WHAT IF Check report

This file was created 2012-01-05 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 pdb1p7c.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: C 2 2 21
Number of matrices in space group: 8
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: 16
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 THM   ( 501-)  B  -
 623 T5A   ( 503-)  A  -

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'.

  28 LEU   (  72-)  A      CG
  28 LEU   (  72-)  A      CD1
  28 LEU   (  72-)  A      CD2
  37 ARG   (  89-)  A      CG
  37 ARG   (  89-)  A      CD
  37 ARG   (  89-)  A      NE
  37 ARG   (  89-)  A      CZ
  37 ARG   (  89-)  A      NH1
  37 ARG   (  89-)  A      NH2
  38 VAL   (  90-)  A      CG1
  38 VAL   (  90-)  A      CG2
  39 LEU   (  91-)  A      CG
  39 LEU   (  91-)  A      CD1
  39 LEU   (  91-)  A      CD2
  42 SER   (  94-)  A      OG
 165 GLN   ( 221-)  A      CG
 165 GLN   ( 221-)  A      CD
 165 GLN   ( 221-)  A      OE1
 165 GLN   ( 221-)  A      NE2
 195 CYS   ( 251-)  A      SG
 296 ARG   ( 366-)  A      CG
 296 ARG   ( 366-)  A      CD
 296 ARG   ( 366-)  A      NE
 296 ARG   ( 366-)  A      CZ
 296 ARG   ( 366-)  A      NH1
And so on for a total of 60 lines.

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: 0

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.

 107 ARG   ( 163-)  A
 248 ARG   ( 318-)  A
 307 ARG   (  51-)  B
 419 ARG   ( 163-)  B
 580 ARG   ( 337-)  B

Warning: Tyrosine convention problem

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

  49 TYR   ( 101-)  A

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   ( 161-)  A
 134 PHE   ( 190-)  A
 568 PHE   ( 325-)  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.

  64 ASP   ( 116-)  A
  84 ASP   ( 136-)  A
 155 ASP   ( 211-)  A
 233 ASP   ( 303-)  A
 293 ASP   ( 363-)  A
 332 ASP   (  76-)  B
 372 ASP   ( 116-)  B
 467 ASP   ( 211-)  B
 546 ASP   ( 303-)  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.

  35 GLU   (  83-)  A
  43 GLU   (  95-)  A
 154 GLU   ( 210-)  A
 301 GLU   ( 371-)  A
 351 GLU   (  95-)  B
 367 GLU   ( 111-)  B
 513 GLU   ( 257-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.996038  0.000449 -0.000165|
 |  0.000449  0.997624  0.000039|
 | -0.000165  0.000039  0.996435|
Proposed new scale matrix

 |  0.008867 -0.000004  0.000001|
 | -0.000004  0.008506  0.000000|
 |  0.000002  0.000000  0.009258|
With corresponding cell

    A    = 112.776  B   = 117.561  C    = 108.015
    Alpha=  90.001  Beta=  90.019  Gamma=  89.948

The CRYST1 cell dimensions

    A    = 113.219  B   = 117.847  C    = 108.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 218.969
(Under-)estimated Z-score: 10.906

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.

  35 GLU   (  83-)  A
  43 GLU   (  95-)  A
  64 ASP   ( 116-)  A
  84 ASP   ( 136-)  A
 107 ARG   ( 163-)  A
 154 GLU   ( 210-)  A
 155 ASP   ( 211-)  A
 233 ASP   ( 303-)  A
 248 ARG   ( 318-)  A
 293 ASP   ( 363-)  A
 301 GLU   ( 371-)  A
 307 ARG   (  51-)  B
 332 ASP   (  76-)  B
 351 GLU   (  95-)  B
 367 GLU   ( 111-)  B
 372 ASP   ( 116-)  B
 419 ARG   ( 163-)  B
 467 ASP   ( 211-)  B
 513 GLU   ( 257-)  B
 546 ASP   ( 303-)  B
 580 ARG   ( 337-)  B

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.

 536 ARG   ( 293-)  B    -2.7
 479 PRO   ( 223-)  B    -2.6
 426 LEU   ( 170-)  B    -2.5
  43 GLU   (  95-)  A    -2.5
  34 PRO   (  82-)  A    -2.4
  18 LYS   (  62-)  A    -2.2
   5 LEU   (  49-)  A    -2.2
 166 ARG   ( 222-)  A    -2.1
 402 GLU   ( 146-)  B    -2.1
 510 SER   ( 254-)  B    -2.1
  11 ASP   (  55-)  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.

  11 ASP   (  55-)  A  Poor phi/psi
  17 GLY   (  61-)  A  Poor phi/psi
  27 ALA   (  71-)  A  Poor phi/psi
  38 VAL   (  90-)  A  Poor phi/psi
  42 SER   (  94-)  A  Poor phi/psi, omega poor
  43 GLU   (  95-)  A  Poor phi/psi
  95 ALA   ( 147-)  A  Poor phi/psi
 107 ARG   ( 163-)  A  Poor phi/psi
 114 LEU   ( 170-)  A  omega poor
 260 ASP   ( 330-)  A  Poor phi/psi
 280 THR   ( 350-)  A  omega poor
 328 LEU   (  72-)  B  omega poor
 330 SER   (  74-)  B  Poor phi/psi
 331 ARG   (  75-)  B  Poor phi/psi
 340 PRO   (  84-)  B  Poor phi/psi
 404 GLY   ( 148-)  B  omega poor
 405 SER   ( 149-)  B  Poor phi/psi, omega poor
 406 SER   ( 150-)  B  Poor phi/psi
 407 HIS   ( 151-)  B  Poor phi/psi
 409 PRO   ( 153-)  B  Poor phi/psi
 419 ARG   ( 163-)  B  Poor phi/psi
 519 SER   ( 263-)  B  Poor phi/psi
 543 PRO   ( 300-)  B  Poor phi/psi
 544 ASN   ( 301-)  B  Poor phi/psi
 573 ASP   ( 330-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.170

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.

 226 GLU   ( 296-)  A    0.33
 379 SER   ( 123-)  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!

  11 ASP   (  55-)  A      0
  14 HIS   (  58-)  A      0
  16 MET   (  60-)  A      0
  26 VAL   (  70-)  A      0
  27 ALA   (  71-)  A      0
  28 LEU   (  72-)  A      0
  29 ASP   (  77-)  A      0
  30 ILE   (  78-)  A      0
  35 GLU   (  83-)  A      0
  36 PRO   (  84-)  A      0
  37 ARG   (  89-)  A      0
  38 VAL   (  90-)  A      0
  39 LEU   (  91-)  A      0
  41 ALA   (  93-)  A      0
  42 SER   (  94-)  A      0
  43 GLU   (  95-)  A      0
  57 GLN   ( 109-)  A      0
  90 HIS   ( 142-)  A      0
  95 ALA   ( 147-)  A      0
  96 GLY   ( 148-)  A      0
  97 PRO   ( 153-)  A      0
  98 PRO   ( 154-)  A      0
 100 ALA   ( 156-)  A      0
 106 ASP   ( 162-)  A      0
 114 LEU   ( 170-)  A      0
And so on for a total of 163 lines.

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].

  34 PRO   (  82-)  A   -35.7 envelop C-alpha (-36 degrees)
  89 PRO   ( 141-)  A  -115.5 envelop C-gamma (-108 degrees)
 109 PRO   ( 165-)  A   103.4 envelop C-beta (108 degrees)
 410 PRO   ( 154-)  B   -41.5 envelop C-alpha (-36 degrees)
 421 PRO   ( 165-)  B   108.1 envelop C-beta (108 degrees)
 452 PRO   ( 196-)  B   113.2 envelop C-beta (108 degrees)
 479 PRO   ( 223-)  B   105.8 envelop C-beta (108 degrees)
 538 PRO   ( 295-)  B  -121.7 half-chair C-delta/C-gamma (-126 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.

 405 SER   ( 149-)  B      CB  <->  590 MET   ( 347-)  B      O      0.66    2.14  INTRA BF
  17 GLY   (  61-)  A      N   <->  623 T5A   ( 503-)  A      O1D    0.42    2.28  INTRA BL
 613 ARG   ( 370-)  B      NH2 <->  625 HOH   ( 531 )  B      O      0.40    2.30  INTRA
 405 SER   ( 149-)  B      O   <->  408 ALA   ( 152-)  B      N      0.39    2.31  INTRA BF
 330 SER   (  74-)  B      O   <->  332 ASP   (  76-)  B      N      0.37    2.33  INTRA BF
 468 ARG   ( 212-)  B      NE  <->  625 HOH   ( 669 )  B      O      0.28    2.42  INTRA
 307 ARG   (  51-)  B      NH2 <->  625 HOH   ( 559 )  B      O      0.23    2.47  INTRA BF
 341 MET   (  85-)  B      CE  <->  345 ARG   (  89-)  B      CG     0.22    2.98  INTRA
 409 PRO   ( 153-)  B      CB  <->  410 PRO   ( 154-)  B      CD     0.22    2.88  INTRA BF
 331 ARG   (  75-)  B      O   <->  609 ARG   ( 366-)  B      NH2    0.22    2.48  INTRA BF
 623 T5A   ( 503-)  A      N7A <->  624 HOH   ( 642 )  A      O      0.19    2.51  INTRA BL
 507 CYS   ( 251-)  B      SG  <->  625 HOH   ( 579 )  B      O      0.19    2.81  INTRA BF
 307 ARG   (  51-)  B      NH1 <->  625 HOH   ( 559 )  B      O      0.17    2.53  INTRA BF
 542 ALA   ( 299-)  B      O   <->  544 ASN   ( 301-)  B      N      0.16    2.54  INTRA BF
 404 GLY   ( 148-)  B      O   <->  406 SER   ( 150-)  B      N      0.16    2.54  INTRA BF
 213 HIS   ( 283-)  A      ND1 <->  215 GLY   ( 285-)  A      N      0.16    2.84  INTRA
 472 ARG   ( 216-)  B      NH1 <->  625 HOH   ( 648 )  B      O      0.15    2.55  INTRA
 526 HIS   ( 283-)  B      ND1 <->  528 GLY   ( 285-)  B      N      0.15    2.85  INTRA BL
 286 GLY   ( 356-)  A      O   <->  290 THR   ( 360-)  A      CG2    0.15    2.65  INTRA BF
 155 ASP   ( 211-)  A      OD2 <->  624 HOH   ( 643 )  A      O      0.15    2.25  INTRA
 302 MET   (  46-)  B      CB  <->  625 HOH   ( 523 )  B      O      0.14    2.66  INTRA BF
  41 ALA   (  93-)  A      O   <->   43 GLU   (  95-)  A      N      0.14    2.56  INTRA BF
 267 ARG   ( 337-)  A      NH1 <->  268 ASP   ( 338-)  A      OD1    0.14    2.56  INTRA
 455 PRO   ( 199-)  B      O   <->  625 HOH   ( 559 )  B      O      0.13    2.27  INTRA BF
 476 ARG   ( 220-)  B      NH2 <->  625 HOH   ( 532 )  B      O      0.13    2.57  INTRA BF
And so on for a total of 73 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.

 524 ARG   ( 281-)  B      -6.40
  35 GLU   (  83-)  A      -5.94
 536 ARG   ( 293-)  B      -5.92
 211 ARG   ( 281-)  A      -5.81
 617 GLU   ( 374-)  B      -5.76
 517 GLN   ( 261-)  B      -5.66
  14 HIS   (  58-)  A      -5.63
 164 ARG   ( 220-)  A      -5.60
 314 HIS   (  58-)  B      -5.59
 478 ARG   ( 222-)  B      -5.57
 194 GLN   ( 250-)  A      -5.47
 506 GLN   ( 250-)  B      -5.41
 166 ARG   ( 222-)  A      -5.39
 261 GLN   ( 331-)  A      -5.18

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.

 477 GLN   ( 221-)  B   -3.73
 331 ARG   (  75-)  B   -3.45
  37 ARG   (  89-)  A   -3.30
  39 LEU   (  91-)  A   -3.26
 165 GLN   ( 221-)  A   -2.80
 112 ALA   ( 168-)  A   -2.50

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.

  36 PRO   (  84-)  A     -   39 LEU   (  91-)  A        -2.25
 162 ALA   ( 218-)  A     -  165 GLN   ( 221-)  A        -2.03

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   ( 599 )  A      O
 625 HOH   ( 523 )  B      O
 625 HOH   ( 638 )  B      O
 625 HOH   ( 678 )  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.

  57 GLN   ( 109-)  A
 253 HIS   ( 323-)  A
 281 HIS   ( 351-)  A
 314 HIS   (  58-)  B
 398 HIS   ( 142-)  B
 441 GLN   ( 185-)  B
 566 HIS   ( 323-)  B
 592 GLN   ( 349-)  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.

  15 GLY   (  59-)  A      N
  18 LYS   (  62-)  A      NZ
  19 THR   (  63-)  A      N
  30 ILE   (  78-)  A      N
  46 ALA   (  98-)  A      N
  49 TYR   ( 101-)  A      OH
  73 GLN   ( 125-)  A      NE2
 107 ARG   ( 163-)  A      NE
 107 ARG   ( 163-)  A      NH1
 107 ARG   ( 163-)  A      NH2
 164 ARG   ( 220-)  A      N
 166 ARG   ( 222-)  A      NH1
 166 ARG   ( 222-)  A      NH2
 170 ARG   ( 226-)  A      N
 191 ARG   ( 247-)  A      NE
 250 ARG   ( 320-)  A      NH2
 259 TYR   ( 329-)  A      OH
 288 ILE   ( 358-)  A      N
 302 MET   (  46-)  B      N
 333 ASP   (  77-)  B      N
 334 ILE   (  78-)  B      N
 345 ARG   (  89-)  B      NE
 349 ALA   (  93-)  B      N
 353 ILE   (  97-)  B      N
 354 ALA   (  98-)  B      N
 357 TYR   ( 101-)  B      OH
 381 GLN   ( 125-)  B      NE2
 405 SER   ( 149-)  B      N
 468 ARG   ( 212-)  B      N
 476 ARG   ( 220-)  B      NH2
 482 ARG   ( 226-)  B      N
 536 ARG   ( 293-)  B      N
 537 ALA   ( 294-)  B      N
 553 TRP   ( 310-)  B      NE1
 572 TYR   ( 329-)  B      OH
 592 GLN   ( 349-)  B      N
 601 ILE   ( 358-)  B      N
 613 ARG   ( 370-)  B      NE

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.

  35 GLU   (  83-)  A      OE1
 418 ASP   ( 162-)  B      OD1

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.

  56 ASP   ( 108-)  A   H-bonding suggests Asn
 268 ASP   ( 338-)  A   H-bonding suggests Asn
 364 ASP   ( 108-)  B   H-bonding suggests Asn; but Alt-Rotamer
 471 ASP   ( 215-)  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 :  -0.112
  2nd generation packing quality :  -1.338
  Ramachandran plot appearance   :  -0.524
  chi-1/chi-2 rotamer normality  :  -2.170
  Backbone conformation          :   0.902

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.486 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.989
  Side chain planarity           :   0.450 (tight)
  Improper dihedral distribution :   0.756
  B-factor distribution          :   0.388
  Inside/Outside distribution    :   0.958

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 :   0.3
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.486 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.989
  Side chain planarity           :   0.450 (tight)
  Improper dihedral distribution :   0.756
  B-factor distribution          :   0.388
  Inside/Outside distribution    :   0.958
==============

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
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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,
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      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.