WHAT IF Check report

This file was created 2012-01-31 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 pdb2qa4.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 3
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
There is also strong SEQRES evidence for a multiplicity of: 1
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 3
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: 1363822.4
Volume of the Unit Cell V= 37492760.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 10.309
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.180 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

6920  MG   (3027-)  3  0
6962  NA   (3065-)  R  0
6977  NA   ( 125-)  0  9
6980  NA   (3076-)  J  0
7003  NA   (3099-)  L  0
7033  CL   (3111-)  Y  0

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

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

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

4173 HIS   (  54-)  G  -   CD2 4513 TYR   ( 115-)  I  -   CE1
4173 HIS   (  54-)  G  -   CE1 4513 TYR   ( 115-)  I  -   CD1
4173 HIS   (  54-)  G  -   CE1 4513 TYR   ( 115-)  I  -   CE1
4173 HIS   (  54-)  G  -   CE1 4513 TYR   ( 115-)  I  -   CZ
4173 HIS   (  54-)  G  -   NE2 4513 TYR   ( 115-)  I  -   CD1
4173 HIS   (  54-)  G  -   NE2 4513 TYR   ( 115-)  I  -   CE1
4173 HIS   (  54-)  G  -   NE2 4513 TYR   ( 115-)  I  -   CZ

Warning: Strange inter-chain connections could NOT be corrected

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

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 105 OURA  ( 115-)  0  -              104 OADE  ( 113-)  0  -           3.8
Delete overlapping entity  104 OADE ( 113-) 0  -
Delete overlapping entity 4174 GLY  (  55-) G  -

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.

 104 OADE  ( 113-)  0  -
4174 GLY   (  55-)  G  -

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

6967  NA   (3070-)  0  -
7032  CL   (3111-)  Y  0

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

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

Warning: Artificial side chains detected

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

3828 SER   ( 168-)  D
4371 LEU   ( 133-)  H
5116 ASN   ( 170-)  M

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'.

1139 OADE  (1181-)  0      O5'
1139 OADE  (1181-)  0      C5'
1139 OADE  (1181-)  0      C4'
1139 OADE  (1181-)  0      O4'
1139 OADE  (1181-)  0      C1'
1139 OADE  (1181-)  0      N9
1139 OADE  (1181-)  0      C5
1139 OADE  (1181-)  0      C6
1139 OADE  (1181-)  0      N6
1139 OADE  (1181-)  0      N1
1139 OADE  (1181-)  0      C2
1139 OADE  (1181-)  0      N3
1139 OADE  (1181-)  0      C4
1518 OURA  (1561-)  0      P
1518 OURA  (1561-)  0      OP1
1518 OURA  (1561-)  0      OP2

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.

  78 OCYT  (  87-)  0    High
  79 OGUA  (  88-)  0    High
  80 OGUA  (  89-)  0    High
 116 OADE  ( 128-)  0    High
 117 OADE  ( 129-)  0    High
 126 OURA  ( 138-)  0    High
 127 OCYT  ( 139-)  0    High
 128 OGUA  ( 140-)  0    High
 186 OADE  ( 198-)  0    High
 187 OADE  ( 199-)  0    High
 188 OURA  ( 200-)  0    High
 189 OGUA  ( 201-)  0    High
 207 OGUA  ( 219-)  0    High
 241 OURA  ( 253-)  0    High
 242 OCYT  ( 254-)  0    High
 243 OADE  ( 255-)  0    High
 244 OCYT  ( 256-)  0    High
 245 OGUA  ( 257-)  0    High
 259 OCYT  ( 271-)  0    High
 260 OADE  ( 272-)  0    High
 261 OGUA  ( 273-)  0    High
 265 OURA  ( 277-)  0    High
 266 OADE  ( 278-)  0    High
 267 OCYT  ( 279-)  0    High
 268 OCYT  ( 280-)  0    High
And so on for a total of 1585 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Nomenclature related problems

Warning: Tyrosine convention problem

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

2897 TYR   (  23-)  A
3203 TYR   (  92-)  B
3310 TYR   ( 199-)  B
3494 TYR   (  46-)  C
3499 TYR   (  51-)  C
4001 TYR   ( 167-)  E
4255 TYR   (   6-)  H
4268 TYR   (  19-)  H
4292 TYR   (  43-)  H
4332 TYR   (  83-)  H
4453 TYR   (  56-)  I
4512 TYR   ( 115-)  I
4593 TYR   (  69-)  J
4628 TYR   ( 104-)  J
4633 TYR   ( 109-)  J
4951 TYR   (   5-)  M
4953 TYR   (   7-)  M
5146 TYR   (   6-)  N
5160 TYR   (  20-)  N
5209 TYR   (  69-)  N
5222 TYR   (  82-)  N
5377 TYR   (  51-)  O
5512 TYR   (  71-)  P
5564 TYR   ( 123-)  P
5581 TYR   ( 140-)  P
5683 TYR   (   4-)  R
5759 TYR   (  80-)  R
5945 TYR   (  35-)  T
6188 TYR   (  41-)  W
6237 TYR   (  90-)  W
6534 TYR   (  18-)  Z
6585 TYR   (  69-)  Z
6646 TYR   (  48-)  1
6710 TYR   (  10-)  3

Warning: Phenylalanine convention problem

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

2890 PHE   (  16-)  A
2934 PHE   (  60-)  A
2992 PHE   ( 118-)  A
3043 PHE   ( 169-)  A
3075 PHE   ( 201-)  A
3137 PHE   (  26-)  B
3216 PHE   ( 105-)  B
3305 PHE   ( 194-)  B
3395 PHE   ( 284-)  B
3422 PHE   ( 311-)  B
3509 PHE   (  61-)  C
3579 PHE   ( 131-)  C
3695 PHE   (  10-)  D
3741 PHE   (  61-)  D
3784 PHE   ( 104-)  D
3786 PHE   ( 106-)  D
3899 PHE   (  65-)  E
3907 PHE   (  73-)  E
3941 PHE   ( 107-)  E
4082 PHE   (  76-)  F
4372 PHE   ( 134-)  H
4388 PHE   ( 150-)  H
4478 PHE   (  81-)  I
4489 PHE   (  92-)  I
4603 PHE   (  79-)  J
4790 PHE   ( 121-)  K
4852 PHE   (  51-)  L
5055 PHE   ( 109-)  M
5106 PHE   ( 160-)  M
5256 PHE   ( 116-)  N
5572 PHE   ( 131-)  P
5617 PHE   (  33-)  Q
5738 PHE   (  59-)  R
5783 PHE   ( 104-)  R
5849 PHE   (  20-)  S
5855 PHE   (  26-)  S
5965 PHE   (  55-)  T
6201 PHE   (  54-)  W
6372 PHE   (  77-)  X
6417 PHE   ( 128-)  Y
6457 PHE   ( 168-)  Y
6471 PHE   ( 182-)  Y
6530 PHE   (  14-)  Z
6580 PHE   (  64-)  Z
6707 PHE   (   7-)  3
6752 PHE   (  52-)  3

Warning: Aspartic acid convention problem

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

2938 ASP   (  64-)  A
3143 ASP   (  32-)  B
3167 ASP   (  56-)  B
3214 ASP   ( 103-)  B
3233 ASP   ( 122-)  B
3284 ASP   ( 173-)  B
3493 ASP   (  45-)  C
3545 ASP   (  97-)  C
3615 ASP   ( 167-)  C
3618 ASP   ( 170-)  C
3805 ASP   ( 145-)  D
3853 ASP   (  19-)  E
3961 ASP   ( 127-)  E
4113 ASP   ( 107-)  F
4349 ASP   ( 111-)  H
4537 ASP   (  13-)  J
4676 ASP   (   7-)  K
4871 ASP   (  70-)  L
4900 ASP   ( 104-)  L
5205 ASP   (  65-)  N
5268 ASP   ( 128-)  N
5381 ASP   (  55-)  O
5453 ASP   (  12-)  P
5562 ASP   ( 121-)  P
5604 ASP   (  20-)  Q
5618 ASP   (  34-)  Q
5690 ASP   (  11-)  R
5888 ASP   (  59-)  S
5964 ASP   (  54-)  T
5978 ASP   (  68-)  T
6010 ASP   ( 100-)  T
6026 ASP   ( 116-)  T
6027 ASP   ( 117-)  T
6051 ASP   (  25-)  U
6197 ASP   (  50-)  W
6225 ASP   (  78-)  W
6346 ASP   (  51-)  X
6400 ASP   ( 111-)  Y
6512 ASP   ( 223-)  Y
6645 ASP   (  47-)  1
6697 ASP   (  46-)  2
6699 ASP   (  48-)  2

Warning: Glutamic acid convention problem

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

2902 GLU   (  28-)  A
2907 GLU   (  33-)  A
2920 GLU   (  46-)  A
2946 GLU   (  72-)  A
2961 GLU   (  87-)  A
3018 GLU   ( 144-)  A
3174 GLU   (  63-)  B
3178 GLU   (  67-)  B
3298 GLU   ( 187-)  B
3375 GLU   ( 264-)  B
3543 GLU   (  95-)  C
3578 GLU   ( 130-)  C
3600 GLU   ( 152-)  C
3669 GLU   ( 221-)  C
3693 GLU   ( 245-)  C
3843 GLU   (   9-)  E
3919 GLU   (  85-)  E
3935 GLU   ( 101-)  E
3983 GLU   ( 149-)  E
4019 GLU   (  13-)  F
4084 GLU   (  78-)  F
4267 GLU   (  18-)  H
4301 GLU   (  52-)  H
4411 GLU   (   6-)  I
4418 GLU   (  13-)  I
And so on for a total of 62 lines.

Warning: Phosphate group convention problem

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

 616 OADE  ( 629-)  0
1518 OURA  (1561-)  0

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.

 615 OGUA  ( 627-)  0      C3'  O3'   1.49    4.5
 840 OGUA  ( 854-)  0      C5   C6    1.37   -4.6
 997 OGUA  (1039-)  0      C5   C6    1.37   -4.4
1328 OGUA  (1370-)  0      C5   C6    1.37   -4.6
1331 OGUA  (1373-)  0      C5   C6    1.37   -4.6
1651 OGUA  (1694-)  0      C5   C6    1.37   -4.5
2650 OADE  (2812-)  0      C5   C6    1.36   -4.6
4127 LYS   (   8-)  G      N    CA    1.36   -5.0
4127 LYS   (   8-)  G      N   -C     1.22   -5.4
4128 THR   (   9-)  G      CA   CB    1.44   -4.5
4429 LEU   (  24-)  I      C    O     1.55   15.8
4429 LEU   (  24-)  I      CA   CB    3.44   95.6
4429 LEU   (  24-)  I      CB   CG    2.53   49.8
4429 LEU   (  24-)  I      CG   CD1   3.38   56.4
4429 LEU   (  24-)  I      CG   CD2   3.65   64.4

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.000629 -0.000039  0.000065|
 | -0.000039  1.000981 -0.000009|
 |  0.000065 -0.000009  1.000940|
Proposed new scale matrix

 |  0.004659  0.000000  0.000000|
 |  0.000000  0.003304  0.000000|
 |  0.000000  0.000000  0.001728|
With corresponding cell

    A    = 214.635  B   = 302.686  C    = 578.578
    Alpha=  90.005  Beta=  90.005  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 214.490  B   = 302.432  C    = 578.056
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1194.889
(Under-)estimated Z-score: 25.476

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.

  11 OGUA  (  20-)  0      N9   C8   N7  113.20    4.2
  19 OGUA  (  28-)  0      N9   C8   N7  113.13    4.1
  23 OGUA  (  32-)  0      N9   C8   N7  113.11    4.0
  24 OGUA  (  33-)  0      N9   C8   N7  113.23    4.3
  30 OGUA  (  39-)  0      N9   C8   N7  113.17    4.1
  32 OGUA  (  41-)  0      N9   C8   N7  113.13    4.1
  35 OGUA  (  44-)  0      N9   C8   N7  113.19    4.2
  38 OGUA  (  47-)  0      N9   C8   N7  113.34    4.5
  41 OGUA  (  50-)  0      N9   C8   N7  113.18    4.2
  42 OGUA  (  51-)  0      N9   C8   N7  113.24    4.3
  45 OGUA  (  54-)  0      N9   C8   N7  113.22    4.2
  55 OGUA  (  64-)  0      N9   C8   N7  113.12    4.0
  57 OGUA  (  66-)  0      N9   C8   N7  113.24    4.3
  67 OGUA  (  76-)  0      N9   C8   N7  113.22    4.2
  68 OGUA  (  77-)  0      N9   C8   N7  113.21    4.2
  70 OGUA  (  79-)  0      N9   C8   N7  113.14    4.1
  72 OGUA  (  81-)  0      N9   C8   N7  113.11    4.0
  75 OGUA  (  84-)  0      N9   C8   N7  113.13    4.1
  79 OGUA  (  88-)  0      N9   C8   N7  113.16    4.1
  88 OGUA  (  97-)  0      N9   C8   N7  113.13    4.1
 106 OGUA  ( 116-)  0      N9   C8   N7  113.16    4.1
 116 OADE  ( 128-)  0      O5'  C5'  C4' 117.67    5.3
 128 OGUA  ( 140-)  0      N9   C8   N7  113.21    4.2
 135 OGUA  ( 147-)  0      N9   C8   N7  113.19    4.2
 136 OADE  ( 148-)  0      C2'  C1'  N9  105.94   -4.7
And so on for a total of 470 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.

2902 GLU   (  28-)  A
2907 GLU   (  33-)  A
2920 GLU   (  46-)  A
2938 ASP   (  64-)  A
2946 GLU   (  72-)  A
2961 GLU   (  87-)  A
3018 GLU   ( 144-)  A
3143 ASP   (  32-)  B
3167 ASP   (  56-)  B
3174 GLU   (  63-)  B
3178 GLU   (  67-)  B
3214 ASP   ( 103-)  B
3233 ASP   ( 122-)  B
3284 ASP   ( 173-)  B
3298 GLU   ( 187-)  B
3375 GLU   ( 264-)  B
3493 ASP   (  45-)  C
3543 GLU   (  95-)  C
3545 ASP   (  97-)  C
3578 GLU   ( 130-)  C
3600 GLU   ( 152-)  C
3615 ASP   ( 167-)  C
3618 ASP   ( 170-)  C
3669 GLU   ( 221-)  C
3693 GLU   ( 245-)  C
And so on for a total of 104 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.

4127 LYS   (   8-)  G      CA     7.5    46.35    33.92
4149 TYR   (  30-)  G      CA    -7.2    22.58    34.03
4158 ALA   (  39-)  G      CA     6.7    42.61    34.09
4159 GLY   (  40-)  G      C      7.7    10.24     0.06
4227 LYS   ( 109-)  G      C      6.5     9.90     0.11
4244 PRO   ( 127-)  G      N     -7.9   -28.48    -2.48
4429 LEU   (  24-)  I      CA   -35.4   -19.98    34.19 Wrong hand
4429 LEU   (  24-)  I      CG   -28.3   -82.86   -33.01
4432 ASP   (  30-)  I      CA   -34.1   -34.15    33.73 Wrong hand
The average deviation= 1.003

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.

4228 THR   ( 110-)  G   12.04
4229 PRO   ( 111-)  G    7.86
4202 TYR   (  84-)  G    7.15
4171 ASP   (  52-)  G    6.68
6186 ASP   (  39-)  W    6.44
4200 ASN   (  82-)  G    6.37
4227 LYS   ( 109-)  G    6.15
3376 LEU   ( 265-)  B    6.02
5111 GLY   ( 165-)  M    5.80
4443 GLN   (  41-)  I    5.74
4199 LEU   (  81-)  G    5.57
6406 LEU   ( 117-)  Y    5.38
3915 GLU   (  81-)  E    5.29
4600 ASP   (  76-)  J    5.25
5154 ARG   (  14-)  N    5.21
4495 VAL   (  98-)  I    5.10
5333 LEU   (   7-)  O    5.10
6492 VAL   ( 203-)  Y    5.08
4420 ASN   (  15-)  I    5.02
4240 ASP   ( 123-)  G    4.98
4724 VAL   (  55-)  K    4.94
5206 LEU   (  66-)  N    4.87
4619 ARG   (  95-)  J    4.75
3720 ILE   (  40-)  D    4.74
5376 ARG   (  50-)  O    4.72
And so on for a total of 66 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.583

Error: Connections to aromatic rings out of plane

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

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

4512 TYR   ( 115-)  I      CB   4.42

Warning: Uncalibrated side chain planarity problems

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

1125 OGUA  (1167-)  0    0.14
1835 OGUA  (1878-)  0    0.12
1792 OURA  (1835-)  0    0.11
2151 OURA  (2306-)  0    0.10
 889 OURA  ( 903-)  0    0.10
 Ramachandran Z-score : -4.170

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 : -4.170

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.

3741 PHE   (  61-)  D    -3.7
3494 TYR   (  46-)  C    -3.3
3209 THR   (  98-)  B    -3.2
6461 THR   ( 172-)  Y    -3.2
4244 PRO   ( 127-)  G    -3.1
3505 PRO   (  57-)  C    -3.0
4485 PRO   (  88-)  I    -2.9
4229 PRO   ( 111-)  G    -2.9
3966 THR   ( 132-)  E    -2.9
3152 PHE   (  41-)  B    -2.9
5056 PRO   ( 110-)  M    -2.8
3539 PRO   (  91-)  C    -2.8
6316 PRO   (  21-)  X    -2.8
4814 HIS   (  13-)  L    -2.7
4632 PRO   ( 108-)  J    -2.7
3433 ARG   ( 322-)  B    -2.7
4242 VAL   ( 125-)  G    -2.7
4231 PRO   ( 113-)  G    -2.7
3475 ARG   (  27-)  C    -2.7
4420 ASN   (  15-)  I    -2.7
3160 THR   (  49-)  B    -2.6
4472 ILE   (  75-)  I    -2.6
4105 THR   (  99-)  F    -2.6
3089 ILE   ( 215-)  A    -2.5
4589 ASN   (  65-)  J    -2.5
And so on for a total of 155 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.

2893 PRO   (  19-)  A  Poor phi/psi
2908 ASP   (  34-)  A  Poor phi/psi
2910 ASP   (  36-)  A  Poor phi/psi
2926 SER   (  52-)  A  Poor phi/psi
2936 ASP   (  62-)  A  Poor phi/psi
2962 ILE   (  88-)  A  Poor phi/psi
2993 ALA   ( 119-)  A  Poor phi/psi
2994 ARG   ( 120-)  A  Poor phi/psi
2999 ASN   ( 125-)  A  Poor phi/psi
3044 VAL   ( 170-)  A  Poor phi/psi
3060 TRP   ( 186-)  A  PRO omega poor
3061 PRO   ( 187-)  A  Poor phi/psi
3073 HIS   ( 199-)  A  Poor phi/psi
3097 ARG   ( 223-)  A  Poor phi/psi
3106 ARG   ( 232-)  A  Poor phi/psi
3108 GLY   ( 234-)  A  Poor phi/psi
3113 GLN   (   2-)  B  Poor phi/psi
3116 ARG   (   5-)  B  Poor phi/psi
3125 GLY   (  14-)  B  PRO omega poor
3127 ARG   (  16-)  B  Poor phi/psi
3144 ASP   (  33-)  B  Poor phi/psi
3152 PHE   (  41-)  B  Poor phi/psi
3213 THR   ( 102-)  B  Poor phi/psi
3214 ASP   ( 103-)  B  Poor phi/psi
3250 ASP   ( 139-)  B  Poor phi/psi
And so on for a total of 193 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.382

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.

3901 SER   (  67-)  E    0.34
3697 GLU   (  12-)  D    0.35
4566 GLU   (  42-)  J    0.35
3894 SER   (  60-)  E    0.36
4314 SER   (  65-)  H    0.36
5342 SER   (  16-)  O    0.37
3561 SER   ( 113-)  C    0.38
5220 SER   (  80-)  N    0.38
4461 ILE   (  64-)  I    0.38
4792 SER   ( 123-)  K    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  (  12-)  0      0
   4 OGUA  (  13-)  0      0
   5 OCYT  (  14-)  0      0
   6 OCYT  (  15-)  0      0
   7 OADE  (  16-)  0      0
   8 OGUA  (  17-)  0      0
   9 OCYT  (  18-)  0      0
  10 OURA  (  19-)  0      0
  11 OGUA  (  20-)  0      0
  12 OGUA  (  21-)  0      0
  13 OURA  (  22-)  0      0
  14 OGUA  (  23-)  0      0
  15 OGUA  (  24-)  0      0
  16 OADE  (  25-)  0      0
  17 OURA  (  26-)  0      0
  18 OURA  (  27-)  0      0
  19 OGUA  (  28-)  0      0
  20 OCYT  (  29-)  0      0
  21 OURA  (  30-)  0      0
  22 OCYT  (  31-)  0      0
  23 OGUA  (  32-)  0      0
  24 OGUA  (  33-)  0      0
  25 OCYT  (  34-)  0      0
  26 OURA  (  35-)  0      0
  27 OCYT  (  36-)  0      0
And so on for a total of 4526 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.685

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!

5590 PRO   (   6-)  Q   2.04   12
4829 GLY   (  28-)  L   2.03   11
3746 GLY   (  66-)  D   1.95   20
4708 GLY   (  39-)  K   1.88   26
5744 GLY   (  65-)  R   1.74   80
4077 GLY   (  71-)  F   1.72   80
3204 GLY   (  93-)  B   1.64   22
4208 GLY   (  90-)  G   1.62   18
4457 GLY   (  60-)  I   1.57   66
3576 GLY   ( 128-)  C   1.55   80

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...

3526 ARG   (  78-)  C   1.56
4227 LYS   ( 109-)  G   3.44

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]

3188 PRO   (  77-)  B    0.47 HIGH
3355 PRO   ( 244-)  B    0.45 HIGH
3363 PRO   ( 252-)  B    0.46 HIGH
3539 PRO   (  91-)  C    0.45 HIGH
3648 PRO   ( 200-)  C    0.45 HIGH
3926 PRO   (  92-)  E    0.45 HIGH
4070 PRO   (  64-)  F    0.45 HIGH
4273 PRO   (  24-)  H    0.45 HIGH
4397 PRO   ( 159-)  H    0.46 HIGH
5270 PRO   ( 130-)  N    0.45 HIGH
6125 PRO   (  43-)  V    0.45 HIGH

Warning: Unusual PRO puckering phases

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

3074 PRO   ( 200-)  A  -129.7 half-chair C-delta/C-gamma (-126 degrees)
3413 PRO   ( 302-)  B  -115.3 envelop C-gamma (-108 degrees)
3428 PRO   ( 317-)  B    32.0 envelop C-delta (36 degrees)
4238 PRO   ( 121-)  G  -113.1 envelop C-gamma (-108 degrees)
4421 PRO   (  16-)  I    49.9 half-chair C-delta/C-gamma (54 degrees)
4424 PRO   (  19-)  I    15.2 half-chair N/C-delta (18 degrees)
4714 PRO   (  45-)  K  -118.3 half-chair C-delta/C-gamma (-126 degrees)
4773 PRO   ( 104-)  K  -114.6 envelop C-gamma (-108 degrees)
4855 PRO   (  54-)  L  -121.7 half-chair C-delta/C-gamma (-126 degrees)
5144 PRO   (   4-)  N    52.0 half-chair C-delta/C-gamma (54 degrees)
5610 PRO   (  26-)  Q    50.6 half-chair C-delta/C-gamma (54 degrees)
5818 PRO   ( 139-)  R    47.7 half-chair C-delta/C-gamma (54 degrees)
6268 PRO   ( 121-)  W  -122.9 half-chair C-delta/C-gamma (-126 degrees)
6316 PRO   (  21-)  X   130.2 half-chair C-beta/C-alpha (126 degrees)
6362 PRO   (  67-)  X  -114.4 envelop C-gamma (-108 degrees)
6435 PRO   ( 146-)  Y  -115.6 envelop C-gamma (-108 degrees)
6468 PRO   ( 179-)  Y  -116.1 envelop C-gamma (-108 degrees)
6604 PRO   (   6-)  1  -115.5 envelop C-gamma (-108 degrees)
6676 PRO   (  22-)  2  -112.2 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

4433 VAL   (  31-)  I      CG2  <->  4436 VAL   (  34-)  I      CB   1.47    1.73  INTRA BF
4433 VAL   (  31-)  I      CG2  <->  4436 VAL   (  34-)  I      CG2  1.38    1.82  INTRA BF
4152 VAL   (  33-)  G      C    <->  4240 ASP   ( 123-)  G      OD2  1.08    1.72  INTRA BF
4151 SER   (  32-)  G      OG   <->  4241 ILE   ( 124-)  G      CD1  0.97    1.83  INTRA BF
4154 VAL   (  35-)  G      CG2  <->  4239 ASN   ( 122-)  G      OD1  0.87    1.93  INTRA BF
4153 GLY   (  34-)  G      N    <->  4240 ASP   ( 123-)  G      OD2  0.74    1.96  INTRA BF
4151 SER   (  32-)  G      CB   <->  4241 ILE   ( 124-)  G      CG1  0.73    2.47  INTRA BF
4152 VAL   (  33-)  G      CA   <->  4240 ASP   ( 123-)  G      OD2  0.66    2.14  INTRA BF
1792 OURA  (1835-)  0      C5   <->  1797 OADE  (1840-)  0      N7   0.60    2.50  INTRA BL
1809 OADE  (1852-)  0      N1   <->  1836 OURA  (1879-)  0      N3   0.60    2.40  INTRA BL
1174 OGUA  (1216-)  0      N7   <->  4126 ARG   (   7-)  G      NH1  0.58    2.42  INTRA BF
1155 OGUA  (1197-)  0      N2   <->  1160 OADE  (1202-)  0      N7   0.58    2.42  INTRA BF
 802 OGUA  ( 816-)  0      C6   <->   803 OGUA  ( 817-)  0      N1   0.58    2.52  INTRA BL
4238 PRO   ( 121-)  G      CB   <->  4244 PRO   ( 127-)  G      CB   0.57    2.63  INTRA BF
1128 OURA  (1170-)  0      C2'  <->  1129 OADE  (1171-)  0      C5'  0.56    2.64  INTRA BF
 859 OGUA  ( 873-)  0      N2   <->   862 OADE  ( 876-)  0      N1   0.54    2.46  INTRA BL
1813 OCYT  (1856-)  0      N3   <->  1830 OGUA  (1873-)  0      N2   0.53    2.47  INTRA BL
1759 OGUA  (1802-)  0      N2   <->  1760 OCYT  (1803-)  0      C2   0.53    2.57  INTRA BF
1174 OGUA  (1216-)  0      N9   <->  4126 ARG   (   7-)  G      NH2  0.52    2.48  INTRA BF
 608 OADE  ( 620-)  0      N6   <->   622 OADE  ( 635-)  0      N1   0.52    2.48  INTRA BL
 441 OADE  ( 453-)  0      C4   <->   467 OGUA  ( 479-)  0      N7   0.51    2.59  INTRA BL
1958 OGUA  (2013-)  0      C2   <->  1959 OGUA  (2014-)  0      N7   0.51    2.59  INTRA BL
2030 OADE  (2085-)  0      N1   <->  2499 OURA  (2659-)  0      N3   0.51    2.49  INTRA BL
1692 OCYT  (1735-)  0      N3   <->  1989 OGUA  (2044-)  0      N1   0.50    2.50  INTRA BL
2044 OGUA  (2099-)  0      N2   <->  2486 OGUA  (2646-)  0      C5   0.50    2.60  INTRA BL
And so on for a total of 4819 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

3109 ARG   ( 235-)  A      -8.75
3830 TYR   ( 170-)  D      -8.20
3106 ARG   ( 232-)  A      -8.17
6269 ARG   ( 122-)  W      -7.89
3203 TYR   (  92-)  B      -7.81
6674 ARG   (  20-)  2      -7.78
3146 GLN   (  35-)  B      -7.78
6458 ARG   ( 169-)  Y      -7.66
6726 ARG   (  26-)  3      -7.66
4822 ARG   (  21-)  L      -7.61
3118 ARG   (   7-)  B      -7.58
5521 ARG   (  80-)  P      -7.55
5014 ARG   (  68-)  M      -7.52
4831 ARG   (  30-)  L      -7.47
4512 TYR   ( 115-)  I      -7.45
4828 ARG   (  27-)  L      -7.37
3346 ARG   ( 235-)  B      -7.36
4945 ARG   ( 149-)  L      -7.34
3447 GLN   ( 336-)  B      -7.33
4809 ARG   (   8-)  L      -7.23
4911 ARG   ( 115-)  L      -7.13
6730 GLN   (  30-)  3      -7.08
4823 ARG   (  22-)  L      -7.02
4849 LYS   (  48-)  L      -7.00
3538 HIS   (  90-)  C      -7.00
And so on for a total of 263 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.

3079 GLY   ( 205-)  A      3082 - HIS    208- ( A)         -5.36
3105 LYS   ( 231-)  A      3111 - GLY    237- ( A)         -5.88
3123 GLY   (  12-)  B      3125 - GLY     14- ( B)         -4.51
3228 GLU   ( 117-)  B      3230 - HIS    119- ( B)         -4.65
3267 LYS   ( 156-)  B      3269 - LYS    158- ( B)         -5.18
3429 ASN   ( 318-)  B      3431 - GLN    320- ( B)         -4.77
3446 ASN   ( 335-)  B      3448 - GLY    337- ( B)         -5.35
3511 SER   (  63-)  C      3513 - ARG     65- ( C)         -5.30
3673 PRO   ( 225-)  C      3675 - GLY    227- ( C)         -4.66
3726 GLY   (  46-)  D      3728 - MET     48- ( D)         -5.39
4200 ASN   (  82-)  G      4202 - TYR     84- ( G)         -4.61
4241 ILE   ( 124-)  G      4243 - ILE    126- ( G)         -4.23
4593 TYR   (  69-)  J      4595 - TYR     71- ( J)         -5.59
4844 HIS   (  43-)  L      4847 - LEU     46- ( L)         -4.85
4849 LYS   (  48-)  L      4854 - ARG     53- ( L)         -5.64
5145 ARG   (   5-)  N      5148 - VAL      8- ( N)         -5.07
5520 SER   (  79-)  P      5522 - LYS     81- ( P)         -5.79
5586 SER   (   2-)  Q      5588 - ASN      4- ( Q)         -4.94
5809 MET   ( 130-)  R      5811 - ARG    132- ( R)         -4.72
6642 LYS   (  44-)  1      6644 - ARG     46- ( 1)         -4.61
6693 TRP   (  42-)  2      6695 - ARG     44- ( 2)         -5.00
6753 SER   (  53-)  3      6757 - GLY     57- ( 3)         -4.70
6779 LEU   (  79-)  3      6781 - GLU     81- ( 3)         -5.47

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 - 6792 : -1.704

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: X

Note: Quality value plot

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

Chain identifier: Y

Note: Quality value plot

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

Chain identifier: Z

Note: Quality value plot

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

Chain identifier: 1

Note: Quality value plot

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

Chain identifier: 2

Note: Quality value plot

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

Chain identifier: 3

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

6610 ASN   (  12-)  1   -3.95
4711 ASN   (  42-)  K   -3.89
5498 ASN   (  57-)  P   -3.88
3349 ASN   ( 238-)  B   -3.57
4254 MET   (   5-)  H   -3.47
3654 ASN   ( 206-)  C   -3.44
3492 GLN   (  44-)  C   -3.38
6694 ARG   (  43-)  2   -3.33
5522 LYS   (  81-)  P   -3.29
3530 GLN   (  82-)  C   -3.26
4842 HIS   (  41-)  L   -3.26
3117 PRO   (   6-)  B   -3.26
4713 LEU   (  44-)  K   -3.20
4354 ALA   ( 116-)  H   -3.20
4812 ARG   (  11-)  L   -3.20
3946 ALA   ( 112-)  E   -3.17
3116 ARG   (   5-)  B   -3.17
5639 ARG   (  55-)  Q   -3.17
4852 PHE   (  51-)  L   -3.16
3447 GLN   ( 336-)  B   -3.16
3061 PRO   ( 187-)  A   -3.16
3538 HIS   (  90-)  C   -3.13
6760 LYS   (  60-)  3   -3.10
6656 LYS   (   2-)  2   -3.09
3357 ARG   ( 246-)  B   -3.09
And so on for a total of 116 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.

3058 THR   ( 184-)  A     - 3064 ARG   ( 190-)  A        -2.12
3077 GLY   ( 203-)  A     - 3082 HIS   ( 208-)  A        -2.10
3083 PRO   ( 209-)  A     - 3088 SER   ( 214-)  A        -2.16
3105 LYS   ( 231-)  A     - 3108 GLY   ( 234-)  A        -2.25
3115 SER   (   4-)  B     - 3118 ARG   (   7-)  B        -2.48
3331 VAL   ( 220-)  B     - 3335 LYS   ( 224-)  B        -1.95
3339 ALA   ( 228-)  B     - 3342 GLY   ( 231-)  B        -2.42
3344 ARG   ( 233-)  B     - 3349 ASN   ( 238-)  B        -2.14
3350 LEU   ( 239-)  B     - 3355 PRO   ( 244-)  B        -2.32
3444 GLU   ( 333-)  B     - 3448 GLY   ( 337-)  B        -2.28
3489 ASN   (  41-)  C     - 3492 GLN   (  44-)  C        -2.28
3513 ARG   (  65-)  C     - 3518 VAL   (  70-)  C        -2.29
3536 SER   (  88-)  C     - 3539 PRO   (  91-)  C        -2.25
3621 LYS   ( 173-)  C     - 3626 GLN   ( 178-)  C        -2.09
3627 GLY   ( 179-)  C     - 3630 ARG   ( 182-)  C        -2.03
4349 ASP   ( 111-)  H     - 4352 ARG   ( 114-)  H        -1.69
4508 ASP   ( 111-)  I     - 4512 TYR   ( 115-)  I        -2.06
4703 VAL   (  34-)  K     - 4706 TYR   (  37-)  K        -1.52
4825 ALA   (  24-)  L     - 4828 ARG   (  27-)  L        -2.10
4846 PRO   (  45-)  L     - 4849 LYS   (  48-)  L        -1.65
4850 SER   (  49-)  L     - 4854 ARG   (  53-)  L        -2.24
5000 TYR   (  54-)  M     - 5004 GLN   (  58-)  M        -1.71
5021 ARG   (  75-)  M     - 5026 GLY   (  80-)  M        -2.34
5037 ILE   (  91-)  M     - 5040 ARG   (  94-)  M        -1.96
5243 ASP   ( 103-)  N     - 5246 LEU   ( 106-)  N        -1.71
5362 PRO   (  36-)  O     - 5365 THR   (  39-)  O        -1.75
5495 LYS   (  54-)  P     - 5498 ASN   (  57-)  P        -2.70
5518 ALA   (  77-)  P     - 5522 LYS   (  81-)  P        -2.11
5586 SER   (   2-)  Q     - 5589 GLY   (   5-)  Q        -1.93
5590 PRO   (   6-)  Q     - 5593 GLY   (   9-)  Q        -1.71
5739 LYS   (  60-)  R     - 5742 ASN   (  63-)  R        -1.84
6156 GLY   (   9-)  W     - 6159 ASN   (  12-)  W        -2.18
6311 ASP   (  16-)  X     - 6314 ALA   (  19-)  X        -1.83
6424 LYS   ( 135-)  Y     - 6428 VAL   ( 139-)  Y        -2.21
6446 ILE   ( 157-)  Y     - 6449 LYS   ( 160-)  Y        -2.08
6454 GLU   ( 165-)  Y     - 6458 ARG   ( 169-)  Y        -2.40
6522 TYR   ( 233-)  Y     - 6525 VAL   ( 236-)  Y        -1.58
6527 SER   (  11-)  Z     - 6530 PHE   (  14-)  Z        -1.95
6606 GLN   (   8-)  1     - 6610 ASN   (  12-)  1        -2.54
6641 ALA   (  43-)  1     - 6644 ARG   (  46-)  1        -2.05
6645 ASP   (  47-)  1     - 6648 TRP   (  50-)  1        -2.04
6654 GLU   (  56-)  1     - 6657 LYS   (   3-)  2        -1.78
6686 ARG   (  35-)  2     - 6689 LYS   (  38-)  2        -1.78
6744 SER   (  44-)  3     - 6748 ASN   (  48-)  3        -1.94
6749 ASP   (  49-)  3     - 6752 PHE   (  52-)  3        -1.97
6786 GLY   (  86-)  3     - 6789 GLU   (  89-)  3        -1.87

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Water, ion, and hydrogenbond related checks

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.

3073 HIS   ( 199-)  A
3138 ASN   (  27-)  B
3256 HIS   ( 145-)  B
3349 ASN   ( 238-)  B
3354 ASN   ( 243-)  B
3443 ASN   ( 332-)  B
3487 GLN   (  39-)  C
3599 GLN   ( 151-)  C
3727 GLN   (  47-)  D
3940 ASN   ( 106-)  E
3977 GLN   ( 143-)  E
3984 GLN   ( 150-)  E
4086 GLN   (  80-)  F
4280 HIS   (  31-)  H
4305 GLN   (  56-)  H
4441 ASN   (  39-)  I
4549 GLN   (  25-)  J
4591 ASN   (  67-)  J
4631 ASN   ( 107-)  J
4679 GLN   (  10-)  K
4839 HIS   (  38-)  L
4842 HIS   (  41-)  L
4960 ASN   (  14-)  M
4965 GLN   (  19-)  M
4970 GLN   (  24-)  M
And so on for a total of 55 lines.

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  24 OGUA  (  33-)  0      N2
  29 OGUA  (  38-)  0      N2
  59 OURA  (  68-)  0      N3
  89 OADE  (  98-)  0      N6
 140 OADE  ( 152-)  0      N6
 145 OGUA  ( 157-)  0      O2'
 158 OURA  ( 170-)  0      N3
 170 OGUA  ( 182-)  0      N2
 178 OGUA  ( 190-)  0      N2
 181 OADE  ( 193-)  0      N6
 183 OCYT  ( 195-)  0      N4
 192 OADE  ( 204-)  0      N6
 207 OGUA  ( 219-)  0      O2'
 215 OADE  ( 227-)  0      N6
 247 OGUA  ( 259-)  0      N2
 314 OGUA  ( 326-)  0      N2
 325 OADE  ( 337-)  0      N6
 345 OADE  ( 357-)  0      N6
 354 OURA  ( 366-)  0      N3
 367 OGUA  ( 379-)  0      N2
 371 OADE  ( 383-)  0      O2'
 381 OGUA  ( 393-)  0      N1
 382 OGUA  ( 394-)  0      N1
 382 OGUA  ( 394-)  0      N2
 405 OGUA  ( 417-)  0      N1
And so on for a total of 709 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.

2903 HIS   (  29-)  A      ND1
2910 ASP   (  36-)  A      OD1
2921 HIS   (  47-)  A      ND1
3072 ASP   ( 198-)  A      OD1
3082 HIS   ( 208-)  A      NE2
3101 ASP   ( 227-)  A      OD2
3217 HIS   ( 106-)  B      ND1
3250 ASP   ( 139-)  B      OD1
3367 GLN   ( 256-)  B      OE1
3377 ASN   ( 266-)  B      OD1
3538 HIS   (  90-)  C      ND1
3611 HIS   ( 163-)  C      ND1
3613 ASP   ( 165-)  C      OD2
3783 ASN   ( 103-)  D      OD1
3793 ASN   ( 133-)  D      OD1
3831 ASP   ( 171-)  D      OD2
4047 GLU   (  41-)  F      OE1
4064 GLU   (  58-)  F      OE1
4156 ASN   (  37-)  G      OD1
4190 ASP   (  72-)  G      OD1
4312 GLU   (  63-)  H      OE2
4428 GLU   (  23-)  I      OE1
4691 ASP   (  22-)  K      OD2
4819 HIS   (  18-)  L      NE2
4842 HIS   (  41-)  L      NE2
4872 GLU   (  71-)  L      OE2
4919 ASP   ( 123-)  L      OD1
4998 GLN   (  52-)  M      OE1
5023 HIS   (  77-)  M      NE2
5075 HIS   ( 129-)  M      ND1
5259 GLN   ( 119-)  N      OE1
5260 GLU   ( 120-)  N      OE1
5304 ASP   ( 164-)  N      OD1
5304 ASP   ( 164-)  N      OD2
5307 ASP   ( 167-)  N      OD1
5307 ASP   ( 167-)  N      OD2
5311 HIS   ( 171-)  N      ND1
5515 GLN   (  74-)  P      OE1
5536 GLU   (  95-)  P      OE2
5854 GLN   (  25-)  S      OE1
6178 HIS   (  31-)  W      ND1
6266 HIS   ( 119-)  W      ND1
6331 HIS   (  36-)  X      ND1
6383 GLU   (  88-)  X      OE2
6442 GLN   ( 153-)  Y      OE1
6720 HIS   (  20-)  3      NE2
6737 ASP   (  37-)  3      OD2
6739 GLN   (  39-)  3      OE1

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+.

6807  MG   (   1-)  0   -.-  -.-  Too few ligands (3)
6808  MG   (2924-)  0   -.-  -.-  Too few ligands (3)
6809  MG   (2925-)  0   -.-  -.-  Too few ligands (3)
6810  MG   (2926-)  0   -.-  -.-  Too few ligands (2)
6811  MG   (2927-)  0   -.-  -.-  Too few ligands (3)
6812  MG   (2928-)  0   -.-  -.-  Too few ligands (3)
6813  MG   (2929-)  0   -.-  -.-  Too few ligands (3)
6814  MG   (2930-)  0     0.72   1.33 Scores about as good as CA
6815  MG   (2931-)  0   -.-  -.-  Part of ionic cluster
6815  MG   (2931-)  0   -.-  -.-  Too few ligands (3)
6816  MG   (2932-)  0   -.-  -.-  Too few ligands (3)
6817  MG   (2933-)  0   -.-  -.-  Too few ligands (2)
6818  MG   (2934-)  0   -.-  -.-  Too few ligands (1)
6819  MG   (2935-)  0   -.-  -.-  Too few ligands (2)
6820  MG   (2936-)  0   -.-  -.-  Too few ligands (3)
6821  MG   (2937-)  0   -.-  -.-  Too few ligands (3)
6822  MG   (2938-)  0     0.58   0.99 Is perhaps CA (Few ligands (4) )
6823  MG   (2939-)  0   -.-  -.-  Too few ligands (2)
6824  MG   (2940-)  0   -.-  -.-  Too few ligands (3)
6825  MG   (2941-)  0   -.-  -.-  Too few ligands (2)
6826  MG   (2942-)  0   -.-  -.-  Too few ligands (1)
6827  MG   (2943-)  0   -.-  -.-  Too few ligands (1)
6828  MG   (2944-)  0   -.-  -.-  Too few ligands (2)
6829  MG   (2945-)  0   -.-  -.-  Part of ionic cluster
6829  MG   (2945-)  0   -.-  -.-  Too few ligands (2)
And so on for a total of 230 lines.

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.

2908 ASP   (  34-)  A   H-bonding suggests Asn
2935 GLU   (  61-)  A   H-bonding suggests Gln
2988 ASP   ( 114-)  A   H-bonding suggests Asn; but Alt-Rotamer
3168 GLU   (  57-)  B   H-bonding suggests Gln
3215 GLU   ( 104-)  B   H-bonding suggests Gln
3229 ASP   ( 118-)  B   H-bonding suggests Asn; but Alt-Rotamer
3241 ASP   ( 130-)  B   H-bonding suggests Asn
3247 ASP   ( 136-)  B   H-bonding suggests Asn; but Alt-Rotamer
3287 ASP   ( 176-)  B   H-bonding suggests Asn
3295 ASP   ( 184-)  B   H-bonding suggests Asn
3388 GLU   ( 277-)  B   H-bonding suggests Gln
3392 ASP   ( 281-)  B   H-bonding suggests Asn
3455 ASP   (   7-)  C   H-bonding suggests Asn; but Alt-Rotamer
3549 ASP   ( 101-)  C   H-bonding suggests Asn; but Alt-Rotamer
3580 ASP   ( 132-)  C   H-bonding suggests Asn
3670 ASP   ( 222-)  C   H-bonding suggests Asn
3719 ASP   (  39-)  D   H-bonding suggests Asn
3747 ASP   (  67-)  D   H-bonding suggests Asn
3805 ASP   ( 145-)  D   H-bonding suggests Asn; but Alt-Rotamer
3831 ASP   ( 171-)  D   H-bonding suggests Asn; but Alt-Rotamer
3939 GLU   ( 105-)  E   H-bonding suggests Gln
4011 ASP   (   5-)  F   H-bonding suggests Asn
4020 ASP   (  14-)  F   H-bonding suggests Asn
4031 ASP   (  25-)  F   H-bonding suggests Asn
4041 GLU   (  35-)  F   H-bonding suggests Gln
And so on for a total of 78 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.011
  2nd generation packing quality :  -3.930 (poor)
  Ramachandran plot appearance   :  -4.170 (bad)
  chi-1/chi-2 rotamer normality  :  -3.382 (poor)
  Backbone conformation          :  -0.202

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.542 (tight)
  Bond angles                    :   0.742
  Omega angle restraints         :   0.488 (tight)
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.896
  B-factor distribution          :   0.894
  Inside/Outside distribution    :   0.992

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.8
  2nd generation packing quality :  -1.7
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.542 (tight)
  Bond angles                    :   0.742
  Omega angle restraints         :   0.488 (tight)
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.896
  B-factor distribution          :   0.894
  Inside/Outside distribution    :   0.992
==============

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.