WHAT IF Check report

This file was created 2012-01-30 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 pdb3i9d.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: 5
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 5 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Error: Matthews Coefficient (Vm) very high

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

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

Molecular weight of all polymer chains: 873804.313
Volume of the Unit Cell V= 59583348.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 17.047
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.

4219  MG   ( 107-)  A  W
4340  MG   ( 177-)  C  2
4601  MG   ( 438-)  A  2
4645  MG   (1679-)  X  A
4900  MG   ( 737-)  C  2
5220  MG   (1870-)  X  A
5450  MG   (1287-)  A  T
5557  MG   (1394-)  V  2
5581  MG   (1975-)  D  A
5600  MG   (1437-)  C  2

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

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

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

4092 OURA  (  80-)  C  -   O3' 4093 OGUA  (  94-)  V  -   P
4093 OGUA  (  94-)  V  -   O3' 4094 OGUA  (1543-)  A  -   P
4096 OGUA  (1545-)  A  -   O3' 4097 OCYT  (  81-)  C  -   P
4103 OGUA  (  86-)  C  -   O3' 4104 OGUA  (  95-)  V  -   P
4107 OGUA  (  98-)  V  -   O3' 4108 OCYT  (  87-)  C  -   P
4108 OCYT  (  87-)  C  -   O3' 4109 OURA  ( 127-)  P  -   P
4109 OURA  ( 127-)  P  -   O3' 4110 OCYT  (1546-)  A  -   P
4112 OURA  (1548-)  A  -   O3' 4113 OCYT  ( 136-)  O  -   P
4113 OCYT  ( 136-)  O  -   O3' 4114 OGUA  (1549-)  A  -   P
4114 OGUA  (1549-)  A  -   O3' 4115 OGUA  ( 128-)  P  -   P
4115 OGUA  ( 128-)  P  -   O3' 4116 OGUA  (1550-)  A  -   P
4119 OCYT  (1553-)  A  -   O3' 4120 OADE  (  35-)  1  -   P
4122 OADE  (  37-)  1  -   O3' 4123 OADE  (1554-)  A  -   P
4123 OADE  (1554-)  A  -   O3' 4124 OCYT  ( 129-)  P  -   P
4126 OCYT  ( 131-)  P  -   O3' 4127 OGUA  (1555-)  A  -   P
4130 OGUA  (1558-)  A  -   O3' 4131 OGUA  (  99-)  V  -   P
4131 OGUA  (  99-)  V  -   O3' 4132 OURA  (  47-)  B  -   P
4133 OCYT  (  48-)  B  -   O3' 4134 OGUA  (  88-)  C  -   P
4135 OURA  (  89-)  C  -   O3' 4136 OCYT  (  51-)  B  -   P
4137 OGUA  (  52-)  B  -   O3' 4138 OGUA  (  90-)  C  -   P
4138 OGUA  (  90-)  C  -   O3' 4139 OURA  (  54-)  B  -   P
4141 OCYT  (  56-)  B  -   O3' 4142 OADE  (  91-)  C  -   P

Warning: Strange inter-chain connections could NOT be corrected

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

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: 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.

   1 OURA  (   5-)  A    High
   2 OGUA  (   6-)  A    High
   3 OGUA  (   7-)  A    High
   4 OADE  (   8-)  A    High
   5 OGUA  (   9-)  A    High
  10 OURA  (  14-)  A    High
  22 OADE  (  26-)  A    High
  33 OURA  (  37-)  A    High
  34 OGUA  (  38-)  A    High
  35 OGUA  (  39-)  A    High
  36 OCYT  (  40-)  A    High
  37 OGUA  (  41-)  A    High
  38 OGUA  (  42-)  A    High
  39 OCYT  (  43-)  A    High
  40 OGUA  (  44-)  A    High
  41 OURA  (  45-)  A    High
  42 OGUA  (  46-)  A    High
  44 OCYT  (  48-)  A    High
  45 OURA  (  49-)  A    High
  46 OADE  (  50-)  A    High
  47 OADE  (  51-)  A    High
  51 OADE  (  55-)  A    High
  52 OURA  (  56-)  A    High
  53 OGUA  (  57-)  A    High
  54 OCYT  (  58-)  A    High
And so on for a total of 3338 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
3633 ARG   ( 101-)  T
3869 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
2379 TYR   (  63-)  I
2460 TYR   (  44-)  J
2501 TYR   (  85-)  J
2570 TYR   ( 154-)  J
2620 TYR   (  48-)  K
2714 TYR   (   5-)  L
2797 TYR   (  88-)  L
2801 TYR   (  92-)  L
2823 TYR   ( 114-)  L
2834 TYR   ( 125-)  L
2946 TYR   (  20-)  N
2976 TYR   (  50-)  N
3156 TYR   ( 105-)  O
3200 TYR   (  21-)  P
3649 TYR   (  34-)  U

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
2035 PHE   (  79-)  G
2049 PHE   (  93-)  G
2167 PHE   (   6-)  H
2413 PHE   (  97-)  I
2727 PHE   (  18-)  L
2746 PHE   (  37-)  L
2810 PHE   ( 101-)  L
2846 PHE   (  11-)  M
3458 PHE   (   9-)  S
3559 PHE   (  27-)  T
3644 PHE   (  29-)  U
3712 PHE   (  10-)  V
3776 PHE   (  74-)  V

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
1787 ASP   (  36-)  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
2645 ASP   (  73-)  K
2814 ASP   ( 105-)  L
2847 ASP   (  12-)  M
2852 ASP   (  17-)  M
2962 ASP   (  36-)  N
3195 ASP   (  16-)  P
3381 ASP   (  21-)  R
3478 ASP   (  29-)  S
3489 ASP   (  40-)  S
3648 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
3178 GLU   ( 127-)  O
3211 GLU   (  32-)  P
3367 GLU   (   7-)  R
3401 GLU   (  41-)  R
3483 GLU   (  34-)  S
3532 GLU   (  83-)  S
3593 GLU   (  61-)  T
3610 GLU   (  78-)  T
3643 GLU   (  28-)  U
3719 GLU   (  17-)  V
3723 GLU   (  21-)  V
3729 GLU   (  27-)  V
3745 GLU   (  43-)  V
3826 GLU   (  46-)  W
3840 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.

4111 OGUA  (1547-)  A
4128 OADE  (1556-)  A

Error: Chain names not unique

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

Chain identifier(s): C, V, A, P, O, 1, B

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.

  67 OCYT  (  74-)  A      C4   N4    1.30   -4.0
  88 OURA  (  97-)  A      N1   C2    1.43    5.4
 656 OURA  ( 677-)  A      N1   C2    1.43    5.0
 767 OURA  ( 788-)  A      N3   C2    1.40    4.2
 767 OURA  ( 788-)  A      C4   N3    1.44    6.8
 771 OADE  ( 792-)  A      P    O5'   1.54   -5.6
 771 OADE  ( 792-)  A      O5'  C5'   1.34   -6.3
 771 OADE  ( 792-)  A      N7   C5    1.33   -9.4
 771 OADE  ( 792-)  A      N3   C4    1.30   -7.6
 771 OADE  ( 792-)  A      C5   C6    1.36   -5.4
 773 OADE  ( 794-)  A      C2   N3    1.38    5.0
1154 OGUA  (1177-)  A      C5   C6    1.47    4.7
3929 OCYT  (  17-)  C      C4   N3    1.38    6.6
3929 OCYT  (  17-)  C      C4   N4    1.23  -11.4
4006 OCYT  (  17-)  D      C4   N3    1.38    6.8
4006 OCYT  (  17-)  D      C4   N4    1.23  -11.6
4102 OCYT  (  77-)  C      C4   N3    1.38    6.5
4102 OCYT  (  77-)  C      C4   N4    1.23  -11.5

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  113.31    4.4
   4 OADE  (   8-)  A      C2'  C1'  N9  121.61    5.1
   7 OGUA  (  11-)  A      N9   C8   N7  113.23    4.3
   9 OURA  (  13-)  A      C2'  C1'  N1  121.70    5.2
  11 OGUA  (  15-)  A      N9   C8   N7  113.18    4.2
  17 OGUA  (  21-)  A      N9   C8   N7  113.12    4.0
  23 OGUA  (  27-)  A      N9   C8   N7  113.40    4.6
  31 OGUA  (  35-)  A      N9   C8   N7  113.16    4.1
  34 OGUA  (  38-)  A      N9   C8   N7  113.24    4.3
  40 OGUA  (  44-)  A      N9   C8   N7  113.11    4.0
  43 OCYT  (  47-)  A      O4'  C1'  N1  113.30    5.1
  43 OCYT  (  47-)  A      C2'  C1'  N1  121.38    5.0
  44 OCYT  (  48-)  A      C2'  C1'  N1  120.96    4.7
  46 OADE  (  50-)  A      C2'  C1'  N9  121.31    4.9
  47 OADE  (  51-)  A      O4'  C1'  N9  112.28    4.1
  48 OGUA  (  52-)  A      N9   C8   N7  113.30    4.4
  57 OGUA  (  61-)  A      N9   C8   N7  113.11    4.0
  62 OGUA  (  66-)  A      N9   C8   N7  113.20    4.2
  65 OGUA  (  69-)  A      N9   C8   N7  113.17    4.1
  66 OGUA  (  73-)  A      C2'  C1'  N9  120.52    4.5
  66 OGUA  (  73-)  A      N9   C8   N7  113.51    4.8
  69 OGUA  (  76-)  A      N9   C8   N7  113.27    4.3
  71 OGUA  (  78-)  A      N9   C8   N7  113.10    4.0
  72 OGUA  (  79-)  A      N9   C8   N7  113.12    4.0
  73 OGUA  (  80-)  A      N9   C8   N7  113.36    4.5
And so on for a total of 473 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
1770 GLU   (  19-)  F
1787 ASP   (  36-)  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
2119 GLU   ( 163-)  G
2148 GLU   ( 192-)  G
And so on for a total of 79 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    -25.3   -85.53    -2.48
The average deviation= 0.739

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    8.59
3343 CYS   (  43-)  Q    6.69
3170 LYS   ( 119-)  O    6.17
3708 LYS   (   6-)  V    6.03
3438 TYR   (  78-)  R    5.83
2795 VAL   (  86-)  L    5.44
3369 GLN   (   9-)  R    5.33
3766 GLU   (  64-)  V    5.32
1987 CYS   (  31-)  G    5.28
3452 LYS   (   3-)  S    5.19
2376 PHE   (  60-)  I    4.89
3830 GLU   (  50-)  W    4.86
3781 THR   (  79-)  V    4.76
3414 ARG   (  54-)  R    4.72
3109 VAL   (  58-)  O    4.60
2796 GLN   (  87-)  L    4.59
1568 ARG   (  56-)  E    4.50
3857 ALA   (  77-)  W    4.49
3592 ILE   (  60-)  T    4.47
3307 ILE   (   7-)  Q    4.47
1598 GLU   (  86-)  E    4.43
2772 ILE   (  63-)  L    4.43
2322 VAL   (   6-)  I    4.38
3747 VAL   (  45-)  V    4.28
3589 VAL   (  57-)  T    4.26
1620 ILE   ( 108-)  E    4.25
3725 ASN   (  23-)  V    4.19
2584 ARG   (  12-)  K    4.18
2172 ILE   (  11-)  H    4.18
3008 VAL   (  82-)  N    4.11
3794 LYS   (  14-)  W    4.09
2029 ARG   (  73-)  G    4.09
2461 ASP   (  45-)  J    4.09
2260 GLY   (  99-)  H    4.08
2402 ARG   (  86-)  I    4.05
3254 ALA   (  75-)  P    4.03
2193 VAL   (  32-)  H    4.02
3212 ALA   (  33-)  P    4.02
1969 ARG   (  13-)  G    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 : 1.555

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    0.16
 554 OGUA  ( 575-)  A    0.14
 Ramachandran Z-score : -6.583

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 : -6.583

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.

3493 THR   (  44-)  S    -3.1
1985 PRO   (  29-)  G    -3.0
1963 PRO   (   7-)  G    -3.0
1518 THR   (   6-)  E    -3.0
1538 PRO   (  26-)  E    -2.9
3099 PRO   (  48-)  O    -2.9
2412 PRO   (  96-)  I    -2.9
1763 LEU   (  12-)  F    -2.9
1818 THR   (  67-)  F    -2.8
3249 LEU   (  70-)  P    -2.8
3765 THR   (  63-)  V    -2.8
1667 LEU   ( 155-)  E    -2.8
2639 PRO   (  67-)  K    -2.8
3712 PHE   (  10-)  V    -2.8
2520 LEU   ( 104-)  J    -2.8
3670 ARG   (  55-)  U    -2.8
1637 PRO   ( 125-)  E    -2.8
1579 THR   (  67-)  E    -2.8
3743 VAL   (  41-)  V    -2.7
2701 VAL   ( 129-)  K    -2.7
3192 LYS   (  13-)  P    -2.7
2889 PHE   (  54-)  M    -2.7
2006 ARG   (  50-)  G    -2.7
2098 PRO   ( 142-)  G    -2.7
1527 VAL   (  15-)  E    -2.7
And so on for a total of 193 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
1530 GLY   (  18-)  E  Poor phi/psi
1534 LYS   (  22-)  E  Poor phi/psi
1536 TRP   (  24-)  E  Poor phi/psi
1537 ASN   (  25-)  E  Poor phi/psi
1538 PRO   (  26-)  E  Poor phi/psi
1548 ARG   (  36-)  E  Poor phi/psi
1549 ASN   (  37-)  E  Poor phi/psi
1550 GLY   (  38-)  E  Poor phi/psi
1574 ALA   (  62-)  E  Poor phi/psi
1577 GLY   (  65-)  E  Poor phi/psi
1595 MET   (  83-)  E  Poor phi/psi
1596 GLU   (  84-)  E  Poor phi/psi
1599 ARG   (  87-)  E  Poor phi/psi
1600 ALA   (  88-)  E  Poor phi/psi
1634 PHE   ( 122-)  E  Poor phi/psi
1636 SER   ( 124-)  E  Poor phi/psi
1638 GLU   ( 126-)  E  Poor phi/psi
1667 LEU   ( 155-)  E  Poor phi/psi
1668 LYS   ( 156-)  E  Poor phi/psi
1671 PRO   ( 159-)  E  Poor phi/psi
1673 ALA   ( 161-)  E  Poor phi/psi
1687 ARG   ( 175-)  E  Poor phi/psi
1689 ALA   ( 177-)  E  Poor phi/psi
1693 PHE   ( 181-)  E  Poor phi/psi
And so on for a total of 321 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 : -5.235

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.

3035 VAL   ( 109-)  N    0.38
3402 HIS   (  42-)  R    0.38
3678 GLN   (  63-)  U    0.38
3862 SER   (  82-)  W    0.39

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 2785 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 : 1.045

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   3.31   41
1829 GLY   (  78-)  F   3.06   10
3279 GLY   ( 100-)  P   2.83   22
3139 GLY   (  88-)  O   2.62   11
1896 GLY   ( 145-)  F   2.53   39
3565 GLY   (  33-)  T   2.41   80
2739 GLY   (  30-)  L   2.25   44
2700 GLY   ( 128-)  K   2.05   21
3172 GLY   ( 121-)  O   2.01   32
2702 GLY   ( 130-)  K   1.89   47
1577 GLY   (  65-)  E   1.77   80
2196 GLY   (  35-)  H   1.67   15
3672 GLY   (  57-)  U   1.63   23
1899 GLY   ( 148-)  F   1.61   10
2128 PRO   ( 172-)  G   1.60   10
2123 GLY   ( 167-)  G   1.59   45
2861 ALA   (  26-)  M   1.56   31
1778 LYS   (  27-)  F   1.55   10

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...

3853 HIS   (  73-)  W   1.86

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].

1538 PRO   (  26-)  E  -132.0 half-chair C-delta/C-gamma (-126 degrees)
1963 PRO   (   7-)  G   102.6 envelop C-beta (108 degrees)
2474 PRO   (  58-)  J  -113.1 envelop C-gamma (-108 degrees)
2509 PRO   (  93-)  J  -114.1 envelop C-gamma (-108 degrees)
3099 PRO   (  48-)  O    -6.0 envelop N (0 degrees)
3314 PRO   (  14-)  Q   114.3 envelop C-beta (108 degrees)
3495 PRO   (  46-)  S  -115.0 envelop C-gamma (-108 degrees)
3695 PRO   (  80-)  U    52.4 half-chair C-delta/C-gamma (54 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.

4202  MG   (  39-)  2     MG    <->  5551  MG   (1388-)  2     MG    1.66    1.54  INTRA BL
4185  MG   (  22-)  2     MG    <->  5156  MG   ( 993-)  2     MG    1.33    1.87  INTRA BL
 791 OCYT  ( 812-)  A      C3'  <->  4951  MG   (1782-)  A     MG    1.22    1.98  INTRA BL
 306 OADE  ( 315-)  A      C3'  <->  4548  MG   (1646-)  A     MG    1.20    2.00  INTRA BL
1279 OURA  (1302-)  A      C3'  <->  5087  MG   (1833-)  A     MG    1.10    2.10  INTRA BF
3997 OGUA  (   9-)  D      C2'  <->  5231  MG   (1068-)  D     MG    1.08    2.12  INTRA BF
3792 ALA   (  12-)  W      CA   <->  5316  MG   (1153-)  W     MG    1.02    2.18  INTRA BL
4303  MG   ( 140-)  2     MG    <->  5461  MG   (1298-)  2     MG    0.95    2.25  INTRA BL
3997 OGUA  (   9-)  D      C3'  <->  5231  MG   (1068-)  D     MG    0.93    2.27  INTRA BF
 567 OGUA  ( 588-)  A      C5'  <->  4595  MG   (1661-)  A     MG    0.93    2.27  INTRA BL
 947 OADE  ( 974-)  A      C3'  <->  5211  MG   (1866-)  A     MG    0.92    2.28  INTRA BF
 306 OADE  ( 315-)  A      C2'  <->  4548  MG   (1646-)  A     MG    0.92    2.28  INTRA BL
1122 OGUA  (1144-)  A      C8   <->  5037  MG   (1811-)  A     MG    0.89    2.31  INTRA BF
3873 GLU   (  93-)  W      CB   <->  4959  MG   ( 796-)  W     MG    0.87    2.33  INTRA BF
4288  MG   ( 125-)  2     MG    <->  4727  MG   ( 564-)  2     MG    0.87    2.33  INTRA BL
4344  MG   ( 181-)  C     MG    <->  5153  MG   ( 990-)  C     MG    0.86    2.34  INTRA BL
4446  MG   ( 283-)  2     MG    <->  5004  MG   ( 841-)  2     MG    0.86    2.34  INTRA BL
3340 CYS   (  40-)  Q      CB   <->  3343 CYS   (  43-)  Q      SG   0.85    2.55  INTRA BL
 333 OCYT  ( 342-)  A      C6   <->  5043  MG   (1813-)  A     MG    0.85    2.35  INTRA BF
 771 OADE  ( 792-)  A      C2'  <->   773 OADE  ( 794-)  A      N6   0.81    2.29  INTRA BL
 791 OCYT  ( 812-)  A      C2'  <->  4951  MG   (1782-)  A     MG    0.81    2.39  INTRA BL
3891 ARG   (   6-)  X      CB   <->  5107  MG   ( 944-)  X     MG    0.81    2.39  INTRA BL
4296  MG   (1578-)  A     MG    <->  5593  MG   (1981-)  A     MG    0.80    2.40  INTRA BL
  80 OCYT  (  88-)  A      C5   <->  4847  MG   (1743-)  A     MG    0.78    2.42  INTRA BF
1233 OADE  (1256-)  A      C3'  <->  5504  MG   (1954-)  A     MG    0.78    2.42  INTRA BF
And so on for a total of 3964 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.

3780 ARG   (  78-)  V      -8.43
1830 ARG   (  79-)  F      -8.20
3705 ARG   (   3-)  V      -7.93
3782 TYR   (  80-)  V      -7.92
2005 ARG   (  49-)  G      -7.89
3448 ARG   (  88-)  R      -7.88
3477 ARG   (  28-)  S      -7.87
3046 ARG   ( 120-)  N      -7.79
1960 TYR   (   4-)  G      -7.71
2006 ARG   (  50-)  G      -7.68
2886 ARG   (  51-)  M      -7.65
3278 ARG   (  99-)  P      -7.53
3909 ARG   (  24-)  X      -7.53
1959 ARG   (   3-)  G      -7.48
2530 ARG   ( 114-)  J      -7.40
2420 ARG   (   4-)  J      -7.37
3783 ARG   (  81-)  V      -7.33
3283 ARG   ( 104-)  P      -7.29
1994 TYR   (  38-)  G      -7.23
2421 ARG   (   5-)  J      -7.20
1923 ARG   ( 172-)  F      -7.20
1998 GLN   (  42-)  G      -7.19
2951 TYR   (  25-)  N      -7.18
3731 ARG   (  29-)  V      -7.17
2422 ARG   (   6-)  J      -7.13
And so on for a total of 194 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)         -5.32
1668 LYS   ( 156-)  E      1670 - LEU    158- ( E)         -5.61
1742 VAL   ( 230-)  E      1744 - PRO    232- ( E)         -4.42
1753 GLY   (   2-)  F      1756 - ILE      5- ( F)         -5.43
1959 ARG   (   3-)  G      1961 - ILE      5- ( G)         -7.05
2040 LYS   (  84-)  G      2042 - LYS     86- ( G)         -5.38
2142 LEU   ( 186-)  G      2144 - LEU    188- ( G)         -4.91
2179 ARG   (  18-)  H      2182 - ALA     21- ( H)         -5.11
2419 ARG   (   3-)  J      2422 - ARG      6- ( J)         -7.07
2426 ARG   (  10-)  J      2429 - GLN     13- ( J)         -5.84
2432 LEU   (  16-)  J      2434 - TYR     18- ( J)         -4.35
2569 HIS   ( 153-)  J      2571 - ARG    155- ( J)         -4.93
2640 ARG   (  68-)  K      2642 - GLN     70- ( K)         -6.37
2718 ARG   (   9-)  L      2721 - GLU     12- ( L)         -5.19
3051 PHE   ( 125-)  N      3054 - ALA    128- ( N)         -4.81
3069 VAL   (  18-)  O      3071 - LYS     20- ( O)         -5.23
3124 GLU   (  73-)  O      3126 - HIS     75- ( O)         -4.81
3164 ARG   ( 113-)  O      3166 - LYS    115- ( O)         -4.56
3190 ARG   (  11-)  P      3192 - LYS     13- ( P)         -5.29
3277 VAL   (  98-)  P      3281 - ARG    102- ( P)         -5.20
3293 ARG   ( 114-)  P      3296 - VAL    117- ( P)         -4.74
3447 ILE   (  87-)  R      3449 - GLY     89- ( R)         -5.64
3461 LYS   (  12-)  S      3463 - ASN     14- ( S)         -5.28
3474 ARG   (  25-)  S      3477 - ARG     28- ( S)         -6.17
3530 ARG   (  81-)  S      3533 - ALA     84- ( S)         -5.27
3707 LEU   (   5-)  V      3709 - LYS      7- ( V)         -5.94
3729 GLU   (  27-)  V      3732 - LEU     30- ( V)         -5.89
3780 ARG   (  78-)  V      3783 - ARG     81- ( V)         -6.94
3884 LEU   ( 104-)  W      3886 - ALA    106- ( W)         -4.72

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 - 4153 : -1.956

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.

2833 GLN   ( 124-)  L   -3.44
3286 ALA   ( 107-)  P   -3.42
2890 LYS   (  55-)  M   -3.36
3474 ARG   (  25-)  S   -3.36
2952 ASN   (  26-)  N   -3.35
1754 ASN   (   3-)  F   -3.27
3780 ARG   (  78-)  V   -3.27
3300 LYS   ( 121-)  P   -3.22
3782 TYR   (  80-)  V   -3.18
3331 ARG   (  31-)  Q   -3.14
3283 ARG   ( 104-)  P   -3.08
2423 ALA   (   7-)  J   -3.06
1913 GLN   ( 162-)  F   -3.04
2889 PHE   (  54-)  M   -3.04
3756 GLY   (  54-)  V   -2.96
3462 HIS   (  13-)  S   -2.96
2720 LYS   (  11-)  L   -2.90
3321 TYR   (  21-)  Q   -2.90
2573 MET   (   1-)  K   -2.87
2419 ARG   (   3-)  J   -2.84
2574 LEU   (   2-)  K   -2.83
3285 ASN   ( 106-)  P   -2.82
3044 GLY   ( 118-)  N   -2.81
3042 HIS   ( 116-)  N   -2.81
2822 LYS   ( 113-)  L   -2.81
1959 ARG   (   3-)  G   -2.79
3281 ARG   ( 102-)  P   -2.79
2821 LYS   ( 112-)  L   -2.78
3705 ARG   (   3-)  V   -2.77
3082 PRO   (  31-)  O   -2.75
3142 LYS   (  91-)  O   -2.72
2813 ARG   ( 104-)  L   -2.71
1992 ARG   (  36-)  G   -2.68
3318 VAL   (  18-)  Q   -2.65
3461 LYS   (  12-)  S   -2.64
1998 GLN   (  42-)  G   -2.63
3595 ARG   (  63-)  T   -2.62
1962 GLY   (   6-)  G   -2.61
3013 THR   (  87-)  N   -2.60
2827 LYS   ( 118-)  L   -2.58
1927 HIS   ( 176-)  F   -2.57
2152 LEU   ( 196-)  G   -2.57
2818 VAL   ( 109-)  L   -2.57
2817 VAL   ( 108-)  L   -2.56
2247 ALA   (  86-)  H   -2.56
2891 HIS   (  56-)  M   -2.52
2091 LEU   ( 135-)  G   -2.51
2005 ARG   (  49-)  G   -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     - 1755 LYS   (   4-)  F        -2.05
1958 GLY   (   2-)  G     - 1962 GLY   (   6-)  G        -2.19
1996 PRO   (  40-)  G     - 1999 HIS   (  43-)  G        -1.98
2417 ALA   ( 101-)  I     - 2420 ARG   (   4-)  J        -1.65
2447 MET   (  31-)  J     - 2452 LYS   (  36-)  J        -1.88
2572 TRP   ( 156-)  J     - 2575 THR   (   3-)  K        -2.23
2819 GLU   ( 110-)  L     - 2823 TYR   ( 114-)  L        -2.15
2882 PHE   (  47-)  M     - 2885 ILE   (  50-)  M        -1.60
2888 PRO   (  53-)  M     - 2892 LYS   (  57-)  M        -2.57
3041 PRO   ( 115-)  N     - 3046 ARG   ( 120-)  N        -2.18
3047 PRO   ( 121-)  N     - 3050 LYS   ( 124-)  N        -1.80
3067 GLU   (  16-)  O     - 3070 ARG   (  19-)  O        -2.00
3096 PRO   (  45-)  O     - 3102 ALA   (  51-)  O        -1.97
3276 PRO   (  97-)  P     - 3281 ARG   ( 102-)  P        -1.86
3282 THR   ( 103-)  P     - 3287 ARG   ( 108-)  P        -2.39
3317 LYS   (  17-)  Q     - 3321 TYR   (  21-)  Q        -2.18
3473 ALA   (  24-)  S     - 3477 ARG   (  28-)  S        -2.42
3545 ASP   (  13-)  T     - 3548 GLN   (  16-)  T        -1.94
3704 PRO   (   2-)  V     - 3710 GLY   (   8-)  V        -1.96
3851 THR   (  71-)  W     - 3854 LYS   (  74-)  W        -1.79
3882 GLY   ( 102-)  W     - 3885 SER   ( 105-)  W        -1.94

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.

1590 GLN   (  78-)  E
1606 ASN   (  94-)  E
1607 GLN   (  95-)  E
1716 ASN   ( 204-)  E
1932 ASN   ( 181-)  F
2033 ASN   (  77-)  G
2343 GLN   (  27-)  I
2380 GLN   (  64-)  I
2416 ASN   ( 100-)  I
2453 ASN   (  37-)  J
2467 GLN   (  51-)  J
2782 GLN   (  73-)  L
2833 GLN   ( 124-)  L
2952 ASN   (  26-)  N
2964 ASN   (  38-)  N
3019 GLN   (  93-)  N
3042 HIS   ( 116-)  N
3060 GLN   (   9-)  O
3241 ASN   (  62-)  P
3271 HIS   (  92-)  P
3280 GLN   ( 101-)  P
3352 GLN   (  52-)  Q
3548 GLN   (  16-)  T

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
  60 OGUA  (  64-)  A      N2
  64 OGUA  (  68-)  A      N2
  67 OCYT  (  74-)  A      N4
  96 OGUA  ( 107-)  A      N1
  97 OGUA  ( 108-)  A      N1
  99 OCYT  ( 110-)  A      N4
 101 OGUA  ( 112-)  A      N2
 104 OGUA  ( 115-)  A      N2
 141 OADE  ( 151-)  A      N6
 142 OADE  ( 152-)  A      N6
 159 OCYT  ( 169-)  A      N4
 170 OURA  ( 180-)  A      N3
 171 OGUA  ( 181-)  A      N1
 171 OGUA  ( 181-)  A      N2
 211 OGUA  ( 220-)  A      N1
 220 OURA  ( 229-)  A      N3
 223 OGUA  ( 232-)  A      N2
 251 OGUA  ( 260-)  A      N1
 257 OGUA  ( 266-)  A      N1
 264 OADE  ( 273-)  A      N6
 281 OCYT  ( 290-)  A      N4
 291 OADE  ( 300-)  A      N6
 309 OGUA  ( 318-)  A      N2
 313 OCYT  ( 322-)  A      N4
And so on for a total of 522 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.

1562 GLU   (  50-)  E      OE1
1596 GLU   (  84-)  E      OE1
1596 GLU   (  84-)  E      OE2
1678 ASP   ( 166-)  E      OD1
1682 GLU   ( 170-)  E      OE1
1701 ASP   ( 189-)  E      OD1
1717 ASP   ( 205-)  E      OD2
1869 GLN   ( 118-)  F      OE1
1998 GLN   (  42-)  G      OE1
2028 GLU   (  72-)  G      OE1
2239 HIS   (  78-)  H      NE2
2431 ASP   (  15-)  J      OD2
2576 ASP   (   4-)  K      OD2
2650 GLN   (  78-)  K      OE1
2757 GLU   (  48-)  L      OE1
2908 ASP   (  73-)  M      OD1
3100 ASN   (  49-)  O      OD1
3211 GLU   (  32-)  P      OE1
3581 GLU   (  49-)  T      OE1
3678 GLN   (  63-)  U      OE1
3759 HIS   (  57-)  V      ND1
3775 GLU   (  73-)  V      OE1
3785 HIS   (  83-)  V      ND1
3840 GLU   (  60-)  W      OE1
3840 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+.

4164  MG   (   1-)  2   -.-  -.-  Too few ligands (0)
4165  MG   (   2-)  2   -.-  -.-  Too few ligands (0)
4166  MG   (   3-)  2   -.-  -.-  Too few ligands (0)
4167  MG   ( 103-)  C   -.-  -.-  Too few ligands (0)
4168  MG   ( 104-)  C   -.-  -.-  Too few ligands (0)
4169  MG   (  77-)  D   -.-  -.-  Too few ligands (0)
4170  MG   (   7-)  2   -.-  -.-  Too few ligands (0)
4171  MG   (   8-)  2   -.-  -.-  Too few ligands (0)
4172  MG   (   9-)  2   -.-  -.-  Too few ligands (0)
4173  MG   ( 105-)  C   -.-  -.-  Too few ligands (0)
4174  MG   (  11-)  2   -.-  -.-  Too few ligands (0)
4175  MG   (  12-)  2   -.-  -.-  Too few ligands (0)
4176  MG   (  13-)  2   -.-  -.-  Too few ligands (0)
4177  MG   (  14-)  2   -.-  -.-  Too few ligands (0)
4178  MG   (  15-)  2   -.-  -.-  Too few ligands (0)
4179  MG   (  16-)  2   -.-  -.-  Too few ligands (0)
4180  MG   (  17-)  2   -.-  -.-  Too few ligands (0)
4181  MG   (  18-)  2   -.-  -.-  Too few ligands (0)
4182  MG   ( 106-)  C   -.-  -.-  Too few ligands (0)
4183  MG   (  20-)  2   -.-  -.-  Too few ligands (0)
4184  MG   (  21-)  2   -.-  -.-  Too few ligands (0)
4185  MG   (  22-)  2   -.-  -.-  Part of ionic cluster
4185  MG   (  22-)  2   -.-  -.-  Too few ligands (0)
4186  MG   (  23-)  2   -.-  -.-  Too few ligands (0)
4187  MG   (1559-)  A   -.-  -.-  Too few ligands (0)
And so on for a total of 1635 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.

1524 GLU   (  12-)  E   H-bonding suggests Gln; but Alt-Rotamer
1561 GLU   (  49-)  E   H-bonding suggests Gln
1562 GLU   (  50-)  E   H-bonding suggests Gln
1655 GLU   ( 143-)  E   H-bonding suggests Gln
1682 GLU   ( 170-)  E   H-bonding suggests Gln; but Alt-Rotamer
1787 ASP   (  36-)  F   H-bonding suggests Asn
1876 GLU   ( 125-)  F   H-bonding suggests Gln
2100 ASP   ( 144-)  G   H-bonding suggests Asn; but Alt-Rotamer
2278 ASP   ( 117-)  H   H-bonding suggests Asn
2308 ASP   ( 147-)  H   H-bonding suggests Asn; but Alt-Rotamer
2411 GLU   (  95-)  I   H-bonding suggests Gln
2461 ASP   (  45-)  J   H-bonding suggests Asn
2542 ASP   ( 126-)  J   H-bonding suggests Asn; but Alt-Rotamer
2545 GLU   ( 129-)  J   H-bonding suggests Gln
2757 GLU   (  48-)  L   H-bonding suggests Gln; but Alt-Rotamer
2769 ASP   (  60-)  L   H-bonding suggests Asn
2860 GLU   (  25-)  M   H-bonding suggests Gln
2908 ASP   (  73-)  M   H-bonding suggests Asn; but Alt-Rotamer
2924 ASP   (  89-)  M   H-bonding suggests Asn; but Alt-Rotamer
2932 GLU   (  97-)  M   H-bonding suggests Gln
2960 ASP   (  34-)  N   H-bonding suggests Asn; but Alt-Rotamer
3007 ASP   (  81-)  N   H-bonding suggests Asn; but Alt-Rotamer
3214 GLU   (  35-)  P   H-bonding suggests Gln
3226 ASP   (  47-)  P   H-bonding suggests Asn
3237 GLU   (  58-)  P   H-bonding suggests Gln
3581 GLU   (  49-)  T   H-bonding suggests Gln
3645 ASP   (  30-)  U   H-bonding suggests Asn; but Alt-Rotamer
3698 GLU   (  83-)  U   H-bonding suggests Gln; but Alt-Rotamer
3826 GLU   (  46-)  W   H-bonding suggests Gln; but Alt-Rotamer
3873 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 :  -3.640
  2nd generation packing quality :  -4.016 (bad)
  Ramachandran plot appearance   :  -6.583 (bad)
  chi-1/chi-2 rotamer normality  :  -5.235 (bad)
  Backbone conformation          :  -0.532

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.487 (tight)
  Bond angles                    :   0.758
  Omega angle restraints         :   0.190 (tight)
  Side chain planarity           :   0.186 (tight)
  Improper dihedral distribution :   0.700
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.007

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 :  -2.2
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -3.4 (poor)
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.487 (tight)
  Bond angles                    :   0.758
  Omega angle restraints         :   0.190 (tight)
  Side chain planarity           :   0.186 (tight)
  Improper dihedral distribution :   0.700
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.007
==============

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.