WHAT IF Check report

This file was created 2011-12-15 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 pdb2f5o.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 4

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: 36792.832
Volume of the Unit Cell V= 446993.156
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.074
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.730 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 4
which would result in the much more normal Vm= 3.037
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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.

 281 GOL   ( 301-)  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: 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'.

  64 ARG   (  38-)  A      CG
  64 ARG   (  38-)  A      CD
  64 ARG   (  38-)  A      NE
  64 ARG   (  38-)  A      CZ
  64 ARG   (  38-)  A      NH1
  64 ARG   (  38-)  A      NH2
 106 ARG   (  80-)  A      CG
 106 ARG   (  80-)  A      CD
 106 ARG   (  80-)  A      NE
 106 ARG   (  80-)  A      CZ
 106 ARG   (  80-)  A      NH1
 106 ARG   (  80-)  A      NH2
 176 GLU   ( 150-)  A      CG
 176 GLU   ( 150-)  A      CD
 176 GLU   ( 150-)  A      OE1
 176 GLU   ( 150-)  A      OE2
 179 VAL   ( 153-)  A      CG1
 179 VAL   ( 153-)  A      CG2
 180 LYS   ( 154-)  A      CG
 180 LYS   ( 154-)  A      CD
 180 LYS   ( 154-)  A      CE
 180 LYS   ( 154-)  A      NZ
 182 LYS   ( 156-)  A      CG
 182 LYS   ( 156-)  A      CD
 182 LYS   ( 156-)  A      CE
 182 LYS   ( 156-)  A      NZ
 231 GLU   ( 205-)  A      CG
 231 GLU   ( 205-)  A      CD
 231 GLU   ( 205-)  A      OE1
 231 GLU   ( 205-)  A      OE2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 DADE  (   1-)  B    High
   2 DGUA  (   2-)  B    High
  15 DGUA  (   3-)  C    High
  16 DTHY  (   4-)  C    High
  26 DCYT  (  14-)  C    High
  27 DCYT  (  15-)  C    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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) : 77.000

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.

  38 ARG   (  12-)  A
  94 ARG   (  68-)  A
 138 ARG   ( 112-)  A
 153 ARG   ( 127-)  A
 183 ARG   ( 157-)  A
 256 ARG   ( 251-)  A
 269 ARG   ( 264-)  A
 276 ARG   ( 271-)  A
 279 ARG   ( 274-)  A

Warning: Tyrosine convention problem

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

 107 TYR   (  81-)  A
 134 TYR   ( 108-)  A
 202 TYR   ( 176-)  A
 245 TYR   ( 240-)  A

Warning: Phenylalanine convention problem

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

  69 PHE   (  43-)  A
  87 PHE   (  61-)  A
  90 PHE   (  64-)  A
 169 PHE   ( 143-)  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.

  51 ASP   (  25-)  A
  65 ASP   (  39-)  A
  95 ASP   (  69-)  A
 152 ASP   ( 126-)  A
 191 ASP   ( 165-)  A
 204 ASP   ( 178-)  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.

  29 GLU   (   3-)  A
 149 GLU   ( 123-)  A
 163 GLU   ( 137-)  A
 239 GLU   ( 213-)  A
 262 GLU   ( 257-)  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.

  12 DGUA  (  12-)  B      O5'  C5'   1.38   -4.0
  60 ILE   (  34-)  A      CA   CB    1.62    4.5
 231 GLU   ( 205-)  A      CA   CB    1.61    4.1

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

 |  0.998100  0.000415 -0.000185|
 |  0.000415  0.998359  0.000089|
 | -0.000185  0.000089  0.998713|
Proposed new scale matrix

 |  0.021999 -0.000009  0.000004|
 | -0.000004  0.010742  0.000000|
 |  0.000002  0.000000  0.009513|
With corresponding cell

    A    =  45.457  B   =  93.096  C    = 105.117
    Alpha=  90.001  Beta=  90.021  Gamma=  89.952

The CRYST1 cell dimensions

    A    =  45.543  B   =  93.253  C    = 105.257
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 58.703
(Under-)estimated Z-score: 5.647

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.

  12 DGUA  (  12-)  B      C3'  C4'  C5' 106.51   -5.5
  15 DGUA  (   3-)  C      N9   C8   N7  113.12    4.0
 132 LEU   ( 106-)  A      N    CA   C    99.26   -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.

  29 GLU   (   3-)  A
  38 ARG   (  12-)  A
  51 ASP   (  25-)  A
  65 ASP   (  39-)  A
  94 ARG   (  68-)  A
  95 ASP   (  69-)  A
 138 ARG   ( 112-)  A
 149 GLU   ( 123-)  A
 152 ASP   ( 126-)  A
 153 ARG   ( 127-)  A
 163 GLU   ( 137-)  A
 183 ARG   ( 157-)  A
 191 ASP   ( 165-)  A
 204 ASP   ( 178-)  A
 239 GLU   ( 213-)  A
 256 ARG   ( 251-)  A
 262 GLU   ( 257-)  A
 269 ARG   ( 264-)  A
 276 ARG   ( 271-)  A
 279 ARG   ( 274-)  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.

 132 LEU   ( 106-)  A    4.39
 171 PRO   ( 145-)  A    4.25
 148 LYS   ( 122-)  A    4.07

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.533

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.

 156 PRO   ( 130-)  A    -2.7
 140 PHE   ( 114-)  A    -2.6
  41 LEU   (  15-)  A    -2.5
 237 ILE   ( 211-)  A    -2.2
 256 ARG   ( 251-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

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

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

  44 ILE   (  18-)  A  Poor phi/psi
  62 HIS   (  36-)  A  PRO omega poor
  92 LEU   (  66-)  A  Poor phi/psi
 102 ARG   (  76-)  A  Poor phi/psi
 119 HIS   (  93-)  A  Poor phi/psi
 139 LYS   ( 113-)  A  Poor phi/psi
 155 PRO   ( 129-)  A  PRO omega poor
 267 ALA   ( 262-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.932

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 DGUA  (   3-)  B      0
   4 DTHY  (   4-)  B      0
   5 DADE  (   5-)  B      0
   6 DGUA  (   6-)  B      0
   7 DADE  (   7-)  B      0
   8 DTHY  (   8-)  B      0
   9 DCYT  (   9-)  B      0
  10 DCYT  (  10-)  B      0
  11 DGUA  (  11-)  B      0
  12 DGUA  (  12-)  B      0
  13 DADE  (  13-)  B      0
  14 DCYT  (  14-)  B      0
  15 DGUA  (   3-)  C      0
  16 DTHY  (   4-)  C      0
  17 DCYT  (   5-)  C      0
  18 DCYT  (   6-)  C      0
  19 DGUA  (   7-)  C      0
  20 DGUA  (   8-)  C      0
  21 DADE  (   9-)  C      0
  22 DTHY  (  10-)  C      0
  23 DCYT  (  11-)  C      0
  24 DTHY  (  12-)  C      0
  25 DADE  (  13-)  C      0
  26 DCYT  (  14-)  C      0
  27 DCYT  (  15-)  C      0
And so on for a total of 116 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 : 2.300

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]

  31 PRO   (   5-)  A    0.48 HIGH
 217 PRO   ( 191-)  A    0.48 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].

  28 PRO   (   2-)  A  -124.6 half-chair C-delta/C-gamma (-126 degrees)
  42 PRO   (  16-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
  63 PRO   (  37-)  A  -122.4 half-chair C-delta/C-gamma (-126 degrees)
 164 PRO   ( 138-)  A  -114.3 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.

 159 GLU   ( 133-)  A      N   <->  284 HOH   ( 426 )  A      O      0.70    2.00  INTRA
  13 DADE  (  13-)  B      N1  <->   16 DTHY  (   4-)  C      N3     0.52    2.48  INTRA BF
 125 CYS   (  99-)  A      SG  <->  284 HOH   ( 305 )  A      O      0.45    2.55  INTRA BL
  19 DGUA  (   7-)  C      N3  <->  103 MET   (  77-)  A      CE     0.43    2.67  INTRA BF
  84 ARG   (  58-)  A      NH2 <->  284 HOH   ( 344 )  A      O      0.32    2.38  INTRA
 117 GLU   (  91-)  A      N   <->  284 HOH   ( 387 )  A      O      0.30    2.40  INTRA BL
   2 DGUA  (   2-)  B      N1  <->   27 DCYT  (  15-)  C      N3     0.29    2.71  INTRA BF
  84 ARG   (  58-)  A      NH1 <->  284 HOH   ( 416 )  A      O      0.25    2.45  INTRA BF
  10 DCYT  (  10-)  B      N3  <->   19 DGUA  (   7-)  C      N1     0.19    2.81  INTRA BF
   8 DTHY  (   8-)  B      N3  <->   21 DADE  (   9-)  C      N1     0.19    2.81  INTRA
  22 DTHY  (  10-)  C      C2' <->   23 DCYT  (  11-)  C      C6     0.17    3.03  INTRA BF
 150 GLU   ( 124-)  A      OE2 <->  154 ARG   ( 128-)  A      NE     0.17    2.53  INTRA BF
 243 HIS   ( 238-)  A      CG  <->  244 LEU   ( 239-)  A      N      0.17    2.83  INTRA BF
 235 ALA   ( 209-)  A      O   <->  239 GLU   ( 213-)  A      CG     0.16    2.64  INTRA
 133 ARG   ( 107-)  A      NH1 <->  284 HOH   ( 383 )  A      O      0.14    2.56  INTRA
   9 DCYT  (   9-)  B      N3  <->   20 DGUA  (   8-)  C      N1     0.14    2.86  INTRA
   5 DADE  (   5-)  B      N1  <->   24 DTHY  (  12-)  C      N3     0.12    2.88  INTRA BF
  22 DTHY  (  10-)  C      C2' <->   23 DCYT  (  11-)  C      C5'    0.12    3.08  INTRA BF
  89 LYS   (  63-)  A      NZ  <->  152 ASP   ( 126-)  A      OD1    0.12    2.58  INTRA BL
  55 PHE   (  29-)  A      N   <->  121 HIS   (  95-)  A      O      0.11    2.59  INTRA BL
  12 DGUA  (  12-)  B      C2' <->   13 DADE  (  13-)  B      C5'    0.11    3.09  INTRA BF
  20 DGUA  (   8-)  C      OP2 <->  283 HOH   (  28 )  C      O      0.11    2.29  INTRA BL
 148 LYS   ( 122-)  A      NZ  <->  284 HOH   ( 354 )  A      O      0.11    2.59  INTRA BL
   2 DGUA  (   2-)  B      N2  <->   27 DCYT  (  15-)  C      O2     0.10    2.60  INTRA BF
 152 ASP   ( 126-)  A      N   <->  284 HOH   ( 377 )  A      O      0.09    2.61  INTRA BL
  85 GLY   (  59-)  A      N   <->  163 GLU   ( 137-)  A      OE2    0.09    2.61  INTRA BL
  94 ARG   (  68-)  A      NE  <->  284 HOH   ( 319 )  A      O      0.09    2.61  INTRA
  69 PHE   (  43-)  A      CE2 <->  145 VAL   ( 119-)  A      CG2    0.08    3.12  INTRA BL
  61 ARG   (  35-)  A      NH2 <->  284 HOH   ( 327 )  A      O      0.08    2.62  INTRA BL
  15 DGUA  (   3-)  C      C2' <->   16 DTHY  (   4-)  C      C7     0.08    3.12  INTRA BF
  41 LEU   (  15-)  A      CB  <->   42 PRO   (  16-)  A      CD     0.06    3.04  INTRA BL
 184 SER   ( 158-)  A      N   <->  284 HOH   ( 407 )  A      O      0.06    2.64  INTRA
 201 ILE   ( 175-)  A      CG2 <->  202 TYR   ( 176-)  A      N      0.05    2.95  INTRA BL
 121 HIS   (  95-)  A      NE2 <->  136 ASP   ( 110-)  A      O      0.04    2.66  INTRA BL
   4 DTHY  (   4-)  B      N3  <->   25 DADE  (  13-)  C      N1     0.04    2.96  INTRA BF
 255 LYS   ( 250-)  A      N   <->  284 HOH   ( 342 )  A      O      0.04    2.66  INTRA BL
  12 DGUA  (  12-)  B      N1  <->   17 DCYT  (   5-)  C      N3     0.03    2.97  INTRA BF
  28 PRO   (   2-)  A      N   <->  284 HOH   ( 414 )  A      O      0.03    2.67  INTRA
  65 ASP   (  39-)  A      OD1 <->   67 GLU   (  41-)  A      N      0.03    2.67  INTRA BL
 241 VAL   ( 215-)  A      CG1 <->  242 MET   ( 216-)  A      N      0.03    2.97  INTRA BF
  13 DADE  (  13-)  B      N6  <->   16 DTHY  (   4-)  C      O4     0.03    2.67  INTRA BF
 257 CYS   ( 252-)  A      SG  <->  259 THR   ( 254-)  A      CB     0.03    3.37  INTRA BL
  38 ARG   (  12-)  A      O   <->  284 HOH   ( 372 )  A      O      0.02    2.38  INTRA BL
 185 VAL   ( 159-)  A      N   <->  216 ARG   ( 190-)  A      O      0.02    2.68  INTRA BL
 102 ARG   (  76-)  A      CB  <->  103 MET   (  77-)  A      N      0.02    2.68  INTRA BL
 100 HIS   (  74-)  A      ND1 <->  102 ARG   (  76-)  A      N      0.02    2.98  INTRA BL
 146 TYR   ( 120-)  A      C   <->  147 ALA   ( 121-)  A      C      0.01    2.79  INTRA BL
  83 ARG   (  57-)  A      NH1 <->  163 GLU   ( 137-)  A      OE1    0.01    2.69  INTRA BL
  86 LYS   (  60-)  A      NZ  <->  283 HOH   (  19 )  C      O      0.01    2.69  INTRA
  30 LEU   (   4-)  A      N   <->   31 PRO   (   5-)  A      CD     0.01    2.99  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.

 256 ARG   ( 251-)  A      -6.48
 113 LEU   (  87-)  A      -6.01
 103 MET   (  77-)  A      -5.96
 153 ARG   ( 127-)  A      -5.71
 209 ARG   ( 183-)  A      -5.19
 140 PHE   ( 114-)  A      -5.17
  61 ARG   (  35-)  A      -5.11
 116 LEU   (  90-)  A      -5.02

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.

 138 ARG   ( 112-)  A       140 - PHE    114- ( A)         -4.58

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.

 101 LEU   (  75-)  A   -2.83
  64 ARG   (  38-)  A   -2.76

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.

 284 HOH   ( 422 )  A      O    -13.05   77.72    0.59

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.

  58 ASN   (  32-)  A
  62 HIS   (  36-)  A
  76 GLN   (  50-)  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.

 103 MET   (  77-)  A      N
 116 LEU   (  90-)  A      N
 140 PHE   ( 114-)  A      N
 244 LEU   ( 239-)  A      N
 248 GLY   ( 243-)  A      N
 250 GLN   ( 245-)  A      N

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.

 284 HOH   ( 315 )  A      O  1.01  K  4
 284 HOH   ( 398 )  A      O  1.05  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.

 131 GLU   ( 105-)  A   H-bonding suggests Gln; 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 :  -0.700
  2nd generation packing quality :  -0.686
  Ramachandran plot appearance   :   0.122
  chi-1/chi-2 rotamer normality  :  -1.932
  Backbone conformation          :   0.156

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.753
  Bond angles                    :   0.902
  Omega angle restraints         :   0.418 (tight)
  Side chain planarity           :   0.390 (tight)
  Improper dihedral distribution :   0.914
  B-factor distribution          :   0.802
  Inside/Outside distribution    :   1.036

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.753
  Bond angles                    :   0.902
  Omega angle restraints         :   0.418 (tight)
  Side chain planarity           :   0.390 (tight)
  Improper dihedral distribution :   0.914
  B-factor distribution          :   0.802
  Inside/Outside distribution    :   1.036
==============

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Checking checks
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