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 pdb1klu.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: 71015.484
Volume of the Unit Cell V= 3075203.3
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.811
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.740

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'.

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  47 ARG   (  50-)  A
 202 ARG   (  23-)  B
 250 ARG   (  71-)  B

Warning: Tyrosine convention problem

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

  10 TYR   (  13-)  A
 147 TYR   ( 150-)  A
 226 TYR   (  47-)  B
 412 TYR   (  28-)  D
 461 TYR   (  77-)  D
 469 TYR   (  85-)  D
 474 TYR   (  90-)  D
 549 TYR   ( 174-)  D
 556 TYR   ( 181-)  D
 573 TYR   ( 198-)  D
 592 TYR   ( 217-)  D

Warning: Phenylalanine convention problem

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

 105 PHE   ( 108-)  A
 109 PHE   ( 112-)  A
 192 PHE   (  13-)  B
 428 PHE   (  44-)  D
 429 PHE   (  45-)  D
 479 PHE   (  95-)  D
 498 PHE   ( 123-)  D
 571 PHE   ( 196-)  D

Warning: Aspartic acid convention problem

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

 168 ASP   ( 171-)  A
 389 ASP   (   5-)  D
 394 ASP   (  10-)  D
 413 ASP   (  29-)  D
 426 ASP   (  42-)  D
 439 ASP   (  55-)  D
 446 ASP   (  62-)  D
 535 ASP   ( 160-)  D

Warning: Glutamic acid convention problem

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

   1 GLU   (   4-)  A
  27 GLU   (  30-)  A
  44 GLU   (  47-)  A
  52 GLU   (  55-)  A
  95 GLU   (  98-)  A
 138 GLU   ( 141-)  A
 155 GLU   ( 158-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 238 GLU   (  59-)  B
 355 GLU   ( 176-)  B
 371 GLU   (  24-)  C
 451 GLU   (  67-)  D
 494 GLU   ( 119-)  D
 533 GLU   ( 158-)  D

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.308
RMS-deviation in bond distances: 0.007

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

 |  0.998382 -0.000427  0.000376|
 | -0.000427  0.999228  0.000300|
 |  0.000376  0.000300  0.998824|
Proposed new scale matrix

 |  0.005849  0.003375 -0.000003|
 |  0.000003  0.006746 -0.000002|
 | -0.000003 -0.000002  0.008273|
With corresponding cell

    A    = 171.014  B   = 171.183  C    = 120.879
    Alpha=  89.992  Beta=  89.957  Gamma= 120.012

The CRYST1 cell dimensions

    A    = 171.296  B   = 171.296  C    = 121.024
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 32.970
(Under-)estimated Z-score: 4.232

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.

   6 GLN   (   9-)  A      N    CA   C    99.77   -4.1
 160 CYS   ( 163-)  A      N    CA   C    98.74   -4.5
 288 LEU   ( 109-)  B      N    CA   C   136.98    9.2
 288 LEU   ( 109-)  B      N    CA   CB  102.52   -4.7
 288 LEU   ( 109-)  B      CB   CG   CD1  96.10   -4.9
 291 HIS   ( 112-)  B      CG   ND1  CE1 109.61    4.0
 500 ASN   ( 125-)  D     -C    N    CA  129.64    4.4

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.

   1 GLU   (   4-)  A
  27 GLU   (  30-)  A
  44 GLU   (  47-)  A
  47 ARG   (  50-)  A
  52 GLU   (  55-)  A
  95 GLU   (  98-)  A
 138 GLU   ( 141-)  A
 155 GLU   ( 158-)  A
 168 ASP   ( 171-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 202 ARG   (  23-)  B
 238 GLU   (  59-)  B
 250 ARG   (  71-)  B
 355 GLU   ( 176-)  B
 371 GLU   (  24-)  C
 389 ASP   (   5-)  D
 394 ASP   (  10-)  D
 413 ASP   (  29-)  D
 426 ASP   (  42-)  D
 439 ASP   (  55-)  D
 446 ASP   (  62-)  D
 451 GLU   (  67-)  D
 494 GLU   ( 119-)  D
 533 GLU   ( 158-)  D
 535 ASP   ( 160-)  D

Error: Tau angle problems

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

 288 LEU   ( 109-)  B   10.42
 545 LYS   ( 170-)  D    4.77
 160 CYS   ( 163-)  A    4.57

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

  13 PRO   (  16-)  A    -2.6
 110 THR   ( 113-)  A    -2.6
 518 ILE   ( 143-)  D    -2.5
 392 PRO   (   8-)  D    -2.5
 306 ILE   ( 127-)  B    -2.4
 289 GLN   ( 110-)  B    -2.4
 553 SER   ( 178-)  D    -2.3
 287 PRO   ( 108-)  B    -2.3
 336 THR   ( 157-)  B    -2.3
 200 THR   (  21-)  B    -2.3
 150 PHE   ( 153-)  A    -2.3
 333 THR   ( 154-)  B    -2.2
 217 VAL   (  38-)  B    -2.2
  98 GLU   ( 101-)  A    -2.2
 442 LEU   (  58-)  D    -2.2
 208 ARG   (  29-)  B    -2.1
 288 LEU   ( 109-)  B    -2.1
 286 GLN   ( 107-)  B    -2.1
 520 PHE   ( 145-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  36 LYS   (  39-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  97 ARG   ( 100-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 112 PRO   ( 115-)  A  Poor phi/psi
 121 ASN   ( 124-)  A  Poor phi/psi
 126 THR   ( 129-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 198 ASN   (  19-)  B  Poor phi/psi
 211 TYR   (  32-)  B  Poor phi/psi
 212 ASN   (  33-)  B  Poor phi/psi
 286 GLN   ( 107-)  B  Poor phi/psi
 287 PRO   ( 108-)  B  omega poor
 288 LEU   ( 109-)  B  Poor phi/psi
 289 GLN   ( 110-)  B  Poor phi/psi
 290 HIS   ( 111-)  B  Poor phi/psi
 302 TYR   ( 123-)  B  PRO omega poor
 313 ASN   ( 134-)  B  Poor phi/psi
 320 GLY   ( 141-)  B  Poor phi/psi
 332 TRP   ( 153-)  B  Poor phi/psi
 416 TYR   (  32-)  D  Poor phi/psi
 421 LYS   (  37-)  D  Poor phi/psi
 441 LYS   (  57-)  D  Poor phi/psi
 476 ASN   (  92-)  D  Poor phi/psi
 479 PHE   (  95-)  D  Poor phi/psi
 500 ASN   ( 125-)  D  Poor phi/psi
 513 ASN   ( 138-)  D  Poor phi/psi
 514 LYS   ( 139-)  D  Poor phi/psi
 553 SER   ( 178-)  D  Poor phi/psi
 595 ASN   ( 220-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.440

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 586 SER   ( 211-)  D    0.36

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!

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  15 GLN   (  18-)  A      0
  16 SER   (  19-)  A      0
  19 PHE   (  22-)  A      0
  23 PHE   (  26-)  A      0
  28 ILE   (  31-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  36 LYS   (  39-)  A      0
  41 ARG   (  44-)  A      0
  48 PHE   (  51-)  A      0
  76 TYR   (  79-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 120 ARG   ( 123-)  A      0
 121 ASN   ( 124-)  A      0
 126 THR   ( 129-)  A      0
And so on for a total of 254 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 : 1.714

Warning: Backbone oxygen evaluation

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

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

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

 304 GLY   ( 125-)  B   1.60   42

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  84 PRO   (  87-)  A    0.45 HIGH
 287 PRO   ( 108-)  B    0.52 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].

 287 PRO   ( 108-)  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.

 423 LYS   (  39-)  D      NZ  <->  463 ASP   (  79-)  D      C      0.56    2.54  INTRA
 289 GLN   ( 110-)  B      O   <->  291 HIS   ( 112-)  B      N      0.52    2.18  INTRA BF
 200 THR   (  21-)  B      O   <->  259 ARG   (  80-)  B      NH1    0.45    2.25  INTRA
 423 LYS   (  39-)  D      NZ  <->  463 ASP   (  79-)  D      CA     0.40    2.70  INTRA
 288 LEU   ( 109-)  B      O   <->  291 HIS   ( 112-)  B      CD2    0.38    2.42  INTRA BF
 593 ASN   ( 218-)  D      ND2 <->  622 HOH   ( 249 )  D      O      0.37    2.33  INTRA
 329 ASN   ( 150-)  B      ND2 <->  333 THR   ( 154-)  B      CG2    0.36    2.74  INTRA BL
 288 LEU   ( 109-)  B      CD1 <->  291 HIS   ( 112-)  B      CE1    0.32    2.88  INTRA BF
 283 SER   ( 104-)  B      O   <->  286 GLN   ( 107-)  B      NE2    0.32    2.38  INTRA BF
 288 LEU   ( 109-)  B      CD1 <->  291 HIS   ( 112-)  B      CG     0.29    2.91  INTRA BF
 288 LEU   ( 109-)  B      CD1 <->  291 HIS   ( 112-)  B      CD2    0.28    2.92  INTRA BF
 203 VAL   (  24-)  B      CG2 <->  259 ARG   (  80-)  B      NH1    0.27    2.83  INTRA
  73 ARG   (  76-)  A      NH2 <->  236 ASP   (  57-)  B      OD2    0.27    2.43  INTRA BL
  43 GLU   (  46-)  A      OE2 <->   47 ARG   (  50-)  A      NE     0.26    2.44  INTRA BF
 392 PRO   (   8-)  D      O   <->  397 LYS   (  13-)  D      NZ     0.26    2.44  INTRA BF
 306 ILE   ( 127-)  B      CD1 <->  307 GLU   ( 128-)  B      N      0.25    2.75  INTRA
 288 LEU   ( 109-)  B      CD1 <->  291 HIS   ( 112-)  B      ND1    0.23    2.87  INTRA BF
 463 ASP   (  79-)  D      N   <->  622 HOH   ( 303 )  D      O      0.22    2.48  INTRA
 288 LEU   ( 109-)  B      CD1 <->  291 HIS   ( 112-)  B      NE2    0.21    2.89  INTRA BF
 197 PHE   (  18-)  B      CG  <->  202 ARG   (  23-)  B      NH1    0.21    2.89  INTRA BF
  14 ASP   (  17-)  A      CG  <->  185 ARG   (   6-)  B      NH1    0.21    2.89  INTRA
  73 ARG   (  76-)  A      CD  <->  619 HOH   ( 305 )  A      O      0.20    2.60  INTRA BL
 289 GLN   ( 110-)  B      O   <->  290 HIS   ( 111-)  B      C      0.19    2.41  INTRA BF
  70 MET   (  73-)  A      SD  <->   73 ARG   (  76-)  A      NH2    0.19    3.11  INTRA BL
 506 VAL   ( 131-)  D      CG1 <->  605 ILE   ( 230-)  D      CD1    0.19    3.01  INTRA BL
And so on for a total of 119 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

  97 ARG   ( 100-)  A      -6.30
 289 GLN   ( 110-)  B      -6.11
 290 HIS   ( 111-)  B      -5.91
 612 LYS   ( 237-)  D      -5.90
 318 LYS   ( 139-)  B      -5.85
 345 ARG   ( 166-)  B      -5.83
 368 ARG   ( 189-)  B      -5.68
 183 ARG   (   4-)  B      -5.30
 453 LEU   (  69-)  D      -5.24
 288 LEU   ( 109-)  B      -5.19
 613 ASN   ( 238-)  D      -5.18
 478 TYR   (  94-)  D      -5.14

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 288 LEU   ( 109-)  B       290 - HIS    111- ( B)         -5.74

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.

 578 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.

 620 HOH   ( 248 )  B      O
 620 HOH   ( 258 )  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.

 140 HIS   ( 143-)  A
 189 GLN   (  10-)  B
 249 GLN   (  70-)  B
 291 HIS   ( 112-)  B
 472 ASN   (  88-)  D
 493 HIS   ( 118-)  D
 496 ASN   ( 121-)  D
 504 GLN   ( 129-)  D
 516 ASN   ( 141-)  D
 523 GLN   ( 148-)  D
 532 GLN   ( 157-)  D
 593 ASN   ( 218-)  D
 608 HIS   ( 233-)  D

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  42 LEU   (  45-)  A      N
 146 HIS   ( 149-)  A      ND1
 185 ARG   (   6-)  B      NH1
 189 GLN   (  10-)  B      NE2
 208 ARG   (  29-)  B      NH1
 212 ASN   (  33-)  B      N
 225 GLU   (  46-)  B      N
 254 VAL   (  75-)  B      N
 259 ARG   (  80-)  B      NH1
 286 GLN   ( 107-)  B      N
 321 VAL   ( 142-)  B      N
 329 ASN   ( 150-)  B      ND2
 403 GLY   (  19-)  D      N
 423 LYS   (  39-)  D      NZ
 424 SER   (  40-)  D      N
 431 TRP   (  47-)  D      N
 435 TYR   (  51-)  D      OH
 442 LEU   (  58-)  D      N
 454 ASN   (  70-)  D      N
 480 SER   (  96-)  D      N
 487 TYR   ( 112-)  D      OH
 549 TYR   ( 174-)  D      N
 554 SER   ( 179-)  D      N
 570 THR   ( 195-)  D      N
 594 ASP   ( 219-)  D      N
 611 THR   ( 236-)  D      OG1
 613 ASN   ( 238-)  D      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  63 ASP   (  66-)  A      OD2

Warning: Unusual water packing

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

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

 619 HOH   ( 203 )  A      O  1.07  K  4
 619 HOH   ( 233 )  A      O  0.89  K  4 Ion-B

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  18 GLU   (  21-)  A   H-bonding suggests Gln
  63 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  95 GLU   (  98-)  A   H-bonding suggests Gln
  98 GLU   ( 101-)  A   H-bonding suggests Gln
 159 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 178 ASP   ( 181-)  A   H-bonding suggests Asn
 432 ASP   (  48-)  D   H-bonding suggests Asn
 446 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 :   0.008
  2nd generation packing quality :  -1.529
  Ramachandran plot appearance   :  -1.176
  chi-1/chi-2 rotamer normality  :  -1.440
  Backbone conformation          :  -0.308

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.308 (tight)
  Bond angles                    :   0.676
  Omega angle restraints         :   0.312 (tight)
  Side chain planarity           :   0.252 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.576
  Inside/Outside distribution    :   1.038

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 : 1.93


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.308 (tight)
  Bond angles                    :   0.676
  Omega angle restraints         :   0.312 (tight)
  Side chain planarity           :   0.252 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.576
  Inside/Outside distribution    :   1.038
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

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
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      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.