WHAT IF Check report

This file was created 2014-02-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb4b3s.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: 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: 771904.563
Volume of the Unit Cell V= 27938844.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.573
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.430 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

4127 RPO   (2800-)  A  -

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.

4025  MG   (2624-)  A  -
4028  MG   (2627-)  A  -
4044  MG   (2643-)  A  -

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: V

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
   2 OGUA  (   6-)  A    High
  69 OGUA  (  73-)  A    High
  70 OCYT  (  76-)  A    High
  71 OGUA  (  77-)  A    High
  79 OADE  (  88-)  A    High
  86 OGUA  (  97-)  A    High
  87 OGUA  (  98-)  A    High
 134 OGUA  ( 144-)  A    High
 135 OGUA  ( 145-)  A    High
 145 OCYT  ( 155-)  A    High
 146 OGUA  ( 156-)  A    High
 147 OGUA  ( 157-)  A    High
 148 OGUA  ( 158-)  A    High
 149 OGUA  ( 159-)  A    High
 150 OADE  ( 160-)  A    High
 151 OADE  ( 161-)  A    High
 152 OADE  ( 162-)  A    High
 153 OCYT  ( 163-)  A    High
 154 OURA  ( 164-)  A    High
 155 OCYT  ( 165-)  A    High
 156 OGUA  ( 166-)  A    High
 157 OGUA  ( 167-)  A    High
 182 OCYT  ( 189-)  A    High
 189 OGUA  ( 189-)  A    High
And so on for a total of 1329 lines.

Warning: C-terminal nitrogen atoms detected.

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

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

3914 LYS   (  25-)  V
3790 GLY   (  81-)  S
3532 ALA   (  84-)  P
3175 ALA   ( 125-)  L
2931 VAL   (  99-)  J
2311 GLU   ( 151-)  E
1952 ILE   ( 207-)  C
1745 GLU   ( 235-)  B

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: 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: V

Nomenclature related problems

Warning: Phosphate group convention problem

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

   2 OGUA  (   6-)  A
   4 OADE  (   8-)  A
   5 OGUA  (   9-)  A
   6 OADE  (  10-)  A
   9 OURA  (  13-)  A
  10 OURA  (  14-)  A
  12 OADE  (  16-)  A
  13 OURA  (  17-)  A
  14 OCYT  (  18-)  A
  17 OGUA  (  21-)  A
  18 OGUA  (  22-)  A
  22 OADE  (  26-)  A
  24 OGUA  (  28-)  A
  26 OURA  (  30-)  A
  33 OURA  (  37-)  A
  34 OGUA  (  38-)  A
  36 OCYT  (  40-)  A
  37 OGUA  (  41-)  A
  40 OGUA  (  44-)  A
  41 OURA  (  45-)  A
  42 OGUA  (  46-)  A
  43 OCYT  (  47-)  A
  44 OCYT  (  48-)  A
  46 OADE  (  50-)  A
  47 OADE  (  51-)  A
And so on for a total of 759 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.

 831 OGUA  ( 858-)  A      C5   C6    1.32   -9.7
 831 OGUA  ( 858-)  A      C6   O6    1.18   -6.3

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

 |  1.000657  0.000139 -0.000173|
 |  0.000139  1.000127  0.000123|
 | -0.000173  0.000123  1.000483|
Proposed new scale matrix

 |  0.002491  0.000000  0.000000|
 |  0.000000  0.002493  0.000000|
 |  0.000001  0.000000  0.005756|
With corresponding cell

    A    = 401.387  B   = 401.174  C    = 173.725
    Alpha=  90.003  Beta=  90.012  Gamma=  90.005

The CRYST1 cell dimensions

    A    = 401.150  B   = 401.150  C    = 173.640
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 175.122
(Under-)estimated Z-score: 9.753

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.

   2 OGUA  (   6-)  A      N9   C8   N7  113.13    4.1
   5 OGUA  (   9-)  A      N9   C8   N7  113.14    4.1
   7 OGUA  (  11-)  A      N9   C8   N7  113.24    4.3
  11 OGUA  (  15-)  A      N9   C8   N7  113.21    4.2
  17 OGUA  (  21-)  A      N9   C8   N7  113.17    4.1
  18 OGUA  (  22-)  A      C3'  C4'  C5' 108.45   -4.7
  18 OGUA  (  22-)  A      N9   C8   N7  113.26    4.3
  23 OGUA  (  27-)  A      N9   C8   N7  113.17    4.1
  31 OGUA  (  35-)  A      N9   C8   N7  113.20    4.2
  34 OGUA  (  38-)  A      N9   C8   N7  113.23    4.3
  37 OGUA  (  41-)  A      N9   C8   N7  113.16    4.1
  38 OGUA  (  42-)  A      N9   C8   N7  113.17    4.1
  40 OGUA  (  44-)  A      N9   C8   N7  113.11    4.0
  42 OGUA  (  46-)  A      N9   C8   N7  113.27    4.3
  46 OADE  (  50-)  A      C2'  C1'  N9  123.79    6.5
  47 OADE  (  51-)  A      C2'  C1'  N9  121.63    5.1
  48 OGUA  (  52-)  A      C3'  C4'  C5' 124.96    6.3
  53 OGUA  (  57-)  A      N9   C8   N7  113.22    4.2
  61 OURA  (  65-)  A      C3'  C4'  C5' 108.56   -4.6
  61 OURA  (  65-)  A      O3'  C3'  C2' 130.03    6.8
  62 OGUA  (  66-)  A      N9   C8   N7  113.36    4.5
  64 OGUA  (  68-)  A      N9   C8   N7  113.29    4.4
  65 OGUA  (  69-)  A      N9   C8   N7  113.14    4.1
  66 OGUA  (  70-)  A      N9   C8   N7  113.11    4.0
  73 OGUA  (  79-)  A      N9   C8   N7  113.17    4.1
And so on for a total of 443 lines.

Error: Tau angle problems

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

1960 LEU   (  10-)  D    6.58
3068 ALA   (  22-)  L    6.45
2788 GLN   (  86-)  I    6.04
3399 VAL   (  44-)  O    5.70
3161 LYS   ( 115-)  L    5.22
3789 LEU   (   6-)  T    4.96
1962 ARG   (  12-)  D    4.87
3834 LYS   (  51-)  T    4.84
2954 GLY   (  27-)  K    4.83
2660 GLY   (  96-)  H    4.78
2182 PHE   (  24-)  E    4.77
3470 LYS   (  27-)  P    4.74
3325 ARG   (  30-)  N    4.72
2460 GLU   (  51-)  G    4.70
2698 ILE   ( 134-)  H    4.67
2458 ILE   (  49-)  G    4.63
2771 LYS   (  69-)  I    4.62
2571 ALA   (   7-)  H    4.60
1831 ARG   (  87-)  C    4.56
3499 ALA   (  56-)  P    4.56
3277 ARG   ( 107-)  M    4.53
2286 ALA   ( 128-)  E    4.51
3808 ALA   (  25-)  T    4.47
1899 ARG   ( 155-)  C    4.36
3447 ILE   (   4-)  P    4.30
2648 ARG   (  84-)  H    4.27
3276 ALA   ( 106-)  M    4.25
2372 GLN   (  64-)  F    4.20
3862 ARG   (  79-)  T    4.17
2707 GLY   (   5-)  I    4.16
3468 ARG   (  25-)  P    4.12
1724 ASP   ( 214-)  B    4.11
1643 LYS   ( 133-)  B    4.10
1681 ALA   ( 171-)  B    4.10
3130 GLY   (  84-)  L    4.07
2692 GLY   ( 128-)  H    4.05
2889 HIS   (  60-)  J    4.03
2326 GLN   (  18-)  F    4.01

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 : 1.551

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.

1187 OCYT  (1210-)  A    0.14
 539 OURA  ( 560-)  A    0.10
 Ramachandran Z-score : -5.310

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 : -5.310

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   ( 164-)  C    -3.3
3004 THR   (  77-)  K    -3.2
3702 ARG   (  72-)  R    -3.1
2588 THR   (  24-)  H    -3.1
1978 PRO   (  28-)  D    -3.1
3293 PRO   ( 123-)  M    -3.1
3744 PRO   (  41-)  S    -3.0
3308 PRO   (  13-)  N    -3.0
3555 PRO   (  29-)  Q    -2.9
2170 THR   (  12-)  E    -2.9
3442 ARG   (  87-)  O    -2.8
3716 HIS   (  13-)  S    -2.8
2282 PRO   ( 124-)  E    -2.8
3232 THR   (  62-)  M    -2.8
1953 TYR   (   3-)  D    -2.7
3192 TYR   (  22-)  M    -2.7
1698 PRO   ( 188-)  B    -2.7
2166 LEU   (   8-)  E    -2.7
1899 ARG   ( 155-)  C    -2.7
3786 LEU   (   3-)  T    -2.6
3278 THR   ( 108-)  M    -2.6
3326 SER   (  31-)  N    -2.6
3178 ILE   (   8-)  M    -2.6
2318 LEU   (  10-)  F    -2.6
2887 ARG   (  58-)  J    -2.6
And so on for a total of 145 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.

1512 LYS   (   2-)  B  Poor phi/psi
1513 GLU   (   3-)  B  Poor phi/psi
1520 HIS   (  10-)  B  Poor phi/psi
1521 PHE   (  11-)  B  Poor phi/psi
1524 GLU   (  14-)  B  Poor phi/psi
1525 ARG   (  15-)  B  Poor phi/psi
1527 ARG   (  17-)  B  Poor phi/psi
1528 TRP   (  18-)  B  Poor phi/psi
1580 GLN   (  70-)  B  Poor phi/psi
1581 ALA   (  71-)  B  Poor phi/psi
1587 MET   (  77-)  B  Poor phi/psi
1592 ALA   (  82-)  B  Poor phi/psi
1593 GLY   (  83-)  B  Poor phi/psi
1599 GLN   (  89-)  B  Poor phi/psi
1627 ALA   ( 117-)  B  Poor phi/psi
1634 ARG   ( 124-)  B  Poor phi/psi
1653 LEU   ( 143-)  B  Poor phi/psi
1669 VAL   ( 159-)  B  Poor phi/psi
1685 PHE   ( 175-)  B  Poor phi/psi
1693 ASP   ( 183-)  B  Poor phi/psi
1711 ALA   ( 201-)  B  Poor phi/psi
1717 LEU   ( 207-)  B  Poor phi/psi
1728 GLN   ( 218-)  B  Poor phi/psi
1731 GLY   ( 221-)  B  Poor phi/psi
1732 GLY   ( 222-)  B  Poor phi/psi
And so on for a total of 248 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.239

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.

3837 SER   (  54-)  T    0.36
3394 SER   (  39-)  O    0.37
1714 SER   ( 204-)  B    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 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 2506 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.107

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!

3175 GLY   (   5-)  M   3.27   27
1888 GLY   ( 144-)  C   3.11   80
2731 GLY   (  29-)  I   2.51   80
2654 GLY   (  90-)  H   2.44   17
2768 GLY   (  66-)  I   2.30   14
1707 GLY   ( 197-)  B   2.19   17
3207 GLY   (  37-)  M   2.08   10
3627 GLY   ( 101-)  Q   2.06   24
2116 GLY   ( 166-)  D   1.97   18
1731 GLY   ( 221-)  B   1.91   80
1827 ILE   (  83-)  C   1.80   16
3130 GLY   (  84-)  L   1.79   24
3269 GLY   (  99-)  M   1.78   29
3628 GLY   ( 102-)  Q   1.77   10
1518 GLY   (   8-)  B   1.70   24
2325 SER   (  17-)  F   1.64   11
1639 GLN   ( 129-)  B   1.63   15
3558 GLY   (  32-)  Q   1.58   26
2694 GLY   ( 130-)  H   1.57   29
2538 GLY   ( 129-)  G   1.56   18
2966 GLY   (  39-)  K   1.55   80
2619 GLY   (  55-)  H   1.52   23

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...

1693 ASP   ( 183-)  B   1.54

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]

1706 PRO   ( 196-)  B    0.45 HIGH
2665 PRO   ( 101-)  H    0.47 HIGH
3032 PRO   ( 105-)  K    0.46 HIGH
3090 PRO   (  44-)  L    0.46 HIGH
3553 PRO   (  27-)  Q    0.45 HIGH
3695 PRO   (  65-)  R    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].

1978 PRO   (  28-)  D   115.4 envelop C-beta (108 degrees)
2868 PRO   (  39-)  J  -113.7 envelop C-gamma (-108 degrees)
3090 PRO   (  44-)  L   -65.7 envelop C-beta (-72 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.

3963  MG   (2570-)  A     MG    <->  3989  MG   (2596-)  A     MG    1.39    1.81  INTRA BF
3068 ALA   (  22-)  L      CB   <->  4115  MG   (1126-)  L     MG    1.16    2.04  INTRA BL
4040  MG   (2647-)  A     MG    <->  4081  MG   (2688-)  A     MG    1.04    2.16  INTRA BL
3321 CYS   (  26-)  N      SG   <->  3337 CYS   (  42-)  N      SG   0.78    2.67  INTRA BL
1600 ARG   (  90-)  B      CG   <->  4107  MG   (1235-)  B     MG    0.76    2.44  INTRA BF
3788 ALA   (   5-)  T      CB   <->  4118  MG   (1100-)  T     MG    0.74    2.46  INTRA BF
3069 LEU   (  23-)  L      O    <->  3071 GLY   (  25-)  L      N    0.64    2.06  INTRA BF
 831 OGUA  ( 858-)  A      C6   <->   842 OGUA  ( 869-)  A      N7   0.62    2.48  INTRA BL
1520 HIS   (  10-)  B      ND1  <->  1521 PHE   (  11-)  B      N    0.59    2.31  INTRA BF
3570 HIS   (  44-)  Q      ND1  <->  3594 LYS   (  68-)  Q      NZ   0.58    2.42  INTRA BL
1975 CYS   (  25-)  D      SG   <->  1980 CYS   (  30-)  D      SG   0.57    2.88  INTRA BL
1282 OGUA  (1305-)  A      P    <->  3883 GLY   (   1-)  V      N    0.55    2.75  INTRA BL
  75 OURA  (  81-)  A      C5   <->  4078  MG   (2685-)  A     MG    0.52    2.68  INTRA BF
3318 CYS   (  23-)  N      SG   <->  3337 CYS   (  42-)  N      SG   0.50    2.95  INTRA BL
 697 OGUA  ( 718-)  A      C5'  <->  3034 ASN   ( 107-)  K      ND2  0.50    2.60  INTRA BL
2888 GLU   (  59-)  J      OE1  <->  3339 ARG   (  44-)  N      NH1  0.49    2.21  INTRA BF
1523 HIS   (  13-)  B      ND1  <->  1708 ASN   ( 198-)  B      ND2  0.48    2.52  INTRA BF
1475 OADE  (1502-)  A      C2   <->  1478 OGUA  (1505-)  A      N1   0.47    2.63  INTRA BL
1166 OCYT  (1189-)  A      P    <->  2878 ARG   (  49-)  J      NH2  0.45    2.85  INTRA BL
1757 ILE   (  13-)  C      O    <->  1759 ARG   (  15-)  C      N    0.45    2.25  INTRA BL
3192 TYR   (  22-)  M      O    <->  3194 ILE   (  24-)  M      N    0.44    2.26  INTRA BF
1166 OCYT  (1189-)  A      OP1  <->  2878 ARG   (  49-)  J      NH2  0.44    2.26  INTRA BL
 626 OCYT  ( 647-)  A      C2'  <->   627 OADE  ( 648-)  A      C5'  0.43    2.77  INTRA BF
3070 LYS   (  24-)  L      O    <->  3072 ALA   (  26-)  L      N    0.43    2.27  INTRA BF
2032 SER   (  82-)  D      CA   <->  2038 THR   (  88-)  D      CG2  0.43    2.77  INTRA BF
And so on for a total of 2406 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: V

Warning: Abnormal packing environment for some residues

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

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

3294 ARG   ( 124-)  M      -8.54
3705 ARG   (   2-)  S      -8.41
1998 ARG   (  48-)  D      -8.38
3442 ARG   (  87-)  O      -8.37
1822 ARG   (  78-)  C      -7.98
3782 TYR   (  79-)  S      -7.98
3905 ARG   (  23-)  V      -7.94
3731 ARG   (  28-)  S      -7.93
2563 ARG   ( 154-)  G      -7.73
3273 ARG   ( 103-)  M      -7.64
3306 ARG   (  11-)  N      -7.61
3268 ARG   (  98-)  M      -7.60
1933 ARG   ( 189-)  C      -7.55
1991 GLN   (  41-)  D      -7.55
2825 GLN   ( 123-)  I      -7.53
1984 ARG   (  34-)  D      -7.47
2412 ARG   (   3-)  G      -7.42
2826 TYR   ( 124-)  I      -7.39
2942 TYR   (  15-)  K      -7.38
2633 ARG   (  69-)  H      -7.32
2411 ARG   (   2-)  G      -7.32
3037 ARG   ( 110-)  K      -7.19
2414 ARG   (   5-)  G      -7.18
2881 PHE   (  52-)  J      -7.15
3588 ARG   (  62-)  Q      -7.15
And so on for a total of 171 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.

1511 VAL   (   1-)  B      1513 - GLU      3- ( B)         -5.15
1525 ARG   (  15-)  B      1528 - TRP     18- ( B)         -5.25
1733 VAL   ( 223-)  B      1735 - GLU    225- ( B)         -4.88
1745 GLY   (   1-)  C      1748 - ILE      4- ( C)         -5.07
1952 ARG   (   2-)  D      1954 - ILE      4- ( D)         -6.29
2172 ARG   (  14-)  E      2175 - ALA     17- ( E)         -5.36
2306 ARG   ( 148-)  E      2308 - GLY    150- ( E)         -4.95
2411 ARG   (   2-)  G      2414 - ARG      5- ( G)         -7.06
2418 ARG   (   9-)  G      2421 - GLN     12- ( G)         -5.51
2424 LEU   (  15-)  G      2426 - TYR     17- ( G)         -4.68
2632 ARG   (  68-)  H      2634 - GLN     70- ( H)         -6.42
2825 GLN   ( 123-)  I      2828 - LYS    126- ( I)         -6.35
3115 GLU   (  69-)  L      3117 - HIS     71- ( L)         -4.75
3168 LYS   ( 122-)  L      3170 - ALA    124- ( L)         -5.01
3267 VAL   (  97-)  M      3269 - GLY     99- ( M)         -5.27
3283 ARG   ( 113-)  M      3287 - ALA    117- ( M)         -4.94
3441 ILE   (  86-)  O      3443 - GLY     88- ( O)         -5.74
3705 ARG   (   2-)  S      3709 - LYS      6- ( S)         -6.12
3729 GLU   (  26-)  S      3732 - LEU     29- ( S)         -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 - 3925 : -1.531

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: V

Warning: Low packing Z-score for some residues

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

2882 LYS   (  53-)  J   -3.35
3275 ASN   ( 105-)  M   -3.31
3325 ARG   (  30-)  N   -3.21
2943 ASN   (  16-)  K   -3.19
1746 ASN   (   2-)  C   -3.13
3273 ARG   ( 103-)  M   -3.13
2825 GLN   ( 123-)  I   -3.12
3780 ARG   (  77-)  S   -3.12
3133 LYS   (  87-)  L   -3.10
2411 ARG   (   2-)  G   -3.08
2881 PHE   (  52-)  J   -3.00
3088 LYS   (  42-)  L   -3.00
1974 ARG   (  24-)  D   -2.97
3037 ARG   ( 110-)  K   -2.96
3756 GLY   (  53-)  S   -2.96
3708 LYS   (   5-)  S   -2.95
2828 LYS   ( 126-)  I   -2.94
1755 LEU   (  11-)  C   -2.93
3269 GLY   (  99-)  M   -2.91
3035 GLY   ( 108-)  K   -2.88
3623 LEU   (  97-)  Q   -2.85
2814 LYS   ( 112-)  I   -2.82
3455 LYS   (  12-)  P   -2.80
1991 GLN   (  41-)  D   -2.80
2805 ARG   ( 103-)  I   -2.79
And so on for a total of 54 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.

1745 GLY   (   1-)  C     - 1748 ILE   (   4-)  C        -2.20
1989 PRO   (  39-)  D     - 1992 HIS   (  42-)  D        -1.82
2173 MET   (  15-)  E     - 2176 GLY   (  18-)  E        -1.77
2439 MET   (  30-)  G     - 2442 GLY   (  33-)  G        -1.76
2564 TRP   ( 155-)  G     - 2567 THR   (   3-)  H        -0.97
2806 ASP   ( 104-)  I     - 2810 VAL   ( 108-)  I        -1.87
2811 GLU   ( 109-)  I     - 2814 LYS   ( 112-)  I        -2.12
2824 PRO   ( 122-)  I     - 2828 LYS   ( 126-)  I        -2.39
2880 PRO   (  51-)  J     - 2884 LYS   (  55-)  J        -2.53
3032 PRO   ( 105-)  K     - 3037 ARG   ( 110-)  K        -2.38
3087 PRO   (  41-)  L     - 3090 PRO   (  44-)  L        -2.09
3267 VAL   (  97-)  M     - 3271 ARG   ( 101-)  M        -2.23
3291 LYS   ( 121-)  M     - 3295 LYS   ( 125-)  M        -2.20
3351 ARG   (  56-)  N     - 3354 SER   (  59-)  N        -1.65
3453 GLY   (  10-)  P     - 3456 HIS   (  13-)  P        -1.91
3469 ARG   (  26-)  P     - 3473 GLY   (  30-)  P        -2.03

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: V

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.

1529 ASN   (  19-)  B
1744 GLN   ( 234-)  B
1749 HIS   (   5-)  C
1812 HIS   (  68-)  C
2011 GLN   (  61-)  D
2023 GLN   (  73-)  D
2174 GLN   (  16-)  E
2281 ASN   ( 123-)  E
2295 GLN   ( 137-)  E
2326 GLN   (  18-)  F
2372 GLN   (  64-)  F
2402 GLN   (  94-)  F
2419 GLN   (  10-)  G
2459 GLN   (  50-)  G
2504 GLN   (  95-)  G
2848 GLN   (  19-)  J
2944 ASN   (  17-)  K
3091 ASN   (  45-)  L
3117 HIS   (  71-)  L
3181 ASN   (  11-)  M
3508 GLN   (  65-)  P
3541 GLN   (  15-)  Q
3767 ASN   (  64-)  S
3821 GLN   (  38-)  T

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.

  53 OGUA  (  57-)  A      N2
  73 OGUA  (  79-)  A      O2'
  76 OURA  (  82-)  A      N3
  77 OURA  (  83-)  A      N3
  96 OGUA  ( 107-)  A      N1
  96 OGUA  ( 107-)  A      N2
  99 OCYT  ( 110-)  A      N4
 141 OADE  ( 151-)  A      N6
 148 OGUA  ( 158-)  A      N1
 171 OGUA  ( 181-)  A      N2
 223 OGUA  ( 232-)  A      N2
 242 OGUA  ( 251-)  A      N2
 245 OGUA  ( 254-)  A      N2
 251 OGUA  ( 260-)  A      N1
 260 OCYT  ( 269-)  A      N4
 269 OGUA  ( 278-)  A      N1
 269 OGUA  ( 278-)  A      N2
 291 OADE  ( 300-)  A      N6
 309 OGUA  ( 318-)  A      N2
 313 OCYT  ( 322-)  A      N4
 345 OGUA  ( 354-)  A      N2
 348 OGUA  ( 357-)  A      N2
 353 OGUA  ( 362-)  A      O2'
 355 OADE  ( 364-)  A      N6
 362 OGUA  ( 371-)  A      N2
And so on for a total of 415 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.

1513 GLU   (   3-)  B      OE1
1544 HIS   (  34-)  B      ND1
1598 ASN   (  88-)  B      OD1
1645 GLU   ( 135-)  B      OE1
1650 GLN   ( 140-)  B      OE1
1693 ASP   ( 183-)  B      OD1
1693 ASP   ( 183-)  B      OD2
1708 ASN   ( 198-)  B      OD1
1779 ASP   (  35-)  C      OD1
2521 GLU   ( 112-)  G      OE2
2568 ASP   (   4-)  H      OD2
2888 GLU   (  59-)  J      OE2
2900 ASP   (  71-)  J      OD1
2939 HIS   (  12-)  K      ND1
3033 HIS   ( 106-)  K      ND1
3275 ASN   ( 105-)  M      OD1
3538 ASP   (  12-)  Q      OD1
3574 GLU   (  48-)  Q      OE1
3716 HIS   (  13-)  S      ND1
3836 GLU   (  53-)  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+.

3938  MG   (2545-)  A     0.27   1.02 Could be  K *1 and *2
3939  MG   (2546-)  A   -.-  -.-  Too few ligands (0)
3940  MG   (2547-)  A   -.-  -.-  Too few ligands (1)
3941  MG   (2548-)  A   -.-  -.-  Too few ligands (1)
3942  MG   (2549-)  A   -.-  -.-  Part of ionic cluster
3942  MG   (2549-)  A   -.-  -.-  Too few ligands (3)
3943  MG   (2550-)  A     0.28   0.93 Could be  K (Few ligands (4) ) *1 and *2
3944  MG   (2551-)  A   -.-  -.-  Low probability ion. B= 81.8
3945  MG   (2552-)  A   -.-  -.-  Part of ionic cluster
3945  MG   (2552-)  A   -.-  -.-  Too few ligands (0)
3946  MG   (2553-)  A   -.-  -.-  Too few ligands (2)
3947  MG   (2554-)  A   -.-  -.-  Low probability ion. B= 82.5
3948  MG   (2555-)  A   -.-  -.-  Too few ligands (1)
3949  MG   (2556-)  A   -.-  -.-  Too few ligands (1)
3950  MG   (2557-)  A   -.-  -.-  Low probability ion. B=118.4
3951  MG   (2558-)  A   -.-  -.-  Too few ligands (1)
3952  MG   (2559-)  A   -.-  -.-  Too few ligands (2)
3953  MG   (2560-)  A   -.-  -.-  Too few ligands (2)
3954  MG   (2561-)  A   -.-  -.-  Part of ionic cluster
3954  MG   (2561-)  A   -.-  -.-  Too few ligands (0)
3955  MG   (2562-)  A   -.-  -.-  Too few ligands (0)
3956  MG   (2563-)  A   -.-  -.-  Too few ligands (2)
3957  MG   (2564-)  A   -.-  -.-  Part of ionic cluster
3957  MG   (2564-)  A   -.-  -.-  Too few ligands (2)
3958  MG   (2565-)  A   -.-  -.-  Too few ligands (0)
And so on for a total of 210 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.

1513 GLU   (   3-)  B   H-bonding suggests Gln; but Alt-Rotamer
1516 GLU   (   6-)  B   H-bonding suggests Gln
1647 GLU   ( 137-)  B   H-bonding suggests Gln
1724 ASP   ( 214-)  B   H-bonding suggests Asn
1787 GLU   (  43-)  C   H-bonding suggests Gln
1868 GLU   ( 124-)  C   H-bonding suggests Gln; but Alt-Rotamer
2093 ASP   ( 143-)  D   H-bonding suggests Asn; but Alt-Rotamer
2271 ASP   ( 113-)  E   H-bonding suggests Asn; but Alt-Rotamer
2301 ASP   ( 143-)  E   H-bonding suggests Asn
2391 ASP   (  83-)  F   H-bonding suggests Asn; but Alt-Rotamer
2453 ASP   (  44-)  G   H-bonding suggests Asn
2616 ASP   (  52-)  H   H-bonding suggests Asn
2703 GLU   (   1-)  I   H-bonding suggests Gln
2761 ASP   (  59-)  I   H-bonding suggests Asn
2844 ASP   (  15-)  J   H-bonding suggests Asn; but Alt-Rotamer
2910 GLU   (  81-)  J   H-bonding suggests Gln
2924 GLU   (  95-)  J   H-bonding suggests Gln; but Alt-Rotamer
3177 GLU   (   7-)  M   H-bonding suggests Gln
3230 GLU   (  60-)  M   H-bonding suggests Gln
3252 ASP   (  82-)  M   H-bonding suggests Asn
3574 GLU   (  48-)  Q   H-bonding suggests Gln
3580 ASP   (  54-)  Q   H-bonding suggests Asn
3643 GLU   (  13-)  R   H-bonding suggests Gln; but Alt-Rotamer
3645 ASP   (  15-)  R   H-bonding suggests Asn; but Alt-Rotamer
3698 GLU   (  68-)  R   H-bonding suggests Gln
3822 GLU   (  39-)  T   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.578
  2nd generation packing quality :  -3.038 (poor)
  Ramachandran plot appearance   :  -5.310 (bad)
  chi-1/chi-2 rotamer normality  :  -4.239 (bad)
  Backbone conformation          :  -0.000

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.482 (tight)
  Bond angles                    :   0.739
  Omega angle restraints         :   0.201 (tight)
  Side chain planarity           :   0.199 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   1.391
  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 : 3.15


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.3
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.482 (tight)
  Bond angles                    :   0.739
  Omega angle restraints         :   0.201 (tight)
  Side chain planarity           :   0.199 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   1.391
  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.