WHAT IF Check report

This file was created 2012-04-04 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 pdb2ybb.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

8361 SF4   ( 439-)  1  -         Atom types
8365 SF4   ( 784-)  3  -         Atom types
8366 SF4   ( 785-)  3  -         Atom types
8367 SF4   ( 786-)  3  -         Atom types
8373 SF4   ( 182-)  6  -         Atom types
8375 SF4   ( 183-)  8  -         Atom types
8376 SF4   ( 184-)  8  -         Atom types
8379 SMA   (2001-)  C  -         OK
8380 UQ1   (2002-)  C  -         OK
8381 HEC   ( 501-)  D  -         Atom types
8383 HEA   ( 515-)  L  -         Atom types
8384 HEA   ( 516-)  L  -         Atom types
8393 HEC   ( 501-)  D  -         Atom types
8396 A12   (3004-)  C  -         OK
8397 A11   (3003-)  C  -         OK
8398 UQ1   (3002-)  C  -         OK
8399 SMA   (3001-)  C  -         OK
8400 A10   (2004-)  G  -         OK
8401 CDL   (2003-)  G  -         OK
8402 NAI   ( 441-)  1  -         OK

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

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

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

2777 ARG   ( 408-)  A  -   NH1 8309 ARG   (  15-)  K  -   CG
4391 LEU   (  23-)  K  -   CD1 8264 SER   (  18-)  J  -   OG
6201 GLN   (  16-)  Y  -   CB  7674 TYR   ( 148-)  D  -   OH

Warning: Strange inter-chain connections could NOT be corrected

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

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.

2591 THR   ( 222-)  A  -   CB
2592 TYR   ( 223-)  A  -   CB
6511 THR   ( 222-)  A  -   CB
6512 TYR   ( 223-)  A  -   CB

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.

2591 THR   ( 222-)  A  -   N
2591 THR   ( 222-)  A  -   CA
2591 THR   ( 222-)  A  -   C
2591 THR   ( 222-)  A  -   O
2592 TYR   ( 223-)  A  -   N
2592 TYR   ( 223-)  A  -   CA
2592 TYR   ( 223-)  A  -   C
2592 TYR   ( 223-)  A  -   O
6511 THR   ( 222-)  A  -   N
6511 THR   ( 222-)  A  -   CA
6511 THR   ( 222-)  A  -   C
6511 THR   ( 222-)  A  -   O
6512 TYR   ( 223-)  A  -   N
6512 TYR   ( 223-)  A  -   CA
6512 TYR   ( 223-)  A  -   C
6512 TYR   ( 223-)  A  -   O
Residue with missing backbone atom(s) 2817 HIS  (  20-) B  -
Residue with missing backbone atom(s) 4138 GLY  (   1-) G  -
Residue with missing backbone atom(s) 4290 SER  (  48-) I  -
Residue with missing backbone atom(s) 4381 ASN  (  61-) J  -
Residue with missing backbone atom(s) 6737 HIS  (  20-) B  -
Residue with missing backbone atom(s) 7162 ASN  (  15-) C  -
Residue with missing backbone atom(s) 8063 GLY  (   1-) G  -
Residue with missing backbone atom(s) 8216 SER  (  48-) I  -
Residue with missing backbone atom(s) 8307 ASN  (  61-) J  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

2817 HIS   (  20-)  B  -
4138 GLY   (   1-)  G  -
4290 SER   (  48-)  I  -
4381 ASN   (  61-)  J  -
6737 HIS   (  20-)  B  -
7162 ASN   (  15-)  C  -
8063 GLY   (   1-)  G  -
8216 SER   (  48-)  I  -
8307 ASN   (  61-)  J  -

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.

8386  MG   ( 518-)  M  -

Note: Ramachandran plot

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

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

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

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

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

2592 TYR   ( 223-)  A      CG
2592 TYR   ( 223-)  A      CD1
2592 TYR   ( 223-)  A      CD2
2592 TYR   ( 223-)  A      CE1
2592 TYR   ( 223-)  A      CE2
2592 TYR   ( 223-)  A      CZ
2592 TYR   ( 223-)  A      OH
2594 GLU   ( 225-)  A      CG
2594 GLU   ( 225-)  A      CD
2594 GLU   ( 225-)  A      OE1
2594 GLU   ( 225-)  A      OE2
2817 HIS   (  20-)  B      N
3240 PHE   (  18-)  C      CD1
3240 PHE   (  18-)  C      CD2
3240 PHE   (  18-)  C      CE1
3240 PHE   (  18-)  C      CE2
3240 PHE   (  18-)  C      CZ
4039 TRP   (  12-)  F      CG
4039 TRP   (  12-)  F      CD1
4039 TRP   (  12-)  F      CD2
4039 TRP   (  12-)  F      NE1
4039 TRP   (  12-)  F      CE2
4039 TRP   (  12-)  F      CE3
4039 TRP   (  12-)  F      CZ2
4039 TRP   (  12-)  F      CZ3
And so on for a total of 98 lines.

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 THR   (   2-)  1    High
   2 GLY   (   3-)  1    High
   3 PRO   (   4-)  1    High
 587 GLU   ( 151-)  2    High
 598 ARG   ( 162-)  2    High
 600 GLU   ( 164-)  2    High
 601 GLU   ( 165-)  2    High
 603 GLU   ( 167-)  2    High
 607 LYS   ( 171-)  2    High
 616 GLU   ( 180-)  2    High
 617 MET   (   1-)  3    High
 619 ARG   (   3-)  3    High
 672 ILE   (  73-)  3    High
 673 GLN   (  74-)  3    High
 741 LYS   ( 142-)  3    High
 742 TYR   ( 143-)  3    High
 743 GLU   ( 150-)  3    High
 905 ARG   ( 312-)  3    High
 906 LYS   ( 313-)  3    High
 907 GLU   ( 314-)  3    High
 908 GLY   ( 315-)  3    High
 909 ARG   ( 316-)  3    High
 910 LEU   ( 317-)  3    High
 916 GLU   ( 323-)  3    High
 924 GLU   ( 331-)  3    High
And so on for a total of 315 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

8138 ALA   (  76-)  G
6732 TRP   ( 443-)  A
6046 HIS   (  57-)  U
4212 ALA   (  75-)  G
3028 GLY   ( 231-)  B
2812 TRP   ( 443-)  A

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

6253 LYS   (  72-)  Y    0.60
6259 THR   (  78-)  Y    0.50

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 not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Note: B-factor plot

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

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 4

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: 8

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

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

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

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

Nomenclature related problems

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

8357 FMN   ( 440-)  1      OP1    O1P
8357 FMN   ( 440-)  1      OP2    O2P
8357 FMN   ( 440-)  1      OP3    O3P

Error: Chain names not unique

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

Chain identifier(s): A, B, C, D, E, F, G, H, I, J, K

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.

4462 HIS   (  61-)  L      CG   CD2   1.44    7.4
4462 HIS   (  61-)  L      ND1  CE1   1.38    4.5
4777 HIS   ( 376-)  L      CG   CD2   1.41    4.6
4777 HIS   ( 376-)  L      ND1  CE1   1.38    4.4
4779 HIS   ( 378-)  L      CG   CD2   1.41    5.3
4779 HIS   ( 378-)  L      ND1  CE1   1.39    5.6
4779 HIS   ( 378-)  L      CE1  NE2   1.26   -4.5
5867 CYS   (  39-)  S      SG  -SG*   2.39    8.8
5881 CYS   (  53-)  S      SG  -SG*   2.39    8.8

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.

 341 TRP   ( 342-)  1      CA   CB   CG  123.37    5.1
 355 CYS   ( 356-)  1      C    CA   CB  100.09   -5.3
 743 GLU   ( 150-)  3      N    CA   C    98.16   -4.7
 801 HIS   ( 208-)  3      CG   ND1  CE1 109.75    4.1
1378 GLY   (  39-)  4      N    CA   C    93.79   -6.5
1444 LEU   ( 105-)  4      CA   CB   CG  131.89    4.5
1669 HIS   ( 330-)  4      CG   ND1  CE1 109.66    4.1
1908 ARG   ( 160-)  5      CB   CG   CD  105.66   -4.2
2182 HIS   (  96-)  7      CG   ND1  CE1 109.62    4.0
2618 PRO   ( 249-)  A      N    CA   C   121.93    4.1
2629 PRO   ( 260-)  A      N    CA   C   123.62    4.7
2988 HIS   ( 192-)  B      CG   ND1  CE1 109.62    4.0
3044 GLY   ( 249-)  B      N    CA   C   124.15    4.0
3237 ALA   (  17-)  C      N    CA   C    98.99   -4.4
3317 HIS   (  97-)  C      CG   ND1  CE1 109.74    4.1
3329 PHE   ( 109-)  C      N    CA   C    96.93   -5.1
3416 HIS   ( 196-)  C      CG   ND1  CE1 109.70    4.1
3426 ASN   ( 206-)  C      N    CA   C    99.51   -4.2
3642 MET   (  43-)  D      N    CA   C    99.97   -4.0
3855 ARG   (  15-)  E      N    CA   C    98.86   -4.4
3976 ILE   ( 136-)  E      N    CA   C    99.15   -4.3
3981 HIS   ( 141-)  E      CG   ND1  CE1 109.81    4.2
3983 GLY   ( 143-)  E      N    CA   C   126.54    4.8
4050 GLY   (  25-)  F      N    CA   C   124.96    4.3
4184 ALA   (  49-)  G      N    CA   C   123.58    4.4
And so on for a total of 83 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.

5019 TRP   ( 104-)  M      CA    -6.3    23.41    34.04
8312 TRP   (  24-)  K      C      7.8    11.69     0.23
The average deviation= 0.835

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.

4184 ALA   (  49-)  G    8.43
8106 ALA   (  49-)  G    8.18
1378 GLY   (  39-)  4    7.10
4483 LEU   (  82-)  L    6.91
3292 ASP   (  72-)  C    6.56
6633 SER   ( 348-)  A    6.53
6940 GLY   ( 228-)  B    6.41
2717 SER   ( 348-)  A    6.38
6194 LYS   (  13-)  Y    5.88
6111 ARG   (  20-)  W    5.75
5533 GLY   ( 133-)  O    5.60
7326 ILE   ( 184-)  C    5.56
3329 PHE   ( 109-)  C    5.51
8193 LEU   (  73-)  H    5.45
 522 LEU   (  86-)  2    5.31
5178 HIS   (  36-)  N    5.31
5759 LYS   (   5-)  R    5.30
7251 PHE   ( 109-)  C    5.29
3237 ALA   (  17-)  C    5.15
2967 ALA   ( 171-)  B    5.13
4116 GLU   (  91-)  F    5.12
6072 GLN   (  35-)  V    5.11
3330 LEU   ( 110-)  C    5.07
6883 ALA   ( 171-)  B    5.06
6165 LEU   (  27-)  X    5.02
And so on for a total of 125 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.

4641 HIS   ( 240-)  L      CB   5.63
4779 HIS   ( 378-)  L      CB   5.49
4645 TYR   ( 244-)  L      OH   4.25
5019 TRP   ( 104-)  M      CB   4.03
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.028

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.

4729 HIS   ( 328-)  L    -3.2
1108 THR   ( 515-)  3    -3.1
   3 PRO   (   4-)  1    -3.1
 544 PRO   ( 108-)  2    -3.1
 960 PRO   ( 367-)  3    -3.1
6602 THR   ( 317-)  A    -3.0
4143 THR   (   8-)  G    -3.0
2686 THR   ( 317-)  A    -3.0
8065 THR   (   8-)  G    -3.0
1033 ARG   ( 440-)  3    -3.0
1836 PHE   (  88-)  5    -3.0
 847 THR   ( 254-)  3    -2.9
  70 PRO   (  71-)  1    -2.9
5709 THR   (  53-)  Q    -2.9
1813 PRO   (  65-)  5    -2.9
5144 THR   (   2-)  N    -2.9
1537 PRO   ( 198-)  4    -2.8
1219 PRO   ( 626-)  3    -2.8
1601 PHE   ( 262-)  4    -2.8
 811 LEU   ( 218-)  3    -2.8
3566 PRO   ( 346-)  C    -2.8
7488 PRO   ( 346-)  C    -2.8
 716 LEU   ( 117-)  3    -2.8
5422 TYR   (  22-)  O    -2.8
5915 THR   (   2-)  T    -2.8
And so on for a total of 296 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.

   3 PRO   (   4-)  1  Poor phi/psi, omega poor
  37 TYR   (  38-)  1  Poor phi/psi
  46 GLU   (  47-)  1  Poor phi/psi
  63 GLY   (  64-)  1  Poor phi/psi
  80 LYS   (  81-)  1  Poor phi/psi
 125 ARG   ( 126-)  1  Poor phi/psi
 162 PHE   ( 163-)  1  Poor phi/psi
 163 GLY   ( 164-)  1  Poor phi/psi
 195 ARG   ( 196-)  1  omega poor
 212 GLY   ( 213-)  1  Poor phi/psi
 293 GLY   ( 294-)  1  omega poor
 320 SER   ( 321-)  1  Poor phi/psi
 359 ARG   ( 360-)  1  Poor phi/psi
 395 GLY   ( 396-)  1  omega poor
 397 SER   ( 398-)  1  Poor phi/psi
 415 HIS   ( 416-)  1  Poor phi/psi
 476 TRP   (  40-)  2  Poor phi/psi
 512 GLY   (  76-)  2  Poor phi/psi
 520 ALA   (  84-)  2  Poor phi/psi
 522 LEU   (  86-)  2  Poor phi/psi
 528 GLY   (  92-)  2  Poor phi/psi
 544 PRO   ( 108-)  2  Poor phi/psi
 560 CYS   ( 124-)  2  Poor phi/psi
 567 ALA   ( 131-)  2  PRO omega poor
 573 ASN   ( 137-)  2  Poor phi/psi, omega poor
And so on for a total of 256 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.

5941 SER   (  28-)  T    0.34
5231 SER   (  89-)  N    0.34
6163 SER   (  25-)  X    0.35
4509 SER   ( 108-)  L    0.35
4557 SER   ( 156-)  L    0.35
4502 SER   ( 101-)  L    0.36
7281 SER   ( 139-)  C    0.36
4656 SER   ( 255-)  L    0.36
 772 GLU   ( 179-)  3    0.36
2766 SER   ( 397-)  A    0.36
3179 SER   ( 384-)  B    0.36
3255 SER   (  35-)  C    0.36
3308 SER   (  88-)  C    0.36
3359 SER   ( 139-)  C    0.36
4328 SER   (  11-)  J    0.36
5246 SER   ( 104-)  N    0.36
6985 SER   ( 273-)  B    0.36
7177 SER   (  35-)  C    0.36
5138 SER   ( 223-)  M    0.37
4995 SER   (  80-)  M    0.38
2665 SER   ( 296-)  A    0.38
6980 GLU   ( 268-)  B    0.38
4588 SER   ( 187-)  L    0.39
2556 SER   ( 187-)  A    0.39
6472 SER   ( 187-)  A    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 PRO   (   4-)  1      0
   4 ILE   (   5-)  1      0
   6 SER   (   7-)  1      0
   8 LEU   (   9-)  1      0
  15 THR   (  16-)  1      0
  16 LEU   (  17-)  1      0
  17 TYR   (  18-)  1      0
  20 VAL   (  21-)  1      0
  23 GLU   (  24-)  1      0
  25 SER   (  26-)  1      0
  26 TRP   (  27-)  1      0
  34 HIS   (  35-)  1      0
  37 TYR   (  38-)  1      0
  64 ARG   (  65-)  1      0
  67 ALA   (  68-)  1      0
  80 LYS   (  81-)  1      0
  81 ASP   (  82-)  1      0
  82 ASP   (  83-)  1      0
  92 ALA   (  93-)  1      0
  94 GLU   (  95-)  1      0
  95 SER   (  96-)  1      0
  97 PRO   (  98-)  1      0
 100 PHE   ( 101-)  1      0
 108 ASP   ( 109-)  1      0
 109 VAL   ( 110-)  1      0
And so on for a total of 2753 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 : 2.988

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!

5742 GLY   (  86-)  Q   3.00   16
3029 GLY   ( 234-)  B   2.21   32
1609 GLY   ( 270-)  4   2.03   26
 175 GLY   ( 176-)  1   2.02   35
2306 GLY   ( 116-)  8   1.97   12
1569 ILE   ( 230-)  4   1.73   18
 931 GLY   ( 338-)  3   1.72   10
3077 GLY   ( 282-)  B   1.65   13
 814 GLY   ( 221-)  3   1.63   13
6994 GLY   ( 282-)  B   1.56   12

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...

 521 THR   (  85-)  2   1.77
5687 TYR   (  31-)  Q   1.61
8128 ARG   (  71-)  G   1.72

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 846 PRO   ( 253-)  3    0.45 HIGH
2054 PRO   ( 141-)  6    0.46 HIGH
3442 PRO   ( 222-)  C    0.46 HIGH
4279 PRO   (  35-)  I    0.00 LOW
4285 PRO   (  41-)  I    0.00 LOW
4384 PRO   (  19-)  K    0.11 LOW
4668 PRO   ( 267-)  L    0.47 HIGH
4799 PRO   ( 398-)  L    0.46 HIGH
4828 PRO   ( 427-)  L    0.46 HIGH
4901 PRO   ( 500-)  L    0.45 HIGH
4919 PRO   (   4-)  M    0.45 HIGH
5104 PRO   ( 189-)  M    0.47 HIGH
5130 PRO   ( 215-)  M    0.47 HIGH
5155 PRO   (  13-)  N    0.46 HIGH
5530 PRO   ( 130-)  O    0.45 HIGH
5569 PRO   (  22-)  P    0.45 HIGH
5624 PRO   (  77-)  P    0.47 HIGH
5648 PRO   ( 101-)  P    0.46 HIGH
5702 PRO   (  46-)  Q    0.46 HIGH
5910 PRO   (  82-)  S    0.46 HIGH
6044 PRO   (   7-)  V    0.45 HIGH
6147 PRO   (   9-)  X    0.45 HIGH
7364 PRO   ( 222-)  C    0.47 HIGH
8202 PRO   (  35-)  I    0.00 LOW
8208 PRO   (  41-)  I    0.00 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].

   3 PRO   (   4-)  1    -2.9 envelop N (0 degrees)
  49 PRO   (  50-)  1    99.5 envelop C-beta (108 degrees)
  70 PRO   (  71-)  1   111.6 envelop C-beta (108 degrees)
 198 PRO   ( 199-)  1  -129.4 half-chair C-delta/C-gamma (-126 degrees)
 202 PRO   ( 203-)  1   115.3 envelop C-beta (108 degrees)
 205 PRO   ( 206-)  1  -112.9 envelop C-gamma (-108 degrees)
 228 PRO   ( 229-)  1  -126.6 half-chair C-delta/C-gamma (-126 degrees)
 300 PRO   ( 301-)  1    46.0 half-chair C-delta/C-gamma (54 degrees)
 400 PRO   ( 401-)  1    48.4 half-chair C-delta/C-gamma (54 degrees)
 408 PRO   ( 409-)  1  -127.5 half-chair C-delta/C-gamma (-126 degrees)
 456 PRO   (  20-)  2  -119.3 half-chair C-delta/C-gamma (-126 degrees)
 465 PRO   (  29-)  2  -131.1 half-chair C-delta/C-gamma (-126 degrees)
 479 PRO   (  43-)  2  -131.5 half-chair C-delta/C-gamma (-126 degrees)
 493 PRO   (  57-)  2    99.8 envelop C-beta (108 degrees)
 510 PRO   (  74-)  2   117.2 half-chair C-beta/C-alpha (126 degrees)
 544 PRO   ( 108-)  2   154.0 half-chair C-alpha/N (162 degrees)
 630 PRO   (  14-)  3  -115.3 envelop C-gamma (-108 degrees)
 631 PRO   (  15-)  3  -121.7 half-chair C-delta/C-gamma (-126 degrees)
 647 PRO   (  31-)  3   115.9 envelop C-beta (108 degrees)
 719 PRO   ( 120-)  3  -123.5 half-chair C-delta/C-gamma (-126 degrees)
 788 PRO   ( 195-)  3    48.3 half-chair C-delta/C-gamma (54 degrees)
 824 PRO   ( 231-)  3  -112.9 envelop C-gamma (-108 degrees)
 876 PRO   ( 283-)  3  -121.0 half-chair C-delta/C-gamma (-126 degrees)
 902 PRO   ( 309-)  3  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 960 PRO   ( 367-)  3   -44.0 envelop C-alpha (-36 degrees)
And so on for a total of 74 lines.

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.

7666 GLU   ( 145-)  D      CB   <->  8407 HOH   ( 323 )  Y      O    2.25    0.55  INTRA BF
7627 ASN   ( 106-)  D      OD1  <->  8407 HOH   ( 305 )  Y      O    1.42    0.98  INTRA BF
7666 GLU   ( 145-)  D      CG   <->  8407 HOH   ( 323 )  Y      O    1.34    1.46  INTRA BF
4335 SER   (  18-)  J      OG   <->  8311 LEU   (  23-)  K      CD1  1.17    1.63  INTRA BF
7627 ASN   ( 106-)  D      CG   <->  8407 HOH   ( 305 )  Y      O    1.15    1.65  INTRA
4346 LEU   (  29-)  J      CD2  <->  8322 SER   (  34-)  K      CB   1.11    2.09  INTRA BF
6195 CYS   (  14-)  Y      SG   <->  8385 HEM   ( 500-)  Y      CAB  1.00    2.40  INTRA BL
7666 GLU   ( 145-)  D      CA   <->  8407 HOH   ( 323 )  Y      O    0.98    1.82  INTRA BF
7666 GLU   ( 145-)  D      CD   <->  8407 HOH   ( 269 )  Y      O    0.95    1.85  INTRA BF
8303 ARG   (  15-)  K      NE   <->  8397 HOH   (4099 )  A      O    0.93    1.77  INTRA BF
8407 HOH   ( 254 )  Y      O    <->  8411 HOH   (3092 )  D      O    0.85    1.55  INTRA BL
4380 ARG   (  15-)  K      CG   <->  6693 ARG   ( 408-)  A      NH2  0.81    2.29  INTRA BF
7627 ASN   ( 106-)  D      CB   <->  8407 HOH   ( 350 )  Y      O    0.69    2.11  INTRA
6208 LYS   (  27-)  Y      CD   <->  7666 GLU   ( 145-)  D      OE1  0.68    2.12  INTRA BF
4346 LEU   (  29-)  J      CD2  <->  8322 SER   (  34-)  K      OG   0.68    2.12  INTRA BF
1562 VAL   ( 223-)  4      CG2  <->  8365  MG   ( 410-)  4     MG    0.66    2.54  INTRA BF
8303 ARG   (  15-)  K      CZ   <->  8397 HOH   (4099 )  A      O    0.63    2.17  INTRA BF
8387 HEC   ( 501-)  D      CBC  <->  8407 HOH   ( 308 )  Y      O    0.63    2.17  INTRA BL
8381  CU   ( 228-)  M     CU    <->  8382  CU   ( 229-)  M     CU    0.62    2.38  INTRA BL
6198 CYS   (  17-)  Y      SG   <->  8385 HEM   ( 500-)  Y      CAC  0.62    2.78  INTRA BL
4335 SER   (  18-)  J      OG   <->  8311 LEU   (  23-)  K      CG   0.60    2.20  INTRA BF
4276 ALA   (  32-)  I      N    <->  4310 ASN   (  71-)  I      CB   0.59    2.51  INTRA BF
8303 ARG   (  15-)  K      NH2  <->  8397 HOH   (4099 )  A      O    0.58    2.12  INTRA BF
7666 GLU   ( 145-)  D      CG   <->  8407 HOH   ( 269 )  Y      O    0.57    2.23  INTRA BF
6206 LYS   (  25-)  Y      CE   <->  7666 GLU   ( 145-)  D      CD   0.56    2.64  INTRA BF
And so on for a total of 1427 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: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

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

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.

3375 TYR   ( 155-)  C      -8.54
7297 TYR   ( 155-)  C      -8.46
3023 ARG   ( 227-)  B      -8.23
6939 ARG   ( 227-)  B      -8.19
1244 ARG   ( 651-)  3      -8.07
1018 ARG   ( 425-)  3      -7.48
1946 ARG   (  16-)  6      -7.38
1642 ARG   ( 303-)  4      -7.27
4246 GLN   (  49-)  H      -7.08
 607 LYS   ( 171-)  2      -6.96
1204 ARG   ( 611-)  3      -6.94
7681 MET   ( 160-)  D      -6.71
5028 TYR   ( 113-)  M      -6.67
1608 ARG   ( 269-)  4      -6.63
6753 TYR   (  41-)  B      -6.60
1033 ARG   ( 440-)  3      -6.59
3759 MET   ( 160-)  D      -6.58
7880 ARG   ( 118-)  E      -6.51
2348 LYS   ( 158-)  8      -6.49
7642 HIS   ( 121-)  D      -6.46
 836 ARG   ( 243-)  3      -6.44
5912 LYS   (  84-)  S      -6.42
3720 HIS   ( 121-)  D      -6.42
3958 ARG   ( 118-)  E      -6.39
 283 LEU   ( 284-)  1      -6.35
And so on for a total of 222 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.

 472 GLN   (  36-)  2       474 - GLU     38- ( 2)         -4.82
 905 ARG   ( 312-)  3       907 - GLU    314- ( 3)         -4.59
1188 GLU   ( 595-)  3      1190 - TYR    597- ( 3)         -4.54
1931 PHE   ( 183-)  5      1933 - LYS    185- ( 5)         -5.74
2130 MET   (  44-)  7      2132 - ARG     46- ( 7)         -4.97
3487 HIS   ( 267-)  C      3489 - LYS    269- ( C)         -5.16
5005 ILE   (  90-)  M      5007 - ASN     92- ( M)         -4.55
5177 PHE   (  35-)  N      5179 - PHE     37- ( N)         -4.50
5666 GLU   (  10-)  Q      5668 - GLN     12- ( Q)         -4.50
5756 SER   (   2-)  R      5759 - LYS      5- ( R)         -4.44
5795 HIS   (  41-)  R      5798 - ARG     44- ( R)         -4.93
7409 HIS   ( 267-)  C      7411 - LYS    269- ( C)         -5.19

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: 1

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: 2

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: 3

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: 4

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: 5

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: 6

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: 7

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: 8

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: 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: 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: 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: 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

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: Y

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: 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: 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: 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: 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

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.

2592 TYR   ( 223-)  A   -3.20
6508 TYR   ( 223-)  A   -3.14
1169 ALA   ( 576-)  3   -2.96
1727 GLU   ( 388-)  4   -2.93
 974 LEU   ( 381-)  3   -2.89
5829 VAL   (  75-)  R   -2.74
5254 LEU   ( 112-)  N   -2.68
4537 LEU   ( 136-)  L   -2.67
4378 ASN   (  61-)  J   -2.63
8301 ASN   (  61-)  J   -2.63
7142 LEU   ( 430-)  B   -2.59
4692 HIS   ( 291-)  L   -2.58
1380 LEU   (  41-)  4   -2.57
1851 THR   ( 103-)  5   -2.55
5847 ARG   (  19-)  S   -2.53
   5 LEU   (   6-)  1   -2.52
2176 HIS   (  90-)  7   -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

1050 PRO   ( 457-)  3     - 1053 LYS   ( 460-)  3        -1.61

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: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

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

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

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

Water, ion, and hydrogenbond related checks

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.

8399 HOH   (2134 )  C      O
8411 HOH   (3047 )  D      O
8414 HOH   (3026 )  G      O
8416 HOH   (1226 )  I      O
Metal-coordinating Histidine residue  34 fixed to   1
Metal-coordinating Histidine residue 714 fixed to   1
Metal-coordinating Histidine residue 760 fixed to   1
Metal-coordinating Histidine residue1892 fixed to   1
Metal-coordinating Histidine residue3303 fixed to   1
Metal-coordinating Histidine residue3402 fixed to   1
Metal-coordinating Histidine residue3640 fixed to   1
Metal-coordinating Histidine residue3317 fixed to   1
Metal-coordinating Histidine residue3416 fixed to   1
Metal-coordinating Histidine residue4462 fixed to   1
Metal-coordinating Histidine residue4779 fixed to   1
Metal-coordinating Histidine residue4777 fixed to   1
Metal-coordinating Histidine residue4641 fixed to   1
Metal-coordinating Histidine residue4691 fixed to   1
Metal-coordinating Histidine residue4692 fixed to   1
Metal-coordinating Histidine residue4769 fixed to   1
Metal-coordinating Histidine residue5076 fixed to   1
Metal-coordinating Histidine residue5119 fixed to   1
Metal-coordinating Histidine residue3981 fixed to   1
Metal-coordinating Histidine residue4001 fixed to   1
Metal-coordinating Histidine residue6199 fixed to   1
Metal-coordinating Histidine residue7225 fixed to   1
Metal-coordinating Histidine residue7324 fixed to   1
Metal-coordinating Histidine residue7562 fixed to   1
Metal-coordinating Histidine residue7239 fixed to   1
Metal-coordinating Histidine residue7338 fixed to   1
Metal-coordinating Histidine residue7903 fixed to   1
Metal-coordinating Histidine residue7923 fixed to   1

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.

 244 GLN   ( 245-)  1
 517 GLN   (  81-)  2
 730 GLN   ( 131-)  3
 891 HIS   ( 298-)  3
1302 GLN   ( 709-)  3
1508 HIS   ( 169-)  4
1631 GLN   ( 292-)  4
1666 HIS   ( 327-)  4
1795 ASN   (  47-)  5
2284 ASN   (  94-)  8
2401 GLN   (  32-)  A
2818 GLN   (  22-)  B
3071 GLN   ( 276-)  B
3288 HIS   (  68-)  C
3565 HIS   ( 345-)  C
3720 HIS   ( 121-)  D
4063 HIS   (  38-)  F
4163 HIS   (  28-)  G
4412 ASN   (  11-)  L
4571 ASN   ( 170-)  L
4823 ASN   ( 422-)  L
4967 HIS   (  52-)  M
5018 GLN   ( 103-)  M
5154 ASN   (  12-)  N
5290 HIS   ( 148-)  N
5581 ASN   (  34-)  P
5805 HIS   (  51-)  R
5806 HIS   (  52-)  R
5851 GLN   (  23-)  S
5853 GLN   (  25-)  S
5856 ASN   (  28-)  S
5860 ASN   (  32-)  S
5921 GLN   (   8-)  T
5989 ASN   (   3-)  U
6002 ASN   (  16-)  U
6133 HIS   (  42-)  W
6223 GLN   (  42-)  Y
6251 ASN   (  70-)  Y
7210 HIS   (  68-)  C
7487 HIS   ( 345-)  C
7642 HIS   ( 121-)  D
7911 ASN   ( 149-)  E
8085 HIS   (  28-)  G

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   2 GLY   (   3-)  1      N
   4 ILE   (   5-)  1      N
  11 ARG   (  12-)  1      N
  18 ALA   (  19-)  1      N
  19 HIS   (  20-)  1      N
  21 GLY   (  22-)  1      N
  26 TRP   (  27-)  1      N
  30 TYR   (  31-)  1      N
  34 HIS   (  35-)  1      ND1
  38 GLU   (  39-)  1      N
  47 LYS   (  48-)  1      N
  48 THR   (  49-)  1      N
  62 ARG   (  63-)  1      N
  64 ARG   (  65-)  1      NH2
  67 ALA   (  68-)  1      N
  69 PHE   (  70-)  1      N
  94 GLU   (  95-)  1      N
  96 GLU   (  97-)  1      N
 103 ARG   ( 104-)  1      NH2
 104 TYR   ( 105-)  1      N
 111 HIS   ( 112-)  1      N
 127 THR   ( 128-)  1      N
 152 ARG   ( 153-)  1      NE
 166 PHE   ( 167-)  1      N
 170 LEU   ( 171-)  1      N
And so on for a total of 765 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.

  93 ASP   (  94-)  1      OD2
 102 ASP   ( 103-)  1      OD1
 108 ASP   ( 109-)  1      OD2
 184 GLU   ( 185-)  1      OE2
 515 HIS   (  79-)  2      NE2
 654 HIS   (  38-)  3      ND1
 730 GLN   ( 131-)  3      OE1
 731 ASP   ( 132-)  3      OD1
 735 GLU   ( 136-)  3      OE1
 756 HIS   ( 163-)  3      ND1
 776 HIS   ( 183-)  3      ND1
 785 GLU   ( 192-)  3      OE2
 797 GLU   ( 204-)  3      OE1
 797 GLU   ( 204-)  3      OE2
 841 GLU   ( 248-)  3      OE2
 874 GLU   ( 281-)  3      OE2
 945 GLU   ( 352-)  3      OE2
 961 HIS   ( 368-)  3      ND1
 998 GLU   ( 405-)  3      OE1
1021 HIS   ( 428-)  3      ND1
1202 GLU   ( 609-)  3      OE2
1342 HIS   ( 749-)  3      NE2
1350 HIS   ( 757-)  3      ND1
1417 ASN   (  78-)  4      OD1
1433 ASP   (  94-)  4      OD2
And so on for a total of 66 lines.

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+.

8356  MG   ( 442-)  1   -.-  -.-  Too few ligands (0)
8358  MG   ( 206-)  2   -.-  -.-  Too few ligands (0)
8363  MG   ( 788-)  3   -.-  -.-  Too few ligands (3)
8364  MG   ( 789-)  3   -.-  -.-  Too few ligands (2)
8365  MG   ( 410-)  4   -.-  -.-  Too few ligands (2)
8366  MG   ( 208-)  5   -.-  -.-  Too few ligands (0)
8368  CA   ( 204-)  7     0.27   0.66 Is perhaps  K (Few ligands (4) )
8380  MG   ( 518-)  M   -.-  -.-  Too few ligands (3)

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.

8397 HOH   (4090 )  A      O  1.15  K  4
8407 HOH   ( 233 )  Y      O  0.96  K  4
8407 HOH   ( 239 )  Y      O  0.96  K  4
8407 HOH   ( 247 )  Y      O  0.86 NA  5
8413 HOH   (2059 )  F      O  0.96  K  4 NCS 1/1

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.

  81 ASP   (  82-)  1   H-bonding suggests Asn
 108 ASP   ( 109-)  1   H-bonding suggests Asn; but Alt-Rotamer
 403 ASP   ( 404-)  1   H-bonding suggests Asn; but Alt-Rotamer
 441 ASP   (   5-)  2   H-bonding suggests Asn
 534 ASP   (  98-)  2   H-bonding suggests Asn
 637 ASP   (  21-)  3   H-bonding suggests Asn
 790 ASP   ( 197-)  3   H-bonding suggests Asn; but Alt-Rotamer
 885 ASP   ( 292-)  3   H-bonding suggests Asn
1059 GLU   ( 466-)  3   H-bonding suggests Gln
1076 ASP   ( 483-)  3   H-bonding suggests Asn
1153 GLU   ( 560-)  3   H-bonding suggests Gln; but Alt-Rotamer
1389 GLU   (  50-)  4   H-bonding suggests Gln; but Alt-Rotamer
1491 GLU   ( 152-)  4   H-bonding suggests Gln; but Alt-Rotamer
1597 GLU   ( 258-)  4   H-bonding suggests Gln; but Alt-Rotamer
1613 ASP   ( 274-)  4   H-bonding suggests Asn
1661 GLU   ( 322-)  4   H-bonding suggests Gln
1699 ASP   ( 360-)  4   H-bonding suggests Asn
1767 ASP   (  19-)  5   H-bonding suggests Asn; but Alt-Rotamer
1799 ASP   (  51-)  5   H-bonding suggests Asn
2122 ASP   (  36-)  7   H-bonding suggests Asn
2593 ASP   ( 224-)  A   H-bonding suggests Asn
3103 ASP   ( 308-)  B   H-bonding suggests Asn
3551 ASP   ( 331-)  C   H-bonding suggests Asn
3844 ASP   (   4-)  E   H-bonding suggests Asn; but Alt-Rotamer
4030 ASP   ( 190-)  E   H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 54 lines.

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 :  -0.959
  2nd generation packing quality :  -1.284
  Ramachandran plot appearance   :  -2.028
  chi-1/chi-2 rotamer normality  :  -2.780
  Backbone conformation          :  -0.213

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.386 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.543 (tight)
  Side chain planarity           :   0.346 (tight)
  Improper dihedral distribution :   0.723
  B-factor distribution          :   0.935
  Inside/Outside distribution    :   1.082

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 : 19.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.386 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.543 (tight)
  Side chain planarity           :   0.346 (tight)
  Improper dihedral distribution :   0.723
  B-factor distribution          :   0.935
  Inside/Outside distribution    :   1.082
==============

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.