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 pdb3i8g.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: 894671.563
Volume of the Unit Cell V= 58237228.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 16.273
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.

4338  MG   (1651-)  D  A
4401  MG   ( 461-)  N  A
4627  MG   ( 220-)  A  2
4785  MG   ( 296-)  D  2
4834  MG   (2016-)  W  A
4866  MG   ( 329-)  D  2
5042  MG   (2160-)  M  A
5144  MG   (2235-)  B  A
5168  MG   (2252-)  S  A
5232  MG   ( 822-)  A  G
5236  MG   ( 942-)  A  G
5254  MG   (1333-)  T  K
5265  MG   (1439-)  A  M
5287  MG   ( 769-)  A  S
5289  MG   ( 801-)  A  S
5327  MG   ( 535-)  C  2
5330  MG   ( 536-)  C  2
5391  MG   ( 569-)  C  2
5653  MG   ( 878-)  C  2
5670  MG   ( 913-)  C  2
5918  MG   (1410-)  A  2
5920  MG   (1417-)  D  2
6031  MG   (1652-)  D  2
6142  MG   (1855-)  C  2
6260  MG   (2060-)  C  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.

2892 HIS   (  56-)  M  -             2891 PHE   (  54-)  M  -           2.6

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.

4946  MG   (2090-)  A  -
4986  MG   (2121-)  A  -
5131  MG   (2226-)  A  -
5259  MG   (1801-)  K  -
5289  MG   ( 801-)  A  S
5292  MG   (1412-)  S  -
5305  MG   (1050-)  V  -
5308  MG   (1326-)  W  -
5571  MG   (1638-)  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 OURA  (   4-)  A    High
   2 OURA  (   5-)  A    High
  66 OGUA  (  69-)  A    High
  67 OGUA  (  73-)  A    High
  68 OCYT  (  74-)  A    High
  69 OCYT  (  75-)  A    High
  70 OGUA  (  76-)  A    High
  71 OCYT  (  77-)  A    High
  72 OGUA  (  78-)  A    High
  73 OGUA  (  79-)  A    High
  74 OGUA  (  80-)  A    High
  75 OGUA  (  81-)  A    High
  76 OURA  (  82-)  A    High
  77 OURA  (  84-)  A    High
  78 OURA  (  85-)  A    High
  79 OURA  (  86-)  A    High
  80 OADE  (  87-)  A    High
  81 OCYT  (  88-)  A    High
  82 OURA  (  89-)  A    High
  83 OCYT  (  90-)  A    High
  84 OCYT  (  91-)  A    High
  85 OGUA  (  92-)  A    High
  86 OURA  (  93-)  A    High
  87 OGUA  (  95-)  A    High
  88 OGUA  (  96-)  A    High
And so on for a total of 1628 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.

1961 ARG   (   3-)  G
2076 ARG   ( 118-)  G
3634 ARG   ( 101-)  T
3871 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

1544 TYR   (  31-)  E
1605 TYR   (  92-)  E
1781 TYR   (  29-)  F
1985 TYR   (  27-)  G
1996 TYR   (  38-)  G
2026 TYR   (  68-)  G
2096 TYR   ( 138-)  G
2165 TYR   ( 207-)  G
2296 TYR   ( 133-)  H
2381 TYR   (  63-)  I
2462 TYR   (  44-)  J
2503 TYR   (  85-)  J
2572 TYR   ( 154-)  J
2825 TYR   ( 114-)  L
2836 TYR   ( 125-)  L
2977 TYR   (  50-)  N
3157 TYR   ( 105-)  O
3201 TYR   (  21-)  P
3203 TYR   (  23-)  P
3467 TYR   (  17-)  S
3482 TYR   (  32-)  S
3565 TYR   (  32-)  T
3652 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.

1665 PHE   ( 152-)  E
1676 PHE   ( 163-)  E
1880 PHE   ( 128-)  F
2051 PHE   (  93-)  G
2748 PHE   (  37-)  L
2848 PHE   (  11-)  M
3530 PHE   (  80-)  S
3777 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.

1573 ASP   (  60-)  E
1679 ASP   ( 166-)  E
1706 ASP   ( 193-)  E
1711 ASP   ( 198-)  E
1935 ASP   ( 183-)  F
2092 ASP   ( 134-)  G
2151 ASP   ( 193-)  G
2310 ASP   ( 147-)  H
2401 ASP   (  83-)  I
2433 ASP   (  15-)  J
2463 ASP   (  45-)  J
2544 ASP   ( 126-)  J
2647 ASP   (  73-)  K
2786 ASP   (  75-)  L
2802 ASP   (  91-)  L
2816 ASP   ( 105-)  L
2849 ASP   (  12-)  M
2909 ASP   (  73-)  M
2961 ASP   (  34-)  N
2963 ASP   (  36-)  N
3008 ASP   (  81-)  N
3037 ASP   ( 110-)  N
3038 ASP   ( 111-)  N
3158 ASP   ( 106-)  O
3164 ASP   ( 112-)  O
3196 ASP   (  16-)  P
3382 ASP   (  21-)  R
3479 ASP   (  29-)  S
3502 ASP   (  52-)  S
3579 ASP   (  46-)  T
3648 ASP   (  30-)  U
3715 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.

1517 GLU   (   4-)  E
1548 GLU   (  35-)  E
1565 GLU   (  52-)  E
1629 GLU   ( 116-)  E
1656 GLU   ( 143-)  E
1771 GLU   (  19-)  F
1842 GLU   (  90-)  F
1958 GLU   ( 206-)  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
2244 GLU   (  81-)  H
2312 GLU   ( 149-)  H
2318 GLU   ( 155-)  H
2340 GLU   (  22-)  I
2360 GLU   (  42-)  I
2470 GLU   (  52-)  J
2485 GLU   (  67-)  J
2492 GLU   (  74-)  J
2508 GLU   (  90-)  J
2557 GLU   ( 139-)  J
2596 GLU   (  22-)  K
2607 GLU   (  33-)  K
2713 GLU   (   2-)  L
2746 GLU   (  35-)  L
2919 GLU   (  83-)  M
2931 GLU   (  95-)  M
3125 GLU   (  73-)  O
3212 GLU   (  32-)  P
3215 GLU   (  35-)  P
3241 GLU   (  61-)  P
3347 GLU   (  46-)  Q
3368 GLU   (   7-)  R
3375 GLU   (  14-)  R
3402 GLU   (  41-)  R
3444 GLU   (  83-)  R
3504 GLU   (  54-)  S
3594 GLU   (  61-)  T
3646 GLU   (  28-)  U
3656 GLU   (  38-)  U
3664 GLU   (  46-)  U
3724 GLU   (  21-)  V
3828 GLU   (  46-)  W
3842 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.

3950 MIA   (  37-)  D
4026 MIA   (  37-)  B
4102 MIA   (  37-)  C

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 768 OURA  ( 788-)  A      N3   C2    1.40    4.3
 768 OURA  ( 788-)  A      C4   N3    1.44    6.7
 774 OADE  ( 794-)  A      C2   N3    1.37    4.1
1970 CYS   (  12-)  G      CA   CB    1.62    4.3

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000495  0.000061  0.000216|
 |  0.000061  1.000661  0.000038|
 |  0.000216  0.000038  1.000504|
Proposed new scale matrix

 |  0.004772  0.000000 -0.000001|
 |  0.000000  0.002240  0.000000|
 |  0.000000  0.000000  0.001604|
With corresponding cell

    A    = 209.572  B   = 446.524  C    = 623.367
    Alpha=  90.006  Beta=  89.991  Gamma=  90.004

The CRYST1 cell dimensions

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

Variance: 314.441
(Under-)estimated Z-score: 13.069

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.

   3 OGUA  (   6-)  A      N9   C8   N7  113.21    4.2
   4 OGUA  (   7-)  A      C4'  O4'  C1' 105.89   -4.1
   4 OGUA  (   7-)  A      C2'  C1'  N9  123.03    6.0
   5 OADE  (   8-)  A      C2'  C1'  N9  122.57    5.7
   8 OGUA  (  11-)  A      N9   C8   N7  113.22    4.2
  12 OGUA  (  15-)  A      N9   C8   N7  113.33    4.5
  24 OGUA  (  27-)  A      N9   C8   N7  113.32    4.4
  25 OGUA  (  28-)  A      N9   C8   N7  113.15    4.1
  28 OGUA  (  31-)  A      C2'  C1'  N9  120.19    4.2
  35 OGUA  (  38-)  A      N9   C8   N7  113.16    4.1
  39 OGUA  (  42-)  A      N9   C8   N7  113.13    4.1
  41 OGUA  (  44-)  A      N9   C8   N7  113.21    4.2
  54 OGUA  (  57-)  A      N9   C8   N7  113.21    4.2
  58 OGUA  (  61-)  A      N9   C8   N7  113.12    4.0
  63 OGUA  (  66-)  A      N9   C8   N7  113.26    4.3
  66 OGUA  (  69-)  A      N9   C8   N7  113.14    4.1
  67 OGUA  (  73-)  A      N9   C8   N7  113.17    4.1
  70 OGUA  (  76-)  A      N9   C8   N7  113.21    4.2
  72 OGUA  (  78-)  A      N9   C8   N7  113.19    4.2
  73 OGUA  (  79-)  A      N9   C8   N7  113.14    4.1
  74 OGUA  (  80-)  A      N9   C8   N7  113.15    4.1
  85 OGUA  (  92-)  A      N9   C8   N7  113.21    4.2
  87 OGUA  (  95-)  A      N9   C8   N7  113.18    4.2
  88 OGUA  (  96-)  A      N9   C8   N7  113.16    4.1
  95 OGUA  ( 105-)  A      N9   C8   N7  113.12    4.0
And so on for a total of 357 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.

1517 GLU   (   4-)  E
1548 GLU   (  35-)  E
1565 GLU   (  52-)  E
1573 ASP   (  60-)  E
1629 GLU   ( 116-)  E
1656 GLU   ( 143-)  E
1679 ASP   ( 166-)  E
1706 ASP   ( 193-)  E
1711 ASP   ( 198-)  E
1771 GLU   (  19-)  F
1842 GLU   (  90-)  F
1935 ASP   ( 183-)  F
1958 GLU   ( 206-)  F
1961 ARG   (   3-)  G
1992 GLU   (  34-)  G
2038 GLU   (  80-)  G
2039 GLU   (  81-)  G
2076 ARG   ( 118-)  G
2092 ASP   ( 134-)  G
2103 GLU   ( 145-)  G
2108 GLU   ( 150-)  G
2114 GLU   ( 156-)  G
2150 GLU   ( 192-)  G
2151 ASP   ( 193-)  G
2163 GLU   ( 205-)  G
And so on for a total of 85 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.

3264 ILE   (  84-)  P      CB     6.8    41.11    32.31
The average deviation= 0.710

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.

1970 CYS   (  12-)  G    8.18
3636 ARG   (  18-)  U    7.49
3199 LEU   (  19-)  P    6.05
3198 ALA   (  18-)  P    6.04
1983 ARG   (  25-)  G    5.95
2763 ALA   (  52-)  L    5.50
1630 GLU   ( 117-)  E    5.42
1968 ARG   (  10-)  G    5.33
3834 ALA   (  52-)  W    5.29
1969 LEU   (  11-)  G    5.29
1991 MET   (  33-)  G    5.21
1984 CYS   (  26-)  G    5.19
1992 GLU   (  34-)  G    5.10
2448 ILE   (  30-)  J    4.79
1990 ALA   (  32-)  G    4.69
2181 ARG   (  18-)  H    4.65
2389 ARG   (  71-)  I    4.65
3716 ASP   (  13-)  V    4.62
2336 GLN   (  18-)  I    4.60
2016 LEU   (  58-)  G    4.54
1625 VAL   ( 112-)  E    4.47
2301 ALA   ( 138-)  H    4.39
2274 GLU   ( 111-)  H    4.38
3525 ARG   (  75-)  S    4.37
3264 ILE   (  84-)  P    4.37
3635 SER   (  17-)  U    4.34
3858 ALA   (  76-)  W    4.31
3439 TYR   (  78-)  R    4.29
2454 LYS   (  36-)  J    4.27
2165 TYR   ( 207-)  G    4.27
2479 VAL   (  61-)  J    4.26
2121 GLU   ( 163-)  G    4.26
2074 GLN   ( 116-)  G    4.22
2404 ARG   (  86-)  I    4.22
2189 PHE   (  26-)  H    4.20
2312 GLU   ( 149-)  H    4.14
3678 ALA   (  60-)  U    4.06
3138 ARG   (  86-)  O    4.06
3510 LEU   (  60-)  S    4.04
2771 ASP   (  60-)  L    4.03

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.

1515 OURA  (1541-)  A    0.18
1514 OURA  (1540-)  A    0.11
 Ramachandran Z-score : -6.372

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 : -6.372

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.

3094 THR   (  42-)  O    -3.6
1519 THR   (   6-)  E    -3.3
1917 THR   ( 165-)  F    -3.2
3315 PRO   (  14-)  Q    -3.1
1987 PRO   (  29-)  G    -3.1
3700 THR   (  82-)  U    -3.1
3243 THR   (  63-)  P    -3.1
2291 PRO   ( 128-)  H    -3.1
2569 TYR   ( 151-)  J    -3.0
3855 HIS   (  73-)  W    -3.0
2241 HIS   (  78-)  H    -2.9
3782 THR   (  79-)  V    -2.9
2472 THR   (  54-)  J    -2.9
1908 ARG   ( 156-)  F    -2.8
1532 HIS   (  19-)  E    -2.8
2732 PRO   (  21-)  L    -2.8
3184 ILE   (   4-)  P    -2.7
2825 TYR   ( 114-)  L    -2.7
1536 ARG   (  23-)  E    -2.7
3655 VAL   (  37-)  U    -2.7
3187 VAL   (   7-)  P    -2.7
2622 TYR   (  48-)  K    -2.6
2214 VAL   (  51-)  H    -2.6
1825 PRO   (  73-)  F    -2.6
2243 ILE   (  80-)  H    -2.6
And so on for a total of 171 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 ILE   (   5-)  E  Poor phi/psi
1519 THR   (   6-)  E  Poor phi/psi
1520 VAL   (   7-)  E  Poor phi/psi
1521 LYS   (   8-)  E  Poor phi/psi
1522 GLU   (   9-)  E  Poor phi/psi
1532 HIS   (  19-)  E  Poor phi/psi
1533 GLU   (  20-)  E  Poor phi/psi
1539 PRO   (  26-)  E  Poor phi/psi
1552 ILE   (  39-)  E  Poor phi/psi
1586 THR   (  73-)  E  Poor phi/psi
1587 LYS   (  74-)  E  Poor phi/psi
1588 LYS   (  75-)  E  Poor phi/psi
1592 ASP   (  79-)  E  Poor phi/psi
1600 ARG   (  87-)  E  Poor phi/psi
1601 ALA   (  88-)  E  Poor phi/psi
1609 ARG   (  96-)  E  Poor phi/psi
1614 MET   ( 101-)  E  Poor phi/psi
1634 LEU   ( 121-)  E  Poor phi/psi
1635 PHE   ( 122-)  E  Poor phi/psi
1642 GLU   ( 129-)  E  Poor phi/psi
1643 ARG   ( 130-)  E  Poor phi/psi
1666 ARG   ( 153-)  E  Poor phi/psi
1667 LEU   ( 154-)  E  Poor phi/psi
1674 ALA   ( 161-)  E  Poor phi/psi
1694 PHE   ( 181-)  E  Poor phi/psi
And so on for a total of 312 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.405

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.

2062 VAL   ( 104-)  G    0.39
3819 SER   (  37-)  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  (   6-)  A      0
   4 OGUA  (   7-)  A      0
   5 OADE  (   8-)  A      0
   6 OGUA  (   9-)  A      0
   7 OADE  (  10-)  A      0
   8 OGUA  (  11-)  A      0
   9 OURA  (  12-)  A      0
  10 OURA  (  13-)  A      0
  11 OURA  (  14-)  A      0
  12 OGUA  (  15-)  A      0
  13 OADE  (  16-)  A      0
  14 OURA  (  17-)  A      0
  15 OCYT  (  18-)  A      0
  16 OCYT  (  19-)  A      0
  17 OURA  (  20-)  A      0
  18 OGUA  (  21-)  A      0
  19 OGUA  (  22-)  A      0
  20 OCYT  (  23-)  A      0
  21 OURA  (  24-)  A      0
  22 OCYT  (  25-)  A      0
  23 OADE  (  26-)  A      0
  24 OGUA  (  27-)  A      0
  25 OGUA  (  28-)  A      0
  26 OGUA  (  29-)  A      0
  27 OURA  (  30-)  A      0
And so on for a total of 2795 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 : 1.034

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!

3513 GLY   (  63-)  S   3.04   32
3829 GLY   (  47-)  W   2.18   18
3140 GLY   (  88-)  O   2.17   17
2868 GLY   (  31-)  M   2.16   51
2704 GLY   ( 130-)  K   1.90   20
3447 GLY   (  86-)  R   1.78   13
3280 GLY   ( 100-)  P   1.74   66
3186 GLY   (   6-)  P   1.70   11
1762 PHE   (  10-)  F   1.69   15
1897 GLY   ( 145-)  F   1.69   80
2277 GLY   ( 114-)  H   1.66   59
2629 GLY   (  55-)  K   1.61   30
2664 GLY   (  90-)  K   1.60   15
2761 LEU   (  50-)  L   1.57   27
3196 ASP   (  16-)  P   1.51   80

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...

1971 ARG   (  13-)  G   1.78

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  -118.0 half-chair C-delta/C-gamma (-126 degrees)
1745 PRO   ( 232-)  E   102.5 envelop C-beta (108 degrees)
3315 PRO   (  14-)  Q   -64.3 envelop C-beta (-72 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.

5589  MG   ( 720-)  2     MG   <-> 5590  MG   ( 721-)  2     MG      1.54    1.46  INTRA BL
5588  MG   ( 719-)  2     MG   <-> 5678  MG   ( 925-)  2     MG      1.53    1.67  INTRA BL
5614  MG   ( 745-)  2     MG   <-> 5775  MG   (1132-)  2     MG      1.31    1.89  INTRA BL
5612  MG   ( 743-)  2     MG   <-> 5699  MG   ( 965-)  2     MG      1.28    1.92  INTRA BL
1979 LEU   (  21-)  G      CD1 <-> 5242  ZN   ( 210-)  G     ZN      1.27    1.93  INTRA BL
5330  MG   ( 536-)  C     MG   <-> 5391  MG   ( 569-)  C     MG      1.27    1.93  INTRA BL
5609  MG   ( 740-)  2     MG   <-> 5883  MG   (1343-)  2     MG      1.26    1.94  INTRA BL
5611  MG   ( 742-)  2     MG   <-> 5883  MG   (1343-)  2     MG      1.21    1.99  INTRA BL
4606  MG   ( 209-)  2     MG   <-> 6096  MG   (1767-)  2     MG      1.20    2.00  INTRA BL
4325  MG   (1642-)  A     MG   <-> 5016  MG   (2142-)  A     MG      1.20    2.00  INTRA BF
4227  MG   (1572-)  A     MG   <-> 4696  MG   (1913-)  A     MG      1.19    2.01  INTRA BL
4545  MG   (1805-)  A     MG   <-> 5289  MG   ( 801-)  A     MG      1.16    2.04  INTRA BL
5627  MG   ( 788-)  2     MG   <-> 6133  MG   (1841-)  2     MG      1.16    2.04  INTRA BL
4503  MG   (1777-)  A     MG   <-> 4504  MG   (1778-)  A     MG      1.16    1.84  INTRA BF
5438  MG   ( 363-)  B     MG   <-> 5473  MG   (1561-)  B     MG      1.15    2.05  INTRA BL
4333  MG   (  70-)  2     MG   <-> 5979  MG   (1548-)  2     MG      1.15    2.05  INTRA BL
4185  MG   (1543-)  A     MG   <-> 4626  MG   (1863-)  A     MG      1.15    2.05  INTRA BL
5322  MG   (  80-)  D     MG   <-> 5413  MG   (1737-)  D     MG      1.14    2.06  INTRA BL
4230  MG   (1574-)  A     MG   <-> 5154  MG   (2242-)  A     MG      1.13    2.07  INTRA BF
4564  MG   (1818-)  A     MG   <-> 4565  MG   (1819-)  A     MG      1.13    1.87  INTRA BL
4518  MG   (1787-)  A     MG   <-> 4789  MG   (1984-)  A     MG      1.10    2.10  INTRA BF
4494  MG   (1771-)  A     MG   <-> 4497  MG   (1773-)  A     MG      1.09    2.11  INTRA BL
4230  MG   (1574-)  A     MG   <-> 5166  MG   (2250-)  A     MG      1.07    2.13  INTRA BL
4315  MG   (  58-)  2     MG   <-> 5950  MG   (1493-)  2     MG      1.06    2.14  INTRA BF
4219  MG   (1566-)  A     MG   <-> 5217  MG   (2290-)  A     MG      1.05    2.15  INTRA BL
And so on for a total of 4551 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.

1831 ARG   (  79-)  F      -8.43
3636 ARG   (  18-)  U      -8.24
3449 ARG   (  88-)  R      -8.09
3596 ARG   (  63-)  T      -7.77
2007 ARG   (  49-)  G      -7.72
3911 ARG   (  24-)  X      -7.71
3279 ARG   (  99-)  P      -7.63
3284 ARG   ( 104-)  P      -7.49
2643 ARG   (  69-)  K      -7.48
3784 ARG   (  81-)  V      -7.47
2421 ARG   (   3-)  J      -7.36
2422 ARG   (   4-)  J      -7.35
2183 GLN   (  20-)  H      -7.33
2000 GLN   (  42-)  G      -7.32
1961 ARG   (   3-)  G      -7.31
3783 TYR   (  80-)  V      -7.31
1972 ARG   (  14-)  G      -7.30
1993 ARG   (  35-)  G      -7.28
3732 ARG   (  29-)  V      -7.28
1996 TYR   (  38-)  G      -7.20
1962 TYR   (   4-)  G      -7.20
2642 ARG   (  68-)  K      -7.17
2450 ARG   (  32-)  J      -7.14
3047 ARG   ( 120-)  N      -7.14
3781 ARG   (  78-)  V      -7.11
And so on for a total of 175 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)         -5.75
1669 LYS   ( 156-)  E      1671 - LEU    158- ( E)         -5.03
1742 VAL   ( 229-)  E      1745 - PRO    232- ( E)         -4.75
1754 GLY   (   2-)  F      1757 - ILE      5- ( F)         -4.93
1961 ARG   (   3-)  G      1963 - ILE      5- ( G)         -6.56
2003 GLN   (  45-)  G      2005 - ARG     47- ( G)         -5.22
2042 LYS   (  84-)  G      2044 - LYS     86- ( G)         -4.94
2181 ARG   (  18-)  H      2184 - ALA     21- ( H)         -5.57
2421 ARG   (   3-)  J      2424 - ARG      6- ( J)         -6.95
2428 ARG   (  10-)  J      2431 - GLN     13- ( J)         -5.06
2434 LEU   (  16-)  J      2436 - TYR     18- ( J)         -4.18
2642 ARG   (  68-)  K      2644 - GLN     70- ( K)         -6.65
2823 LYS   ( 112-)  L      2825 - TYR    114- ( L)         -5.12
3052 PHE   ( 125-)  N      3054 - LYS    127- ( N)         -5.05
3070 VAL   (  18-)  O      3072 - LYS     20- ( O)         -5.16
3125 GLU   (  73-)  O      3127 - HIS     75- ( O)         -4.72
3297 VAL   ( 117-)  P      3299 - GLY    119- ( P)         -4.25
3374 GLN   (  13-)  R      3376 - PHE     15- ( R)         -4.49
3462 LYS   (  12-)  S      3464 - ASN     14- ( S)         -5.35
3530 PHE   (  80-)  S      3534 - ALA     84- ( S)         -5.47
3635 SER   (  17-)  U      3637 - LYS     19- ( U)         -6.25
3708 LEU   (   5-)  V      3710 - LYS      7- ( V)         -5.56
3731 LYS   (  28-)  V      3733 - LEU     30- ( V)         -5.71
3885 GLY   ( 103-)  W      3888 - ALA    106- ( W)         -4.89
3907 LYS   (  20-)  X      3909 - ARG     22- ( X)         -5.19

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 - 4171 : -1.774

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.

2000 GLN   (  42-)  G   -3.54
2835 GLN   ( 124-)  L   -3.42
2953 ASN   (  26-)  N   -3.26
3286 ASN   ( 106-)  P   -3.25
3098 LYS   (  46-)  O   -3.21
2839 ARG   ( 128-)  L   -3.18
3143 LYS   (  91-)  O   -3.15
2183 GLN   (  20-)  H   -3.10
3709 LYS   (   6-)  V   -3.10
3475 ARG   (  25-)  S   -3.09
3284 ARG   ( 104-)  P   -3.05
1914 GLN   ( 162-)  F   -3.02
2823 LYS   ( 112-)  L   -3.02
3322 TYR   (  21-)  Q   -3.02
3332 ARG   (  31-)  Q   -3.00
3281 GLN   ( 101-)  P   -2.99
1755 ASN   (   3-)  F   -2.98
2575 MET   (   1-)  K   -2.91
1983 ARG   (  25-)  G   -2.90
3640 VAL   (  22-)  U   -2.90
3262 MET   (  82-)  P   -2.89
3851 GLY   (  69-)  W   -2.86
1764 LEU   (  12-)  F   -2.84
3786 HIS   (  83-)  V   -2.83
2368 TYR   (  50-)  I   -2.82
And so on for a total of 55 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        -2.15
1997 PRO   (  39-)  G     - 2001 HIS   (  43-)  G        -1.82
2420 ALA   (   2-)  J     - 2423 ARG   (   5-)  J        -2.28
2449 MET   (  31-)  J     - 2452 GLY   (  34-)  J        -1.80
2574 TRP   ( 156-)  J     - 2577 THR   (   3-)  K        -2.24
2821 GLU   ( 110-)  L     - 2825 TYR   ( 114-)  L        -2.14
2834 PRO   ( 123-)  L     - 2839 ARG   ( 128-)  L        -2.49
2875 ILE   (  38-)  M     - 2878 PRO   (  41-)  M        -2.07
2884 PHE   (  47-)  M     - 2887 ILE   (  50-)  M        -1.79
3042 PRO   ( 115-)  N     - 3047 ARG   ( 120-)  N        -2.12
3048 PRO   ( 121-)  N     - 3051 LYS   ( 124-)  N        -1.58
3097 PRO   (  45-)  O     - 3103 ALA   (  51-)  O        -2.10
3260 ARG   (  80-)  P     - 3263 ASP   (  83-)  P        -2.21
3278 VAL   (  98-)  P     - 3282 ARG   ( 102-)  P        -2.16
3283 THR   ( 103-)  P     - 3286 ASN   ( 106-)  P        -2.19
3297 VAL   ( 117-)  P     - 3300 LYS   ( 120-)  P        -2.19
3358 ARG   (  57-)  Q     - 3361 SER   (  60-)  Q        -1.99
3460 GLY   (  10-)  S     - 3463 HIS   (  13-)  S        -2.12
3476 ARG   (  26-)  S     - 3479 ASP   (  29-)  S        -1.99
3849 ALA   (  67-)  W     - 3853 THR   (  71-)  W        -2.11

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.

1888 GLN   ( 136-)  F
2020 GLN   (  62-)  G
2228 ASN   (  65-)  H
2418 ASN   ( 100-)  I
2469 GLN   (  51-)  J
2566 ASN   ( 148-)  J
2740 ASN   (  29-)  L
2858 GLN   (  21-)  M
3044 ASN   ( 117-)  N
3060 ASN   (   8-)  O
3061 GLN   (   9-)  O
3101 ASN   (  49-)  O
3272 HIS   (  92-)  P
3281 GLN   ( 101-)  P
3800 GLN   (  18-)  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.

   1 OURA  (   4-)  A      N3
   2 OURA  (   5-)  A      N3
   3 OGUA  (   6-)  A      N1
  48 OADE  (  51-)  A      N6
  62 OURA  (  65-)  A      O2'
  94 OGUA  ( 104-)  A      N2
  97 OGUA  ( 107-)  A      N1
  98 OGUA  ( 108-)  A      N1
  98 OGUA  ( 108-)  A      N2
 100 OCYT  ( 110-)  A      N4
 102 OGUA  ( 112-)  A      N2
 143 OADE  ( 152-)  A      N6
 193 OURA  ( 191-)  A      N3
 194 OGUA  ( 191-)  A      N2
 218 OGUA  ( 226-)  A      N2
 224 OGUA  ( 232-)  A      N2
 246 OGUA  ( 254-)  A      N2
 260 OCYT  ( 268-)  A      N4
 261 OCYT  ( 269-)  A      N4
 271 OADE  ( 279-)  A      N6
 282 OCYT  ( 290-)  A      N4
 310 OGUA  ( 318-)  A      N2
 314 OCYT  ( 322-)  A      N4
 335 OURA  ( 343-)  A      N3
 338 OGUA  ( 346-)  A      N2
And so on for a total of 560 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.

1597 GLU   (  84-)  E      OE1
1607 ASN   (  94-)  E      OD1
1654 GLU   ( 141-)  E      OE1
1679 ASP   ( 166-)  E      OD2
1683 GLU   ( 170-)  E      OE1
1702 ASP   ( 189-)  E      OD1
1702 ASP   ( 189-)  E      OD2
1718 ASP   ( 205-)  E      OD2
1719 ASP   ( 206-)  E      OD1
1787 GLU   (  35-)  F      OE2
1788 ASP   (  36-)  F      OD2
1928 HIS   ( 176-)  F      NE2
1973 GLU   (  15-)  G      OE1
1982 GLU   (  24-)  G      OE2
2001 HIS   (  43-)  G      ND1
2158 GLU   ( 200-)  G      OE1
2241 HIS   (  78-)  H      ND1
2340 GLU   (  22-)  I      OE1
2433 ASP   (  15-)  J      OD2
2582 ASP   (   8-)  K      OD2
2723 GLU   (  12-)  L      OE1
2905 ASN   (  69-)  M      OD1
2909 ASP   (  73-)  M      OD1
2994 ASP   (  67-)  N      OD1
3026 GLN   (  99-)  N      OE1
3101 ASN   (  49-)  O      OD1
3263 ASP   (  83-)  P      OD1
3382 ASP   (  21-)  R      OD1
3466 HIS   (  16-)  S      NE2
3578 HIS   (  45-)  T      ND1
3681 GLN   (  63-)  U      OE1
3715 ASP   (  12-)  V      OD2
3750 HIS   (  47-)  V      NE2
3776 GLU   (  73-)  V      OE1

Warning: Unusual ion packing

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

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

4182  MG   (   1-)  2   -.-  -.-  Too few ligands (0)
4183  MG   (   2-)  2   -.-  -.-  Part of ionic cluster
4183  MG   (   2-)  2   -.-  -.-  Too few ligands (0)
4184  MG   (   3-)  A   -.-  -.-  Part of ionic cluster
4184  MG   (   3-)  A   -.-  -.-  Too few ligands (0)
4185  MG   (1543-)  A   -.-  -.-  Part of ionic cluster
4185  MG   (1543-)  A   -.-  -.-  Too few ligands (0)
4186  MG   (1544-)  A   -.-  -.-  Part of ionic cluster
4186  MG   (1544-)  A   -.-  -.-  Too few ligands (2)
4187  MG   (   4-)  2   -.-  -.-  Too few ligands (0)
4188  MG   (1545-)  A   -.-  -.-  Too few ligands (0)
4189  MG   (1546-)  A   -.-  -.-  Part of ionic cluster
4189  MG   (1546-)  A   -.-  -.-  Too few ligands (0)
4190  MG   (   5-)  2   -.-  -.-  Too few ligands (0)
4191  MG   (1547-)  A   -.-  -.-  Part of ionic cluster
4191  MG   (1547-)  A   -.-  -.-  Too few ligands (2)
4192  MG   (1548-)  A   -.-  -.-  Part of ionic cluster
4192  MG   (1548-)  A   -.-  -.-  Too few ligands (0)
4193  MG   (1549-)  A   -.-  -.-  Too few ligands (2)
4194  MG   (1550-)  A   -.-  -.-  Low probability ion. B= 93.2
4195  MG   (1551-)  A   -.-  -.-  Part of ionic cluster
4195  MG   (1551-)  A   -.-  -.-  Too few ligands (1)
4196  MG   (   7-)  2   -.-  -.-  Too few ligands (0)
4197  MG   (1552-)  A   -.-  -.-  Part of ionic cluster
4198  MG   (1553-)  A   -.-  -.-  Part of ionic cluster
And so on for a total of 2846 lines.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

1562 GLU   (  49-)  E   H-bonding suggests Gln
1597 GLU   (  84-)  E   H-bonding suggests Gln; but Alt-Rotamer
1683 GLU   ( 170-)  E   H-bonding suggests Gln
1769 ASP   (  17-)  F   H-bonding suggests Asn
1771 GLU   (  19-)  F   H-bonding suggests Gln; but Alt-Rotamer
1877 GLU   ( 125-)  F   H-bonding suggests Gln
1973 GLU   (  15-)  G   H-bonding suggests Gln; but Alt-Rotamer
1982 GLU   (  24-)  G   H-bonding suggests Gln
2102 ASP   ( 144-)  G   H-bonding suggests Asn
2213 GLU   (  50-)  H   H-bonding suggests Gln; but Alt-Rotamer
2285 GLU   ( 122-)  H   H-bonding suggests Gln
2310 ASP   ( 147-)  H   H-bonding suggests Asn; but Alt-Rotamer
2392 ASP   (  74-)  I   H-bonding suggests Asn
2544 ASP   ( 126-)  J   H-bonding suggests Asn
2560 GLU   ( 142-)  J   H-bonding suggests Gln; but Alt-Rotamer
2673 GLU   (  99-)  K   H-bonding suggests Gln
2723 GLU   (  12-)  L   H-bonding suggests Gln
2771 ASP   (  60-)  L   H-bonding suggests Asn
2909 ASP   (  73-)  M   H-bonding suggests Asn; but Alt-Rotamer
2933 GLU   (  97-)  M   H-bonding suggests Gln; but Alt-Rotamer
3179 GLU   ( 127-)  O   H-bonding suggests Gln
3188 GLU   (   8-)  P   H-bonding suggests Gln
3227 ASP   (  47-)  P   H-bonding suggests Asn
3263 ASP   (  83-)  P   H-bonding suggests Asn
3309 GLU   (   8-)  Q   H-bonding suggests Gln
3402 GLU   (  41-)  R   H-bonding suggests Gln
3579 ASP   (  46-)  T   H-bonding suggests Asn
3588 ASP   (  55-)  T   H-bonding suggests Asn
3648 ASP   (  30-)  U   H-bonding suggests Asn
3724 GLU   (  21-)  V   H-bonding suggests Gln
3730 GLU   (  27-)  V   H-bonding suggests Gln
3846 ASP   (  64-)  W   H-bonding suggests Asn; but Alt-Rotamer
3875 GLU   (  93-)  W   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.185
  2nd generation packing quality :  -3.881 (poor)
  Ramachandran plot appearance   :  -6.372 (bad)
  chi-1/chi-2 rotamer normality  :  -4.405 (bad)
  Backbone conformation          :  -0.377

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.445 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   0.188 (tight)
  Side chain planarity           :   0.168 (tight)
  Improper dihedral distribution :   0.617
  B-factor distribution          :   0.373
  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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.0
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -3.5 (poor)
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.445 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   0.188 (tight)
  Side chain planarity           :   0.168 (tight)
  Improper dihedral distribution :   0.617
  B-factor distribution          :   0.373
  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.