WHAT IF Check report

This file was created 2011-12-21 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 pdb1aqd.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.398
CA-only RMS fit for the two chains : 0.314

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 0.287
CA-only RMS fit for the two chains : 0.167

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and G

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and J

All-atom RMS fit for the two chains : 0.365
CA-only RMS fit for the two chains : 0.281

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and J

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 0.723
CA-only RMS fit for the two chains : 0.572

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and H

All-atom RMS fit for the two chains : 0.430
CA-only RMS fit for the two chains : 0.241

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and H

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   2 GLU   (   4-)  A  -   CB
   2 GLU   (   4-)  A  -   CG
   2 GLU   (   4-)  A  -   CD
   2 GLU   (   4-)  A  -   OE1
   2 GLU   (   4-)  A  -   OE2
  17 SER   (  19-)  A  -   OG
  37 LYS   (  39-)  A  -   CD
  37 LYS   (  39-)  A  -   CE
  37 LYS   (  39-)  A  -   NZ
  48 ARG   (  50-)  A  -   CG
  48 ARG   (  50-)  A  -   CD
  48 ARG   (  50-)  A  -   NE
  48 ARG   (  50-)  A  -   CZ
  48 ARG   (  50-)  A  -   NH1
  48 ARG   (  50-)  A  -   NH2
  51 SER   (  53-)  A  -   OG
  53 GLU   (  55-)  A  -   CG
  53 GLU   (  55-)  A  -   CD
  53 GLU   (  55-)  A  -   OE1
  53 GLU   (  55-)  A  -   OE2
  58 LEU   (  60-)  A  -   CG
  58 LEU   (  60-)  A  -   CD1
  58 LEU   (  60-)  A  -   CD2
  65 LYS   (  67-)  A  -   CE
  65 LYS   (  67-)  A  -   NZ
And so on for a total of 575 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 240 GLN   (  64-)  B  -   N
 240 GLN   (  64-)  B  -   CA
 240 GLN   (  64-)  B  -   C
 240 GLN   (  64-)  B  -   O
 665 HIS   ( 111-)  E  -   C
 665 HIS   ( 111-)  E  -   O
1373 GLN   (  64-)  K  -   N
1373 GLN   (  64-)  K  -   CA
1373 GLN   (  64-)  K  -   C
1373 GLN   (  64-)  K  -   O
1415 THR   ( 106-)  K  -   N
1415 THR   ( 106-)  K  -   CA
1415 THR   ( 106-)  K  -   C
1415 THR   ( 106-)  K  -   O
1416 GLN   ( 107-)  K  -   N
1416 GLN   ( 107-)  K  -   CA
1416 GLN   ( 107-)  K  -   C
1416 GLN   ( 107-)  K  -   O
1417 PRO   ( 108-)  K  -   N
1417 PRO   ( 108-)  K  -   CA
1417 PRO   ( 108-)  K  -   C
1417 PRO   ( 108-)  K  -   O
1418 LEU   ( 109-)  K  -   N
1418 LEU   ( 109-)  K  -   CA
1418 LEU   ( 109-)  K  -   C
1418 LEU   ( 109-)  K  -   O
1419 GLN   ( 110-)  K  -   N
1419 GLN   ( 110-)  K  -   CA
1419 GLN   ( 110-)  K  -   C
1419 GLN   ( 110-)  K  -   O
1420 HIS   ( 111-)  K  -   N
1420 HIS   ( 111-)  K  -   CA
1420 HIS   ( 111-)  K  -   C
1420 HIS   ( 111-)  K  -   O
1475 ARG   ( 166-)  K  -   N
1475 ARG   ( 166-)  K  -   CA
1475 ARG   ( 166-)  K  -   C
1475 ARG   ( 166-)  K  -   O
1476 SER   ( 167-)  K  -   N
1476 SER   ( 167-)  K  -   CA
1476 SER   ( 167-)  K  -   C
1476 SER   ( 167-)  K  -   O
1477 GLY   ( 168-)  K  -   N
1477 GLY   ( 168-)  K  -   CA
1477 GLY   ( 168-)  K  -   C
1477 GLY   ( 168-)  K  -   O
1500 ARG   ( 191-)  K  -   C
1500 ARG   ( 191-)  K  -   O
Residue with missing backbone atom(s)  380 ALA  (  15-) C  -
Residue with missing backbone atom(s)  757 ALA  (  15-) F  -
Residue with missing backbone atom(s) 1135 ALA  (  15-) I  -
Residue with missing backbone atom(s) 1514 ALA  (  15-) L  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 380 ALA   (  15-)  C  -
 757 ALA   (  15-)  F  -
1135 ALA   (  15-)  I  -
1514 ALA   (  15-)  L  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: 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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 380 ALA   (  15-)  C      O
 757 ALA   (  15-)  F      O
1135 ALA   (  15-)  I      O
1514 ALA   (  15-)  L      O

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) : 98.000

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

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

RMS Z-score : 1.628 over 11332 bonds
Average difference in B over a bond : 4.06
RMS difference in B over a bond : 6.15

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

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.

 158 VAL   ( 160-)  A      C    O     1.14   -4.6
 243 LEU   (  67-)  B      CG   CD1   1.39   -4.1
 653 VAL   (  99-)  E      CA   CB    1.61    4.1
 859 VAL   ( 104-)  G      CA   CB    1.61    4.1
 891 VAL   ( 136-)  G      CA   CB    1.62    4.4
1347 VAL   (  38-)  K      CA   CB    1.62    4.3

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  31 HIS   (  33-)  A      CG   ND1  CE1 109.90    4.3
 141 HIS   ( 143-)  A      CG   ND1  CE1 109.61    4.0
 158 VAL   ( 160-)  A      CA   C    O   111.77   -5.3
 159 TYR   ( 161-)  A     -CA  -C    N   127.00    5.4
 179 ASP   ( 181-)  A      N    CA   C   123.01    4.2
 183 PHE   (   7-)  B      N    CA   C    99.51   -4.2
 274 LYS   (  98-)  B      N    CA   C    98.37   -4.6
 285 LEU   ( 109-)  B      N    CA   C   124.40    4.7
 286 GLN   ( 110-)  B      CA   CB   CG  106.10   -4.0
 288 HIS   ( 112-)  B      CG   ND1  CE1 110.01    4.4
 340 VAL   ( 164-)  B      N    CA   C    96.82   -5.1
 368 SER   (   3-)  C      N    CA   C   125.23    5.0
 383 HIS   (   5-)  D      CG   ND1  CE1 109.78    4.2
 478 ARG   ( 100-)  D      CB   CG   CD  103.06   -5.5
 478 ARG   ( 100-)  D      CG   CD   NE  117.83    4.3
 541 CYS   ( 163-)  D      N    CA   C    98.78   -4.4
 718 VAL   ( 164-)  E      N    CA   C    97.31   -5.0
 731 HIS   ( 177-)  E      CG   ND1  CE1 109.64    4.0
 760 HIS   (   5-)  G      CG   ND1  CE1 109.63    4.0
 764 GLN   (   9-)  G      N    CA   C    98.37   -4.6
 856 GLU   ( 101-)  G      N    CA   C    98.81   -4.4
 898 HIS   ( 143-)  G      CG   ND1  CE1 109.68    4.1
 918 CYS   ( 163-)  G      N    CA   C    99.06   -4.3
1043 HIS   ( 112-)  H      CG   ND1  CE1 109.72    4.1
1095 VAL   ( 164-)  H      N    CA   C    95.79   -5.5
1132 HIS   (  12-)  I      CG   ND1  CE1 109.65    4.0
1138 HIS   (   5-)  J      CG   ND1  CE1 109.74    4.1
1142 GLN   (   9-)  J      N    CA   C    99.40   -4.2
1276 HIS   ( 143-)  J      CG   ND1  CE1 109.79    4.2
1374 LYS   (  65-)  K      N    CA   C   125.98    5.3
1390 HIS   (  81-)  K      CG   ND1  CE1 109.74    4.1
1473 VAL   ( 164-)  K      N    CA   C    95.09   -5.8
1486 HIS   ( 177-)  K      CG   ND1  CE1 109.85    4.2
1498 ARG   ( 189-)  K      CB   CG   CD  104.51   -4.8

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.

 241 LYS   (  65-)  B    6.11
 242 ASP   (  66-)  B    5.97
1018 GLU   (  87-)  H    5.95
1473 VAL   ( 164-)  K    5.77
1374 LYS   (  65-)  K    5.64
1095 VAL   ( 164-)  H    5.50
 285 LEU   ( 109-)  B    5.32
1375 ASP   (  66-)  K    5.26
 368 SER   (   3-)  C    5.19
 340 VAL   ( 164-)  B    5.11
 274 LYS   (  98-)  B    5.08
 259 TYR   (  83-)  B    5.05
 718 VAL   ( 164-)  E    4.92
 541 CYS   ( 163-)  D    4.55
 992 TRP   (  61-)  H    4.53
 183 PHE   (   7-)  B    4.52
 764 GLN   (   9-)  G    4.48
 866 LYS   ( 111-)  G    4.46
 918 CYS   ( 163-)  G    4.44
 109 LYS   ( 111-)  A    4.38
 983 GLU   (  52-)  H    4.36
 856 GLU   ( 101-)  G    4.31
1256 ARG   ( 123-)  J    4.22
1431 PHE   ( 122-)  K    4.21
 614 TYR   (  60-)  E    4.14
1502 SER   (   3-)  L    4.10
 652 LYS   (  98-)  E    4.06
1142 GLN   (   9-)  J    4.06

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 : 1.695

Error: Side chain planarity problems

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

1328 ASN   (  19-)  K    5.18
 122 ASN   ( 124-)  A    4.89
 240 GLN   (  64-)  B    4.83

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.

1276 HIS   ( 143-)  J      CB   4.44
 299 TYR   ( 123-)  B      CB   4.42
 521 HIS   ( 143-)  D      CB   4.34
1042 HIS   ( 111-)  H      CB   4.12
1325 HIS   (  16-)  K      CB   4.11
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.123

Torsion-related checks

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.

 111 THR   ( 113-)  A    -2.7
 368 SER   (   3-)  C    -2.7
1037 THR   ( 106-)  H    -2.6
 282 THR   ( 106-)  B    -2.6
1415 THR   ( 106-)  K    -2.6
 868 THR   ( 113-)  G    -2.6
 491 THR   ( 113-)  D    -2.6
1246 THR   ( 113-)  J    -2.5
1151 GLN   (  18-)  J    -2.4
 991 TYR   (  60-)  H    -2.4
 531 PHE   ( 153-)  D    -2.4
 396 GLN   (  18-)  D    -2.4
 773 GLN   (  18-)  G    -2.4
1149 PRO   (  16-)  J    -2.3
1466 THR   ( 157-)  K    -2.3
 303 ILE   ( 127-)  B    -2.3
1088 THR   ( 157-)  H    -2.2
1045 LEU   ( 114-)  H    -2.2
1423 LEU   ( 114-)  K    -2.2
 648 ARG   (  94-)  E    -2.2
 115 VAL   ( 117-)  A    -2.2
 753 TYR   (  11-)  F    -2.2
 681 ILE   ( 127-)  E    -2.2
1330 THR   (  21-)  K    -2.1
 662 PRO   ( 108-)  E    -2.1
1269 VAL   ( 136-)  J    -2.1
 333 THR   ( 157-)  B    -2.1
 668 LEU   ( 114-)  E    -2.1
1336 LEU   (  27-)  K    -2.1
 969 VAL   (  38-)  H    -2.1
 512 GLU   ( 134-)  D    -2.1
1436 ILE   ( 127-)  K    -2.1
 290 LEU   ( 114-)  B    -2.1
 577 ARG   (  23-)  E    -2.1
 270 ARG   (  94-)  B    -2.1
1478 GLU   ( 169-)  K    -2.1
1131 TYR   (  11-)  I    -2.1
 659 LYS   ( 105-)  E    -2.1
1058 ILE   ( 127-)  H    -2.0
 157 ASP   ( 159-)  A    -2.0
 908 PHE   ( 153-)  G    -2.0
 365 ARG   ( 189-)  B    -2.0
 711 THR   ( 157-)  E    -2.0
 514 VAL   ( 136-)  D    -2.0
1347 VAL   (  38-)  K    -2.0
 203 LEU   (  27-)  B    -2.0

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.

  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 127 THR   ( 129-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 209 ASN   (  33-)  B  Poor phi/psi
 286 GLN   ( 110-)  B  Poor phi/psi
 299 TYR   ( 123-)  B  PRO omega poor
 329 TRP   ( 153-)  B  Poor phi/psi
 368 SER   (   3-)  C  Poor phi/psi
 393 ASN   (  15-)  D  PRO omega poor
 396 GLN   (  18-)  D  Poor phi/psi
 456 ASN   (  78-)  D  Poor phi/psi
 478 ARG   ( 100-)  D  Poor phi/psi
 489 LYS   ( 111-)  D  Poor phi/psi
 491 THR   ( 113-)  D  PRO omega poor
 507 THR   ( 129-)  D  Poor phi/psi
 521 HIS   ( 143-)  D  Poor phi/psi
 587 ASN   (  33-)  E  Poor phi/psi
 644 THR   (  90-)  E  Poor phi/psi
 659 LYS   ( 105-)  E  Poor phi/psi
 664 GLN   ( 110-)  E  Poor phi/psi
And so on for a total of 60 lines.

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!

   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  16 GLN   (  18-)  A      0
  19 GLU   (  21-)  A      0
  20 PHE   (  22-)  A      0
  24 PHE   (  26-)  A      0
  30 PHE   (  32-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  92 ASN   (  94-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 101 ASN   ( 103-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
 114 VAL   ( 116-)  A      0
 121 ARG   ( 123-)  A      0
 127 THR   ( 129-)  A      0
And so on for a total of 600 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 : 2.399

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!

1099 GLY   ( 168-)  H   2.11   63
1056 GLY   ( 125-)  H   1.92   43
 679 GLY   ( 125-)  E   1.83   26
 301 GLY   ( 125-)  B   1.81   30
1434 GLY   ( 125-)  K   1.66   42

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]

  14 PRO   (  16-)  A    0.46 HIGH
  94 PRO   (  96-)  A    0.46 HIGH
 125 PRO   ( 127-)  A    0.45 HIGH
 300 PRO   ( 124-)  B    0.48 HIGH
 533 PRO   ( 155-)  D    0.18 LOW
 559 PRO   (   5-)  E    0.47 HIGH
 678 PRO   ( 124-)  E    0.45 HIGH
 771 PRO   (  16-)  G    0.45 HIGH
 936 PRO   (   5-)  H    0.45 HIGH
1039 PRO   ( 108-)  H    0.47 HIGH
1055 PRO   ( 124-)  H    0.49 HIGH
1114 PRO   ( 183-)  H    0.17 LOW
1214 PRO   (  81-)  J    0.48 HIGH
1229 PRO   (  96-)  J    0.45 HIGH
1235 PRO   ( 102-)  J    0.50 HIGH
1248 PRO   ( 115-)  J    0.47 HIGH
1272 PRO   ( 139-)  J    0.45 HIGH
1288 PRO   ( 155-)  J    0.19 LOW
1433 PRO   ( 124-)  K    0.49 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].

 341 PRO   ( 165-)  B    39.0 envelop C-delta (36 degrees)
 354 PRO   ( 178-)  B  -123.2 half-chair C-delta/C-gamma (-126 degrees)
 732 PRO   ( 178-)  E  -136.4 envelop C-delta (-144 degrees)
 737 PRO   ( 183-)  E  -114.6 envelop C-gamma (-108 degrees)
1096 PRO   ( 165-)  H    52.2 half-chair C-delta/C-gamma (54 degrees)
1474 PRO   ( 165-)  K    47.1 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 145 LYS   ( 147-)  A      NZ  <->  147 HIS   ( 149-)  A      CE1    0.48    2.62  INTRA
 902 LYS   ( 147-)  G      NZ  <->  904 HIS   ( 149-)  G      CE1    0.40    2.70  INTRA BL
1276 HIS   ( 143-)  J      CD2 <-> 1321 LYS   (  12-)  K      NZ     0.37    2.73  INTRA BL
 247 ARG   (  71-)  B      NH2 <->  376 TYR   (  11-)  C      CE2    0.35    2.75  INTRA BL
1442 ARG   ( 133-)  K      CD  <-> 1480 TYR   ( 171-)  K      CE1    0.34    2.86  INTRA BF
 247 ARG   (  71-)  B      CZ  <->  376 TYR   (  11-)  C      CE2    0.29    2.91  INTRA BL
 591 SER   (  37-)  E      O   <->  604 VAL   (  50-)  E      N      0.28    2.42  INTRA
 121 ARG   ( 123-)  A      N   <->  124 LYS   ( 126-)  A      O      0.28    2.42  INTRA BL
 949 PHE   (  18-)  H      CE2 <->  954 ARG   (  23-)  H      NH2    0.25    2.85  INTRA
 965 GLN   (  34-)  H      CG  <-> 1521 HOH   ( 215 )  H      O      0.25    2.55  INTRA BF
 284 PRO   ( 108-)  B      O   <->  287 HIS   ( 111-)  B      ND1    0.24    2.46  INTRA BF
 243 LEU   (  67-)  B      CD1 <->  376 TYR   (  11-)  C      CE2    0.24    2.96  INTRA BF
 305 VAL   ( 129-)  B      CG1 <->  349 CYS   ( 173-)  B      SG     0.24    3.16  INTRA BL
1280 LYS   ( 147-)  J      NZ  <-> 1282 HIS   ( 149-)  J      CE1    0.22    2.88  INTRA
1390 HIS   (  81-)  K      CD2 <-> 1505 ARG   (   6-)  L      CD     0.22    2.98  INTRA
1361 GLU   (  52-)  K      OE1 <-> 1364 ARG   (  55-)  K      NH2    0.22    2.48  INTRA BF
1123 SER   (   3-)  I      N   <-> 1124 ASP   (   4-)  I      N      0.22    2.38  INTRA BF
1373 GLN   (  64-)  K      O   <-> 1375 ASP   (  66-)  K      N      0.22    2.48  INTRA
 243 LEU   (  67-)  B      CD1 <->  376 TYR   (  11-)  C      CD2    0.21    2.99  INTRA BF
1502 SER   (   3-)  L      N   <-> 1503 ASP   (   4-)  L      N      0.21    2.39  INTRA BF
1138 HIS   (   5-)  J      CE1 <-> 1523 HOH   ( 202 )  J      O      0.21    2.59  INTRA
  12 LEU   (  14-)  A      O   <->   16 GLN   (  18-)  A      N      0.21    2.49  INTRA
 600 GLU   (  46-)  E      OE2 <->  602 ARG   (  48-)  E      NH1    0.21    2.49  INTRA BF
 635 HIS   (  81-)  E      CD2 <->  748 ARG   (   6-)  F      CD     0.21    2.99  INTRA
 799 ARG   (  44-)  G      NH2 <-> 1082 GLY   ( 151-)  H      O      0.20    2.50  INTRA
And so on for a total of 285 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

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.

  98 ARG   ( 100-)  A      -7.35
 855 ARG   ( 100-)  G      -7.14
 379 TYR   (  14-)  C      -7.01
 756 TYR   (  14-)  F      -6.97
1513 TYR   (  14-)  L      -6.96
1134 TYR   (  14-)  I      -6.81
 478 ARG   ( 100-)  D      -6.74
1475 ARG   ( 166-)  K      -6.51
 365 ARG   ( 189-)  B      -6.00
1070 LYS   ( 139-)  H      -5.94
 315 LYS   ( 139-)  B      -5.91
1233 ARG   ( 100-)  J      -5.86
1448 LYS   ( 139-)  K      -5.76
 693 LYS   ( 139-)  E      -5.76
1040 LEU   ( 109-)  H      -5.48
 283 GLN   ( 107-)  B      -5.47
1419 GLN   ( 110-)  K      -5.34
  48 ARG   (  50-)  A      -5.34
1038 GLN   ( 107-)  H      -5.33
 285 LEU   ( 109-)  B      -5.29
 457 TYR   (  79-)  D      -5.27
1025 ARG   (  94-)  H      -5.26
1498 ARG   ( 189-)  K      -5.25
1131 TYR   (  11-)  I      -5.25
1120 ARG   ( 189-)  H      -5.20
1097 ARG   ( 166-)  H      -5.19
1418 LEU   ( 109-)  K      -5.17
 396 GLN   (  18-)  D      -5.15
 805 ARG   (  50-)  G      -5.12
1183 ARG   (  50-)  J      -5.03
1416 GLN   ( 107-)  K      -5.03
 428 ARG   (  50-)  D      -5.01

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.

 659 LYS   ( 105-)  E       661 - GLN    107- ( E)         -4.38
 753 TYR   (  11-)  F       756 - TYR     14- ( F)         -4.97
1131 TYR   (  11-)  I      1134 - TYR     14- ( I)         -5.13
1511 HIS   (  12-)  L      1513 - TYR     14- ( L)         -5.18

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: 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

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1515 HOH   ( 204 )  A      O
1517 HOH   ( 202 )  D      O
1518 HOH   ( 206 )  E      O
1521 HOH   ( 203 )  H      O

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.

 116 ASN   ( 118-)  A
 147 HIS   ( 149-)  A
 186 GLN   (  10-)  B
 332 GLN   ( 156-)  B
 496 ASN   ( 118-)  D
 527 HIS   ( 149-)  D
 564 GLN   (  10-)  E
 635 HIS   (  81-)  E
 636 ASN   (  82-)  E
 710 GLN   ( 156-)  E
 898 HIS   ( 143-)  G
 904 HIS   ( 149-)  G
 941 GLN   (  10-)  H
1087 GLN   ( 156-)  H
1282 HIS   ( 149-)  J
1319 GLN   (  10-)  K
1421 HIS   ( 112-)  K
1465 GLN   ( 156-)  K

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.

  43 LEU   (  45-)  A      N
  45 GLU   (  47-)  A      N
  48 ARG   (  50-)  A      N
  74 ARG   (  76-)  A      NH1
 119 TRP   ( 121-)  A      NE1
 123 GLY   ( 125-)  A      N
 157 ASP   ( 159-)  A      N
 186 GLN   (  10-)  B      NE2
 205 ARG   (  29-)  B      NE
 213 SER   (  37-)  B      OG
 222 GLU   (  46-)  B      N
 227 THR   (  51-)  B      OG1
 231 ARG   (  55-)  B      NE
 247 ARG   (  71-)  B      NH2
 251 VAL   (  75-)  B      N
 287 HIS   ( 111-)  B      N
 327 GLY   ( 151-)  B      N
 365 ARG   ( 189-)  B      N
 370 TRP   (   5-)  C      NE1
 378 GLN   (  13-)  C      NE2
 395 ASP   (  17-)  D      N
 423 LEU   (  45-)  D      N
 437 ALA   (  59-)  D      N
 499 TRP   ( 121-)  D      NE1
 503 GLY   ( 125-)  D      N
And so on for a total of 75 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.

   9 GLU   (  11-)  A      OE1
  60 ASN   (  62-)  A      OD1
  64 ASP   (  66-)  A      OD2
 175 HIS   ( 177-)  A      NE2
 177 GLU   ( 179-)  A      OE1
 378 GLN   (  13-)  C      OE1
 395 ASP   (  17-)  D      OD2
 440 ASN   (  62-)  D      OD1
 590 GLU   (  36-)  E      OE2
 661 GLN   ( 107-)  E      OE1
 666 HIS   ( 112-)  E      ND1
 755 GLN   (  13-)  F      OE1
 780 ASP   (  25-)  G      OD2
 817 ASN   (  62-)  G      OD1
 821 ASP   (  66-)  G      OD2
 932 HIS   ( 177-)  G      NE2
 983 GLU   (  52-)  H      OE2
 988 ASP   (  57-)  H      OD2
1038 GLN   ( 107-)  H      OE1
1133 GLN   (  13-)  I      OE1
1195 ASN   (  62-)  J      OD1
1512 GLN   (  13-)  L      OE1

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.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  99 GLU   ( 101-)  A   H-bonding suggests Gln
 160 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 399 GLU   (  21-)  D   H-bonding suggests Gln
 444 ASP   (  66-)  D   H-bonding suggests Asn
 479 GLU   ( 101-)  D   H-bonding suggests Gln
 540 ASP   ( 162-)  D   H-bonding suggests Asn
 613 GLU   (  59-)  E   H-bonding suggests Gln
 776 GLU   (  21-)  G   H-bonding suggests Gln
 856 GLU   ( 101-)  G   H-bonding suggests Gln
 914 ASP   ( 159-)  G   H-bonding suggests Asn
 917 ASP   ( 162-)  G   H-bonding suggests Asn; but Alt-Rotamer
1100 GLU   ( 169-)  H   H-bonding suggests Gln; but Alt-Rotamer
1154 GLU   (  21-)  J   H-bonding suggests Gln
1199 ASP   (  66-)  J   H-bonding suggests Asn
1295 ASP   ( 162-)  J   H-bonding suggests Asn
1478 GLU   ( 169-)  K   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 :   0.557
  2nd generation packing quality :  -0.575
  Ramachandran plot appearance   :  -1.123
  chi-1/chi-2 rotamer normality  :  -1.930
  Backbone conformation          :   0.021

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.756
  Bond angles                    :   0.945
  Omega angle restraints         :   0.436 (tight)
  Side chain planarity           :   0.776
  Improper dihedral distribution :   1.334
  B-factor distribution          :   1.628 (loose)
  Inside/Outside distribution    :   1.040

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.45


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.5
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.756
  Bond angles                    :   0.945
  Omega angle restraints         :   0.436 (tight)
  Side chain planarity           :   0.776
  Improper dihedral distribution :   1.334
  B-factor distribution          :   1.628 (loose)
  Inside/Outside distribution    :   1.040
==============

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.