WHAT IF Check report

This file was created 2013-12-19 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 pdb4kfk.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

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

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

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

Molecular weight of all polymer chains: 851584.938
Volume of the Unit Cell V= 59592040.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 34.989
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.980 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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.

4355  MG   (1609-)  I  A
4677  MG   (1931-)  N  A
4777  MG   (2031-)  W  A
5222  MG   (2476-)  K  A

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

4555  MG   (1809-)  A  -
5165  MG   (2419-)  A  -

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: Y

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

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

Warning: B-factors outside the range 0.0 - 100.0

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

   1 OURA  (   5-)  A    High
   2 OGUA  (   6-)  A    High
   3 OGUA  (   7-)  A    High
   4 OADE  (   8-)  A    High
   6 OADE  (  10-)  A    High
   9 OURA  (  13-)  A    High
  11 OGUA  (  15-)  A    High
  12 OADE  (  16-)  A    High
  13 OURA  (  17-)  A    High
  22 OADE  (  26-)  A    High
  23 OGUA  (  27-)  A    High
  24 OGUA  (  28-)  A    High
  25 OGUA  (  29-)  A    High
  26 OURA  (  30-)  A    High
  27 OGUA  (  31-)  A    High
  28 OADE  (  32-)  A    High
  29 OADE  (  33-)  A    High
  32 OCYT  (  36-)  A    High
  33 OURA  (  37-)  A    High
  34 OGUA  (  38-)  A    High
  35 OGUA  (  39-)  A    High
  36 OCYT  (  40-)  A    High
  37 OGUA  (  41-)  A    High
  38 OGUA  (  42-)  A    High
  39 OCYT  (  43-)  A    High
And so on for a total of 3613 lines.

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) :100.000

Note: B-factor plot

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

Chain identifier: Y

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

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.

1634 ARG   (  59-)  Y
1642 ARG   (  67-)  Y
1644 ARG   (  69-)  Y
1645 ARG   (  70-)  Y
1726 ARG   ( 151-)  Y
1734 ARG   ( 159-)  Y
1789 ARG   ( 214-)  Y
1870 ARG   ( 295-)  Y
1879 ARG   ( 304-)  Y
1891 ARG   ( 316-)  Y
1918 ARG   ( 343-)  Y
1943 ARG   ( 368-)  Y
2395 ARG   (   3-)  D
2510 ARG   ( 118-)  D
4284 ARG   (  89-)  T

Warning: Tyrosine convention problem

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

1754 TYR   ( 179-)  Y
1902 TYR   ( 327-)  Y
1908 TYR   ( 333-)  Y
1978 TYR   (  31-)  B
2039 TYR   (  92-)  B
2146 TYR   ( 199-)  B
2209 TYR   (  23-)  C
2370 TYR   ( 184-)  C
2396 TYR   (   4-)  D
2412 TYR   (  20-)  D
2599 TYR   ( 207-)  D
2785 TYR   (  33-)  F
2802 TYR   (  50-)  F
2815 TYR   (  63-)  F
2896 TYR   (  44-)  G
2937 TYR   (  85-)  G
3006 TYR   ( 154-)  G
3056 TYR   (  48-)  H
3066 TYR   (  58-)  H
3102 TYR   (  94-)  H
3150 TYR   (   5-)  I
3259 TYR   ( 114-)  I
3270 TYR   ( 125-)  I
3381 TYR   (  20-)  K
3386 TYR   (  25-)  K
3411 TYR   (  50-)  K
3579 TYR   (  97-)  L
3586 TYR   ( 104-)  L
3629 TYR   (  23-)  M
3693 TYR   (  87-)  M
3744 TYR   (  21-)  N
3889 TYR   (  17-)  P
3904 TYR   (  32-)  P
3986 TYR   (  32-)  Q
3996 TYR   (  42-)  Q
4005 TYR   (  51-)  Q
4049 TYR   (  95-)  Q

Warning: Phenylalanine convention problem

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

1697 PHE   ( 122-)  Y
1783 PHE   ( 208-)  Y
1964 PHE   (  17-)  B
2099 PHE   ( 152-)  B
2128 PHE   ( 181-)  B
2314 PHE   ( 128-)  C
2467 PHE   (  75-)  D
2485 PHE   (  93-)  D
2577 PHE   ( 185-)  D
2598 PHE   ( 206-)  D
2603 PHE   (   6-)  E
2849 PHE   (  97-)  F
3163 PHE   (  18-)  I
3182 PHE   (  37-)  I
3282 PHE   (  11-)  J
3318 PHE   (  47-)  J
3334 PHE   (  63-)  J
3513 PHE   (  31-)  L
3739 PHE   (  16-)  N
3760 PHE   (  37-)  N
3798 PHE   (  15-)  O
3881 PHE   (   9-)  P
3952 PHE   (  80-)  P
3981 PHE   (  27-)  Q
4025 PHE   (  71-)  Q
4117 PHE   (  81-)  R
4131 PHE   (  10-)  S
4195 PHE   (  74-)  S

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.

1606 ASP   (  31-)  Y
1623 ASP   (  48-)  Y
1687 ASP   ( 112-)  Y
1719 ASP   ( 144-)  Y
1743 ASP   ( 168-)  Y
1784 ASP   ( 209-)  Y
1803 ASP   ( 228-)  Y
1920 ASP   ( 345-)  Y
1926 ASP   ( 351-)  Y
2026 ASP   (  79-)  B
2107 ASP   ( 160-)  B
2113 ASP   ( 166-)  B
2140 ASP   ( 193-)  B
2142 ASP   ( 195-)  B
2145 ASP   ( 198-)  B
2203 ASP   (  17-)  C
2248 ASP   (  62-)  C
2369 ASP   ( 183-)  C
2526 ASP   ( 134-)  D
2714 ASP   ( 117-)  E
2767 ASP   (  15-)  F
2867 ASP   (  15-)  G
2897 ASP   (  45-)  G
2978 ASP   ( 126-)  G
2992 ASP   ( 140-)  G
3081 ASP   (  73-)  H
3236 ASP   (  91-)  I
3250 ASP   ( 105-)  I
3283 ASP   (  12-)  J
3395 ASP   (  34-)  K
3397 ASP   (  36-)  K
3471 ASP   ( 110-)  K
3472 ASP   ( 111-)  K
3622 ASP   (  16-)  M
3804 ASP   (  21-)  O
3857 ASP   (  74-)  O
3912 ASP   (  40-)  P
4000 ASP   (  46-)  Q
4069 ASP   (  33-)  R
4133 ASP   (  12-)  S
4305 ASP   (   5-)  U

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.

1616 GLU   (  41-)  Y
1639 GLU   (  64-)  Y
1662 GLU   (  87-)  Y
1665 GLU   (  90-)  Y
1671 GLU   (  96-)  Y
1678 GLU   ( 103-)  Y
1681 GLU   ( 106-)  Y
1701 GLU   ( 126-)  Y
1722 GLU   ( 147-)  Y
1733 GLU   ( 158-)  Y
1762 GLU   ( 187-)  Y
1797 GLU   ( 222-)  Y
1801 GLU   ( 226-)  Y
1813 GLU   ( 238-)  Y
1880 GLU   ( 305-)  Y
1882 GLU   ( 307-)  Y
1894 GLU   ( 319-)  Y
1948 GLU   ( 373-)  Y
1951 GLU   ( 376-)  Y
1953 GLU   ( 378-)  Y
1956 GLU   (   9-)  B
1982 GLU   (  35-)  B
1996 GLU   (  49-)  B
1999 GLU   (  52-)  B
2063 GLU   ( 116-)  B
And so on for a total of 86 lines.

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.

1466 OADE  (1493-)  A      P    OP1   1.34   -8.8
1466 OADE  (1493-)  A      P    OP2   1.34   -8.6

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

 |  1.000259 -0.000052 -0.000016|
 | -0.000052  1.000130 -0.000026|
 | -0.000016 -0.000026  1.000392|
Proposed new scale matrix

 |  0.004714  0.000000  0.000000|
 |  0.000000  0.002201  0.000000|
 |  0.000000  0.000000  0.001616|
With corresponding cell

    A    = 212.144  B   = 454.398  C    = 618.671
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 212.089  B   = 454.339  C    = 618.429
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 64.237
(Under-)estimated Z-score: 5.907

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.

   2 OGUA  (   6-)  A      N9   C8   N7  113.72    5.2
   5 OGUA  (   9-)  A      N9   C8   N7  113.11    4.0
   7 OGUA  (  11-)  A      N9   C8   N7  113.43    4.7
  11 OGUA  (  15-)  A      N9   C8   N7  113.45    4.7
  17 OGUA  (  21-)  A      N9   C8   N7  113.76    5.3
  23 OGUA  (  27-)  A      N9   C8   N7  113.27    4.3
  24 OGUA  (  28-)  A      N9   C8   N7  113.30    4.4
  31 OGUA  (  35-)  A      N9   C8   N7  113.39    4.6
  34 OGUA  (  38-)  A      N9   C8   N7  113.14    4.1
  37 OGUA  (  41-)  A      N9   C8   N7  113.17    4.1
  48 OGUA  (  52-)  A      N9   C8   N7  113.33    4.5
  62 OGUA  (  66-)  A      N9   C8   N7  113.27    4.3
  64 OGUA  (  68-)  A      N9   C8   N7  113.26    4.3
  66 OGUA  (  68-)  A      N9   C8   N7  113.14    4.1
  72 OGUA  (  68-)  A      N9   C8   N7  113.24    4.3
  97 OGUA  ( 108-)  A      N9   C8   N7  113.83    5.5
 101 OGUA  ( 112-)  A      N9   C8   N7  113.11    4.0
 102 OGUA  ( 113-)  A      N9   C8   N7  113.72    5.2
 104 OGUA  ( 115-)  A      N9   C8   N7  113.76    5.3
 106 OGUA  ( 117-)  A      N9   C8   N7  113.20    4.2
 111 OGUA  ( 122-)  A      N9   C8   N7  113.11    4.0
 115 OGUA  ( 126-)  A      N9   C8   N7  113.16    4.1
 116 OGUA  ( 127-)  A      N9   C8   N7  113.19    4.2
 129 OGUA  ( 139-)  A      N9   C8   N7  113.30    4.4
 134 OGUA  ( 144-)  A      N9   C8   N7  113.28    4.4
And so on for a total of 295 lines.

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.

1606 ASP   (  31-)  Y
1616 GLU   (  41-)  Y
1623 ASP   (  48-)  Y
1634 ARG   (  59-)  Y
1639 GLU   (  64-)  Y
1642 ARG   (  67-)  Y
1644 ARG   (  69-)  Y
1645 ARG   (  70-)  Y
1662 GLU   (  87-)  Y
1665 GLU   (  90-)  Y
1671 GLU   (  96-)  Y
1678 GLU   ( 103-)  Y
1681 GLU   ( 106-)  Y
1687 ASP   ( 112-)  Y
1701 GLU   ( 126-)  Y
1719 ASP   ( 144-)  Y
1722 GLU   ( 147-)  Y
1726 ARG   ( 151-)  Y
1733 GLU   ( 158-)  Y
1734 ARG   ( 159-)  Y
1743 ASP   ( 168-)  Y
1762 GLU   ( 187-)  Y
1784 ASP   ( 209-)  Y
1789 ARG   ( 214-)  Y
1797 GLU   ( 222-)  Y
And so on for a total of 142 lines.

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.660

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.

3722 THR   ( 116-)  M    -3.5
4308 THR   (   8-)  U    -3.3
3325 PHE   (  54-)  J    -3.2
2281 THR   (  95-)  C    -3.0
3736 THR   (  13-)  N    -3.0
3112 ARG   ( 104-)  H    -2.9
2673 ILE   (  76-)  E    -2.8
4118 THR   (  82-)  R    -2.7
3508 LEU   (  26-)  L    -2.7
1890 VAL   ( 315-)  Y    -2.7
3363 THR   (  92-)  J    -2.6
1893 ILE   ( 318-)  Y    -2.6
2200 ILE   (  14-)  C    -2.6
2609 LEU   (  12-)  E    -2.6
3709 THR   ( 103-)  M    -2.6
3960 LEU   (   6-)  Q    -2.6
1693 THR   ( 118-)  Y    -2.6
2725 PRO   ( 128-)  E    -2.5
3965 VAL   (  11-)  Q    -2.5
2297 LEU   ( 111-)  C    -2.5
3088 ILE   (  80-)  H    -2.5
3519 THR   (  37-)  L    -2.5
3120 LEU   ( 112-)  H    -2.5
3526 PRO   (  44-)  L    -2.5
2624 ARG   (  27-)  E    -2.5
And so on for a total of 120 lines.

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.

1630 PRO   (  55-)  Y  Poor phi/psi
1662 GLU   (  87-)  Y  Poor phi/psi
1664 MET   (  89-)  Y  Poor phi/psi
1667 LEU   (  92-)  Y  Poor phi/psi
1669 ALA   (  94-)  Y  Poor phi/psi
1670 GLU   (  95-)  Y  Poor phi/psi
1693 THR   ( 118-)  Y  Poor phi/psi
1698 PRO   ( 123-)  Y  Poor phi/psi
1713 GLY   ( 138-)  Y  Poor phi/psi
1750 ALA   ( 175-)  Y  Poor phi/psi
1751 GLY   ( 176-)  Y  Poor phi/psi
1763 ASN   ( 188-)  Y  Poor phi/psi
1779 ARG   ( 204-)  Y  Poor phi/psi
1800 PRO   ( 225-)  Y  Poor phi/psi
1802 VAL   ( 227-)  Y  Poor phi/psi
1803 ASP   ( 228-)  Y  Poor phi/psi
1810 LEU   ( 235-)  Y  Poor phi/psi
1845 GLY   ( 270-)  Y  Poor phi/psi
1884 LYS   ( 309-)  Y  Poor phi/psi
1890 VAL   ( 315-)  Y  Poor phi/psi
1891 ARG   ( 316-)  Y  Poor phi/psi
1893 ILE   ( 318-)  Y  Poor phi/psi
1894 GLU   ( 319-)  Y  Poor phi/psi
1925 LEU   ( 350-)  Y  Poor phi/psi
1926 ASP   ( 351-)  Y  Poor phi/psi
And so on for a total of 239 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.192

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.

3823 SER   (  40-)  O    0.36
2163 SER   ( 216-)  B    0.36
3790 GLU   (   7-)  O    0.38

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 OGUA  (   7-)  A      0
   4 OADE  (   8-)  A      0
   5 OGUA  (   9-)  A      0
   6 OADE  (  10-)  A      0
   7 OGUA  (  11-)  A      0
   8 OURA  (  12-)  A      0
   9 OURA  (  13-)  A      0
  10 OURA  (  14-)  A      0
  11 OGUA  (  15-)  A      0
  12 OADE  (  16-)  A      0
  13 OURA  (  17-)  A      0
  14 OCYT  (  18-)  A      0
  15 OCYT  (  19-)  A      0
  16 OURA  (  20-)  A      0
  17 OGUA  (  21-)  A      0
  18 OGUA  (  22-)  A      0
  19 OCYT  (  23-)  A      0
  20 OURA  (  24-)  A      0
  21 OCYT  (  25-)  A      0
  22 OADE  (  26-)  A      0
  23 OGUA  (  27-)  A      0
  24 OGUA  (  28-)  A      0
  25 OGUA  (  29-)  A      0
  26 OURA  (  30-)  A      0
  27 OGUA  (  31-)  A      0
And so on for a total of 2716 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 : 3.646

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!

2331 GLY   ( 145-)  C   2.84   65
3935 GLY   (  63-)  P   2.71   26
3569 GLY   (  87-)  L   2.51   33
3202 GLY   (  57-)  I   2.34   15
3245 GLY   ( 100-)  I   2.06   17
3987 GLY   (  33-)  Q   2.05   16
4167 GLY   (  46-)  S   1.98   10
3644 GLY   (  38-)  M   1.81   65
3882 GLY   (  10-)  P   1.81   16
3179 ASN   (  34-)  I   1.78   11
3151 GLY   (   6-)  I   1.61   56

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].

1973 PRO   (  26-)  B  -123.8 half-chair C-delta/C-gamma (-126 degrees)
2106 PRO   ( 159-)  B   104.2 envelop C-beta (108 degrees)
2181 PRO   ( 234-)  B  -113.7 envelop C-gamma (-108 degrees)
2399 PRO   (   7-)  D   104.2 envelop C-beta (108 degrees)
2429 PRO   (  37-)  D    32.5 envelop C-delta (36 degrees)
2581 PRO   ( 189-)  D  -158.2 half-chair N/C-delta (-162 degrees)
2646 PRO   (  49-)  E    99.5 envelop C-beta (108 degrees)
2725 PRO   ( 128-)  E   100.1 envelop C-beta (108 degrees)
3035 PRO   (  27-)  H   103.1 envelop C-beta (108 degrees)
3529 PRO   (  47-)  L    30.5 envelop C-delta (36 degrees)
3606 PRO   ( 124-)  L   -14.5 half-chair C-alpha/N (-18 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.

4928  MG   (2182-)  A     MG   <-> 4994  MG   (2248-)  A     MG      0.56    2.64  INTRA BL
4798  MG   (2052-)  A     MG   <-> 5202  MG   (2456-)  A     MG      0.51    2.69  INTRA BL
 897 OCYT  ( 924-)  A      N3  <-> 1370 OGUA  (1392-)  A      N1     0.46    2.54  INTRA BL
4540  MG   (1794-)  A     MG   <-> 4859  MG   (2113-)  A     MG      0.46    2.74  INTRA BL
1087 OCYT  (1109-)  A      C5  <-> 5142  MG   (2396-)  A     MG      0.45    2.75  INTRA BL
 488 OADE  ( 509-)  A      O2' <->  489 OADE  ( 510-)  A      N7     0.41    2.29  INTRA BF
1059 OGUA  (1081-)  A      N7  <-> 2644 LYS   (  47-)  E      NZ     0.41    2.59  INTRA BL
4724  MG   (1978-)  A     MG   <-> 5342  MG   (2596-)  A     MG      0.40    2.80  INTRA BL
1475 OADE  (1502-)  A      N7  <-> 1478 OGUA  (1505-)  A      N2     0.39    2.61  INTRA BL
 346 OCYT  ( 355-)  A      C4  <->  347 OADE  ( 356-)  A      N7     0.39    2.71  INTRA BL
1086 OGUA  (1108-)  A      C3' <-> 5142  MG   (2396-)  A     MG      0.39    2.81  INTRA BL
 597 OCYT  ( 618-)  A      N3  <->  601 OADE  ( 622-)  A      N6     0.38    2.62  INTRA BF
1105 OGUA  (1127-)  A      N2  <-> 1123 OCYT  (1145-)  A      N3     0.38    2.62  INTRA BF
2404 CYS   (  12-)  D      SG  <-> 2423 CYS   (  31-)  D      SG     0.37    3.08  INTRA BF
 331 OURA  ( 340-)  A      N3  <->  340 OADE  ( 349-)  A      N1     0.37    2.63  INTRA BF
 911 OADE  ( 938-)  A      N6  <->  912 OGUA  ( 939-)  A      C6     0.37    2.73  INTRA BL
3270 TYR   ( 125-)  I      CD1 <-> 3271 SER   ( 126-)  I      N      0.37    2.63  INTRA BL
4463  MG   (1717-)  A     MG   <-> 5106  MG   (2360-)  A     MG      0.37    2.83  INTRA BL
 356 OURA  ( 365-)  A      C5  <-> 4957  MG   (2211-)  A     MG      0.35    2.85  INTRA BF
1190 OADE  (1213-)  A      N6  <-> 1192 OGUA  (1215-)  A      N3     0.35    2.65  INTRA BF
1420 OGUA  (1440-)  A      N7  <-> 1422 OADE  (1440-)  A      C2     0.35    2.75  INTRA BF
  34 OGUA  (  38-)  A      C2  <->  388 OADE  ( 397-)  A      C2     0.34    2.86  INTRA BL
4360  MG   (1614-)  A     MG   <-> 5167  MG   (2421-)  A     MG      0.34    2.86  INTRA BL
 142 OADE  ( 152-)  A      N6  <->  159 OCYT  ( 169-)  A      N3     0.33    2.67  INTRA BF
  51 OADE  (  55-)  A      N7  <->   52 OURA  (  56-)  A      N3     0.33    2.67  INTRA BL
And so on for a total of 2103 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: Y

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

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.

3270 TYR   ( 125-)  I      -8.61
2441 ARG   (  49-)  D      -8.18
4324 ARG   (  24-)  U      -8.13
3871 ARG   (  88-)  O      -8.05
3710 ARG   ( 104-)  M      -7.94
2265 ARG   (  79-)  C      -7.87
2858 ARG   (   6-)  G      -7.87
2376 ARG   ( 190-)  C      -7.82
3481 ARG   ( 120-)  K      -7.66
4201 TYR   (  80-)  S      -7.51
2434 GLN   (  42-)  D      -7.45
3900 ARG   (  28-)  P      -7.42
3705 ARG   (  99-)  M      -7.41
3386 TYR   (  25-)  K      -7.32
3252 ARG   ( 107-)  I      -7.26
2396 TYR   (   4-)  D      -7.26
2856 ARG   (   4-)  G      -7.19
2104 ARG   ( 157-)  B      -7.17
2855 ARG   (   3-)  G      -7.16
2430 TYR   (  38-)  D      -7.13
2293 GLN   ( 107-)  C      -7.12
1854 ARG   ( 279-)  Y      -7.11
3954 GLN   (  82-)  P      -7.09
3077 ARG   (  69-)  H      -7.08
3708 ARG   ( 102-)  M      -7.04
And so on for a total of 188 lines.

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.

1801 GLU   ( 226-)  Y      1804 - GLU    229- ( Y)         -4.60
1823 SER   ( 248-)  Y      1826 - GLY    251- ( Y)         -4.27
1889 GLU   ( 314-)  Y      1891 - ARG    316- ( Y)         -5.35
1983 ARG   (  36-)  B      1985 - GLY     38- ( B)         -4.93
2103 LYS   ( 156-)  B      2105 - LEU    158- ( B)         -5.98
2176 VAL   ( 229-)  B      2178 - GLU    231- ( B)         -4.82
2189 ASN   (   3-)  C      2191 - ILE      5- ( C)         -5.00
2312 ARG   ( 126-)  C      2314 - PHE    128- ( C)         -4.76
2395 ARG   (   3-)  D      2397 - ILE      5- ( D)         -6.45
2437 GLN   (  45-)  D      2439 - ARG     47- ( D)         -5.83
2476 LYS   (  84-)  D      2478 - LYS     86- ( D)         -5.45
2560 ARG   ( 168-)  D      2562 - VAL    170- ( D)         -5.74
2615 ARG   (  18-)  E      2619 - GLY     22- ( E)         -5.04
2855 ARG   (   3-)  G      2858 - ARG      6- ( G)         -6.75
2868 LEU   (  16-)  G      2870 - TYR     18- ( G)         -4.46
3076 ARG   (  68-)  H      3078 - GLN     70- ( H)         -6.29
3154 ARG   (   9-)  I      3156 - LYS     11- ( I)         -4.58
3269 GLN   ( 124-)  I      3272 - LYS    127- ( I)         -6.34
3496 ARG   (  14-)  L      3501 - LYS     19- ( L)         -5.17
3554 GLU   (  72-)  L      3556 - HIS     74- ( L)         -5.05
3870 ILE   (  87-)  O      3872 - GLY     89- ( O)         -5.62
4051 SER   (  97-)  Q      4053 - SER     99- ( Q)         -4.26
4125 SER   (   4-)  S      4128 - LYS      7- ( S)         -5.58
4149 LYS   (  28-)  S      4151 - LEU     30- ( S)         -5.54
4320 LYS   (  20-)  U      4322 - ARG     22- ( U)         -5.34

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 4325 : -1.641

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: Y

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

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: E

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: F

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: G

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: H

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: I

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: J

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: K

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: L

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: M

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: N

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: O

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: P

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: Q

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: R

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: T

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: U

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.

3326 LYS   (  55-)  J   -3.54
3269 GLN   ( 124-)  I   -3.28
3272 LYS   ( 127-)  I   -3.17
3754 ARG   (  31-)  N   -3.16
3387 ASN   (  26-)  K   -3.15
2855 ARG   (   3-)  G   -3.10
4205 LEU   (  10-)  T   -3.08
4127 LYS   (   6-)  S   -3.07
3710 ARG   ( 104-)  M   -3.07
3914 ARG   (  42-)  P   -2.99
3572 LYS   (  90-)  L   -2.96
4175 GLY   (  54-)  S   -2.96
3744 TYR   (  21-)  N   -2.96
2189 ASN   (   3-)  C   -2.95
3325 PHE   (  54-)  J   -2.92
3479 GLY   ( 118-)  K   -2.92
3512 PRO   (  30-)  L   -2.90
1786 SER   ( 211-)  Y   -2.89
3009 MET   (   1-)  H   -2.88
3706 GLY   ( 100-)  M   -2.86
2434 GLN   (  42-)  D   -2.84
2570 VAL   ( 178-)  D   -2.84
2859 ALA   (   7-)  G   -2.82
3249 ARG   ( 104-)  I   -2.82
3477 HIS   ( 116-)  K   -2.80
And so on for a total of 56 lines.

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.

2187 GLN   ( 240-)  B     - 2191 ILE   (   5-)  C        -2.13
2393 VAL   ( 207-)  C     - 2398 GLY   (   6-)  D        -1.90
2413 LEU   (  21-)  D     - 2417 ARG   (  25-)  D        -1.89
2432 PRO   (  40-)  D     - 2435 HIS   (  43-)  D        -1.92
2853 ALA   ( 101-)  F     - 2857 ARG   (   5-)  G        -2.00
2883 MET   (  31-)  G     - 2886 GLY   (  34-)  G        -1.93
3008 TRP   ( 156-)  G     - 3011 THR   (   3-)  H        -2.23
3255 GLU   ( 110-)  I     - 3259 TYR   ( 114-)  I        -2.01
3322 ARG   (  51-)  J     - 3329 ASP   (  58-)  J        -2.28
3475 VAL   ( 114-)  K     - 3481 ARG   ( 120-)  K        -2.21
3597 SER   ( 115-)  L     - 3600 LYS   ( 118-)  L        -1.84
3703 PRO   (  97-)  M     - 3708 ARG   ( 102-)  M        -1.90
3709 THR   ( 103-)  M     - 3712 ASN   ( 106-)  M        -2.32
3736 THR   (  13-)  N     - 3742 ARG   (  19-)  N        -1.94
3780 ARG   (  57-)  N     - 3783 SER   (  60-)  N        -1.85
3878 LEU   (   6-)  P     - 3881 PHE   (   9-)  P        -1.78
3896 ALA   (  24-)  P     - 3900 ARG   (  28-)  P        -2.08
4125 SER   (   4-)  S     - 4128 LYS   (   7-)  S        -2.19

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: Y

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Water, ion, and hydrogenbond related checks

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.

1756 GLN   ( 181-)  Y
1851 GLN   ( 276-)  Y
1992 GLN   (  45-)  B
2151 ASN   ( 204-)  B
2217 HIS   (  31-)  C
2367 ASN   ( 181-)  C
2434 GLN   (  42-)  D
2454 GLN   (  62-)  D
2517 HIS   ( 125-)  D
2591 ASN   ( 199-)  D
2675 HIS   (  78-)  E
2759 ASN   (   7-)  F
2936 ASN   (  84-)  G
3218 GLN   (  73-)  I
3269 GLN   ( 124-)  I
3292 GLN   (  21-)  J
3333 HIS   (  62-)  J
3477 HIS   ( 116-)  K
3489 ASN   (   7-)  L
3490 GLN   (   8-)  L
3556 HIS   (  74-)  L
4072 ASN   (  36-)  R
4174 ASN   (  53-)  S

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.

  53 OGUA  (  57-)  A      N2
  73 OGUA  (  68-)  A      N2
  75 OURA  (  68-)  A      N3
  81 OURA  (  68-)  A      N3
  85 OURA  (  68-)  A      N3
  99 OCYT  ( 110-)  A      N4
 104 OGUA  ( 115-)  A      N2
 126 OCYT  ( 136-)  A      O2'
 134 OGUA  ( 144-)  A      N1
 141 OADE  ( 151-)  A      N6
 147 OGUA  ( 157-)  A      N1
 167 OCYT  ( 177-)  A      N4
 171 OGUA  ( 181-)  A      N2
 179 OGUA  ( 186-)  A      N1
 190 OURA  ( 186-)  A      N3
 192 OURA  ( 186-)  A      N3
 202 OGUA  ( 200-)  A      N1
 207 OGUA  ( 216-)  A      N1
 217 OGUA  ( 226-)  A      N2
 242 OGUA  ( 251-)  A      N2
 245 OGUA  ( 254-)  A      N2
 309 OGUA  ( 318-)  A      N2
 313 OCYT  ( 322-)  A      N4
 316 OADE  ( 325-)  A      N6
 353 OGUA  ( 362-)  A      O2'
And so on for a total of 604 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.

1611 GLU   (  36-)  Y      OE1
1771 GLU   ( 196-)  Y      OE2
1898 GLN   ( 323-)  Y      OE1
1905 ASP   ( 330-)  Y      OD2
2031 GLU   (  84-)  B      OE1
2066 GLU   ( 119-)  B      OE1
2088 GLU   ( 141-)  B      OE1
2136 ASP   ( 189-)  B      OD2
2152 ASP   ( 205-)  B      OD1
2222 ASP   (  36-)  C      OD1
2867 ASP   (  15-)  G      OD2
3327 HIS   (  56-)  J      NE2
3344 ASP   (  73-)  J      OD1
3546 GLU   (  64-)  L      OE1
3614 GLU   (   8-)  M      OE1
3673 GLU   (  67-)  M      OE1
3809 GLU   (  26-)  O      OE2
4194 GLU   (  73-)  S      OE1
4255 GLU   (  60-)  T      OE2

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+.

4347  MG   (1601-)  A   -.-  -.-  Too few ligands (0)
4348  MG   (1602-)  A   -.-  -.-  Too few ligands (1)
4349  MG   (1603-)  A   -.-  -.-  Too few ligands (0)
4350  MG   (1604-)  A   -.-  -.-  Too few ligands (0)
4351  MG   (1605-)  A   -.-  -.-  Low probability ion. B=112.6
4352  MG   (1606-)  A   -.-  -.-  Low probability ion. B=255.5
4353  MG   (1607-)  A   -.-  -.-  Part of ionic cluster
4353  MG   (1607-)  A   -.-  -.-  Too few ligands (0)
4354  MG   (1608-)  A   -.-  -.-  Low probability ion. B= 87.9
4355  MG   (1609-)  I   -.-  -.-  Low probability ion. B= 99.9
4356  MG   (1610-)  A   -.-  -.-  Low probability ion. B=159.5
4357  MG   (1611-)  A   -.-  -.-  Too few ligands (0)
4358  MG   (1612-)  A   -.-  -.-  Low probability ion. B=115.3
4359  MG   (1613-)  A   -.-  -.-  Too few ligands (0)
4360  MG   (1614-)  A   -.-  -.-  Low probability ion. B=138.6
4361  MG   (1615-)  A   -.-  -.-  Too few ligands (0)
4362  MG   (1616-)  A   -.-  -.-  Low probability ion. B= 86.1
4363  MG   (1617-)  A   -.-  -.-  Low probability ion. B= 86.0
4364  MG   (1618-)  A   -.-  -.-  Too few ligands (0)
4365  MG   (1619-)  A   -.-  -.-  Low probability ion. B= 90.6
4366  MG   (1620-)  A   -.-  -.-  Low probability ion. B=100.4
4367  MG   (1621-)  A   -.-  -.-  Low probability ion. B= 84.3
4368  MG   (1622-)  A   -.-  -.-  Too few ligands (1)
4369  MG   (1623-)  A   -.-  -.-  Too few ligands (2)
4370  MG   (1624-)  A   -.-  -.-  Low probability ion. B= 82.2
And so on for a total of 1339 lines.

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.

1611 GLU   (  36-)  Y   H-bonding suggests Gln
1648 ASP   (  73-)  Y   H-bonding suggests Asn; but Alt-Rotamer
1662 GLU   (  87-)  Y   H-bonding suggests Gln
1665 GLU   (  90-)  Y   H-bonding suggests Gln
1673 GLU   (  98-)  Y   H-bonding suggests Gln
1688 GLU   ( 113-)  Y   H-bonding suggests Gln
1733 GLU   ( 158-)  Y   H-bonding suggests Gln
1801 GLU   ( 226-)  Y   H-bonding suggests Gln
1814 GLU   ( 239-)  Y   H-bonding suggests Gln
1881 GLU   ( 306-)  Y   H-bonding suggests Gln
1889 GLU   ( 314-)  Y   H-bonding suggests Gln
1911 ASP   ( 336-)  Y   H-bonding suggests Asn; but Alt-Rotamer
1938 GLU   ( 363-)  Y   H-bonding suggests Gln; but Alt-Rotamer
1951 GLU   ( 376-)  Y   H-bonding suggests Gln
1959 GLU   (  12-)  B   H-bonding suggests Gln
1997 GLU   (  50-)  B   H-bonding suggests Gln; but Alt-Rotamer
2064 GLU   ( 117-)  B   H-bonding suggests Gln
2066 GLU   ( 119-)  B   H-bonding suggests Gln; but Alt-Rotamer
2073 GLU   ( 126-)  B   H-bonding suggests Gln
2117 GLU   ( 170-)  B   H-bonding suggests Gln
2167 ASP   ( 220-)  B   H-bonding suggests Asn; but Alt-Rotamer
2178 GLU   ( 231-)  B   H-bonding suggests Gln; but Alt-Rotamer
2205 GLU   (  19-)  C   H-bonding suggests Gln
2221 GLU   (  35-)  C   H-bonding suggests Gln
2291 GLU   ( 105-)  C   H-bonding suggests Gln
2311 GLU   ( 125-)  C   H-bonding suggests Gln; but Alt-Rotamer
2536 ASP   ( 144-)  D   H-bonding suggests Asn; but Alt-Rotamer
2719 GLU   ( 122-)  E   H-bonding suggests Gln
2807 ASP   (  55-)  F   H-bonding suggests Asn; but Alt-Rotamer
2897 ASP   (  45-)  G   H-bonding suggests Asn
2975 GLU   ( 123-)  G   H-bonding suggests Gln
3042 GLU   (  34-)  H   H-bonding suggests Gln
3060 ASP   (  52-)  H   H-bonding suggests Asn
3107 GLU   (  99-)  H   H-bonding suggests Gln
3199 ASP   (  54-)  I   H-bonding suggests Asn
3205 ASP   (  60-)  I   H-bonding suggests Asn; but Alt-Rotamer
3344 ASP   (  73-)  J   H-bonding suggests Asn; but Alt-Rotamer
3368 GLU   (  97-)  J   H-bonding suggests Gln
3395 ASP   (  34-)  K   H-bonding suggests Asn
3614 GLU   (   8-)  M   H-bonding suggests Gln
3673 GLU   (  67-)  M   H-bonding suggests Gln; but Alt-Rotamer
3689 ASP   (  83-)  M   H-bonding suggests Asn
3856 GLU   (  73-)  O   H-bonding suggests Gln
4009 ASP   (  55-)  Q   H-bonding suggests Asn
4066 ASP   (  30-)  R   H-bonding suggests Asn; but Alt-Rotamer
4119 GLU   (  83-)  R   H-bonding suggests Gln
4148 GLU   (  27-)  S   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.852
  2nd generation packing quality :  -3.517 (poor)
  Ramachandran plot appearance   :  -4.660 (bad)
  chi-1/chi-2 rotamer normality  :  -4.192 (bad)
  Backbone conformation          :  -0.839

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.651 (tight)
  Omega angle restraints         :   0.663 (tight)
  Side chain planarity           :   0.127 (tight)
  Improper dihedral distribution :   0.366
  B-factor distribution          :   0.349
  Inside/Outside distribution    :   1.009

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 : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.651 (tight)
  Omega angle restraints         :   0.663 (tight)
  Side chain planarity           :   0.127 (tight)
  Improper dihedral distribution :   0.366
  B-factor distribution          :   0.349
  Inside/Outside distribution    :   1.009
==============

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.