WHAT IF Check report

This file was created 2013-12-10 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 pdb4egj.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: A and B

All-atom RMS fit for the two chains : 13.718
CA-only RMS fit for the two chains : 13.631

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

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 43
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 4
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: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 3 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 267 ARG   ( 293-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 267 ARG   ( 293-)  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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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'.

  55 LYS   (  58-)  A      CG
  55 LYS   (  58-)  A      CD
  55 LYS   (  58-)  A      CE
  55 LYS   (  58-)  A      NZ
 126 ASP   ( 129-)  A      CG
 126 ASP   ( 129-)  A      OD1
 126 ASP   ( 129-)  A      OD2
 128 GLU   ( 131-)  A      CG
 128 GLU   ( 131-)  A      CD
 128 GLU   ( 131-)  A      OE1
 128 GLU   ( 131-)  A      OE2
 132 LYS   ( 135-)  A      CG
 132 LYS   ( 135-)  A      CD
 132 LYS   ( 135-)  A      CE
 132 LYS   ( 135-)  A      NZ
 133 GLU   ( 136-)  A      CG
 133 GLU   ( 136-)  A      CD
 133 GLU   ( 136-)  A      OE1
 133 GLU   ( 136-)  A      OE2
 137 LYS   ( 140-)  A      CG
 137 LYS   ( 140-)  A      CD
 137 LYS   ( 140-)  A      CE
 137 LYS   ( 140-)  A      NZ
 149 ILE   ( 159-)  A      CG1
 149 ILE   ( 159-)  A      CG2
And so on for a total of 248 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

 696 ASP   ( 129-)  C    High
 697 TYR   ( 130-)  C    High
 698 GLU   ( 131-)  C    High
 699 ALA   ( 132-)  C    High
 700 ARG   ( 133-)  C    High
 715 ALA   ( 164-)  C    High
 716 ASP   ( 165-)  C    High
 717 ALA   ( 166-)  C    High
 726 VAL   ( 175-)  C    High
 727 LYS   ( 176-)  C    High
 728 PHE   ( 177-)  C    High
 729 ASP   ( 178-)  C    High
 730 ARG   ( 179-)  C    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: 4

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: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

 215 ARG   ( 241-)  A
 506 ARG   ( 247-)  B
 598 ARG   (  31-)  C
 782 ARG   ( 241-)  C
1034 ARG   ( 247-)  D

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.

  57 GLU   (  60-)  A
 212 GLU   ( 238-)  A
 306 GLU   (  24-)  B
 342 GLU   (  60-)  B
 497 GLU   ( 238-)  B
 626 GLU   (  59-)  C
 627 GLU   (  60-)  C
 779 GLU   ( 238-)  C
 816 GLU   ( 275-)  C
 911 GLU   (  60-)  D
1025 GLU   ( 238-)  D
1062 GLU   ( 275-)  D

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.

  42 HIS   (  45-)  A      CG   CD2   1.41    4.5
  67 HIS   (  70-)  A      CG   CD2   1.41    4.7
 327 HIS   (  45-)  B      CG   CD2   1.40    4.4
 352 HIS   (  70-)  B      CG   CD2   1.42    5.5
 393 TRP   ( 111-)  B      NE1  CE2   1.32   -4.8
 544 HIS   ( 285-)  B      CG   CD2   1.42    5.5
 612 HIS   (  45-)  C      CG   CD2   1.40    4.3
 826 HIS   ( 285-)  C      CG   CD2   1.41    4.7
 896 HIS   (  45-)  D      CG   CD2   1.42    5.4
 896 HIS   (  45-)  D      ND1  CE1   1.38    4.3
1072 HIS   ( 285-)  D      CG   CD2   1.40    4.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998509 -0.000326  0.000133|
 | -0.000326  0.998236 -0.000224|
 |  0.000133 -0.000224  0.996450|
Proposed new scale matrix

 |  0.012688  0.000004 -0.000002|
 |  0.000004  0.012691  0.000003|
 |  0.000000  0.000001  0.004466|
With corresponding cell

    A    =  78.815  B   =  78.794  C    = 223.921
    Alpha=  90.026  Beta=  89.994  Gamma=  90.037

The CRYST1 cell dimensions

    A    =  78.930  B   =  78.930  C    = 224.740
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 187.746
(Under-)estimated Z-score: 10.098

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.

  67 HIS   (  70-)  A      CG   ND1  CE1 109.67    4.1
 267 ARG   ( 293-)  A      CB   CG   CD  122.67    4.3
 306 GLU   (  24-)  B      CB   CG   CD  119.93    4.3
 352 HIS   (  70-)  B      CG   ND1  CE1 109.80    4.2
 371 ARG   (  89-)  B      CG   CD   NE  102.52   -4.7
 506 ARG   ( 247-)  B      CG   CD   NE  117.45    4.1
 572 ASP   (   5-)  C      C    CA   CB  102.46   -4.0
 602 GLN   (  35-)  C      CA   CB   CG  123.86    4.9
 637 HIS   (  70-)  C      CG   ND1  CE1 110.18    4.6
 782 ARG   ( 241-)  C      C    CA   CB   99.69   -5.5
 782 ARG   ( 241-)  C      CA   CB   CG  122.39    4.1
 782 ARG   ( 241-)  C      CB   CG   CD  103.56   -5.3
 782 ARG   ( 241-)  C      CG   CD   NE  120.13    5.7
 886 GLN   (  35-)  D      CA   CB   CG  123.62    4.8
 921 HIS   (  70-)  D      CG   ND1  CE1 110.29    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.

  57 GLU   (  60-)  A
 212 GLU   ( 238-)  A
 215 ARG   ( 241-)  A
 306 GLU   (  24-)  B
 342 GLU   (  60-)  B
 497 GLU   ( 238-)  B
 506 ARG   ( 247-)  B
 598 ARG   (  31-)  C
 626 GLU   (  59-)  C
 627 GLU   (  60-)  C
 779 GLU   ( 238-)  C
 782 ARG   ( 241-)  C
 816 GLU   ( 275-)  C
 911 GLU   (  60-)  D
1025 GLU   ( 238-)  D
1034 ARG   ( 247-)  D
1062 GLU   ( 275-)  D

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.

 423 LEU   ( 141-)  B    4.03

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.

 115 THR   ( 118-)  A    -2.3
 685 THR   ( 118-)  C    -2.3
 400 THR   ( 118-)  B    -2.3
 969 THR   ( 118-)  D    -2.2
  99 LEU   ( 102-)  A    -2.2
 184 THR   ( 194-)  A    -2.2
 953 LEU   ( 102-)  D    -2.1
 763 GLY   ( 212-)  C    -2.1
 669 LEU   ( 102-)  C    -2.1
 470 THR   ( 194-)  B    -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.

  48 GLU   (  51-)  A  Poor phi/psi
  62 ALA   (  65-)  A  omega poor
  89 GLY   (  92-)  A  omega poor
 140 LEU   ( 143-)  A  PRO omega poor
 173 VAL   ( 183-)  A  omega poor
 178 GLU   ( 188-)  A  omega poor
 180 GLY   ( 190-)  A  Poor phi/psi
 202 TYR   ( 228-)  A  omega poor
 204 ILE   ( 230-)  A  PRO omega poor
 230 THR   ( 256-)  A  omega poor
 231 ASP   ( 257-)  A  Poor phi/psi
 333 GLU   (  51-)  B  Poor phi/psi
 347 ALA   (  65-)  B  omega poor
 425 LEU   ( 143-)  B  PRO omega poor
 459 VAL   ( 183-)  B  omega poor
 464 GLU   ( 188-)  B  omega poor
 466 GLY   ( 190-)  B  Poor phi/psi
 489 ILE   ( 230-)  B  PRO omega poor
 515 THR   ( 256-)  B  omega poor
 516 ASP   ( 257-)  B  Poor phi/psi
 618 GLU   (  51-)  C  Poor phi/psi
 632 ALA   (  65-)  C  omega poor
 659 GLY   (  92-)  C  omega poor
 704 LEU   ( 143-)  C  PRO omega poor
 739 GLU   ( 188-)  C  omega poor
 741 GLY   ( 190-)  C  Poor phi/psi
 769 TYR   ( 228-)  C  omega poor
 771 ILE   ( 230-)  C  PRO omega poor
 797 THR   ( 256-)  C  omega poor
 798 ASP   ( 257-)  C  Poor phi/psi
 864 ALA   (  13-)  D  omega poor
 902 GLU   (  51-)  D  Poor phi/psi
 916 ALA   (  65-)  D  omega poor
 943 GLY   (  92-)  D  omega poor
 972 PHE   ( 121-)  D  omega poor
 976 LEU   ( 143-)  D  PRO omega poor
 989 GLU   ( 188-)  D  omega poor
 991 GLY   ( 190-)  D  Poor phi/psi
1017 ILE   ( 230-)  D  PRO omega poor
1043 THR   ( 256-)  D  omega poor
1044 ASP   ( 257-)  D  Poor phi/psi, omega poor
 chi-1/chi-2 correlation Z-score : -0.639

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.

 880 SER   (  29-)  D    0.35
  26 SER   (  29-)  A    0.38
 596 SER   (  29-)  C    0.39

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 PHE   (   9-)  A      0
   8 LYS   (  11-)  A      0
  13 LEU   (  16-)  A      0
  49 ARG   (  52-)  A      0
  57 GLU   (  60-)  A      0
  59 PHE   (  62-)  A      0
  65 ALA   (  68-)  A      0
  67 HIS   (  70-)  A      0
  70 TYR   (  73-)  A      0
  72 GLU   (  75-)  A      0
  73 ASN   (  76-)  A      0
  83 TYR   (  86-)  A      0
  88 THR   (  91-)  A      0
  92 VAL   (  95-)  A      0
  99 LEU   ( 102-)  A      0
 111 LEU   ( 114-)  A      0
 123 ARG   ( 126-)  A      0
 125 ASP   ( 128-)  A      0
 126 ASP   ( 129-)  A      0
 138 LEU   ( 141-)  A      0
 140 LEU   ( 143-)  A      0
 147 ALA   ( 150-)  A      0
 148 SER   ( 151-)  A      0
 149 ILE   ( 159-)  A      0
 150 LYS   ( 160-)  A      0
And so on for a total of 353 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 254 PRO   ( 280-)  A    0.17 LOW
 539 PRO   ( 280-)  B    0.18 LOW
 821 PRO   ( 280-)  C    0.16 LOW
1067 PRO   ( 280-)  D    0.17 LOW

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].

   3 PRO   (   6-)  A  -122.8 half-chair C-delta/C-gamma (-126 degrees)
 117 PRO   ( 120-)  A   105.6 envelop C-beta (108 degrees)
 158 PRO   ( 168-)  A   110.7 envelop C-beta (108 degrees)
 200 PRO   ( 210-)  A   -50.6 half-chair C-beta/C-alpha (-54 degrees)
 288 PRO   (   6-)  B  -124.1 half-chair C-delta/C-gamma (-126 degrees)
 402 PRO   ( 120-)  B   101.7 envelop C-beta (108 degrees)
 444 PRO   ( 168-)  B   114.9 envelop C-beta (108 degrees)
 573 PRO   (   6-)  C  -130.1 half-chair C-delta/C-gamma (-126 degrees)
 719 PRO   ( 168-)  C   112.9 envelop C-beta (108 degrees)
 857 PRO   (   6-)  D  -121.2 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.

 293 LYS   (  11-)  B      NZ  <-> 1101 HOH   ( 492 )  B      O      0.39    2.31  INTRA
 179 GLY   ( 189-)  A      N   <-> 1100 HOH   ( 463 )  A      O      0.37    2.33  INTRA
 327 HIS   (  45-)  B      ND1 <-> 1101 HOH   ( 417 )  B      O      0.36    2.34  INTRA BL
 487 TYR   ( 228-)  B      O   <->  549 LYS   ( 290-)  B      NZ     0.33    2.37  INTRA
  75 GLN   (  78-)  A    A NE2 <-> 1100 HOH   ( 502 )  A      O      0.31    2.39  INTRA BL
 478 ASP   ( 202-)  B      OD1 <->  502 LYS   ( 243-)  B      NZ     0.30    2.40  INTRA
 313 ARG   (  31-)  B      NH2 <-> 1101 HOH   ( 436 )  B      O      0.28    2.42  INTRA BF
 578 LYS   (  11-)  C      NZ  <->  627 GLU   (  60-)  C      O      0.21    2.49  INTRA BF
 192 ASP   ( 202-)  A      OD1 <->  217 LYS   ( 243-)  A      NZ     0.21    2.49  INTRA
 234 ARG   ( 260-)  A      NE  <->  261 LEU   ( 287-)  A      CD1    0.18    2.92  INTRA
 862 LYS   (  11-)  D      NZ  <->  911 GLU   (  60-)  D      O      0.18    2.52  INTRA
 430 LYS   ( 148-)  B      NZ  <->  460 GLU   ( 184-)  B      OE1    0.17    2.53  INTRA BL
1003 ASP   ( 202-)  D      OD1 <-> 1030 LYS   ( 243-)  D      NZ     0.15    2.55  INTRA
  42 HIS   (  45-)  A      ND1 <-> 1100 HOH   ( 408 )  A      O      0.14    2.56  INTRA BL
  68 GLY   (  71-)  A      N   <->   72 GLU   (  75-)  A      OE1    0.14    2.56  INTRA BL
 801 ARG   ( 260-)  C      NH2 <->  828 LEU   ( 287-)  C      CD1    0.14    2.96  INTRA
 353 GLY   (  71-)  B      N   <->  357 GLU   (  75-)  B      OE1    0.14    2.56  INTRA BL
 753 ASP   ( 202-)  C      OD1 <->  784 LYS   ( 243-)  C      NZ     0.14    2.56  INTRA BL
 638 GLY   (  71-)  C      N   <->  642 GLU   (  75-)  C      OE1    0.14    2.56  INTRA
 651 ASP   (  84-)  C      OD2 <-> 1102 HOH   ( 404 )  C      O      0.13    2.27  INTRA
 922 GLY   (  71-)  D      N   <->  926 GLU   (  75-)  D      OE1    0.13    2.57  INTRA BL
 494 THR   ( 235-)  B      OG1 <-> 1101 HOH   ( 488 )  B      O      0.11    2.29  INTRA
  40 ASP   (  43-)  A      OD2 <-> 1100 HOH   ( 401 )  A      O      0.11    2.29  INTRA BL
 145 LYS   ( 148-)  A      NZ  <->  174 GLU   ( 184-)  A      OE1    0.11    2.59  INTRA
 610 ASP   (  43-)  C      OD1 <->  612 HIS   (  45-)  C      NE2    0.11    2.59  INTRA
And so on for a total of 89 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 408 ARG   ( 126-)  B      -7.47
 713 LYS   ( 162-)  C      -6.42
 123 ARG   ( 126-)  A      -6.29
 395 GLN   ( 113-)  B      -5.58
 110 GLN   ( 113-)  A      -5.58
 680 GLN   ( 113-)  C      -5.55
 964 GLN   ( 113-)  D      -5.49
 859 GLN   (   8-)  D      -5.47
 575 GLN   (   8-)  C      -5.42
 290 GLN   (   8-)  B      -5.41
   5 GLN   (   8-)  A      -5.36
 544 HIS   ( 285-)  B      -5.31
 980 VAL   ( 147-)  D      -5.29
 407 LEU   ( 125-)  B      -5.23
 259 HIS   ( 285-)  A      -5.22
 936 PHE   (  85-)  D      -5.16
 140 LEU   ( 143-)  A      -5.10
  82 PHE   (  85-)  A      -5.05
 367 PHE   (  85-)  B      -5.04
 652 PHE   (  85-)  C      -5.02

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: 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: C

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: D

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.

 693 ARG   ( 126-)  C   -3.41
 455 ARG   ( 179-)  B   -2.77
 169 ARG   ( 179-)  A   -2.71
 700 ARG   ( 133-)  C   -2.58
1066 ALA   ( 279-)  D   -2.53
 730 ARG   ( 179-)  C   -2.50

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.

 725 ALA   ( 174-)  C     -  730 ARG   ( 179-)  C        -1.65

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

1100 HOH   ( 424 )  A      O
1100 HOH   ( 466 )  A      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.

  25 ASN   (  28-)  A
 317 GLN   (  35-)  B
 879 ASN   (  28-)  D

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.

 122 LEU   ( 125-)  A      N
 257 THR   ( 283-)  A      OG1
 337 ALA   (  55-)  B      N
 434 GLU   ( 152-)  B      N
 466 GLY   ( 190-)  B      N
 542 THR   ( 283-)  B      OG1
 622 ALA   (  55-)  C      N
 637 HIS   (  70-)  C      N
 653 TYR   (  86-)  C      OH
 879 ASN   (  28-)  D      ND2
 991 GLY   ( 190-)  D      N

Warning: Unusual water packing

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

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

1100 HOH   ( 410 )  A      O  1.05  K  4

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.

  45 ASP   (  48-)  A   H-bonding suggests Asn; but Alt-Rotamer
 125 ASP   ( 128-)  A   H-bonding suggests Asn; but Alt-Rotamer
 168 ASP   ( 178-)  A   H-bonding suggests Asn; but Alt-Rotamer
 330 ASP   (  48-)  B   H-bonding suggests Asn; but Alt-Rotamer
 615 ASP   (  48-)  C   H-bonding suggests Asn; but Alt-Rotamer
 899 ASP   (  48-)  D   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 :  -0.145
  2nd generation packing quality :  -0.953
  Ramachandran plot appearance   :  -0.302
  chi-1/chi-2 rotamer normality  :  -0.639
  Backbone conformation          :   0.833

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.760
  Bond angles                    :   0.824
  Omega angle restraints         :   1.077
  Side chain planarity           :   1.047
  Improper dihedral distribution :   0.985
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   1.026

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :   0.6
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.760
  Bond angles                    :   0.824
  Omega angle restraints         :   1.077
  Side chain planarity           :   1.047
  Improper dihedral distribution :   0.985
  B-factor distribution          :   0.418
  Inside/Outside distribution    :   1.026
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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Ramachandran plot
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
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    M.Nayal and E.Di Cera,
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      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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    Acta Cryst. D 59 32--37 (2003).

Checking checks
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      Who checks the checkers
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