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.
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
20 ASP ( 20 ) CA -5.2 22.1 34.0 90 ALA ( 93 ) CA -4.1 26.8 34.4 121 LYS ( 124 ) CA -4.5 24.9 34.3 123 TRP ( 126 ) CA -4.9 22.4 34.3
34 THR ( 34 ) C 159 LYS ( 162 ) C
20 ASP ( 20 ) CA CB CG 117.628 5.0 25 TYR ( 25 ) C CA CB 118.406 4.4 31 HIS ( 31 ) CA CB CG 108.660 -5.1 50 ASN ( 53 ) CA CB CG 107.674 -4.9 111 PHE ( 114 ) CA CB CG 117.935 4.1
83 PRO ( 86 ) 0.10 LOW 140 PRO ( 143 ) 0.16 LOW
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.
27 ILE ( 27 ) -2.6171 21 THR ( 21 ) -2.4165 121 LYS ( 124 ) -2.3458 22 GLU ( 22 ) -2.2220 14 ARG ( 14 ) -2.1030
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.
52 ASN ( 55 ) Poor phi/psi
Standard deviation of omega values : 2.402
Note: Ramachandran plot
In this Ramachandran plot X-signs represent glycines, squares represent
prolines and small plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse).
In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. "Allowed" regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green.
Chain without chain identifier
Accessibility related checks
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 without chain identifier
Bump checks
Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually
short distance.
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 centers 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 criterium 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 aren't there anyway.
Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction.
162 CL ( 173 ) CL -- 174 HOH ( 291 ) 1.117 1.683 INTER 16 LYS ( 16 ) O -- 17 ILE ( 17 ) C 0.325 2.475 INTRA BF 25 TYR ( 25 ) N -- 34 THR ( 34 ) CG2 0.310 2.790 INTRA BF 14 ARG ( 14 ) NH1 -- 167 HOH ( 236 ) 0.251 2.299 INTRA BF 17 ILE ( 17 ) CG2 -- 18 TYR ( 18 ) N 0.246 2.854 INTRA 69 ASP ( 72 ) OD2 -- 93 ARG ( 96 ) NH1 0.241 2.309 INTER HB 16 LYS ( 16 ) CE -- 54 VAL ( 57 ) CG2 0.212 2.988 INTRA BF 82 LYS ( 85 ) N -- 83 PRO ( 86 ) CD 0.207 2.793 INTRA 16 LYS ( 16 ) CD -- 54 VAL ( 57 ) CG2 0.207 2.993 INTRA BF 99 MET ( 102 ) CE -- 103 MET ( 106 ) CE 0.200 3.000 INTRA 11 GLU ( 11 ) OE2 -- 142 ARG ( 145 ) NH1 0.195 2.355 INTRA HB 26 THR ( 26 ) CG2 -- 27 ILE ( 27 ) N 0.167 2.933 INTRA 20 ASP ( 20 ) O -- 23 GLY ( 23 ) N 0.162 2.388 INTRA BF 137 ASN ( 140 ) ND2 -- 171 HOH ( 300 ) 0.156 2.394 INTRA HB 62 LYS ( 65 ) NZ -- 173 HOH ( 273 ) 0.147 2.403 INTER BF 45 LYS ( 48 ) CE -- 174 HOH ( 197 ) 0.136 2.664 INTER 142 ARG ( 145 ) O -- 143 ALA ( 146 ) C 0.131 2.669 INTRA 129 ASN ( 132 ) O -- 130 LEU ( 133 ) C 0.118 2.682 INTRA 73 ARG ( 76 ) CD -- 171 HOH ( 328 ) 0.113 2.687 INTER BF 74 GLY ( 77 ) O -- 75 ILE ( 78 ) C 0.110 2.690 INTRA 20 ASP ( 20 ) C -- 22 GLU ( 22 ) N 0.109 2.791 INTRA BF 11 GLU ( 11 ) CD -- 142 ARG ( 145 ) NH1 0.104 2.996 INTRA 49 ARG ( 52 ) NH2 -- 167 HOH ( 196 ) 0.098 2.452 INTRA BF 51 THR ( 54 ) C -- 53 GLY ( 56 ) N 0.098 2.802 INTRA BF 1 MET ( 1 ) CG -- 155 TRP ( 158 ) CD2 0.094 3.106 INTRA BFAnd so on for a total of 65 lines
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.
77 ARG ( 80 ) -5.75 138 GLN ( 141 ) -5.53 151 ARG ( 154 ) -5.33 102 GLN ( 105 ) -5.23 132 LYS ( 135 ) -5.17
Chain without chain identifier
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 without chain identifier
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 constraints on the neighboring 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!
32 LEU ( 32 ) 3.19 19 81 LEU ( 84 ) 2.75 53 10 ASP ( 10 ) 2.43 51 151 ARG ( 154 ) 2.26 47 12 GLY ( 12 ) 2.13 11 138 GLN ( 141 ) 2.04 18 141 ASN ( 144 ) 1.85 80 55 ILE ( 58 ) 1.55 31
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!
21 THR ( 21 ) 0 29 ILE ( 29 ) 0 47 ILE ( 50 ) 0 103 MET ( 106 ) 0 111 PHE ( 114 ) 0 155 TRP ( 158 ) 0 27 ILE ( 27 ) 1 132 LYS ( 135 ) 1 51 THR ( 54 ) 2 139 THR ( 142 ) 2
172 HOH ( 325 ) 172 HOH ( 333 ) 173 HOH ( 334 )
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation.
168 HOH ( 246 ) 32.843 17.969 -11.651 171 HOH ( 324 ) 34.130 -2.577 9.400 171 HOH ( 328 ) 23.817 -3.141 9.908 172 HOH ( 325 ) 29.178 24.440 16.767 172 HOH ( 326 ) 46.775 21.536 33.679 172 HOH ( 329 ) 43.881 20.882 35.381 172 HOH ( 333 ) 29.282 18.611 2.894 173 HOH ( 296 ) 41.751 6.727 26.081 173 HOH ( 297 ) 40.329 9.145 28.929 173 HOH ( 334 ) 48.343 -1.238 13.371 174 HOH ( 327 ) 39.908 23.082 3.638 174 HOH ( 332 ) 46.431 12.675 5.467
167 HOH ( 304 ) 168 HOH ( 246 ) 169 HOH ( 227 ) 169 HOH ( 283 ) 169 HOH ( 294 ) 169 HOH ( 295 ) 172 HOH ( 303 ) 172 HOH ( 325 ) 172 HOH ( 326 ) 172 HOH ( 329 ) 172 HOH ( 333 ) 173 HOH ( 250 ) 173 HOH ( 271 ) 173 HOH ( 334 )
RMS Z-score : 3.496 over 1020 bonds
Average difference in B over a bond : 8.86
RMS difference in B over a bond : 13.34
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of
the residue number.
Chain without chain identifier
Hydrogen bond 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 favorable 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. If a
residue is marked ``flexible'' the flipped conformation is only
slightly better than the non-flipped conformation.
50 ASN ( 53 ) 137 ASN ( 140 )
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.
2 ASN ( 2 ) N 25 TYR ( 25 ) N 89 ASP ( 92 ) N
The second part of the table mostly gives an impression of how well the model conforms to common refinement constraint values. The first part of the table shows a number of constraint-independent quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.913 2nd generation packing quality : 1.482 Ramachandran plot appearance : -0.520 chi-1/chi-2 rotamer normality : -1.413 Backbone conformation : -0.382
Bond lengths : 0.887 Bond angles : 1.143 Omega angle restraints : 0.437 (tight) Side chain planarity : 0.934 Improper dihedral distribution : 1.065 B-factor distribution : 3.496 (loose) Inside/Outside distribution : 0.931
The second part of the table mostly gives an impression of how well the model conforms to common refinement constraint values. The first part of the table shows a number of constraint-independent quality indicators, which have been calibrated against structures of similar resolution.
Resolution found in PDB file : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : 1.4 2nd generation packing quality : 0.6 Ramachandran plot appearance : -0.2 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : -0.7
Bond lengths : 0.887 Bond angles : 1.143 Omega angle restraints : 0.437 (tight) Side chain planarity : 0.934 Improper dihedral distribution : 1.065 B-factor distribution : 3.496 (loose) Inside/Outside distribution : 0.931