WHAT IF Check report

This file was created 2013-12-10 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 pdb4kja.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: P 1 21 1
Number of matrices in space group: 2
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: 2
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

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

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 837627.750
Volume of the Unit Cell V= 54471920.0
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 65.031
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.650 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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.

4632 GCP   ( 801-)  V  -
4633 5OH   (   6-)  W  -
4634 UAL   (   5-)  W  -
4635 DPP   (   2-)  W  -
4636 KBE   (   1-)  W  -

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.

4577 SER   (   3-)  W  -

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.

4577 SER   (   3-)  W  -   N   bound to 4635 DPP   (   2-)  W  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: 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

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'.

3992 VAL   ( 116-)  V      CG2
4034 ILE   ( 158-)  V      CG2
4034 ILE   ( 158-)  V      CD1
4045 LEU   ( 169-)  V      CD1
4045 LEU   ( 169-)  V      CD2
4061 LEU   ( 185-)  V      CD1
4061 LEU   ( 185-)  V      CD2
4067 ILE   ( 191-)  V      CG2
4067 ILE   ( 191-)  V      CD1
4090 LEU   ( 214-)  V      CD1
4090 LEU   ( 214-)  V      CD2
4099 ILE   ( 223-)  V      CD1
4109 LEU   ( 233-)  V      CD1
4109 LEU   ( 233-)  V      CD2
4119 LEU   ( 243-)  V      CD1
4119 LEU   ( 243-)  V      CD2
4128 LEU   ( 252-)  V      CD1
4128 LEU   ( 252-)  V      CD2
4133 LEU   ( 257-)  V      CD1
4133 LEU   ( 257-)  V      CD2
4175 LEU   ( 299-)  V      CD1
4175 LEU   ( 299-)  V      CD2

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.

   3 OURA  (   4-)  A    High
   4 OURA  (   5-)  A    High
  74 OGUA  (  75-)  A    High
  77 OADE  (  78-)  A    High
  78 OGUA  (  79-)  A    High
  79 OADE  (  80-)  A    High
  80 OADE  (  81-)  A    High
  81 OGUA  (  82-)  A    High
  82 OCYT  (  83-)  A    High
  83 OURA  (  84-)  A    High
  84 OURA  (  85-)  A    High
  85 OGUA  (  86-)  A    High
  86 OCYT  (  87-)  A    High
  87 OURA  (  88-)  A    High
  88 OURA  (  89-)  A    High
  89 OCYT  (  90-)  A    High
  90 OURA  (  91-)  A    High
  91 OURA  (  92-)  A    High
 208 OURA  ( 209-)  A    High
 209 OCYT  ( 210-)  A    High
 210 OGUA  ( 211-)  A    High
 461 OGUA  ( 462-)  A    High
 531 OADE  ( 532-)  A    High
 839 OCYT  ( 840-)  A    High
 840 OCYT  ( 841-)  A    High
 841 OURA  ( 842-)  A    High
 842 OURA  ( 843-)  A    High
 843 OGUA  ( 844-)  A    High
 844 OADE  ( 845-)  A    High
 845 OGUA  ( 846-)  A    High
 846 OGUA  ( 847-)  A    High
 847 OCYT  ( 848-)  A    High
 848 OGUA  ( 849-)  A    High
1136 OCYT  (1137-)  A    High
1167 OURA  (1168-)  A    High
1451 OCYT  (1452-)  A    High
1452 OGUA  (1453-)  A    High
1453 OGUA  (1454-)  A    High
1533 OADE  (1534-)  A    High
1661 MET   ( 135-)  B    High
2305 MET   ( 152-)  E    High
3926 MET   (  50-)  V    High
3979 MET   ( 103-)  V    High
4020 MET   ( 144-)  V    High
4087 MET   ( 211-)  V    High
4242 MET   ( 366-)  V    High
4450 MET   ( 574-)  V    High
4493 MET   ( 617-)  V    High
4517 MET   ( 641-)  V    High

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.

4577 SER   (   3-)  W    0.56
4578 SER   (   4-)  W    0.56

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.974 over 21187 bonds
Average difference in B over a bond : 6.12
RMS difference in B over a bond : 7.98

Note: B-factor plot

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

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

1881 ARG   ( 131-)  C
2813 ARG   ( 124-)  I
3089 ARG   (  56-)  L
3483 ARG   (  28-)  P
4235 ARG   ( 359-)  V
4238 ARG   ( 362-)  V
4367 ARG   ( 491-)  V
4388 ARG   ( 512-)  V
4547 ARG   ( 671-)  V

Warning: Tyrosine convention problem

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

1943 TYR   ( 193-)  C
2316 TYR   (   4-)  F
2727 TYR   (  38-)  I
4080 TYR   ( 204-)  V
4161 TYR   ( 285-)  V

Warning: Phenylalanine convention problem

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

1555 PHE   (  29-)  B
3918 PHE   (  32-)  V
4481 PHE   ( 605-)  V

Warning: Aspartic acid convention problem

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

1713 ASP   ( 187-)  B
2055 ASP   (  99-)  D
3303 ASP   (  33-)  N

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.

1581 GLU   (  55-)  B
1670 GLU   ( 144-)  B
1700 GLU   ( 174-)  B
1832 GLU   (  82-)  C
1860 GLU   ( 110-)  C
1875 GLU   ( 125-)  C
1938 GLU   ( 188-)  C
2208 GLU   (  55-)  E
2269 GLU   ( 116-)  E
2317 GLU   (   5-)  F
2345 GLU   (  33-)  F
2377 GLU   (  65-)  F
2410 GLU   (  98-)  F
2432 GLU   (  21-)  G
2451 GLU   (  40-)  G
2469 GLU   (  58-)  G
2474 GLU   (  63-)  G
2605 GLU   (  43-)  H
2609 GLU   (  47-)  H
2614 GLU   (  52-)  H
2620 GLU   (  58-)  H
2653 GLU   (  91-)  H
2686 GLU   ( 124-)  H
2781 GLU   (  92-)  I
2842 GLU   (  27-)  J
And so on for a total of 64 lines.

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.

 413 OADE  ( 414-)  A      N9   C4    1.40    4.3
 460 OADE  ( 461-)  A      N9   C4    1.41    5.9
 732 OGUA  ( 733-)  A      N9   C4    1.34   -4.0
 902 OGUA  ( 903-)  A      N7   C5    1.36   -4.9
 921 OGUA  ( 922-)  A      C1'  N9    1.50    4.0
1356 OADE  (1357-)  A      N9   C4    1.35   -4.2
1499 OADE  (1500-)  A      N9   C4    1.35   -4.5
4578 SER   (   4-)  W      N   -C     1.48    7.7

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

 |  0.999254  0.000282  0.000228|
 |  0.000282  0.999523  0.000068|
 |  0.000228  0.000068  0.999885|
Proposed new scale matrix

 |  0.002771  0.000000  0.000649|
 |  0.000000  0.002775  0.000000|
 |  0.000000  0.000000  0.002390|
With corresponding cell

    A    = 360.895  B   = 360.318  C    = 429.704
    Alpha=  90.004  Beta= 103.193  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 361.141  B   = 360.490  C    = 429.783
    Alpha=  90.000  Beta= 103.211  Gamma=  90.000

Variance: 239.662
(Under-)estimated Z-score: 11.409

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.

  14 OGUA  (  15-)  A      N9   C8   N7  113.58    5.0
  15 OADE  (  16-)  A      N6   C6   N1  115.54   -5.1
  21 OGUA  (  22-)  A      N9   C8   N7  113.50    4.8
  26 OGUA  (  27-)  A      N9   C8   N7  114.52    6.8
  26 OGUA  (  27-)  A      C8   N9   C4  104.67   -4.3
  26 OGUA  (  27-)  A      C5   C4   N3  126.28   -4.6
  27 OADE  (  28-)  A      C8   N9   C4  103.82   -4.9
  31 OADE  (  32-)  A      C5   C6   N6  126.98    4.1
  31 OADE  (  32-)  A      N6   C6   N1  115.87   -4.6
  34 OGUA  (  35-)  A      N9   C8   N7  113.45    4.7
  37 OGUA  (  38-)  A      N9   C8   N7  113.61    5.0
  38 OGUA  (  39-)  A      N9   C8   N7  113.13    4.1
  41 OGUA  (  42-)  A      N9   C8   N7  113.39    4.6
  45 OGUA  (  46-)  A      N9   C8   N7  113.29    4.4
  48 OURA  (  49-)  A      O4   C4   N3  116.45   -4.2
  51 OCYT  (  52-)  A      P   -C3* -O3* 130.31    8.8
  52 OADE  (  53-)  A      N9   C8   N7  116.08    4.6
  52 OADE  (  53-)  A      C8   N9   C4  103.32   -6.2
  56 OGUA  (  57-)  A      N9   C8   N7  113.52    4.8
  59 OADE  (  60-)  A      C2   N3   C4  108.59   -4.0
  67 OGUA  (  68-)  A      N9   C8   N7  113.57    4.9
  68 OGUA  (  69-)  A      N9   C8   N7  113.53    4.9
  69 OURA  (  70-)  A      C1'  N1   C2  123.08    4.5
  69 OURA  (  70-)  A      N1   C6   C5  125.03    4.7
  72 OCYT  (  73-)  A      O5'  C5'  C4' 116.33    4.4
And so on for a total of 671 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.

1581 GLU   (  55-)  B
1670 GLU   ( 144-)  B
1700 GLU   ( 174-)  B
1713 ASP   ( 187-)  B
1832 GLU   (  82-)  C
1860 GLU   ( 110-)  C
1875 GLU   ( 125-)  C
1881 ARG   ( 131-)  C
1938 GLU   ( 188-)  C
2055 ASP   (  99-)  D
2208 GLU   (  55-)  E
2269 GLU   ( 116-)  E
2317 GLU   (   5-)  F
2345 GLU   (  33-)  F
2377 GLU   (  65-)  F
2410 GLU   (  98-)  F
2432 GLU   (  21-)  G
2451 GLU   (  40-)  G
2469 GLU   (  58-)  G
2474 GLU   (  63-)  G
2605 GLU   (  43-)  H
2609 GLU   (  47-)  H
2614 GLU   (  52-)  H
2620 GLU   (  58-)  H
2653 GLU   (  91-)  H
And so on for a total of 76 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

4433 ILE   ( 557-)  V    5.30
3969 VAL   (  93-)  V    5.18
4466 GLU   ( 590-)  V    4.72
3234 LYS   (  78-)  M    4.50
2732 THR   (  43-)  I    4.35
3410 ALA   (  44-)  O    4.34
4098 LEU   ( 222-)  V    4.29
1992 GLN   (  36-)  D    4.17
3263 ARG   ( 107-)  M    4.10
3005 LEU   ( 100-)  K    4.04
3846 ASP   (  13-)  U    4.04
4578 SER   (   4-)  W    4.03
3758 LYS   (   9-)  T    4.02
1732 ILE   ( 206-)  B    4.02

Error: Side chain planarity problems

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

4434 GLN   ( 558-)  V    4.57

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 : -4.685

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.

4078 PHE   ( 202-)  V    -3.8
3870 PHE   (  37-)  U    -3.5
2732 THR   (  43-)  I    -3.2
4369 THR   ( 493-)  V    -3.0
4077 THR   ( 201-)  V    -3.0
4080 TYR   ( 204-)  V    -3.0
3871 TYR   (  38-)  U    -3.0
2994 PRO   (  89-)  K    -2.9
3891 THR   (   5-)  V    -2.9
3818 LYS   (  69-)  T    -2.9
2286 PRO   ( 133-)  E    -2.8
3453 LEU   (  87-)  O    -2.8
2177 THR   (  24-)  E    -2.8
1976 PHE   (  20-)  D    -2.7
4076 VAL   ( 200-)  V    -2.7
1593 LEU   (  67-)  B    -2.7
1765 VAL   (  15-)  C    -2.7
4179 LYS   ( 303-)  V    -2.7
1655 THR   ( 129-)  B    -2.7
4551 LYS   ( 675-)  V    -2.6
3867 ARG   (  34-)  U    -2.6
3890 THR   (   4-)  V    -2.6
2496 TYR   (  85-)  G    -2.6
3969 VAL   (  93-)  V    -2.6
2319 VAL   (   7-)  F    -2.6
And so on for a total of 173 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.

1535 LEU   (   9-)  B  Poor phi/psi
1537 ALA   (  11-)  B  Poor phi/psi
1538 GLY   (  12-)  B  Poor phi/psi
1543 HIS   (  17-)  B  Poor phi/psi
1544 GLN   (  18-)  B  Poor phi/psi, omega poor
1546 ARG   (  20-)  B  Poor phi/psi, omega poor
1547 TYR   (  21-)  B  Poor phi/psi
1548 TRP   (  22-)  B  Poor phi/psi
1559 ALA   (  33-)  B  Poor phi/psi
1561 ASN   (  35-)  B  Poor phi/psi
1562 LYS   (  36-)  B  Poor phi/psi
1566 ILE   (  40-)  B  Poor phi/psi
1568 LEU   (  42-)  B  omega poor
1589 LYS   (  63-)  B  Poor phi/psi
1593 LEU   (  67-)  B  Poor phi/psi
1597 THR   (  71-)  B  Poor phi/psi
1598 LYS   (  72-)  B  Poor phi/psi
1601 ALA   (  75-)  B  Poor phi/psi
1606 LYS   (  80-)  B  Poor phi/psi
1607 ASP   (  81-)  B  Poor phi/psi
1610 LEU   (  84-)  B  Poor phi/psi
1644 THR   ( 118-)  B  Poor phi/psi
1645 GLN   ( 119-)  B  Poor phi/psi
1649 GLY   ( 123-)  B  Poor phi/psi
1650 THR   ( 124-)  B  Poor phi/psi
And so on for a total of 362 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.214

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.

3279 ARG   (   9-)  N    0.38
1968 SER   (  12-)  D    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 OURA  (   4-)  A      0
   4 OURA  (   5-)  A      0
   5 OGUA  (   6-)  A      0
   6 OADE  (   7-)  A      0
   7 OADE  (   8-)  A      0
   8 OGUA  (   9-)  A      0
   9 OADE  (  10-)  A      0
  10 OGUA  (  11-)  A      0
  11 OURA  (  12-)  A      0
  12 OURA  (  13-)  A      0
  13 OURA  (  14-)  A      0
  14 OGUA  (  15-)  A      0
  15 OADE  (  16-)  A      0
  16 OURA  (  17-)  A      0
  17 OCYT  (  18-)  A      0
  18 OADE  (  19-)  A      0
  19 OURA  (  20-)  A      0
  20 OGUA  (  21-)  A      0
  21 OGUA  (  22-)  A      0
  22 OCYT  (  23-)  A      0
  23 OURA  (  24-)  A      0
  24 OCYT  (  25-)  A      0
  25 OADE  (  26-)  A      0
  26 OGUA  (  27-)  A      0
  27 OADE  (  28-)  A      0
And so on for a total of 2834 lines.

Warning: Backbone oxygen evaluation

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

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

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

3357 GLY   (  91-)  N   2.77   80
3465 GLY   (  10-)  P   2.37   12
3118 GLY   (  85-)  L   2.23   13
3009 GLY   ( 104-)  K   1.93   80
2244 GLY   (  91-)  E   1.89   15
3974 GLU   (  98-)  V   1.83   14
2504 PRO   (  93-)  G   1.74   13
2303 PRO   ( 150-)  E   1.72   13
3678 GLY   (   8-)  S   1.69   12
3641 ARG   (  43-)  R   1.63   80
3192 ALA   (  36-)  M   1.62   10

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].

1726 PRO   ( 200-)  B  -115.9 envelop C-gamma (-108 degrees)
1767 PRO   (  17-)  C   -57.0 half-chair C-beta/C-alpha (-54 degrees)
1848 PRO   (  98-)  C  -116.3 envelop C-gamma (-108 degrees)
1924 PRO   ( 174-)  C    50.1 half-chair C-delta/C-gamma (54 degrees)
2286 PRO   ( 133-)  E   169.0 half-chair C-alpha/N (162 degrees)
2324 PRO   (  12-)  F  -118.7 half-chair C-delta/C-gamma (-126 degrees)
2331 PRO   (  19-)  F  -114.8 envelop C-gamma (-108 degrees)
2643 PRO   (  81-)  H  -115.1 envelop C-gamma (-108 degrees)
2712 PRO   (  23-)  I  -112.4 envelop C-gamma (-108 degrees)
2994 PRO   (  89-)  K   -64.0 envelop C-beta (-72 degrees)
3078 PRO   (  45-)  L   -56.2 half-chair C-beta/C-alpha (-54 degrees)
3252 PRO   (  96-)  M  -121.2 half-chair C-delta/C-gamma (-126 degrees)
3318 PRO   (  52-)  N    99.5 envelop C-beta (108 degrees)
3470 PRO   (  15-)  P  -115.5 envelop C-gamma (-108 degrees)
3639 PRO   (  41-)  R  -112.5 envelop C-gamma (-108 degrees)
3667 PRO   (  69-)  R    46.8 half-chair C-delta/C-gamma (54 degrees)
3746 PRO   (  76-)  S  -133.0 half-chair C-delta/C-gamma (-126 degrees)
3844 PRO   (  11-)  U    48.9 half-chair C-delta/C-gamma (54 degrees)
4012 PRO   ( 136-)  V   101.0 envelop C-beta (108 degrees)
4084 PRO   ( 208-)  V   -26.6 half-chair C-alpha/N (-18 degrees)
4279 PRO   ( 403-)  V     6.9 envelop N (0 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.

4633 5OH   (   6-)  W      N   <-> 4634 UAL   (   5-)  W      C      1.29    1.41  INTRA BL
4578 SER   (   4-)  W      C   <-> 4634 UAL   (   5-)  W      N      1.27    1.43  INTRA BL
4577 SER   (   3-)  W      N   <-> 4635 DPP   (   2-)  W      C      1.22    1.48  INTRA BL
4633 5OH   (   6-)  W      C   <-> 4635 DPP   (   2-)  W      NG     1.22    1.48  INTRA BL
4635 DPP   (   2-)  W      N   <-> 4636 KBE   (   1-)  W      C      1.20    1.50  INTRA BL
2746 MET   (  57-)  I      SD  <-> 2747 VAL   (  58-)  I      N      0.74    2.46  INTRA BF
3031 LYS   ( 126-)  K      O   <-> 3867 ARG   (  34-)  U      NH1    0.73    1.97  INTRA BF
 410 OADE  ( 411-)  A      OP1 <-> 1982 ARG   (  26-)  D      NH2    0.73    1.97  INTRA BL
1319 OCYT  (1320-)  A      N3  <-> 3706 ARG   (  36-)  S      NH1    0.70    2.30  INTRA BL
2479 ASN   (  68-)  G      OD1 <-> 2541 ASN   ( 130-)  G      ND2    0.64    2.06  INTRA BF
4577 SER   (   3-)  W      CA  <-> 4635 DPP   (   2-)  W      C      0.64    2.56  INTRA
4578 SER   (   4-)  W      CA  <-> 4634 UAL   (   5-)  W      N      0.64    2.46  INTRA
 180 OADE  ( 181-)  A      N7  <-> 4637 HOH   (1876 )  A      O      0.64    2.06  INTRA BL
2731 GLU   (  42-)  I      O   <-> 2733 ALA   (  44-)  I      N      0.62    2.08  INTRA BF
3968 HIS   (  92-)  V      O   <-> 3998 GLN   ( 122-)  V      NE2    0.61    2.09  INTRA BF
 194 OADE  ( 195-)  A      OP1 <-> 3809 ARG   (  60-)  T      NH1    0.60    2.10  INTRA
3108 GLN   (  75-)  L      O   <-> 3110 HIS   (  77-)  L      N      0.60    2.10  INTRA BL
 461 OGUA  ( 462-)  A      N1  <->  469 OCYT  ( 470-)  A      N3     0.59    2.41  INTRA BF
1531 OURA  (1532-)  A      O4  <-> 3880 ARG   (  47-)  U      NH1    0.58    2.12  INTRA BF
1786 ASP   (  36-)  C      OD1 <-> 1809 ARG   (  59-)  C      NH1    0.57    2.13  INTRA BL
4079 GLU   ( 203-)  V      O   <-> 4081 GLU   ( 205-)  V      N      0.57    2.13  INTRA BF
3909 LYS   (  23-)  V      NZ  <-> 4632 GCP   ( 801-)  V      O2G    0.53    2.17  INTRA
4633 5OH   (   6-)  W      CA  <-> 4634 UAL   (   5-)  W      C      0.53    2.47  INTRA BL
4521 GLN   ( 645-)  V      O   <-> 4523 SER   ( 647-)  V      N      0.53    2.17  INTRA BF
4095 HIS   ( 219-)  V      O   <-> 4098 LEU   ( 222-)  V      N      0.52    2.18  INTRA BF
And so on for a total of 2461 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: 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

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.

3269 ARG   ( 113-)  M      -8.61
3750 TYR   (  80-)  S      -8.39
3033 ARG   ( 128-)  K      -8.31
2414 ARG   (   3-)  G      -8.23
1982 ARG   (  26-)  D      -8.11
3383 ARG   (  17-)  O      -7.97
3027 ARG   ( 122-)  K      -7.93
1857 ARG   ( 107-)  C      -7.86
3889 ARG   (   3-)  V      -7.84
1960 TYR   (   4-)  D      -7.62
1996 GLN   (  40-)  D      -7.54
3254 ARG   (  98-)  M      -7.54
3671 ARG   (  73-)  R      -7.44
1750 ARG   ( 224-)  B      -7.40
2000 ARG   (  44-)  D      -7.36
3725 ARG   (  55-)  S      -7.24
4384 GLN   ( 508-)  V      -7.22
3270 LYS   ( 114-)  M      -7.18
3540 ARG   (   6-)  Q      -7.17
3327 ARG   (  61-)  N      -7.10
1943 TYR   ( 193-)  C      -7.07
2942 ARG   (  37-)  K      -7.05
3483 ARG   (  28-)  P      -6.95
2852 ARG   (  37-)  J      -6.92
2566 GLN   (   4-)  H      -6.89
And so on for a total of 174 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.

1752 GLY   (   2-)  C      1755 - VAL      5- ( C)         -4.87
1959 ARG   (   3-)  D      1961 - LEU      5- ( D)         -6.01
2364 ASN   (  52-)  F      2367 - HIS     55- ( F)         -5.13
2414 ARG   (   3-)  G      2418 - ILE      7- ( G)         -5.69
2420 GLN   (   9-)  G      2424 - LEU     13- ( G)         -4.92
2700 ARG   (  11-)  I      2702 - LYS     13- ( I)         -4.88
2811 ARG   ( 122-)  I      2813 - ARG    124- ( I)         -4.59
3030 LYS   ( 125-)  K      3033 - ARG    128- ( K)         -6.56
3103 GLU   (  70-)  L      3106 - ASN     73- ( L)         -4.54
3269 ARG   ( 113-)  M      3271 - PRO    115- ( M)         -6.69
3467 LYS   (  12-)  P      3469 - ARG     14- ( P)         -5.68
3500 GLU   (  45-)  P      3503 - GLU     48- ( P)         -5.16
3550 LYS   (  16-)  Q      3552 - GLU     18- ( Q)         -5.17
3675 LEU   (   5-)  S      3677 - LYS      7- ( S)         -5.79
3748 ARG   (  78-)  S      3750 - TYR     80- ( S)         -6.57
3840 ARG   (   7-)  U      3843 - GLU     10- ( U)         -4.96
3866 ARG   (  33-)  U      3868 - ARG     35- ( U)         -5.18
3870 PHE   (  37-)  U      3872 - GLU     39- ( U)         -5.54
3954 GLN   (  78-)  V      3956 - GLU     80- ( V)         -4.44
4351 ARG   ( 475-)  V      4353 - PHE    477- ( V)         -4.74
4384 GLN   ( 508-)  V      4388 - ARG    512- ( V)         -4.92
4513 ARG   ( 637-)  V      4515 - ARG    639- ( V)         -4.40

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 - 4578 : -1.589

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

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.

1546 ARG   (  20-)  B   -3.54
3259 LYS   ( 103-)  M   -3.52
3261 ASN   ( 105-)  M   -3.27
2566 GLN   (   4-)  H   -3.23
3748 ARG   (  78-)  S   -3.13
1926 HIS   ( 176-)  C   -3.11
1762 LEU   (  12-)  C   -3.07
3121 LYS   (  88-)  L   -3.04
3754 LYS   (   5-)  T   -3.03
3868 ARG   (  35-)  U   -3.03
2871 HIS   (  56-)  J   -3.01
1753 GLN   (   3-)  C   -2.98
2815 GLN   ( 126-)  I   -2.97
3676 LYS   (   6-)  S   -2.97
3724 GLY   (  54-)  S   -2.94
3061 PRO   (  28-)  L   -2.92
3468 LYS   (  13-)  P   -2.89
2777 MET   (  88-)  I   -2.88
3327 ARG   (  61-)  N   -2.87
2876 ALA   (  61-)  J   -2.86
2817 SER   ( 128-)  I   -2.82
2802 ARG   ( 113-)  I   -2.80
3023 HIS   ( 118-)  K   -2.79
3031 LYS   ( 126-)  K   -2.78
1996 GLN   (  40-)  D   -2.78
And so on for a total of 51 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.

1994 PRO   (  38-)  D     - 1998 GLY   (  42-)  D        -1.67
2412 SER   ( 100-)  F     - 2416 ARG   (   5-)  G        -1.57
2814 PRO   ( 125-)  I     - 2817 SER   ( 128-)  I        -2.48
2870 PRO   (  55-)  J     - 2874 LYS   (  59-)  J        -2.20
3022 PRO   ( 117-)  K     - 3028 PRO   ( 123-)  K        -2.14
3029 PRO   ( 124-)  K     - 3033 ARG   ( 128-)  K        -2.18
3058 GLU   (  25-)  L     - 3062 GLN   (  29-)  L        -1.99
3253 VAL   (  97-)  M     - 3257 ARG   ( 101-)  M        -1.91
3258 THR   ( 102-)  M     - 3261 ASN   ( 105-)  M        -2.48
3312 LEU   (  46-)  N     - 3315 GLN   (  49-)  N        -1.85
3673 ARG   (   3-)  S     - 3676 LYS   (   6-)  S        -2.41

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: 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

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.

4637 HOH   (1717 )  A      O
4637 HOH   (1782 )  A      O
Unrecognized bound group for 4578
  Bound atom= 4634 UAL  (   5-) W      N

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.

1564 HIS   (  38-)  B
1703 ASN   ( 177-)  B
1715 ASN   ( 189-)  B
1756 HIS   (   6-)  C
1926 HIS   ( 176-)  C
2045 ASN   (  89-)  D
2072 GLN   ( 116-)  D
2087 ASN   ( 131-)  D
2349 HIS   (  37-)  F
2420 GLN   (   9-)  G
2583 ASN   (  21-)  H
2714 ASN   (  25-)  I
2764 GLN   (  75-)  I
2770 HIS   (  81-)  I
2933 ASN   (  28-)  K
3023 HIS   ( 118-)  K
3145 GLN   ( 112-)  L
3518 GLN   (  63-)  P
3652 GLN   (  54-)  R
3722 HIS   (  52-)  S
3727 HIS   (  57-)  S
3769 HIS   (  20-)  T
4152 GLN   ( 276-)  V
4341 HIS   ( 465-)  V
4434 GLN   ( 558-)  V
4460 HIS   ( 584-)  V

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.

  21 OGUA  (  22-)  A      N2
  56 OGUA  (  57-)  A      N2
  69 OURA  (  70-)  A      N3
  71 OADE  (  72-)  A      N6
  86 OCYT  (  87-)  A      N4
  87 OURA  (  88-)  A      N3
  90 OURA  (  91-)  A      N3
  92 OURA  (  93-)  A      N3
 101 OGUA  ( 102-)  A      N2
 106 OGUA  ( 107-)  A      N1
 109 OCYT  ( 110-)  A      N4
 146 OGUA  ( 147-)  A      N2
 150 OADE  ( 151-)  A      N6
 193 OCYT  ( 194-)  A      N4
 201 OGUA  ( 202-)  A      N2
 202 OGUA  ( 203-)  A      N2
 210 OGUA  ( 211-)  A      N1
 231 OGUA  ( 232-)  A      N2
 253 OGUA  ( 254-)  A      N2
 259 OGUA  ( 260-)  A      N1
 268 OCYT  ( 269-)  A      N4
 321 OCYT  ( 322-)  A      N4
 326 OADE  ( 327-)  A      N6
 381 OADE  ( 382-)  A      N6
 390 OGUA  ( 391-)  A      N2
And so on for a total of 529 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.

1544 GLN   (  18-)  B      OE1
1614 GLN   (  88-)  B      OE1
1713 ASP   ( 187-)  B      OD2
1875 GLU   ( 125-)  C      OE1
1916 GLU   ( 166-)  C      OE1
1940 HIS   ( 190-)  C      ND1
2051 GLU   (  95-)  D      OE2
2072 GLN   ( 116-)  D      OE1
2076 HIS   ( 120-)  D      NE2
2108 GLN   ( 152-)  D      OE1
2329 GLN   (  17-)  F      OE1
2370 HIS   (  58-)  F      ND1
2426 ASP   (  15-)  G      OD2
2469 GLU   (  58-)  G      OE1
2551 ASP   ( 140-)  G      OD1
2686 GLU   ( 124-)  H      OE1
2929 HIS   (  24-)  K      ND1
3017 ASP   ( 112-)  K      OD2
3039 GLN   (   6-)  L      OE1
3401 GLN   (  35-)  O      OE1
3464 HIS   (   9-)  P      ND1
3514 HIS   (  59-)  P      ND1
3857 GLU   (  24-)  U      OE1
3869 GLU   (  36-)  U      OE1
3958 HIS   (  82-)  V      ND1
3961 ASN   (  85-)  V      OD1
4005 GLN   ( 129-)  V      OE1
4073 ASP   ( 197-)  V      OD1
4095 HIS   ( 219-)  V      ND1
4176 ASP   ( 300-)  V      OD1
4227 ASN   ( 351-)  V      OD1
4503 ASN   ( 627-)  V      OD1

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+.

4588  MG   (1601-)  A     0.33   1.41 Could be  K (Few ligands (4) ) *2
4589  MG   (1602-)  A   -.-  -.-  Too few ligands (3)
4590  MG   (1603-)  A   -.-  -.-  Too few ligands (3)
4591  MG   (1604-)  A     0.37   0.75 Is perhaps NA
4592  MG   (1605-)  A     0.52   1.03 Is perhaps NA
4593  MG   (1606-)  A     0.65   1.07 Is perhaps CA (Few ligands (4) )
4594  MG   (1607-)  A     0.60   1.07 Is perhaps CA
4595  MG   (1608-)  A     0.73   1.37 Scores about as good as CA
4596  MG   (1609-)  A     0.49   0.97 Is perhaps NA
4597  MG   (1610-)  A   -.-  -.-  Too few ligands (1)
4598  MG   (1611-)  A   -.-  -.-  Too few ligands (3)
4599  MG   (1612-)  A     0.35   1.68 Is perhaps  K (Few ligands (4) ) *2
4600  MG   (1613-)  A     0.80   1.40 Scores about as good as CA (Few ligands (4) )
4601  MG   (1614-)  A     0.58   0.94 Is perhaps CA
4602  MG   (1615-)  A     0.69   1.22 Scores about as good as CA
4603  MG   (1616-)  A   -.-  -.-  Too few ligands (2)
4604  MG   (1617-)  A     0.68   1.21 Scores about as good as CA (Few ligands (4) )
4605  MG   (1618-)  A     0.59   0.98 Is perhaps CA (Few ligands (4) )
4606  MG   (1619-)  A   -.-  -.-  Too few ligands (3)
4607  MG   (1620-)  A   -.-  -.-  Part of ionic cluster
4607  MG   (1620-)  A     0.75   1.29 Scores about as good as CA
4608  MG   (1621-)  A     0.55   1.00 Is perhaps CA
4609  MG   (1622-)  A     0.59   1.01 Is perhaps CA (Few ligands (4) )
4611  MG   (1624-)  A   -.-  -.-  Too few ligands (3)
4612  MG   (1625-)  A     0.55   0.97 Is perhaps CA (Few ligands (4) )
4614  MG   (1627-)  A   -.-  -.-  Too few ligands (3)
4615  MG   (1628-)  A   -.-  -.-  Too few ligands (0)
4616  MG   (1629-)  A     0.70   1.23 Scores about as good as CA
4617  MG   (1630-)  A     0.42   0.84 Is perhaps NA (Few ligands (4) )
4618  MG   (1631-)  A     0.38   0.76 Is perhaps NA (Few ligands (4) )
4619  MG   (1632-)  A     0.54   1.09 Is perhaps NA (Few ligands (4) )
4620  MG   (1633-)  A     0.67   1.21 Scores about as good as CA
4621  MG   (1634-)  A     0.48   0.97 Is perhaps NA
4622  MG   (1635-)  A   -.-  -.-  Part of ionic cluster
4622  MG   (1635-)  A     0.71   1.28 Scores about as good as CA
4623  MG   (1636-)  A   -.-  -.-  Too few ligands (2)
4624  MG   (1637-)  A     0.59   0.94 Is perhaps CA (Few ligands (4) )
4625  MG   (1638-)  A     0.37   0.75 Is perhaps NA (Few ligands (4) )
4626  MG   (1639-)  A     0.61   1.06 Is perhaps CA (Few ligands (4) )
4627  MG   (1640-)  A   -.-  -.-  Too few ligands (3)
4628  MG   (1641-)  A     0.38   0.76 Is perhaps NA
4629  MG   ( 201-)  E   -.-  -.-  Too few ligands (0)
4630  MG   ( 101-)  A   -.-  -.-  Too few ligands (2)
4631  MG   ( 802-)  V     0.38   0.75 Is perhaps NA

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.

1607 ASP   (  81-)  B   H-bonding suggests Asn
1613 ASP   (  87-)  B   H-bonding suggests Asn
1641 ASP   ( 115-)  B   H-bonding suggests Asn; but Alt-Rotamer
1652 ASP   ( 126-)  B   H-bonding suggests Asn; but Alt-Rotamer
1678 ASP   ( 152-)  B   H-bonding suggests Asn; but Alt-Rotamer
1722 ASP   ( 196-)  B   H-bonding suggests Asn
1832 GLU   (  82-)  C   H-bonding suggests Gln
1843 ASP   (  93-)  C   H-bonding suggests Asn
1875 GLU   ( 125-)  C   H-bonding suggests Gln; but Alt-Rotamer
2146 ASP   ( 190-)  D   H-bonding suggests Asn; but Alt-Rotamer
2194 ASP   (  41-)  E   H-bonding suggests Asn
2254 GLU   ( 101-)  E   H-bonding suggests Gln
2295 ASP   ( 142-)  E   H-bonding suggests Asn
2352 GLU   (  40-)  F   H-bonding suggests Gln
2432 GLU   (  21-)  G   H-bonding suggests Gln; but Alt-Rotamer
2501 GLU   (  90-)  G   H-bonding suggests Gln
2551 ASP   ( 140-)  G   H-bonding suggests Asn; but Alt-Rotamer
2725 GLU   (  36-)  I   H-bonding suggests Gln; but Alt-Rotamer
2731 GLU   (  42-)  I   H-bonding suggests Gln
2742 GLU   (  53-)  I   H-bonding suggests Gln
2751 ASP   (  62-)  I   H-bonding suggests Asn
2834 ASP   (  19-)  J   H-bonding suggests Asn; but Alt-Rotamer
2906 ASP   (  91-)  J   H-bonding suggests Asn; but Alt-Rotamer
3017 ASP   ( 112-)  K   H-bonding suggests Asn; but Alt-Rotamer
3109 GLU   (  76-)  L   H-bonding suggests Gln
3122 ASP   (  89-)  L   H-bonding suggests Asn
3210 ASP   (  54-)  M   H-bonding suggests Asn; but Alt-Rotamer
3288 ASP   (  18-)  N   H-bonding suggests Asn; but Alt-Rotamer
3303 ASP   (  33-)  N   H-bonding suggests Asn
3380 GLU   (  14-)  O   H-bonding suggests Gln
3384 ASP   (  18-)  O   H-bonding suggests Asn; but Alt-Rotamer
3449 GLU   (  83-)  O   H-bonding suggests Gln
3582 ASP   (  48-)  Q   H-bonding suggests Asn
3591 ASP   (  57-)  Q   H-bonding suggests Asn; but Alt-Rotamer
3697 ASP   (  27-)  S   H-bonding suggests Asn
3964 ASP   (  88-)  V   H-bonding suggests Asn; but Alt-Rotamer
3970 ASP   (  94-)  V   H-bonding suggests Asn; but Alt-Rotamer
4073 ASP   ( 197-)  V   H-bonding suggests Asn; but Alt-Rotamer
4160 ASP   ( 284-)  V   H-bonding suggests Asn
4249 GLU   ( 373-)  V   H-bonding suggests Gln
4271 ASP   ( 395-)  V   H-bonding suggests Asn
4305 GLU   ( 429-)  V   H-bonding suggests Gln
4326 ASP   ( 450-)  V   H-bonding suggests Asn; but Alt-Rotamer
4368 GLU   ( 492-)  V   H-bonding suggests Gln
4397 ASP   ( 521-)  V   H-bonding suggests Asn; but Alt-Rotamer
4576 GLU   ( 700-)  V   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.722
  2nd generation packing quality :  -3.225 (poor)
  Ramachandran plot appearance   :  -4.685 (bad)
  chi-1/chi-2 rotamer normality  :  -4.214 (bad)
  Backbone conformation          :  -0.680

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.703
  Bond angles                    :   1.093
  Omega angle restraints         :   1.141
  Side chain planarity           :   0.729
  Improper dihedral distribution :   0.752
  B-factor distribution          :   1.974 (loose)
  Inside/Outside distribution    :   1.009

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.7
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -2.1
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.703
  Bond angles                    :   1.093
  Omega angle restraints         :   1.141
  Side chain planarity           :   0.729
  Improper dihedral distribution :   0.752
  B-factor distribution          :   1.974 (loose)
  Inside/Outside distribution    :   1.009
==============

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.