WHAT IF Check report

This file was created 2013-07-12 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 pdb4i1f.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  15 GLN   ( 155-)  A  -   CB
  15 GLN   ( 155-)  A  -   CG
  15 GLN   ( 155-)  A  -   CD
  15 GLN   ( 155-)  A  -   OE1
  15 GLN   ( 155-)  A  -   NE2
  30 ARG   ( 170-)  A  -   CD
  30 ARG   ( 170-)  A  -   NE
  30 ARG   ( 170-)  A  -   CZ
  55 GLU   ( 195-)  A  -   CD
  55 GLU   ( 195-)  A  -   OE1
  55 GLU   ( 195-)  A  -   OE2
  60 HIS   ( 200-)  A  -   ND1
  60 HIS   ( 200-)  A  -   CE1
  60 HIS   ( 200-)  A  -   NE2
  71 LYS   ( 211-)  A  -   CD
  71 LYS   ( 211-)  A  -   CE
  71 LYS   ( 211-)  A  -   NZ
 138 GLN   ( 282-)  A  -   CG
 138 GLN   ( 282-)  A  -   CD
 138 GLN   ( 282-)  A  -   OE1
 138 GLN   ( 282-)  A  -   NE2
 155 LYS   ( 299-)  A  -   CG
 155 LYS   ( 299-)  A  -   CD
 155 LYS   ( 299-)  A  -   CE
 155 LYS   ( 299-)  A  -   NZ
 202 ASP   ( 346-)  A  -   CG
 202 ASP   ( 346-)  A  -   OD1
 202 ASP   ( 346-)  A  -   OD2
 203 GLN   ( 347-)  A  -   CG
 203 GLN   ( 347-)  A  -   CD
 203 GLN   ( 347-)  A  -   OE1
 203 GLN   ( 347-)  A  -   NE2
 219 GLU   ( 367-)  A  -   CG
 219 GLU   ( 367-)  A  -   CD
 219 GLU   ( 367-)  A  -   OE1
 219 GLU   ( 367-)  A  -   OE2
 228 GLU   ( 376-)  A  -   CG
 228 GLU   ( 376-)  A  -   CD
 228 GLU   ( 376-)  A  -   OE1
 228 GLU   ( 376-)  A  -   OE2
 233 ARG   ( 392-)  A  -   CG
 233 ARG   ( 392-)  A  -   CD
 233 ARG   ( 392-)  A  -   NE
 233 ARG   ( 392-)  A  -   CZ
 233 ARG   ( 392-)  A  -   NH1
 233 ARG   ( 392-)  A  -   NH2

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: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  76 PRO   ( 216-)  A    0.50
  77 THR   ( 217-)  A    0.50
  78 THR   ( 222-)  A    0.50

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

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.

  90 ARG   ( 234-)  A
 131 ARG   ( 275-)  A
 237 ARG   ( 396-)  A

Warning: Tyrosine convention problem

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

   3 TYR   ( 143-)  A
   7 TYR   ( 147-)  A
 141 TYR   ( 285-)  A
 174 TYR   ( 318-)  A
 224 TYR   ( 372-)  A
 232 TYR   ( 391-)  A

Warning: Phenylalanine convention problem

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

   6 PHE   ( 146-)  A
  69 PHE   ( 209-)  A
  70 PHE   ( 210-)  A
 133 PHE   ( 277-)  A
 216 PHE   ( 364-)  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.

 226 GLU   ( 374-)  A
 267 GLU   ( 426-)  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.

   5 SER   ( 145-)  A      CA   CB    1.62    4.4
   5 SER   ( 145-)  A      CB   OG    1.33   -4.3
  61 CYS   ( 201-)  A      C    O     1.43   10.0
  72 CYS   ( 212-)  A      CA   CB    1.62    4.7
  83 HIS   ( 227-)  A      N    CA    1.54    4.3
 113 HIS   ( 257-)  A      ND1  CE1   1.38    4.7
 135 HIS   ( 279-)  A      CG   CD2   1.41    4.5
 158 HIS   ( 302-)  A      CG   CD2   1.41    4.8
 159 HIS   ( 303-)  A      CG   CD2   1.42    6.1
 159 HIS   ( 303-)  A      ND1  CE1   1.40    6.1
 225 HIS   ( 373-)  A      CG   CD2   1.41    4.9
 244 TRP   ( 403-)  A      NE1  CE2   1.42    4.6
 274 HIS   ( 433-)  A      ND1  CE1   1.41    6.9
 286 TRP   ( 445-)  A      CD2  CE2   1.48    4.1
 294 TRP   ( 453-)  A      CD1  NE1   1.53    7.4
 300 GLY   ( 459-)  A      CA   C     1.58    4.0

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

 |  0.991039  0.001380 -0.001585|
 |  0.001380  0.995453  0.001132|
 | -0.001585  0.001132  0.993982|
Proposed new scale matrix

 |  0.011604 -0.000016  0.000019|
 | -0.000011  0.007544 -0.000009|
 |  0.000025 -0.000018  0.015387|
With corresponding cell

    A    =  86.178  B   = 132.551  C    =  64.992
    Alpha=  89.870  Beta=  90.183  Gamma=  89.841

The CRYST1 cell dimensions

    A    =  86.955  B   = 133.155  C    =  65.385
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 457.257
(Under-)estimated Z-score: 15.760

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.

  16 ARG   ( 156-)  A      CB   CG   CD  106.02   -4.0
  30 ARG   ( 170-)  A      CB   CG   CD  106.07   -4.0
  51 ARG   ( 191-)  A      CB   CG   CD  106.03   -4.0
  62 PRO   ( 202-)  A     -CA  -C    N   109.72   -4.8
  81 ALA   ( 225-)  A      C    CA   CB  104.14   -4.2
 115 ILE   ( 259-)  A      CA   CB   CG2 118.11    4.5
 156 GLU   ( 300-)  A      N    CA   C    99.95   -4.0
 159 HIS   ( 303-)  A      CG   ND1  CE1 109.97    4.4
 172 GLN   ( 316-)  A      CB   CG   CD  104.65   -4.7
 225 HIS   ( 373-)  A      CG   ND1  CE1 110.05    4.5
 243 ARG   ( 402-)  A      CG   CD   NE  103.34   -4.2
 274 HIS   ( 433-)  A      N    CA   CB  103.17   -4.3
 276 LYS   ( 435-)  A      CA   CB   CG  105.49   -4.3

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.

  90 ARG   ( 234-)  A
 131 ARG   ( 275-)  A
 226 GLU   ( 374-)  A
 237 ARG   ( 396-)  A
 267 GLU   ( 426-)  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.

  47 LEU   ( 187-)  A    4.25
  38 GLN   ( 178-)  A    4.08

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.

  50 ASN   ( 190-)  A    5.94
 302 HIS   ( 461-)  A    4.76
  25 GLN   ( 165-)  A    4.67
 172 GLN   ( 316-)  A    4.48
 135 HIS   ( 279-)  A    4.08

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   ( 153-)  A    -2.9
 144 PRO   ( 288-)  A    -2.9
 131 ARG   ( 275-)  A    -2.2
 302 HIS   ( 461-)  A    -2.2
  62 PRO   ( 202-)  A    -2.2
 156 GLU   ( 300-)  A    -2.2
  34 LEU   ( 174-)  A    -2.0
 281 GLN   ( 440-)  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 LYS   ( 151-)  A  Poor phi/psi
  12 GLY   ( 152-)  A  PRO omega poor
  30 ARG   ( 170-)  A  Poor phi/psi
  32 ALA   ( 172-)  A  Poor phi/psi
  50 ASN   ( 190-)  A  Poor phi/psi
  75 HIS   ( 215-)  A  Poor phi/psi
  91 ASN   ( 235-)  A  Poor phi/psi
  98 THR   ( 242-)  A  Poor phi/psi
 102 SER   ( 246-)  A  PRO omega poor
 131 ARG   ( 275-)  A  Poor phi/psi
 132 GLN   ( 276-)  A  omega poor
 139 LEU   ( 283-)  A  omega poor
 193 CYS   ( 337-)  A  Poor phi/psi
 209 GLU   ( 353-)  A  omega poor
 221 LYS   ( 369-)  A  Poor phi/psi
 242 ALA   ( 401-)  A  Poor phi/psi
 263 HIS   ( 422-)  A  Poor phi/psi
 265 PRO   ( 424-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.485

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 LYS   ( 151-)  A      0
  14 CYS   ( 154-)  A      0
  15 GLN   ( 155-)  A      0
  16 ARG   ( 156-)  A      0
  17 VAL   ( 157-)  A      0
  25 GLN   ( 165-)  A      0
  28 THR   ( 168-)  A      0
  29 CYS   ( 169-)  A      0
  30 ARG   ( 170-)  A      0
  32 ALA   ( 172-)  A      0
  33 THR   ( 173-)  A      0
  38 GLN   ( 178-)  A      0
  40 PRO   ( 180-)  A      0
  42 CYS   ( 182-)  A      0
  43 TRP   ( 183-)  A      0
  49 PRO   ( 189-)  A      0
  50 ASN   ( 190-)  A      0
  51 ARG   ( 191-)  A      0
  52 MET   ( 192-)  A      0
  53 SER   ( 193-)  A      0
  55 GLU   ( 195-)  A      0
  56 CYS   ( 196-)  A      0
  57 GLN   ( 197-)  A      0
  60 HIS   ( 200-)  A      0
  61 CYS   ( 201-)  A      0
And so on for a total of 156 lines.

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]

  19 PRO   ( 159-)  A    0.51 HIGH
 103 PRO   ( 247-)  A    0.19 LOW
 189 PRO   ( 333-)  A    0.09 LOW
 258 PRO   ( 417-)  A    0.46 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].

  13 PRO   ( 153-)  A   -64.6 envelop C-beta (-72 degrees)
  62 PRO   ( 202-)  A   -57.5 half-chair C-beta/C-alpha (-54 degrees)
 201 PRO   ( 345-)  A   154.6 half-chair C-alpha/N (162 degrees)
 260 PRO   ( 419-)  A   103.0 envelop C-beta (108 degrees)
 280 PRO   ( 439-)  A  -115.7 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 317 HOH   ( 609 )  A      O   <->  317 HOH   ( 730 )  A      O      1.05    1.15  INTRA
 317 HOH   ( 632 )  A      O   <->  317 HOH   ( 732 )  A      O      0.96    1.24  INTRA
 317 HOH   ( 654 )  A      O   <->  317 HOH   ( 736 )  A      O      0.96    1.24  INTRA
 317 HOH   ( 850 )  A      O   <->  317 HOH   ( 855 )  A      O      0.65    1.55  INTRA
 317 HOH   ( 672 )  A      O   <->  317 HOH   ( 836 )  A      O      0.58    1.62  INTRA
 317 HOH   ( 628 )  A      O   <->  317 HOH   ( 731 )  A      O      0.46    1.74  INTRA BF
 317 HOH   ( 706 )  A      O   <->  317 HOH   ( 809 )  A      O      0.39    1.81  INTRA
 205 LYS   ( 349-)  A      NZ  <->  317 HOH   ( 861 )  A      O      0.37    2.33  INTRA BF
  56 CYS   ( 196-)  A      SG  <->   61 CYS   ( 201-)  A      CB     0.36    3.04  INTRA
 256 THR   ( 415-)  A      OG1 <->  317 HOH   ( 776 )  A      O      0.32    2.08  INTRA BL
 317 HOH   ( 652 )  A      O   <->  317 HOH   ( 716 )  A      O      0.31    1.89  INTRA BF
 101 ARG   ( 245-)  A      NH1 <->  317 HOH   ( 632 )  A      O      0.25    2.45  INTRA
 317 HOH   ( 745 )  A      O   <->  317 HOH   ( 847 )  A      O      0.24    1.96  INTRA
 273 MET   ( 432-)  A      CE  <->  289 ASN   ( 448-)  A      CB     0.23    2.97  INTRA
  61 CYS   ( 201-)  A      CA  <->   62 PRO   ( 202-)  A      CD     0.23    2.57  INTRA BF
 158 HIS   ( 302-)  A      CD2 <->  161 ARG   ( 305-)  A      NE     0.22    2.88  INTRA
 129 ASN   ( 273-)  A      OD1 <->  170 ARG   ( 314-)  A      NH2    0.20    2.50  INTRA
 296 ARG   ( 455-)  A      NE  <->  317 HOH   ( 839 )  A      O      0.19    2.51  INTRA
  14 CYS   ( 154-)  A      SG  <->   18 GLN   ( 158-)  A      NE2    0.18    3.12  INTRA BF
 261 ARG   ( 420-)  A      CD  <->  282 CYS   ( 441-)  A      SG     0.17    3.23  INTRA
 190 ARG   ( 334-)  A      NE  <->  212 CYS   ( 360-)  A      SG     0.15    3.15  INTRA
 277 CYS   ( 436-)  A      O   <->  283 ARG   ( 442-)  A      NH1    0.13    2.57  INTRA
 273 MET   ( 432-)  A      CE  <->  289 ASN   ( 448-)  A      N      0.13    2.97  INTRA
 131 ARG   ( 275-)  A      NH2 <->  178 GLU   ( 322-)  A      OE1    0.12    2.58  INTRA
 274 HIS   ( 433-)  A      ND1 <->  317 HOH   ( 765 )  A      O      0.11    2.59  INTRA BL
 121 HIS   ( 265-)  A      CD2 <->  317 HOH   ( 629 )  A      O      0.10    2.70  INTRA
  26 CYS   ( 166-)  A      SG  <->   56 CYS   ( 196-)  A      SG     0.08    3.37  INTRA
 243 ARG   ( 402-)  A      NH1 <->  317 HOH   ( 753 )  A      O      0.07    2.63  INTRA
 190 ARG   ( 334-)  A      NH1 <->  317 HOH   ( 851 )  A      O      0.03    2.67  INTRA BF
  19 PRO   ( 159-)  A      O   <->   73 GLY   ( 213-)  A      N      0.03    2.67  INTRA
 112 ARG   ( 256-)  A      NH1 <->  245 GLU   ( 404-)  A      OE2    0.03    2.67  INTRA BL
  29 CYS   ( 169-)  A      SG  <->   56 CYS   ( 196-)  A      SG     0.03    3.42  INTRA
  61 CYS   ( 201-)  A      SG  <->   62 PRO   ( 202-)  A      CD     0.02    3.38  INTRA
 240 GLU   ( 399-)  A      O   <->  243 ARG   ( 402-)  A      NE     0.02    2.68  INTRA BL
 199 PRO   ( 343-)  A      CG  <->  218 ARG   ( 366-)  A      NH1    0.02    3.08  INTRA BF
 317 HOH   ( 649 )  A      O   <->  317 HOH   ( 733 )  A      O      0.02    2.18  INTRA BF
 295 ASN   ( 454-)  A      ND2 <->  298 CYS   ( 457-)  A      SG     0.01    3.29  INTRA BL

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.

  38 GLN   ( 178-)  A      -7.06
 138 GLN   ( 282-)  A      -6.40
  60 HIS   ( 200-)  A      -5.85
  51 ARG   ( 191-)  A      -5.75
 226 GLU   ( 374-)  A      -5.60
 269 ASN   ( 428-)  A      -5.59
 263 HIS   ( 422-)  A      -5.57
 182 GLN   ( 326-)  A      -5.56
 281 GLN   ( 440-)  A      -5.51
  57 GLN   ( 197-)  A      -5.47
 268 LYS   ( 427-)  A      -5.47
 209 GLU   ( 353-)  A      -5.41
   2 ILE   ( 142-)  A      -5.13
  90 ARG   ( 234-)  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.

  75 HIS   ( 215-)  A        77 - THR    217- ( A)         -4.57

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.

  90 ARG   ( 234-)  A   -2.61

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.

 149 CYS   ( 293-)  A     -  152 SER   ( 296-)  A        -1.55

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 317 HOH   ( 648 )  A      O     63.50   31.15  -28.61
 317 HOH   ( 698 )  A      O     57.25   37.05  -37.47
 317 HOH   ( 832 )  A      O     46.28   32.86  -30.47

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.

 108 GLN   ( 252-)  A
 121 HIS   ( 265-)  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.

  42 CYS   ( 182-)  A      N
  58 SER   ( 198-)  A      N
  61 CYS   ( 201-)  A      N
  75 HIS   ( 215-)  A      N
  83 HIS   ( 227-)  A      N
  98 THR   ( 242-)  A      OG1
 146 VAL   ( 290-)  A      N
 161 ARG   ( 305-)  A      NE
 190 ARG   ( 334-)  A      NH2
 218 ARG   ( 366-)  A      NH1
 225 HIS   ( 373-)  A      N
 281 GLN   ( 440-)  A      N
 286 TRP   ( 445-)  A      NE1
 295 ASN   ( 454-)  A      N
 304 PHE   ( 463-)  A      N
Only metal coordination for   75 HIS  ( 215-) A      NE2
Only metal coordination for  113 HIS  ( 257-) A      ND1
Only metal coordination for  225 HIS  ( 373-) A      NE2
Only metal coordination for  302 HIS  ( 461-) 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.

 135 HIS   ( 279-)  A      ND1

Warning: Unusual water packing

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

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

 317 HOH   ( 685 )  A      O  1.07  K  4 Ion-B

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 :  -2.052
  2nd generation packing quality :  -2.729
  Ramachandran plot appearance   :  -0.404
  chi-1/chi-2 rotamer normality  :  -1.485
  Backbone conformation          :  -1.316

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.218
  Bond angles                    :   1.181
  Omega angle restraints         :   1.188
  Side chain planarity           :   1.762
  Improper dihedral distribution :   1.504 (loose)
  B-factor distribution          :   1.187
  Inside/Outside distribution    :   0.972

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 : 1.58


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.9
  2nd generation packing quality :  -2.0
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :  -1.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.218
  Bond angles                    :   1.181
  Omega angle restraints         :   1.188
  Side chain planarity           :   1.762
  Improper dihedral distribution :   1.504 (loose)
  B-factor distribution          :   1.187
  Inside/Outside distribution    :   0.972
==============

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
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      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      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
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      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.