WHAT IF Check report

This file was created 2011-12-13 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 pdb3cme.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Warning: Matthews Coefficient (Vm) high

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

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 1359590.6
Volume of the Unit Cell V= 35952608.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.611
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.040 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

6975 ACA   (  78-)  6  -
6976 8AN   (  76-)  6  -

Administrative problems that can generate validation failures

Warning: Amino acids observed inside ligands

Ligands were detected that contain amino acids. This is not a wise thing to do. Please rename those ligand fragments and call them DRG, XXX, or whatever, but do not give them the name of a valid amino acid, nucleotide, or sugar.

Crystallographers and NMR spectroscopists have an understandable dislike for organic chemistry and quantum chemistry. And they hate making topology entries for small molecules. So, if they find a funny small molecular ligand in their molecule, they generally try to 'recycle' old topologies. If the ligand contains a group that, for example, looks like an amino acid, it is common practice to split the ligand into several 'ligand-residues' and use the amino acid topology for the amino acid fragment. This is all fine, but please change the name into DRG, XXX, or whatever, before depositing the ligand. If you think that the validation software makes errors that are related to these ligands, I suggest you first change the name of the ligand (and make one ligand out of the fragments) and run the validation again. The table lists the residues, or residue-like things, that are found bound between ligands or unrecognized things, and that thus are suspect of actually being part of one big ligand.

6656 PHE   (  77-)  6  -

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.

6656 PHE   (  77-)  6  -   N   bound to 6975 ACA   (  78-)  6  -   C1

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.

  78 ASP   (  78-)  A  -
 315 PRO   (  78-)  B  -
 652 ARG   (  78-)  C  -
 884 GLU   (  78-)  D  -
1038 GLU   (  78-)  E  -
1210 GLU   (  78-)  F  -
1355 LYS   (  78-)  H  -
1453 ALA   (  78-)  I  -
1585 ILE   (  78-)  J  -
1730 LYS   (  78-)  K  -
1862 ALA   (  78-)  L  -
2007 LYS   (  78-)  M  -
2201 MET   (  78-)  N  -
2387 ALA   (  78-)  O  -
2502 GLY   (  78-)  P  -
2645 GLY   (  78-)  Q  -
2740 GLY   (  78-)  R  -
2890 ALA   (  78-)  S  -
2971 THR   (  78-)  T  -
3208 ASP   (  78-)  W  -
3356 GLU   (  78-)  X  -
3553 ILE   (  78-)  Z  -
3761 HIS   (  78-)  3  -

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.

6671  MG   (8025-)  A  -
6680  MG   (8043-)  B  -
6684  MG   (8012-)  C  -
6691  SR   (8907-)  0  -
6777  NA   (8515-)  0  -
6797  NA   (8537-)  0  -
6867  SR   (8940-)  0  -
6898  SR   (8978-)  0  -
6946  MG   (8054-)  0  -
6956  CL   (8811-)  Q  -

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: 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: Z

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

2113 ARG   ( 184-)  M
3670 ASN   (  36-)  2

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'.

  78 ASP   (  78-)  A      N
 315 PRO   (  78-)  B      N
 652 ARG   (  78-)  C      N
 884 GLU   (  78-)  D      N
1038 GLU   (  78-)  E      N
1210 GLU   (  78-)  F      N
1355 LYS   (  78-)  H      N
1453 ALA   (  78-)  I      N
1585 ILE   (  78-)  J      N
1730 LYS   (  78-)  K      N
1862 ALA   (  78-)  L      N
2007 LYS   (  78-)  M      N
2201 MET   (  78-)  N      N
2387 ALA   (  78-)  O      N
2502 GLY   (  78-)  P      N
2645 GLY   (  78-)  Q      N
2740 GLY   (  78-)  R      N
2890 ALA   (  78-)  S      N
2971 THR   (  78-)  T      N
3208 ASP   (  78-)  W      N
3356 GLU   (  78-)  X      N
3553 ILE   (  78-)  Z      N
3761 HIS   (  78-)  3      N
3844 OGUA  (  78-)  0      C5
3844 OGUA  (  78-)  0      C6
3844 OGUA  (  78-)  0      C2
3844 OGUA  (  78-)  0      C4
5295 OURA  (1561-)  0      P
5295 OURA  (1561-)  0      OP1
5295 OURA  (1561-)  0      OP2
6607 OGUA  (  78-)  9      C5
6607 OGUA  (  78-)  9      C6
6607 OGUA  (  78-)  9      C2
6607 OGUA  (  78-)  9      C4

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.

  33 GLU   (  33-)  A    High
  34 ASP   (  34-)  A    High
  35 GLY   (  35-)  A    High
  36 ASP   (  36-)  A    High
  37 VAL   (  37-)  A    High
 821 PHE   (  10-)  D    High
 822 HIS   (  11-)  D    High
 823 GLU   (  12-)  D    High
 824 MET   (  13-)  D    High
 825 ARG   (  14-)  D    High
 828 ARG   (  17-)  D    High
 841 ALA   (  35-)  D    High
 842 ASN   (  36-)  D    High
 843 ALA   (  37-)  D    High
 844 GLU   (  38-)  D    High
 845 ASP   (  39-)  D    High
 849 GLU   (  43-)  D    High
 859 LYS   (  53-)  D    High
 860 ALA   (  54-)  D    High
 861 LYS   (  55-)  D    High
 862 ARG   (  56-)  D    High
 863 THR   (  57-)  D    High
 864 VAL   (  58-)  D    High
 865 GLY   (  59-)  D    High
 866 GLU   (  60-)  D    High
And so on for a total of 368 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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: Z

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Nomenclature related problems

Warning: Tyrosine convention problem

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

  23 TYR   (  23-)  A
 329 TYR   (  92-)  B
 436 TYR   ( 199-)  B
 620 TYR   (  46-)  C
 625 TYR   (  51-)  C
1299 TYR   (  22-)  H
1576 TYR   (  69-)  J
1616 TYR   ( 109-)  J
2205 TYR   (  82-)  N
2360 TYR   (  51-)  O
2547 TYR   ( 123-)  P
2638 TYR   (  71-)  Q
3171 TYR   (  41-)  W
3517 TYR   (  42-)  Z
3568 TYR   (  93-)  Z

Warning: Phenylalanine convention problem

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

  16 PHE   (  16-)  A
 169 PHE   ( 169-)  A
 201 PHE   ( 201-)  A
 263 PHE   (  26-)  B
 342 PHE   ( 105-)  B
 867 PHE   (  61-)  D
 910 PHE   ( 104-)  D
1025 PHE   (  65-)  E
1033 PHE   (  73-)  E
1051 PHE   (  91-)  E
1208 PHE   (  76-)  F
1403 PHE   ( 137-)  H
1419 PHE   ( 153-)  H
1466 PHE   (  91-)  I
1586 PHE   (  79-)  J
1773 PHE   ( 121-)  K
1835 PHE   (  51-)  L
2038 PHE   ( 109-)  M
2089 PHE   ( 160-)  M
2239 PHE   ( 116-)  N
2555 PHE   ( 131-)  P
2721 PHE   (  59-)  R
2832 PHE   (  20-)  S
3040 PHE   (  31-)  U
3184 PHE   (  54-)  W
3400 PHE   ( 128-)  Y
3440 PHE   ( 168-)  Y
3454 PHE   ( 182-)  Y
3513 PHE   (  38-)  Z
3735 PHE   (  52-)  3

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 561 ASP   ( 324-)  B
 619 ASP   (  45-)  C
 671 ASP   (  97-)  C
 741 ASP   ( 167-)  C
 744 ASP   ( 170-)  C
 931 ASP   ( 145-)  D
1380 ASP   ( 114-)  H
2436 ASP   (  12-)  P
2439 ASP   (  15-)  P
2545 ASP   ( 121-)  P
2871 ASP   (  59-)  S
2947 ASP   (  54-)  T
3034 ASP   (  25-)  U
3208 ASP   (  78-)  W
3305 ASP   (  27-)  X
3329 ASP   (  51-)  X
3682 ASP   (  48-)  2

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  28 GLU   (  28-)  A
  33 GLU   (  33-)  A
  46 GLU   (  46-)  A
  72 GLU   (  72-)  A
 144 GLU   ( 144-)  A
 300 GLU   (  63-)  B
 424 GLU   ( 187-)  B
1013 GLU   (  53-)  E
1145 GLU   (  13-)  F
1549 GLU   (  42-)  J
1557 GLU   (  50-)  J
2191 GLU   (  68-)  N
2195 GLU   (  72-)  N
2222 GLU   (  99-)  N
2343 GLU   (  34-)  O
2516 GLU   (  92-)  P
2806 GLU   ( 144-)  R
3008 GLU   ( 115-)  T
3046 GLU   (  37-)  U
3456 GLU   ( 184-)  Y

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

5295 OURA  (1561-)  0

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): 6

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000653  0.000086 -0.000008|
 |  0.000086  1.000615  0.000029|
 | -0.000008  0.000029  1.000443|
Proposed new scale matrix

 |  0.004741  0.000000  0.000000|
 |  0.000000  0.003356  0.000000|
 |  0.000000  0.000000  0.001745|
With corresponding cell

    A    = 210.930  B   = 297.979  C    = 572.992
    Alpha=  90.005  Beta=  90.004  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 210.793  B   = 297.796  C    = 572.738
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 534.002
(Under-)estimated Z-score: 17.031

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.

 238 PRO   (   1-)  B      N    CA   CB  107.46    4.1
2286 PHE   ( 163-)  N      N    CA   C    97.02   -5.1
2568 PRO   (   1-)  Q      N    CA   CB  107.52    4.1
2839 ALA   (  27-)  S      N    CA   C    97.04   -5.1
2947 ASP   (  54-)  T      N    CA   C    99.13   -4.3
3182 VAL   (  52-)  W      CA   CB   CG2  75.59  -20.5
3182 VAL   (  52-)  W      CG1  CB   CG2 168.52   26.2
3474 ALA   ( 202-)  Y      N    CA   C    99.44   -4.2
3786 OGUA  (  20-)  0      N9   C8   N7  113.15    4.1
3787 OGUA  (  21-)  0      N9   C8   N7  113.14    4.1
3789 OGUA  (  23-)  0      N9   C8   N7  113.23    4.3
3794 OGUA  (  28-)  0      N9   C8   N7  113.12    4.0
3799 OGUA  (  33-)  0      N9   C8   N7  113.33    4.5
3805 OGUA  (  39-)  0      N9   C8   N7  113.13    4.1
3807 OGUA  (  41-)  0      N9   C8   N7  113.13    4.1
3810 OGUA  (  44-)  0      N9   C8   N7  113.18    4.2
3813 OGUA  (  47-)  0      N9   C8   N7  113.19    4.2
3816 OGUA  (  50-)  0      N9   C8   N7  113.17    4.1
3817 OGUA  (  51-)  0      N9   C8   N7  113.21    4.2
3820 OGUA  (  54-)  0      N9   C8   N7  113.25    4.3
3822 OGUA  (  56-)  0      N9   C8   N7  113.21    4.2
3830 OGUA  (  64-)  0      N9   C8   N7  113.16    4.1
3832 OGUA  (  66-)  0      N9   C8   N7  113.26    4.3
3837 OGUA  (  71-)  0      N9   C8   N7  113.18    4.2
3840 OGUA  (  74-)  0      N9   C8   N7  113.11    4.0
And so on for a total of 461 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  28 GLU   (  28-)  A
  33 GLU   (  33-)  A
  46 GLU   (  46-)  A
  72 GLU   (  72-)  A
 144 GLU   ( 144-)  A
 300 GLU   (  63-)  B
 424 GLU   ( 187-)  B
 561 ASP   ( 324-)  B
 619 ASP   (  45-)  C
 671 ASP   (  97-)  C
 741 ASP   ( 167-)  C
 744 ASP   ( 170-)  C
 931 ASP   ( 145-)  D
1013 GLU   (  53-)  E
1145 GLU   (  13-)  F
1380 ASP   ( 114-)  H
1549 GLU   (  42-)  J
1557 GLU   (  50-)  J
2191 GLU   (  68-)  N
2195 GLU   (  72-)  N
2222 GLU   (  99-)  N
2343 GLU   (  34-)  O
2436 ASP   (  12-)  P
2439 ASP   (  15-)  P
2516 GLU   (  92-)  P
2545 ASP   ( 121-)  P
2806 GLU   ( 144-)  R
2871 ASP   (  59-)  S
2947 ASP   (  54-)  T
3008 GLU   ( 115-)  T
3034 ASP   (  25-)  U
3046 GLU   (  37-)  U
3208 ASP   (  78-)  W
3305 ASP   (  27-)  X
3329 ASP   (  51-)  X
3456 GLU   ( 184-)  Y
3682 ASP   (  48-)  2

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.

3182 VAL   (  52-)  W      CB    19.0    -8.06   -32.96
The average deviation= 0.711

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.

2286 PHE   ( 163-)  N    5.48
 319 VAL   (  82-)  B    5.37
2839 ALA   (  27-)  S    5.28
2256 ASP   ( 133-)  N    5.27
2803 VAL   ( 141-)  R    5.04
2409 GLN   ( 100-)  O    4.94
1191 ILE   (  59-)  F    4.93
 412 LEU   ( 175-)  B    4.91
3723 ARG   (  40-)  3    4.80
2928 TYR   (  35-)  T    4.75
6656 PHE   (  77-)  6    4.64
2136 ARG   (  13-)  N    4.52
3199 ARG   (  69-)  W    4.46
 778 ALA   ( 204-)  C    4.40
1666 LYS   (  14-)  K    4.27
3474 ALA   ( 202-)  Y    4.26
 454 ARG   ( 217-)  B    4.24
2909 LEU   (  16-)  T    4.23
2359 ARG   (  50-)  O    4.23
2584 LYS   (  17-)  Q    4.15
2527 THR   ( 103-)  P    4.13
2947 ASP   (  54-)  T    4.11
2534 ASP   ( 110-)  P    4.10
3006 GLU   ( 113-)  T    4.10
 779 ARG   ( 205-)  C    4.07
2635 GLY   (  68-)  Q    4.03
3300 ASN   (  22-)  X    4.03

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

6607 OGUA  (  78-)  9    0.30
3844 OGUA  (  78-)  0    0.24
 Ramachandran Z-score : -4.002

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.002

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.

 867 PHE   (  61-)  D    -3.4
 923 PRO   ( 137-)  D    -3.1
 631 PRO   (  57-)  C    -3.1
 601 ARG   (  27-)  C    -2.8
 855 PRO   (  49-)  D    -2.7
3573 PRO   (  98-)  Z    -2.7
 314 PRO   (  77-)  B    -2.7
2277 LEU   ( 154-)  N    -2.6
3692 THR   (   9-)  3    -2.6
 808 VAL   ( 234-)  C    -2.6
3218 THR   (  88-)  W    -2.6
3108 PRO   (  43-)  V    -2.6
 541 PRO   ( 304-)  B    -2.5
2537 THR   ( 113-)  P    -2.5
3517 TYR   (  42-)  Z    -2.5
1076 THR   ( 116-)  E    -2.5
 955 THR   ( 169-)  D    -2.5
2642 ILE   (  75-)  Q    -2.5
1697 PRO   (  45-)  K    -2.4
1231 THR   (  99-)  F    -2.4
1572 ASN   (  65-)  J    -2.4
 205 GLY   ( 205-)  A    -2.4
2417 GLY   ( 108-)  O    -2.4
2384 THR   (  75-)  O    -2.4
2675 THR   (  13-)  R    -2.4
And so on for a total of 118 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.

  10 GLY   (  10-)  A  Poor phi/psi
  19 PRO   (  19-)  A  Poor phi/psi
  24 LYS   (  24-)  A  Poor phi/psi
  27 LEU   (  27-)  A  Poor phi/psi
  34 ASP   (  34-)  A  Poor phi/psi
  35 GLY   (  35-)  A  Poor phi/psi
  36 ASP   (  36-)  A  Poor phi/psi
  37 VAL   (  37-)  A  Poor phi/psi
  77 GLY   (  77-)  A  Impossible psi
  78 ASP   (  78-)  A  Impossible phi
  88 ILE   (  88-)  A  Poor phi/psi
 107 ASN   ( 107-)  A  Poor phi/psi
 134 ASN   ( 134-)  A  Poor phi/psi
 170 VAL   ( 170-)  A  Poor phi/psi
 173 GLY   ( 173-)  A  Poor phi/psi
 186 TRP   ( 186-)  A  PRO omega poor
 205 GLY   ( 205-)  A  Poor phi/psi
 208 HIS   ( 208-)  A  Poor phi/psi
 232 ARG   ( 232-)  A  Poor phi/psi
 239 GLN   (   2-)  B  Poor phi/psi
 251 GLY   (  14-)  B  PRO omega poor
 270 ASP   (  33-)  B  Poor phi/psi
 314 PRO   (  77-)  B  Impossible psi
 315 PRO   (  78-)  B  Impossible phi
 338 TRP   ( 101-)  B  Poor phi/psi
And so on for a total of 243 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.210

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.

 817 VAL   ( 243-)  C    0.33
2903 SER   (  10-)  T    0.33
 729 SER   ( 155-)  C    0.35
 409 SER   ( 172-)  B    0.35
1531 SER   (  24-)  J    0.37
3530 SER   (  55-)  Z    0.37
1348 SER   (  71-)  H    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  19 PRO   (  19-)  A      0
  22 ARG   (  22-)  A      0
  27 LEU   (  27-)  A      0
  33 GLU   (  33-)  A      0
  34 ASP   (  34-)  A      0
  35 GLY   (  35-)  A      0
  36 ASP   (  36-)  A      0
  37 VAL   (  37-)  A      0
  38 ILE   (  38-)  A      0
  39 ALA   (  39-)  A      0
  44 ASP   (  44-)  A      0
  46 GLU   (  46-)  A      0
  66 ARG   (  66-)  A      0
  72 GLU   (  72-)  A      0
  76 VAL   (  76-)  A      0
  78 ASP   (  78-)  A      0
  82 VAL   (  82-)  A      0
  87 GLU   (  87-)  A      0
  88 ILE   (  88-)  A      0
  90 PRO   (  90-)  A      0
  94 LEU   (  94-)  A      0
 101 GLU   ( 101-)  A      0
 106 CYS   ( 106-)  A      0
 107 ASN   ( 107-)  A      0
 112 PRO   ( 112-)  A      0
And so on for a total of 4449 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.058

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!

3553 ILE   (  78-)  Z   4.99   32
2890 ALA   (  78-)  S   3.40   27
  78 ASP   (  78-)  A   3.30   80
1355 LYS   (  78-)  H   3.29   10
2193 GLY   (  70-)  N   1.98   46
1458 GLY   (  83-)  I   1.81   19
  73 GLY   (  73-)  A   1.78   18
1691 GLY   (  39-)  K   1.73   41
 405 GLY   ( 168-)  B   1.71   15
3025 GLY   (  16-)  U   1.64   54
1737 GLY   (  85-)  K   1.58   80
3741 GLY   (  58-)  3   1.57   14
 102 GLY   ( 102-)  A   1.56   26

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...

 502 LEU   ( 265-)  B   2.18

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]

 315 PRO   (  78-)  B    0.00 LOW
 541 PRO   ( 304-)  B    0.45 HIGH
 665 PRO   (  91-)  C    0.45 HIGH
3503 PRO   ( 231-)  Y    0.46 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  95 PRO   (  95-)  A  -114.0 envelop C-gamma (-108 degrees)
 150 PRO   ( 150-)  A  -118.5 half-chair C-delta/C-gamma (-126 degrees)
 593 PRO   (  19-)  C  -112.6 envelop C-gamma (-108 degrees)
 799 PRO   ( 225-)  C  -116.4 envelop C-gamma (-108 degrees)
 923 PRO   ( 137-)  D    99.4 envelop C-beta (108 degrees)
1697 PRO   (  45-)  K  -118.3 half-chair C-delta/C-gamma (-126 degrees)
1838 PRO   (  54-)  L  -116.7 envelop C-gamma (-108 degrees)
2039 PRO   ( 110-)  M  -116.1 envelop C-gamma (-108 degrees)
3659 PRO   (  22-)  2  -114.9 envelop C-gamma (-108 degrees)
3739 PRO   (  56-)  3   124.7 half-chair C-beta/C-alpha (126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

6656 PHE   (  77-)  6      N   <-> 6975 ACA   (  78-)  6      C1     1.36    1.34  INTRA BF
6656 PHE   (  77-)  6      C   <-> 6976 8AN   (  76-)  6      N3'    1.09    1.61  INTRA BF
6655 OCYT  (  75-)  6      O3' <-> 6976 8AN   (  76-)  6      P      1.01    1.59  INTRA BF
6656 PHE   (  77-)  6      CA  <-> 6975 ACA   (  78-)  6      C1     0.80    2.40  INTRA BF
6655 OCYT  (  75-)  6      C3' <-> 6976 8AN   (  76-)  6      P      0.79    2.61  INTRA BF
2790 ARG   ( 128-)  R      NH2 <-> 5776 OADE  (2054-)  0      N3     0.61    2.39  INTRA BL
5052 OADE  (1317-)  0      N7  <-> 5075 OGUA  (1340-)  0      N2     0.56    2.44  INTRA BL
2160 ARG   (  37-)  N      NH1 <-> 6535 OCYT  (   6-)  9      C5'    0.54    2.56  INTRA BF
4854 OGUA  (1119-)  0      N2  <-> 4981 OADE  (1246-)  0      C2     0.54    2.56  INTRA BF
1276 ARG   (  69-)  G      NH2 <-> 4885 OADE  (1150-)  0      N7     0.53    2.47  INTRA BF
3182 VAL   (  52-)  W      CG2 <-> 3183 ALA   (  53-)  W      N      0.51    2.49  INTRA BL
6205 OMG   (2588-)  0      N1  <-> 6653 OADE  (  76-)  5      N1     0.48    2.52  INTRA BF
  36 ASP   (  36-)  A      O   <->   38 ILE   (  38-)  A      N      0.47    2.23  INTRA BF
5586 OADE  (1852-)  0      N1  <-> 5613 OURA  (1879-)  0      N3     0.47    2.53  INTRA BL
1559 GLN   (  52-)  J      NE2 <-> 4854 OGUA  (1119-)  0      C2'    0.47    2.63  INTRA BL
5845 OADE  (2123-)  0      N7  <-> 5892 OGUA  (2270-)  0      N2     0.46    2.54  INTRA BL
5416 OADE  (1682-)  0      N7  <-> 5430 OURA  (1696-)  0      N3     0.46    2.54  INTRA BL
5851 OURA  (2129-)  0      N3  <-> 5886 OADE  (2264-)  0      N1     0.46    2.54  INTRA BL
4331 OURA  ( 567-)  0      N3  <-> 4355 OADE  ( 591-)  0      N1     0.46    2.54  INTRA BL
4559 OADE  ( 796-)  0      N7  <-> 4580 OGUA  ( 817-)  0      N2     0.45    2.55  INTRA BL
6119 OCYT  (2502-)  0      N3  <-> 6135 OCYT  (2518-)  0      N4     0.45    2.55  INTRA BL
5789 OADE  (2067-)  0      N1  <-> 5800 OURA  (2078-)  0      N3     0.45    2.55  INTRA BL
6214 OURA  (2597-)  0      N3  <-> 6218 OADE  (2601-)  0      N7     0.45    2.55  INTRA BL
6304 OADE  (2689-)  0      N1  <-> 6320 OURA  (2705-)  0      N3     0.44    2.56  INTRA BF
4544 OCYT  ( 781-)  0      N3  <-> 4628 OGUA  ( 865-)  0      N1     0.44    2.56  INTRA BL
And so on for a total of 4550 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: 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: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

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.

 235 ARG   ( 235-)  A      -8.99
 956 TYR   ( 170-)  D      -8.31
 232 ARG   ( 232-)  A      -8.15
2005 ARG   (  76-)  M      -8.12
3252 ARG   ( 122-)  W      -7.80
1805 ARG   (  21-)  L      -7.76
3657 ARG   (  20-)  2      -7.75
 272 GLN   (  35-)  B      -7.75
1928 ARG   ( 149-)  L      -7.73
3709 ARG   (  26-)  3      -7.72
 329 TYR   (  92-)  B      -7.70
2504 ARG   (  80-)  P      -7.53
3441 ARG   ( 169-)  Y      -7.52
3712 ARG   (  29-)  3      -7.47
2128 ARG   (   5-)  N      -7.43
 133 ARG   ( 133-)  A      -7.40
3580 ARG   ( 105-)  Z      -7.35
3763 ARG   (  80-)  3      -7.34
 244 ARG   (   7-)  B      -7.31
3713 GLN   (  30-)  3      -7.29
 472 ARG   ( 235-)  B      -7.25
1383 ARG   ( 117-)  H      -7.24
1806 ARG   (  22-)  L      -7.20
1792 ARG   (   8-)  L      -7.19
1832 LYS   (  48-)  L      -7.12
And so on for a total of 250 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.

 206 ARG   ( 206-)  A       208 - HIS    208- ( A)         -6.01
 231 LYS   ( 231-)  A       237 - GLY    237- ( A)         -5.99
 253 ARG   (  16-)  B       255 - ARG     18- ( B)         -4.78
 354 GLU   ( 117-)  B       356 - HIS    119- ( B)         -4.52
 393 LYS   ( 156-)  B       395 - LYS    158- ( B)         -4.73
 555 ASN   ( 318-)  B       557 - GLN    320- ( B)         -4.66
 635 PHE   (  61-)  C       639 - ARG     65- ( C)         -5.16
 799 PRO   ( 225-)  C       801 - GLY    227- ( C)         -4.66
 958 VAL   ( 172-)  D       960 - VAL    174- ( D)         -4.85
1368 ARG   (  91-)  H      1370 - PHE     93- ( H)         -4.41
1576 TYR   (  69-)  J      1578 - TYR     71- ( J)         -5.82
1826 ASN   (  42-)  L      1828 - GLU     44- ( L)         -4.75
1832 LYS   (  48-)  L      1837 - ARG     53- ( L)         -5.41
2004 ARG   (  75-)  M      2006 - HIS     77- ( M)         -6.58
2277 LEU   ( 154-)  N      2279 - GLU    156- ( N)         -4.50
2569 SER   (   2-)  Q      2571 - ASN      4- ( Q)         -5.01
2586 ARG   (  19-)  Q      2588 - ARG     21- ( Q)         -5.23
2792 MET   ( 130-)  R      2794 - ARG    132- ( R)         -4.58
2855 GLU   (  43-)  S      2857 - TYR     45- ( S)         -4.31
3548 ARG   (  73-)  Z      3551 - THR     76- ( Z)         -5.09
3625 LYS   (  44-)  1      3627 - ARG     46- ( 1)         -4.57
3676 TRP   (  42-)  2      3678 - ARG     44- ( 2)         -5.07
3735 PHE   (  52-)  3      3739 - PRO     56- ( 3)         -4.79
3762 LEU   (  79-)  3      3764 - GLU     81- ( 3)         -5.83

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6656 : -1.548

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: Z

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

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.

 480 ASN   ( 243-)  B   -4.02
3593 ASN   (  12-)  1   -3.87
1694 ASN   (  42-)  K   -3.86
2481 ASN   (  57-)  P   -3.82
 475 ASN   ( 238-)  B   -3.61
3677 ARG   (  43-)  2   -3.57
 618 GLN   (  44-)  C   -3.47
 206 ARG   ( 206-)  A   -3.47
1285 MET   (   8-)  H   -3.43
 670 LYS   (  96-)  C   -3.43
1424 ASN   ( 158-)  H   -3.42
3591 LYS   (  10-)  1   -3.33
 242 ARG   (   5-)  B   -3.32
2505 LYS   (  81-)  P   -3.30
3297 ALA   (  19-)  X   -3.29
2502 GLY   (  78-)  P   -3.29
 243 PRO   (   6-)  B   -3.28
1825 HIS   (  41-)  L   -3.28
2574 LEU   (   7-)  Q   -3.26
 780 ASN   ( 206-)  C   -3.24
1795 ARG   (  11-)  L   -3.18
1835 PHE   (  51-)  L   -3.17
 211 LYS   ( 211-)  A   -3.17
 483 ARG   ( 246-)  B   -3.17
3711 GLY   (  28-)  3   -3.16
And so on for a total of 139 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

   8 ARG   (   8-)  A     -   11 ARG   (  11-)  A        -1.70
 181 ALA   ( 181-)  A     -  185 LYS   ( 185-)  A        -2.06
 203 GLY   ( 203-)  A     -  208 HIS   ( 208-)  A        -2.40
 209 PRO   ( 209-)  A     -  212 PRO   ( 212-)  A        -2.42
 230 SER   ( 230-)  A     -  234 GLY   ( 234-)  A        -2.15
 241 SER   (   4-)  B     -  244 ARG   (   7-)  B        -2.53
 451 PRO   ( 214-)  B     -  454 ARG   ( 217-)  B        -1.65
 457 VAL   ( 220-)  B     -  461 LYS   ( 224-)  B        -1.79
 464 HIS   ( 227-)  B     -  468 GLY   ( 231-)  B        -2.18
 472 ARG   ( 235-)  B     -  475 ASN   ( 238-)  B        -2.39
 476 LEU   ( 239-)  B     -  483 ARG   ( 246-)  B        -2.62
 569 ASN   ( 332-)  B     -  574 GLY   ( 337-)  B        -2.04
 619 ASP   (  45-)  C     -  622 SER   (  48-)  C        -1.67
 639 ARG   (  65-)  C     -  644 VAL   (  70-)  C        -2.23
 662 SER   (  88-)  C     -  665 PRO   (  91-)  C        -2.27
 668 THR   (  94-)  C     -  671 ASP   (  97-)  C        -2.28
 748 ILE   ( 174-)  C     -  752 GLN   ( 178-)  C        -2.33
 855 PRO   (  49-)  D     -  858 THR   (  52-)  D        -1.87
1113 ARG   ( 153-)  E     - 1117 LYS   ( 157-)  E        -2.10
1380 ASP   ( 114-)  H     - 1386 PHE   ( 120-)  H        -2.00
1573 ASP   (  66-)  J     - 1576 TYR   (  69-)  J        -2.07
1687 HIS   (  35-)  K     - 1691 GLY   (  39-)  K        -2.12
1818 GLY   (  34-)  L     - 1822 HIS   (  38-)  L        -2.16
1833 SER   (  49-)  L     - 1836 LYS   (  52-)  L        -2.38
1983 TYR   (  54-)  M     - 1987 GLN   (  58-)  M        -1.49
2001 ALA   (  72-)  M     - 2009 GLY   (  80-)  M        -2.28
2012 SER   (  83-)  M     - 2015 GLN   (  86-)  M        -2.09
2087 ARG   ( 158-)  M     - 2090 ARG   ( 161-)  M        -2.15
2104 GLY   ( 175-)  M     - 2108 GLY   ( 179-)  M        -2.23
2159 ALA   (  36-)  N     - 2164 LYS   (  41-)  N        -1.94
2257 ASP   ( 134-)  N     - 2260 ALA   ( 137-)  N        -1.90
2345 PRO   (  36-)  O     - 2348 THR   (  39-)  O        -1.74
2477 ASP   (  53-)  P     - 2483 ARG   (  59-)  P        -2.27
2569 SER   (   2-)  Q     - 2572 GLY   (   5-)  Q        -2.07
2573 PRO   (   6-)  Q     - 2576 GLY   (   9-)  Q        -1.93
3139 GLY   (   9-)  W     - 3142 ASN   (  12-)  W        -2.15
3396 GLY   ( 124-)  Y     - 3399 GLN   ( 127-)  Y        -2.01
3407 LYS   ( 135-)  Y     - 3411 VAL   ( 139-)  Y        -2.23
3437 GLU   ( 165-)  Y     - 3440 PHE   ( 168-)  Y        -2.45
3513 PHE   (  38-)  Z     - 3516 ARG   (  41-)  Z        -1.99
3589 GLN   (   8-)  1     - 3595 THR   (  14-)  1        -2.45
3624 ALA   (  43-)  1     - 3632 GLN   (  51-)  1        -2.27
3637 GLU   (  56-)  1     - 3640 LYS   (   3-)  2        -1.72
3727 SER   (  44-)  3     - 3731 ASN   (  48-)  3        -2.15
3735 PHE   (  52-)  3     - 3738 VAL   (  55-)  3        -2.03
3742 ASP   (  59-)  3     - 3745 THR   (  62-)  3        -1.85
3760 ALA   (  77-)  3     - 3763 ARG   (  80-)  3        -1.91

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: 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: Z

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

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.

6999 HOH   (2786 )  V      O     65.46  120.64   -5.14
7004 HOH   (7106 )  0      O     50.81   10.67   98.48

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.

6980 HOH   (8568 )  C      O
6981 HOH   (4886 )  D      O
6981 HOH   (5708 )  D      O
6981 HOH   (6555 )  D      O
6985 HOH   (9024 )  H      O
6985 HOH   (9034 )  H      O
6987 HOH   (2664 )  J      O
6987 HOH   (5249 )  J      O
6987 HOH   (6256 )  J      O
6989 HOH   (8995 )  L      O
6989 HOH   (9020 )  L      O
6991 HOH   (8816 )  N      O
6995 HOH   (8984 )  R      O
6996 HOH   (8525 )  S      O
6996 HOH   (8541 )  S      O
7000 HOH   (5084 )  W      O
7000 HOH   (6694 )  W      O
7002 HOH   (8848 )  Y      O
7004 HOH   (3301 )  0      O
7004 HOH   (3686 )  0      O
7004 HOH   (3969 )  0      O
7004 HOH   (4295 )  0      O
7004 HOH   (4786 )  0      O
7004 HOH   (5070 )  0      O
7004 HOH   (5340 )  0      O
7004 HOH   (5565 )  0      O
7004 HOH   (5601 )  0      O
7004 HOH   (5908 )  0      O
7004 HOH   (6301 )  0      O
7004 HOH   (6420 )  0      O
7004 HOH   (7273 )  0      O
7004 HOH   (7446 )  0      O
7004 HOH   (7473 )  0      O
7004 HOH   (7546 )  0      O
7004 HOH   (9018 )  0      O
7004 HOH   (9020 )  0      O
7004 HOH   (9194 )  0      O
7004 HOH   (9651 )  0      O
7004 HOH   (9668 )  0      O
7006 HOH   (5444 )  2      O
7007 HOH   (9031 )  3      O
Marked this atom as acceptor 6694  CL  (8816-) 0     CL
Marked this atom as acceptor 6830  CL  (8803-) 0     CL
Marked this atom as acceptor 6831  CL  (8805-) 0     CL
Marked this atom as acceptor 6832  CL  (8812-) 0     CL
Marked this atom as acceptor 6833  CL  (8813-) 0     CL
Marked this atom as acceptor 6834  CL  (8815-) 0     CL
Marked this atom as acceptor 6835  CL  (8822-) 0     CL
Marked this atom as acceptor 6931  CL  (8809-) A     CL
Marked this atom as acceptor 6936  CL  (8819-) B     CL
Marked this atom as acceptor 6943  CL  (8801-) J     CL
Marked this atom as acceptor 6944  CL  (8802-) J     CL
Marked this atom as acceptor 6945  CL  (8821-) J     CL
Marked this atom as acceptor 6947  CL  (8810-) L     CL
Marked this atom as acceptor 6948  CL  (8814-) L     CL
Marked this atom as acceptor 6951  CL  (8818-) M     CL
Marked this atom as acceptor 6952  CL  (8807-) N     CL
Marked this atom as acceptor 6954  CL  (8808-) O     CL
Marked this atom as acceptor 6956  CL  (8811-) Q     CL
Marked this atom as acceptor 6958  CL  (8806-) R     CL
Marked this atom as acceptor 6964  CL  (8817-) Y     CL
Marked this atom as acceptor 6965  CL  (8820-) 0     CL
Marked this atom as acceptor 6972  CL  (8804-) 3     CL
Unrecognized bound group for 6656
  Bound atom= 6976 8AN  (  76-) 6      N3'

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.

 199 HIS   ( 199-)  A
 475 ASN   ( 238-)  B
 497 HIS   ( 260-)  B
 647 GLN   (  73-)  C
 737 HIS   ( 163-)  C
 853 GLN   (  47-)  D
 909 ASN   ( 103-)  D
 919 ASN   ( 133-)  D
1103 GLN   ( 143-)  E
1212 GLN   (  80-)  F
1336 GLN   (  59-)  H
1532 GLN   (  25-)  J
1614 ASN   ( 107-)  J
1802 HIS   (  18-)  L
1943 ASN   (  14-)  M
1953 GLN   (  24-)  M
1987 GLN   (  58-)  M
2144 HIS   (  21-)  N
2145 GLN   (  22-)  N
2230 ASN   ( 107-)  N
2452 GLN   (  28-)  P
2474 GLN   (  50-)  P
2490 GLN   (  66-)  P
2512 GLN   (  88-)  P
2542 GLN   ( 118-)  P
And so on for a total of 58 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.

  24 LYS   (  24-)  A      N
  30 ARG   (  30-)  A      NH1
  33 GLU   (  33-)  A      N
  34 ASP   (  34-)  A      N
  36 ASP   (  36-)  A      N
  37 VAL   (  37-)  A      N
  51 ARG   (  51-)  A      NH1
  66 ARG   (  66-)  A      NH1
  75 GLY   (  75-)  A      N
  85 SER   (  85-)  A      N
 122 SER   ( 122-)  A      OG
 135 VAL   ( 135-)  A      N
 153 ARG   ( 153-)  A      NH1
 158 VAL   ( 158-)  A      N
 162 GLY   ( 162-)  A      N
 164 ARG   ( 164-)  A      NH2
 167 LYS   ( 167-)  A      N
 170 VAL   ( 170-)  A      N
 208 HIS   ( 208-)  A      N
 230 SER   ( 230-)  A      N
 255 ARG   (  18-)  B      NE
 255 ARG   (  18-)  B      NH1
 260 THR   (  23-)  B      N
 263 PHE   (  26-)  B      N
 265 SER   (  28-)  B      N
And so on for a total of 391 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.

 292 ASN   (  55-)  B      OD1
 303 GLU   (  66-)  B      OE1
 467 GLN   ( 230-)  B      OE1
 493 GLN   ( 256-)  B      OE1
 703 HIS   ( 129-)  C      NE2
 739 ASP   ( 165-)  C      OD2
 873 ASP   (  67-)  D      OD1
 957 ASP   ( 171-)  D      OD2
1173 GLU   (  41-)  F      OE1
1485 ASP   ( 110-)  I      OD2
1696 HIS   (  44-)  K      ND1
1825 HIS   (  41-)  L      NE2
1854 ASP   (  70-)  L      OD1
1981 GLN   (  52-)  M      OE1
2006 HIS   (  77-)  M      NE2
2086 ASP   ( 157-)  M      OD2
2099 ASN   ( 170-)  M      OD1
2274 ASP   ( 151-)  N      OD1
2287 ASP   ( 164-)  N      OD1
2290 ASP   ( 167-)  N      OD2
2296 ASP   ( 173-)  N      OD2
3255 HIS   ( 125-)  W      ND1
3360 GLU   (  82-)  X      OE2
3366 GLU   (  88-)  X      OE2
3421 GLN   ( 149-)  Y      OE1
3667 ASP   (  30-)  2      OD2
3683 GLU   (  49-)  2      OE1
3703 HIS   (  20-)  3      NE2

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+.

6670  MG   (8001-)  0     0.38   0.76 Scores about as good as NA *1
6671  MG   (8025-)  A     0.28   0.92 Is perhaps  K *1 and *2
6672  MG   (8002-)  0     0.36   1.75 Scores about as good as  K *1 and *2
6673  MG   (8044-)  0     0.30   1.04 Is perhaps  K *1 and *2
6674  MG   (8003-)  0     0.43   0.86 Scores about as good as NA *1
6675  MG   (8004-)  0     0.45   0.89 Is perhaps NA *1
6676  MG   (8005-)  0     0.30   1.25 Is perhaps  K *1 and *2
6677  MG   (8006-)  0     0.41   0.82 Scores about as good as NA *1
6678  MG   (8007-)  0   -.-  -.-  Part of ionic cluster
6678  MG   (8007-)  0     0.32   1.25 Is perhaps  K *1 and *2
6679  MG   (8008-)  0     0.32   1.44 Is perhaps  K *1 and *2
6680  MG   (8043-)  B     0.26   0.97 Is perhaps  K *1 and *2
6681  MG   (8009-)  0     0.47   0.93 Is perhaps NA *1
6682  MG   (8010-)  0     0.22   0.52 Scores about as good as  K *1 and *2
6683  MG   (8011-)  0     0.55   1.11 Scores about as good as NA *1
6684  MG   (8012-)  C     0.45   0.90 Is perhaps NA *1
6685  MG   (8013-)  0     0.34   1.42 Is perhaps  K *1 and *2
6686  MG   (8014-)  0     0.42   0.85 Scores about as good as NA *1
6687  MG   (8015-)  0     0.32   1.38 Is perhaps  K *1 and *2
6688  MG   (8016-)  0   -.-  -.-  Low probability ion. B=131.7
6689  NA   (8518-)  H   -.-  -.-  Too few ligands (0)
6690  MG   (8017-)  0   -.-  -.-  Low probability ion. B=123.4
6692  MG   (8018-)  0   -.-  -.-  Part of ionic cluster
6692  MG   (8018-)  0     0.40   0.79 Scores about as good as NA *1
6693  MG   (8019-)  0     0.41   0.82 Scores about as good as NA *1
And so on for a total of 201 lines.

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.

6978 HOH   (9040 )  A      O  0.79  K  5 *1 and *2
6982 HOH   (3940 )  E      O  0.79  K  4 *1 and *2 Ion-B
6985 HOH   (9050 )  H      O  1.04  K  4 *1 and *2 ION-B
6994 HOH   (5903 )  Q      O  1.09  K  4 *1 and *2
6995 HOH   (8985 )  R      O  0.83  K  5 *1 and *2
6996 HOH   (8526 )  S      O  1.10  K  4 *1 and *2 Ion-B
6998 HOH   ( 310 )  U      O  1.04  K  7 *1 and *2
7004 HOH   (4406 )  0      O  1.04  K  4 *1 and *2 ION-B
7004 HOH   (5299 )  0      O  0.78  K  4 *1 and *2 Ion-B
7004 HOH   (5361 )  0      O  0.92  K  5 *1 and *2
7005 HOH   (6146 )  1      O  0.80  K  4 *1 and *2 Ion-B

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.

 114 ASP   ( 114-)  A   H-bonding suggests Asn
 166 ASP   ( 166-)  A   H-bonding suggests Asn
 270 ASP   (  33-)  B   H-bonding suggests Asn; but Alt-Rotamer
 351 ASP   ( 114-)  B   H-bonding suggests Asn
 355 ASP   ( 118-)  B   H-bonding suggests Asn
 413 ASP   ( 176-)  B   H-bonding suggests Asn; but Alt-Rotamer
 417 ASP   ( 180-)  B   H-bonding suggests Asn
 421 ASP   ( 184-)  B   H-bonding suggests Asn
 435 GLU   ( 198-)  B   H-bonding suggests Gln; but Alt-Rotamer
 518 ASP   ( 281-)  B   H-bonding suggests Asn
 581 ASP   (   7-)  C   H-bonding suggests Asn; but Alt-Rotamer
 675 ASP   ( 101-)  C   H-bonding suggests Asn; but Alt-Rotamer
 700 ASP   ( 126-)  C   H-bonding suggests Asn
 704 GLU   ( 130-)  C   H-bonding suggests Gln; but Alt-Rotamer
 719 GLU   ( 145-)  C   H-bonding suggests Gln
 796 ASP   ( 222-)  C   H-bonding suggests Asn; but Alt-Rotamer
 849 GLU   (  43-)  D   H-bonding suggests Gln
 873 ASP   (  67-)  D   H-bonding suggests Asn
 957 ASP   ( 171-)  D   H-bonding suggests Asn
1089 GLU   ( 129-)  E   H-bonding suggests Gln; but Alt-Rotamer
1107 ASP   ( 147-)  E   H-bonding suggests Asn; but Alt-Rotamer
1146 ASP   (  14-)  F   H-bonding suggests Asn
1157 ASP   (  25-)  F   H-bonding suggests Asn
1173 GLU   (  41-)  F   H-bonding suggests Gln; but Alt-Rotamer
1200 ASP   (  68-)  F   H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 81 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 :  -2.620
  2nd generation packing quality :  -3.970 (poor)
  Ramachandran plot appearance   :  -4.002 (bad)
  chi-1/chi-2 rotamer normality  :  -3.210 (poor)
  Backbone conformation          :  -0.032

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.420 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.192 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   0.985

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 : 2.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.6
  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.420 (tight)
  Bond angles                    :   0.667
  Omega angle restraints         :   0.192 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.419
  Inside/Outside distribution    :   0.985
==============

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.