WHAT IF Check report

This file was created 2011-12-28 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 pdb1h7k.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: 54651.891
Volume of the Unit Cell V= 2632273.3
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.014
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 3.820

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.

 479 ACT   ( 700-)  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

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

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 476 GLU   ( 479-)  A

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

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.

  96 ARG   (  99-)  A
 103 ARG   ( 106-)  A
 149 ARG   ( 152-)  A
 153 ARG   ( 156-)  A
 179 ARG   ( 182-)  A
 368 ARG   ( 371-)  A
 410 ARG   ( 413-)  A

Warning: Tyrosine convention problem

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

 270 TYR   ( 273-)  A
 379 TYR   ( 382-)  A
 423 TYR   ( 426-)  A

Warning: Phenylalanine convention problem

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

  89 PHE   (  92-)  A
 112 PHE   ( 115-)  A
 242 PHE   ( 245-)  A

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.

 100 ASP   ( 103-)  A
 139 ASP   ( 142-)  A
 224 ASP   ( 227-)  A
 233 ASP   ( 236-)  A
 240 ASP   ( 243-)  A
 249 ASP   ( 252-)  A
 283 ASP   ( 286-)  A
 299 ASP   ( 302-)  A
 414 ASP   ( 417-)  A

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   (  38-)  A
  43 GLU   (  46-)  A
  84 GLU   (  87-)  A
 225 GLU   ( 228-)  A
 246 GLU   ( 249-)  A
 264 GLU   ( 267-)  A
 411 GLU   ( 414-)  A
 424 GLU   ( 427-)  A
 463 GLU   ( 466-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   3 LEU   (   6-)  A      CA   CB    1.43   -4.9
  15 ASN   (  18-)  A      C    O     1.38    7.6
  16 ASN   (  19-)  A      N   -C     1.13  -10.1
  96 ARG   (  99-)  A      NE   CZ    1.55   16.0
  96 ARG   (  99-)  A      CZ   NH2   1.14  -10.3
 100 ASP   ( 103-)  A      CB   CG    1.63    4.7
 100 ASP   ( 103-)  A      CG   OD1   1.37    6.3
 100 ASP   ( 103-)  A      CG   OD2   1.13   -6.0
 150 THR   ( 153-)  A      CA   CB    1.34   -9.5
 151 ASN   ( 154-)  A      CA   CB    1.62    4.6
 346 HIS   ( 349-)  A      CB   CG    1.57    5.3
 346 HIS   ( 349-)  A      CG   ND1   1.51    8.3
 346 HIS   ( 349-)  A      CG   CD2   1.19  -14.7
 354 PRO   ( 357-)  A      N    CA    1.66   12.9
 354 PRO   ( 357-)  A      N   -C     1.19   -6.8
 361 TYR   ( 364-)  A      CA   CB    1.63    4.9
 361 TYR   ( 364-)  A      CB   CG    1.36   -6.8
 362 HIS   ( 365-)  A      N   -C     1.53   10.0
 469 GLU   ( 472-)  A      CD   OE2   1.40    7.7

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

 |  0.997825  0.000381 -0.000344|
 |  0.000381  0.998050 -0.000052|
 | -0.000344 -0.000052  0.999469|
Proposed new scale matrix

 |  0.009109  0.005256  0.000003|
 | -0.000004  0.010518  0.000000|
 |  0.000001  0.000000  0.003983|
With corresponding cell

    A    = 109.760  B   = 109.748  C    = 251.060
    Alpha=  89.981  Beta=  90.041  Gamma= 119.963

The CRYST1 cell dimensions

    A    = 110.000  B   = 110.000  C    = 251.200
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 43.275
(Under-)estimated Z-score: 4.848

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.

  15 ASN   (  18-)  A      CA   C    O   105.65   -8.9
  16 ASN   (  19-)  A     -CA  -C    N   124.67    4.2
  51 HIS   (  54-)  A      CA   C    O   130.25    5.6
  52 ALA   (  55-)  A     -O   -C    N   112.47   -6.6
  96 ARG   (  99-)  A      NE   CZ   NH1 106.07   -7.3
  96 ARG   (  99-)  A      NH1  CZ   NH2 136.82    9.5
 100 ASP   ( 103-)  A      CB   CG   OD1 107.64   -4.7
 150 THR   ( 153-)  A      CA   CB   CG2 120.75    6.0
 150 THR   ( 153-)  A      CA   CB   OG1 120.29    7.1
 314 ASN   ( 317-)  A      CA   C    O   112.02   -5.2
 315 ILE   ( 318-)  A     -O   -C    N   132.53    6.0
 346 HIS   ( 349-)  A      CA   CB   CG  119.08    5.3
 346 HIS   ( 349-)  A      CB   CG   ND1 109.60   -8.0
 346 HIS   ( 349-)  A      NE2  CD2  CG  110.79    4.3
 346 HIS   ( 349-)  A      CB   CG   CD2 139.18    7.8
 347 HIS   ( 350-)  A      CG   ND1  CE1 109.63    4.0
 354 PRO   ( 357-)  A     -O   -C    N   127.97    4.3
 354 PRO   ( 357-)  A     -CA  -C    N   110.83   -4.0
 354 PRO   ( 357-)  A      CD   N    CA  100.18   -8.4
 361 TYR   ( 364-)  A      C    CA   CB  101.27   -4.6
 361 TYR   ( 364-)  A      CB   CG   CD1 128.55    5.2
 361 TYR   ( 364-)  A      CB   CG   CD2 113.16   -5.1
 362 HIS   ( 365-)  A     -C    N    CA  108.56   -7.3
 362 HIS   ( 365-)  A      N    CA   CB   99.76   -6.3

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   (  38-)  A
  43 GLU   (  46-)  A
  84 GLU   (  87-)  A
  96 ARG   (  99-)  A
 100 ASP   ( 103-)  A
 103 ARG   ( 106-)  A
 139 ASP   ( 142-)  A
 149 ARG   ( 152-)  A
 153 ARG   ( 156-)  A
 179 ARG   ( 182-)  A
 224 ASP   ( 227-)  A
 225 GLU   ( 228-)  A
 233 ASP   ( 236-)  A
 240 ASP   ( 243-)  A
 246 GLU   ( 249-)  A
 249 ASP   ( 252-)  A
 264 GLU   ( 267-)  A
 283 ASP   ( 286-)  A
 299 ASP   ( 302-)  A
 368 ARG   ( 371-)  A
 410 ARG   ( 413-)  A
 411 GLU   ( 414-)  A
 414 ASP   ( 417-)  A
 424 GLU   ( 427-)  A
 463 GLU   ( 466-)  A

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.

 333 SER   ( 336-)  A    6.52
 304 ASP   ( 307-)  A    4.29
  93 ALA   (  96-)  A    4.12
 416 PHE   ( 419-)  A    4.10
 146 ARG   ( 149-)  A    4.10

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 100 ASP   ( 103-)  A   14.34
 346 HIS   ( 349-)  A    8.59
 469 GLU   ( 472-)  A    4.20

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.

 350 PRO   ( 353-)  A    -2.5
  60 THR   (  63-)  A    -2.3
 143 ILE   ( 146-)  A    -2.3
 363 ARG   ( 366-)  A    -2.2
 181 LEU   ( 184-)  A    -2.2
 129 PHE   ( 132-)  A    -2.1
 144 VAL   ( 147-)  A    -2.1
 321 PHE   ( 324-)  A    -2.1
 376 GLY   ( 379-)  A    -2.1
 132 ARG   ( 135-)  A    -2.0
 122 VAL   ( 125-)  A    -2.0
 110 LEU   ( 113-)  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.

  51 HIS   (  54-)  A  Poor phi/psi
 101 ALA   ( 104-)  A  Poor phi/psi
 145 LYS   ( 148-)  A  Poor phi/psi
 151 ASN   ( 154-)  A  Poor phi/psi
 193 SER   ( 196-)  A  Poor phi/psi
 203 ASN   ( 206-)  A  Poor phi/psi
 320 SER   ( 323-)  A  Poor phi/psi
 321 PHE   ( 324-)  A  Poor phi/psi
 364 ASP   ( 367-)  A  Poor phi/psi
 372 ASN   ( 375-)  A  Poor phi/psi
 380 GLU   ( 383-)  A  PRO omega poor
 387 PHE   ( 390-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.712

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!

  14 ASN   (  17-)  A      0
  15 ASN   (  18-)  A      0
  16 ASN   (  19-)  A      0
  20 ALA   (  23-)  A      0
  23 ARG   (  26-)  A      0
  29 GLN   (  32-)  A      0
  42 ARG   (  45-)  A      0
  43 GLU   (  46-)  A      0
  49 ARG   (  52-)  A      0
  50 OMT   (  53-)  A      0
  53 LYS   (  56-)  A      0
  67 ILE   (  70-)  A      0
  70 TYR   (  73-)  A      0
  71 THR   (  74-)  A      0
  72 ARG   (  75-)  A      0
  79 VAL   (  82-)  A      0
  81 LYS   (  84-)  A      0
  84 GLU   (  87-)  A      0
  85 MET   (  88-)  A      0
  92 VAL   (  95-)  A      0
  93 ALA   (  96-)  A      0
  98 ALA   ( 101-)  A      0
 101 ALA   ( 104-)  A      0
 103 ARG   ( 106-)  A      0
 104 ASP   ( 107-)  A      0
And so on for a total of 189 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 : 1.488

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]

 357 PRO   ( 360-)  A    0.45 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 419 PRO   ( 422-)  A  -112.9 envelop C-gamma (-108 degrees)
 462 PRO   ( 465-)  A  -118.8 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.

 189 HIS   ( 192-)  A      ND1 <->  214 CYS   ( 217-)  A      N      0.19    2.81  INTRA BL
 192 GLY   ( 195-)  A      O   <->  194 HIS   ( 197-)  A      N      0.13    2.57  INTRA BL
  67 ILE   (  70-)  A      N   <->  479 HOH   (2030 )  A      O      0.13    2.57  INTRA BF
 103 ARG   ( 106-)  A      NH2 <->  479 HOH   (2045 )  A      O      0.13    2.57  INTRA BF
  90 SER   (  93-)  A      O   <->  107 GLY   ( 110-)  A      N      0.11    2.59  INTRA BL
 153 ARG   ( 156-)  A      NH2 <->  479 HOH   (2066 )  A      O      0.08    2.62  INTRA BF
 338 HIS   ( 341-)  A      O   <->  342 LEU   ( 345-)  A      N      0.08    2.62  INTRA BL
  53 LYS   (  56-)  A      CE  <->   98 ALA   ( 101-)  A      O      0.07    2.73  INTRA BF
  88 ARG   (  91-)  A      NH1 <->  476 HEM   ( 600-)  A      O1D    0.05    2.65  INTRA BL
 194 HIS   ( 197-)  A      NE2 <->  330 ARG   ( 333-)  A      NH1    0.05    2.95  INTRA BL
 126 THR   ( 129-)  A      OG1 <->  171 GLN   ( 174-)  A      NE2    0.05    2.65  INTRA BL
 155 MET   ( 158-)  A      CE  <->  441 GLU   ( 444-)  A      CD     0.05    3.15  INTRA BF
 103 ARG   ( 106-)  A      NH1 <->  223 ASP   ( 226-)  A      OD1    0.04    2.66  INTRA BF
 208 VAL   ( 211-)  A      CG2 <->  209 LYS   ( 212-)  A      N      0.04    2.96  INTRA BL
  50 OMT   (  53-)  A      SD  <->  141 ASN   ( 144-)  A      ND2    0.04    3.26  INTRA
  15 ASN   (  18-)  A      C   <->   16 ASN   (  19-)  A      CA     0.04    2.26  INTRA BL
   5 THR   (   8-)  A      N   <->    9 ALA   (  12-)  A      O      0.04    2.66  INTRA BL
 192 GLY   ( 195-)  A      N   <->  193 SER   ( 196-)  A      N      0.03    2.57  INTRA BL
 194 HIS   ( 197-)  A      CD2 <->  330 ARG   ( 333-)  A      NH1    0.03    3.07  INTRA BL
 356 CYS   ( 359-)  A      CB  <->  357 PRO   ( 360-)  A      CD     0.02    3.08  INTRA BF
 376 GLY   ( 379-)  A      N   <->  479 HOH   (2141 )  A      O      0.02    2.68  INTRA BF
 411 GLU   ( 414-)  A      N   <->  412 ASP   ( 415-)  A      N      0.02    2.58  INTRA BF
 364 ASP   ( 367-)  A      CB  <->  365 GLY   ( 368-)  A      N      0.02    2.68  INTRA BL
  64 THR   (  67-)  A      OG1 <->   65 HIS   (  68-)  A      ND1    0.02    2.68  INTRA BF
 229 LEU   ( 232-)  A      O   <->  233 ASP   ( 236-)  A      N      0.02    2.68  INTRA BF
 196 TYR   ( 199-)  A      N   <->  208 VAL   ( 211-)  A      O      0.01    2.69  INTRA BL
 423 TYR   ( 426-)  A      O   <->  431 HIS   ( 434-)  A      NE2    0.01    2.69  INTRA BF
 104 ASP   ( 107-)  A      O   <->  106 ARG   ( 109-)  A      NH1    0.01    2.69  INTRA

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

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.

  23 ARG   (  26-)  A      -8.98
  49 ARG   (  52-)  A      -7.96
 270 TYR   ( 273-)  A      -6.75
  48 ARG   (  51-)  A      -6.74
 363 ARG   ( 366-)  A      -6.53
 355 LYS   ( 358-)  A      -6.10
 375 ASN   ( 378-)  A      -6.04
 401 GLU   ( 404-)  A      -5.94
 394 LYS   ( 397-)  A      -5.90
 146 ARG   ( 149-)  A      -5.90
 379 TYR   ( 382-)  A      -5.86
 400 ILE   ( 403-)  A      -5.68
 348 GLN   ( 351-)  A      -5.34
 398 LEU   ( 401-)  A      -5.34
 389 GLU   ( 392-)  A      -5.33
 103 ARG   ( 106-)  A      -5.30
 215 GLN   ( 218-)  A      -5.28
 341 ARG   ( 344-)  A      -5.21
 358 PHE   ( 361-)  A      -5.09
 352 ASN   ( 355-)  A      -5.05

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.

 361 TYR   ( 364-)  A       363 - ARG    366- ( A)         -5.15
 393 PHE   ( 396-)  A       395 - GLU    398- ( A)         -5.23

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

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.

  98 ALA   ( 101-)  A   -2.82
 153 ARG   ( 156-)  A   -2.69
 270 TYR   ( 273-)  A   -2.67
 342 LEU   ( 345-)  A   -2.62
 145 LYS   ( 148-)  A   -2.56

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

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.

 479 HOH   (2032 )  A      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.

  16 ASN   (  19-)  A
 171 GLN   ( 174-)  A
 215 GLN   ( 218-)  A
 256 GLN   ( 259-)  A
 297 ASN   ( 300-)  A
 328 GLN   ( 331-)  A
 360 ASN   ( 363-)  A
 388 GLN   ( 391-)  A
 461 HIS   ( 464-)  A

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.

  48 ARG   (  51-)  A      NE
  50 OMT   (  53-)  A      N
  54 GLY   (  57-)  A      N
  78 GLU   (  81-)  A      N
  88 ARG   (  91-)  A      NH1
  94 GLY   (  97-)  A      N
  95 GLU   (  98-)  A      N
  97 GLY   ( 100-)  A      N
 124 ASN   ( 127-)  A      ND2
 126 THR   ( 129-)  A      N
 130 TYR   ( 133-)  A      N
 131 LEU   ( 134-)  A      N
 141 ASN   ( 144-)  A      ND2
 153 ARG   ( 156-)  A      NH1
 184 SER   ( 187-)  A      N
 188 VAL   ( 191-)  A      N
 205 ARG   ( 208-)  A      NE
 212 TYR   ( 215-)  A      OH
 220 ASN   ( 223-)  A      ND2
 270 TYR   ( 273-)  A      N
 270 TYR   ( 273-)  A      OH
 279 TRP   ( 282-)  A      N
 316 VAL   ( 319-)  A      N
 322 SER   ( 325-)  A      N
 328 GLN   ( 331-)  A      NE2
 330 ARG   ( 333-)  A      NH2
 334 TYR   ( 337-)  A      OH
 341 ARG   ( 344-)  A      NE
 341 ARG   ( 344-)  A      NH2
 360 ASN   ( 363-)  A      ND2
 363 ARG   ( 366-)  A      NE
 379 TYR   ( 382-)  A      N
 387 PHE   ( 390-)  A      N
 410 ARG   ( 413-)  A      NH2
 452 ARG   ( 455-)  A      NH1
 453 GLN   ( 456-)  A      NE2

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.

  39 HIS   (  42-)  A      NE2
  41 ASP   (  44-)  A      OD2
 359 HIS   ( 362-)  A      ND1
 453 GLN   ( 456-)  A      OE1

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.

  41 ASP   (  44-)  A   H-bonding suggests Asn
 304 ASP   ( 307-)  A   H-bonding suggests Asn
 455 ASP   ( 458-)  A   H-bonding suggests Asn

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 :  -1.757
  2nd generation packing quality :  -1.760
  Ramachandran plot appearance   :  -0.825
  chi-1/chi-2 rotamer normality  :  -1.712
  Backbone conformation          :  -0.842

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.556 (tight)
  Bond angles                    :   0.798
  Omega angle restraints         :   0.271 (tight)
  Side chain planarity           :   1.251
  Improper dihedral distribution :   0.837
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.099

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.1
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.556 (tight)
  Bond angles                    :   0.798
  Omega angle restraints         :   0.271 (tight)
  Side chain planarity           :   1.251
  Improper dihedral distribution :   0.837
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.099
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

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

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.