 ARG   ( 368-)  A
 347 ASP   (  39-)  B
 410 ASP   ( 162-)  B
 467 ARG   ( 219-)  B
 478 GLU   ( 230-)  B
 487 GLU   ( 239-)  B
 505 GLU   ( 257-)  B
 515 GLU   ( 267-)  B
 520 ASP   ( 272-)  B
 558 ASP   ( 310-)  B
 566 ASP   ( 318-)  B
 572 ASP   ( 324-)  B
 578 GLU   ( 330-)  B

Error: Tau angle problems

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

 360 PRO   (  52-)  B    8.72
  51 ASN   (  62-)  A    7.09
 391 VAL   ( 143-)  B    5.25
 357 GLY   (  49-)  B    4.56

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.

 423 PRO   ( 175-)  B    -2.5
 391 VAL   ( 143-)  B    -2.5
 369 PHE   ( 114-)  B    -2.5
 445 ARG   ( 197-)  B    -2.5
  69 PHE   ( 114-)  A    -2.4
 359 THR   (  51-)  B    -2.3
 155 SER   ( 200-)  A    -2.3
 130 PRO   ( 175-)  A    -2.2
 363 GLU   ( 108-)  B    -2.2
  72 LEU   ( 117-)  A    -2.2
 413 PRO   ( 165-)  B    -2.1
 367 VAL   ( 112-)  B    -2.1
 134 LEU   ( 179-)  A    -2.1

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.

   3 ARG   (   9-)  A  Poor phi/psi
  33 ASP   (  44-)  A  omega poor
  50 ALA   (  61-)  A  omega poor
 129 PRO   ( 174-)  A  PRO omega poor
 144 LEU   ( 189-)  A  PRO omega poor
 156 SER   ( 201-)  A  Poor phi/psi
 241 VAL   ( 286-)  A  PRO omega poor
 265 ASP   ( 310-)  A  Poor phi/psi
 274 PHE   ( 319-)  A  omega poor
 285 GLU   ( 330-)  A  omega poor
 333 ALA   (  25-)  B  Poor phi/psi
 356 VAL   (  48-)  B  omega poor
 357 GLY   (  49-)  B  omega poor
 359 THR   (  51-)  B  PRO omega poor
 362 LEU   ( 107-)  B  Poor phi/psi, omega poor
 363 GLU   ( 108-)  B  Poor phi/psi
 364 SER   ( 109-)  B  Poor phi/psi
 390 GLY   ( 142-)  B  omega poor
 391 VAL   ( 143-)  B  Poor phi/psi
 422 PRO   ( 174-)  B  PRO omega poor
 425 SER   ( 177-)  B  Poor phi/psi
 437 LEU   ( 189-)  B  PRO omega poor
 507 ARG   ( 259-)  B  omega poor
 509 ALA   ( 261-)  B  Poor phi/psi
 511 VAL   ( 263-)  B  Poor phi/psi
 514 ARG   ( 266-)  B  Poor phi/psi, omega poor
 534 VAL   ( 286-)  B  PRO omega poor
 558 ASP   ( 310-)  B  Poor phi/psi
 567 PHE   ( 319-)  B  omega poor
 617 GLY   ( 369-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -1.843

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.

  22 SER   (  33-)  A    0.35
  19 SER   (  30-)  A    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 ARG   (   9-)  A      0
  12 GLY   (  18-)  A      0
  13 GLY   (  19-)  A      0
  14 ALA   (  25-)  A      0
  15 ILE   (  26-)  A      0
  31 ARG   (  42-)  A      0
  50 ALA   (  61-)  A      0
  51 ASN   (  62-)  A      0
  52 VAL   (  97-)  A      0
  53 SER   (  98-)  A      0
  56 PRO   ( 101-)  A      0
  64 SER   ( 109-)  A      0
  72 LEU   ( 117-)  A      0
  73 HIS   ( 118-)  A      0
  76 TYR   ( 121-)  A      0
  78 GLU   ( 123-)  A      0
  89 ALA   ( 134-)  A      0
  94 VAL   ( 139-)  A      0
  96 ALA   ( 141-)  A      0
 105 MET   ( 150-)  A      0
 123 ALA   ( 168-)  A      0
 128 ARG   ( 173-)  A      0
 129 PRO   ( 174-)  A      0
 130 PRO   ( 175-)  A      0
 131 ARG   ( 176-)  A      0
And so on for a total of 194 lines.

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!

 513 GLY   ( 265-)  B   3.23   23
 494 PRO   ( 246-)  B   1.54   10

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]

 360 PRO   (  52-)  B    0.00 LOW

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].

  41 PRO   (  52-)  A   101.7 envelop C-beta (108 degrees)
 120 PRO   ( 165-)  A    38.0 envelop C-delta (36 degrees)
 130 PRO   ( 175-)  A    30.2 envelop C-delta (36 degrees)
 145 PRO   ( 190-)  A   -23.7 half-chair C-alpha/N (-18 degrees)
 169 PRO   ( 214-)  A   100.4 envelop C-beta (108 degrees)
 180 PRO   ( 225-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 413 PRO   ( 165-)  B    10.3 half-chair N/C-delta (18 degrees)
 423 PRO   ( 175-)  B    12.1 half-chair N/C-delta (18 degrees)
 438 PRO   ( 190-)  B     0.3 envelop N (0 degrees)
 535 PRO   ( 287-)  B    48.1 half-chair C-delta/C-gamma (54 degrees)
 574 PRO   ( 326-)  B  -113.5 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.

  50 ALA   (  61-)  A      C   <->   51 ASN   (  62-)  A      C      0.50    2.30  INTRA BF
 616 ARG   ( 368-)  B      CG  <->  617 GLY   ( 369-)  B      N      0.34    2.66  INTRA BF
 149 LYS   ( 194-)  A      NZ  <->  624 HOH   ( 404 )  A      O      0.28    2.42  INTRA BL
 363 GLU   ( 108-)  B      C   <->  365 VAL   ( 110-)  B      N      0.27    2.63  INTRA BF
 442 LYS   ( 194-)  B      NZ  <->  625 HOH   ( 482 )  B      O      0.24    2.46  INTRA BF
 616 ARG   ( 368-)  B      NE  <->  625 HOH   ( 380 )  B      O      0.21    2.49  INTRA BF
 117 ASP   ( 162-)  A      OD2 <->  405 LYS   ( 157-)  B      NZ     0.21    2.49  INTRA BF
  50 ALA   (  61-)  A      O   <->   51 ASN   (  62-)  A      C      0.20    2.40  INTRA BF
 513 GLY   ( 265-)  B      O   <->  515 GLU   ( 267-)  B      N      0.19    2.51  INTRA BF
 454 ARG   ( 206-)  B    A NH2 <->  625 HOH   ( 483 )  B      O      0.16    2.54  INTRA BF
 363 GLU   ( 108-)  B      CG  <->  364 SER   ( 109-)  B      N      0.14    2.86  INTRA BF
 328 ALA   (  14-)  B      O   <->  369 PHE   ( 114-)  B      N      0.14    2.56  INTRA BF
 357 GLY   (  49-)  B      N   <->  358 ILE   (  50-)  B      N      0.13    2.47  INTRA BF
 359 THR   (  51-)  B      CG2 <->  360 PRO   (  52-)  B      N      0.13    2.87  INTRA BF
 562 LEU   ( 314-)  B      CD1 <->  585 PHE   ( 337-)  B      CZ     0.10    3.10  INTRA BF
 117 ASP   ( 162-)  A      CG  <->  405 LYS   ( 157-)  B      NZ     0.10    3.00  INTRA BF
 345 ASN   (  37-)  B      CG  <->  602 TYR   ( 354-)  B      CD2    0.10    3.10  INTRA BF
 428 HIS   ( 180-)  B      N   <->  431 GLU   ( 183-)  B      OE1    0.09    2.61  INTRA BL
 461 LEU   ( 213-)  B      N   <->  462 PRO   ( 214-)  B      CD     0.09    2.91  INTRA BL
 539 ASP   ( 291-)  B      OD1 <->  541 GLN   ( 293-)  B      N      0.08    2.62  INTRA BF
  40 THR   (  51-)  A      O   <->   43 GLY   (  54-)  A      N      0.08    2.62  INTRA BL
 602 TYR   ( 354-)  B      N   <->  603 PRO   ( 355-)  B      CD     0.06    2.94  INTRA BL
 104 GLY   ( 149-)  A      O   <->  624 HOH   ( 551 )  A      O      0.06    2.34  INTRA BF
 168 LEU   ( 213-)  A      N   <->  169 PRO   ( 214-)  A      CD     0.06    2.94  INTRA BL
 309 TYR   ( 354-)  A      N   <->  310 PRO   ( 355-)  A      CD     0.06    2.94  INTRA BL
And so on for a total of 59 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  76 TYR   ( 121-)  A      -9.46
 219 ARG   ( 264-)  A      -8.67
 582 MET   ( 334-)  B      -7.77
 152 ARG   ( 197-)  A      -6.52
 620 LEU   ( 372-)  B      -6.24
 445 ARG   ( 197-)  B      -6.03
 244 LYS   ( 289-)  A      -5.96
 537 LYS   ( 289-)  B      -5.86
  30 ARG   (  41-)  A      -5.60
 616 ARG   ( 368-)  B      -5.59
 128 ARG   ( 173-)  A      -5.57
 421 ARG   ( 173-)  B      -5.51
 131 ARG   ( 176-)  A      -5.50
 434 ARG   ( 186-)  B      -5.47
 141 ARG   ( 186-)  A      -5.42
 363 GLU   ( 108-)  B      -5.42
 289 MET   ( 334-)  A      -5.29
 560 ARG   ( 312-)  B      -5.22
 450 ILE   ( 202-)  B      -5.15
 359 THR   (  51-)  B      -5.08
 267 ARG   ( 312-)  A      -5.00

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 221 ARG   ( 266-)  A   -3.42
  54 LEU   (  99-)  A   -3.10
 372 LEU   ( 117-)  B   -3.04
 358 ILE   (  50-)  B   -2.91
 621 HIS   ( 373-)  B   -2.75
 512 ARG   ( 264-)  B   -2.60
 362 LEU   ( 107-)  B   -2.59
   3 ARG   (   9-)  A   -2.53
 344 ARG   (  36-)  B   -2.52
 349 ARG   (  41-)  B   -2.51
 514 ARG   ( 266-)  B   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 510 GLY   ( 262-)  B     -  514 ARG   ( 266-)  B        -2.10

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 624 HOH   ( 402 )  A      O
 624 HOH   ( 513 )  A      O
 624 HOH   ( 523 )  A      O
 624 HOH   ( 583 )  A      O
 624 HOH   ( 605 )  A      O
 625 HOH   ( 457 )  B      O
 625 HOH   ( 504 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  26 ASN   (  37-)  A
 178 HIS   ( 223-)  A
 345 ASN   (  37-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   3 ARG   (   9-)  A      N
  51 ASN   (  62-)  A      N
 133 THR   ( 178-)  A      N
 158 GLY   ( 203-)  A      N
 159 VAL   ( 204-)  A      N
 164 SER   ( 209-)  A      N
 219 ARG   ( 264-)  A      N
 221 ARG   ( 266-)  A      N
 249 VAL   ( 294-)  A      N
 271 ARG   ( 316-)  A      NE
 298 TYR   ( 343-)  A      N
 302 TRP   ( 347-)  A      NE1
 364 SER   ( 109-)  B      N
 365 VAL   ( 110-)  B      N
 377 GLY   ( 129-)  B      N
 386 TYR   ( 138-)  B      OH
 391 VAL   ( 143-)  B      N
 405 LYS   ( 157-)  B      NZ
 421 ARG   ( 173-)  B      NH2
 449 SER   ( 201-)  B      N
 564 ARG   ( 316-)  B      NE
 590 MET   ( 342-)  B      N
 591 TYR   ( 343-)  B      N
 595 TRP   ( 347-)  B      NE1

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.

 194 GLU   ( 239-)  A      OE2
 273 ASP   ( 318-)  A      OD1
 487 GLU   ( 239-)  B      OE2
 566 ASP   ( 318-)  B      OD1

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.

 624 HOH   ( 440 )  A      O  0.84  K  5 *2
 624 HOH   ( 520 )  A      O  0.86  K  4 *2 Ion-B H2O-B
 625 HOH   ( 432 )  B      O  0.86  K  4 *2

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.

  60 GLU   ( 105-)  A   H-bonding suggests Gln
 194 GLU   ( 239-)  A   H-bonding suggests Gln
 487 GLU   ( 239-)  B   H-bonding suggests Gln
 515 GLU   ( 267-)  B   H-bonding suggests Gln
 520 ASP   ( 272-)  B   H-bonding suggests Asn; but Alt-Rotamer
 533 ASP   ( 285-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.091
  2nd generation packing quality :  -1.045
  Ramachandran plot appearance   :  -0.157
  chi-1/chi-2 rotamer normality  :  -1.843
  Backbone conformation          :   0.903

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.261 (tight)
  Bond angles                    :   0.527 (tight)
  Omega angle restraints         :   1.025
  Side chain planarity           :   0.237 (tight)
  Improper dihedral distribution :   0.532
  B-factor distribution          :   1.345
  Inside/Outside distribution    :   1.080

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.261 (tight)
  Bond angles                    :   0.527 (tight)
  Omega angle restraints         :   1.025
  Side chain planarity           :   0.237 (tight)
  Improper dihedral distribution :   0.532
  B-factor distribution          :   1.345
  Inside/Outside distribution    :   1.080
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      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.