WHAT IF Check report

This file was created 2011-12-17 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 pdb3pyo.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: 1330572.9
Volume of the Unit Cell V= 59680028.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 22.426
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

Warning: Chain identifier inconsistency

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

6287  MG   (2943-)  M  A
6428  MG   (3042-)  K  A
6664  MG   ( 438-)  A  Y
6929  MG   ( 703-)  A  F
6997  MG   (3415-)  N  A
7089  MG   (3491-)  Q  A
7205  MG   (3573-)  Q  A
7228  MG   (3591-)  2  A
7383  MG   (3692-)  L  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.

6977  MG   (3401-)  A  -
7116  MG   (3510-)  A  -
7289  MG   (3635-)  A  -

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

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: 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

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 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
  16 OADE  (  21-)  A    High
  29 OCYT  (  34-)  A    High
  36 OCYT  (  41-)  A    High
  37 OGUA  (  43-)  A    High
  38 OADE  (  44-)  A    High
  44 OURA  (  50-)  A    High
  54 OGUA  (  60-)  A    High
  56 OCYT  (  62-)  A    High
  57 OURA  (  63-)  A    High
  58 OADE  (  64-)  A    High
  61 OURA  (  67-)  A    High
  63 OCYT  (  69-)  A    High
  65 OADE  (  71-)  A    High
  67 OADE  (  73-)  A    High
  68 OADE  (  74-)  A    High
  69 OGUA  (  75-)  A    High
  70 OCYT  (  76-)  A    High
  71 OCYT  (  77-)  A    High
And so on for a total of 3592 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: 0

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: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

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: 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

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.

3117 ARG   ( 239-)  C
4044 ARG   (   5-)  I
4058 ARG   (  19-)  I
4066 ARG   (  60-)  I
4369 ARG   (  41-)  L
4383 ARG   (  55-)  L
4430 ARG   ( 102-)  L
4439 ARG   ( 111-)  L
4677 ARG   (  64-)  N
4701 ARG   (  88-)  N
5014 ARG   (  50-)  Q

Warning: Tyrosine convention problem

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

2940 TYR   (  62-)  C
3050 TYR   ( 172-)  C
3310 TYR   ( 160-)  D
3408 TYR   (  59-)  E
3448 TYR   (  99-)  E
3809 TYR   (  83-)  G
3921 TYR   (  25-)  H
4022 TYR   ( 126-)  H
4408 TYR   (  80-)  L
4610 TYR   ( 137-)  M
4634 TYR   (  21-)  N
4813 TYR   (  92-)  O
4815 TYR   (  94-)  O
4897 TYR   (  68-)  P
4989 TYR   (  24-)  Q
5009 TYR   (  45-)  Q
5040 TYR   (  76-)  Q
5094 TYR   (  12-)  R
5163 TYR   (  81-)  R
5173 TYR   (  91-)  R
5192 TYR   (   9-)  S
5253 TYR   (  70-)  S
5258 TYR   (  75-)  S
5298 TYR   (   5-)  T
5319 TYR   (  26-)  T
5362 TYR   (  69-)  T
5493 TYR   (   8-)  V
5514 TYR   (  29-)  V
5523 TYR   (  38-)  V
5584 TYR   (  99-)  V
5692 TYR   (  26-)  W
5787 TYR   (  43-)  X
5815 TYR   (  71-)  X
5916 TYR   (  15-)  Z
5983 TYR   (  58-)  1
6055 TYR   (  21-)  3

Warning: Phenylalanine convention problem

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

2893 PHE   (  15-)  C
2899 PHE   (  21-)  C
2945 PHE   (  67-)  C
3217 PHE   (  67-)  D
3234 PHE   (  84-)  D
3246 PHE   (  96-)  D
3263 PHE   ( 113-)  D
3432 PHE   (  83-)  E
3578 PHE   (  23-)  F
3635 PHE   (  80-)  F
3657 PHE   ( 102-)  F
3680 PHE   ( 125-)  F
3733 PHE   ( 178-)  F
3735 PHE   ( 180-)  F
3835 PHE   ( 109-)  G
4289 PHE   (  79-)  K
4458 PHE   ( 130-)  L
4577 PHE   ( 104-)  M
4660 PHE   (  47-)  N
4733 PHE   (  12-)  O
4750 PHE   (  29-)  O
4851 PHE   (  22-)  P
4874 PHE   (  45-)  P
4886 PHE   (  57-)  P
4890 PHE   (  61-)  P
4905 PHE   (  76-)  P
4930 PHE   ( 101-)  P
5004 PHE   (  40-)  Q
5084 PHE   (   2-)  R
5314 PHE   (  21-)  T
5446 PHE   (  60-)  U
5573 PHE   (  88-)  V
5574 PHE   (  89-)  V
5621 PHE   ( 136-)  V
5726 PHE   (  60-)  W
5804 PHE   (  60-)  X
6104 PHE   (  18-)  4

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.

2963 ASP   (  85-)  C
2977 ASP   (  99-)  C
2987 ASP   ( 109-)  C
3000 ASP   ( 122-)  C
3192 ASP   (  42-)  D
3324 ASP   ( 174-)  D
3711 ASP   ( 156-)  F
4089 ASP   (  40-)  J
4222 ASP   (  12-)  K
4266 ASP   (  56-)  K
4291 ASP   (  81-)  K
4333 ASP   (   5-)  L
4672 ASP   (  59-)  N
4682 ASP   (  69-)  N
4685 ASP   (  72-)  N
4720 ASP   ( 107-)  N
4809 ASP   (  88-)  O
4936 ASP   ( 107-)  P
5055 ASP   (  91-)  Q
5205 ASP   (  22-)  S
5246 ASP   (  63-)  S
5277 ASP   (  94-)  S
5530 ASP   (  45-)  V
5625 ASP   ( 140-)  V
5639 ASP   ( 154-)  V
5681 ASP   (  15-)  W

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.

2979 GLU   ( 101-)  C
3026 GLU   ( 148-)  C
3047 GLU   ( 169-)  C
3059 GLU   ( 181-)  C
3115 GLU   ( 237-)  C
3223 GLU   (  73-)  D
3568 GLU   (  13-)  F
3692 GLU   ( 137-)  F
3698 GLU   ( 143-)  F
3812 GLU   (  86-)  G
3830 GLU   ( 104-)  G
4047 GLU   (   8-)  I
4054 GLU   (  15-)  I
4071 GLU   (  65-)  I
4264 GLU   (  54-)  K
4278 GLU   (  68-)  K
4402 GLU   (  74-)  L
4511 GLU   (  38-)  M
4553 GLU   (  80-)  M
4564 GLU   (  91-)  M
4585 GLU   ( 112-)  M
4656 GLU   (  43-)  N
4764 GLU   (  43-)  O
4785 GLU   (  64-)  O
5053 GLU   (  89-)  Q
5075 GLU   ( 111-)  Q
5175 GLU   (  93-)  R
5235 GLU   (  52-)  S
5426 GLU   (  40-)  U
5528 GLU   (  43-)  V
5545 GLU   (  60-)  V
5623 GLU   ( 138-)  V
5647 GLU   ( 162-)  V

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.

  53 OURA  (  59-)  A      C1'  N1    1.51    4.2
 151 OURA  ( 161-)  A      C1'  N1    1.51    4.2
 325 OURA  ( 305-)  A      C1'  N1    1.51    4.0
 348 OURA  ( 328-)  A      C1'  N1    1.51    4.1
 587 OURA  ( 568-)  A      C1'  N1    1.52    5.9
 688 OURA  ( 667-)  A      C1'  N1    1.51    4.9
 849 OURA  ( 828-)  A      C1'  N1    1.51    4.1
1081 OURA  (1108-)  A      C1'  N1    1.51    4.7
1213 OURA  (1240-)  A      C1'  N1    1.51    4.4
1228 OURA  (1255-)  A      C1'  N1    1.51    4.2
1345 OURA  (1372-)  A      C1'  N1    1.51    4.1
1367 OURA  (1394-)  A      C1'  N1    1.52    5.6
1644 OURA  (1671-)  A      C1'  N1    1.51    4.9
1699 OURA  (1735-)  A      C1'  N1    1.51    4.0
1791 OURA  (1834-)  A      C1'  N1    1.51    4.3
1871 OURA  (1923-)  A      C1'  N1    1.51    4.1
1924 OURA  (1976-)  A      C1'  N1    1.51    4.5
1976 OURA  (2028-)  A      C1'  N1    1.54    8.2
2256 OURA  (2390-)  A      C1'  N1    1.51    4.8
2303 OURA  (2437-)  A      C1'  N1    1.51    4.3
2372 OURA  (2506-)  A      C1'  N1    1.53    7.0
2554 OURA  (2688-)  A      C1'  N1    1.51    4.1
2751 OURA  (2887-)  A      C1'  N1    1.51    4.6

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000554  0.000067  0.000039|
 |  0.000067  1.000432  0.000044|
 |  0.000039  0.000044  1.000799|
Proposed new scale matrix

 |  0.004715  0.000000  0.000000|
 |  0.000000  0.002194  0.000000|
 |  0.000000  0.000000  0.001617|
With corresponding cell

    A    = 212.072  B   = 455.778  C    = 618.541
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 211.940  B   = 455.590  C    = 618.020
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 583.823
(Under-)estimated Z-score: 17.808

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  113.62    5.0
   5 OGUA  (  10-)  A      N9   C8   N7  113.30    4.4
   6 OGUA  (  11-)  A      N9   C8   N7  113.63    5.1
  10 OGUA  (  15-)  A      N9   C8   N7  113.21    4.2
  11 OGUA  (  16-)  A      C3'  C2'  C1'  97.79   -4.1
  11 OGUA  (  16-)  A      N9   C8   N7  113.53    4.9
  18 OGUA  (  23-)  A      C4'  C3'  C2'  98.03   -4.7
  18 OGUA  (  23-)  A      N9   C8   N7  113.77    5.3
  19 OGUA  (  24-)  A      N9   C8   N7  113.79    5.4
  21 OGUA  (  26-)  A      N9   C8   N7  113.53    4.9
  22 OGUA  (  27-)  A      N9   C8   N7  113.72    5.2
  30 OGUA  (  35-)  A      C4'  C3'  C2'  97.59   -5.1
  30 OGUA  (  35-)  A      N9   C8   N7  113.81    5.4
  31 OGUA  (  36-)  A      N9   C8   N7  113.62    5.0
  37 OGUA  (  43-)  A      N9   C8   N7  113.54    4.9
  39 OGUA  (  45-)  A      N9   C8   N7  113.57    4.9
  42 OGUA  (  48-)  A      N9   C8   N7  113.72    5.2
  45 OGUA  (  51-)  A      N9   C8   N7  113.41    4.6
  48 OGUA  (  54-)  A      N9   C8   N7  113.66    5.1
  49 OGUA  (  55-)  A      N9   C8   N7  113.22    4.2
  52 OGUA  (  58-)  A      N9   C8   N7  113.58    5.0
  54 OGUA  (  60-)  A      N9   C8   N7  113.41    4.6
  55 OGUA  (  61-)  A      N9   C8   N7  113.32    4.4
  62 OGUA  (  68-)  A      N9   C8   N7  113.45    4.7
  64 OGUA  (  70-)  A      N9   C8   N7  114.35    6.5
And so on for a total of 1273 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.

2963 ASP   (  85-)  C
2977 ASP   (  99-)  C
2979 GLU   ( 101-)  C
2987 ASP   ( 109-)  C
3000 ASP   ( 122-)  C
3026 GLU   ( 148-)  C
3047 GLU   ( 169-)  C
3059 GLU   ( 181-)  C
3115 GLU   ( 237-)  C
3117 ARG   ( 239-)  C
3192 ASP   (  42-)  D
3223 GLU   (  73-)  D
3324 ASP   ( 174-)  D
3568 GLU   (  13-)  F
3692 GLU   ( 137-)  F
3698 GLU   ( 143-)  F
3711 ASP   ( 156-)  F
3812 GLU   (  86-)  G
3830 GLU   ( 104-)  G
4044 ARG   (   5-)  I
4047 GLU   (   8-)  I
4054 GLU   (  15-)  I
4058 ARG   (  19-)  I
4066 ARG   (  60-)  I
4071 GLU   (  65-)  I
And so on for a total of 70 lines.

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.776

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.

3626 THR   (  71-)  F    -3.4
2905 THR   (  27-)  C    -3.2
6040 TYR   (  51-)  2    -3.1
4812 PRO   (  91-)  O    -3.1
4214 PRO   (   4-)  K    -3.1
3884 HIS   ( 158-)  G    -3.1
3432 PHE   (  83-)  E    -3.0
5755 ARG   (  11-)  X    -3.0
5392 HIS   (   6-)  U    -2.9
3848 THR   ( 122-)  G    -2.9
4756 ILE   (  35-)  O    -2.9
3843 PRO   ( 117-)  G    -2.9
5253 TYR   (  70-)  S    -2.9
3418 HIS   (  69-)  E    -2.9
5321 PHE   (  28-)  T    -2.9
2888 THR   (  10-)  C    -2.8
4649 THR   (  36-)  N    -2.8
4376 PRO   (  48-)  L    -2.8
5538 ILE   (  53-)  V    -2.7
2984 ILE   ( 106-)  C    -2.7
3643 ILE   (  88-)  F    -2.7
4301 LEU   (  91-)  K    -2.6
5100 LEU   (  18-)  R    -2.6
2996 VAL   ( 118-)  C    -2.6
4377 ARG   (  49-)  L    -2.6
And so on for a total of 204 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.

2890 SER   (  12-)  C  Poor phi/psi
2911 LEU   (  33-)  C  Poor phi/psi
2915 LEU   (  37-)  C  Poor phi/psi
2923 ASN   (  45-)  C  omega poor
2928 THR   (  50-)  C  Poor phi/psi
2931 PHE   (  53-)  C  Poor phi/psi
2948 TRP   (  70-)  C  Poor phi/psi
2952 GLY   (  74-)  C  Poor phi/psi
3003 ILE   ( 125-)  C  Poor phi/psi
3028 LYS   ( 150-)  C  Poor phi/psi
3032 LYS   ( 154-)  C  Poor phi/psi
3069 ALA   ( 191-)  C  Poor phi/psi
3075 GLY   ( 197-)  C  Poor phi/psi
3112 GLY   ( 234-)  C  Poor phi/psi
3114 GLY   ( 236-)  C  Poor phi/psi
3115 GLU   ( 237-)  C  Poor phi/psi
3117 ARG   ( 239-)  C  Poor phi/psi
3134 GLY   ( 256-)  C  Poor phi/psi
3138 ARG   ( 260-)  C  Poor phi/psi
3154 ILE   (   4-)  D  Poor phi/psi
3166 ARG   (  16-)  D  Poor phi/psi
3168 ASP   (  18-)  D  Poor phi/psi
3192 ASP   (  42-)  D  Poor phi/psi
3193 GLY   (  43-)  D  Poor phi/psi
3196 ALA   (  46-)  D  Poor phi/psi
And so on for a total of 313 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.236

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.

3789 SER   (  63-)  G    0.38
3787 HIS   (  61-)  G    0.38
4326 SER   ( 116-)  K    0.38
5423 VAL   (  37-)  U    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 4329 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!

5828 GLY   (  84-)  X   2.62   12
4421 GLY   (  93-)  L   2.44   10
6039 GLY   (  50-)  2   2.31   19
5599 GLY   ( 114-)  V   2.26   61
4432 GLY   ( 104-)  L   2.06   19
3336 GLY   ( 186-)  D   2.05   21
5136 GLY   (  54-)  R   1.81   11
3644 GLY   (  89-)  F   1.77   19
4372 GLY   (  44-)  L   1.74   38
6161 GLY   (  28-)  5   1.73   14
5970 GLY   (  45-)  1   1.65   16
4310 GLY   ( 100-)  K   1.63   20
3179 GLY   (  29-)  D   1.57   19

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...

3631 SER   (  76-)  F   1.53

Warning: Unusual PRO puckering amplitudes

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

3339 PRO   ( 189-)  D    0.16 LOW
3415 PRO   (  66-)  E    0.50 HIGH
5067 PRO   ( 103-)  Q    0.51 HIGH
5510 PRO   (  25-)  V    0.53 HIGH
5568 PRO   (  83-)  V    0.11 LOW
5619 PRO   ( 134-)  V    0.56 HIGH

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].

3097 PRO   ( 219-)  C  -117.9 half-chair C-delta/C-gamma (-126 degrees)
3106 PRO   ( 228-)  C  -112.7 envelop C-gamma (-108 degrees)
3119 PRO   ( 241-)  C    27.8 envelop C-delta (36 degrees)
3124 PRO   ( 246-)  C   101.8 envelop C-beta (108 degrees)
3224 PRO   (  74-)  D  -118.9 half-chair C-delta/C-gamma (-126 degrees)
3441 PRO   (  92-)  E  -119.5 half-chair C-delta/C-gamma (-126 degrees)
3843 PRO   ( 117-)  G    32.9 envelop C-delta (36 degrees)
3904 PRO   (   8-)  H  -116.2 envelop C-gamma (-108 degrees)
4214 PRO   (   4-)  K   136.1 envelop C-alpha (144 degrees)
4303 PRO   (  93-)  K  -118.0 half-chair C-delta/C-gamma (-126 degrees)
4338 PRO   (  10-)  L    29.8 envelop C-delta (36 degrees)
4376 PRO   (  48-)  L    24.4 half-chair N/C-delta (18 degrees)
4543 PRO   (  70-)  M   -31.3 envelop C-alpha (-36 degrees)
4812 PRO   (  91-)  O   136.9 envelop C-alpha (144 degrees)
4853 PRO   (  24-)  P  -134.3 half-chair C-delta/C-gamma (-126 degrees)
5118 PRO   (  36-)  R  -123.9 half-chair C-delta/C-gamma (-126 degrees)
5132 PRO   (  50-)  R   102.1 envelop C-beta (108 degrees)
5172 PRO   (  90-)  R    52.7 half-chair C-delta/C-gamma (54 degrees)
5304 PRO   (  11-)  T    49.3 half-chair C-delta/C-gamma (54 degrees)
5325 PRO   (  32-)  T    99.6 envelop C-beta (108 degrees)
5463 PRO   (  77-)  U   126.9 half-chair C-beta/C-alpha (126 degrees)
5500 PRO   (  15-)  V    99.6 envelop C-beta (108 degrees)
5553 PRO   (  68-)  V    -7.9 envelop N (0 degrees)
5756 PRO   (  12-)  X   104.5 envelop C-beta (108 degrees)
5913 PRO   (  12-)  Z   -21.4 half-chair C-alpha/N (-18 degrees)
5917 PRO   (  16-)  Z   105.2 envelop C-beta (108 degrees)
6016 PRO   (  27-)  2  -115.9 envelop C-gamma (-108 degrees)
6023 PRO   (  34-)  2  -122.6 half-chair C-delta/C-gamma (-126 degrees)
6065 PRO   (  31-)  3   101.2 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

2259 OADE  (2393-)  A      N6  <-> 2288 OADE  (2422-)  A      N1     0.56    2.44  INTRA BL
1631 OCYT  (1658-)  A      OP1 <-> 3282 HIS   ( 132-)  D      ND1    0.54    2.16  INTRA BL
 211 OGUA  ( 226-)  A      N3  <->  213 OADE  ( 228-)  A      N6     0.49    2.51  INTRA BF
2004 OGUA  (2056-)  A      N2  <-> 5993 HIS   (   4-)  2      O      0.49    2.21  INTRA BL
 992 OADE  ( 973-)  A      OP2 <-> 5160 LYS   (  78-)  R      NZ     0.49    2.21  INTRA BL
4377 ARG   (  49-)  L      CG  <-> 4378 ARG   (  50-)  L      N      0.48    2.52  INTRA BL
 754 OGUA  ( 733-)  A      N7  <->  782 OADE  ( 761-)  A      C6     0.48    2.62  INTRA BL
1847 OGUA  (1899-)  A      N2  <-> 1850 OCYT  (1902-)  A      N4     0.46    2.39  INTRA BL
4811 GLY   (  90-)  O      O   <-> 4813 TYR   (  92-)  O      N      0.45    2.25  INTRA BF
2547 OCYT  (2681-)  A      C5  <-> 2592 OADE  (2725-)  A      N6     0.45    2.65  INTRA BL
1459 OADE  (1486-)  A      N1  <-> 1477 OCYT  (1504-)  A      N4     0.43    2.57  INTRA BF
3282 HIS   ( 132-)  D      CD2 <-> 3285 HIS   ( 135-)  D      NE2    0.42    2.68  INTRA BL
 881 OURA  ( 860-)  A      C5  <->  937 OADE  ( 917-)  A      N7     0.42    2.68  INTRA BL
1381 OCYT  (1408-)  A      C2  <-> 1567 OGUA  (1595-)  A      N2     0.42    2.68  INTRA BL
1759 OADE  (1802-)  A      N7  <-> 1772 OADE  (1815-)  A      N6     0.41    2.59  INTRA BL
5467 LYS   (  81-)  U      NZ  <-> 5485 CYS   (  99-)  U      SG     0.39    2.91  INTRA BF
6024 GLU   (  35-)  2      CB  <-> 6038 CYS   (  49-)  2      SG     0.39    3.01  INTRA BF
 835 OCYT  ( 814-)  A      C5  <-> 4355 HIS   (  27-)  L      NE2    0.39    2.71  INTRA BF
2908 GLU   (  30-)  C      CD  <-> 2941 ARG   (  63-)  C      NE     0.39    2.71  INTRA BF
3282 HIS   ( 132-)  D      CG  <-> 3285 HIS   ( 135-)  D      NE2    0.38    2.72  INTRA BL
 117 OGUA  ( 124-)  A      N7  <-> 6105 ARG   (  19-)  4      NH2    0.38    2.62  INTRA BL
1378 OURA  (1405-)  A      N3  <-> 1569 OADE  (1597-)  A      N1     0.38    2.62  INTRA BL
2004 OGUA  (2056-)  A      N2  <-> 2005 OADE  (2057-)  A      C1'    0.38    2.72  INTRA BL
 605 OADE  ( 586-)  A      N7  <-> 1224 OCYT  (1251-)  A      N4     0.37    2.63  INTRA BL
 585 OURA  ( 566-)  A      N3  <->  594 OADE  ( 575-)  A      N1     0.37    2.63  INTRA BL
And so on for a total of 3196 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: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

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: 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

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.

3117 ARG   ( 239-)  C      -8.47
4349 ARG   (  21-)  L      -8.44
6041 TYR   (  52-)  2      -8.44
4555 ARG   (  82-)  M      -8.08
5680 ARG   (  14-)  W      -8.02
3883 TYR   ( 157-)  G      -7.98
6133 ARG   (  47-)  4      -7.94
3122 ARG   ( 244-)  C      -7.90
5740 ARG   (  74-)  W      -7.79
4395 MET   (  67-)  L      -7.76
2962 TYR   (  84-)  C      -7.75
5443 GLN   (  57-)  U      -7.74
3423 ARG   (  74-)  E      -7.72
5686 ARG   (  20-)  W      -7.71
5825 ARG   (  81-)  X      -7.69
4924 ARG   (  95-)  P      -7.69
4487 ARG   (  14-)  M      -7.64
2887 TYR   (   9-)  C      -7.63
4346 ARG   (  18-)  L      -7.58
4480 MET   (   7-)  M      -7.56
5707 ARG   (  41-)  W      -7.43
3299 ARG   ( 149-)  D      -7.42
4718 ARG   ( 105-)  N      -7.39
4438 TYR   ( 110-)  L      -7.37
4483 ARG   (  10-)  M      -7.35
And so on for a total of 313 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.

2883 LYS   (   5-)  C      2885 - LYS      7- ( C)         -4.42
2916 LYS   (  38-)  C      2921 - ARG     43- ( C)         -5.25
2936 HIS   (  58-)  C      2938 - ARG     60- ( C)         -5.08
3003 ILE   ( 125-)  C      3005 - VAL    127- ( C)         -4.83
3119 PRO   ( 241-)  C      3122 - ARG    244- ( C)         -5.80
3136 LYS   ( 258-)  C      3138 - ARG    260- ( C)         -4.83
3277 ASP   ( 127-)  D      3279 - HIS    129- ( D)         -5.05
3290 SER   ( 140-)  D      3296 - THR    146- ( D)         -5.14
3352 LYS   ( 202-)  D      3354 - ALA    204- ( D)         -5.23
3393 ARG   (  44-)  E      3395 - ARG     46- ( E)         -5.56
3416 GLN   (  67-)  E      3418 - HIS     69- ( E)         -5.95
3431 ILE   (  82-)  E      3433 - VAL     84- ( E)         -5.11
4079 LYS   (  30-)  J      4081 - VAL     32- ( J)         -5.30
4257 ILE   (  47-)  K      4259 - ARG     49- ( K)         -5.38
4342 LYS   (  14-)  L      4346 - ARG     18- ( L)         -5.70
4378 ARG   (  50-)  L      4380 - GLU     52- ( L)         -5.35
4395 MET   (  67-)  L      4399 - VAL     71- ( L)         -6.34
4402 GLU   (  74-)  L      4405 - ARG     77- ( L)         -5.16
4475 LEU   ( 147-)  L      4478 - ALA    150- ( L)         -4.83
4480 MET   (   7-)  M      4487 - ARG     14- ( M)         -6.68
4489 ARG   (  16-)  M      4491 - LYS     18- ( M)         -5.04
4552 LEU   (  79-)  M      4556 - MET     83- ( M)         -6.36
4616 HIS   (   3-)  N      4618 - LYS      5- ( N)         -5.26
4620 GLY   (   7-)  N      4625 - ARG     12- ( N)         -5.16
4814 LYS   (  93-)  O      4816 - HIS     95- ( O)         -5.29
4850 GLU   (  21-)  P      4852 - ARG     23- ( P)         -5.53
5243 ASN   (  60-)  S      5245 - HIS     62- ( S)         -5.34
5293 LYS   ( 110-)  S      5295 - GLY    112- ( S)         -5.63
5357 LYS   (  64-)  T      5359 - LEU     66- ( T)         -6.13
5361 ARG   (  68-)  T      5363 - LEU     70- ( T)         -5.36
5389 VAL   (   3-)  U      5391 - MET      5- ( U)         -5.22
5435 VAL   (  49-)  U      5437 - VAL     51- ( U)         -5.62
5494 TYR   (   9-)  V      5496 - GLU     11- ( V)         -4.52
5563 LYS   (  78-)  V      5566 - ARG     81- ( V)         -6.25
5685 LYS   (  19-)  W      5687 - LEU     21- ( W)         -5.51
5763 GLN   (  19-)  X      5765 - ARG     21- ( X)         -4.98
5825 ARG   (  81-)  X      5827 - GLU     83- ( X)         -5.83
5992 LYS   (   3-)  2      5994 - PRO      5- ( 2)         -5.18
5997 LYS   (   8-)  2      5999 - LYS     10- ( 2)         -4.89
6071 ARG   (  37-)  3      6074 - CYS     40- ( 3)         -4.51
6076 TRP   (  42-)  3      6080 - HIS     46- ( 3)         -5.51
6125 ARG   (  39-)  4      6128 - LEU     42- ( 4)         -5.06
6163 ARG   (  30-)  5      6165 - LEU     32- ( 5)         -5.44

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 - 6197 : -1.878

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

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: 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

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.

5678 ASN   (  12-)  W   -4.10
4367 LYS   (  39-)  L   -3.57
5998 LYS   (   9-)  2   -3.41
3444 ARG   (  95-)  E   -3.36
4618 LYS   (   5-)  N   -3.35
5684 ALA   (  18-)  W   -3.29
4970 LYS   (   5-)  Q   -3.28
3299 ARG   ( 149-)  D   -3.23
4349 ARG   (  21-)  L   -3.21
6165 LEU   (  32-)  5   -3.19
3423 ARG   (  74-)  E   -3.15
5159 ALA   (  77-)  R   -3.15
3122 ARG   ( 244-)  C   -3.14
4992 LEU   (  27-)  Q   -3.13
3518 ASN   ( 169-)  E   -3.13
3267 MET   ( 117-)  D   -3.11
4617 LEU   (   4-)  N   -3.09
4371 GLY   (  43-)  L   -3.08
4486 GLN   (  13-)  M   -3.08
4491 LYS   (  18-)  M   -3.08
4555 ARG   (  82-)  M   -3.06
6093 PRO   (   7-)  4   -3.04
5388 ARG   (   2-)  U   -3.04
5160 LYS   (  78-)  R   -3.03
2923 ASN   (  45-)  C   -3.02
And so on for a total of 140 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.

2884 PHE   (   6-)  C     - 2887 TYR   (   9-)  C        -1.95
2921 ARG   (  43-)  C     - 2924 GLN   (  46-)  C        -2.34
2926 ARG   (  48-)  C     - 2930 ARG   (  52-)  C        -2.01
2935 GLY   (  57-)  C     - 2938 ARG   (  60-)  C        -2.03
3114 GLY   ( 236-)  C     - 3122 ARG   ( 244-)  C        -2.42
3160 GLY   (  10-)  D     - 3163 ARG   (  13-)  D        -1.57
3276 PRO   ( 126-)  D     - 3281 ALA   ( 131-)  D        -2.08
3282 HIS   ( 132-)  D     - 3285 HIS   ( 135-)  D        -2.06
3288 PRO   ( 138-)  D     - 3295 LYS   ( 145-)  D        -2.46
3296 THR   ( 146-)  D     - 3301 TYR   ( 151-)  D        -2.33
3391 ALA   (  42-)  E     - 3395 ARG   (  46-)  E        -1.58
3405 GLU   (  56-)  E     - 3412 LYS   (  63-)  E        -1.75
3627 ARG   (  72-)  F     - 3630 LYS   (  75-)  F        -1.49
4145 THR   (  96-)  J     - 4148 SER   (  99-)  J        -1.84
4202 HIS   ( 153-)  J     - 4205 GLN   ( 156-)  J        -1.99
4236 LYS   (  26-)  K     - 4239 ASN   (  29-)  K        -2.06
4342 LYS   (  14-)  L     - 4346 ARG   (  18-)  L        -2.24
4354 GLY   (  26-)  L     - 4359 ALA   (  31-)  L        -1.93
4360 THR   (  32-)  L     - 4364 LYS   (  36-)  L        -2.12
4365 GLY   (  37-)  L     - 4375 ASP   (  47-)  L        -2.21
4376 PRO   (  48-)  L     - 4379 PHE   (  51-)  L        -1.90
4380 GLU   (  52-)  L     - 4383 ARG   (  55-)  L        -2.39
4389 ARG   (  61-)  L     - 4395 MET   (  67-)  L        -2.44
4396 GLN   (  68-)  L     - 4401 GLY   (  73-)  L        -2.18
4402 GLU   (  74-)  L     - 4405 ARG   (  77-)  L        -2.19
4432 GLY   ( 104-)  L     - 4435 LYS   ( 107-)  L        -2.04
4479 ARG   (   6-)  M     - 4482 TYR   (   9-)  M        -1.76
4488 GLY   (  15-)  M     - 4492 GLY   (  19-)  M        -2.26
4548 THR   (  75-)  M     - 4552 LEU   (  79-)  M        -1.96
4614 GLN   ( 141-)  M     - 4618 LYS   (   5-)  N        -2.38
4775 LEU   (  54-)  O     - 4778 LYS   (  57-)  O        -2.07
4921 GLY   (  92-)  P     - 4927 LYS   (  98-)  P        -2.24
4966 LYS   ( 137-)  P     - 4973 VAL   (   8-)  Q        -2.40
4994 SER   (  29-)  Q     - 4997 ARG   (  33-)  Q        -1.64
5158 LYS   (  76-)  R     - 5163 TYR   (  81-)  R        -2.49
5352 VAL   (  59-)  T     - 5355 LYS   (  62-)  T        -1.92
5387 GLY   (  94-)  T     - 5395 LYS   (   9-)  U        -2.27
5431 VAL   (  45-)  U     - 5434 ALA   (  48-)  U        -1.80
5679 GLY   (  13-)  W     - 5686 ARG   (  20-)  W        -2.38
5719 MET   (  53-)  W     - 5722 ASP   (  56-)  W        -1.26
5786 GLN   (  42-)  X     - 5789 ASN   (  45-)  X        -1.96
5990 CYS   (  65-)  1     - 6000 THR   (  11-)  2        -2.47
6056 ALA   (  22-)  3     - 6059 LYS   (  25-)  3        -1.90
6078 ARG   (  44-)  3     - 6081 THR   (  47-)  3        -1.80
6086 VAL   (  52-)  3     - 6089 ARG   (   3-)  4        -2.04
6090 THR   (   4-)  4     - 6094 ASN   (   8-)  4        -2.27
6135 PRO   (   2-)  5     - 6138 LYS   (   5-)  5        -2.28
6161 GLY   (  28-)  5     - 6166 ASN   (  33-)  5        -2.34

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: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

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: 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

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.

3105 ASN   ( 227-)  C
3111 HIS   ( 233-)  C
3210 ASN   (  60-)  D
3271 ASN   ( 121-)  D
3285 HIS   ( 135-)  D
3319 ASN   ( 169-)  D
3509 ASN   ( 160-)  E
3582 ASN   (  27-)  F
3621 GLN   (  66-)  F
4035 GLN   ( 139-)  H
4128 ASN   (  79-)  J
4239 ASN   (  29-)  K
4292 ASN   (  82-)  K
4299 ASN   (  89-)  K
4341 ASN   (  13-)  L
4363 HIS   (  35-)  L
4409 GLN   (  81-)  L
4614 GLN   ( 141-)  M
4666 HIS   (  53-)  N
4755 HIS   (  34-)  O
4908 HIS   (  79-)  P
5013 HIS   (  49-)  Q
5240 ASN   (  57-)  S
5285 HIS   ( 102-)  S
5294 HIS   ( 111-)  S
5324 HIS   (  31-)  T
5348 ASN   (  55-)  T
5535 GLN   (  50-)  V
5539 HIS   (  54-)  V
5701 ASN   (  35-)  W
5736 GLN   (  70-)  W
5763 GLN   (  19-)  X
5789 ASN   (  45-)  X
5920 GLN   (  19-)  Z
5933 GLN   (  32-)  Z
5947 ASN   (  46-)  Z
5953 HIS   (  52-)  Z
5993 HIS   (   4-)  2
6011 HIS   (  22-)  2
6032 HIS   (  43-)  2
6080 HIS   (  46-)  3
6094 ASN   (   8-)  4
6166 ASN   (  33-)  5

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.

  19 OGUA  (  24-)  A      N2
  45 OGUA  (  51-)  A      N2
  46 OADE  (  52-)  A      N6
  54 OGUA  (  60-)  A      N2
  64 OGUA  (  70-)  A      N2
  88 OGUA  (  94-)  A      N1
  88 OGUA  (  94-)  A      N2
  97 OURA  ( 104-)  A      N3
 131 OGUA  ( 137-)  A      N2
 132 OGUA  ( 138-)  A      N1
 133 OGUA  ( 139-)  A      N2
 135 OADE  ( 141-)  A      N6
 183 OCYT  ( 198-)  A      N4
 184 OADE  ( 199-)  A      N6
 185 OURA  ( 200-)  A      N3
 186 OCYT  ( 201-)  A      N4
 205 OGUA  ( 220-)  A      N2
 206 OADE  ( 221-)  A      N6
 207 OADE  ( 222-)  A      N6
 211 OGUA  ( 226-)  A      N1
 231 OCYT  ( 246-)  A      N4
 233 OGUA  ( 248-)  A      N2
 301 OGUA  ( 281-)  A      N2
 319 OADE  ( 299-)  A      N6
 327 OGUA  ( 307-)  A      N2
And so on for a total of 777 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.

2922 ASN   (  44-)  C      OD1
3021 HIS   ( 143-)  C      ND1
3064 HIS   ( 186-)  C      ND1
3198 GLN   (  48-)  D      OE1
3279 HIS   ( 129-)  D      ND1
3285 HIS   ( 135-)  D      NE2
3319 ASN   ( 169-)  D      OD1
3518 ASN   ( 169-)  E      OD1
3596 GLN   (  41-)  F      OE1
3698 GLU   ( 143-)  F      OE2
3865 GLN   ( 139-)  G      OE1
4000 GLN   ( 104-)  H      OE1
4071 GLU   (  65-)  I      OE1
4203 GLN   ( 154-)  J      OE1
4292 ASN   (  82-)  K      OD1
4412 ASN   (  84-)  L      OD1
4486 GLN   (  13-)  M      OE1
4498 ASP   (  25-)  M      OD2
4530 HIS   (  57-)  M      ND1
4612 GLU   ( 139-)  M      OE2
4614 GLN   ( 141-)  M      OE1
4629 HIS   (  16-)  N      ND1
4662 ASP   (  49-)  N      OD1
4755 HIS   (  34-)  O      ND1
4840 GLU   (  11-)  P      OE2
4875 GLU   (  46-)  P      OE2
5055 ASP   (  91-)  Q      OD1
5348 ASN   (  55-)  T      OD1
5572 ASP   (  87-)  V      OD2
5633 ASP   ( 148-)  V      OD1
5886 ASN   (  47-)  Y      OD1
5935 GLU   (  34-)  Z      OE1
5974 GLU   (  49-)  1      OE1
6083 HIS   (  49-)  3      NE2
6085 GLU   (  51-)  3      OE1
6168 GLN   (  35-)  5      OE1
6176 GLN   (  43-)  5      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+.

6227  MG   (   1-)  A   -.-  -.-  Part of ionic cluster
6227  MG   (   1-)  A   -.-  -.-  Too few ligands (2)
6228  MG   (   2-)  A   -.-  -.-  Too few ligands (1)
6229  MG   (   3-)  A   -.-  -.-  Too few ligands (1)
6230  MG   (   4-)  A     0.14   0.20 Is perhaps  K (Few ligands (4) ) *2
6231  MG   (   5-)  A   -.-  -.-  Too few ligands (2)
6232  MG   (2898-)  A   -.-  -.-  Part of ionic cluster
6232  MG   (2898-)  A   -.-  -.-  Too few ligands (3)
6233  MG   (2899-)  A   -.-  -.-  Part of ionic cluster
6233  MG   (2899-)  A   -.-  -.-  Too few ligands (2)
6234  MG   (2900-)  A   -.-  -.-  Part of ionic cluster
6234  MG   (2900-)  A   -.-  -.-  Too few ligands (2)
6235  MG   (2901-)  A   -.-  -.-  Too few ligands (1)
6236  MG   (  63-)  Y   -.-  -.-  Too few ligands (1)
6237  MG   (2902-)  A   -.-  -.-  Too few ligands (2)
6238  MG   (2903-)  A   -.-  -.-  Too few ligands (2)
6239  MG   (2904-)  A   -.-  -.-  Too few ligands (1)
6240  MG   (2905-)  A   -.-  -.-  Too few ligands (1)
6241  MG   (2906-)  A   -.-  -.-  Too few ligands (1)
6242  MG   (2907-)  A   -.-  -.-  Too few ligands (2)
6243  MG   (2908-)  A   -.-  -.-  Too few ligands (2)
6244  MG   (  18-)  6   -.-  -.-  Part of ionic cluster
6244  MG   (  18-)  6   -.-  -.-  Too few ligands (0)
6245  MG   (2909-)  A   -.-  -.-  Too few ligands (2)
6246  MG   (2910-)  A   -.-  -.-  Part of ionic cluster
And so on for a total of 1345 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.

2898 ASP   (  20-)  C   H-bonding suggests Asn; but Alt-Rotamer
3168 ASP   (  18-)  D   H-bonding suggests Asn
3239 ASP   (  89-)  D   H-bonding suggests Asn; but Alt-Rotamer
3329 GLU   ( 179-)  D   H-bonding suggests Gln; but Alt-Rotamer
3487 GLU   ( 138-)  E   H-bonding suggests Gln
3569 GLU   (  14-)  F   H-bonding suggests Gln
3590 GLU   (  35-)  F   H-bonding suggests Gln
3681 ASP   ( 126-)  F   H-bonding suggests Asn; but Alt-Rotamer
3721 ASP   ( 166-)  F   H-bonding suggests Asn; but Alt-Rotamer
3760 GLU   (  34-)  G   H-bonding suggests Gln
3812 GLU   (  86-)  G   H-bonding suggests Gln; but Alt-Rotamer
3969 GLU   (  73-)  H   H-bonding suggests Gln; but Alt-Rotamer
3981 GLU   (  85-)  H   H-bonding suggests Gln
3992 ASP   (  96-)  H   H-bonding suggests Asn
4333 ASP   (   5-)  L   H-bonding suggests Asn
4420 GLU   (  92-)  L   H-bonding suggests Gln
4477 GLU   ( 149-)  L   H-bonding suggests Gln
4553 GLU   (  80-)  M   H-bonding suggests Gln
4612 GLU   ( 139-)  M   H-bonding suggests Gln
4662 ASP   (  49-)  N   H-bonding suggests Asn
4694 ASP   (  81-)  N   H-bonding suggests Asn
4840 GLU   (  11-)  P   H-bonding suggests Gln; but Alt-Rotamer
4855 ASP   (  26-)  P   H-bonding suggests Asn
4873 ASP   (  44-)  P   H-bonding suggests Asn; but Alt-Rotamer
4916 ASP   (  87-)  P   H-bonding suggests Asn; but Alt-Rotamer
4936 ASP   ( 107-)  P   H-bonding suggests Asn; but Alt-Rotamer
4951 ASP   ( 122-)  P   H-bonding suggests Asn
4953 ASP   ( 124-)  P   H-bonding suggests Asn; but Alt-Rotamer
5055 ASP   (  91-)  Q   H-bonding suggests Asn; but Alt-Rotamer
5125 GLU   (  43-)  R   H-bonding suggests Gln
5205 ASP   (  22-)  S   H-bonding suggests Asn; but Alt-Rotamer
5246 ASP   (  63-)  S   H-bonding suggests Asn
5277 ASP   (  94-)  S   H-bonding suggests Asn
5397 ASP   (  11-)  U   H-bonding suggests Asn; but Alt-Rotamer
5415 GLU   (  29-)  U   H-bonding suggests Gln
5426 GLU   (  40-)  U   H-bonding suggests Gln; but Alt-Rotamer
5562 ASP   (  77-)  V   H-bonding suggests Asn
5630 GLU   ( 145-)  V   H-bonding suggests Gln
5639 ASP   ( 154-)  V   H-bonding suggests Asn; but Alt-Rotamer
5663 GLU   ( 178-)  V   H-bonding suggests Gln
5681 ASP   (  15-)  W   H-bonding suggests Asn
5833 GLU   (  89-)  X   H-bonding suggests Gln
5850 GLU   (  11-)  Y   H-bonding suggests Gln; but Alt-Rotamer
5958 GLU   (  57-)  Z   H-bonding suggests Gln
5974 GLU   (  49-)  1   H-bonding suggests Gln
6187 GLU   (  54-)  5   H-bonding suggests Gln
6189 GLU   (  56-)  5   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.445
  2nd generation packing quality :  -4.289 (bad)
  Ramachandran plot appearance   :  -4.776 (bad)
  chi-1/chi-2 rotamer normality  :  -4.236 (bad)
  Backbone conformation          :  -0.404

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.545 (tight)
  Bond angles                    :   0.925
  Omega angle restraints         :   0.809
  Side chain planarity           :   0.160 (tight)
  Improper dihedral distribution :   0.467
  B-factor distribution          :   0.533
  Inside/Outside distribution    :   1.022

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.0
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.545 (tight)
  Bond angles                    :   0.925
  Omega angle restraints         :   0.809
  Side chain planarity           :   0.160 (tight)
  Improper dihedral distribution :   0.467
  B-factor distribution          :   0.533
  Inside/Outside distribution    :   1.022
==============

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.