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 pdb3i9b.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: 848336.500
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= 17.559
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.

4107  MG   (   6-)  C  2
4369  MG   (1605-)  S  A
4468  MG   ( 367-)  A  2
4625  MG   ( 524-)  T  2
4706  MG   ( 605-)  A  2

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

2896 HIS   (  56-)  M  -             2895 PHE   (  54-)  M  -           2.8

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.

5251  MG   (1150-)  1  -

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 OGUA  (   3-)  A    High
   2 OURA  (   4-)  A    High
   3 OURA  (   5-)  A    High
   4 OGUA  (   6-)  A    High
   6 OADE  (   8-)  A    High
  10 OURA  (  12-)  A    High
  12 OURA  (  14-)  A    High
  13 OGUA  (  15-)  A    High
  14 OADE  (  16-)  A    High
  15 OURA  (  17-)  A    High
  24 OADE  (  26-)  A    High
  29 OGUA  (  31-)  A    High
  36 OGUA  (  38-)  A    High
  37 OGUA  (  39-)  A    High
  38 OCYT  (  40-)  A    High
  39 OGUA  (  41-)  A    High
  46 OCYT  (  48-)  A    High
  53 OADE  (  55-)  A    High
  54 OURA  (  56-)  A    High
  55 OGUA  (  57-)  A    High
  56 OCYT  (  58-)  A    High
  57 OADE  (  59-)  A    High
  60 OURA  (  62-)  A    High
  61 OCYT  (  63-)  A    High
  62 OGUA  (  64-)  A    High
And so on for a total of 3341 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.

1650 ARG   ( 137-)  E
1961 ARG   (   3-)  G
2076 ARG   ( 118-)  G
3637 ARG   ( 101-)  T
3872 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

1605 TYR   (  92-)  E
1712 TYR   ( 199-)  E
1781 TYR   (  29-)  F
1936 TYR   ( 184-)  F
1978 TYR   (  20-)  G
1996 TYR   (  38-)  G
2096 TYR   ( 138-)  G
2165 TYR   ( 207-)  G
2299 TYR   ( 133-)  H
2371 TYR   (  50-)  I
2384 TYR   (  63-)  I
2465 TYR   (  44-)  J
2575 TYR   ( 154-)  J
2719 TYR   (   4-)  L
2829 TYR   ( 114-)  L
2953 TYR   (  20-)  N
2983 TYR   (  50-)  N
3127 TYR   (  69-)  O
3163 TYR   ( 105-)  O
3207 TYR   (  21-)  P
3209 TYR   (  23-)  P
3568 TYR   (  32-)  T

Warning: Phenylalanine convention problem

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

1541 PHE   (  28-)  E
1665 PHE   ( 152-)  E
1676 PHE   ( 163-)  E
2051 PHE   (  93-)  G
2172 PHE   (   6-)  H
2752 PHE   (  37-)  L
2852 PHE   (  11-)  M
3533 PHE   (  80-)  S
3649 PHE   (  29-)  U
3663 PHE   (  43-)  U
3715 PHE   (  10-)  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.

1573 ASP   (  60-)  E
1679 ASP   ( 166-)  E
1706 ASP   ( 193-)  E
1711 ASP   ( 198-)  E
1719 ASP   ( 206-)  E
1808 ASP   (  56-)  F
1935 ASP   ( 183-)  F
2060 ASP   ( 102-)  G
2092 ASP   ( 134-)  G
2151 ASP   ( 193-)  G
2313 ASP   ( 147-)  H
2404 ASP   (  83-)  I
2441 ASP   (  20-)  J
2466 ASP   (  45-)  J
2547 ASP   ( 126-)  J
2650 ASP   (  73-)  K
2790 ASP   (  75-)  L
2806 ASP   (  91-)  L
2820 ASP   ( 105-)  L
2853 ASP   (  12-)  M
2913 ASP   (  73-)  M
2967 ASP   (  34-)  N
2969 ASP   (  36-)  N
3044 ASP   ( 111-)  N
3164 ASP   ( 106-)  O
3170 ASP   ( 112-)  O
3202 ASP   (  16-)  P
3269 ASP   (  83-)  P
3385 ASP   (  21-)  R
3482 ASP   (  29-)  S
3505 ASP   (  52-)  S
3582 ASP   (  46-)  T
3650 ASP   (  30-)  U
3717 ASP   (  12-)  V

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.

1548 GLU   (  35-)  E
1562 GLU   (  49-)  E
1565 GLU   (  52-)  E
1629 GLU   ( 116-)  E
1630 GLU   ( 117-)  E
1632 GLU   ( 119-)  E
1641 GLU   ( 128-)  E
1656 GLU   ( 143-)  E
1771 GLU   (  19-)  F
1834 GLU   (  82-)  F
1992 GLU   (  34-)  G
2038 GLU   (  80-)  G
2039 GLU   (  81-)  G
2103 GLU   ( 145-)  G
2108 GLU   ( 150-)  G
2114 GLU   ( 156-)  G
2150 GLU   ( 192-)  G
2163 GLU   ( 205-)  G
2169 GLU   (   3-)  H
2315 GLU   ( 149-)  H
2343 GLU   (  22-)  I
2363 GLU   (  42-)  I
2473 GLU   (  52-)  J
2488 GLU   (  67-)  J
2495 GLU   (  74-)  J
2511 GLU   (  90-)  J
2560 GLU   ( 139-)  J
2599 GLU   (  22-)  K
2610 GLU   (  33-)  K
2923 GLU   (  83-)  M
2935 GLU   (  95-)  M
3131 GLU   (  73-)  O
3194 GLU   (   8-)  P
3221 GLU   (  35-)  P
3247 GLU   (  61-)  P
3350 GLU   (  46-)  Q
3371 GLU   (   7-)  R
3378 GLU   (  14-)  R
3405 GLU   (  41-)  R
3447 GLU   (  83-)  R
3507 GLU   (  54-)  S
3597 GLU   (  61-)  T
3648 GLU   (  28-)  U
3658 GLU   (  38-)  U
3726 GLU   (  21-)  V
3769 GLU   (  64-)  V
3829 GLU   (  46-)  W
3843 GLU   (  60-)  W

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.

 658 OURA  ( 677-)  A      N1   C2    1.42    4.6
 769 OURA  ( 788-)  A      C4   N3    1.44    6.1
 775 OADE  ( 794-)  A      C2   N3    1.37    4.2
1970 CYS   (  12-)  G      CA   CB    1.61    4.1
3303 VAL   ( 117-)  P      CA   CB    1.69    8.2
3932 OCYT  (  17-)  C      C4   N3    1.38    6.8
3932 OCYT  (  17-)  C      C4   N4    1.23  -11.3
4009 OCYT  (  17-)  D      C4   N3    1.39    7.3
4009 OCYT  (  17-)  D      C4   N4    1.23  -11.4

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.

   4 OGUA  (   6-)  A      N9   C8   N7  113.21    4.2
   5 OGUA  (   7-)  A      C4'  O4'  C1' 105.49   -4.6
   5 OGUA  (   7-)  A      O4'  C1'  N9  113.43    5.2
   5 OGUA  (   7-)  A      C2'  C1'  N9  122.77    5.9
   6 OADE  (   8-)  A      C2'  C1'  N9  123.23    6.1
   7 OGUA  (   9-)  A      N9   C8   N7  113.13    4.1
   9 OGUA  (  11-)  A      N9   C8   N7  113.14    4.1
  13 OGUA  (  15-)  A      N9   C8   N7  113.15    4.1
  25 OGUA  (  27-)  A      N9   C8   N7  113.27    4.3
  26 OGUA  (  28-)  A      N9   C8   N7  113.20    4.2
  27 OGUA  (  29-)  A      N9   C8   N7  113.12    4.0
  33 OGUA  (  35-)  A      N9   C8   N7  113.41    4.6
  40 OGUA  (  42-)  A      N9   C8   N7  113.30    4.4
  42 OGUA  (  44-)  A      N9   C8   N7  113.18    4.2
  44 OGUA  (  46-)  A      N9   C8   N7  113.15    4.1
  45 OCYT  (  47-)  A      O4'  C1'  N1  113.32    5.1
  47 OURA  (  49-)  A      C2'  C1'  N1  121.83    5.3
  59 OGUA  (  61-)  A      N9   C8   N7  113.26    4.3
  64 OGUA  (  66-)  A      N9   C8   N7  113.35    4.5
  66 OGUA  (  68-)  A      N9   C8   N7  113.12    4.0
  68 OGUA  (  73-)  A      N9   C8   N7  113.19    4.2
  71 OGUA  (  76-)  A      N9   C8   N7  113.13    4.1
  73 OGUA  (  78-)  A      N9   C8   N7  113.29    4.4
  75 OGUA  (  80-)  A      N9   C8   N7  113.16    4.1
  76 OGUA  (  81-)  A      N9   C8   N7  113.13    4.1
And so on for a total of 424 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.

1548 GLU   (  35-)  E
1562 GLU   (  49-)  E
1565 GLU   (  52-)  E
1573 ASP   (  60-)  E
1629 GLU   ( 116-)  E
1630 GLU   ( 117-)  E
1632 GLU   ( 119-)  E
1641 GLU   ( 128-)  E
1650 ARG   ( 137-)  E
1656 GLU   ( 143-)  E
1679 ASP   ( 166-)  E
1706 ASP   ( 193-)  E
1711 ASP   ( 198-)  E
1719 ASP   ( 206-)  E
1771 GLU   (  19-)  F
1808 ASP   (  56-)  F
1834 GLU   (  82-)  F
1935 ASP   ( 183-)  F
1961 ARG   (   3-)  G
1992 GLU   (  34-)  G
2038 GLU   (  80-)  G
2039 GLU   (  81-)  G
2060 ASP   ( 102-)  G
2076 ARG   ( 118-)  G
2092 ASP   ( 134-)  G
And so on for a total of 87 lines.

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.

2016 LEU   (  58-)  G    5.76
3835 ALA   (  52-)  W    5.70
3860 ALA   (  77-)  W    5.55
1970 CYS   (  12-)  G    5.46
3389 THR   (  25-)  R    5.38
2767 ALA   (  52-)  L    5.27
1708 ASP   ( 195-)  E    5.19
2791 ALA   (  76-)  L    5.03
2564 ARG   ( 143-)  J    5.00
1984 CYS   (  26-)  G    4.80
3231 VAL   (  45-)  P    4.78
2500 ARG   (  79-)  J    4.75
3523 ALA   (  70-)  S    4.74
3442 TYR   (  78-)  R    4.72
2944 LYS   (  11-)  N    4.63
1640 ILE   ( 127-)  E    4.57
3524 ARG   (  71-)  S    4.56
3069 VAL   (  11-)  O    4.52
2501 VAL   (  80-)  J    4.52
2051 PHE   (  93-)  G    4.51
2517 GLN   (  96-)  J    4.49
1528 VAL   (  15-)  E    4.48
1731 ALA   ( 218-)  E    4.48
1968 ARG   (  10-)  G    4.47
1599 GLU   (  86-)  E    4.43
2298 ALA   ( 132-)  H    4.42
2465 TYR   (  44-)  J    4.35
2943 VAL   (  10-)  N    4.34
2741 VAL   (  26-)  L    4.33
1882 VAL   ( 130-)  F    4.32
1623 GLN   ( 110-)  E    4.30
1639 GLU   ( 126-)  E    4.16
2407 ARG   (  86-)  I    4.15
2349 ARG   (  28-)  I    4.15
1677 VAL   ( 164-)  E    4.11
3815 ALA   (  32-)  W    4.08
1906 SER   ( 154-)  F    4.08
3694 ARG   (  74-)  U    4.02

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 : 1.583

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.

  77 OURA  (  82-)  A    0.16
 360 OURA  ( 367-)  A    0.14
 Ramachandran Z-score : -6.805

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 : -6.805

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.

1917 THR   ( 165-)  F    -3.6
1605 TYR   (  92-)  E    -3.6
2719 TYR   (   4-)  L    -3.5
2720 TYR   (   5-)  L    -3.5
3235 THR   (  49-)  P    -3.4
3856 HIS   (  73-)  W    -3.3
3196 PRO   (  10-)  P    -3.1
2576 ARG   ( 155-)  J    -3.1
2736 PRO   (  21-)  L    -3.1
1536 ARG   (  23-)  E    -3.0
1987 PRO   (  29-)  G    -3.0
1995 PRO   (  37-)  G    -3.0
2572 TYR   ( 151-)  J    -3.0
2888 PHE   (  47-)  M    -3.0
3700 PRO   (  80-)  U    -2.9
1546 TYR   (  33-)  E    -2.8
1580 THR   (  67-)  E    -2.8
1530 PHE   (  17-)  E    -2.8
3195 ILE   (   9-)  P    -2.7
2961 THR   (  28-)  N    -2.7
3469 HIS   (  16-)  S    -2.7
1756 LYS   (   4-)  F    -2.7
2597 TYR   (  20-)  K    -2.7
2742 THR   (  27-)  L    -2.7
3772 VAL   (  67-)  V    -2.7
And so on for a total of 248 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.

1519 THR   (   6-)  E  Poor phi/psi
1521 LYS   (   8-)  E  Poor phi/psi
1526 ALA   (  13-)  E  Poor phi/psi
1530 PHE   (  17-)  E  Poor phi/psi
1533 GLU   (  20-)  E  Poor phi/psi
1535 LYS   (  22-)  E  Poor phi/psi
1536 ARG   (  23-)  E  Poor phi/psi
1537 TRP   (  24-)  E  Poor phi/psi
1541 PHE   (  28-)  E  Poor phi/psi
1542 ALA   (  29-)  E  Poor phi/psi
1545 ILE   (  32-)  E  Poor phi/psi
1546 TYR   (  33-)  E  Poor phi/psi
1552 ILE   (  39-)  E  Poor phi/psi
1558 GLN   (  45-)  E  Poor phi/psi
1566 ARG   (  53-)  E  Poor phi/psi
1576 MET   (  63-)  E  Poor phi/psi
1578 GLY   (  65-)  E  Poor phi/psi
1587 LYS   (  74-)  E  Poor phi/psi
1588 LYS   (  75-)  E  Poor phi/psi
1600 ARG   (  87-)  E  Poor phi/psi
1614 MET   ( 101-)  E  Poor phi/psi
1615 LEU   ( 102-)  E  Poor phi/psi
1616 THR   ( 103-)  E  Poor phi/psi
1634 LEU   ( 121-)  E  Poor phi/psi
1638 PRO   ( 125-)  E  Poor phi/psi
And so on for a total of 410 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 : -5.344

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.

1641 GLU   ( 128-)  E    0.36
3661 LYS   (  41-)  U    0.36
3514 SER   (  61-)  S    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 OURA  (   5-)  A      0
   4 OGUA  (   6-)  A      0
   5 OGUA  (   7-)  A      0
   6 OADE  (   8-)  A      0
   7 OGUA  (   9-)  A      0
   8 OADE  (  10-)  A      0
   9 OGUA  (  11-)  A      0
  10 OURA  (  12-)  A      0
  11 OURA  (  13-)  A      0
  12 OURA  (  14-)  A      0
  13 OGUA  (  15-)  A      0
  14 OADE  (  16-)  A      0
  15 OURA  (  17-)  A      0
  16 OCYT  (  18-)  A      0
  17 OCYT  (  19-)  A      0
  18 OURA  (  20-)  A      0
  19 OGUA  (  21-)  A      0
  20 OGUA  (  22-)  A      0
  21 OCYT  (  23-)  A      0
  22 OURA  (  24-)  A      0
  23 OCYT  (  25-)  A      0
  24 OADE  (  26-)  A      0
  25 OGUA  (  27-)  A      0
  26 OGUA  (  28-)  A      0
  27 OGUA  (  29-)  A      0
And so on for a total of 2786 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 : 1.126

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!

1911 GLY   ( 159-)  F   3.34   13
3087 GLY   (  29-)  O   2.49   21
3904 GLY   (  16-)  X   2.29   45
2067 GLY   ( 109-)  G   2.20   67
3387 GLY   (  23-)  R   2.06   13
3146 GLY   (  88-)  O   1.94   31
3830 GLY   (  47-)  W   1.80   14
3224 GLY   (  38-)  P   1.70   80
3377 GLN   (  13-)  R   1.67   16
2783 GLY   (  68-)  L   1.64   25
2765 LEU   (  50-)  L   1.61   42
2125 GLY   ( 167-)  G   1.59   74
2624 GLY   (  47-)  K   1.59   11
3254 GLY   (  68-)  P   1.56   12
1957 GLY   ( 205-)  F   1.54   13
3286 GLY   ( 100-)  P   1.53   46
2707 GLY   ( 130-)  K   1.52   14
2551 GLY   ( 130-)  J   1.51   16

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...

1529 HIS   (  16-)  E   2.48
2499 ARG   (  78-)  J   2.81
2500 ARG   (  79-)  J   2.67
2825 GLU   ( 110-)  L   1.90
2944 LYS   (  11-)  N   2.66
3229 THR   (  43-)  P   1.63

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]

3103 PRO   (  45-)  O    0.47 HIGH
3196 PRO   (  10-)  P    0.45 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].

1539 PRO   (  26-)  E  -112.1 envelop C-gamma (-108 degrees)
1604 PRO   (  91-)  E    43.6 envelop C-delta (36 degrees)
1995 PRO   (  37-)  G    45.0 envelop C-delta (36 degrees)
2736 PRO   (  21-)  L    99.5 envelop C-beta (108 degrees)
3183 PRO   ( 125-)  O  -119.4 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

5241  MG   (1970-)  A     MG   <-> 5243  MG   (1972-)  A     MG      1.67    1.53  INTRA BF
4239  MG   ( 138-)  2     MG   <-> 4790  MG   ( 689-)  2     MG      1.31    1.89  INTRA BL
 106 OGUA  ( 115-)  A      C2' <-> 4930  MG   (1804-)  A     MG      1.30    1.90  INTRA BL
4455  MG   (1644-)  A     MG   <-> 5168  MG   (1897-)  A     MG      1.29    1.91  INTRA BL
4361  MG   (1601-)  A     MG   <-> 5168  MG   (1897-)  A     MG      1.13    2.07  INTRA BL
3877 ALA   (  94-)  W      CB  <-> 4715  MG   ( 614-)  W     MG      1.13    2.07  INTRA BF
 443 OADE  ( 451-)  A      C2' <-> 5198  MG   (1927-)  A     MG      1.13    2.07  INTRA BL
 444 OADE  ( 452-)  A      C3' <-> 4398  MG   (1620-)  A     MG      1.12    2.08  INTRA BL
 239 OADE  ( 246-)  A      C2' <-> 5191  MG   (1920-)  A     MG      1.10    2.10  INTRA BL
 547 OGUA  ( 566-)  A      C3' <-> 5200  MG   (1929-)  A     MG      1.10    2.10  INTRA BL
4251  MG   ( 150-)  2     MG   <-> 4757  MG   ( 656-)  2     MG      1.08    2.12  INTRA BL
 733 OGUA  ( 752-)  A      C3' <-> 4484  MG   (1653-)  A     MG      1.05    2.15  INTRA BL
1979 LEU   (  21-)  G      CD1 <-> 5318  ZN   ( 210-)  G     ZN      1.04    2.16  INTRA BF
4788  MG   ( 687-)  2     MG   <-> 4874  MG   ( 773-)  2     MG      0.99    2.21  INTRA BL
4460  MG   ( 359-)  2     MG   <-> 4764  MG   ( 663-)  2     MG      0.93    2.27  INTRA BL
 966 OURA  ( 991-)  A      C5  <-> 4989  MG   (1822-)  A     MG      0.93    2.27  INTRA BF
 374 OCYT  ( 381-)  A      C2' <-> 5049  MG   (1843-)  A     MG      0.91    2.29  INTRA BL
 443 OADE  ( 451-)  A      C3' <-> 5198  MG   (1927-)  A     MG      0.90    2.30  INTRA BL
  62 OGUA  (  64-)  A      C3' <-> 5291  MG   (1994-)  A     MG      0.89    2.31  INTRA BL
1367 OGUA  (1387-)  A      C5' <-> 5217  MG   (1946-)  A     MG      0.89    2.31  INTRA BL
 897 OGUA  ( 922-)  A      C5' <-> 4670  MG   (1719-)  A     MG      0.88    2.32  INTRA BL
 444 OADE  ( 452-)  A      C2' <-> 4398  MG   (1620-)  A     MG      0.88    2.32  INTRA BL
 547 OGUA  ( 566-)  A      C2' <-> 5200  MG   (1929-)  A     MG      0.87    2.33  INTRA BL
 365 OCYT  ( 372-)  A      C5' <-> 4418  MG   (1628-)  A     MG      0.86    2.34  INTRA BL
 377 OGUA  ( 384-)  A      C5' <-> 4751  MG   (1751-)  A     MG      0.86    2.34  INTRA BL
And so on for a total of 3957 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.

3452 ARG   (  88-)  R      -8.00
2007 ARG   (  49-)  G      -7.94
2840 TYR   ( 125-)  L      -7.84
1942 ARG   ( 190-)  F      -7.80
3912 ARG   (  24-)  X      -7.79
3290 ARG   ( 104-)  P      -7.69
1962 TYR   (   4-)  G      -7.67
3077 ARG   (  19-)  O      -7.59
3786 ARG   (  81-)  V      -7.57
1961 ARG   (   3-)  G      -7.51
1549 ARG   (  36-)  E      -7.38
3785 TYR   (  80-)  V      -7.36
2646 ARG   (  69-)  K      -7.29
1996 TYR   (  38-)  G      -7.19
2645 ARG   (  68-)  K      -7.19
3285 ARG   (  99-)  P      -7.19
2453 ARG   (  32-)  J      -7.18
2292 ARG   ( 126-)  H      -7.17
2839 GLN   ( 124-)  L      -7.16
2892 ARG   (  51-)  M      -7.15
1945 TYR   ( 193-)  F      -7.15
2958 TYR   (  25-)  N      -7.10
2186 GLN   (  20-)  H      -7.04
2576 ARG   ( 155-)  J      -7.03
2945 ARG   (  12-)  N      -7.01
And so on for a total of 200 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.

1534 ARG   (  21-)  E      1536 - ARG     23- ( E)         -5.60
1669 LYS   ( 156-)  E      1671 - LEU    158- ( E)         -5.91
1754 GLY   (   2-)  F      1757 - ILE      5- ( F)         -5.43
1961 ARG   (   3-)  G      1963 - ILE      5- ( G)         -6.96
2042 LYS   (  84-)  G      2044 - LYS     86- ( G)         -5.19
2184 ARG   (  18-)  H      2188 - GLY     22- ( H)         -5.41
2366 LEU   (  45-)  I      2368 - ARG     47- ( I)         -5.18
2424 ARG   (   3-)  J      2427 - ARG      6- ( J)         -6.29
2431 ARG   (  10-)  J      2434 - GLN     13- ( J)         -5.15
2499 ARG   (  78-)  J      2501 - VAL     80- ( J)         -5.07
2574 HIS   ( 153-)  J      2576 - ARG    155- ( J)         -5.33
2645 ARG   (  68-)  K      2647 - GLN     70- ( K)         -6.43
2681 ARG   ( 104-)  K      2683 - GLY    106- ( K)         -5.00
2724 ARG   (   9-)  L      2726 - LYS     11- ( L)         -4.59
2943 VAL   (  10-)  N      2946 - GLN     13- ( N)         -5.82
3058 PHE   ( 125-)  N      3062 - SER    129- ( N)         -4.92
3073 ARG   (  15-)  O      3079 - LYS     21- ( O)         -5.38
3131 GLU   (  73-)  O      3133 - HIS     75- ( O)         -4.93
3300 ARG   ( 114-)  P      3305 - GLY    119- ( P)         -4.96
3451 ILE   (  87-)  R      3453 - GLY     89- ( R)         -5.49
3478 ARG   (  25-)  S      3481 - ARG     28- ( S)         -5.15
3534 ARG   (  81-)  S      3536 - GLU     83- ( S)         -5.67
3785 TYR   (  80-)  V      3789 - GLY     84- ( V)         -5.88
3886 GLY   ( 103-)  W      3889 - ALA    106- ( W)         -4.87
3908 LYS   (  20-)  X      3910 - ARG     22- ( X)         -5.21

Error: Abnormal average packing environment

The average packing score for the structure is very low.

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

Average for range 1 - 4091 : -2.018

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.

2843 ARG   ( 128-)  L   -3.51
3292 ASN   ( 106-)  P   -3.24
3287 GLN   ( 101-)  P   -3.23
3567 LEU   (  31-)  T   -3.20
3783 ARG   (  78-)  V   -3.19
3290 ARG   ( 104-)  P   -3.13
3495 ARG   (  42-)  S   -3.13
2428 ALA   (   7-)  J   -3.12
1764 LEU   (  12-)  F   -3.11
2839 GLN   ( 124-)  L   -3.10
3173 LYS   ( 115-)  O   -3.09
3335 ARG   (  31-)  Q   -3.08
2959 ASN   (  26-)  N   -3.07
1993 ARG   (  35-)  G   -3.06
1755 ASN   (   3-)  F   -3.04
1914 GLN   ( 162-)  F   -3.04
1983 ARG   (  25-)  G   -3.03
2186 GLN   (  20-)  H   -2.96
3903 ARG   (  15-)  X   -2.95
3759 GLY   (  54-)  V   -2.90
3466 HIS   (  13-)  S   -2.90
3480 LYS   (  27-)  S   -2.82
3051 GLY   ( 118-)  N   -2.82
2826 ARG   ( 111-)  L   -2.81
2841 SER   ( 126-)  L   -2.79
And so on for a total of 57 lines.

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1754 GLY   (   2-)  F     - 1757 ILE   (   5-)  F        -2.32
1998 PRO   (  40-)  G     - 2001 HIS   (  43-)  G        -1.86
2185 MET   (  19-)  H     - 2188 GLY   (  22-)  H        -2.15
2422 ALA   ( 101-)  I     - 2426 ARG   (   5-)  J        -1.68
2577 TRP   ( 156-)  J     - 2580 THR   (   3-)  K        -2.13
2825 GLU   ( 110-)  L     - 2829 TYR   ( 114-)  L        -2.02
2834 ALA   ( 119-)  L     - 2837 ALA   ( 122-)  L        -1.84
2838 PRO   ( 123-)  L     - 2843 ARG   ( 128-)  L        -2.56
2878 PRO   (  37-)  M     - 2882 PRO   (  41-)  M        -1.84
2888 PHE   (  47-)  M     - 2891 ILE   (  50-)  M        -1.96
3048 PRO   ( 115-)  N     - 3051 GLY   ( 118-)  N        -2.25
3174 SER   ( 116-)  O     - 3177 LYS   ( 119-)  O        -1.88
3283 PRO   (  97-)  P     - 3288 ARG   ( 102-)  P        -1.99
3289 THR   ( 103-)  P     - 3292 ASN   ( 106-)  P        -2.46
3305 GLY   ( 119-)  P     - 3310 LEU   (   6-)  Q        -1.88
3361 ARG   (  57-)  Q     - 3364 SER   (  60-)  Q        -1.48
3463 GLY   (  10-)  S     - 3466 HIS   (  13-)  S        -2.13
3476 ASP   (  23-)  S     - 3482 ASP   (  29-)  S        -2.13
3549 ASP   (  13-)  T     - 3552 GLN   (  16-)  T        -1.84
3598 SER   (  62-)  T     - 3601 ILE   (  65-)  T        -1.88
3633 SER   (  97-)  T     - 3636 LYS   ( 100-)  T        -1.78
3756 VAL   (  51-)  V     - 3760 LYS   (  55-)  V        -1.89
3885 GLY   ( 102-)  W     - 3888 SER   ( 105-)  W        -1.78

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.

1550 ASN   (  37-)  E
1607 ASN   (  94-)  E
1623 GLN   ( 110-)  E
1648 GLN   ( 135-)  E
1653 HIS   ( 140-)  E
1753 GLN   ( 240-)  E
1815 ASN   (  63-)  F
2020 GLN   (  62-)  G
2087 ASN   ( 129-)  G
2421 ASN   ( 100-)  I
2505 ASN   (  84-)  J
2832 HIS   ( 117-)  L
2946 GLN   (  13-)  N
3026 GLN   (  93-)  N
3049 HIS   ( 116-)  N
3067 GLN   (   9-)  O
3107 ASN   (  49-)  O
3157 HIS   (  99-)  O
3248 ASN   (  62-)  P
3287 GLN   ( 101-)  P
3353 HIS   (  49-)  Q
3535 GLN   (  82-)  S
3809 ASN   (  26-)  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.

   2 OURA  (   4-)  A      N3
  13 OGUA  (  15-)  A      N2
  24 OADE  (  26-)  A      N6
  55 OGUA  (  57-)  A      N2
  92 OADE  ( 101-)  A      N6
  99 OGUA  ( 108-)  A      N2
 101 OCYT  ( 110-)  A      N4
 103 OGUA  ( 112-)  A      N2
 114 OCYT  ( 123-)  A      N4
 121 OGUA  ( 129-)  A      N2
 173 OGUA  ( 181-)  A      N2
 179 OCYT  ( 186-)  A      O2'
 186 OURA  ( 188-)  A      O2'
 187 OURA  ( 189-)  A      N3
 195 OGUA  ( 191-)  A      N2
 203 OGUA  ( 199-)  A      N2
 213 OGUA  ( 220-)  A      N1
 225 OGUA  ( 232-)  A      N2
 230 OCYT  ( 237-)  A      N4
 239 OADE  ( 246-)  A      N6
 247 OGUA  ( 254-)  A      N2
 262 OCYT  ( 269-)  A      N4
 294 OGUA  ( 301-)  A      N2
 311 OGUA  ( 318-)  A      N2
 315 OCYT  ( 322-)  A      N4
And so on for a total of 591 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.

1553 HIS   (  40-)  E      ND1
1679 ASP   ( 166-)  E      OD1
1689 GLU   ( 176-)  E      OE2
1702 ASP   ( 189-)  E      OD1
1702 ASP   ( 189-)  E      OD2
1755 ASN   (   3-)  F      OD1
1787 GLU   (  35-)  F      OE2
1788 ASP   (  36-)  F      OD2
1821 HIS   (  69-)  F      ND1
2151 ASP   ( 193-)  G      OD2
2288 GLU   ( 122-)  H      OE1
2441 ASP   (  20-)  J      OD2
2569 ASN   ( 148-)  J      OD1
2585 ASP   (   8-)  K      OD2
2904 GLU   (  64-)  M      OE1
2955 HIS   (  22-)  N      ND1
3253 GLU   (  67-)  P      OE1
3385 ASP   (  21-)  R      OD1
3417 HIS   (  53-)  R      ND1
3717 ASP   (  12-)  V      OD2
3788 HIS   (  83-)  V      ND1
3843 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+.

4102  MG   (   1-)  2   -.-  -.-  Too few ligands (0)
4103  MG   (   2-)  2   -.-  -.-  Too few ligands (0)
4104  MG   (  77-)  C   -.-  -.-  Low probability ion. B= 82.4
4105  MG   (  78-)  C   -.-  -.-  Low probability ion. B=101.6
4106  MG   (  79-)  C   -.-  -.-  Low probability ion. B=136.1
4107  MG   (   6-)  C   -.-  -.-  Low probability ion. B=101.4
4108  MG   (  80-)  C   -.-  -.-  Low probability ion. B=106.8
4109  MG   (   8-)  2   -.-  -.-  Low probability ion. B=102.7
4110  MG   (  81-)  C   -.-  -.-  Too few ligands (0)
4111  MG   (  10-)  2   -.-  -.-  Low probability ion. B=149.1
4112  MG   (  11-)  2   -.-  -.-  Low probability ion. B=120.1
4113  MG   (  12-)  2   -.-  -.-  Low probability ion. B=138.5
4114  MG   (  13-)  2   -.-  -.-  Low probability ion. B=115.9
4115  MG   (  14-)  2   -.-  -.-  Too few ligands (0)
4116  MG   (  15-)  2   -.-  -.-  Too few ligands (0)
4117  MG   (  16-)  2   -.-  -.-  Too few ligands (0)
4118  MG   (  17-)  2   -.-  -.-  Too few ligands (0)
4119  MG   (  18-)  2   -.-  -.-  Too few ligands (0)
4120  MG   (  19-)  2   -.-  -.-  Too few ligands (0)
4121  MG   (  20-)  2   -.-  -.-  Too few ligands (0)
4122  MG   (  21-)  2   -.-  -.-  Too few ligands (0)
4123  MG   (  22-)  2   -.-  -.-  Too few ligands (0)
4124  MG   (  23-)  2   -.-  -.-  Too few ligands (0)
4125  MG   (  24-)  2   -.-  -.-  Too few ligands (0)
4126  MG   (1543-)  A   -.-  -.-  Too few ligands (1)
And so on for a total of 1374 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.

1563 GLU   (  50-)  E   H-bonding suggests Gln; but Alt-Rotamer
1683 GLU   ( 170-)  E   H-bonding suggests Gln
1744 GLU   ( 231-)  E   H-bonding suggests Gln
1771 GLU   (  19-)  F   H-bonding suggests Gln
1874 GLU   ( 122-)  F   H-bonding suggests Gln; but Alt-Rotamer
1913 GLU   ( 161-)  F   H-bonding suggests Gln
2102 ASP   ( 144-)  G   H-bonding suggests Asn
2135 ASP   ( 177-)  G   H-bonding suggests Asn; but Alt-Rotamer
2216 GLU   (  50-)  H   H-bonding suggests Gln; but Alt-Rotamer
2283 ASP   ( 117-)  H   H-bonding suggests Asn; but Alt-Rotamer
2313 ASP   ( 147-)  H   H-bonding suggests Asn; but Alt-Rotamer
2436 ASP   (  15-)  J   H-bonding suggests Asn
2547 ASP   ( 126-)  J   H-bonding suggests Asn; but Alt-Rotamer
2629 ASP   (  52-)  K   H-bonding suggests Asn
2631 ASP   (  54-)  K   H-bonding suggests Asn
2676 GLU   (  99-)  K   H-bonding suggests Gln
2727 GLU   (  12-)  L   H-bonding suggests Gln
2775 ASP   (  60-)  L   H-bonding suggests Asn
2913 ASP   (  73-)  M   H-bonding suggests Asn; but Alt-Rotamer
2969 ASP   (  36-)  N   H-bonding suggests Asn
3043 ASP   ( 110-)  N   H-bonding suggests Asn
3202 ASP   (  16-)  P   H-bonding suggests Asn; but Alt-Rotamer
3233 ASP   (  47-)  P   H-bonding suggests Asn; but Alt-Rotamer
3247 GLU   (  61-)  P   H-bonding suggests Gln
3269 ASP   (  83-)  P   H-bonding suggests Asn; but Alt-Rotamer
3591 ASP   (  55-)  T   H-bonding suggests Asn
3614 GLU   (  78-)  T   H-bonding suggests Gln; but Alt-Rotamer
3748 GLU   (  43-)  V   H-bonding suggests Gln
3876 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 :  -3.794 (poor)
  2nd generation packing quality :  -4.265 (bad)
  Ramachandran plot appearance   :  -6.805 (bad)
  chi-1/chi-2 rotamer normality  :  -5.344 (bad)
  Backbone conformation          :  -0.801

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.469 (tight)
  Bond angles                    :   0.749
  Omega angle restraints         :   0.205 (tight)
  Side chain planarity           :   0.183 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.379
  Inside/Outside distribution    :   1.010

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 :  -2.3
  2nd generation packing quality :  -1.7
  Ramachandran plot appearance   :  -3.6 (poor)
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.469 (tight)
  Bond angles                    :   0.749
  Omega angle restraints         :   0.205 (tight)
  Side chain planarity           :   0.183 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.379
  Inside/Outside distribution    :   1.010
==============

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.