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 pdb3hll.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 338 I45   ( 401-)  A  -         Fragmented
 339 PO2   ( 501-)  A  -
 340 I46   ( 402-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

  60 HIS   (  64-)  A  -   NE2 bound to  339 PO2   ( 501-)  A  -   P

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'.

 168 VAL   ( 183-)  A      CG1
 168 VAL   ( 183-)  A      CG2
 170 THR   ( 185-)  A      OG1
 170 THR   ( 185-)  A      CG2

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: 1

Crystal temperature (K) :110.000

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.

  45 ARG   (  49-)  A
  63 ARG   (  67-)  A
 132 ARG   ( 136-)  A
 145 ARG   ( 149-)  A
 174 ARG   ( 189-)  A
 205 ARG   ( 220-)  A
 241 ARG   ( 256-)  A
 281 ARG   ( 296-)  A

Warning: Tyrosine convention problem

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

  20 TYR   (  24-)  A
  31 TYR   (  35-)  A
 136 TYR   ( 140-)  A
 185 TYR   ( 200-)  A
 296 TYR   ( 311-)  A

Warning: Phenylalanine convention problem

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

  55 PHE   (  59-)  A
  95 PHE   (  99-)  A
 208 PHE   ( 223-)  A
 293 PHE   ( 308-)  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.

 141 ASP   ( 145-)  A
 157 ASP   ( 161-)  A
 190 ASP   ( 205-)  A
 212 ASP   ( 227-)  A
 301 ASP   ( 316-)  A
 316 ASP   ( 331-)  A
 320 ASP   ( 335-)  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.

   8 GLU   (  12-)  A
  15 GLU   (  19-)  A
  67 GLU   (  71-)  A
 156 GLU   ( 160-)  A
 159 GLU   ( 163-)  A
 238 GLU   ( 253-)  A
 313 GLU   ( 328-)  A

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.465
RMS-deviation in bond distances: 0.011

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

 |  0.997762  0.000220  0.000324|
 |  0.000220  0.998534  0.000256|
 |  0.000324  0.000256  0.997169|
Proposed new scale matrix

 |  0.015392 -0.000003 -0.000005|
 | -0.000003  0.013417 -0.000003|
 | -0.000004 -0.000003  0.013013|
With corresponding cell

    A    =  64.967  B   =  74.534  C    =  76.847
    Alpha=  89.971  Beta=  89.963  Gamma=  89.975

The CRYST1 cell dimensions

    A    =  65.114  B   =  74.645  C    =  77.066
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 56.137
(Under-)estimated Z-score: 5.522

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.

  60 HIS   (  64-)  A      CG   ND1  CE1 109.65    4.1
 290 HIS   ( 305-)  A      CG   ND1  CE1 109.64    4.0

Warning: Low bond angle variability

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

RMS Z-score for bond angles: 0.659
RMS-deviation in bond angles: 1.329

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.

   8 GLU   (  12-)  A
  15 GLU   (  19-)  A
  45 ARG   (  49-)  A
  63 ARG   (  67-)  A
  67 GLU   (  71-)  A
 132 ARG   ( 136-)  A
 141 ASP   ( 145-)  A
 145 ARG   ( 149-)  A
 156 GLU   ( 160-)  A
 157 ASP   ( 161-)  A
 159 GLU   ( 163-)  A
 174 ARG   ( 189-)  A
 190 ASP   ( 205-)  A
 205 ARG   ( 220-)  A
 212 ASP   ( 227-)  A
 238 GLU   ( 253-)  A
 241 ARG   ( 256-)  A
 281 ARG   ( 296-)  A
 301 ASP   ( 316-)  A
 313 GLU   ( 328-)  A
 316 ASP   ( 331-)  A
 320 ASP   ( 335-)  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.

 170 THR   ( 185-)  A    4.38

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.

 317 LEU   ( 332-)  A    -2.3
 260 ILE   ( 275-)  A    -2.2
 114 LYS   ( 118-)  A    -2.1
  31 TYR   (  35-)  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.

  10 ASN   (  14-)  A  Poor phi/psi
  11 LYS   (  15-)  A  Poor phi/psi
  22 ASN   (  26-)  A  Poor phi/psi
  30 ALA   (  34-)  A  Poor phi/psi
  31 TYR   (  35-)  A  Poor phi/psi
  35 CYS   (  39-)  A  omega poor
 115 CYS   ( 119-)  A  Poor phi/psi
 141 ASP   ( 145-)  A  Poor phi/psi
 145 ARG   ( 149-)  A  Poor phi/psi
 158 CYS   ( 162-)  A  Poor phi/psi
 164 ASP   ( 168-)  A  Poor phi/psi
 169 ALA   ( 184-)  A  omega poor
 181 ASN   ( 196-)  A  Poor phi/psi
 188 THR   ( 203-)  A  omega poor
 223 LEU   ( 238-)  A  omega poor
 260 ILE   ( 275-)  A  Poor phi/psi
 336 PRO   ( 351-)  A  PRO omega poor
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
 chi-1/chi-2 correlation Z-score : -1.547

Warning: Unusual rotamers

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

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

 239 SER   ( 254-)  A    0.36
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P

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!

   6 ARG   (  10-)  A      0
   9 LEU   (  13-)  A      0
  10 ASN   (  14-)  A      0
  11 LYS   (  15-)  A      0
  20 TYR   (  24-)  A      0
  21 GLN   (  25-)  A      0
  25 PRO   (  29-)  A      0
  30 ALA   (  34-)  A      0
  31 TYR   (  35-)  A      0
  52 SER   (  56-)  A      0
  53 ARG   (  57-)  A      0
  55 PHE   (  59-)  A      0
  56 GLN   (  60-)  A      0
  73 HIS   (  77-)  A      0
  74 MET   (  78-)  A      0
  75 LYS   (  79-)  A      0
  83 LEU   (  87-)  A      0
  84 ASP   (  88-)  A      0
  88 PRO   (  92-)  A      0
  95 PHE   (  99-)  A      0
  96 ASN   ( 100-)  A      0
 105 MET   ( 109-)  A      0
 113 VAL   ( 117-)  A      0
 114 LYS   ( 118-)  A      0
 115 CYS   ( 119-)  A      0
And so on for a total of 112 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].

 307 PRO   ( 322-)  A   106.0 envelop C-beta (108 degrees)
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P
IAT=   60 HIS  (  64-) A      NE2
JAT=  339 PO2  ( 501-) A      P

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.

  60 HIS   (  64-)  A      NE2 <->  339 PO2   ( 501-)  A      P      1.61    1.69  INTRA BF
  60 HIS   (  64-)  A      CE1 <->  339 PO2   ( 501-)  A      P      1.00    2.40  INTRA BF
  60 HIS   (  64-)  A      CD2 <->  339 PO2   ( 501-)  A      P      0.54    2.86  INTRA BF
  84 ASP   (  88-)  A      CB  <->  101 VAL   ( 105-)  A      CG2    0.46    2.74  INTRA BL
  84 ASP   (  88-)  A      N   <->  101 VAL   ( 105-)  A      CG2    0.35    2.75  INTRA BL
  49 LYS   (  53-)  A      NZ  <->   51 LEU   (  55-)  A      CD2    0.27    2.83  INTRA BF
 117 LYS   ( 121-)  A      NZ  <->  341 HOH   (5180 )  A      O      0.26    2.44  INTRA BF
  80 ILE   (  84-)  A      CG1 <->  163 LEU   ( 167-)  A      CD2    0.24    2.96  INTRA BF
 113 VAL   ( 117-)  A      CG2 <->  201 LEU   ( 216-)  A      CD2    0.23    2.97  INTRA BF
  95 PHE   (  99-)  A      O   <->  323 LYS   ( 338-)  A      CE     0.21    2.59  INTRA BF
  84 ASP   (  88-)  A      CA  <->  101 VAL   ( 105-)  A      CG2    0.18    3.02  INTRA BL
 234 LYS   ( 249-)  A      NZ  <->  277 ASP   ( 292-)  A      OD2    0.16    2.54  INTRA BL
 124 GLN   ( 128-)  A      NE2 <->  341 HOH   (5198 )  A      O      0.13    2.57  INTRA BF
 268 ASP   ( 283-)  A      OD2 <->  290 HIS   ( 305-)  A      NE2    0.13    2.57  INTRA
  93 GLU   (  97-)  A      O   <->  341 HOH   (5171 )  A      O      0.12    2.28  INTRA BF
  76 HIS   (  80-)  A      CD2 <->   78 ASN   (  82-)  A      N      0.09    3.01  INTRA BL
   7 GLN   (  11-)  A      NE2 <->  341 HOH   (5088 )  A      O      0.08    2.62  INTRA BF
  13 ILE   (  17-)  A      O   <->   50 LYS   (  54-)  A      NZ     0.08    2.62  INTRA BF
 304 VAL   ( 319-)  A      CG1 <->  305 ALA   ( 320-)  A      N      0.07    2.93  INTRA BF
 308 TYR   ( 323-)  A      CE2 <->  310 GLN   ( 325-)  A      CG     0.07    3.13  INTRA BF
  90 ARG   (  94-)  A      N   <->   94 GLU   (  98-)  A      OE1    0.07    2.63  INTRA BF
 244 ILE   ( 259-)  A      CD1 <->  340 I46   ( 402-)  A      F18    0.06    3.14  INTRA
 145 ARG   ( 149-)  A      NE  <->  185 TYR   ( 200-)  A      OH     0.06    2.64  INTRA BF
  73 HIS   (  77-)  A      ND1 <->   74 MET   (  78-)  A      CE     0.05    3.05  INTRA BF
  60 HIS   (  64-)  A      NE2 <->  339 PO2   ( 501-)  A      O2     0.05    2.65  INTRA BF
  50 LYS   (  54-)  A      NZ  <->  341 HOH   (5142 )  A      O      0.04    2.66  INTRA BF
  72 LYS   (  76-)  A      NZ  <->  329 GLU   ( 344-)  A      OE1    0.04    2.66  INTRA
 244 ILE   ( 259-)  A      CG1 <->  340 I46   ( 402-)  A      F18    0.04    3.16  INTRA
 168 VAL   ( 183-)  A      N   <->  341 HOH   (5054 )  A      O      0.03    2.67  INTRA BF
 242 ASN   ( 257-)  A      O   <->  246 SER   ( 261-)  A      OG     0.03    2.37  INTRA BF
  56 GLN   (  60-)  A      NE2 <->  341 HOH   (5050 )  A      O      0.03    2.67  INTRA BF
 192 TRP   ( 207-)  A      NE1 <->  196 CYS   ( 211-)  A      SG     0.03    3.27  INTRA BL
 336 PRO   ( 351-)  A      N   <->  337 PRO   ( 352-)  A      CD     0.03    2.97  INTRA BF
 268 ASP   ( 283-)  A      OD2 <->  272 LYS   ( 287-)  A      NZ     0.02    2.68  INTRA BF
 295 GLN   ( 310-)  A      CG  <->  296 TYR   ( 311-)  A      CE2    0.02    3.18  INTRA BF
  60 HIS   (  64-)  A      CE1 <->  339 PO2   ( 501-)  A      O1     0.02    2.78  INTRA BF
 138 HIS   ( 142-)  A      ND1 <->  341 HOH   (5024 )  A      O      0.02    2.68  INTRA BL
 183 MET   ( 198-)  A      N   <->  341 HOH   (5202 )  A      O      0.02    2.68  INTRA BF
  47 ALA   (  51-)  A      CB  <->  338 I45   ( 401-)  A      F21    0.01    3.19  INTRA BL
   9 LEU   (  13-)  A      N   <->   12 THR   (  16-)  A      O      0.01    2.69  INTRA BF

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.

  90 ARG   (  94-)  A      -7.46
  31 TYR   (  35-)  A      -6.78
  56 GLN   (  60-)  A      -6.12
 249 GLN   ( 264-)  A      -5.99
  75 LYS   (  79-)  A      -5.56
  73 HIS   (  77-)  A      -5.54

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.

 183 MET   ( 198-)  A       185 - TYR    200- ( A)         -4.15

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.

 205 ARG   ( 220-)  A   -2.88
 183 MET   ( 198-)  A   -2.57

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.

 341 HOH   (5158 )  A      O     38.54   14.35   -1.67

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 341 HOH   (5008 )  A      O
 341 HOH   (5162 )  A      O
 341 HOH   (5175 )  A      O
 341 HOH   (5183 )  A      O
 341 HOH   (5185 )  A      O
 341 HOH   (5203 )  A      O
Marked this atom as acceptor  338 I45  ( 401-) A      F21
Marked this atom as acceptor  338 I45  ( 401-) A      F22
Marked this atom as acceptor  340 I46  ( 402-) A      F19
Marked this atom as acceptor  340 I46  ( 402-) A      F18

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.

  56 GLN   (  60-)  A
  73 HIS   (  77-)  A
 124 GLN   ( 128-)  A
 184 HIS   ( 199-)  A
 295 GLN   ( 310-)  A
 310 GLN   ( 325-)  A
Atom is not a donor   60 HIS  (  64-) A      NE2

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.

  57 SER   (  61-)  A      N
  57 SER   (  61-)  A      OG
  63 ARG   (  67-)  A      NH2
  78 ASN   (  82-)  A      N
  91 SER   (  95-)  A      N
 105 MET   ( 109-)  A      N
 106 GLY   ( 110-)  A      N
 108 ASP   ( 112-)  A      N
 118 LEU   ( 122-)  A      N
 119 THR   ( 123-)  A      N
 148 LYS   ( 152-)  A      N
 165 PHE   ( 169-)  A      N
 171 ARG   ( 186-)  A      N
 171 ARG   ( 186-)  A      NE
 184 HIS   ( 199-)  A      N
 185 TYR   ( 200-)  A      N
 191 ILE   ( 206-)  A      N
 212 ASP   ( 227-)  A      N
 231 LEU   ( 246-)  A      N
 243 TYR   ( 258-)  A      OH
 275 VAL   ( 290-)  A      N
 278 SER   ( 293-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

  76 HIS   (  80-)  A      ND1
 157 ASP   ( 161-)  A      OD1

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.

  97 ASP   ( 101-)  A   H-bonding suggests Asn; but Alt-Rotamer
 302 GLU   ( 317-)  A   H-bonding suggests Gln
 328 ASP   ( 343-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.640
  2nd generation packing quality :  -1.123
  Ramachandran plot appearance   :  -0.210
  chi-1/chi-2 rotamer normality  :  -1.547
  Backbone conformation          :  -0.152

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.659 (tight)
  Omega angle restraints         :   0.986
  Side chain planarity           :   0.592 (tight)
  Improper dihedral distribution :   0.621
  B-factor distribution          :   0.366
  Inside/Outside distribution    :   1.046

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 : 1.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.659 (tight)
  Omega angle restraints         :   0.986
  Side chain planarity           :   0.592 (tight)
  Improper dihedral distribution :   0.621
  B-factor distribution          :   0.366
  Inside/Outside distribution    :   1.046
==============

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.