WHAT IF Check report

This file was created 2011-12-13 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 pdb3c58.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 41 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
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 8

Error: Matthews Coefficient (Vm) very 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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 39267.785
Volume of the Unit Cell V= 1176350.5
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.489
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.670 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 8
which would result in the much more normal Vm= 3.745
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.

 300 GOL   ( 402-)  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'.

  15 LYS   (  15-)  A      CE
  15 LYS   (  15-)  A      NZ
  31 ARG   (  31-)  A      CZ
  31 ARG   (  31-)  A      NH1
  31 ARG   (  31-)  A      NH2
  42 LYS   (  42-)  A      CD
  42 LYS   (  42-)  A      CE
  42 LYS   (  42-)  A      NZ
  88 ARG   (  88-)  A      CG
  88 ARG   (  88-)  A      CD
  88 ARG   (  88-)  A      NE
  88 ARG   (  88-)  A      CZ
  88 ARG   (  88-)  A      NH1
  88 ARG   (  88-)  A      NH2
 130 LYS   ( 130-)  A      CE
 130 LYS   ( 130-)  A      NZ
 138 GLU   ( 138-)  A      CG
 138 GLU   ( 138-)  A      CD
 138 GLU   ( 138-)  A      OE1
 138 GLU   ( 138-)  A      OE2
 150 ARG   ( 150-)  A      CD
 150 ARG   ( 150-)  A      NE
 150 ARG   ( 150-)  A      CZ
 150 ARG   ( 150-)  A      NH1
 150 ARG   ( 150-)  A      NH2
 151 LYS   ( 151-)  A      CE
 151 LYS   ( 151-)  A      NZ
 213 LYS   ( 213-)  A      CD
 213 LYS   ( 213-)  A      CE
 213 LYS   ( 213-)  A      NZ
 220 ARG   ( 220-)  A      CG
 220 ARG   ( 220-)  A      CD
 220 ARG   ( 220-)  A      NE
 220 ARG   ( 220-)  A      CZ
 220 ARG   ( 220-)  A      NH1
 220 ARG   ( 220-)  A      NH2
 221 SER   ( 223-)  A      OG
 228 LYS   ( 230-)  A      CE
 228 LYS   ( 230-)  A      NZ
 242 LYS   ( 244-)  A      NZ
 269 LYS   ( 271-)  A      CE
 269 LYS   ( 271-)  A      NZ

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.

  26 GLU   (  26-)  A    0.50
  50 GLN   (  50-)  A    0.50
 100 ASP   ( 100-)  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: 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.

  66 ASP   (  66-)  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.

 277 DTHY  (   8-)  B      C6   C5    1.37    4.4

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

 |  0.996286  0.001252 -0.000428|
 |  0.001252  0.996680  0.000689|
 | -0.000428  0.000689  0.996022|
Proposed new scale matrix

 |  0.010987 -0.000014  0.000005|
 | -0.000014  0.010982 -0.000008|
 |  0.000003 -0.000005  0.007123|
With corresponding cell

    A    =  91.018  B   =  91.054  C    = 140.384
    Alpha=  89.921  Beta=  90.049  Gamma=  89.856

The CRYST1 cell dimensions

    A    =  91.356  B   =  91.356  C    = 140.943
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 322.903
(Under-)estimated Z-score: 13.243

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.

  40 LEU   (  40-)  A      CA   CB   CG  133.07    4.8
  65 ASP   (  65-)  A     -O   -C    N   116.36   -4.2
  68 ARG   (  68-)  A      CG   CD   NE  117.93    4.4
  96 MET   (  96-)  A      CG   SD   CE   91.61   -4.2
 198 HIS   ( 198-)  A      CG   ND1  CE1 109.75    4.2
 273 DTHY  (   4-)  B      C6   C5   C7  119.90   -5.0
 274 DTHY  (   5-)  B      C6   C5   C7  120.50   -4.0
 274 DTHY  (   5-)  B      C4   C5   C7  121.42    4.0
 275 DTHY  (   6-)  B      C3'  C4'  O4' 100.95   -4.6
 275 DTHY  (   6-)  B      O4'  C1'  N1  111.58    4.7
 276 SOS   (   7-)  B      O5*  P   -O3*  95.23   -4.6
 276 SOS   (   7-)  B      P   -C3* -O3* 130.49    9.0
 277 DTHY  (   8-)  B      P   -C3* -O3* 131.22    9.6
 277 DTHY  (   8-)  B      N3   C2   O2  118.67   -6.0
 279 DTHY  (  10-)  B      C4   C5   C7  121.45    4.1
 280 DCYT  (  11-)  B      O5*  P   -O3*  95.90   -4.3
 280 DCYT  (  11-)  B      C5   C4   N3  123.81    4.8
 280 DCYT  (  11-)  B      C4   N3   C2  117.23   -5.3
 281 DTHY  (  12-)  B      C5   C4   O4  120.96   -5.6
 281 DTHY  (  12-)  B      O4   C4   N3  122.66    4.6
 282 DCYT  (  13-)  B      O4'  C1'  N1  103.91   -4.9
 283 DGUA  (  14-)  B      N9   C8   N7  113.19    4.2
 284 DGUA  (  15-)  C      N9   C8   N7  114.27    6.3
 286 DGUA  (  17-)  C      O5'  C5'  C4' 103.33   -4.9
 286 DGUA  (  17-)  C      N9   C8   N7  113.77    5.3
 287 DADE  (  18-)  C      O4'  C1'  N9  104.20   -4.5
 289 DADE  (  20-)  C      C8   N9   C4  107.49    4.2
 289 DADE  (  20-)  C      N6   C6   N1  121.75    5.2
 290 DADE  (  21-)  C      O4'  C1'  N9  104.09   -4.6
 290 DADE  (  21-)  C      N1   C2   N3  126.90   -4.8
 291 DADE  (  22-)  C      OP1  P    OP2 126.15    4.4
 291 DADE  (  22-)  C      N9   C4   C5  104.15   -4.1
 291 DADE  (  22-)  C      N1   C2   N3  127.26   -4.1
 292 DCYT  (  23-)  C      OP1  P    OP2 126.22    4.4
 293 DADE  (  24-)  C      O4'  C1'  N9  104.49   -4.1
 293 DADE  (  24-)  C      N1   C2   N3  126.77   -5.1
 294 DADE  (  25-)  C      O4'  C1'  N9  104.58   -4.0
 296 DGUA  (  27-)  C      N9   C8   N7  113.44    4.7

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.

  66 ASP   (  66-)  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.

  16 ARG   (  16-)  A    4.89
 222 ALA   ( 224-)  A    4.39

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.

 166 VAL   ( 166-)  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.

  27 ALA   (  27-)  A  omega poor
  74 ARG   (  74-)  A  Poor phi/psi
 110 LYS   ( 110-)  A  Poor phi/psi
 130 LYS   ( 130-)  A  Poor phi/psi
 163 GLN   ( 163-)  A  Poor phi/psi
 167 ALA   ( 167-)  A  omega poor
 182 LYS   ( 182-)  A  Poor phi/psi
 219 ILE   ( 219-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.021

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!

  16 ARG   (  16-)  A      0
  17 ILE   (  17-)  A      0
  18 VAL   (  18-)  A      0
  24 SER   (  24-)  A      0
  29 TYR   (  29-)  A      0
  32 MET   (  32-)  A      0
  35 THR   (  35-)  A      0
  37 PHE   (  37-)  A      0
  45 THR   (  45-)  A      0
  50 GLN   (  50-)  A      0
  55 ARG   (  55-)  A      0
  57 LYS   (  57-)  A      0
  63 ILE   (  63-)  A      0
  66 ASP   (  66-)  A      0
  67 PHE   (  67-)  A      0
  74 ARG   (  74-)  A      0
  75 MET   (  75-)  A      0
  76 GLU   (  76-)  A      0
  92 ASP   (  92-)  A      0
  93 HIS   (  93-)  A      0
  94 LEU   (  94-)  A      0
  98 PHE   (  98-)  A      0
 100 ASP   ( 100-)  A      0
 109 ARG   ( 109-)  A      0
 111 PHE   ( 111-)  A      0
And so on for a total of 123 lines.

Warning: Unusual PRO puckering phases

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

 158 PRO   ( 158-)  A  -121.5 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.

 271 DTHY  (   2-)  B      N3  <->  297 DADE  (  28-)  C      N1     0.33    2.67  INTRA
 281 DTHY  (  12-)  B      N3  <->  287 DADE  (  18-)  C      N1     0.24    2.76  INTRA
 280 DCYT  (  11-)  B      N3  <->  288 DGUA  (  19-)  C      N1     0.24    2.76  INTRA
 242 LYS   ( 244-)  A      CE  <->  301 HOH   ( 571 )  A      O      0.23    2.57  INTRA BF
 274 DTHY  (   5-)  B      N3  <->  294 DADE  (  25-)  C      N1     0.23    2.77  INTRA
 279 DTHY  (  10-)  B      N3  <->  289 DADE  (  20-)  C      N1     0.21    2.79  INTRA
 277 DTHY  (   8-)  B      N3  <->  291 DADE  (  22-)  C      N1     0.21    2.79  INTRA BL
 278 DTHY  (   9-)  B      N3  <->  290 DADE  (  21-)  C      N1     0.19    2.81  INTRA
  65 ASP   (  65-)  A    A O   <->  301 HOH   ( 675 )  A      O      0.19    2.21  INTRA
 275 DTHY  (   6-)  B      N3  <->  293 DADE  (  24-)  C      N1     0.19    2.81  INTRA BL
 282 DCYT  (  13-)  B      N3  <->  286 DGUA  (  17-)  C      N1     0.19    2.81  INTRA
  78 LYS   (  78-)  A      NZ  <->  301 HOH   ( 566 )  A      O      0.19    2.51  INTRA
   5 GLU   (   5-)  A      CD  <->  276 SOS   (   7-)  B      N2     0.19    2.91  INTRA BL
 301 HOH   ( 484 )  A      O   <->  301 HOH   ( 669 )  A      O      0.19    2.01  INTRA
 273 DTHY  (   4-)  B      N3  <->  295 DADE  (  26-)  C      N1     0.18    2.82  INTRA
 301 HOH   ( 630 )  A      O   <->  302 HOH   (  22 )  B      O      0.17    2.23  INTRA
 272 DCYT  (   3-)  B      N3  <->  296 DGUA  (  27-)  C      N1     0.17    2.83  INTRA
 283 DGUA  (  14-)  B      N1  <->  285 DCYT  (  16-)  C      N3     0.13    2.87  INTRA
 148 LYS   ( 148-)  A      NZ  <->  301 HOH   ( 450 )  A      O      0.12    2.58  INTRA
 157 LYS   ( 157-)  A      NZ  <->  171 ASN   ( 171-)  A      OD1    0.11    2.59  INTRA BL
 217 SER   ( 217-)  A      O   <->  276 SOS   (   7-)  B      N1     0.10    2.60  INTRA BL
  26 GLU   (  26-)  A      OE2 <->   97 LYS   (  97-)  A      NZ     0.10    2.60  INTRA
  16 ARG   (  16-)  A      NH2 <->  301 HOH   ( 619 )  A      O      0.09    2.61  INTRA
 284 DGUA  (  15-)  C      N3  <->  303 HOH   (  45 )  C      O      0.08    2.62  INTRA BF
 294 DADE  (  25-)  C      N3  <->  303 HOH   (  40 )  C      O      0.08    2.62  INTRA
  26 GLU   (  26-)  A      OE2 <->  301 HOH   ( 626 )  A      O      0.07    2.33  INTRA
  68 ARG   (  68-)  A      NH2 <->  301 HOH   ( 675 )  A      O      0.07    2.63  INTRA
  57 LYS   (  57-)  A      NZ  <->  277 DTHY  (   8-)  B      OP1    0.07    2.63  INTRA BL
  91 HIS   (  91-)  A      N   <->  301 HOH   ( 491 )  A      O      0.07    2.63  INTRA
 298 LYS   ( 271-)  A      O'' <->  301 HOH   ( 636 )  A      O      0.06    2.34  INTRA BF
 275 DTHY  (   6-)  B      O2  <->  302 HOH   (  41 )  B      O      0.06    2.34  INTRA
 154 LYS   ( 154-)  A      NZ  <->  162 GLU   ( 162-)  A      OE2    0.06    2.64  INTRA
  72 HIS   (  72-)  A      ND1 <->   74 ARG   (  74-)  A      N      0.06    2.94  INTRA BL
 293 DADE  (  24-)  C      N3  <->  303 HOH   (  30 )  C      O      0.05    2.65  INTRA
 188 GLU   ( 188-)  A      OE1 <->  301 HOH   ( 582 )  A      O      0.05    2.35  INTRA
  41 LYS   (  41-)  A      NZ  <->  301 HOH   ( 643 )  A      O      0.05    2.65  INTRA BF
 261 HIS   ( 263-)  A      NE2 <->  301 HOH   ( 437 )  A      O      0.04    2.66  INTRA BL
 249 GLU   ( 251-)  A      OE2 <->  301 HOH   ( 571 )  A      O      0.04    2.36  INTRA
 293 DADE  (  24-)  C      N7  <->  303 HOH   (  41 )  C      O      0.04    2.66  INTRA
 132 GLY   ( 132-)  A      N   <->  163 GLN   ( 163-)  A      O      0.03    2.67  INTRA BL
 179 TRP   ( 179-)  A      NE1 <->  243 CYS   ( 245-)  A      SG     0.02    3.28  INTRA BL
 243 CYS   ( 245-)  A      N   <->  248 ALA   ( 250-)  A      O      0.02    2.68  INTRA BL
 210 LYS   ( 210-)  A      NZ  <->  301 HOH   ( 563 )  A      O      0.02    2.68  INTRA
 142 GLU   ( 142-)  A      OE1 <->  198 HIS   ( 198-)  A      ND1    0.01    2.69  INTRA BL
 179 TRP   ( 179-)  A      O   <->  245 ARG   ( 247-)  A      NH2    0.01    2.69  INTRA BL
 271 DTHY  (   2-)  B      O4  <->  302 HOH   (  38 )  B      O      0.01    2.39  INTRA
 176 GLU   ( 176-)  A      OE1 <->  234 GLN   ( 236-)  A      N      0.01    2.69  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.

  75 MET   (  75-)  A      -6.79
 268 GLN   ( 270-)  A      -6.45
 245 ARG   ( 247-)  A      -6.38
 191 GLN   ( 191-)  A      -5.50
 219 ILE   ( 219-)  A      -5.41

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.

 109 ARG   ( 109-)  A       111 - PHE    111- ( A)         -4.54

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.

  73 LEU   (  73-)  A   -2.79
 109 ARG   ( 109-)  A   -2.72
 256 ALA   ( 258-)  A   -2.72
  88 ARG   (  88-)  A   -2.71
 269 LYS   ( 271-)  A   -2.70
 220 ARG   ( 220-)  A   -2.59

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.

  72 HIS   (  72-)  A     -   75 MET   (  75-)  A        -1.73

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.

 301 HOH   ( 616 )  A      O    -18.04   32.61   52.62

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.

  18 VAL   (  18-)  A      N
  74 ARG   (  74-)  A      NE
 101 GLY   ( 101-)  A      N
 111 PHE   ( 111-)  A      N
 166 VAL   ( 166-)  A      N
 184 HIS   ( 184-)  A      ND1
 186 GLU   ( 186-)  A      N
 237 GLY   ( 239-)  A      N
 258 ARG   ( 260-)  A      NH2

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.

 301 HOH   ( 614 )  A      O  1.04  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.

   5 GLU   (   5-)  A   H-bonding suggests Gln

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 :   0.016
  2nd generation packing quality :  -0.917
  Ramachandran plot appearance   :   0.447
  chi-1/chi-2 rotamer normality  :  -0.021
  Backbone conformation          :   0.003

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.860
  Bond angles                    :   1.090
  Omega angle restraints         :   1.024
  Side chain planarity           :   0.808
  Improper dihedral distribution :   0.871
  B-factor distribution          :   0.551
  Inside/Outside distribution    :   0.998

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.860
  Bond angles                    :   1.090
  Omega angle restraints         :   1.024
  Side chain planarity           :   0.808
  Improper dihedral distribution :   0.871
  B-factor distribution          :   0.551
  Inside/Outside distribution    :   0.998
==============

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.