WHAT IF Check report

This file was created 2013-12-09 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 pdb3axk.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: S and T

All-atom RMS fit for the two chains : 0.568
CA-only RMS fit for the two chains : 0.176

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1111 GOL   ( 503-)  A  B
1113 GOL   ( 504-)  A  B

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.

1106 GOL   ( 501-)  A  -         OK
1108 NDP   ( 479-)  A  -
1109 NDP   ( 480-)  A  -
1110 GOL   ( 502-)  A  -         OK
1111 GOL   ( 503-)  A  B         OK
1113 GOL   ( 504-)  A  B         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.

 435 MET   (   1-)  S  -   N   bound to 1104 NME   (   0-)  S  -   C
 985 MET   (   1-)  T  -   N   bound to 1105 NME   (   0-)  T  -   C

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

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: T

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 510 CYS   (  77-)  S
 898 VAL   ( 377-)  B

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'.

   1 TYR   (  20-)  A      CG
   1 TYR   (  20-)  A      CD1
   1 TYR   (  20-)  A      CD2
   1 TYR   (  20-)  A      CE1
   1 TYR   (  20-)  A      CE2
   1 TYR   (  20-)  A      CZ
   1 TYR   (  20-)  A      OH
   2 LYS   (  21-)  A      CG
   2 LYS   (  21-)  A      CD
   2 LYS   (  21-)  A      CE
   2 LYS   (  21-)  A      NZ
  70 GLU   (  93-)  A      CG
  70 GLU   (  93-)  A      CD
  70 GLU   (  93-)  A      OE1
  70 GLU   (  93-)  A      OE2
 555 LYS   (  21-)  B      CG
 555 LYS   (  21-)  B      CD
 555 LYS   (  21-)  B      CE
 555 LYS   (  21-)  B      NZ
 859 GLU   ( 338-)  B      CG
 859 GLU   ( 338-)  B      CD
 859 GLU   ( 338-)  B      OE1
 859 GLU   ( 338-)  B      OE2

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: T

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.

  56 ARG   (  79-)  A

Warning: Phenylalanine convention problem

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

 446 PHE   (  12-)  S
 996 PHE   (  12-)  T

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.

 180 ASP   ( 203-)  A
 245 ASP   ( 268-)  A
 459 ASP   (  25-)  S
 538 ASP   ( 105-)  S
 622 ASP   (  94-)  B
 731 ASP   ( 203-)  B
1009 ASP   (  25-)  T

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.

   9 GLU   (  28-)  A
 310 GLU   ( 338-)  A
 522 GLU   (  89-)  S
 594 GLU   (  60-)  B
 616 GLU   (  88-)  B
 876 GLU   ( 355-)  B
1008 GLU   (  24-)  T
1015 GLU   (  31-)  T

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 178 KCX   ( 201-)  A      CH     CX
 178 KCX   ( 201-)  A      OX1    OQ1
 178 KCX   ( 201-)  A      OX2    OQ2
 729 KCX   ( 201-)  B      CH     CX
 729 KCX   ( 201-)  B      OX1    OQ1
 729 KCX   ( 201-)  B      OX2    OQ2

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.

 555 LYS   (  21-)  B      CA   C     1.44   -4.1
 556 LEU   (  22-)  B      CA   CB    1.45   -4.0

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: 0.268
RMS-deviation in bond distances: 0.007

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

 |  0.998750  0.000082  0.000057|
 |  0.000082  0.998856 -0.000024|
 |  0.000057 -0.000024  0.998712|
Proposed new scale matrix

 |  0.009082  0.000000  0.000000|
 |  0.000000  0.009081  0.000000|
 |  0.000000  0.000000  0.005012|
With corresponding cell

    A    = 110.104  B   = 110.115  C    = 199.503
    Alpha=  90.002  Beta=  90.002  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 110.246  B   = 110.246  C    = 199.768
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 56.175
(Under-)estimated Z-score: 5.524

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.

   3 LEU   (  22-)  A      CA   CB   CG   92.32   -6.9
   4 THR   (  23-)  A      N    CA   C    96.47   -5.3
  17 ILE   (  36-)  A      N    CA   C    99.02   -4.3
 177 THR   ( 200-)  A      N    CA   C    98.67   -4.5
 610 GLY   (  82-)  B      N    CA   C   100.20   -4.2
 728 THR   ( 200-)  B      N    CA   C    98.26   -4.6

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: 0.646
RMS-deviation in bond angles: 1.421

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.

   9 GLU   (  28-)  A
  56 ARG   (  79-)  A
 180 ASP   ( 203-)  A
 245 ASP   ( 268-)  A
 310 GLU   ( 338-)  A
 459 ASP   (  25-)  S
 522 GLU   (  89-)  S
 538 ASP   ( 105-)  S
 594 GLU   (  60-)  B
 616 GLU   (  88-)  B
 622 ASP   (  94-)  B
 731 ASP   ( 203-)  B
 876 GLU   ( 355-)  B
1008 GLU   (  24-)  T
1009 ASP   (  25-)  T
1015 GLU   (  31-)  T

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 556 LEU   (  22-)  B      C     -6.1    -9.49     0.20
The average deviation= 0.677

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.

   4 THR   (  23-)  A    8.92
 652 VAL   ( 124-)  B    6.55
 101 VAL   ( 124-)  A    6.01
 279 ASP   ( 302-)  A    5.69
 830 ASP   ( 302-)  B    5.33
 871 ARG   ( 350-)  B    5.23
 797 TYR   ( 269-)  B    4.84
 610 GLY   (  82-)  B    4.80
 728 THR   ( 200-)  B    4.72
 177 THR   ( 200-)  A    4.55
  59 GLY   (  82-)  A    4.52
 683 ILE   ( 155-)  B    4.44
 322 ARG   ( 350-)  A    4.21
 905 VAL   ( 384-)  B    4.15
  83 ASP   ( 106-)  A    4.08
 246 TYR   ( 269-)  A    4.04
 278 ILE   ( 301-)  A    4.01
   3 LEU   (  22-)  A    4.01

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.

 603 THR   (  75-)  B    -3.1
  52 THR   (  75-)  A    -3.1
 543 VAL   ( 110-)  S    -2.5
1093 VAL   ( 110-)  T    -2.5
 890 VAL   ( 369-)  B    -2.4
 115 LEU   ( 138-)  A    -2.3
 489 HIS   (  56-)  S    -2.3
 666 LEU   ( 138-)  B    -2.3
 341 VAL   ( 369-)  A    -2.3
1039 HIS   (  56-)  T    -2.2
 375 GLY   ( 403-)  A    -2.2
 615 ILE   (  87-)  B    -2.1
  54 LEU   (  77-)  A    -2.1
1050 TRP   (  67-)  T    -2.1
 850 GLY   ( 322-)  B    -2.1
 904 HIS   ( 383-)  B    -2.0
 901 GLY   ( 380-)  B    -2.0
 299 GLY   ( 322-)  A    -2.0
1035 TYR   (  52-)  T    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  43 SER   (  62-)  A  Poor phi/psi
  52 THR   (  75-)  A  Poor phi/psi
  71 ASP   (  94-)  A  Poor phi/psi
 140 ASN   ( 163-)  A  Poor phi/psi
 152 LYS   ( 175-)  A  PRO omega poor
 173 GLY   ( 196-)  A  Poor phi/psi
 184 ASN   ( 207-)  A  Poor phi/psi
 274 MET   ( 297-)  A  Poor phi/psi
 342 SER   ( 370-)  A  Poor phi/psi
 413 GLY   ( 441-)  A  Poor phi/psi
 447 GLU   (  13-)  S  Poor phi/psi
 449 LEU   (  15-)  S  Poor phi/psi
 471 LYS   (  37-)  S  Poor phi/psi
 504 LYS   (  71-)  S  Poor phi/psi
 556 LEU   (  22-)  B  Poor phi/psi
 596 SER   (  62-)  B  Poor phi/psi
 623 ASN   (  95-)  B  Poor phi/psi
 691 ASN   ( 163-)  B  Poor phi/psi
 703 LYS   ( 175-)  B  PRO omega poor
 735 ASN   ( 207-)  B  Poor phi/psi
 825 MET   ( 297-)  B  Poor phi/psi
 891 SER   ( 370-)  B  Poor phi/psi
 997 GLU   (  13-)  T  Poor phi/psi
 999 LEU   (  15-)  T  Poor phi/psi
1021 LYS   (  37-)  T  Poor phi/psi
1054 LYS   (  71-)  T  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.533

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.

 205 SER   ( 228-)  A    0.36
 756 SER   ( 228-)  B    0.36

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 LEU   (  22-)  A      0
   5 TYR   (  24-)  A      0
   7 THR   (  26-)  A      0
  27 PRO   (  46-)  A      0
  42 SER   (  61-)  A      0
  43 SER   (  62-)  A      0
  44 THR   (  63-)  A      0
  45 THR   (  68-)  A      0
  46 VAL   (  69-)  A      0
  47 TRP   (  70-)  A      0
  51 LEU   (  74-)  A      0
  52 THR   (  75-)  A      0
  53 SER   (  76-)  A      0
  62 TYR   (  85-)  A      0
  67 VAL   (  90-)  A      0
  68 VAL   (  91-)  A      0
  69 GLY   (  92-)  A      0
  70 GLU   (  93-)  A      0
  71 ASP   (  94-)  A      0
  72 ASN   (  95-)  A      0
  73 GLN   (  96-)  A      0
  84 LEU   ( 107-)  A      0
  87 GLU   ( 110-)  A      0
  98 VAL   ( 121-)  A      0
 100 ASN   ( 123-)  A      0
And so on for a total of 415 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.419

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 926 GLY   ( 405-)  B   1.52   80

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 224 CYS   ( 247-)  A      SG   <->   775 CYS   ( 247-)  B      SG   0.78    2.67  INTRA
 903 ILE   ( 382-)  B      N    <->  1116 HOH   (1125 )  B      O    0.58    2.12  INTRA BF
 733 ASN   ( 205-)  B      CG   <->  1116 HOH   (1112 )  B      O    0.46    2.34  INTRA
 717 CYS   ( 189-)  B      CB   <->  1116 HOH   ( 705 )  B      O    0.42    2.38  INTRA BL
 133 GLN   ( 156-)  A      CD   <->   543 VAL   ( 110-)  S      CG2  0.41    2.79  INTRA
 732 GLU   ( 204-)  B      CD   <->  1116 HOH   (1112 )  B      O    0.37    2.43  INTRA
 731 ASP   ( 203-)  B      OD2  <->  1116 HOH   (1112 )  B      O    0.35    2.05  INTRA
   2 LYS   (  21-)  A      O    <->     6 TYR   (  25-)  A      N    0.34    2.36  INTRA
 575 ARG   (  41-)  B      NH2  <->   833 LYS   ( 305-)  B      NZ   0.33    2.52  INTRA
 133 GLN   ( 156-)  A      NE2  <->   543 VAL   ( 110-)  S      CG1  0.33    2.77  INTRA
 607 ARG   (  79-)  B      NE   <->  1116 HOH   ( 784 )  B      O    0.33    2.37  INTRA BF
 983 TRP   ( 462-)  B      NE1  <->  1116 HOH   (1079 )  B      O    0.32    2.38  INTRA BF
 135 GLU   ( 158-)  A      OE2  <->   302 HIS   ( 325-)  A      NE2  0.32    2.38  INTRA BL
 903 ILE   ( 382-)  B      CG1  <->  1116 HOH   (1125 )  B      O    0.31    2.49  INTRA BF
  67 VAL   (  90-)  A      CG1  <->    75 ILE   (  98-)  A      CG1  0.30    2.90  INTRA
1030 LYS   (  46-)  T      NZ   <->  1079 ASP   (  96-)  T      OD2  0.29    2.41  INTRA
 902 GLY   ( 381-)  B      N    <->  1109 NDP   ( 480-)  A      PN   0.28    3.02  INTRA BF
 555 LYS   (  21-)  B      CB   <->   559 TYR   (  25-)  B      CB   0.27    2.93  INTRA
 507 MET   (  74-)  S      CE   <->   515 GLN   (  82-)  S      NE2  0.26    2.84  INTRA
 715 ARG   ( 187-)  B      NE   <->  1116 HOH   ( 533 )  B      O    0.25    2.45  INTRA
   2 LYS   (  21-)  A      O    <->     6 TYR   (  25-)  A      CB   0.25    2.55  INTRA
 374 PHE   ( 402-)  A      CB   <->   378 THR   ( 406-)  A      CG2  0.25    2.95  INTRA
 686 GLU   ( 158-)  B      OE2  <->   853 HIS   ( 325-)  B      NE2  0.24    2.46  INTRA BL
 541 ARG   ( 108-)  S      NH1  <->  1115 HOH   ( 719 )  S      O    0.24    2.46  INTRA BF
 598 TRP   (  70-)  B      N    <->  1116 HOH   (1118 )  B      O    0.22    2.48  INTRA BF
And so on for a total of 212 lines.

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

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.

 499 TYR   (  66-)  S      -8.53
1049 TYR   (  66-)  T      -8.44
 490 ARG   (  57-)  S      -7.37
1040 ARG   (  57-)  T      -7.33
 659 ARG   ( 131-)  B      -6.47
 108 ARG   ( 131-)  A      -6.29
 126 GLN   ( 149-)  A      -5.99
 677 GLN   ( 149-)  B      -5.95
1058 PHE   (  75-)  T      -5.84
1102 LYS   ( 119-)  T      -5.82
 960 ARG   ( 439-)  B      -5.81
 411 ARG   ( 439-)  A      -5.79
1054 LYS   (  71-)  T      -5.54
 508 PHE   (  75-)  S      -5.53
 990 ILE   (   6-)  T      -5.48
 504 LYS   (  71-)  S      -5.41
 440 ILE   (   6-)  S      -5.35
 619 VAL   (  91-)  B      -5.30
 437 VAL   (   3-)  S      -5.28
 987 VAL   (   3-)  T      -5.27
 871 ARG   ( 350-)  B      -5.20
  68 VAL   (  91-)  A      -5.20
 552 LYS   ( 119-)  S      -5.19
 322 ARG   ( 350-)  A      -5.16
 815 ASN   ( 287-)  B      -5.10
 264 ASN   ( 287-)  A      -5.09
 171 ARG   ( 194-)  A      -5.07
 722 ARG   ( 194-)  B      -5.06
 332 ARG   ( 360-)  A      -5.04
 953 ASN   ( 432-)  B      -5.01
 404 ASN   ( 432-)  A      -5.00

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.

 540 VAL   ( 107-)  S       542 - GLN    109- ( S)         -4.57

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

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: S

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: B

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: T

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.

 379 LEU   ( 407-)  A   -2.89
 276 ALA   ( 299-)  A   -2.69
 827 ALA   ( 299-)  B   -2.69
  82 LEU   ( 105-)  A   -2.61
1093 VAL   ( 110-)  T   -2.61
 633 LEU   ( 105-)  B   -2.52
  84 LEU   ( 107-)  A   -2.52

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 149 CYS   ( 172-)  A     -  152 LYS   ( 175-)  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

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: T

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.

1114 HOH   ( 663 )  A      O     23.48   -0.67   -9.22
1114 HOH   ( 682 )  A      O     52.45   11.89   -6.45
1114 HOH   ( 711 )  A      O     53.25   13.29    0.58
1114 HOH   ( 725 )  A      O     53.21   37.63   -5.29
1114 HOH   ( 895 )  A      O     54.39   28.54    1.86
1114 HOH   ( 980 )  A      O     29.48   31.39   50.47
1114 HOH   ( 987 )  A      O     38.21   25.21   51.17
1114 HOH   (1067 )  A      O     22.01    0.60   -7.45
1114 HOH   (1110 )  A      O     54.08   29.13   -6.53
1115 HOH   ( 471 )  S      O     37.24   63.30  -49.99
1115 HOH   ( 700 )  S      O     43.93   58.41  -43.76
1115 HOH   ( 763 )  S      O     20.95   35.23   47.08
1116 HOH   ( 495 )  B      O      1.86   34.30   -6.52
1116 HOH   ( 496 )  B      O      0.89   42.21   -4.43
1116 HOH   ( 773 )  B      O      1.81   32.09   -2.15
1116 HOH   ( 780 )  B      O     14.33   58.94  -29.79
1116 HOH   ( 813 )  B      O     -3.18   29.40   10.07
1116 HOH   ( 976 )  B      O     -2.43   38.78   -2.38
1117 HOH   ( 829 )  T      O     65.68   25.32   48.68

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.

1114 HOH   ( 628 )  A      O
1114 HOH   ( 675 )  A      O
1114 HOH   ( 740 )  A      O
1114 HOH   ( 755 )  A      O
1114 HOH   ( 804 )  A      O
1114 HOH   ( 883 )  A      O
1114 HOH   ( 886 )  A      O
1114 HOH   ( 892 )  A      O
1114 HOH   ( 912 )  A      O
1114 HOH   ( 916 )  A      O
1114 HOH   ( 917 )  A      O
1114 HOH   (1001 )  A      O
1114 HOH   (1004 )  A      O
1114 HOH   (1074 )  A      O
1114 HOH   (1086 )  A      O
1114 HOH   (1101 )  A      O
1115 HOH   ( 493 )  S      O
1115 HOH   (1016 )  S      O
1115 HOH   (1038 )  S      O
1116 HOH   ( 745 )  B      O
1116 HOH   ( 800 )  B      O
1116 HOH   ( 801 )  B      O
1116 HOH   ( 809 )  B      O
1116 HOH   ( 812 )  B      O
1116 HOH   ( 952 )  B      O
1116 HOH   ( 953 )  B      O
1117 HOH   ( 831 )  T      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 283 ASN   ( 306-)  A
 284 HIS   ( 307-)  A
 355 HIS   ( 383-)  A
 463 GLN   (  29-)  S
 488 ASN   (  55-)  S
 614 HIS   (  86-)  B
 623 ASN   (  95-)  B
 684 GLN   ( 156-)  B
 832 GLN   ( 304-)  B
 963 ASN   ( 442-)  B
1013 GLN   (  29-)  T
1089 ASN   ( 106-)  T

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.

  32 GLU   (  51-)  A      N
 144 ARG   ( 167-)  A      NE
 158 SER   ( 181-)  A      OG
 161 ASN   ( 184-)  A      ND2
 164 ARG   ( 187-)  A      NH1
 184 ASN   ( 207-)  A      ND2
 188 PHE   ( 211-)  A      N
 194 ARG   ( 217-)  A      NH1
 223 THR   ( 246-)  A      N
 246 TYR   ( 269-)  A      N
 248 THR   ( 271-)  A      OG1
 272 ARG   ( 295-)  A      NE
 300 GLY   ( 323-)  A      N
 308 VAL   ( 331-)  A      N
 312 GLU   ( 340-)  A      N
 357 TRP   ( 385-)  A      N
 373 GLN   ( 401-)  A      NE2
 376 GLY   ( 404-)  A      N
 385 ASN   ( 413-)  A      ND2
 436 GLN   (   2-)  S      N
 449 LEU   (  15-)  S      N
 456 THR   (  22-)  S      OG1
 458 GLU   (  24-)  S      N
 483 PHE   (  50-)  S      N
 495 TYR   (  62-)  S      N
And so on for a total of 57 lines.

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.

 133 GLN   ( 156-)  A      OE1
 275 HIS   ( 298-)  A      NE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1107  MG   ( 478-)  A     0.74   1.32 Scores about as good as CA
1112  MG   ( 478-)  B     0.72   1.27 Scores about as good as CA

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.

1114 HOH   ( 566 )  A      O  0.85  K  4 *2 NCS 1/1
1114 HOH   ( 633 )  A      O  0.81  K  4 *2 NCS 1/1
1114 HOH   ( 667 )  A      O  0.90  K  4 *2
1114 HOH   ( 790 )  A      O  1.14  K  4 *2 NCS 1/1
1115 HOH   ( 229 )  S      O  0.82  K  4 *2 NCS 1/1
1115 HOH   ( 266 )  S      O  0.95  K  4 *2 NCS 1/1
1115 HOH   ( 350 )  S      O  0.82  K  5 *2 NCS 1/1
1115 HOH   ( 938 )  S      O  0.95  K  4 *2 ION-B
1115 HOH   ( 992 )  S      O  1.09  K  4 *2 ION-B
1116 HOH   ( 640 )  B      O  0.84  K  4 *2
1116 HOH   ( 683 )  B      O  0.80  K  6 *2 NCS 1/1
1116 HOH   ( 994 )  B      O  1.19  K  4 *2 ION-B
1117 HOH   ( 359 )  T      O  1.08  K  4 *2 Ion-B
1117 HOH   ( 546 )  T      O  0.92  K  4 *2 NCS 1/1
1117 HOH   ( 790 )  T      O  0.78  K  5 *2 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.

  49 ASP   (  72-)  A   H-bonding suggests Asn
 263 ASP   ( 286-)  A   H-bonding suggests Asn
 279 ASP   ( 302-)  A   H-bonding suggests Asn
 796 ASP   ( 268-)  B   H-bonding suggests Asn
 814 ASP   ( 286-)  B   H-bonding suggests Asn
 830 ASP   ( 302-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.667
  2nd generation packing quality :  -0.167
  Ramachandran plot appearance   :  -0.791
  chi-1/chi-2 rotamer normality  :  -1.533
  Backbone conformation          :  -0.470

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.268 (tight)
  Bond angles                    :   0.646 (tight)
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.584
  B-factor distribution          :   0.620
  Inside/Outside distribution    :   1.072

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 :  -0.2
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.268 (tight)
  Bond angles                    :   0.646 (tight)
  Omega angle restraints         :   0.258 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.584
  B-factor distribution          :   0.620
  Inside/Outside distribution    :   1.072
==============

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.