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 pdb4kbw.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the space group: MONOCLINIC

Space group name: C 1 2 1

Error: CRYST1 cell represents wrong crystal class

The crystal class for the unit cell on the CRYST1 card is different from the crystal class derived from the SCALE matrix. The SCALE matrix is compatible with the SPACE group.

The CRYST1 cell dimensions

    A    = 302.391  B   = 683.918  C    = 356.698
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Cell as derived from the SCALE matrix

    A    = 302.297  B   = 683.060  C    = 358.299
    Alpha=  90.000  Beta=  90.294  Gamma=  90.000

Space group name: C 1 2 1

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: C 1 2 1
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: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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: 1381149.3
Volume of the Unit Cell V= 73983272.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.392
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.040

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

2230 ARG   (  64-)  U  -   CG  3135 PRO   (  40-)  N  -   O
3173 TYR   (  78-)  N  -   CD2 6441 OGUA  (2642-)  A  -   C5'

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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: 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: K

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

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 0

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

Note: Ramachandran plot

Chain identifier: E

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 PRO   (   2-)  C    High
   2 LYS   (   3-)  C    High
   3 HIS   (   4-)  C    High
   4 GLY   (   5-)  C    High
   5 LYS   (   6-)  C    High
   6 ARG   (   7-)  C    High
   7 TYR   (   8-)  C    High
   8 ARG   (   9-)  C    High
   9 ALA   (  10-)  C    High
  10 LEU   (  11-)  C    High
  11 LEU   (  12-)  C    High
  12 GLU   (  13-)  C    High
  13 LYS   (  14-)  C    High
  14 VAL   (  15-)  C    High
  16 PRO   (  17-)  C    High
  17 ASN   (  18-)  C    High
  18 LYS   (  19-)  C    High
  19 VAL   (  20-)  C    High
  20 TYR   (  21-)  C    High
  21 THR   (  22-)  C    High
  22 ILE   (  23-)  C    High
  23 ASP   (  24-)  C    High
  24 GLU   (  25-)  C    High
  25 ALA   (  26-)  C    High
  26 ALA   (  27-)  C    High
And so on for a total of 2508 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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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: K

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

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 0

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: 8

Note: B-factor plot

Chain identifier: 9

Note: B-factor plot

Chain identifier: E

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.

  53 ARG   (  54-)  C
 466 ARG   ( 239-)  D
 561 ARG   (  58-)  E
1563 ARG   (  41-)  P
1572 ARG   (  50-)  P
1577 ARG   (  55-)  P
1624 ARG   ( 102-)  P
1633 ARG   ( 111-)  P
1876 ARG   (  64-)  R
1900 ARG   (  88-)  R
2158 ARG   ( 129-)  T
2216 ARG   (  50-)  U
2230 ARG   (  64-)  U
2914 ARG   (  32-)  0
3017 ARG   (  52-)  1
3287 ARG   (  55-)  2
3418 ARG   (  55-)  5
3437 ARG   (  18-)  6
3522 ARG   (  49-)  7

Warning: Tyrosine convention problem

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

 213 TYR   ( 214-)  C
 289 TYR   (  62-)  D
 331 TYR   ( 104-)  D
 399 TYR   ( 172-)  D
 663 TYR   ( 160-)  E
 767 TYR   (  59-)  F
 805 TYR   (  97-)  F
 926 TYR   (  11-)  G
 927 TYR   (  12-)  G
1243 TYR   ( 157-)  H
1698 TYR   (  26-)  Q
1704 TYR   (  32-)  Q
1833 TYR   (  21-)  R
2061 TYR   (  32-)  T
2190 TYR   (  24-)  U
2211 TYR   (  45-)  U
2365 TYR   (  81-)  V
2565 TYR   (  69-)  X
2610 TYR   (  20-)  Y
2645 TYR   (  55-)  Y
2705 TYR   (   9-)  Z
2725 TYR   (  29-)  Z
2795 TYR   (  99-)  Z
2908 TYR   (  26-)  0
3218 TYR   ( 123-)  N
3585 TYR   (  64-)  8

Warning: Phenylalanine convention problem

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

 163 PHE   ( 164-)  C
 242 PHE   (  15-)  D
 248 PHE   (  21-)  D
 280 PHE   (  53-)  D
 294 PHE   (  67-)  D
 362 PHE   ( 135-)  D
 518 PHE   (  15-)  E
 587 PHE   (  84-)  E
 616 PHE   ( 113-)  E
 798 PHE   (  90-)  F
1017 PHE   ( 102-)  G
1056 PHE   ( 141-)  G
1328 PHE   (  65-)  K
1503 PHE   (  99-)  O
1573 PHE   (  51-)  P
1613 PHE   (  91-)  P
1652 PHE   ( 130-)  P
1701 PHE   (  29-)  Q
1892 PHE   (  80-)  R
1949 PHE   (  29-)  S
2086 PHE   (  57-)  T
2090 PHE   (  61-)  T
2105 PHE   (  76-)  T
2198 PHE   (  32-)  U
2206 PHE   (  40-)  U
2245 PHE   (  79-)  U
2517 PHE   (  21-)  X
2543 PHE   (  47-)  X
2650 PHE   (  60-)  Y
2784 PHE   (  88-)  Z
2785 PHE   (  89-)  Z
2832 PHE   ( 136-)  Z
2927 PHE   (  45-)  0
2942 PHE   (  60-)  0
3633 PHE   (  60-)  E

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.

 118 ASP   ( 119-)  C
 326 ASP   (  99-)  D
 398 ASP   ( 171-)  D
 520 ASP   (  17-)  E
 586 ASP   (  83-)  E
 677 ASP   ( 174-)  E
 731 ASP   (  23-)  F
 824 ASP   ( 116-)  F
 903 ASP   ( 195-)  F
 905 ASP   ( 197-)  F
 919 ASP   (   4-)  G
 964 ASP   (  49-)  G
1031 ASP   ( 116-)  G
1041 ASP   ( 126-)  G
1081 ASP   ( 166-)  G
1325 ASP   (  62-)  K
1382 ASP   ( 119-)  K
1416 ASP   (  12-)  O
1460 ASP   (  56-)  O
1485 ASP   (  81-)  O
1569 ASP   (  47-)  P
1861 ASP   (  49-)  R
1884 ASP   (  72-)  R
1919 ASP   ( 107-)  R
2008 ASP   (  88-)  S
2055 ASP   (  26-)  T
2073 ASP   (  44-)  T
2407 ASP   (  22-)  W
2479 ASP   (  94-)  W
2601 ASP   (  11-)  Y
2741 ASP   (  45-)  Z
2773 ASP   (  77-)  Z
2836 ASP   ( 140-)  Z
2850 ASP   ( 154-)  Z
2897 ASP   (  15-)  0
2938 ASP   (  56-)  0
3112 ASP   (  17-)  N
3343 ASP   (  39-)  3
3380 ASP   (  17-)  5

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.

  24 GLU   (  25-)  C
  39 GLU   (  40-)  C
  42 GLU   (  43-)  C
  97 GLU   (  98-)  C
  98 GLU   (  99-)  C
 151 GLU   ( 152-)  C
 197 GLU   ( 198-)  C
 202 GLU   ( 203-)  C
 250 GLU   (  23-)  D
 310 GLU   (  83-)  D
 373 GLU   ( 146-)  D
 375 GLU   ( 148-)  D
 408 GLU   ( 181-)  D
 576 GLU   (  73-)  E
 597 GLU   (  94-)  E
 703 GLU   ( 200-)  E
 743 GLU   (  35-)  F
 828 GLU   ( 120-)  F
 835 GLU   ( 127-)  F
 908 GLU   ( 200-)  F
 928 GLU   (  13-)  G
 929 GLU   (  14-)  G
 950 GLU   (  35-)  G
 960 GLU   (  45-)  G
 963 GLU   (  48-)  G
And so on for a total of 79 lines.

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): E

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.

 306 VAL   (  79-)  D      CA   CB    1.61    4.0
 862 VAL   ( 154-)  F      CA   CB    1.61    4.0
 864 LEU   ( 156-)  F      CA   C     1.44   -4.1
1028 ARG   ( 113-)  G      CA   C     1.42   -4.8
1029 ILE   ( 114-)  G      N    CA    1.31   -7.9
2978 ILE   (  13-)  1      CA   CB    1.62    4.5
3770 OGUA  (  75-)  B      N9   C4    1.41    4.0
4238 OADE  ( 401-)  A      N9   C4    1.40    4.0
4840 OCYT  (1006-)  A      N1   C2    1.45    5.1
4854 OADE  (1020-)  A      N9   C8    1.33   -5.5
4970 OGUA  (1137-)  A      C1'  N9    1.50    4.3
4970 OGUA  (1137-)  A      N9   C4    1.42    5.5

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

 |  0.999696 -0.000011 -0.000029|
 | -0.000011  0.999957  0.000045|
 | -0.000029  0.000045  0.999665|
Proposed new scale matrix

 |  0.003309  0.000000  0.000017|
 |  0.000000  0.001464  0.000000|
 |  0.000000  0.000000  0.002792|
With corresponding cell

    A    = 302.205  B   = 683.030  C    = 358.179
    Alpha=  90.006  Beta=  90.298  Gamma=  90.006

The CRYST1 cell dimensions

    A    = 302.297  B   = 683.060  C    = 358.299
    Alpha=  90.000  Beta=  90.294  Gamma=  90.000

Variance: 103.363
(Under-)estimated Z-score: 7.493

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.

  11 LEU   (  12-)  C      CA   CB   CG  131.85    4.4
  41 VAL   (  42-)  C      C    CA   CB  102.12   -4.2
  44 HIS   (  45-)  C     -C    N    CA  109.86   -6.6
  61 THR   (  62-)  C      C    CA   CB  102.42   -4.0
 137 LEU   ( 138-)  C      N    CA   C   125.41    5.1
 163 PHE   ( 164-)  C      N    CA   CB  120.40    5.8
 212 VAL   ( 213-)  C      N    CA   C    96.73   -5.2
 213 TYR   ( 214-)  C      N    CA   C    92.76   -6.6
 263 PRO   (  36-)  D      N    CA   C   122.76    4.4
 565 PRO   (  62-)  E     -C    N    CD  141.73    4.1
 862 VAL   ( 154-)  F     -C    N    CA  112.15   -5.3
 862 VAL   ( 154-)  F      C    CA   CB  118.42    4.4
 863 LEU   ( 155-)  F      N    CA   C    88.61   -8.1
 864 LEU   ( 156-)  F      N    CA   C    93.94   -6.2
 865 VAL   ( 157-)  F     -C    N    CA  111.95   -5.4
 865 VAL   ( 157-)  F      N    CA   CB  118.23    4.5
 865 VAL   ( 157-)  F      C    CA   CB  120.03    5.2
 882 VAL   ( 174-)  F      N    CA   C    98.01   -4.7
 882 VAL   ( 174-)  F      N    CA   CB  117.60    4.2
 898 GLU   ( 190-)  F      N    CA   C   122.69    4.1
 899 ARG   ( 191-)  F     -C    N    CA  114.39   -4.1
 899 ARG   ( 191-)  F      N    CA   C   125.80    5.2
 901 VAL   ( 193-)  F      C    CA   CB  121.81    6.2
 902 MET   ( 194-)  F     -CA  -C    N   107.39   -4.4
 903 ASP   ( 195-)  F      N    CA   C    98.28   -4.6
And so on for a total of 1192 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.

  24 GLU   (  25-)  C
  39 GLU   (  40-)  C
  42 GLU   (  43-)  C
  53 ARG   (  54-)  C
  97 GLU   (  98-)  C
  98 GLU   (  99-)  C
 118 ASP   ( 119-)  C
 151 GLU   ( 152-)  C
 197 GLU   ( 198-)  C
 202 GLU   ( 203-)  C
 250 GLU   (  23-)  D
 310 GLU   (  83-)  D
 326 ASP   (  99-)  D
 373 GLU   ( 146-)  D
 375 GLU   ( 148-)  D
 398 ASP   ( 171-)  D
 408 GLU   ( 181-)  D
 466 ARG   ( 239-)  D
 520 ASP   (  17-)  E
 561 ARG   (  58-)  E
 576 GLU   (  73-)  E
 586 ASP   (  83-)  E
 597 GLU   (  94-)  E
 677 ASP   ( 174-)  E
 703 GLU   ( 200-)  E
And so on for a total of 137 lines.

Warning: Chirality deviations detected

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

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

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

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

 181 PRO   ( 182-)  C      N      7.4    21.82    -2.48
 862 VAL   ( 154-)  F      CA    -6.5    23.78    33.23
 865 VAL   ( 157-)  F      CA    -7.0    23.02    33.23
 899 ARG   ( 191-)  F      CA    -8.2    20.47    33.91
1026 LEU   ( 111-)  G      C      8.5    13.62     0.20
2334 PRO   (  50-)  V      N      7.8    23.10    -2.48
The average deviation= 0.750

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.

 863 LEU   ( 155-)  F    9.19
3005 ARG   (  40-)  1    8.07
 213 TYR   ( 214-)  C    7.03
 864 LEU   ( 156-)  F    7.03
1992 ALA   (  72-)  S    6.09
2982 SER   (  17-)  1    5.75
 137 LEU   ( 138-)  C    5.73
1081 ASP   ( 166-)  G    5.55
2380 ILE   (  96-)  V    5.49
 899 ARG   ( 191-)  F    5.42
 308 ALA   (  81-)  D    5.19
 212 VAL   ( 213-)  C    5.14
3209 ARG   ( 114-)  N    4.85
1011 ARG   (  96-)  G    4.72
 882 VAL   ( 174-)  F    4.65
 120 MET   ( 121-)  C    4.61
2979 VAL   (  14-)  1    4.58
 307 ALA   (  80-)  D    4.51
1880 ARG   (  68-)  R    4.51
 524 VAL   (  21-)  E    4.50
 903 ASP   ( 195-)  F    4.40
 153 ILE   ( 154-)  C    4.36
 568 GLY   (  65-)  E    4.28
2458 ALA   (  73-)  W    4.27
3427 LYS   (   8-)  6    4.27
 114 VAL   ( 115-)  C    4.25
 526 VAL   (  23-)  E    4.21
1029 ILE   ( 114-)  G    4.14
2021 LEU   ( 101-)  S    4.13
 513 GLY   (  10-)  E    4.12
2590 GLY   (  94-)  X    4.05

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 : -6.113

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.

3585 TYR   (  64-)  8    -3.7
 252 THR   (  25-)  D    -3.7
2725 TYR   (  29-)  Z    -3.7
1967 THR   (  47-)  S    -3.7
2056 THR   (  27-)  T    -3.6
 554 PHE   (  51-)  E    -3.5
1632 TYR   ( 110-)  P    -3.5
2999 THR   (  34-)  1    -3.4
2394 TYR   (   9-)  W    -3.4
3468 HIS   (  49-)  6    -3.3
3569 PHE   (  48-)  8    -3.3
1580 THR   (  58-)  P    -3.3
1438 THR   (  34-)  O    -3.2
 718 PRO   (  10-)  F    -3.1
2334 PRO   (  50-)  V    -3.1
2622 PRO   (  32-)  Y    -3.1
1107 PRO   (  21-)  H    -3.1
1452 PRO   (  48-)  O    -3.1
 181 PRO   ( 182-)  C    -3.1
 559 PRO   (  56-)  E    -3.1
 174 PRO   ( 175-)  C    -3.1
1204 PRO   ( 118-)  H    -3.1
1667 PRO   ( 145-)  P    -3.1
 140 PRO   ( 141-)  C    -3.1
2791 PRO   (  95-)  Z    -3.1
And so on for a total of 557 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.

   2 LYS   (   3-)  C  Poor phi/psi
   7 TYR   (   8-)  C  omega poor
  10 LEU   (  11-)  C  omega poor
  12 GLU   (  13-)  C  omega poor
  16 PRO   (  17-)  C  Poor phi/psi
  18 LYS   (  19-)  C  omega poor
  20 TYR   (  21-)  C  Poor phi/psi
  21 THR   (  22-)  C  Poor phi/psi
  23 ASP   (  24-)  C  Poor phi/psi
  29 VAL   (  30-)  C  omega poor
  35 ALA   (  36-)  C  Poor phi/psi
  36 LYS   (  37-)  C  Poor phi/psi, omega poor
  37 PHE   (  38-)  C  Poor phi/psi, omega poor
  41 VAL   (  42-)  C  Poor phi/psi
  42 GLU   (  43-)  C  Poor phi/psi, omega poor
  43 VAL   (  44-)  C  omega poor
  44 HIS   (  45-)  C  omega poor
  47 LEU   (  48-)  C  Poor phi/psi
  51 PRO   (  52-)  C  Poor phi/psi
  53 ARG   (  54-)  C  Poor phi/psi
  54 SER   (  55-)  C  Poor phi/psi
  57 ASN   (  58-)  C  omega poor
  58 VAL   (  59-)  C  Poor phi/psi
  59 ARG   (  60-)  C  Poor phi/psi, omega poor
  60 GLY   (  61-)  C  Poor phi/psi
And so on for a total of 738 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 : -6.301

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.

1839 SER   (  27-)  R    0.37

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 HIS   (   4-)  C      0
   7 TYR   (   8-)  C      0
  13 LYS   (  14-)  C      0
  14 VAL   (  15-)  C      0
  15 ASP   (  16-)  C      0
  16 PRO   (  17-)  C      0
  17 ASN   (  18-)  C      0
  18 LYS   (  19-)  C      0
  19 VAL   (  20-)  C      0
  20 TYR   (  21-)  C      0
  21 THR   (  22-)  C      0
  22 ILE   (  23-)  C      0
  27 ARG   (  28-)  C      0
  29 VAL   (  30-)  C      0
  33 ALA   (  34-)  C      0
  34 THR   (  35-)  C      0
  35 ALA   (  36-)  C      0
  36 LYS   (  37-)  C      0
  37 PHE   (  38-)  C      0
  38 ASP   (  39-)  C      0
  40 THR   (  41-)  C      0
  41 VAL   (  42-)  C      0
  42 GLU   (  43-)  C      0
  43 VAL   (  44-)  C      0
  44 HIS   (  45-)  C      0
And so on for a total of 5050 lines.

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!

2016 GLY   (  96-)  S   3.39   13
 627 GLY   ( 124-)  E   3.36   10
 461 GLY   ( 234-)  D   3.25   13
2810 GLY   ( 114-)  Z   3.09   23
2974 GLY   (   9-)  1   2.81   10
1533 GLY   (  11-)  P   2.48   10
2325 GLY   (  41-)  V   2.33   15
3274 GLY   (  42-)  2   2.19   32
2890 GLY   (   8-)  0   1.87   16
 553 GLY   (  50-)  E   1.86   55
 106 GLY   ( 107-)  C   1.85   10
1090 LEU   ( 175-)  G   1.81   48
 366 GLY   ( 139-)  D   1.80   74
2722 GLY   (  26-)  Z   1.79   38
1687 GLY   (  15-)  Q   1.76   12
3511 GLY   (  38-)  7   1.66   14
2557 GLY   (  61-)  X   1.61   23
2567 GLY   (  71-)  X   1.59   30
 450 GLY   ( 223-)  D   1.54   15
1566 GLY   (  44-)  P   1.51   28
2314 GLY   (  30-)  V   1.51   80

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

2361 ALA   (  77-)  V   1.62

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].

  16 PRO   (  17-)  C   123.5 half-chair C-beta/C-alpha (126 degrees)
  51 PRO   (  52-)  C   116.1 envelop C-beta (108 degrees)
  65 PRO   (  66-)  C   110.2 envelop C-beta (108 degrees)
 138 PRO   ( 139-)  C   131.5 half-chair C-beta/C-alpha (126 degrees)
 140 PRO   ( 141-)  C   118.6 half-chair C-beta/C-alpha (126 degrees)
 174 PRO   ( 175-)  C   -20.2 half-chair C-alpha/N (-18 degrees)
 181 PRO   ( 182-)  C   135.8 envelop C-alpha (144 degrees)
 182 PRO   ( 183-)  C   163.2 half-chair C-alpha/N (162 degrees)
 220 PRO   ( 221-)  C   110.2 envelop C-beta (108 degrees)
 226 PRO   ( 227-)  C   121.0 half-chair C-beta/C-alpha (126 degrees)
 263 PRO   (  36-)  D   124.5 half-chair C-beta/C-alpha (126 degrees)
 303 PRO   (  76-)  D  -116.6 envelop C-gamma (-108 degrees)
 359 PRO   ( 132-)  D   107.6 envelop C-beta (108 degrees)
 405 PRO   ( 178-)  D  -143.6 envelop C-delta (-144 degrees)
 446 PRO   ( 219-)  D  -117.7 half-chair C-delta/C-gamma (-126 degrees)
 492 PRO   ( 265-)  D   100.1 envelop C-beta (108 degrees)
 525 PRO   (  22-)  E  -135.2 envelop C-delta (-144 degrees)
 535 PRO   (  32-)  E   110.2 envelop C-beta (108 degrees)
 542 PRO   (  39-)  E  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 559 PRO   (  56-)  E   -20.9 half-chair C-alpha/N (-18 degrees)
 577 PRO   (  74-)  E  -128.8 half-chair C-delta/C-gamma (-126 degrees)
 629 PRO   ( 126-)  E   166.1 half-chair C-alpha/N (162 degrees)
 718 PRO   (  10-)  F   -31.7 envelop C-alpha (-36 degrees)
 722 PRO   (  14-)  F   104.6 envelop C-beta (108 degrees)
 800 PRO   (  92-)  F  -118.4 half-chair C-delta/C-gamma (-126 degrees)
And so on for a total of 76 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance; each bump is listed in only one direction,

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

2230 ARG   (  64-)  U      CD   <->  3136 ASP   (  41-)  N      CA   1.30    1.90  INTRA BF
6480 OCYT  (2681-)  A      C5   <->  6525 OADE  (2725-)  A      N6   1.01    2.09  INTRA BL
4717 OGUA  ( 882-)  A      N2   <->  4728 OCYT  ( 894-)  A      N3   1.00    2.00  INTRA BF
3161 LYS   (  66-)  N      NZ   <->  4973 OCYT  (1140-)  A      OP2  0.92    1.78  INTRA BF
3171 SER   (  76-)  N      CB   <->  6440 OGUA  (2641-)  A      C5'  0.89    2.31  INTRA BL
5250 OGUA  (1416-)  A      N2   <->  5416 OCYT  (1582-)  A      N3   0.84    2.16  INTRA BF
4853 OURA  (1019-)  A      O2   <->  4854 OADE  (1020-)  A      N7   0.84    1.71  INTRA BL
6304 OGUA  (2505-)  A      N1   <->  6409 OCYT  (2610-)  A      N3   0.79    2.21  INTRA BF
6498 OCYT  (2699-)  A      N3   <->  6507 OGUA  (2708-)  A      N2   0.78    2.22  INTRA BF
2230 ARG   (  64-)  U      CD   <->  3136 ASP   (  41-)  N      C    0.78    2.42  INTRA BF
4853 OURA  (1019-)  A      C2   <->  4854 OADE  (1020-)  A      N7   0.77    2.33  INTRA BL
6089 OGUA  (2290-)  A      N2   <->  6141 OCYT  (2342-)  A      N3   0.76    2.24  INTRA BF
3891 OGUA  (  83-)  A      N2   <->  3910 OADE  ( 103-)  A      N7   0.75    2.25  INTRA BF
5139 OCYT  (1305-)  A      N3   <->  5456 OGUA  (1623-)  A      N2   0.75    2.25  INTRA BL
5321 OGUA  (1487-)  A      N2   <->  5336 OCYT  (1502-)  A      N3   0.75    2.25  INTRA BF
4837 OGUA  (1003-)  A      N2   <->  4986 OCYT  (1152-)  A      N3   0.75    2.25  INTRA BF
4531 OGUA  ( 696-)  A      N2   <->  4601 OCYT  ( 766-)  A      N3   0.74    2.26  INTRA BF
6129 OGUA  (2330-)  A      N2   <->  6184 OCYT  (2385-)  A      N3   0.74    2.26  INTRA BF
2230 ARG   (  64-)  U      NE   <->  3136 ASP   (  41-)  N      CA   0.74    2.36  INTRA BF
5145 OGUA  (1311-)  A      N2   <->  5436 OADE  (1603-)  A      N6   0.74    2.11  INTRA BF
3833 OGUA  (  24-)  A      N1   <->  4351 OCYT  ( 516-)  A      O2   0.73    1.97  INTRA BF
4864 OGUA  (1030-)  A      N2   <->  4958 OCYT  (1124-)  A      N3   0.73    2.27  INTRA BL
5188 OADE  (1354-)  A      N6   <->  5211 OGUA  (1377-)  A      N2   0.73    2.12  INTRA BL
5248 OGUA  (1414-)  A      N2   <->  5421 OCYT  (1588-)  A      N3   0.71    2.29  INTRA BF
4717 OGUA  ( 882-)  A      N2   <->  4728 OCYT  ( 894-)  A      C2   0.71    2.39  INTRA BF
And so on for a total of 4055 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: 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: K

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 0

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

 471 ARG   ( 244-)  D      -8.79
3415 TYR   (  52-)  5      -8.72
1543 ARG   (  21-)  P      -8.71
1453 ARG   (  49-)  O      -8.51
2124 ARG   (  95-)  T      -8.47
 466 ARG   ( 239-)  D      -8.32
2052 ARG   (  23-)  T      -8.26
2937 ARG   (  55-)  0      -8.24
2902 ARG   (  20-)  0      -8.23
2169 ARG   (   3-)  U      -8.22
1943 ARG   (  23-)  S      -7.96
 236 TYR   (   9-)  D      -7.96
1256 ARG   ( 170-)  H      -7.95
2808 ARG   ( 112-)  Z      -7.90
1537 ARG   (  15-)  P      -7.89
2893 ARG   (  11-)  0      -7.89
1754 ARG   (  82-)  Q      -7.83
2956 ARG   (  74-)  0      -7.77
1677 ARG   (   5-)  Q      -7.74
1755 MET   (  83-)  Q      -7.70
3514 ARG   (  41-)  7      -7.64
2083 ARG   (  54-)  T      -7.64
1540 ARG   (  18-)  P      -7.63
 311 TYR   (  84-)  D      -7.57
2647 GLN   (  57-)  Y      -7.55
And so on for a total of 375 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.

 231 LYS   (   4-)  D       233 - PHE      6- ( D)         -4.52
 279 ARG   (  52-)  D       281 - ARG     54- ( D)         -5.27
 469 ARG   ( 242-)  D       471 - ARG    244- ( D)         -6.92
 484 LEU   ( 257-)  D       487 - ARG    260- ( D)         -5.02
 500 ARG   ( 273-)  D       502 - LYS    275- ( D)         -5.81
 630 ASP   ( 127-)  E       632 - HIS    129- ( E)         -5.05
 638 HIS   ( 135-)  E       640 - HIS    137- ( E)         -5.42
 643 SER   ( 140-)  E       649 - THR    146- ( E)         -4.92
 652 ARG   ( 149-)  E       655 - LYS    152- ( E)         -5.22
 657 LYS   ( 154-)  E       659 - MET    156- ( E)         -5.37
 752 ARG   (  44-)  F       754 - ARG     46- ( F)         -5.50
 770 ARG   (  62-)  F       772 - ILE     64- ( F)         -5.25
 775 GLN   (  67-)  F       777 - HIS     69- ( F)         -5.57
 790 ILE   (  82-)  F       793 - GLY     85- ( F)         -4.55
 796 VAL   (  88-)  F       798 - PHE     90- ( F)         -5.26
1243 TYR   ( 157-)  H      1246 - LYS    160- ( H)         -4.67
1255 VAL   ( 169-)  H      1258 - LYS    172- ( H)         -5.84
1493 ASN   (  89-)  O      1495 - LEU     91- ( O)         -4.62
1535 ASN   (  13-)  P      1538 - ARG     16- ( P)         -6.16
1540 ARG   (  18-)  P      1543 - ARG     21- ( P)         -6.19
1571 ARG   (  49-)  P      1574 - GLU     52- ( P)         -5.38
1581 LEU   (  59-)  P      1584 - LEU     62- ( P)         -4.52
1597 ILE   (  75-)  P      1599 - ARG     77- ( P)         -5.40
1612 ARG   (  90-)  P      1614 - GLU     92- ( P)         -4.67
1669 LEU   ( 147-)  P      1672 - ALA    150- ( P)         -4.71
And so on for a total of 54 lines.

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6693 : -2.280

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: 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: 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

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: V

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: W

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: X

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: Z

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: 0

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: 1

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: 4

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: 2

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: 3

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: 5

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: 6

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: 7

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: 8

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: 9

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

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.

2894 ASN   (  12-)  0   -3.95
 877 ASN   ( 169-)  F   -3.55
 776 LYS   (  68-)  F   -3.51
2598 LYS   (   8-)  Y   -3.39
2173 GLY   (   7-)  U   -3.38
1592 GLN   (  70-)  P   -3.36
3366 LYS   (   3-)  5   -3.32
3553 LEU   (  32-)  8   -3.31
 564 ARG   (  61-)  E   -3.31
2171 LYS   (   5-)  U   -3.30
3588 LYS   (   2-)  9   -3.30
3373 LYS   (  10-)  5   -3.28
3552 HIS   (  31-)  8   -3.26
1543 ARG   (  21-)  P   -3.22
2013 LYS   (  93-)  S   -3.18
1538 ARG   (  16-)  P   -3.16
 501 ARG   ( 274-)  D   -3.15
2170 ALA   (   4-)  U   -3.14
3010 ASN   (  45-)  1   -3.11
2169 ARG   (   3-)  U   -3.10
 236 TYR   (   9-)  D   -3.09
3556 GLN   (  35-)  8   -3.07
2015 HIS   (  95-)  S   -3.07
1471 LYS   (  67-)  O   -3.07
 286 LYS   (  59-)  D   -3.06
And so on for a total of 147 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.

 165 ASN   ( 166-)  C     -  168 THR   ( 169-)  C        -1.90
 271 ASN   (  44-)  D     -  276 ILE   (  49-)  D        -2.13
 277 THR   (  50-)  D     -  280 PHE   (  53-)  D        -2.20
 325 VAL   (  98-)  D     -  328 GLU   ( 101-)  D        -1.88
 447 HIS   ( 220-)  D     -  450 GLY   ( 223-)  D        -2.20
 451 ALA   ( 224-)  D     -  456 VAL   ( 229-)  D        -2.15
 462 GLY   ( 235-)  D     -  471 ARG   ( 244-)  D        -2.26
 480 GLN   ( 253-)  D     -  485 LYS   ( 258-)  D        -2.10
 625 PHE   ( 122-)  E     -  628 GLY   ( 125-)  E        -2.34
 640 HIS   ( 137-)  E     -  648 LYS   ( 145-)  E        -2.35
 649 THR   ( 146-)  E     -  654 TYR   ( 151-)  E        -2.19
 754 ARG   (  46-)  F     -  758 SER   (  50-)  F        -1.81
 764 GLU   (  56-)  F     -  767 TYR   (  59-)  F        -1.80
 769 GLY   (  61-)  F     -  772 ILE   (  64-)  F        -1.90
 778 THR   (  70-)  F     -  782 ARG   (  74-)  F        -2.13
 788 ALA   (  80-)  F     -  794 GLY   (  86-)  F        -1.93
 795 GLY   (  87-)  F     -  799 GLY   (  91-)  F        -2.29
1424 MET   (  20-)  O     - 1427 ARG   (  23-)  O        -1.81
1536 LYS   (  14-)  P     - 1543 ARG   (  21-)  P        -2.26
1548 GLY   (  26-)  P     - 1551 LYS   (  29-)  P        -2.14
1554 THR   (  32-)  P     - 1558 LYS   (  36-)  P        -2.02
1559 GLY   (  37-)  P     - 1562 SER   (  40-)  P        -2.09
1566 GLY   (  44-)  P     - 1577 ARG   (  55-)  P        -2.30
1580 THR   (  58-)  P     - 1584 LEU   (  62-)  P        -2.31
1590 GLN   (  68-)  P     - 1599 ARG   (  77-)  P        -2.35
And so on for a total of 57 lines.

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: 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: K

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

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 0

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: 9

Note: Second generation quality Z-score plot

Chain identifier: E

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.

 314 ASN   (  87-)  D
 323 HIS   (  96-)  D
 391 GLN   ( 164-)  D
 425 ASN   ( 198-)  D
 460 HIS   ( 233-)  D
 638 HIS   ( 135-)  E
 737 ASN   (  29-)  F
 911 GLN   ( 203-)  F
 981 GLN   (  66-)  G
1047 ASN   ( 132-)  G
1366 GLN   ( 103-)  K
1535 ASN   (  13-)  P
1603 GLN   (  81-)  P
1813 GLN   ( 141-)  Q
1862 HIS   (  50-)  R
2067 ASN   (  38-)  T
2283 GLN   ( 117-)  U
2487 HIS   ( 102-)  W
2551 ASN   (  55-)  X
2771 ASN   (  75-)  Z
3021 GLN   (  56-)  1
3140 ASN   (  45-)  N
3189 HIS   (  94-)  N
3241 GLN   (   9-)  2
3280 HIS   (  48-)  2
3554 ASN   (  33-)  8

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.

   7 TYR   (   8-)  C      N
  11 LEU   (  12-)  C      N
  19 VAL   (  20-)  C      N
  20 TYR   (  21-)  C      N
  23 ASP   (  24-)  C      N
  38 ASP   (  39-)  C      N
  40 THR   (  41-)  C      N
  52 ARG   (  53-)  C      N
  54 SER   (  55-)  C      N
  56 GLN   (  57-)  C      N
  59 ARG   (  60-)  C      N
  64 LEU   (  65-)  C      N
  73 ARG   (  74-)  C      N
  74 VAL   (  75-)  C      N
  77 ILE   (  78-)  C      N
  82 LYS   (  83-)  C      N
  90 GLY   (  91-)  C      N
  98 GLU   (  99-)  C      N
  99 ILE   ( 100-)  C      N
 100 ILE   ( 101-)  C      N
 114 VAL   ( 115-)  C      N
 116 THR   ( 117-)  C      N
 119 VAL   ( 120-)  C      N
 127 LEU   ( 128-)  C      N
 129 ARG   ( 130-)  C      N
And so on for a total of 1199 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.

  44 HIS   (  45-)  C      ND1
  97 GLU   (  98-)  C      OE1
 162 GLU   ( 163-)  C      OE1
 172 HIS   ( 173-)  C      ND1
 197 GLU   ( 198-)  C      OE2
 310 GLU   (  83-)  D      OE2
 328 GLU   ( 101-)  D      OE1
 370 HIS   ( 143-)  D      ND1
 458 HIS   ( 231-)  D      ND1
 646 ASN   ( 143-)  E      OD1
 739 HIS   (  31-)  F      NE2
 748 GLN   (  40-)  F      OE1
 783 HIS   (  75-)  F      ND1
 857 ASP   ( 149-)  F      OD1
 942 ASN   (  27-)  G      OD1
 981 GLN   (  66-)  G      OE1
1019 GLU   ( 104-)  G      OE1
1019 GLU   ( 104-)  G      OE2
1041 ASP   ( 126-)  G      OD1
1045 ASN   ( 130-)  G      OD1
1053 GLN   ( 138-)  G      OE1
1058 GLU   ( 143-)  G      OE1
1089 GLU   ( 174-)  G      OE2
1147 HIS   (  61-)  H      ND1
1293 HIS   (  30-)  K      ND1
And so on for a total of 60 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.

  39 GLU   (  40-)  C   H-bonding suggests Gln; but Alt-Rotamer
  97 GLU   (  98-)  C   H-bonding suggests Gln
 111 ASP   ( 112-)  C   H-bonding suggests Asn
 197 GLU   ( 198-)  C   H-bonding suggests Gln
 257 GLU   (  30-)  D   H-bonding suggests Gln
 373 GLU   ( 146-)  D   H-bonding suggests Gln; but Alt-Rotamer
 396 GLU   ( 169-)  D   H-bonding suggests Gln
 398 ASP   ( 171-)  D   H-bonding suggests Asn; but Alt-Rotamer
 520 ASP   (  17-)  E   H-bonding suggests Asn
 545 ASP   (  42-)  E   H-bonding suggests Asn
 576 GLU   (  73-)  E   H-bonding suggests Gln
 606 ASP   ( 103-)  E   H-bonding suggests Asn
 630 ASP   ( 127-)  E   H-bonding suggests Asn
 666 GLU   ( 163-)  E   H-bonding suggests Gln
 727 GLU   (  19-)  F   H-bonding suggests Gln
 743 GLU   (  35-)  F   H-bonding suggests Gln; but Alt-Rotamer
 785 ASP   (  77-)  F   H-bonding suggests Asn; but Alt-Rotamer
 828 GLU   ( 120-)  F   H-bonding suggests Gln
 898 GLU   ( 190-)  F   H-bonding suggests Gln
 903 ASP   ( 195-)  F   H-bonding suggests Asn
 945 GLU   (  30-)  G   H-bonding suggests Gln
 964 ASP   (  49-)  G   H-bonding suggests Asn
1058 GLU   ( 143-)  G   H-bonding suggests Gln
1071 ASP   ( 156-)  G   H-bonding suggests Asn; but Alt-Rotamer
1079 GLU   ( 164-)  G   H-bonding suggests Gln
And so on for a total of 85 lines.

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 :  -4.450 (poor)
  2nd generation packing quality :  -5.251 (bad)
  Ramachandran plot appearance   :  -6.113 (bad)
  chi-1/chi-2 rotamer normality  :  -6.301 (bad)
  Backbone conformation          :  -1.419

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.524 (tight)
  Bond angles                    :   1.003
  Omega angle restraints         :   1.237
  Side chain planarity           :   0.271 (tight)
  Improper dihedral distribution :   0.722
  B-factor distribution          :   0.463
  Inside/Outside distribution    :   1.064

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 : 3.86


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.0
  2nd generation packing quality :  -2.6
  Ramachandran plot appearance   :  -3.0
  chi-1/chi-2 rotamer normality  :  -3.7 (poor)
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.524 (tight)
  Bond angles                    :   1.003
  Omega angle restraints         :   1.237
  Side chain planarity           :   0.271 (tight)
  Improper dihedral distribution :   0.722
  B-factor distribution          :   0.463
  Inside/Outside distribution    :   1.064
==============

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.