WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1rbl.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 223.900  B   = 111.900  C    = 199.700
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 223.900  B   = 111.900  C    = 199.700
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 111.900  B   = 199.700  C    = 223.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 111.900  B   = 199.700  C    = 223.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  1.000000  0.000000  0.000000|

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

4626 CAP   ( 476-)  A  -
4628 CAP   ( 476-)  B  -
4631 CAP   ( 476-)  C  -
4634 CAP   ( 476-)  D  -
4637 CAP   ( 476-)  E  -
4640 CAP   ( 476-)  F  -
4643 CAP   ( 476-)  G  -
4648 CAP   ( 476-)  H  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 193 LYS   ( 201-)  A  -   NZ  bound to 4629 FMT   ( 478-)  A  -   C
 769 LYS   ( 201-)  B  -   NZ  bound to 4632 FMT   ( 478-)  B  -   C
1345 LYS   ( 201-)  C  -   NZ  bound to 4635 FMT   ( 478-)  C  -   C
1921 LYS   ( 201-)  D  -   NZ  bound to 4638 FMT   ( 478-)  D  -   C
2497 LYS   ( 201-)  E  -   NZ  bound to 4641 FMT   ( 478-)  E  -   C
3073 LYS   ( 201-)  F  -   NZ  bound to 4644 FMT   ( 478-)  F  -   C
3649 LYS   ( 201-)  G  -   NZ  bound to 4646 FMT   ( 478-)  G  -   C
4225 LYS   ( 201-)  H  -   NZ  bound to 4647 FMT   ( 478-)  H  -   C

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 SER   (   9-)  A  -   CB
   1 SER   (   9-)  A  -   OG
   2 ALA   (  10-)  A  -   CB
   3 ALA   (  11-)  A  -   CB
 576 ARG   ( 122-)  M  -   CB
 576 ARG   ( 122-)  M  -   CG
 576 ARG   ( 122-)  M  -   CD
 576 ARG   ( 122-)  M  -   NE
 576 ARG   ( 122-)  M  -   CZ
 576 ARG   ( 122-)  M  -   NH1
 576 ARG   ( 122-)  M  -   NH2
 577 SER   (   9-)  B  -   CB
 577 SER   (   9-)  B  -   OG
 578 ALA   (  10-)  B  -   CB
 579 ALA   (  11-)  B  -   CB
1152 ARG   ( 122-)  I  -   CB
1152 ARG   ( 122-)  I  -   CG
1152 ARG   ( 122-)  I  -   CD
1152 ARG   ( 122-)  I  -   NE
1152 ARG   ( 122-)  I  -   CZ
1152 ARG   ( 122-)  I  -   NH1
1152 ARG   ( 122-)  I  -   NH2
1153 SER   (   9-)  C  -   CB
1153 SER   (   9-)  C  -   OG
1154 ALA   (  10-)  C  -   CB
And so on for a total of 88 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

   1 SER   (   9-)  A  -   N
   1 SER   (   9-)  A  -   CA
   1 SER   (   9-)  A  -   C
   1 SER   (   9-)  A  -   O
   2 ALA   (  10-)  A  -   N
   2 ALA   (  10-)  A  -   CA
   2 ALA   (  10-)  A  -   C
   2 ALA   (  10-)  A  -   O
   3 ALA   (  11-)  A  -   N
   3 ALA   (  11-)  A  -   CA
   3 ALA   (  11-)  A  -   C
   3 ALA   (  11-)  A  -   O
 576 ARG   ( 122-)  M  -   N
 576 ARG   ( 122-)  M  -   CA
 576 ARG   ( 122-)  M  -   C
 576 ARG   ( 122-)  M  -   O
 577 SER   (   9-)  B  -   N
 577 SER   (   9-)  B  -   CA
 577 SER   (   9-)  B  -   C
 577 SER   (   9-)  B  -   O
 578 ALA   (  10-)  B  -   N
 578 ALA   (  10-)  B  -   CA
 578 ALA   (  10-)  B  -   C
 578 ALA   (  10-)  B  -   O
 579 ALA   (  11-)  B  -   N
And so on for a total of 136 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: L

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: L

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.

 126 ARG   ( 134-)  A
 151 ARG   ( 159-)  A
 207 ARG   ( 215-)  A
 209 ARG   ( 217-)  A
 476 ARG   (  10-)  M
 545 ARG   (  91-)  M
 702 ARG   ( 134-)  B
 727 ARG   ( 159-)  B
 783 ARG   ( 215-)  B
 785 ARG   ( 217-)  B
1052 ARG   (  10-)  I
1121 ARG   (  91-)  I
1278 ARG   ( 134-)  C
1303 ARG   ( 159-)  C
1359 ARG   ( 215-)  C
1361 ARG   ( 217-)  C
1628 ARG   (  10-)  N
1697 ARG   (  91-)  N
1854 ARG   ( 134-)  D
1879 ARG   ( 159-)  D
1935 ARG   ( 215-)  D
1937 ARG   ( 217-)  D
2204 ARG   (  10-)  J
2273 ARG   (  91-)  J
2430 ARG   ( 134-)  E
2455 ARG   ( 159-)  E
2511 ARG   ( 215-)  E
2513 ARG   ( 217-)  E
2780 ARG   (  10-)  O
2849 ARG   (  91-)  O
3006 ARG   ( 134-)  F
3031 ARG   ( 159-)  F
3087 ARG   ( 215-)  F
3089 ARG   ( 217-)  F
3356 ARG   (  10-)  K
3425 ARG   (  91-)  K
3582 ARG   ( 134-)  G
3607 ARG   ( 159-)  G
3663 ARG   ( 215-)  G
3665 ARG   ( 217-)  G
3932 ARG   (  10-)  P
4001 ARG   (  91-)  P
4158 ARG   ( 134-)  H
4183 ARG   ( 159-)  H
4239 ARG   ( 215-)  H
4241 ARG   ( 217-)  H
4508 ARG   (  10-)  L
4577 ARG   (  91-)  L

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.

3695 CYS   ( 247-)  G      SG  -SG*   2.23    4.7
4271 CYS   ( 247-)  H      SG  -SG*   2.23    4.7

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.

  28 LEU   (  36-)  A      CA   CB   CG  130.61    4.1
 259 HIS   ( 267-)  A      CG   ND1  CE1 109.70    4.1
 317 HIS   ( 325-)  A      CG   ND1  CE1 109.67    4.1
 319 HIS   ( 327-)  A      CG   ND1  CE1 109.74    4.1
 342 ARG   ( 350-)  A      CB   CG   CD  105.07   -4.5
 604 LEU   (  36-)  B      CA   CB   CG  130.62    4.1
 835 HIS   ( 267-)  B      CG   ND1  CE1 109.68    4.1
 893 HIS   ( 325-)  B      CG   ND1  CE1 109.71    4.1
 895 HIS   ( 327-)  B      CG   ND1  CE1 109.77    4.2
 918 ARG   ( 350-)  B      CB   CG   CD  105.06   -4.5
1180 LEU   (  36-)  C      CA   CB   CG  130.59    4.1
1411 HIS   ( 267-)  C      CG   ND1  CE1 109.67    4.1
1469 HIS   ( 325-)  C      CG   ND1  CE1 109.69    4.1
1471 HIS   ( 327-)  C      CG   ND1  CE1 109.77    4.2
1494 ARG   ( 350-)  C      CB   CG   CD  105.07   -4.5
1756 LEU   (  36-)  D      CA   CB   CG  130.62    4.1
1987 HIS   ( 267-)  D      CG   ND1  CE1 109.71    4.1
2045 HIS   ( 325-)  D      CG   ND1  CE1 109.72    4.1
2047 HIS   ( 327-)  D      CG   ND1  CE1 109.73    4.1
2070 ARG   ( 350-)  D      CB   CG   CD  105.10   -4.5
2332 LEU   (  36-)  E      CA   CB   CG  130.57    4.1
2563 HIS   ( 267-)  E      CG   ND1  CE1 109.73    4.1
2621 HIS   ( 325-)  E      CG   ND1  CE1 109.70    4.1
2623 HIS   ( 327-)  E      CG   ND1  CE1 109.72    4.1
2646 ARG   ( 350-)  E      CB   CG   CD  105.02   -4.5
2908 LEU   (  36-)  F      CA   CB   CG  130.63    4.1
3139 HIS   ( 267-)  F      CG   ND1  CE1 109.71    4.1
3197 HIS   ( 325-)  F      CG   ND1  CE1 109.69    4.1
3199 HIS   ( 327-)  F      CG   ND1  CE1 109.78    4.2
3222 ARG   ( 350-)  F      CB   CG   CD  105.04   -4.5
3484 LEU   (  36-)  G      CA   CB   CG  130.62    4.1
3715 HIS   ( 267-)  G      CG   ND1  CE1 109.74    4.1
3773 HIS   ( 325-)  G      CG   ND1  CE1 109.65    4.1
3775 HIS   ( 327-)  G      CG   ND1  CE1 109.72    4.1
3798 ARG   ( 350-)  G      CB   CG   CD  105.09   -4.5
4028 HIS   ( 118-)  P      CG   ND1  CE1 109.60    4.0
4060 LEU   (  36-)  H      CA   CB   CG  130.60    4.1
4291 HIS   ( 267-)  H      CG   ND1  CE1 109.69    4.1
4349 HIS   ( 325-)  H      CG   ND1  CE1 109.66    4.1
4351 HIS   ( 327-)  H      CG   ND1  CE1 109.70    4.1
4374 ARG   ( 350-)  H      CB   CG   CD  105.07   -4.5

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.

 126 ARG   ( 134-)  A
 151 ARG   ( 159-)  A
 207 ARG   ( 215-)  A
 209 ARG   ( 217-)  A
 476 ARG   (  10-)  M
 545 ARG   (  91-)  M
 702 ARG   ( 134-)  B
 727 ARG   ( 159-)  B
 783 ARG   ( 215-)  B
 785 ARG   ( 217-)  B
1052 ARG   (  10-)  I
1121 ARG   (  91-)  I
1278 ARG   ( 134-)  C
1303 ARG   ( 159-)  C
1359 ARG   ( 215-)  C
1361 ARG   ( 217-)  C
1628 ARG   (  10-)  N
1697 ARG   (  91-)  N
1854 ARG   ( 134-)  D
1879 ARG   ( 159-)  D
1935 ARG   ( 215-)  D
1937 ARG   ( 217-)  D
2204 ARG   (  10-)  J
2273 ARG   (  91-)  J
2430 ARG   ( 134-)  E
2455 ARG   ( 159-)  E
2511 ARG   ( 215-)  E
2513 ARG   ( 217-)  E
2780 ARG   (  10-)  O
2849 ARG   (  91-)  O
3006 ARG   ( 134-)  F
3031 ARG   ( 159-)  F
3087 ARG   ( 215-)  F
3089 ARG   ( 217-)  F
3356 ARG   (  10-)  K
3425 ARG   (  91-)  K
3582 ARG   ( 134-)  G
3607 ARG   ( 159-)  G
3663 ARG   ( 215-)  G
3665 ARG   ( 217-)  G
3932 ARG   (  10-)  P
4001 ARG   (  91-)  P
4158 ARG   ( 134-)  H
4183 ARG   ( 159-)  H
4239 ARG   ( 215-)  H
4241 ARG   ( 217-)  H
4508 ARG   (  10-)  L
4577 ARG   (  91-)  L

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.

 329 GLY   ( 337-)  A      C     -6.7    -8.78     0.06
 342 ARG   ( 350-)  A      C     -6.2    -9.24     0.13
 905 GLY   ( 337-)  B      C     -6.7    -8.79     0.06
 918 ARG   ( 350-)  B      C     -6.2    -9.22     0.13
1481 GLY   ( 337-)  C      C     -6.7    -8.81     0.06
1494 ARG   ( 350-)  C      C     -6.2    -9.22     0.13
2057 GLY   ( 337-)  D      C     -6.7    -8.78     0.06
2070 ARG   ( 350-)  D      C     -6.1    -9.20     0.13
2633 GLY   ( 337-)  E      C     -6.7    -8.81     0.06
2646 ARG   ( 350-)  E      C     -6.2    -9.24     0.13
3209 GLY   ( 337-)  F      C     -6.7    -8.82     0.06
3222 ARG   ( 350-)  F      C     -6.1    -9.20     0.13
3785 GLY   ( 337-)  G      C     -6.7    -8.73     0.06
3798 ARG   ( 350-)  G      C     -6.2    -9.25     0.13
4361 GLY   ( 337-)  H      C     -6.7    -8.79     0.06
4374 ARG   ( 350-)  H      C     -6.2    -9.29     0.13
The average deviation= 1.719

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.

2022 ASP   ( 302-)  D    4.20
1446 ASP   ( 302-)  C    4.18
2598 ASP   ( 302-)  E    4.17
 294 ASP   ( 302-)  A    4.17
3174 ASP   ( 302-)  F    4.16
 870 ASP   ( 302-)  B    4.16
3750 ASP   ( 302-)  G    4.15
4326 ASP   ( 302-)  H    4.15

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1876 GLN   ( 156-)  D    6.75
3028 GLN   ( 156-)  F    6.74
2452 GLN   ( 156-)  E    6.73
 724 GLN   ( 156-)  B    6.72
1300 GLN   ( 156-)  C    6.72
 148 GLN   ( 156-)  A    6.71
3604 GLN   ( 156-)  G    6.69
4180 GLN   ( 156-)  H    6.66
4239 ARG   ( 215-)  H    6.58
1935 ARG   ( 215-)  D    6.58
1359 ARG   ( 215-)  C    6.56
2511 ARG   ( 215-)  E    6.56
3663 ARG   ( 215-)  G    6.56
 207 ARG   ( 215-)  A    6.49
3087 ARG   ( 215-)  F    6.46
1303 ARG   ( 159-)  C    6.39
4183 ARG   ( 159-)  H    6.39
2455 ARG   ( 159-)  E    6.39
3607 ARG   ( 159-)  G    6.38
 727 ARG   ( 159-)  B    6.37
3031 ARG   ( 159-)  F    6.35
 783 ARG   ( 215-)  B    6.34
1879 ARG   ( 159-)  D    6.34
 151 ARG   ( 159-)  A    6.25
3356 ARG   (  10-)  K    6.17
And so on for a total of 127 lines.

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

4177 HIS   ( 153-)  H      CB   4.66
3601 HIS   ( 153-)  G      CB   4.65
 145 HIS   ( 153-)  A      CB   4.64
3025 HIS   ( 153-)  F      CB   4.64
1873 HIS   ( 153-)  D      CB   4.63
2449 HIS   ( 153-)  E      CB   4.63
1297 HIS   ( 153-)  C      CB   4.63
 721 HIS   ( 153-)  B      CB   4.62
1657 HIS   (  39-)  N      CB   4.31
 505 HIS   (  39-)  M      CB   4.30
2233 HIS   (  39-)  J      CB   4.30
3961 HIS   (  39-)  P      CB   4.30
4537 HIS   (  39-)  L      CB   4.30
1081 HIS   (  39-)  I      CB   4.29
3385 HIS   (  39-)  K      CB   4.29
2809 HIS   (  39-)  O      CB   4.28
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.545

Torsion-related checks

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.

3615 ARG   ( 167-)  G    -2.6
2463 ARG   ( 167-)  E    -2.6
4191 ARG   ( 167-)  H    -2.6
 735 ARG   ( 167-)  B    -2.6
1887 ARG   ( 167-)  D    -2.6
3039 ARG   ( 167-)  F    -2.6
 159 ARG   ( 167-)  A    -2.6
1311 ARG   ( 167-)  C    -2.6
2310 LYS   (  14-)  E    -2.5
1734 LYS   (  14-)  D    -2.5
1158 LYS   (  14-)  C    -2.5
   6 LYS   (  14-)  A    -2.5
2886 LYS   (  14-)  F    -2.5
3462 LYS   (  14-)  G    -2.5
4038 LYS   (  14-)  H    -2.5
 582 LYS   (  14-)  B    -2.5
2460 LYS   ( 164-)  E    -2.5
3612 LYS   ( 164-)  G    -2.5
1884 LYS   ( 164-)  D    -2.5
1308 LYS   ( 164-)  C    -2.5
 732 LYS   ( 164-)  B    -2.5
4188 LYS   ( 164-)  H    -2.5
 156 LYS   ( 164-)  A    -2.5
3036 LYS   ( 164-)  F    -2.5
3743 ARG   ( 295-)  G    -2.4
And so on for a total of 120 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.

   2 ALA   (  10-)  A  omega poor
  15 THR   (  23-)  A  omega poor
  54 SER   (  62-)  A  Poor phi/psi
  55 THR   (  63-)  A  omega poor
  57 THR   (  65-)  A  omega poor
  87 ASN   (  95-)  A  Poor phi/psi
  89 TYR   (  97-)  A  omega poor
 155 ASN   ( 163-)  A  Poor phi/psi
 157 TYR   ( 165-)  A  omega poor
 167 LYS   ( 175-)  A  PRO omega poor
 191 PHE   ( 199-)  A  omega poor
 199 ASN   ( 207-)  A  Poor phi/psi
 235 THR   ( 243-)  A  omega poor
 289 MET   ( 297-)  A  Poor phi/psi
 293 ILE   ( 301-)  A  omega poor
 323 VAL   ( 331-)  A  Poor phi/psi
 362 SER   ( 370-)  A  Poor phi/psi
 469 MET   (   3-)  M  Poor phi/psi
 479 GLU   (  13-)  M  Poor phi/psi, omega poor
 481 PHE   (  15-)  M  Poor phi/psi
 525 LYS   (  71-)  M  Poor phi/psi
 551 CYS   (  97-)  M  omega poor
 578 ALA   (  10-)  B  omega poor
 591 THR   (  23-)  B  omega poor
 630 SER   (  62-)  B  Poor phi/psi
And so on for a total of 176 lines.

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.

 333 SER   ( 341-)  A    0.39
 909 SER   ( 341-)  B    0.39
1485 SER   ( 341-)  C    0.39
2061 SER   ( 341-)  D    0.39
2637 SER   ( 341-)  E    0.39
3213 SER   ( 341-)  F    0.39
3789 SER   ( 341-)  G    0.39
4365 SER   ( 341-)  H    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 ALA   (  11-)  A      0
   5 TYR   (  13-)  A      0
   7 ALA   (  15-)  A      0
  15 THR   (  23-)  A      0
  16 TYR   (  24-)  A      0
  17 TYR   (  25-)  A      0
  18 THR   (  26-)  A      0
  38 PRO   (  46-)  A      0
  53 SER   (  61-)  A      0
  54 SER   (  62-)  A      0
  55 THR   (  63-)  A      0
  58 TRP   (  66-)  A      0
  62 TRP   (  70-)  A      0
  66 LEU   (  74-)  A      0
  67 THR   (  75-)  A      0
  77 TYR   (  85-)  A      0
  80 GLU   (  88-)  A      0
  83 ALA   (  91-)  A      0
  86 GLU   (  94-)  A      0
  99 LEU   ( 107-)  A      0
 102 GLU   ( 110-)  A      0
 112 ILE   ( 120-)  A      0
 113 VAL   ( 121-)  A      0
 115 ASN   ( 123-)  A      0
 116 VAL   ( 124-)  A      0
And so on for a total of 1633 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

3209 GLY   ( 337-)  F   1.66   20
3785 GLY   ( 337-)  G   1.66   20
4361 GLY   ( 337-)  H   1.66   20
 905 GLY   ( 337-)  B   1.66   20
 329 GLY   ( 337-)  A   1.66   20
2633 GLY   ( 337-)  E   1.65   20
1481 GLY   ( 337-)  C   1.65   20
2057 GLY   ( 337-)  D   1.65   20
3277 GLY   ( 405-)  F   1.55   80
3853 GLY   ( 405-)  G   1.54   80
4429 GLY   ( 405-)  H   1.54   80
1549 GLY   ( 405-)  C   1.54   80
 397 GLY   ( 405-)  A   1.54   80
 973 GLY   ( 405-)  B   1.54   80
2125 GLY   ( 405-)  D   1.54   80
2701 GLY   ( 405-)  E   1.54   80

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]

 407 PRO   ( 415-)  A    0.20 LOW
 983 PRO   ( 415-)  B    0.20 LOW
1559 PRO   ( 415-)  C    0.20 LOW
2135 PRO   ( 415-)  D    0.20 LOW
2711 PRO   ( 415-)  E    0.20 LOW
3287 PRO   ( 415-)  F    0.20 LOW
3863 PRO   ( 415-)  G    0.20 LOW
4439 PRO   ( 415-)  H    0.20 LOW

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].

  38 PRO   (  46-)  A  -124.6 half-chair C-delta/C-gamma (-126 degrees)
 380 PRO   ( 388-)  A  -124.3 half-chair C-delta/C-gamma (-126 degrees)
 402 PRO   ( 410-)  A  -127.1 half-chair C-delta/C-gamma (-126 degrees)
 614 PRO   (  46-)  B  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 956 PRO   ( 388-)  B  -124.3 half-chair C-delta/C-gamma (-126 degrees)
 978 PRO   ( 410-)  B  -127.0 half-chair C-delta/C-gamma (-126 degrees)
1190 PRO   (  46-)  C  -124.4 half-chair C-delta/C-gamma (-126 degrees)
1532 PRO   ( 388-)  C  -124.3 half-chair C-delta/C-gamma (-126 degrees)
1554 PRO   ( 410-)  C  -127.1 half-chair C-delta/C-gamma (-126 degrees)
1766 PRO   (  46-)  D  -124.6 half-chair C-delta/C-gamma (-126 degrees)
2108 PRO   ( 388-)  D  -124.3 half-chair C-delta/C-gamma (-126 degrees)
2130 PRO   ( 410-)  D  -127.2 half-chair C-delta/C-gamma (-126 degrees)
2342 PRO   (  46-)  E  -124.6 half-chair C-delta/C-gamma (-126 degrees)
2684 PRO   ( 388-)  E  -124.2 half-chair C-delta/C-gamma (-126 degrees)
2706 PRO   ( 410-)  E  -127.0 half-chair C-delta/C-gamma (-126 degrees)
2918 PRO   (  46-)  F  -124.6 half-chair C-delta/C-gamma (-126 degrees)
3260 PRO   ( 388-)  F  -124.4 half-chair C-delta/C-gamma (-126 degrees)
3282 PRO   ( 410-)  F  -127.2 half-chair C-delta/C-gamma (-126 degrees)
3494 PRO   (  46-)  G  -124.6 half-chair C-delta/C-gamma (-126 degrees)
3836 PRO   ( 388-)  G  -124.4 half-chair C-delta/C-gamma (-126 degrees)
3858 PRO   ( 410-)  G  -127.0 half-chair C-delta/C-gamma (-126 degrees)
4070 PRO   (  46-)  H  -124.5 half-chair C-delta/C-gamma (-126 degrees)
4412 PRO   ( 388-)  H  -124.3 half-chair C-delta/C-gamma (-126 degrees)
4434 PRO   ( 410-)  H  -127.1 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 distance; each bump is listed in only one direction,

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

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

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

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

1494 ARG   ( 350-)  C      NH2  <->  1538 PHE   ( 394-)  C      O    0.49    2.21  INTRA
 918 ARG   ( 350-)  B      NH2  <->   962 PHE   ( 394-)  B      O    0.49    2.21  INTRA
2646 ARG   ( 350-)  E      NH2  <->  2690 PHE   ( 394-)  E      O    0.49    2.21  INTRA
3222 ARG   ( 350-)  F      NH2  <->  3266 PHE   ( 394-)  F      O    0.49    2.21  INTRA
 342 ARG   ( 350-)  A      NH2  <->   386 PHE   ( 394-)  A      O    0.49    2.21  INTRA
3798 ARG   ( 350-)  G      NH2  <->  3842 PHE   ( 394-)  G      O    0.49    2.21  INTRA
2070 ARG   ( 350-)  D      NH2  <->  2114 PHE   ( 394-)  D      O    0.49    2.21  INTRA
4374 ARG   ( 350-)  H      NH2  <->  4418 PHE   ( 394-)  H      O    0.49    2.21  INTRA
3307 ARG   ( 435-)  F      NH2  <->  3319 GLU   ( 447-)  F      OE2  0.42    2.28  INTRA BF
3883 ARG   ( 435-)  G      NH2  <->  3895 GLU   ( 447-)  G      OE2  0.42    2.28  INTRA BF
1579 ARG   ( 435-)  C      NH2  <->  1591 GLU   ( 447-)  C      OE2  0.42    2.28  INTRA BF
2155 ARG   ( 435-)  D      NH2  <->  2167 GLU   ( 447-)  D      OE2  0.42    2.28  INTRA BF
 427 ARG   ( 435-)  A      NH2  <->   439 GLU   ( 447-)  A      OE2  0.42    2.28  INTRA BF
4459 ARG   ( 435-)  H      NH2  <->  4471 GLU   ( 447-)  H      OE2  0.42    2.28  INTRA BF
1003 ARG   ( 435-)  B      NH2  <->  1015 GLU   ( 447-)  B      OE2  0.42    2.28  INTRA BF
2731 ARG   ( 435-)  E      NH2  <->  2743 GLU   ( 447-)  E      OE2  0.41    2.29  INTRA BF
1107 CYS   (  77-)  I      SG   <->  1112 GLN   (  82-)  I      NE2  0.33    2.97  INTRA BF
1683 CYS   (  77-)  N      SG   <->  1688 GLN   (  82-)  N      NE2  0.33    2.97  INTRA BF
2259 CYS   (  77-)  J      SG   <->  2264 GLN   (  82-)  J      NE2  0.33    2.97  INTRA BF
 531 CYS   (  77-)  M      SG   <->   536 GLN   (  82-)  M      NE2  0.33    2.97  INTRA BF
4563 CYS   (  77-)  L      SG   <->  4568 GLN   (  82-)  L      NE2  0.33    2.97  INTRA BF
3411 CYS   (  77-)  K      SG   <->  3416 GLN   (  82-)  K      NE2  0.33    2.97  INTRA BF
2835 CYS   (  77-)  O      SG   <->  2840 GLN   (  82-)  O      NE2  0.33    2.97  INTRA BF
3987 CYS   (  77-)  P      SG   <->  3992 GLN   (  82-)  P      NE2  0.33    2.97  INTRA BF
 511 ASN   (  45-)  M      ND2  <->  4650 HOH   ( 145 )  M      O    0.29    2.41  INTRA
And so on for a total of 310 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: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

2301 ARG   ( 119-)  J      -6.93
 573 ARG   ( 119-)  M      -6.93
4605 ARG   ( 119-)  L      -6.93
3453 ARG   ( 119-)  K      -6.93
1149 ARG   ( 119-)  I      -6.90
1725 ARG   ( 119-)  N      -6.90
4029 ARG   ( 119-)  P      -6.89
2877 ARG   ( 119-)  O      -6.89
1851 ARG   ( 131-)  D      -5.86
1275 ARG   ( 131-)  C      -5.83
3003 ARG   ( 131-)  F      -5.82
4173 GLN   ( 149-)  H      -5.79
2445 GLN   ( 149-)  E      -5.79
 717 GLN   ( 149-)  B      -5.79
 141 GLN   ( 149-)  A      -5.79
1293 GLN   ( 149-)  C      -5.79
3021 GLN   ( 149-)  F      -5.79
3597 GLN   ( 149-)  G      -5.79
2427 ARG   ( 131-)  E      -5.75
1869 GLN   ( 149-)  D      -5.75
 123 ARG   ( 131-)  A      -5.75
4155 ARG   ( 131-)  H      -5.72
3323 TRP   ( 451-)  F      -5.71
2747 TRP   ( 451-)  E      -5.71
2171 TRP   ( 451-)  D      -5.71
And so on for a total of 99 lines.

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: A

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: B

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: C

Note: Quality value plot

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

Chain identifier: 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: D

Note: Quality value plot

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

Chain identifier: 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: 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: 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: 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: 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: 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: 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: 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: L

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.

3171 ALA   ( 299-)  F   -2.83
2019 ALA   ( 299-)  D   -2.83
1443 ALA   ( 299-)  C   -2.82
3747 ALA   ( 299-)  G   -2.82
4323 ALA   ( 299-)  H   -2.82
2595 ALA   ( 299-)  E   -2.82
 291 ALA   ( 299-)  A   -2.82
 867 ALA   ( 299-)  B   -2.81
 673 LEU   ( 105-)  B   -2.64
2977 LEU   ( 105-)  F   -2.64
3553 LEU   ( 105-)  G   -2.64
1249 LEU   ( 105-)  C   -2.63
1825 LEU   ( 105-)  D   -2.63
2401 LEU   ( 105-)  E   -2.62
  97 LEU   ( 105-)  A   -2.62
4129 LEU   ( 105-)  H   -2.62

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.

1621 MET   (   3-)  N     - 1624 LEU   (   6-)  N        -1.86
3349 MET   (   3-)  K     - 3352 LEU   (   6-)  K        -1.77

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: A

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: L

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

4650 HOH   ( 135 )  M      O    113.17  -10.02  -55.04

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

4649 HOH   ( 548 )  A      O
4649 HOH   ( 549 )  A      O
4652 HOH   ( 487 )  C      O

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.

 145 HIS   ( 153-)  A
 204 GLN   ( 212-)  A
 221 GLN   ( 229-)  A
 230 HIS   ( 238-)  A
 233 ASN   ( 241-)  A
 259 HIS   ( 267-)  A
 269 ASN   ( 277-)  A
 296 GLN   ( 304-)  A
 319 HIS   ( 327-)  A
 345 HIS   ( 353-)  A
 378 HIS   ( 386-)  A
 393 GLN   ( 401-)  A
 412 ASN   ( 420-)  A
 511 ASN   (  45-)  M
 535 GLN   (  81-)  M
 560 ASN   ( 106-)  M
 780 GLN   ( 212-)  B
 797 GLN   ( 229-)  B
 806 HIS   ( 238-)  B
 809 ASN   ( 241-)  B
 835 HIS   ( 267-)  B
 845 ASN   ( 277-)  B
 872 GLN   ( 304-)  B
 895 HIS   ( 327-)  B
 921 HIS   ( 353-)  B
And so on for a total of 113 lines.

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.

   4 GLY   (  12-)  A      N
  57 THR   (  65-)  A      OG1
  58 TRP   (  66-)  A      NE1
  59 THR   (  67-)  A      N
  88 SER   (  96-)  A      N
 126 ARG   ( 134-)  A      NE
 151 ARG   ( 159-)  A      NE
 159 ARG   ( 167-)  A      N
 159 ARG   ( 167-)  A      NE
 167 LYS   ( 175-)  A      N
 167 LYS   ( 175-)  A      NZ
 169 LYS   ( 177-)  A      NZ
 170 LEU   ( 178-)  A      N
 171 GLY   ( 179-)  A      N
 176 ASN   ( 184-)  A      ND2
 203 PHE   ( 211-)  A      N
 204 GLN   ( 212-)  A      NE2
 207 ARG   ( 215-)  A      N
 236 ALA   ( 244-)  A      N
 238 THR   ( 246-)  A      N
 268 ALA   ( 276-)  A      N
 291 ALA   ( 299-)  A      N
 295 ARG   ( 303-)  A      NE
 311 ARG   ( 319-)  A      NE
 315 GLY   ( 323-)  A      N
And so on for a total of 525 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.

 259 HIS   ( 267-)  A      NE2
 260 ASP   ( 268-)  A      OD1
 260 ASP   ( 268-)  A      OD2
 284 HIS   ( 292-)  A      NE2
 726 GLU   ( 158-)  B      OE1
 835 HIS   ( 267-)  B      NE2
 836 ASP   ( 268-)  B      OD1
 836 ASP   ( 268-)  B      OD2
 860 HIS   ( 292-)  B      NE2
 988 ASN   ( 420-)  B      OD1
1232 GLU   (  88-)  C      OE1
1302 GLU   ( 158-)  C      OE1
1411 HIS   ( 267-)  C      NE2
1412 ASP   ( 268-)  C      OD1
1412 ASP   ( 268-)  C      OD2
1436 HIS   ( 292-)  C      NE2
1564 ASN   ( 420-)  C      OD1
1878 GLU   ( 158-)  D      OE1
1988 ASP   ( 268-)  D      OD1
1988 ASP   ( 268-)  D      OD2
2012 HIS   ( 292-)  D      NE2
2140 ASN   ( 420-)  D      OD1
2454 GLU   ( 158-)  E      OE1
2564 ASP   ( 268-)  E      OD1
2564 ASP   ( 268-)  E      OD2
2588 HIS   ( 292-)  E      NE2
2716 ASN   ( 420-)  E      OD1
2756 ASP   ( 460-)  E      OD2
3030 GLU   ( 158-)  F      OE1
3139 HIS   ( 267-)  F      NE2
3140 ASP   ( 268-)  F      OD1
3140 ASP   ( 268-)  F      OD2
3164 HIS   ( 292-)  F      NE2
3292 ASN   ( 420-)  F      OD1
3715 HIS   ( 267-)  G      NE2
3716 ASP   ( 268-)  G      OD1
3716 ASP   ( 268-)  G      OD2
3740 HIS   ( 292-)  G      NE2
3868 ASN   ( 420-)  G      OD1
4177 HIS   ( 153-)  H      ND1
4182 GLU   ( 158-)  H      OE1
4292 ASP   ( 268-)  H      OD1
4292 ASP   ( 268-)  H      OD2
4316 HIS   ( 292-)  H      NE2
4444 ASN   ( 420-)  H      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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+.

4625  MG   ( 477-)  A     0.53   1.07 Is perhaps NA
4627  MG   ( 477-)  B     0.53   1.07 Is perhaps NA
4630  MG   ( 477-)  C     0.53   1.07 Is perhaps NA
4633  MG   ( 477-)  D     0.53   1.07 Is perhaps NA
4636  MG   ( 477-)  E     0.53   1.07 Is perhaps NA
4639  MG   ( 477-)  F     0.53   1.07 Is perhaps NA
4642  MG   ( 477-)  G     0.53   1.07 Is perhaps NA
4645  MG   ( 477-)  H     0.53   1.07 Is perhaps NA

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

4649 HOH   ( 567 )  A      O  0.87  K  5
4652 HOH   ( 484 )  C      O  1.07  K  4

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.

 152 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 260 ASP   ( 268-)  A   H-bonding suggests Asn
 294 ASP   ( 302-)  A   H-bonding suggests Asn
 518 GLU   (  64-)  M   H-bonding suggests Gln; but Alt-Rotamer
 563 GLU   ( 109-)  M   H-bonding suggests Gln
 728 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 836 ASP   ( 268-)  B   H-bonding suggests Asn
 870 ASP   ( 302-)  B   H-bonding suggests Asn
1094 GLU   (  64-)  I   H-bonding suggests Gln; but Alt-Rotamer
1139 GLU   ( 109-)  I   H-bonding suggests Gln
1304 ASP   ( 160-)  C   H-bonding suggests Asn; but Alt-Rotamer
1412 ASP   ( 268-)  C   H-bonding suggests Asn
1446 ASP   ( 302-)  C   H-bonding suggests Asn
1670 GLU   (  64-)  N   H-bonding suggests Gln; but Alt-Rotamer
1715 GLU   ( 109-)  N   H-bonding suggests Gln
1880 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
1988 ASP   ( 268-)  D   H-bonding suggests Asn
2022 ASP   ( 302-)  D   H-bonding suggests Asn
2246 GLU   (  64-)  J   H-bonding suggests Gln; but Alt-Rotamer
2291 GLU   ( 109-)  J   H-bonding suggests Gln
2456 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2564 ASP   ( 268-)  E   H-bonding suggests Asn
2598 ASP   ( 302-)  E   H-bonding suggests Asn
2822 GLU   (  64-)  O   H-bonding suggests Gln; but Alt-Rotamer
2867 GLU   ( 109-)  O   H-bonding suggests Gln
3032 ASP   ( 160-)  F   H-bonding suggests Asn; but Alt-Rotamer
3140 ASP   ( 268-)  F   H-bonding suggests Asn
3174 ASP   ( 302-)  F   H-bonding suggests Asn
3398 GLU   (  64-)  K   H-bonding suggests Gln; but Alt-Rotamer
3443 GLU   ( 109-)  K   H-bonding suggests Gln
3608 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
3716 ASP   ( 268-)  G   H-bonding suggests Asn
3750 ASP   ( 302-)  G   H-bonding suggests Asn
3974 GLU   (  64-)  P   H-bonding suggests Gln; but Alt-Rotamer
4019 GLU   ( 109-)  P   H-bonding suggests Gln
4184 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
4292 ASP   ( 268-)  H   H-bonding suggests Asn
4326 ASP   ( 302-)  H   H-bonding suggests Asn
4550 GLU   (  64-)  L   H-bonding suggests Gln; but Alt-Rotamer
4595 GLU   ( 109-)  L   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 :  -0.485
  2nd generation packing quality :  -0.129
  Ramachandran plot appearance   :  -0.545
  chi-1/chi-2 rotamer normality  :  -1.686
  Backbone conformation          :  -0.514

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.309 (tight)
  Bond angles                    :   0.567 (tight)
  Omega angle restraints         :   1.137
  Side chain planarity           :   1.726
  Improper dihedral distribution :   1.990 (loose)
  B-factor distribution          :   0.573
  Inside/Outside distribution    :   1.054

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.309 (tight)
  Bond angles                    :   0.567 (tight)
  Omega angle restraints         :   1.137
  Side chain planarity           :   1.726
  Improper dihedral distribution :   1.990 (loose)
  B-factor distribution          :   0.573
  Inside/Outside distribution    :   1.054
==============

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.