WHAT IF Check report

This file was created 2011-12-16 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 pdb3i8h.ent

Checks that need to be done early-on in validation

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: 923447.500
Volume of the Unit Cell V= 58237228.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 15.766
Vm by authors and this calculated Vm do not agree very well

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.

4205  MG   (  10-)  C  2
4331  MG   (  82-)  C  2
4564  MG   (1757-)  1  A
4569  MG   ( 227-)  A  2
4737  MG   ( 325-)  D  2
5221  MG   (2514-)  G  A
5346  MG   (2801-)  S  A
5420  MG   (3020-)  L  A
5539  MG   (1227-)  A  G
5545  MG   ( 832-)  C  2
5550  MG   ( 566-)  A  H
5570  MG   (1283-)  A  K
5571  MG   (1284-)  A  K
5574  MG   (2077-)  E  K
5581  MG   ( 191-)  A  L
5590  MG   (3006-)  A  P
5605  MG   (1014-)  A  S
5611  MG   (2778-)  A  S
5639  MG   (  78-)  C  B
5695  MG   ( 808-)  C  B
5761  MG   ( 976-)  N  2
5763  MG   ( 977-)  D  2
5774  MG   ( 987-)  D  2
5776  MG   ( 988-)  D  2
5829  MG   (1024-)  A  2
And so on for a total of 51 lines.

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.

5221  MG   (2514-)  G  A
5570  MG   (1283-)  A  K
5571  MG   (1284-)  A  K
5582  MG   (2668-)  M  -

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: 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

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.

  60 OGUA  (  64-)  A    High
  61 OURA  (  65-)  A    High
  62 OGUA  (  66-)  A    High
  63 OCYT  (  67-)  A    High
  64 OGUA  (  68-)  A    High
  65 OGUA  (  69-)  A    High
  66 OGUA  (  73-)  A    High
  67 OCYT  (  74-)  A    High
  68 OCYT  (  75-)  A    High
  69 OGUA  (  76-)  A    High
  70 OCYT  (  77-)  A    High
  71 OGUA  (  78-)  A    High
  72 OGUA  (  79-)  A    High
  73 OGUA  (  80-)  A    High
  74 OGUA  (  81-)  A    High
  75 OURA  (  82-)  A    High
  76 OURA  (  84-)  A    High
  77 OURA  (  85-)  A    High
  78 OURA  (  86-)  A    High
  79 OADE  (  87-)  A    High
  80 OCYT  (  88-)  A    High
  81 OURA  (  89-)  A    High
  82 OCYT  (  90-)  A    High
  83 OCYT  (  91-)  A    High
  84 OGUA  (  92-)  A    High
And so on for a total of 1066 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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

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.

1959 ARG   (   3-)  G
2074 ARG   ( 118-)  G
2571 ARG   ( 155-)  J
3637 ARG   ( 101-)  T
3879 ARG   (  89-)  W

Warning: Tyrosine convention problem

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

1543 TYR   (  31-)  E
1711 TYR   ( 199-)  E
1780 TYR   (  29-)  F
1983 TYR   (  27-)  G
2094 TYR   ( 138-)  G
2349 TYR   (  33-)  I
2379 TYR   (  63-)  I
2460 TYR   (  44-)  J
2501 TYR   (  85-)  J
2567 TYR   ( 151-)  J
2570 TYR   ( 154-)  J
2714 TYR   (   5-)  L
2797 TYR   (  88-)  L
2801 TYR   (  92-)  L
2823 TYR   ( 114-)  L
2834 TYR   ( 125-)  L
2951 TYR   (  25-)  N
2976 TYR   (  50-)  N
3156 TYR   ( 105-)  O
3171 TYR   ( 120-)  O
3200 TYR   (  21-)  P
3485 TYR   (  32-)  S
3568 TYR   (  32-)  T
3587 TYR   (  51-)  T
3769 TYR   (  61-)  V

Warning: Phenylalanine convention problem

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

1664 PHE   ( 152-)  E
1675 PHE   ( 163-)  E
2031 PHE   (  75-)  G
2035 PHE   (  79-)  G
2049 PHE   (  93-)  G
2167 PHE   (   6-)  H
2727 PHE   (  18-)  L
2746 PHE   (  37-)  L
2810 PHE   ( 101-)  L
2846 PHE   (  11-)  M
3462 PHE   (   9-)  S
3607 PHE   (  71-)  T
3650 PHE   (  29-)  U
3702 PHE   (  81-)  U

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.

1572 ASP   (  60-)  E
1678 ASP   ( 166-)  E
1703 ASP   ( 191-)  E
1705 ASP   ( 193-)  E
1710 ASP   ( 198-)  E
1768 ASP   (  17-)  F
1787 ASP   (  36-)  F
1807 ASP   (  56-)  F
1934 ASP   ( 183-)  F
2090 ASP   ( 134-)  G
2166 ASP   (   5-)  H
2308 ASP   ( 147-)  H
2399 ASP   (  83-)  I
2431 ASP   (  15-)  J
2461 ASP   (  45-)  J
2542 ASP   ( 126-)  J
2576 ASP   (   4-)  K
2624 ASP   (  52-)  K
2645 ASP   (  73-)  K
2814 ASP   ( 105-)  L
2847 ASP   (  12-)  M
2852 ASP   (  17-)  M
2962 ASP   (  36-)  N
2993 ASP   (  67-)  N
3195 ASP   (  16-)  P
3385 ASP   (  21-)  R
3482 ASP   (  29-)  S
3493 ASP   (  40-)  S
3505 ASP   (  52-)  S
3654 ASP   (  33-)  U

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

1516 GLU   (   4-)  E
1521 GLU   (   9-)  E
1547 GLU   (  35-)  E
1564 GLU   (  52-)  E
1638 GLU   ( 126-)  E
1641 GLU   ( 129-)  E
1770 GLU   (  19-)  F
1990 GLU   (  34-)  G
2028 GLU   (  72-)  G
2036 GLU   (  80-)  G
2037 GLU   (  81-)  G
2101 GLU   ( 145-)  G
2112 GLU   ( 156-)  G
2119 GLU   ( 163-)  G
2148 GLU   ( 192-)  G
2161 GLU   ( 205-)  G
2168 GLU   (   7-)  H
2272 GLU   ( 111-)  H
2316 GLU   ( 155-)  H
2338 GLU   (  22-)  I
2358 GLU   (  42-)  I
2468 GLU   (  52-)  J
2483 GLU   (  67-)  J
2490 GLU   (  74-)  J
2506 GLU   (  90-)  J
2555 GLU   ( 139-)  J
2594 GLU   (  22-)  K
2605 GLU   (  33-)  K
2671 GLU   (  99-)  K
2711 GLU   (   2-)  L
2744 GLU   (  35-)  L
2896 GLU   (  61-)  M
2918 GLU   (  83-)  M
2930 GLU   (  95-)  M
3211 GLU   (  32-)  P
3371 GLU   (   7-)  R
3405 GLU   (  41-)  R
3487 GLU   (  34-)  S
3536 GLU   (  83-)  S
3597 GLU   (  61-)  T
3614 GLU   (  78-)  T
3649 GLU   (  28-)  U
3725 GLU   (  17-)  V
3751 GLU   (  43-)  V
3794 GLU   (  86-)  V
3836 GLU   (  46-)  W
3850 GLU   (  60-)  W

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

3958 MIA   (  37-)  D
4034 MIA   (  37-)  B
4110 MIA   (  37-)  C

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.

  66 OGUA  (  73-)  A      C6   N1    1.36   -4.6
  88 OURA  (  97-)  A      N1   C2    1.42    4.7
  88 OURA  (  97-)  A      C2   O2    1.26    4.1
 608 OGUA  ( 629-)  A      C5   C4    1.35   -4.7
 767 OURA  ( 788-)  A      C2   O2    1.26    4.6
 767 OURA  ( 788-)  A      N3   C2    1.41    4.9
 767 OURA  ( 788-)  A      C4   N3    1.44    6.8
 773 OADE  ( 794-)  A      C2   N3    1.37    4.1
1154 OGUA  (1177-)  A      C5   C6    1.47    4.8
1508 OCYT  (1535-)  A      C4   N4    1.30   -4.2
1968 CYS   (  12-)  G      CA   CB    1.61    4.2
3714 LYS   (   6-)  V      CA   CB    1.63    5.1
4093 OURA  (  20-)  C      C1'  N1    1.55    8.6

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000839  0.000098 -0.000078|
 |  0.000098  1.000863 -0.000137|
 | -0.000078 -0.000137  1.000686|
Proposed new scale matrix

 |  0.004770  0.000000  0.000000|
 |  0.000000  0.002239  0.000000|
 |  0.000000  0.000000  0.001604|
With corresponding cell

    A    = 209.644  B   = 446.614  C    = 623.480
    Alpha=  90.006  Beta=  90.005  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 209.460  B   = 446.200  C    = 623.050
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 645.922
(Under-)estimated Z-score: 18.731

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   2 OGUA  (   6-)  A      N9   C8   N7  113.13    4.1
   4 OADE  (   8-)  A      C2'  C1'  N9  120.30    4.3
   7 OGUA  (  11-)  A      N9   C8   N7  113.12    4.0
   9 OURA  (  13-)  A      C2'  C1'  N1  123.66    6.4
  11 OGUA  (  15-)  A      N9   C8   N7  113.27    4.3
  17 OGUA  (  21-)  A      N9   C8   N7  113.14    4.1
  31 OGUA  (  35-)  A      N9   C8   N7  113.26    4.3
  34 OGUA  (  38-)  A      N9   C8   N7  113.31    4.4
  43 OCYT  (  47-)  A      C4'  O4'  C1' 105.67   -4.4
  43 OCYT  (  47-)  A      O4'  C1'  N1  112.48    4.3
  43 OCYT  (  47-)  A      C2'  C1'  N1  122.38    5.6
  46 OADE  (  50-)  A      C2'  C1'  N9  121.75    5.2
  48 OGUA  (  52-)  A      N9   C8   N7  113.33    4.5
  57 OGUA  (  61-)  A      N9   C8   N7  113.14    4.1
  62 OGUA  (  66-)  A      N9   C8   N7  113.32    4.4
  64 OGUA  (  68-)  A      N9   C8   N7  113.10    4.0
  65 OGUA  (  69-)  A      N9   C8   N7  113.13    4.1
  66 OGUA  (  73-)  A      N9   C8   N7  113.53    4.9
  69 OGUA  (  76-)  A      N9   C8   N7  113.25    4.3
  71 OGUA  (  78-)  A      N9   C8   N7  113.19    4.2
  73 OGUA  (  80-)  A      N9   C8   N7  113.26    4.3
  74 OGUA  (  81-)  A      N9   C8   N7  113.16    4.1
  84 OGUA  (  92-)  A      N9   C8   N7  113.19    4.2
  86 OGUA  (  95-)  A      N9   C8   N7  113.24    4.3
  87 OGUA  (  96-)  A      N9   C8   N7  113.23    4.3
And so on for a total of 389 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.

1516 GLU   (   4-)  E
1521 GLU   (   9-)  E
1547 GLU   (  35-)  E
1564 GLU   (  52-)  E
1572 ASP   (  60-)  E
1638 GLU   ( 126-)  E
1641 GLU   ( 129-)  E
1678 ASP   ( 166-)  E
1703 ASP   ( 191-)  E
1705 ASP   ( 193-)  E
1710 ASP   ( 198-)  E
1768 ASP   (  17-)  F
1770 GLU   (  19-)  F
1787 ASP   (  36-)  F
1807 ASP   (  56-)  F
1934 ASP   ( 183-)  F
1959 ARG   (   3-)  G
1990 GLU   (  34-)  G
2028 GLU   (  72-)  G
2036 GLU   (  80-)  G
2037 GLU   (  81-)  G
2074 ARG   ( 118-)  G
2090 ASP   ( 134-)  G
2101 GLU   ( 145-)  G
2112 GLU   ( 156-)  G
And so on for a total of 82 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.

3099 PRO   (  48-)  O      N     10.5    31.83    -2.48
3303 PRO   ( 124-)  P      N     -7.9   -28.36    -2.48
The average deviation= 0.742

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.

1968 CYS   (  12-)  G    8.62
3793 LYS   (  85-)  V    7.27
3731 ASN   (  23-)  V    6.67
1987 CYS   (  31-)  G    6.28
2796 GLN   (  87-)  L    5.62
2160 ILE   ( 204-)  G    5.52
1652 HIS   ( 140-)  E    5.28
1966 ARG   (  10-)  G    5.22
3732 ALA   (  24-)  V    5.09
3346 ILE   (  42-)  Q    5.09
3170 LYS   ( 119-)  O    5.07
1969 ARG   (  13-)  G    4.99
2584 ARG   (  12-)  K    4.99
3862 LEU   (  72-)  W    4.98
2193 VAL   (  32-)  H    4.94
3827 SER   (  37-)  W    4.83
3418 ARG   (  54-)  R    4.74
2795 VAL   (  86-)  L    4.58
2219 ALA   (  58-)  H    4.54
1986 LYS   (  30-)  G    4.50
3524 ARG   (  71-)  S    4.39
3190 ARG   (  11-)  P    4.37
3867 ALA   (  77-)  W    4.37
1712 ILE   ( 200-)  E    4.34
3347 CYS   (  43-)  Q    4.31
2855 ALA   (  20-)  M    4.27
2402 ARG   (  86-)  I    4.22
2341 ILE   (  25-)  I    4.21
3447 GLU   (  83-)  R    4.20
3772 GLU   (  64-)  V    4.17
2159 VAL   ( 203-)  G    4.14
3473 VAL   (  20-)  S    4.13
3866 ALA   (  76-)  W    4.10
3528 ARG   (  75-)  S    4.07
3412 LYS   (  48-)  R    4.07
3881 LEU   (  91-)  W    4.07
3194 VAL   (  15-)  P    4.05
1559 THR   (  47-)  E    4.05
3623 LYS   (  87-)  T    4.04
3835 GLN   (  45-)  W    4.04
1624 VAL   ( 112-)  E    4.02
3840 GLU   (  50-)  W    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.510

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  88 OURA  (  97-)  A    0.19
1514 OURA  (1541-)  A    0.14
3966 OURA  (  45-)  D    0.11
 Ramachandran Z-score : -6.092

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -6.092

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.

3787 THR   (  79-)  V    -3.6
1916 THR   ( 165-)  F    -3.3
1963 PRO   (   7-)  G    -3.1
3303 PRO   ( 124-)  P    -3.1
2926 PRO   (  91-)  M    -3.0
1985 PRO   (  29-)  G    -2.9
1637 PRO   ( 125-)  E    -2.9
1763 LEU   (  12-)  F    -2.9
2213 PRO   (  52-)  H    -2.8
3713 LEU   (   5-)  V    -2.8
3099 PRO   (  48-)  O    -2.8
2412 PRO   (  96-)  I    -2.8
2967 THR   (  41-)  N    -2.8
2098 PRO   ( 142-)  G    -2.8
3749 VAL   (  41-)  V    -2.7
1527 VAL   (  15-)  E    -2.7
3718 PHE   (  10-)  V    -2.7
3078 LEU   (  27-)  O    -2.7
2279 ILE   ( 118-)  H    -2.7
3639 ARG   (  18-)  U    -2.7
3863 HIS   (  73-)  W    -2.7
3712 SER   (   4-)  V    -2.7
1579 THR   (  67-)  E    -2.6
2894 SER   (  59-)  M    -2.6
2983 THR   (  57-)  N    -2.6
And so on for a total of 178 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.

1518 THR   (   6-)  E  Poor phi/psi
1520 LYS   (   8-)  E  Poor phi/psi
1527 VAL   (  15-)  E  Poor phi/psi
1534 LYS   (  22-)  E  Poor phi/psi
1540 PHE   (  28-)  E  Poor phi/psi
1549 ASN   (  37-)  E  Poor phi/psi
1579 THR   (  67-)  E  Poor phi/psi
1589 ALA   (  77-)  E  Poor phi/psi
1590 GLN   (  78-)  E  Poor phi/psi
1595 MET   (  83-)  E  Poor phi/psi
1599 ARG   (  87-)  E  Poor phi/psi
1600 ALA   (  88-)  E  Poor phi/psi
1608 ARG   (  96-)  E  Poor phi/psi
1634 PHE   ( 122-)  E  Poor phi/psi
1638 GLU   ( 126-)  E  Poor phi/psi
1641 GLU   ( 129-)  E  Poor phi/psi
1651 LYS   ( 139-)  E  Poor phi/psi
1667 LEU   ( 155-)  E  Poor phi/psi
1673 ALA   ( 161-)  E  Poor phi/psi
1677 VAL   ( 165-)  E  Poor phi/psi
1693 PHE   ( 181-)  E  Poor phi/psi
1704 SER   ( 192-)  E  Poor phi/psi
1706 PRO   ( 194-)  E  Poor phi/psi
1707 ASP   ( 195-)  E  Poor phi/psi
1720 ILE   ( 208-)  E  Poor phi/psi
And so on for a total of 287 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 : -4.700

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.

2973 VAL   (  47-)  N    0.33
1728 SER   ( 216-)  E    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 OGUA  (   7-)  A      0
   4 OADE  (   8-)  A      0
   5 OGUA  (   9-)  A      0
   6 OADE  (  10-)  A      0
   7 OGUA  (  11-)  A      0
   8 OURA  (  12-)  A      0
   9 OURA  (  13-)  A      0
  10 OURA  (  14-)  A      0
  11 OGUA  (  15-)  A      0
  12 OADE  (  16-)  A      0
  13 OURA  (  17-)  A      0
  14 OCYT  (  18-)  A      0
  15 OCYT  (  19-)  A      0
  16 OURA  (  20-)  A      0
  17 OGUA  (  21-)  A      0
  18 OGUA  (  22-)  A      0
  19 OCYT  (  23-)  A      0
  20 OURA  (  24-)  A      0
  21 OCYT  (  25-)  A      0
  22 OADE  (  26-)  A      0
  23 OGUA  (  27-)  A      0
  24 OGUA  (  28-)  A      0
  25 OGUA  (  29-)  A      0
  26 OURA  (  30-)  A      0
  27 OGUA  (  31-)  A      0
And so on for a total of 2787 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.160

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!

2275 GLY   ( 114-)  H   2.89   80
1896 GLY   ( 145-)  F   2.69   67
1829 GLY   (  78-)  F   2.48   24
3279 GLY   ( 100-)  P   2.46   50
3298 GLY   ( 119-)  P   2.42   24
1550 GLY   (  38-)  E   2.34   16
3028 GLY   ( 102-)  N   2.02   80
2435 GLY   (  19-)  J   1.83   11
1737 ALA   ( 225-)  E   1.78   10
3837 GLY   (  47-)  W   1.76   13
1578 GLY   (  66-)  E   1.72   16
3569 GLY   (  33-)  T   1.68   76
2196 GLY   (  35-)  H   1.66   24
2731 GLY   (  22-)  L   1.65   11
3450 GLY   (  86-)  R   1.65   40
1577 GLY   (  65-)  E   1.59   80
2471 GLY   (  55-)  J   1.58   29
3002 GLY   (  76-)  N   1.56   16
2733 GLY   (  24-)  L   1.55   80
1715 GLY   ( 203-)  E   1.52   15

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...

3190 ARG   (  11-)  P   2.72

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]

3041 PRO   ( 115-)  N    0.46 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].

1963 PRO   (   7-)  G   103.0 envelop C-beta (108 degrees)
2474 PRO   (  58-)  J  -120.5 half-chair C-delta/C-gamma (-126 degrees)
3096 PRO   (  45-)  O    42.9 envelop C-delta (36 degrees)
3099 PRO   (  48-)  O  -139.0 envelop C-delta (-144 degrees)
3276 PRO   (  97-)  P  -112.7 envelop C-gamma (-108 degrees)
3318 PRO   (  14-)  Q   141.6 envelop C-alpha (144 degrees)
3366 PRO   (   2-)  R  -114.2 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

5889  MG   (1055-)  2     MG    <->  6369  MG   (1486-)  2     MG    1.49    1.71  INTRA BL
4632  MG   (1792-)  A     MG    <->  4634  MG   (1793-)  A     MG    1.47    1.73  INTRA BL
6100  MG   (1164-)  2     MG    <->  6102  MG   (1165-)  2     MG    1.41    1.79  INTRA BL
6166  MG   (1197-)  2     MG    <->  6168  MG   (1198-)  2     MG    1.40    1.80  INTRA BL
6255  MG   (1317-)  C     MG    <->  6713  MG   (2057-)  C     MG    1.39    1.81  INTRA BL
6063  MG   (1145-)  2     MG    <->  6065  MG   (1146-)  2     MG    1.35    1.85  INTRA BF
4229  MG   (  24-)  2     MG    <->  6517  MG   (1728-)  2     MG    1.34    1.86  INTRA BL
5833  MG   (1026-)  2     MG    <->  5835  MG   (1027-)  2     MG    1.34    1.86  INTRA BL
4222  MG   (  20-)  2     MG    <->  6584  MG   (1825-)  2     MG    1.33    1.87  INTRA BL
6158  MG   (1193-)  2     MG    <->  6160  MG   (1194-)  2     MG    1.32    1.88  INTRA BF
4229  MG   (  24-)  2     MG    <->  6656  MG   (1952-)  2     MG    1.32    1.88  INTRA BL
6062  MG   ( 980-)  D     MG    <->  6066  MG   ( 982-)  D     MG    1.32    1.88  INTRA BL
4650  MG   (1801-)  A     MG    <->  4652  MG   (1802-)  A     MG    1.31    1.89  INTRA BF
4718  MG   (1846-)  A     MG    <->  5013  MG   (2037-)  A     MG    1.27    1.93  INTRA BL
6015  MG   (  79-)  D     MG    <->  6121  MG   (1986-)  D     MG    1.27    1.93  INTRA BL
6066  MG   ( 982-)  D     MG    <->  6068  MG   ( 983-)  D     MG    1.27    1.93  INTRA BL
6277  MG   (1341-)  2     MG    <->  6278  MG   (1342-)  2     MG    1.25    1.75  INTRA BL
4348  MG   (  92-)  2     MG    <->  6392  MG   (1531-)  2     MG    1.24    1.96  INTRA BL
4237  MG   (  29-)  2     MG    <->  7191  MG   (2865-)  2     MG    1.24    1.96  INTRA BL
4569  MG   ( 227-)  A     MG    <->  4830  MG   (1918-)  A     MG    1.24    1.96  INTRA BF
5782  MG   (  77-)  C     MG    <->  5916  MG   (1665-)  C     MG    1.24    1.96  INTRA BL
4293  MG   (1598-)  A     MG    <->  5433  MG   (3064-)  A     MG    1.23    1.97  INTRA BL
4363  MG   ( 101-)  2     MG    <->  6488  MG   (1687-)  2     MG    1.23    1.97  INTRA BL
4235  MG   (  28-)  2     MG    <->  6774  MG   (2164-)  2     MG    1.23    1.97  INTRA BL
4237  MG   (  29-)  2     MG    <->  7010  MG   (2562-)  2     MG    1.23    1.97  INTRA BL
And so on for a total of 5088 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: 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

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.

3304 ARG   ( 125-)  P      -8.92
3711 ARG   (   3-)  V      -8.90
2005 ARG   (  49-)  G      -8.17
3283 ARG   ( 104-)  P      -7.98
1830 ARG   (  79-)  F      -7.88
3639 ARG   (  18-)  U      -7.80
2641 ARG   (  69-)  K      -7.74
2422 ARG   (   6-)  J      -7.73
3452 ARG   (  88-)  R      -7.72
1960 TYR   (   4-)  G      -7.70
2419 ARG   (   3-)  J      -7.61
3788 TYR   (  80-)  V      -7.60
3919 ARG   (  24-)  X      -7.52
2834 TYR   ( 125-)  L      -7.50
3316 ARG   (  12-)  Q      -7.40
3278 ARG   (  99-)  P      -7.35
2640 ARG   (  68-)  K      -7.31
2775 ARG   (  66-)  L      -7.25
2287 ARG   ( 126-)  H      -7.21
3769 TYR   (  61-)  V      -7.18
3786 ARG   (  78-)  V      -7.18
1959 ARG   (   3-)  G      -7.16
1548 ARG   (  36-)  E      -7.15
2495 ARG   (  79-)  J      -7.15
2448 ARG   (  32-)  J      -7.10
And so on for a total of 183 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.

1533 ARG   (  21-)  E      1536 - TRP     24- ( E)         -5.19
1668 LYS   ( 156-)  E      1670 - LEU    158- ( E)         -6.00
1753 GLY   (   2-)  F      1756 - ILE      5- ( F)         -5.05
1959 ARG   (   3-)  G      1961 - ILE      5- ( G)         -6.93
2040 LYS   (  84-)  G      2042 - LYS     86- ( G)         -5.22
2180 MET   (  19-)  H      2183 - GLY     22- ( H)         -4.91
2419 ARG   (   3-)  J      2422 - ARG      6- ( J)         -6.85
2426 ARG   (  10-)  J      2429 - GLN     13- ( J)         -5.26
2569 HIS   ( 153-)  J      2572 - TRP    156- ( J)         -4.83
2640 ARG   (  68-)  K      2642 - GLN     70- ( K)         -6.76
2676 ARG   ( 104-)  K      2678 - GLY    106- ( K)         -4.91
2718 ARG   (   9-)  L      2720 - LYS     11- ( L)         -4.60
2821 LYS   ( 112-)  L      2823 - TYR    114- ( L)         -5.05
2889 PHE   (  54-)  M      2892 - LYS     57- ( M)         -5.58
3051 PHE   ( 125-)  N      3053 - LYS    127- ( N)         -4.42
3069 VAL   (  18-)  O      3072 - LYS     21- ( O)         -5.45
3124 GLU   (  73-)  O      3126 - HIS     75- ( O)         -4.82
3164 ARG   ( 113-)  O      3166 - LYS    115- ( O)         -4.20
3177 LYS   ( 126-)  O      3180 - ALA    129- ( O)         -4.88
3295 THR   ( 116-)  P      3304 - ARG    125- ( P)         -5.52
3377 GLN   (  13-)  R      3379 - PHE     15- ( R)         -4.20
3478 ARG   (  25-)  S      3481 - ARG     28- ( S)         -5.53
3534 ARG   (  81-)  S      3537 - ALA     84- ( S)         -5.64
3710 PRO   (   2-)  V      3715 - LYS      7- ( V)         -5.70
3736 LYS   (  28-)  V      3738 - LEU     30- ( V)         -5.69
3894 LEU   ( 104-)  W      3896 - ALA    106- ( W)         -4.31

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 - 4179 : -1.741

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

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.

1998 GLN   (  42-)  G   -3.41
2890 LYS   (  55-)  M   -3.33
2952 ASN   (  26-)  N   -3.27
2833 GLN   ( 124-)  L   -3.26
2837 ARG   ( 128-)  L   -3.21
1754 ASN   (   3-)  F   -3.18
3286 ALA   ( 107-)  P   -3.15
3335 ARG   (  31-)  Q   -3.12
3283 ARG   ( 104-)  P   -3.11
3788 TYR   (  80-)  V   -3.11
3303 PRO   ( 124-)  P   -3.03
2889 PHE   (  54-)  M   -2.98
3762 GLY   (  54-)  V   -2.94
1913 GLN   ( 162-)  F   -2.91
3142 LYS   (  91-)  O   -2.90
3325 TYR   (  21-)  Q   -2.85
3786 ARG   (  78-)  V   -2.84
3864 LYS   (  74-)  W   -2.82
3082 PRO   (  31-)  O   -2.82
2573 MET   (   1-)  K   -2.82
2813 ARG   ( 104-)  L   -2.80
2822 LYS   ( 113-)  L   -2.80
1959 ARG   (   3-)  G   -2.78
2419 ARG   (   3-)  J   -2.77
3495 ARG   (  42-)  S   -2.77
2165 ARG   ( 209-)  G   -2.73
2720 LYS   (  11-)  L   -2.72
2834 TYR   ( 125-)  L   -2.71
1992 ARG   (  36-)  G   -2.71
3279 GLY   ( 100-)  P   -2.68
2821 LYS   ( 112-)  L   -2.66
3302 ALA   ( 123-)  P   -2.66
3042 HIS   ( 116-)  N   -2.66
3044 GLY   ( 118-)  N   -2.66
3599 ARG   (  63-)  T   -2.63
2818 VAL   ( 109-)  L   -2.63
3140 ARG   (  89-)  O   -2.60
3753 VAL   (  45-)  V   -2.59
2426 ARG   (  10-)  J   -2.58
2891 HIS   (  56-)  M   -2.58
1927 HIS   ( 176-)  F   -2.55
3322 VAL   (  18-)  Q   -2.54
2423 ALA   (   7-)  J   -2.52
3363 ALA   (  59-)  Q   -2.52
2366 TYR   (  50-)  I   -2.51

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.

1752 GLN   ( 240-)  E     - 1756 ILE   (   5-)  F        -2.11
1996 PRO   (  40-)  G     - 1999 HIS   (  43-)  G        -2.13
2180 MET   (  19-)  H     - 2183 GLY   (  22-)  H        -1.89
2572 TRP   ( 156-)  J     - 2575 THR   (   3-)  K        -2.11
2819 GLU   ( 110-)  L     - 2823 TYR   ( 114-)  L        -2.02
2887 GLY   (  52-)  M     - 2893 ASP   (  58-)  M        -2.36
3041 PRO   ( 115-)  N     - 3046 ARG   ( 120-)  N        -2.20
3096 PRO   (  45-)  O     - 3102 ALA   (  51-)  O        -1.94
3277 VAL   (  98-)  P     - 3281 ARG   ( 102-)  P        -2.26
3284 THR   ( 105-)  P     - 3287 ARG   ( 108-)  P        -2.29
3300 LYS   ( 121-)  P     - 3305 LYS   ( 126-)  P        -2.29
3463 GLY   (  10-)  S     - 3466 HIS   (  13-)  S        -2.08
3477 ALA   (  24-)  S     - 3483 GLY   (  30-)  S        -1.99
3572 ILE   (  36-)  T     - 3575 SER   (  39-)  T        -1.74
3712 SER   (   4-)  V     - 3715 LYS   (   7-)  V        -1.95
3801 SER   (  11-)  W     - 3804 LYS   (  14-)  W        -1.73

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: 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

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.

1552 HIS   (  40-)  E
1588 GLN   (  76-)  E
1716 ASN   ( 204-)  E
1869 GLN   ( 118-)  F
1874 GLN   ( 123-)  F
1927 HIS   ( 176-)  F
2075 GLN   ( 119-)  G
2502 GLN   (  86-)  J
2525 ASN   ( 109-)  J
2654 HIS   (  82-)  K
2782 GLN   (  73-)  L
2833 GLN   ( 124-)  L
2903 HIS   (  68-)  M
3042 HIS   ( 116-)  N
3060 GLN   (   9-)  O
3100 ASN   (  49-)  O
3271 HIS   (  92-)  P
3280 GLN   ( 101-)  P
3630 ASN   (  94-)  T
3773 ASN   (  65-)  V
3808 GLN   (  18-)  W
3880 GLN   (  90-)  W

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.

  33 OURA  (  37-)  A      N3
  49 OADE  (  53-)  A      N6
  53 OGUA  (  57-)  A      N2
  64 OGUA  (  68-)  A      N2
  66 OGUA  (  73-)  A      N1
  67 OCYT  (  74-)  A      N4
  95 OCYT  ( 106-)  A      N4
  96 OGUA  ( 107-)  A      N1
  99 OCYT  ( 110-)  A      N4
 104 OGUA  ( 115-)  A      N2
 141 OADE  ( 151-)  A      N6
 171 OGUA  ( 181-)  A      N1
 171 OGUA  ( 181-)  A      N2
 185 OURA  ( 189-)  A      N3
 234 OADE  ( 243-)  A      N6
 242 OGUA  ( 251-)  A      N1
 245 OGUA  ( 254-)  A      N2
 251 OGUA  ( 260-)  A      N1
 257 OGUA  ( 266-)  A      N1
 257 OGUA  ( 266-)  A      N2
 259 OCYT  ( 268-)  A      N4
 280 OGUA  ( 289-)  A      N2
 288 OGUA  ( 297-)  A      N1
 309 OGUA  ( 318-)  A      N2
 313 OCYT  ( 322-)  A      N4
And so on for a total of 500 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.

1524 GLU   (  12-)  E      OE1
1562 GLU   (  50-)  E      OE1
1606 ASN   (  94-)  E      OD1
1678 ASP   ( 166-)  E      OD1
1682 GLU   ( 170-)  E      OE1
1701 ASP   ( 189-)  E      OD2
1718 ASP   ( 206-)  E      OD1
1788 GLN   (  37-)  F      OE1
2161 GLU   ( 205-)  G      OE2
2338 GLU   (  22-)  I      OE1
2453 ASN   (  37-)  J      OD1
2576 ASP   (   4-)  K      OD2
2653 HIS   (  81-)  K      NE2
2704 GLU   ( 132-)  K      OE2
2757 GLU   (  48-)  L      OE1
2948 HIS   (  22-)  N      ND1
2953 ASN   (  27-)  N      OD1
3036 ASP   ( 110-)  N      OD1
3211 GLU   (  32-)  P      OE1
3582 ASP   (  46-)  T      OD2
3585 GLU   (  49-)  T      OE1
3657 ASN   (  36-)  U      OD1
3781 GLU   (  73-)  V      OE1
3850 GLU   (  60-)  W      OE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

4191  MG   (   2-)  2   -.-  -.-  Part of ionic cluster
4191  MG   (   2-)  2   -.-  -.-  Too few ligands (0)
4192  MG   (1543-)  A   -.-  -.-  Too few ligands (2)
4193  MG   (   3-)  2   -.-  -.-  Part of ionic cluster
4193  MG   (   3-)  2   -.-  -.-  Too few ligands (0)
4194  MG   (1544-)  A   -.-  -.-  Part of ionic cluster
4194  MG   (1544-)  A   -.-  -.-  Too few ligands (0)
4195  MG   (   4-)  2   -.-  -.-  Part of ionic cluster
4195  MG   (   4-)  2   -.-  -.-  Too few ligands (0)
4196  MG   (1545-)  A   -.-  -.-  Too few ligands (0)
4197  MG   (1546-)  A   -.-  -.-  Part of ionic cluster
4197  MG   (1546-)  A   -.-  -.-  Too few ligands (0)
4198  MG   (   6-)  2   -.-  -.-  Part of ionic cluster
4198  MG   (   6-)  2   -.-  -.-  Too few ligands (0)
4199  MG   (1547-)  A   -.-  -.-  Part of ionic cluster
4199  MG   (1547-)  A   -.-  -.-  Too few ligands (1)
4200  MG   (   7-)  2   -.-  -.-  Too few ligands (0)
4201  MG   (1548-)  A   -.-  -.-  Part of ionic cluster
4201  MG   (1548-)  A   -.-  -.-  Too few ligands (2)
4202  MG   (   8-)  2   -.-  -.-  Part of ionic cluster
4202  MG   (   8-)  2   -.-  -.-  Too few ligands (0)
4203  MG   (1549-)  A   -.-  -.-  Too few ligands (0)
4204  MG   (1550-)  A   -.-  -.-  Part of ionic cluster
4204  MG   (1550-)  A   -.-  -.-  Too few ligands (2)
4205  MG   (  10-)  C   -.-  -.-  Part of ionic cluster
And so on for a total of 4796 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.

1562 GLU   (  50-)  E   H-bonding suggests Gln
1598 GLU   (  86-)  E   H-bonding suggests Gln; but Alt-Rotamer
1682 GLU   ( 170-)  E   H-bonding suggests Gln
1718 ASP   ( 206-)  E   H-bonding suggests Asn
1917 GLU   ( 166-)  F   H-bonding suggests Gln
2058 ASP   ( 102-)  G   H-bonding suggests Asn
2100 ASP   ( 144-)  G   H-bonding suggests Asn
2278 ASP   ( 117-)  H   H-bonding suggests Asn; but Alt-Rotamer
2308 ASP   ( 147-)  H   H-bonding suggests Asn
2461 ASP   (  45-)  J   H-bonding suggests Asn; but Alt-Rotamer
2626 ASP   (  54-)  K   H-bonding suggests Asn
2757 GLU   (  48-)  L   H-bonding suggests Gln
2763 ASP   (  54-)  L   H-bonding suggests Asn
2769 ASP   (  60-)  L   H-bonding suggests Asn; but Alt-Rotamer
2860 GLU   (  25-)  M   H-bonding suggests Gln
2924 ASP   (  89-)  M   H-bonding suggests Asn; but Alt-Rotamer
2960 ASP   (  34-)  N   H-bonding suggests Asn; but Alt-Rotamer
3007 ASP   (  81-)  N   H-bonding suggests Asn; but Alt-Rotamer
3036 ASP   ( 110-)  N   H-bonding suggests Asn; but Alt-Rotamer
3178 GLU   ( 127-)  O   H-bonding suggests Gln
3585 GLU   (  49-)  T   H-bonding suggests Gln
3591 ASP   (  55-)  T   H-bonding suggests Asn
3651 ASP   (  30-)  U   H-bonding suggests Asn; but Alt-Rotamer
3704 GLU   (  83-)  U   H-bonding suggests Gln; but Alt-Rotamer
3854 ASP   (  64-)  W   H-bonding suggests Asn; but Alt-Rotamer
3883 GLU   (  93-)  W   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 :  -3.102
  2nd generation packing quality :  -3.637 (poor)
  Ramachandran plot appearance   :  -6.092 (bad)
  chi-1/chi-2 rotamer normality  :  -4.700 (bad)
  Backbone conformation          :  -0.319

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.506 (tight)
  Bond angles                    :   0.757
  Omega angle restraints         :   0.211 (tight)
  Side chain planarity           :   0.192 (tight)
  Improper dihedral distribution :   0.656
  B-factor distribution          :   0.382
  Inside/Outside distribution    :   1.000

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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.9
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -3.3 (poor)
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.506 (tight)
  Bond angles                    :   0.757
  Omega angle restraints         :   0.211 (tight)
  Side chain planarity           :   0.192 (tight)
  Improper dihedral distribution :   0.656
  B-factor distribution          :   0.382
  Inside/Outside distribution    :   1.000
==============

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.