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 pdb4jv5.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 41 21 2
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

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: 763279.125
Volume of the Unit Cell V= 28294752.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 9.267
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.600 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.

3936 PSU   (   4-)  X  -

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

1898 SER   ( 154-)  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

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 OURA  (   5-)  A    High
  27 OGUA  (  31-)  A    High
  34 OGUA  (  38-)  A    High
  37 OGUA  (  41-)  A    High
  44 OCYT  (  48-)  A    High
  52 OURA  (  56-)  A    High
  55 OADE  (  59-)  A    High
  61 OURA  (  65-)  A    High
  68 OCYT  (  72-)  A    High
  69 OGUA  (  73-)  A    High
  70 OCYT  (  76-)  A    High
  75 OURA  (  81-)  A    High
  76 OURA  (  82-)  A    High
  77 OURA  (  83-)  A    High
  78 OURA  (  84-)  A    High
  79 OADE  (  88-)  A    High
  80 OCYT  (  89-)  A    High
  86 OGUA  (  97-)  A    High
  87 OGUA  (  98-)  A    High
 128 OGUA  ( 138-)  A    High
 130 OADE  ( 140-)  A    High
 131 OADE  ( 141-)  A    High
 133 OADE  ( 143-)  A    High
 134 OGUA  ( 144-)  A    High
 135 OGUA  ( 145-)  A    High
And so on for a total of 1834 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. 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) : 77.000

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

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.

1952 ARG   (   3-)  D
2067 ARG   ( 118-)  D
3851 ARG   (  89-)  T

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.

1540 GLU   (  35-)  B
1557 GLU   (  52-)  B
1564 GLU   (  59-)  B
1621 GLU   ( 116-)  B
1646 GLU   ( 141-)  B
1763 GLU   (  19-)  C
1779 GLU   (  35-)  C
1790 GLU   (  46-)  C
1983 GLU   (  34-)  D
2009 GLU   (  60-)  D
2029 GLU   (  80-)  D
2030 GLU   (  81-)  D
2105 GLU   ( 156-)  D
2112 GLU   ( 163-)  D
2154 GLU   ( 205-)  D
2162 GLU   (   8-)  E
2235 GLU   (  81-)  E
2237 GLU   (  83-)  E
2265 GLU   ( 111-)  E
2330 GLU   (  22-)  F
2349 GLU   (  41-)  F
2350 GLU   (  42-)  F
2374 GLU   (  66-)  F
2386 GLU   (  78-)  F
2403 GLU   (  95-)  F
And so on for a total of 66 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.

 553 OADE  ( 574-)  A      P    OP2   1.56    4.5
 745 OADE  ( 766-)  A      P    OP2   1.59    6.0
1961 CYS   (  12-)  D      CA   CB    1.62    4.5
3314 CYS   (  24-)  N      SG  -SG*   1.78   -6.6
3317 CYS   (  27-)  N      SG  -SG*   1.78   -6.6
3317 CYS   (  27-)  N      SG  -SG*   2.45   10.2
3333 CYS   (  43-)  N      SG  -SG*   1.87   -4.3

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.

   1 OURA  (   5-)  A      C3'  C4'  C5' 122.58    4.7
   1 OURA  (   5-)  A      C5'  C4'  O4' 116.72    5.4
   2 OGUA  (   6-)  A      O3'  C3'  C4'  93.66   -6.5
  11 OGUA  (  15-)  A      N9   C8   N7  113.12    4.0
  23 OGUA  (  27-)  A      N9   C8   N7  113.17    4.1
  24 OGUA  (  28-)  A      N9   C8   N7  113.24    4.3
  25 OGUA  (  29-)  A      N9   C8   N7  113.12    4.0
  31 OGUA  (  35-)  A      N9   C8   N7  113.15    4.1
  37 OGUA  (  41-)  A      N9   C8   N7  113.14    4.1
  38 OGUA  (  42-)  A      N9   C8   N7  113.14    4.1
  53 OGUA  (  57-)  A      N9   C8   N7  113.12    4.0
  57 OGUA  (  61-)  A      N9   C8   N7  113.14    4.1
  60 OGUA  (  64-)  A      N9   C8   N7  113.10    4.0
  62 OGUA  (  66-)  A      N9   C8   N7  113.21    4.2
  66 OGUA  (  70-)  A      N9   C8   N7  113.14    4.1
  69 OGUA  (  73-)  A      N9   C8   N7  113.13    4.1
  71 OGUA  (  77-)  A      N9   C8   N7  113.11    4.0
  76 OURA  (  82-)  A      C4'  C3'  C2'  98.28   -4.4
  76 OURA  (  82-)  A      C2'  C1'  N1  121.67    5.2
  77 OURA  (  83-)  A      P   -C3* -O3* 125.65    5.0
  78 OURA  (  84-)  A      P   -C3* -O3* 126.04    5.3
  78 OURA  (  84-)  A      C2'  C1'  N1  121.70    5.2
  91 OGUA  ( 102-)  A      N9   C8   N7  113.14    4.1
  94 OGUA  ( 105-)  A      N9   C8   N7  113.17    4.1
  95 OCYT  ( 106-)  A      O3'  C3'  C2' 126.64    5.6
And so on for a total of 334 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.

1540 GLU   (  35-)  B
1557 GLU   (  52-)  B
1564 GLU   (  59-)  B
1621 GLU   ( 116-)  B
1646 GLU   ( 141-)  B
1763 GLU   (  19-)  C
1779 GLU   (  35-)  C
1790 GLU   (  46-)  C
1952 ARG   (   3-)  D
1983 GLU   (  34-)  D
2009 GLU   (  60-)  D
2029 GLU   (  80-)  D
2030 GLU   (  81-)  D
2067 ARG   ( 118-)  D
2105 GLU   ( 156-)  D
2112 GLU   ( 163-)  D
2154 GLU   ( 205-)  D
2162 GLU   (   8-)  E
2235 GLU   (  81-)  E
2237 GLU   (  83-)  E
2265 GLU   ( 111-)  E
2330 GLU   (  22-)  F
2349 GLU   (  41-)  F
2350 GLU   (  42-)  F
2374 GLU   (  66-)  F
And so on for a total of 69 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

1978 PRO   (  29-)  D      N      6.3    18.23    -2.48
3768 TYR   (  80-)  S      CA    -6.7    23.42    34.03
The average deviation= 0.962

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.

1980 CYS   (  31-)  D    7.87
1958 CYS   (   9-)  D    7.00
2553 ALA   ( 145-)  G    6.71
3333 CYS   (  43-)  N    6.22
3239 GLU   (  69-)  M    5.95
3849 LYS   (  87-)  T    5.54
3260 LEU   (  90-)  M    5.10
2221 VAL   (  67-)  E    4.97
3335 ARG   (  45-)  N    4.95
2661 VAL   (  97-)  H    4.82
3318 GLY   (  28-)  N    4.63
2648 ARG   (  84-)  H    4.48
1678 ALA   ( 173-)  B    4.40
2651 SER   (  87-)  H    4.28
3820 LYS   (  58-)  T    4.22
2180 PHE   (  26-)  E    4.17
1616 ARG   ( 111-)  B    4.04
3068 ALA   (  26-)  L    4.02
3130 GLY   (  88-)  L    4.01

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 : -5.102

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.

1908 THR   ( 165-)  C    -3.4
1572 THR   (  67-)  B    -3.3
3283 PRO   ( 113-)  M    -3.1
3090 PRO   (  48-)  L    -3.1
1636 PRO   ( 131-)  B    -3.1
1978 PRO   (  29-)  D    -3.1
3860 PRO   (  98-)  T    -3.0
3730 PRO   (  42-)  S    -3.0
2638 PRO   (  74-)  H    -3.0
2826 TYR   ( 125-)  I    -3.0
1872 PHE   ( 128-)  C    -2.9
2881 PHE   (  54-)  J    -2.9
3862 ILE   ( 100-)  T    -2.9
3444 ARG   (   5-)  P    -2.8
2712 LYS   (  11-)  I    -2.8
2655 ARG   (  91-)  H    -2.8
3089 LYS   (  47-)  L    -2.8
2181 ARG   (  27-)  E    -2.8
1743 LEU   ( 238-)  B    -2.8
2793 TYR   (  92-)  I    -2.7
3835 HIS   (  73-)  T    -2.7
2283 ILE   ( 129-)  E    -2.7
3190 THR   (  20-)  M    -2.7
2404 PRO   (  96-)  F    -2.7
3066 VAL   (  24-)  L    -2.7
And so on for a total of 249 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.

1513 LYS   (   8-)  B  Poor phi/psi
1514 GLU   (   9-)  B  Poor phi/psi
1520 VAL   (  15-)  B  omega poor
1521 HIS   (  16-)  B  Poor phi/psi
1522 PHE   (  17-)  B  Poor phi/psi
1524 HIS   (  19-)  B  Poor phi/psi, omega poor
1525 GLU   (  20-)  B  Poor phi/psi
1528 ARG   (  23-)  B  omega poor
1539 ALA   (  34-)  B  omega poor
1542 ASN   (  37-)  B  Poor phi/psi
1546 ILE   (  41-)  B  omega poor
1583 GLN   (  78-)  B  Poor phi/psi
1591 GLU   (  86-)  B  omega poor
1598 VAL   (  93-)  B  omega poor
1610 PHE   ( 105-)  B  Poor phi/psi
1621 GLU   ( 116-)  B  omega poor
1623 LEU   ( 118-)  B  omega poor
1625 ALA   ( 120-)  B  omega poor
1626 LEU   ( 121-)  B  omega poor
1629 SER   ( 124-)  B  PRO omega poor
1635 ARG   ( 130-)  B  Poor phi/psi
1636 PRO   ( 131-)  B  Poor phi/psi, omega poor
1637 LYS   ( 132-)  B  Poor phi/psi
1638 LYS   ( 133-)  B  omega poor
1640 GLN   ( 135-)  B  omega poor
And so on for a total of 381 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 : -5.993

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.

2053 VAL   ( 104-)  D    0.36
2772 SER   (  71-)  I    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!

   3 OGUA  (   7-)  A      0
   4 OADE  (   8-)  A      0
   5 OGUA  (   9-)  A      0
   6 OADE  (  10-)  A      0
   7 OGUA  (  11-)  A      0
   8 OURA  (  12-)  A      0
   9 OURA  (  13-)  A      0
  10 OURA  (  14-)  A      0
  11 OGUA  (  15-)  A      0
  12 OADE  (  16-)  A      0
  13 OURA  (  17-)  A      0
  14 OCYT  (  18-)  A      0
  15 OCYT  (  19-)  A      0
  16 OURA  (  20-)  A      0
  17 OGUA  (  21-)  A      0
  18 OGUA  (  22-)  A      0
  19 OCYT  (  23-)  A      0
  20 OURA  (  24-)  A      0
  21 OCYT  (  25-)  A      0
  22 OADE  (  26-)  A      0
  23 OGUA  (  27-)  A      0
  24 OGUA  (  28-)  A      0
  25 OGUA  (  29-)  A      0
  26 OURA  (  30-)  A      0
  27 OGUA  (  31-)  A      0
And so on for a total of 2512 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 8.928

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!

2489 GLY   (  81-)  G   2.70   11
2768 GLY   (  67-)  I   2.65   13
3863 GLY   ( 101-)  T   2.61   80
3019 GLY   ( 102-)  K   2.51   80
3502 GLY   (  63-)  P   2.37   59
3071 GLY   (  29-)  L   2.34   23
3809 GLY   (  47-)  T   2.16   18
3554 GLY   (  33-)  Q   1.90   44
2079 GLY   ( 130-)  D   1.85   67
1708 GLY   ( 203-)  B   1.77   16
3270 GLY   ( 100-)  M   1.69   39
2731 GLY   (  30-)  I   1.63   39
3151 GLY   ( 109-)  L   1.60   19
1939 LEU   ( 196-)  C   1.59   10
2627 LEU   (  63-)  H   1.53   10

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...

3698 PHE   (  10-)  S   1.98

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]

1858 PRO   ( 114-)  C    0.18 LOW
2496 PRO   (  88-)  G    0.11 LOW
2904 PRO   (  77-)  J    0.17 LOW
3352 PRO   (   2-)  O    0.17 LOW

Warning: Unusual PRO puckering phases

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

1630 PRO   ( 125-)  B   102.5 envelop C-beta (108 degrees)
1636 PRO   ( 131-)  B   134.9 half-chair C-beta/C-alpha (126 degrees)
1672 PRO   ( 167-)  B   -16.3 half-chair C-alpha/N (-18 degrees)
1688 PRO   ( 183-)  B  -144.4 envelop C-delta (-144 degrees)
1707 PRO   ( 202-)  B     1.6 envelop N (0 degrees)
1737 PRO   ( 232-)  B   125.7 half-chair C-beta/C-alpha (126 degrees)
1751 PRO   (   7-)  C     3.4 envelop N (0 degrees)
1853 PRO   ( 109-)  C   -59.5 half-chair C-beta/C-alpha (-54 degrees)
1956 PRO   (   7-)  D   147.5 envelop C-alpha (144 degrees)
1978 PRO   (  29-)  D   152.5 envelop C-alpha (144 degrees)
1986 PRO   (  37-)  D   -49.1 half-chair C-beta/C-alpha (-54 degrees)
1988 PRO   (  39-)  D  -151.1 envelop C-delta (-144 degrees)
2000 PRO   (  51-)  D   -43.9 envelop C-alpha (-36 degrees)
2091 PRO   ( 142-)  D    50.1 half-chair C-delta/C-gamma (54 degrees)
2121 PRO   ( 172-)  D   139.7 envelop C-alpha (144 degrees)
2146 PRO   ( 197-)  D   -64.8 envelop C-beta (-72 degrees)
2203 PRO   (  49-)  E   107.3 envelop C-beta (108 degrees)
2376 PRO   (  68-)  F  -142.8 envelop C-delta (-144 degrees)
2404 PRO   (  96-)  F   -56.2 half-chair C-beta/C-alpha (-54 degrees)
2466 PRO   (  58-)  G   102.9 envelop C-beta (108 degrees)
2591 PRO   (  27-)  H   -54.6 half-chair C-beta/C-alpha (-54 degrees)
2631 PRO   (  67-)  H   -46.9 half-chair C-beta/C-alpha (-54 degrees)
2636 PRO   (  72-)  H   -24.1 half-chair C-alpha/N (-18 degrees)
2638 PRO   (  74-)  H   -42.0 envelop C-alpha (-36 degrees)
2640 PRO   (  76-)  H   179.1 envelop N (180 degrees)
2653 PRO   (  89-)  H  -120.5 half-chair C-delta/C-gamma (-126 degrees)
2722 PRO   (  21-)  I   -61.3 half-chair C-beta/C-alpha (-54 degrees)
2791 PRO   (  90-)  I   101.6 envelop C-beta (108 degrees)
2799 PRO   (  98-)  I   135.0 half-chair C-beta/C-alpha (126 degrees)
2824 PRO   ( 123-)  I    29.4 envelop C-delta (36 degrees)
2866 PRO   (  39-)  J   -27.9 envelop C-alpha (-36 degrees)
3032 PRO   ( 115-)  K   -37.5 envelop C-alpha (-36 degrees)
3038 PRO   ( 121-)  K    29.1 envelop C-delta (36 degrees)
3090 PRO   (  48-)  L   -23.4 half-chair C-alpha/N (-18 degrees)
3113 PRO   (  71-)  L   -36.3 envelop C-alpha (-36 degrees)
3136 PRO   (  94-)  L   138.5 envelop C-alpha (144 degrees)
3180 PRO   (  10-)  M  -122.5 half-chair C-delta/C-gamma (-126 degrees)
3267 PRO   (  97-)  M   100.6 envelop C-beta (108 degrees)
3283 PRO   ( 113-)  M   162.5 half-chair C-alpha/N (162 degrees)
3304 PRO   (  14-)  N   -16.7 half-chair C-alpha/N (-18 degrees)
3425 PRO   (  75-)  O   111.9 envelop C-beta (108 degrees)
3454 PRO   (  15-)  P    50.9 half-chair C-delta/C-gamma (54 degrees)
3523 PRO   (   2-)  Q   165.8 half-chair C-alpha/N (162 degrees)
3549 PRO   (  28-)  Q  -113.7 envelop C-gamma (-108 degrees)
3551 PRO   (  30-)  Q  -128.5 half-chair C-delta/C-gamma (-126 degrees)
3568 PRO   (  47-)  Q    50.5 half-chair C-delta/C-gamma (54 degrees)
3730 PRO   (  42-)  S   136.0 envelop C-alpha (144 degrees)
3860 PRO   (  98-)  T    -5.0 envelop N (0 degrees)
3890 PRO   (  23-)  U   -20.2 half-chair C-alpha/N (-18 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.

1980 CYS   (  31-)  D      O   <-> 1982 MET   (  33-)  D      N      0.93    1.77  INTRA BF
3070 LYS   (  28-)  L      O   <-> 3072 ALA   (  30-)  L      N      0.73    1.97  INTRA BF
1226 OCYT  (1249-)  A      N4  <-> 1265 OADE  (1288-)  A      N6     0.71    2.14  INTRA BF
3587 SER   (  66-)  Q      O   <-> 3591 ARG   (  70-)  Q      NH1    0.69    2.01  INTRA BL
1980 CYS   (  31-)  D      CA  <-> 3932  ZN   ( 301-)  D     ZN      0.66    2.54  INTRA BF
1975 CYS   (  26-)  D      CB  <-> 1980 CYS   (  31-)  D      SG     0.61    2.39  INTRA BF
1958 CYS   (   9-)  D      SG  <-> 1980 CYS   (  31-)  D      CA     0.59    2.81  INTRA BF
 883 OCYT  ( 910-)  A      OP2 <-> 3063 LYS   (  21-)  L      NZ     0.57    2.13  INTRA BF
1106 OCYT  (1128-)  A      O2' <-> 1108 OADE  (1130-)  A      N7     0.56    2.14  INTRA BF
1009 OGUA  (1031-)  A      N3  <-> 1010 OGUA  (1032-)  A      N1     0.56    2.44  INTRA BF
1030 OURA  (1052-)  A      O2' <-> 1033 OADE  (1055-)  A      OP2    0.55    1.85  INTRA BL
2440 ARG   (  32-)  G      O   <-> 2442 GLY   (  34-)  G      N      0.55    2.15  INTRA BL
1980 CYS   (  31-)  D      C   <-> 1982 MET   (  33-)  D      N      0.54    2.36  INTRA BF
1203 OCYT  (1226-)  A      N4  <-> 3274 ARG   ( 104-)  M      CG     0.54    2.56  INTRA BL
 664 OGUA  ( 685-)  A      OP1 <-> 2928 LYS   (  11-)  K      NZ     0.53    2.17  INTRA BF
1511 OURA  (1544-)  A      O3' <-> 3935 PSU   (   4-)  X      O5'    0.53    1.87  INTRA BL
3069 LEU   (  27-)  L      O   <-> 3071 GLY   (  29-)  L      N      0.52    2.18  INTRA BL
1032 OCYT  (1054-)  A      N4  <-> 3900   I   (  34-)  Y      C8     0.50    2.60  INTRA BF
1227 OADE  (1250-)  A      C1' <-> 1228 OADE  (1251-)  A      N7     0.49    2.61  INTRA BF
3314 CYS   (  24-)  N      SG  <-> 3317 CYS   (  27-)  N      N      0.48    2.82  INTRA BF
1641 VAL   ( 136-)  B      O   <-> 1645 HIS   ( 140-)  B      N      0.48    2.22  INTRA BF
1247 OCYT  (1270-)  A      OP2 <-> 3891 ARG   (  24-)  U      NH2    0.48    2.22  INTRA BF
1005 OGUA  (1030-)  A      N1  <-> 1010 OGUA  (1032-)  A      N7     0.47    2.53  INTRA BF
1240 OCYT  (1263-)  A      N3  <-> 1249 OGUA  (1272-)  A      N1     0.47    2.53  INTRA BF
1102 OGUA  (1124-)  A      C2  <-> 1105 OGUA  (1127-)  A      N2     0.45    2.65  INTRA BF
And so on for a total of 1744 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

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.

3768 TYR   (  80-)  S      -8.27
3891 ARG   (  24-)  U      -8.19
1823 ARG   (  79-)  C      -8.19
2414 ARG   (   6-)  G      -8.17
1998 ARG   (  49-)  D      -7.95
3438 ARG   (  88-)  O      -7.93
2412 ARG   (   4-)  G      -7.71
1953 TYR   (   4-)  D      -7.71
1999 ARG   (  50-)  D      -7.68
3274 ARG   ( 104-)  M      -7.53
1991 GLN   (  42-)  D      -7.51
2942 TYR   (  25-)  K      -7.47
3272 ARG   ( 102-)  M      -7.33
3302 ARG   (  12-)  N      -7.33
2826 TYR   ( 125-)  I      -7.30
2632 ARG   (  68-)  H      -7.28
3584 ARG   (  63-)  Q      -7.24
3293 ARG   (   3-)  N      -7.22
3284 ARG   ( 114-)  M      -7.19
3521 GLN   (  82-)  P      -7.17
3766 ARG   (  78-)  S      -7.14
3269 ARG   (  99-)  M      -7.13
2563 ARG   ( 155-)  G      -7.09
3290 LYS   ( 120-)  M      -7.03
1987 TYR   (  38-)  D      -7.01
And so on for a total of 169 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.

1526 ARG   (  21-)  B      1529 - TRP     24- ( B)         -5.23
1734 VAL   ( 229-)  B      1736 - GLU    231- ( B)         -4.71
1747 ASN   (   3-)  C      1749 - ILE      5- ( C)         -5.06
1951 GLY   (   2-)  D      1954 - ILE      5- ( D)         -5.69
1994 GLN   (  45-)  D      1996 - ARG     47- ( D)         -5.09
2033 LYS   (  84-)  D      2035 - LYS     86- ( D)         -5.06
2173 MET   (  19-)  E      2176 - GLY     22- ( E)         -4.99
2306 ARG   ( 152-)  E      2308 - GLY    154- ( E)         -4.50
2411 ARG   (   3-)  G      2414 - ARG      6- ( G)         -6.91
2418 ARG   (  10-)  G      2421 - GLN     13- ( G)         -5.21
2424 LEU   (  16-)  G      2426 - TYR     18- ( G)         -4.42
2632 ARG   (  68-)  H      2634 - GLN     70- ( H)         -6.64
2668 ARG   ( 104-)  H      2670 - GLY    106- ( H)         -4.89
2915 LEU   (  88-)  J      2917 - LEU     90- ( J)         -4.74
3061 ARG   (  19-)  L      3063 - LYS     21- ( L)         -5.63
3155 ARG   ( 113-)  L      3157 - LYS    115- ( L)         -4.18
3168 LYS   ( 126-)  L      3170 - ALA    128- ( L)         -4.58
3284 ARG   ( 114-)  M      3290 - LYS    120- ( M)         -5.44
3535 LYS   (  14-)  Q      3537 - GLN     16- ( Q)         -5.25
3692 SER   (   4-)  S      3695 - LYS      7- ( S)         -5.44
3866 LEU   ( 104-)  T      3868 - ALA    106- ( T)         -4.48

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 - 3906 : -1.691

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

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.

2943 ASN   (  26-)  K   -3.59
2882 LYS   (  55-)  J   -3.58
2825 GLN   ( 124-)  I   -3.53
3276 ASN   ( 106-)  M   -3.51
3321 ARG   (  31-)  N   -3.20
1747 ASN   (   3-)  C   -3.13
2927 THR   ( 100-)  J   -3.11
3088 LYS   (  46-)  L   -3.11
2881 PHE   (  54-)  J   -3.04
3481 ARG   (  42-)  P   -2.99
1991 GLN   (  42-)  D   -2.98
2712 LYS   (  11-)  I   -2.98
3742 GLY   (  54-)  S   -2.93
3274 ARG   ( 104-)  M   -2.93
3693 LEU   (   5-)  S   -2.92
1951 GLY   (   2-)  D   -2.92
2814 LYS   ( 113-)  I   -2.91
3133 LYS   (  91-)  L   -2.90
1974 ARG   (  25-)  D   -2.89
2565 MET   (   1-)  H   -2.87
2883 HIS   (  56-)  J   -2.83
3033 HIS   ( 116-)  K   -2.79
1756 LEU   (  12-)  C   -2.78
2411 ARG   (   3-)  G   -2.78
3584 ARG   (  63-)  Q   -2.75
3073 PRO   (  31-)  L   -2.75
1919 HIS   ( 176-)  C   -2.74
2415 ALA   (   7-)  G   -2.73
2358 TYR   (  50-)  F   -2.73
1819 VAL   (  75-)  C   -2.65
1952 ARG   (   3-)  D   -2.65
3308 VAL   (  18-)  N   -2.65
3521 GLN   (  82-)  P   -2.62
1850 VAL   ( 106-)  C   -2.60
3136 PRO   (  94-)  L   -2.59
3035 GLY   ( 118-)  K   -2.59
3766 ARG   (  78-)  S   -2.58
2418 ARG   (  10-)  G   -2.57
3725 ARG   (  37-)  S   -2.55
2805 ARG   ( 104-)  I   -2.54
2828 LYS   ( 127-)  I   -2.53
2810 VAL   ( 109-)  I   -2.53
3311 TYR   (  21-)  N   -2.52
3464 ARG   (  25-)  P   -2.52
2679 SER   ( 115-)  H   -2.51
3350 SER   (  60-)  N   -2.50
3480 PRO   (  41-)  P   -2.50

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.

2564 TRP   ( 156-)  G     - 2567 THR   (   3-)  H        -2.21
2811 GLU   ( 110-)  I     - 2814 LYS   ( 113-)  I        -1.91
2878 ARG   (  51-)  J     - 2884 LYS   (  57-)  J        -2.46
3032 PRO   ( 115-)  K     - 3036 CYS   ( 119-)  K        -2.17
3087 PRO   (  45-)  L     - 3093 ALA   (  51-)  L        -2.12
3268 VAL   (  98-)  M     - 3272 ARG   ( 102-)  M        -2.02
3273 THR   ( 103-)  M     - 3276 ASN   ( 106-)  M        -2.42
3291 LYS   ( 121-)  M     - 3294 LYS   (   4-)  N        -1.77
3306 PHE   (  16-)  N     - 3309 ARG   (  19-)  N        -2.07
3465 ARG   (  26-)  P     - 3468 ASP   (  29-)  P        -2.05
3717 ARG   (  29-)  S     - 3720 LYS   (  32-)  S        -1.81

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

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

1542 ASN   (  37-)  B
1581 GLN   (  76-)  B
1651 GLN   ( 146-)  B
1729 GLN   ( 224-)  B
1992 HIS   (  43-)  D
2174 GLN   (  20-)  E
2381 ASN   (  73-)  F
2825 GLN   ( 124-)  I
2905 ASN   (  78-)  J
3182 ASN   (  12-)  M
3232 ASN   (  62-)  M
3363 GLN   (  13-)  O
3396 HIS   (  46-)  O
3547 GLN   (  26-)  Q

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 OGUA  (  28-)  A      N2
  53 OGUA  (  57-)  A      N2
  72 OGUA  (  78-)  A      N1
  72 OGUA  (  78-)  A      N2
  96 OGUA  ( 107-)  A      N1
  99 OCYT  ( 110-)  A      N4
 104 OGUA  ( 115-)  A      N2
 141 OADE  ( 151-)  A      N6
 159 OCYT  ( 169-)  A      N4
 242 OGUA  ( 251-)  A      N2
 257 OGUA  ( 266-)  A      N1
 259 OCYT  ( 268-)  A      N4
 280 OGUA  ( 289-)  A      N2
 282 OCYT  ( 291-)  A      N4
 292 OGUA  ( 301-)  A      N2
 309 OGUA  ( 318-)  A      N2
 313 OCYT  ( 322-)  A      N4
 347 OADE  ( 356-)  A      N6
 362 OGUA  ( 371-)  A      N2
 404 OGUA  ( 413-)  A      N1
 453 OADE  ( 472-)  A      N6
 473 OGUA  ( 493-)  A      N2
 476 OADE  ( 496-)  A      N6
 499 OADE  ( 520-)  A      N6
 501 OCYT  ( 522-)  A      N4
And so on for a total of 434 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.

1545 HIS   (  40-)  B      ND1
1555 GLU   (  50-)  B      OE1
1599 ASN   (  94-)  B      OD1
1671 ASP   ( 166-)  B      OD1
1780 ASP   (  36-)  C      OD1
1781 GLN   (  37-)  C      OE1
1802 GLU   (  58-)  C      OE1
1862 GLN   ( 118-)  C      OE1
1964 GLU   (  15-)  D      OE2
2232 HIS   (  78-)  E      ND1
2436 ASN   (  28-)  G      OD1
2806 ASP   ( 105-)  I      OD1
2811 GLU   ( 110-)  I      OE1
2900 ASP   (  73-)  J      OD1
3115 GLU   (  73-)  L      OE1
3570 GLU   (  49-)  Q      OE1
3822 GLU   (  60-)  T      OE2

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+.

3917  MG   (1601-)  A   -.-  -.-  Too few ligands (1)
3918  MG   (1602-)  A   -.-  -.-  Too few ligands (0)
3919  MG   (1603-)  A   -.-  -.-  Too few ligands (1)
3920  MG   (1604-)  A   -.-  -.-  Too few ligands (1)
3921  MG   (1605-)  A   -.-  -.-  Too few ligands (0)
3922  MG   (1606-)  A   -.-  -.-  Too few ligands (0)
3923  MG   (1607-)  A   -.-  -.-  Too few ligands (1)
3924  MG   (1608-)  A   -.-  -.-  Too few ligands (1)
3925  MG   (1609-)  A   -.-  -.-  Too few ligands (0)
3926  MG   (1610-)  A   -.-  -.-  Too few ligands (1)
3927  MG   (1611-)  A   -.-  -.-  Too few ligands (1)
3928  MG   (1612-)  A   -.-  -.-  Too few ligands (0)
3929  MG   (1613-)  A   -.-  -.-  Too few ligands (0)
3930  MG   (1614-)  A   -.-  -.-  Too few ligands (3)
3931  MG   (1615-)  A   -.-  -.-  Too few ligands (1)
3933  MG   ( 101-)  X     0.28   1.06 Is perhaps  K *2
3934  MG   ( 101-)  Y   -.-  -.-  Too few ligands (2)
Since there are no waters, the water check has been skipped.

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.

1517 GLU   (  12-)  B   H-bonding suggests Gln; but Alt-Rotamer
1648 GLU   ( 143-)  B   H-bonding suggests Gln; but Alt-Rotamer
1833 GLU   (  89-)  C   H-bonding suggests Gln
1869 GLU   ( 125-)  C   H-bonding suggests Gln; but Alt-Rotamer
1887 GLU   ( 143-)  C   H-bonding suggests Gln
1949 GLU   ( 206-)  C   H-bonding suggests Gln
2271 ASP   ( 117-)  E   H-bonding suggests Asn
2301 ASP   ( 147-)  E   H-bonding suggests Asn
2453 ASP   (  45-)  G   H-bonding suggests Asn
2548 ASP   ( 140-)  G   H-bonding suggests Asn
2616 ASP   (  52-)  H   H-bonding suggests Asn
2663 GLU   (  99-)  H   H-bonding suggests Gln
2761 ASP   (  60-)  I   H-bonding suggests Asn; but Alt-Rotamer
2844 ASP   (  17-)  J   H-bonding suggests Asn
2852 GLU   (  25-)  J   H-bonding suggests Gln
2900 ASP   (  73-)  J   H-bonding suggests Asn; but Alt-Rotamer
2910 GLU   (  83-)  J   H-bonding suggests Gln
2922 GLU   (  95-)  J   H-bonding suggests Gln
2924 GLU   (  97-)  J   H-bonding suggests Gln; but Alt-Rotamer
2953 ASP   (  36-)  K   H-bonding suggests Asn
3148 ASP   ( 106-)  L   H-bonding suggests Asn
3178 GLU   (   8-)  M   H-bonding suggests Gln
3231 GLU   (  61-)  M   H-bonding suggests Gln; but Alt-Rotamer
3486 ASP   (  47-)  P   H-bonding suggests Asn
3570 GLU   (  49-)  Q   H-bonding suggests Gln
3576 ASP   (  55-)  Q   H-bonding suggests Asn; but Alt-Rotamer
3633 ASP   (  30-)  R   H-bonding suggests Asn; but Alt-Rotamer
3686 GLU   (  83-)  R   H-bonding suggests Gln; but Alt-Rotamer
3808 GLU   (  46-)  T   H-bonding suggests Gln
3813 GLU   (  51-)  T   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.978
  2nd generation packing quality :  -3.358 (poor)
  Ramachandran plot appearance   :  -5.102 (bad)
  chi-1/chi-2 rotamer normality  :  -5.993 (bad)
  Backbone conformation          :  -0.278

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.499 (tight)
  Bond angles                    :   0.899
  Omega angle restraints         :   1.623 (loose)
  Side chain planarity           :   0.467 (tight)
  Improper dihedral distribution :   0.817
  B-factor distribution          :   0.983
  Inside/Outside distribution    :   1.004

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.16


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.6
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -2.1
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.499 (tight)
  Bond angles                    :   0.899
  Omega angle restraints         :   1.623 (loose)
  Side chain planarity           :   0.467 (tight)
  Improper dihedral distribution :   0.817
  B-factor distribution          :   0.983
  Inside/Outside distribution    :   1.004
==============

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.