WHAT IF Check report

This file was created 2012-04-04 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 pdb3f1f.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: 1377927.9
Volume of the Unit Cell V= 59715164.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 21.668
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.450 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

6441  MG   (5004-)  A  D
6443  MG   (5006-)  D  A
6445  MG   (5008-)  A  D
6452  MG   (5015-)  E  A
6458  MG   (5021-)  A  F
6476  MG   (5039-)  U  N
6495  MG   (5058-)  R  A
6499  MG   (5062-)  U  A
6515  MG   (5078-)  A  0
6580  MG   (5143-)  1  A
6748  MG   (5311-)  F  A
6870  MG   (5433-)  B  A
6871  MG   (5434-)  A  B
6900  MG   (5463-)  Q  A
6933  MG   (5496-)  P  A
7317  MG   (5880-)  F  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.

6446  MG   (5009-)  A  -
6486  MG   (5049-)  A  -
6900  MG   (5463-)  Q  A
6933  MG   (5496-)  P  A
7473  MG   (6036-)  S  -

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: 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: K

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

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: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

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

Warning: Artificial side chains detected

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

3442 VAL   ( 173-)  E
5042 ARG   (  89-)  S

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 OADE  (   6-)  A    High
   2 OGUA  (   7-)  A    High
   3 OADE  (   8-)  A    High
   4 OURA  (   9-)  A    High
   5 OGUA  (  10-)  A    High
   6 OGUA  (  11-)  A    High
   7 OURA  (  12-)  A    High
  17 OCYT  (  22-)  A    High
  29 OCYT  (  34-)  A    High
  44 OURA  (  50-)  A    High
  76 OGUA  (  82-)  A    High
  80 OCYT  (  86-)  A    High
  81 OCYT  (  87-)  A    High
  83 OGUA  (  89-)  A    High
  84 OURA  (  90-)  A    High
  85 OADE  (  91-)  A    High
  86 OGUA  (  92-)  A    High
  87 OCYT  (  93-)  A    High
  88 OGUA  (  94-)  A    High
  89 OGUA  (  95-)  A    High
  92 OGUA  (  98-)  A    High
  93 OURA  (  99-)  A    High
  94 OGUA  ( 101-)  A    High
  95 OGUA  ( 102-)  A    High
  96 OADE  ( 103-)  A    High
And so on for a total of 2545 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: 120

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.564 over 13626 bonds
Average difference in B over a bond : 5.71
RMS difference in B over a bond : 7.44

Note: B-factor plot

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

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: K

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

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: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 4

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

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.

3236 ARG   ( 239-)  D
4603 ARG   (  41-)  P
4612 ARG   (  50-)  P
4617 ARG   (  55-)  P
4664 ARG   ( 102-)  P
4673 ARG   ( 111-)  P
4909 ARG   (  64-)  R
4933 ARG   (  88-)  R
5247 ARG   (  50-)  U
5987 ARG   (  11-)  1

Warning: Tyrosine convention problem

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

3006 TYR   (   9-)  D
3059 TYR   (  62-)  D
3094 TYR   (  97-)  D
3187 TYR   ( 190-)  D
3429 TYR   ( 160-)  E
3527 TYR   (  59-)  F
3565 TYR   (  97-)  F
3567 TYR   (  99-)  F
3699 TYR   (  25-)  G
4008 TYR   ( 163-)  H
4040 TYR   (  25-)  I
4141 TYR   ( 126-)  I
4145 TYR   ( 130-)  I
4429 TYR   ( 146-)  N
4476 TYR   (  32-)  O
4716 TYR   (   9-)  Q
4800 TYR   (  93-)  Q
4866 TYR   (  21-)  R
4939 TYR   (  94-)  R
5045 TYR   (  92-)  S
5129 TYR   (  68-)  T
5221 TYR   (  24-)  U
5242 TYR   (  45-)  U
5273 TYR   (  76-)  U
5396 TYR   (  81-)  V
5406 TYR   (  91-)  V
5425 TYR   (   9-)  W
5454 TYR   (  38-)  W
5461 TYR   (  45-)  W
5486 TYR   (  70-)  W
5531 TYR   (   5-)  X
5552 TYR   (  26-)  X
5595 TYR   (  69-)  X
5654 TYR   (  35-)  Y
5726 TYR   (   8-)  Z
5727 TYR   (   9-)  Z
5756 TYR   (  38-)  Z
5817 TYR   (  99-)  Z
5924 TYR   (  26-)  0
6019 TYR   (  43-)  1
6148 TYR   (  15-)  3
6208 TYR   (  51-)  4
6215 TYR   (  58-)  4
6272 TYR   (  51-)  5
6287 TYR   (  21-)  6

Warning: Phenylalanine convention problem

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

3003 PHE   (   6-)  D
3012 PHE   (  15-)  D
3018 PHE   (  21-)  D
3064 PHE   (  67-)  D
3284 PHE   (  15-)  E
3336 PHE   (  67-)  E
3353 PHE   (  84-)  E
3365 PHE   (  96-)  E
3382 PHE   ( 113-)  E
3551 PHE   (  83-)  F
3697 PHE   (  23-)  G
3776 PHE   ( 102-)  G
3799 PHE   ( 125-)  G
3854 PHE   ( 180-)  G
4225 PHE   (  65-)  K
4357 PHE   (  74-)  N
4543 PHE   (  99-)  O
4692 PHE   ( 130-)  P
4736 PHE   (  29-)  Q
4811 PHE   ( 104-)  Q
4965 PHE   (  12-)  S
4982 PHE   (  29-)  S
5083 PHE   (  22-)  T
5118 PHE   (  57-)  T
5122 PHE   (  61-)  T
5137 PHE   (  76-)  T
5162 PHE   ( 101-)  T
5237 PHE   (  40-)  U
5317 PHE   (   2-)  V
5390 PHE   (  75-)  V
5547 PHE   (  21-)  X
5573 PHE   (  47-)  X
5762 PHE   (  44-)  Z
5766 PHE   (  48-)  Z
5806 PHE   (  88-)  Z
5807 PHE   (  89-)  Z
5822 PHE   ( 104-)  Z
5854 PHE   ( 136-)  Z
5958 PHE   (  60-)  0
6036 PHE   (  60-)  1
6336 PHE   (  18-)  7
6413 PHE   (  48-)  8

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.

3068 ASP   (  71-)  D
3082 ASP   (  85-)  D
3096 ASP   (  99-)  D
3106 ASP   ( 109-)  D
3119 ASP   ( 122-)  D
3358 ASP   (  89-)  E
3443 ASP   ( 174-)  E
3678 ASP   (   4-)  G
3771 ASP   (  97-)  G
3830 ASP   ( 156-)  G
3982 ASP   ( 137-)  H
4279 ASP   ( 119-)  K
4323 ASP   (  40-)  N
4456 ASP   (  12-)  O
4500 ASP   (  56-)  O
4567 ASP   (   5-)  P
4609 ASP   (  47-)  P
4904 ASP   (  59-)  R
4914 ASP   (  69-)  R
4917 ASP   (  72-)  R
4926 ASP   (  81-)  R
4952 ASP   ( 107-)  R
5041 ASP   (  88-)  S
5105 ASP   (  44-)  T
5178 ASP   ( 117-)  T
5288 ASP   (  91-)  U
5438 ASP   (  22-)  W
5510 ASP   (  94-)  W
5630 ASP   (  11-)  Y
5805 ASP   (  87-)  Z
5858 ASP   ( 140-)  Z
5872 ASP   ( 154-)  Z
5897 ASP   ( 179-)  Z
5913 ASP   (  15-)  0

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.

3145 GLU   ( 148-)  D
3234 GLU   ( 237-)  D
3342 GLU   (  73-)  E
3356 GLU   (  87-)  E
3363 GLU   (  94-)  E
3447 GLU   ( 178-)  E
3613 GLU   ( 145-)  F
3687 GLU   (  13-)  G
3811 GLU   ( 137-)  G
3817 GLU   ( 143-)  G
3842 GLU   ( 168-)  G
3931 GLU   (  86-)  H
3949 GLU   ( 104-)  H
4114 GLU   (  99-)  I
4245 GLU   (  85-)  K
4281 GLU   ( 121-)  K
4498 GLU   (  54-)  O
4512 GLU   (  68-)  O
4636 GLU   (  74-)  P
4698 GLU   ( 136-)  P
4745 GLU   (  38-)  Q
4787 GLU   (  80-)  Q
4798 GLU   (  91-)  Q
4888 GLU   (  43-)  R
4960 GLU   ( 115-)  R
4996 GLU   (  43-)  S
5017 GLU   (  64-)  S
5286 GLU   (  89-)  U
5308 GLU   ( 111-)  U
5358 GLU   (  43-)  V
5468 GLU   (  52-)  W
5549 GLU   (  23-)  X
5659 GLU   (  40-)  Y
5761 GLU   (  43-)  Z
5778 GLU   (  60-)  Z
5812 GLU   (  94-)  Z
5856 GLU   ( 138-)  Z
5880 GLU   ( 162-)  Z
5925 GLU   (  27-)  0

Error: Decreasing residue numbers

At least one residue in each of the chains mentioned below has a residue number that is lower than the previous residue in that chain ('-' represents a chain without chain identifier).

Chain identifier(s): A

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.

   4 OURA  (   9-)  A      C1'  N1    1.51    4.2
  53 OURA  (  59-)  A      C1'  N1    1.52    6.1
 151 OURA  ( 161-)  A      C1'  N1    1.51    4.5
 152 OURA  ( 162-)  A      C1'  N1    1.51    4.5
 154 OURA  ( 164-)  A      C1'  N1    1.51    4.7
 261 OURA  ( 270-)  A      C1'  N1    1.51    4.4
 262 OCYT  ( 270-)  A      C1'  N1    1.52    4.3
 267 OURA  ( 270-)  A      C1'  N1    1.51    4.6
 284 OURA  ( 271-)  A      C1'  N1    1.51    4.6
 382 OURA  ( 362-)  A      C1'  N1    1.51    4.6
 634 OURA  ( 614-)  A      C1'  N1    1.51    4.3
 660 OURA  ( 639-)  A      C1'  N1    1.51    4.6
 735 OURA  ( 714-)  A      C1'  N1    1.51    4.5
 843 OURA  ( 822-)  A      C1'  N1    1.51    4.8
 892 OURA  ( 871-)  A      C1'  N1    1.51    4.2
 898 OURA  ( 877-)  A      C1'  N1    1.51    4.4
 977 OURA  ( 958-)  A      C1'  N1    1.52    5.3
1085 OURA  (1065-)  A      C1'  N1    1.51    4.1
1102 OURA  (1082-)  A      C1'  N1    1.51    4.2
1133 OURA  (1113-)  A      C1'  N1    1.51    4.5
1194 OURA  (1175-)  A      C1'  N1    1.51    4.5
1392 OURA  (1372-)  A      C1'  N1    1.52    5.6
1414 OURA  (1394-)  A      C1'  N1    1.53    6.5
1509 OURA  (1489-)  A      C1'  N1    1.51    4.2
1513 OCYT  (1493-)  A      C1'  N1    1.53    4.6
And so on for a total of 55 lines.

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

 |  1.000841  0.000081  0.000036|
 |  0.000081  1.000636  0.000017|
 |  0.000036  0.000017  1.000470|
Proposed new scale matrix

 |  0.004730  0.000000  0.000000|
 |  0.000000  0.002188  0.000000|
 |  0.000000  0.000000  0.001615|
With corresponding cell

    A    = 211.416  B   = 457.120  C    = 619.103
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 211.238  B   = 456.830  C    = 618.812
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 729.182
(Under-)estimated Z-score: 19.901

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  (   7-)  A      N9   C8   N7  113.64    5.1
   5 OGUA  (  10-)  A      N9   C8   N7  113.72    5.2
   6 OGUA  (  11-)  A      N9   C8   N7  113.95    5.7
   9 OADE  (  14-)  A      O4'  C1'  N9  104.17   -4.0
  10 OGUA  (  15-)  A      N9   C8   N7  113.57    4.9
  11 OGUA  (  16-)  A      N9   C8   N7  113.93    5.7
  12 OGUA  (  17-)  A      N9   C8   N7  113.27    4.3
  19 OGUA  (  24-)  A      N9   C8   N7  113.88    5.6
  21 OGUA  (  26-)  A      N9   C8   N7  113.49    4.8
  22 OGUA  (  27-)  A      C3'  C2'  C1' 105.22    4.1
  22 OGUA  (  27-)  A      C5'  C4'  O4' 102.93   -4.5
  25 OGUA  (  30-)  A      N9   C8   N7  113.40    4.6
  30 OGUA  (  35-)  A      N9   C8   N7  114.04    5.9
  31 OGUA  (  36-)  A      N9   C8   N7  113.21    4.2
  37 OGUA  (  43-)  A      N9   C8   N7  113.39    4.6
  39 OGUA  (  45-)  A      N9   C8   N7  113.67    5.1
  40 OCYT  (  46-)  A      C4'  C3'  C2'  96.09   -6.6
  42 OGUA  (  48-)  A      C4'  C3'  C2'  97.85   -4.9
  42 OGUA  (  48-)  A      N9   C8   N7  113.43    4.7
  43 OADE  (  49-)  A      C3'  C2'  C1'  96.89   -5.1
  49 OGUA  (  55-)  A      O5'  C5'  C4' 116.33    4.4
  52 OGUA  (  58-)  A      N9   C8   N7  114.00    5.8
  55 OGUA  (  61-)  A      N9   C8   N7  113.40    4.6
  62 OGUA  (  68-)  A      N9   C8   N7  113.67    5.1
  64 OGUA  (  70-)  A      N9   C8   N7  113.81    5.4
And so on for a total of 1606 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.

3068 ASP   (  71-)  D
3082 ASP   (  85-)  D
3096 ASP   (  99-)  D
3106 ASP   ( 109-)  D
3119 ASP   ( 122-)  D
3145 GLU   ( 148-)  D
3234 GLU   ( 237-)  D
3236 ARG   ( 239-)  D
3342 GLU   (  73-)  E
3356 GLU   (  87-)  E
3358 ASP   (  89-)  E
3363 GLU   (  94-)  E
3443 ASP   ( 174-)  E
3447 GLU   ( 178-)  E
3613 GLU   ( 145-)  F
3678 ASP   (   4-)  G
3687 GLU   (  13-)  G
3771 ASP   (  97-)  G
3811 GLU   ( 137-)  G
3817 GLU   ( 143-)  G
3830 ASP   ( 156-)  G
3842 GLU   ( 168-)  G
3931 GLU   (  86-)  H
3949 GLU   ( 104-)  H
3982 ASP   ( 137-)  H
And so on for a total of 83 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.

5696 PRO   (  77-)  Y      N      6.9    20.10    -2.48
The average deviation= 0.651

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.

3038 GLY   (  41-)  D    5.73
6082 GLU   (  11-)  2    5.55
6011 THR   (  35-)  1    5.29
5255 ARG   (  58-)  U    5.04
3043 GLN   (  46-)  D    4.99
4590 GLY   (  28-)  P    4.93
6003 GLU   (  27-)  1    4.89
3220 GLY   ( 223-)  D    4.44
5986 LYS   (  10-)  1    4.27
4789 ARG   (  82-)  Q    4.13

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 : -5.393

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.

6272 TYR   (  51-)  5    -3.9
4619 THR   (  57-)  P    -3.7
6273 TYR   (  52-)  5    -3.4
3189 THR   ( 192-)  D    -3.4
4334 THR   (  51-)  N    -3.4
4218 THR   (  58-)  K    -3.3
3024 THR   (  27-)  D    -3.3
3537 HIS   (  69-)  F    -3.2
4716 TYR   (   9-)  Q    -3.2
5625 HIS   (   6-)  Y    -3.1
5696 PRO   (  77-)  Y    -3.1
3754 PHE   (  80-)  G    -3.1
5365 PRO   (  50-)  V    -3.0
6207 THR   (  50-)  4    -3.0
3050 PHE   (  53-)  D    -3.0
5360 THR   (  45-)  V    -3.0
4613 PHE   (  51-)  P    -3.0
5016 THR   (  63-)  S    -3.0
5103 ILE   (  42-)  T    -3.0
6313 THR   (  47-)  6    -2.9
3516 THR   (  48-)  F    -2.9
6297 PRO   (  31-)  6    -2.9
3690 ARG   (  16-)  G    -2.9
5989 ILE   (  13-)  1    -2.9
3962 PRO   ( 117-)  H    -2.9
And so on for a total of 340 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.

3010 ARG   (  13-)  D  Poor phi/psi
3023 LYS   (  26-)  D  Poor phi/psi
3030 LEU   (  33-)  D  Poor phi/psi
3031 VAL   (  34-)  D  Poor phi/psi
3037 THR   (  40-)  D  omega poor
3042 ASN   (  45-)  D  omega poor
3050 PHE   (  53-)  D  Poor phi/psi
3054 GLY   (  57-)  D  Poor phi/psi
3056 LYS   (  59-)  D  Poor phi/psi
3067 TRP   (  70-)  D  Poor phi/psi
3071 GLY   (  74-)  D  Poor phi/psi
3140 HIS   ( 143-)  D  Poor phi/psi
3147 LYS   ( 150-)  D  Poor phi/psi
3151 LYS   ( 154-)  D  Poor phi/psi
3159 SER   ( 162-)  D  Poor phi/psi
3166 GLU   ( 169-)  D  Poor phi/psi
3172 LEU   ( 175-)  D  omega poor
3188 ALA   ( 191-)  D  Poor phi/psi
3189 THR   ( 192-)  D  Poor phi/psi
3207 GLY   ( 210-)  D  Poor phi/psi
3230 HIS   ( 233-)  D  Poor phi/psi
3232 GLY   ( 235-)  D  Poor phi/psi
3233 GLY   ( 236-)  D  Poor phi/psi
3241 ARG   ( 244-)  D  Poor phi/psi, PRO omega poor
3251 THR   ( 254-)  D  Poor phi/psi
And so on for a total of 378 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 : -6.031

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.

3906 HIS   (  61-)  H    0.36
4290 SER   ( 130-)  K    0.36
4695 SER   ( 133-)  P    0.36
3908 SER   (  63-)  H    0.37
6075 SER   (   4-)  2    0.38
5734 SER   (  16-)  Z    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 OADE  (   8-)  A      0
   4 OURA  (   9-)  A      0
   5 OGUA  (  10-)  A      0
   6 OGUA  (  11-)  A      0
   7 OURA  (  12-)  A      0
   8 OADE  (  13-)  A      0
   9 OADE  (  14-)  A      0
  10 OGUA  (  15-)  A      0
  11 OGUA  (  16-)  A      0
  12 OGUA  (  17-)  A      0
  13 OCYT  (  18-)  A      0
  14 OCYT  (  19-)  A      0
  15 OCYT  (  20-)  A      0
  16 OADE  (  21-)  A      0
  17 OCYT  (  22-)  A      0
  18 OGUA  (  23-)  A      0
  19 OGUA  (  24-)  A      0
  20 OURA  (  25-)  A      0
  21 OGUA  (  26-)  A      0
  22 OGUA  (  27-)  A      0
  23 OADE  (  28-)  A      0
  24 OURA  (  29-)  A      0
  25 OGUA  (  30-)  A      0
  26 OCYT  (  31-)  A      0
  27 OCYT  (  32-)  A      0
And so on for a total of 4568 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!

6271 GLY   (  50-)  5   2.89   39
5832 GLY   ( 114-)  Z   2.84   80
5034 GLY   (  81-)  S   2.29   40
3054 GLY   (  57-)  D   2.26   12
3298 GLY   (  29-)  E   2.25   16
3828 GLY   ( 154-)  G   2.14   17
3938 GLY   (  93-)  H   2.05   80
3602 GLY   ( 134-)  F   2.02   80
4731 GLY   (  24-)  Q   2.01   16
5730 GLY   (  12-)  Z   1.99   13
3876 GLY   (  31-)  H   1.98   31
5612 GLY   (  86-)  X   1.98   54
5587 GLY   (  61-)  X   1.88   16
3253 GLY   ( 256-)  D   1.78   22
5223 GLY   (  26-)  U   1.77   12
5926 GLY   (  28-)  0   1.64   80
4295 GLY   ( 135-)  K   1.64   36
3455 GLY   ( 186-)  E   1.60   54
4342 GLY   (  59-)  N   1.57   23
4631 GLY   (  69-)  P   1.56   21
6174 PRO   (  41-)  3   1.55   11

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...

4716 TYR   (   9-)  Q   1.51

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].

3146 PRO   ( 149-)  D  -119.7 half-chair C-delta/C-gamma (-126 degrees)
3216 PRO   ( 219-)  D  -114.4 envelop C-gamma (-108 degrees)
3225 PRO   ( 228-)  D  -125.1 half-chair C-delta/C-gamma (-126 degrees)
3229 PRO   ( 232-)  D   100.5 envelop C-beta (108 degrees)
3242 PRO   ( 245-)  D    51.2 half-chair C-delta/C-gamma (54 degrees)
3243 PRO   ( 246-)  D   112.2 envelop C-beta (108 degrees)
3246 PRO   ( 249-)  D   118.8 half-chair C-beta/C-alpha (126 degrees)
3301 PRO   (  32-)  E    46.4 half-chair C-delta/C-gamma (54 degrees)
3343 PRO   (  74-)  E  -121.1 half-chair C-delta/C-gamma (-126 degrees)
3407 PRO   ( 138-)  E    33.9 envelop C-delta (36 degrees)
3446 PRO   ( 177-)  E  -113.0 envelop C-gamma (-108 degrees)
3458 PRO   ( 189-)  E  -115.0 envelop C-gamma (-108 degrees)
3460 PRO   ( 191-)  E   -59.1 half-chair C-beta/C-alpha (-54 degrees)
3534 PRO   (  66-)  F   126.2 half-chair C-beta/C-alpha (126 degrees)
3549 PRO   (  81-)  F  -116.8 envelop C-gamma (-108 degrees)
3560 PRO   (  92-)  F  -112.8 envelop C-gamma (-108 degrees)
3562 PRO   (  94-)  F  -113.4 envelop C-gamma (-108 degrees)
3646 PRO   ( 178-)  F  -119.2 half-chair C-delta/C-gamma (-126 degrees)
3706 PRO   (  32-)  G   102.0 envelop C-beta (108 degrees)
3786 PRO   ( 112-)  G   100.1 envelop C-beta (108 degrees)
3796 PRO   ( 122-)  G  -112.2 envelop C-gamma (-108 degrees)
3816 PRO   ( 142-)  G  -126.6 half-chair C-delta/C-gamma (-126 degrees)
3866 PRO   (  21-)  H   103.2 envelop C-beta (108 degrees)
3881 PRO   (  36-)  H  -126.8 half-chair C-delta/C-gamma (-126 degrees)
3884 PRO   (  39-)  H    47.2 half-chair C-delta/C-gamma (54 degrees)
And so on for a total of 74 lines.

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.

1894 OGUA  (1899-)  A      N2  <-> 1897 OCYT  (1902-)  A      N4     0.65    2.20  INTRA BL
1678 OCYT  (1658-)  A      OP1 <-> 3401 HIS   ( 132-)  E      ND1    0.63    2.07  INTRA BL
 274 OGUA  ( 270-)  A      C5' <-> 6619  MG   (5182-)  A     MG      0.59    2.61  INTRA BL
 211 OGUA  ( 226-)  A      N3  <->  213 OADE  ( 228-)  A      N6     0.57    2.43  INTRA BL
2819 OURA  (2836-)  A      C4  <-> 2866 OADE  (2883-)  A      N6     0.56    2.54  INTRA BL
3022 THR   (  25-)  D      CG2 <-> 3079 ILE   (  82-)  D      N      0.53    2.57  INTRA BL
3030 LEU   (  33-)  D      O   <-> 3032 LYS   (  35-)  D      N      0.53    2.17  INTRA BL
1076 OGUA  (1056-)  A      N3  <-> 1123 OADE  (1103-)  A      N6     0.52    2.48  INTRA BF
  77 OGUA  (  83-)  A      N2  <->   96 OADE  ( 103-)  A      N7     0.52    2.48  INTRA BF
1623 OCYT  (1604-)  A      C3' <-> 7063  MG   (5626-)  A     MG      0.52    2.68  INTRA BL
 154 OURA  ( 164-)  A      C6  <-> 6586  MG   (5149-)  A     MG      0.51    2.69  INTRA BF
4612 ARG   (  50-)  P      CG  <-> 4613 PHE   (  51-)  P      N      0.50    2.50  INTRA BF
3400 ALA   ( 131-)  E      O   <-> 3402 LYS   ( 133-)  E      N      0.50    2.20  INTRA BL
1561 OGUA  (1542-)  A      C5' <-> 7042  MG   (5605-)  A     MG      0.49    2.71  INTRA BF
2128 OGUA  (2133-)  A      N3  <-> 2153 OADE  (2158-)  A      N6     0.49    2.51  INTRA BF
 622 OADE  ( 603-)  A      N1  <->  676 OADE  ( 655-)  A      C5     0.49    2.61  INTRA BF
6118 ASN   (  47-)  2      O   <-> 6120 LYS   (  49-)  2      N      0.48    2.22  INTRA BF
4585 PRO   (  23-)  P      CD  <-> 4595 ARG   (  33-)  P      NH2    0.48    2.62  INTRA BF
 172 OGUA  ( 187-)  A      C3' <-> 6596  MG   (5159-)  A     MG      0.48    2.72  INTRA BL
2244 OGUA  (2259-)  A      C2  <-> 2267 OGUA  (2282-)  A      N1     0.47    2.63  INTRA BL
3401 HIS   ( 132-)  E      CD2 <-> 3404 HIS   ( 135-)  E      NE2    0.47    2.63  INTRA BF
4620 THR   (  58-)  P      C   <-> 4623 ARG   (  61-)  P      NE     0.47    2.63  INTRA BL
2959 OURA  (  80-)  B      C2  <-> 2960 OGUA  (  81-)  B      N2     0.46    2.64  INTRA BF
2272 OADE  (2287-)  A      N6  <-> 2329 OURA  (2344-)  A      N3     0.46    2.39  INTRA BF
2330 OGUA  (2345-)  A      N7  <-> 2356 OGUA  (2371-)  A      N2     0.46    2.54  INTRA BF
And so on for a total of 4707 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: 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: K

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

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: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

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

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.

3241 ARG   ( 244-)  D      -8.99
3236 ARG   ( 239-)  D      -8.75
4583 ARG   (  21-)  P      -8.60
6273 TYR   (  52-)  5      -8.39
4789 ARG   (  82-)  Q      -8.20
4617 ARG   (  55-)  P      -8.12
3418 ARG   ( 149-)  E      -8.05
6057 ARG   (  81-)  1      -8.01
5972 ARG   (  74-)  0      -7.98
5918 ARG   (  20-)  0      -7.90
4716 TYR   (   9-)  Q      -7.87
4580 ARG   (  18-)  P      -7.83
4721 ARG   (  14-)  Q      -7.75
6365 ARG   (  47-)  7      -7.75
5912 ARG   (  14-)  0      -7.72
5156 ARG   (  95-)  T      -7.71
3081 TYR   (  84-)  D      -7.71
6395 ARG   (  30-)  8      -7.70
3542 ARG   (  74-)  F      -7.63
4493 ARG   (  49-)  O      -7.61
4936 GLN   (  91-)  R      -7.60
5749 ARG   (  31-)  Z      -7.54
4629 MET   (  67-)  P      -7.52
4632 GLN   (  70-)  P      -7.50
4002 TYR   ( 157-)  H      -7.49
And so on for a total of 303 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.

3002 LYS   (   5-)  D      3004 - LYS      7- ( D)         -4.63
3010 ARG   (  13-)  D      3012 - PHE     15- ( D)         -4.74
3035 LYS   (  38-)  D      3037 - THR     40- ( D)         -5.70
3051 ARG   (  54-)  D      3053 - GLY     56- ( D)         -4.85
3055 HIS   (  58-)  D      3057 - ARG     60- ( D)         -5.19
3238 PRO   ( 241-)  D      3241 - ARG    244- ( D)         -6.08
3396 ASP   ( 127-)  E      3398 - HIS    129- ( E)         -5.24
3409 SER   ( 140-)  E      3415 - THR    146- ( E)         -5.13
3471 LYS   ( 202-)  E      3473 - ALA    204- ( E)         -5.18
3512 ARG   (  44-)  F      3514 - ARG     46- ( F)         -5.45
3535 GLN   (  67-)  F      3537 - HIS     69- ( F)         -6.11
3550 ILE   (  82-)  F      3552 - VAL     84- ( F)         -4.67
4314 GLN   (  31-)  N      4316 - GLU     33- ( N)         -4.73
4491 ILE   (  47-)  O      4493 - ARG     49- ( O)         -5.38
4575 ASN   (  13-)  P      4580 - ARG     18- ( P)         -6.03
4611 ARG   (  49-)  P      4614 - GLU     52- ( P)         -5.29
4637 ILE   (  75-)  P      4639 - ARG     77- ( P)         -6.05
4652 ARG   (  90-)  P      4654 - GLU     92- ( P)         -4.59
4710 LEU   ( 148-)  P      4712 - ALA    150- ( P)         -5.02
4714 MET   (   7-)  Q      4721 - ARG     14- ( Q)         -6.59
4723 ARG   (  16-)  Q      4725 - LYS     18- ( Q)         -5.66
4786 LEU   (  79-)  Q      4790 - MET     83- ( Q)         -6.47
4848 HIS   (   3-)  R      4857 - ARG     12- ( R)         -5.47
4949 ARG   ( 104-)  R      4951 - GLY    106- ( R)         -5.90
5128 SER   (  67-)  T      5130 - GLY     69- ( T)         -4.35
5476 ASN   (  60-)  W      5478 - HIS     62- ( W)         -5.30
5506 ARG   (  90-)  W      5508 - ARG     92- ( W)         -4.90
5526 LYS   ( 110-)  W      5528 - GLY    112- ( W)         -5.53
5590 LYS   (  64-)  X      5592 - LEU     66- ( X)         -5.71
5594 ARG   (  68-)  X      5596 - LEU     70- ( X)         -5.56
5623 LYS   (   4-)  Y      5627 - LYS      8- ( Y)         -4.97
5668 VAL   (  49-)  Y      5670 - VAL     51- ( Y)         -4.80
5796 LYS   (  78-)  Z      5799 - ARG     81- ( Z)         -5.77
5917 LYS   (  19-)  0      5919 - LEU     21- ( 0)         -5.78
6006 VAL   (  30-)  1      6009 - LYS     33- ( 1)         -4.79
6224 LYS   (   3-)  5      6226 - PRO      5- ( 5)         -5.45
6229 LYS   (   8-)  5      6231 - LYS     10- ( 5)         -5.18
6272 TYR   (  51-)  5      6274 - ALA     53- ( 5)         -6.38
6283 LYS   (  17-)  6      6285 - ARG     19- ( 6)         -5.37
6304 LYS   (  38-)  6      6306 - CYS     40- ( 6)         -4.27
6308 TRP   (  42-)  6      6312 - HIS     46- ( 6)         -5.61
6357 ARG   (  39-)  7      6360 - LEU     42- ( 7)         -5.08
6368 LYS   (   3-)  8      6370 - LYS      5- ( 8)         -4.67
6394 LYS   (  29-)  8      6397 - LEU     32- ( 8)         -5.66
6410 GLY   (  45-)  8      6412 - LYS     47- ( 8)         -4.64

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 - 6429 : -1.922

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: 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: 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

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: 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: 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: 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

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.

5910 ASN   (  12-)  0   -4.00
5393 LYS   (  78-)  V   -3.56
4473 ASN   (  29-)  O   -3.43
3563 ARG   (  95-)  F   -3.36
5916 ALA   (  18-)  0   -3.32
3637 ASN   ( 169-)  F   -3.31
3252 LYS   ( 255-)  D   -3.29
5202 LYS   (   5-)  U   -3.26
6396 HIS   (  31-)  8   -3.25
5917 LYS   (  19-)  0   -3.25
3418 ARG   ( 149-)  E   -3.22
6398 ASN   (  33-)  8   -3.18
4850 LYS   (   5-)  R   -3.18
3241 ARG   ( 244-)  D   -3.16
4590 GLY   (  28-)  P   -3.16
4583 ARG   (  21-)  P   -3.16
5392 ALA   (  77-)  V   -3.12
5623 LYS   (   4-)  Y   -3.12
4352 VAL   (  69-)  N   -3.10
6325 PRO   (   7-)  7   -3.09
6243 HIS   (  22-)  5   -3.06
6118 ASN   (  47-)  2   -3.03
3042 ASN   (  45-)  D   -3.03
4789 ARG   (  82-)  Q   -3.02
3539 GLY   (  71-)  F   -3.02
And so on for a total of 131 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.

3003 PHE   (   6-)  D     - 3006 TYR   (   9-)  D        -1.88
3040 ARG   (  43-)  D     - 3044 GLY   (  47-)  D        -2.18
3045 ARG   (  48-)  D     - 3049 ARG   (  52-)  D        -1.99
3220 GLY   ( 223-)  D     - 3223 MET   ( 226-)  D        -2.26
3231 GLY   ( 234-)  D     - 3236 ARG   ( 239-)  D        -2.22
3237 ALA   ( 240-)  D     - 3241 ARG   ( 244-)  D        -2.51
3251 THR   ( 254-)  D     - 3255 LYS   ( 258-)  D        -2.35
3256 THR   ( 259-)  D     - 3263 SER   ( 266-)  D        -2.07
3325 PRO   (  56-)  E     - 3328 VAL   (  59-)  E        -1.74
3396 ASP   ( 127-)  E     - 3404 HIS   ( 135-)  E        -2.30
3405 ARG   ( 136-)  E     - 3409 SER   ( 140-)  E        -2.08
3410 ILE   ( 141-)  E     - 3414 LYS   ( 145-)  E        -2.51
3415 THR   ( 146-)  E     - 3420 TYR   ( 151-)  E        -2.35
3524 GLU   (  56-)  F     - 3531 LYS   (  63-)  F        -1.90
4471 GLY   (  27-)  O     - 4475 LYS   (  31-)  O        -2.16
4568 LEU   (   6-)  P     - 4575 ASN   (  13-)  P        -2.06
4576 LYS   (  14-)  P     - 4580 ARG   (  18-)  P        -2.32
4588 GLY   (  26-)  P     - 4591 LYS   (  29-)  P        -1.99
4599 GLY   (  37-)  P     - 4609 ASP   (  47-)  P        -2.25
4614 GLU   (  52-)  P     - 4617 ARG   (  55-)  P        -2.38
4619 THR   (  57-)  P     - 4622 MET   (  60-)  P        -2.04
4625 PRO   (  63-)  P     - 4629 MET   (  67-)  P        -2.27
4630 GLN   (  68-)  P     - 4637 ILE   (  75-)  P        -2.21
4714 MET   (   7-)  Q     - 4718 LYS   (  11-)  Q        -2.04
4722 GLY   (  15-)  Q     - 4726 GLY   (  19-)  Q        -2.24
4782 THR   (  75-)  Q     - 4786 LEU   (  79-)  Q        -1.97
4846 GLU   ( 139-)  Q     - 4850 LYS   (   5-)  R        -2.49
5153 GLY   (  92-)  T     - 5159 LYS   (  98-)  T        -2.22
5160 LEU   (  99-)  T     - 5163 ILE   ( 102-)  T        -1.77
5198 LYS   ( 137-)  T     - 5205 VAL   (   8-)  U        -2.32
5294 ASP   (  97-)  U     - 5297 VAL   ( 100-)  U        -1.85
5391 LYS   (  76-)  V     - 5396 TYR   (  81-)  V        -2.56
5502 LEU   (  86-)  W     - 5506 ARG   (  90-)  W        -1.89
5620 GLY   (  94-)  X     - 5627 LYS   (   8-)  Y        -2.41
5911 GLY   (  13-)  0     - 5914 SER   (  16-)  0        -2.14
5915 GLN   (  17-)  0     - 5919 LEU   (  21-)  0        -2.68
5951 MET   (  53-)  0     - 5954 ASP   (  56-)  0        -1.60
6018 GLN   (  42-)  1     - 6022 LEU   (  46-)  1        -1.88
6222 CYS   (  65-)  4     - 6232 THR   (  11-)  5        -2.40
6241 ARG   (  20-)  5     - 6244 HIS   (  23-)  5        -2.04
6310 ARG   (  44-)  6     - 6313 THR   (  47-)  6        -1.64
6318 VAL   (  52-)  6     - 6321 ARG   (   3-)  7        -1.87
6322 THR   (   4-)  7     - 6325 PRO   (   7-)  7        -2.35
6367 PRO   (   2-)  8     - 6370 LYS   (   5-)  8        -2.14
6393 GLY   (  28-)  8     - 6398 ASN   (  33-)  8        -2.21
6424 LYS   (  59-)  8     - 6428 PRO   (  63-)  8        -1.93

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: 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: K

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

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: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

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

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.

3093 HIS   (  96-)  D
3183 HIS   ( 186-)  D
3195 ASN   ( 198-)  D
3335 HIS   (  66-)  E
3438 ASN   ( 169-)  E
3637 ASN   ( 169-)  F
3701 ASN   (  27-)  G
3714 ASN   (  40-)  G
3732 GLN   (  58-)  G
4003 HIS   ( 158-)  H
4249 HIS   (  89-)  K
4351 ASN   (  68-)  N
4407 HIS   ( 124-)  N
4434 HIS   ( 151-)  N
4447 GLN   (   3-)  O
4796 ASN   (  89-)  Q
4858 HIS   (  13-)  R
5246 HIS   (  49-)  U
5272 ASN   (  75-)  U
5326 GLN   (  11-)  V
5473 ASN   (  57-)  W
5478 HIS   (  62-)  W
5518 HIS   ( 102-)  W
5581 ASN   (  55-)  X
5662 ASN   (  43-)  Y
5772 HIS   (  54-)  Z
5791 GLN   (  73-)  Z
5933 ASN   (  35-)  0
5968 GLN   (  70-)  0
5995 GLN   (  19-)  1
6021 ASN   (  45-)  1
6119 HIS   (  48-)  2
6152 GLN   (  19-)  3
6165 GLN   (  32-)  3
6326 ASN   (   8-)  7
6396 HIS   (  31-)  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.

  23 OADE  (  28-)  A      N6
  26 OCYT  (  31-)  A      N4
  64 OGUA  (  70-)  A      N2
  66 OURA  (  72-)  A      N3
  74 OGUA  (  80-)  A      N2
 130 OCYT  ( 137-)  A      N4
 132 OGUA  ( 138-)  A      N1
 133 OGUA  ( 139-)  A      N1
 133 OGUA  ( 139-)  A      N2
 135 OADE  ( 141-)  A      N6
 150 OCYT  ( 155-)  A      N4
 151 OURA  ( 161-)  A      N3
 158 OGUA  ( 173-)  A      N2
 184 OADE  ( 199-)  A      N6
 185 OURA  ( 200-)  A      N3
 205 OGUA  ( 220-)  A      N2
 206 OADE  ( 221-)  A      N6
 218 OADE  ( 233-)  A      N6
 231 OCYT  ( 246-)  A      N4
 232 OGUA  ( 247-)  A      N1
 233 OGUA  ( 248-)  A      N2
 257 OADE  ( 270-)  A      N6
 273 OGUA  ( 270-)  A      O2'
 295 OGUA  ( 275-)  A      N2
 322 OCYT  ( 302-)  A      N4
And so on for a total of 816 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.

3027 GLU   (  30-)  D      OE1
3027 GLU   (  30-)  D      OE2
3041 ASN   (  44-)  D      OD1
3140 HIS   ( 143-)  D      NE2
3250 GLN   ( 253-)  D      OE1
3304 GLN   (  35-)  E      OE1
3372 ASP   ( 103-)  E      OD2
3398 HIS   ( 129-)  E      ND1
3438 ASN   ( 169-)  E      OD1
3543 HIS   (  75-)  F      ND1
3545 ASP   (  77-)  F      OD1
3709 GLU   (  35-)  G      OE2
3740 GLN   (  66-)  G      OE1
3778 GLU   ( 104-)  G      OE2
3817 GLU   ( 143-)  G      OE2
3931 GLU   (  86-)  H      OE2
4088 GLU   (  73-)  I      OE1
4356 ASP   (  73-)  N      OD2
4456 ASP   (  12-)  O      OD1
4456 ASP   (  12-)  O      OD2
4690 HIS   ( 128-)  P      ND1
4720 GLN   (  13-)  Q      OE1
4732 ASP   (  25-)  Q      OD2
4764 HIS   (  57-)  Q      ND1
4812 GLU   ( 105-)  Q      OE1
4894 ASP   (  49-)  R      OD1
5087 ASP   (  26-)  T      OD1
5140 HIS   (  79-)  T      ND1
5581 ASN   (  55-)  X      OD1
5625 HIS   (   6-)  Y      NE2
5630 ASP   (  11-)  Y      OD1
5896 GLU   ( 178-)  Z      OE1
6042 HIS   (  66-)  1      ND1
6152 GLN   (  19-)  3      OE1
6172 ASP   (  39-)  3      OD1
6185 HIS   (  52-)  3      ND1
6290 GLU   (  24-)  6      OE2
6292 ASN   (  26-)  6      OD1
6298 ASN   (  32-)  6      OD1
6301 GLU   (  35-)  6      OE1
6301 GLU   (  35-)  6      OE2
6315 HIS   (  49-)  6      NE2
6317 GLU   (  51-)  6      OE1

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+.

6438  MG   (5001-)  D   -.-  -.-  Too few ligands (2)
6439  MG   (5002-)  D   -.-  -.-  Low probability ion. B= 82.1
6440  MG   (5003-)  D   -.-  -.-  Too few ligands (0)
6441  MG   (5004-)  A   -.-  -.-  Part of ionic cluster
6441  MG   (5004-)  A   -.-  -.-  Too few ligands (1)
6442  MG   (5005-)  D   -.-  -.-  Too few ligands (0)
6443  MG   (5006-)  D   -.-  -.-  Too few ligands (0)
6444  MG   (5007-)  D   -.-  -.-  Part of ionic cluster
6444  MG   (5007-)  D   -.-  -.-  Too few ligands (0)
6445  MG   (5008-)  A   -.-  -.-  Part of ionic cluster
6445  MG   (5008-)  A   -.-  -.-  Too few ligands (0)
6446  MG   (5009-)  A   -.-  -.-  Too few ligands (2)
6447  MG   (5010-)  E   -.-  -.-  Too few ligands (3)
6448  MG   (5011-)  E   -.-  -.-  Too few ligands (0)
6449  MG   (5012-)  E   -.-  -.-  Too few ligands (1)
6450  MG   (5013-)  E   -.-  -.-  Too few ligands (1)
6451  MG   (5014-)  E   -.-  -.-  Part of ionic cluster
6451  MG   (5014-)  E   -.-  -.-  Too few ligands (1)
6452  MG   (5015-)  E   -.-  -.-  Too few ligands (2)
6453  MG   (5016-)  A   -.-  -.-  Too few ligands (0)
6454  MG   (5017-)  E   -.-  -.-  Too few ligands (1)
6455  MG   (5018-)  F   -.-  -.-  Too few ligands (0)
6456  MG   (5019-)  F   -.-  -.-  Part of ionic cluster
6456  MG   (5019-)  F   -.-  -.-  Too few ligands (1)
6457  MG   (5020-)  F   -.-  -.-  Too few ligands (2)
And so on for a total of 1490 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.

3286 ASP   (  17-)  E   H-bonding suggests Asn
3287 ASP   (  18-)  E   H-bonding suggests Asn; but Alt-Rotamer
3432 GLU   ( 163-)  E   H-bonding suggests Gln
3606 GLU   ( 138-)  F   H-bonding suggests Gln; but Alt-Rotamer
3692 GLU   (  18-)  G   H-bonding suggests Gln
3709 GLU   (  35-)  G   H-bonding suggests Gln
3800 ASP   ( 126-)  G   H-bonding suggests Asn
3840 ASP   ( 166-)  G   H-bonding suggests Asn; but Alt-Rotamer
3969 GLU   ( 124-)  H   H-bonding suggests Gln
4081 GLU   (  66-)  I   H-bonding suggests Gln
4137 GLU   ( 122-)  I   H-bonding suggests Gln
4210 ASP   (  50-)  K   H-bonding suggests Asn
4323 ASP   (  40-)  N   H-bonding suggests Asn
4567 ASP   (   5-)  P   H-bonding suggests Asn
4681 GLU   ( 119-)  P   H-bonding suggests Gln
4732 ASP   (  25-)  Q   H-bonding suggests Asn; but Alt-Rotamer
4787 GLU   (  80-)  Q   H-bonding suggests Gln
4812 GLU   ( 105-)  Q   H-bonding suggests Gln; but Alt-Rotamer
5072 GLU   (  11-)  T   H-bonding suggests Gln
5087 ASP   (  26-)  T   H-bonding suggests Asn
5168 ASP   ( 107-)  T   H-bonding suggests Asn
5183 ASP   ( 122-)  T   H-bonding suggests Asn
5185 ASP   ( 124-)  T   H-bonding suggests Asn
5288 ASP   (  91-)  U   H-bonding suggests Asn; but Alt-Rotamer
5294 ASP   (  97-)  U   H-bonding suggests Asn; but Alt-Rotamer
5358 GLU   (  43-)  V   H-bonding suggests Gln; but Alt-Rotamer
5438 ASP   (  22-)  W   H-bonding suggests Asn
5479 ASP   (  63-)  W   H-bonding suggests Asn
5564 GLU   (  38-)  X   H-bonding suggests Gln
5601 ASP   (  75-)  X   H-bonding suggests Asn
5630 ASP   (  11-)  Y   H-bonding suggests Asn
5659 GLU   (  40-)  Y   H-bonding suggests Gln
5795 ASP   (  77-)  Z   H-bonding suggests Asn; but Alt-Rotamer
5805 ASP   (  87-)  Z   H-bonding suggests Asn; but Alt-Rotamer
5896 GLU   ( 178-)  Z   H-bonding suggests Gln
5925 GLU   (  27-)  0   H-bonding suggests Gln
6076 GLU   (   5-)  2   H-bonding suggests Gln
6082 GLU   (  11-)  2   H-bonding suggests Gln
6083 GLU   (  12-)  2   H-bonding suggests Gln
6123 ASP   (  52-)  2   H-bonding suggests Asn
6238 ASP   (  17-)  5   H-bonding suggests Asn
6421 GLU   (  56-)  8   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 :  -3.555
  2nd generation packing quality :  -4.379 (bad)
  Ramachandran plot appearance   :  -5.393 (bad)
  chi-1/chi-2 rotamer normality  :  -6.031 (bad)
  Backbone conformation          :  -0.643

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.665 (tight)
  Bond angles                    :   1.106
  Omega angle restraints         :   1.010
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   1.564 (loose)
  Inside/Outside distribution    :   1.018

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.4
  2nd generation packing quality :  -2.1
  Ramachandran plot appearance   :  -2.7
  chi-1/chi-2 rotamer normality  :  -3.5 (poor)
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.665 (tight)
  Bond angles                    :   1.106
  Omega angle restraints         :   1.010
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   1.564 (loose)
  Inside/Outside distribution    :   1.018
==============

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.