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.
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
Coordinate problems, unexpected atoms, B-factor and occupancy checks
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) :293.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
56 ARG ( 58-) A
5 TYR ( 7-) A
12 GLU ( 14-) A 24 GLU ( 26-) A 184 GLU ( 187-) A
RMS Z-score for bond lengths: 0.239
RMS-deviation in bond distances: 0.005
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.608
RMS-deviation in bond angles: 1.256
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
12 GLU ( 14-) A 24 GLU ( 26-) A 56 ARG ( 58-) A 184 GLU ( 187-) A
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
199 PRO ( 202-) A N -6.3 -23.12 -2.48 The average deviation= 0.731
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.
199 PRO ( 202-) A -3.1 81 PRO ( 83-) A -2.5 173 PHE ( 176-) A -2.2 205 THR ( 208-) A -2.2 2 HIS ( 4-) A -2.2 190 THR ( 193-) A -2.1 148 GLY ( 151-) A -2.1 90 GLN ( 92-) A -2.0
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.
27 SER ( 29-) A PRO omega poor 63 ALA ( 65-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 194 SER ( 197-) A omega poor 198 PRO ( 201-) A PRO omega poor 199 PRO ( 202-) A omega poor 200 LEU ( 203-) A Poor phi/psi 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi 250 ASN ( 253-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.162
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 17 ASP ( 19-) A 0 18 PHE ( 20-) A 0 20 ILE ( 22-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 50 ASP ( 52-) A 0 52 ALA ( 54-) A 0 60 LEU ( 62-) A 0 62 HIS ( 64-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 90 GLN ( 92-) A 0 101 GLN ( 103-) A 0And so on for a total of 115 lines.
Standard deviation of omega values : 3.749
Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone oxygen
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!
126 GLY ( 129-) A 1.87 17
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.
249 LYS ( 252-) A NZ <-> 260 HOH ( 465 ) A O 0.33 2.37 INTRA 121 TRP ( 123-) A CH2 <-> 126 GLY ( 129-) A O 0.29 2.51 INTRA BL 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.15 2.55 INTRA BL 76 VAL ( 78-) A CG2 <-> 78 LYS ( 80-) A NZ 0.14 2.96 INTRA 23 GLY ( 25-) A O <-> 249 LYS ( 252-) A NZ 0.13 2.57 INTRA 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.12 2.88 INTRA BL 194 SER ( 197-) A C <-> 204 VAL ( 207-) A CG2 0.11 3.09 INTRA BL 73 ASP ( 75-) A OD1 <-> 87 ARG ( 89-) A NE 0.09 2.61 INTRA 196 THR ( 199-) A OG1 <-> 260 HOH ( 461 ) A O 0.07 2.33 INTRA BL 158 VAL ( 161-) A CG1 <-> 222 LYS ( 225-) A CD 0.07 3.13 INTRA 249 LYS ( 252-) A CE <-> 260 HOH ( 465 ) A O 0.06 2.74 INTRA 121 TRP ( 123-) A CZ3 <-> 126 GLY ( 129-) A O 0.04 2.76 INTRA BL 118 LEU ( 120-) A O <-> 120 HIS ( 122-) A ND1 0.04 2.66 INTRA BL 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.04 2.66 INTRA BL 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.03 2.67 INTRA BL 56 ARG ( 58-) A CG <-> 57 ILE ( 59-) A N 0.03 2.97 INTRA 118 LEU ( 120-) A O <-> 120 HIS ( 122-) A CE1 0.03 2.77 INTRA BL 34 HIS ( 36-) A ND1 <-> 260 HOH ( 463 ) A O 0.02 2.68 INTRA 121 TRP ( 123-) A CZ3 <-> 126 GLY ( 129-) A C 0.01 3.19 INTRA BL
Chain identifier: A
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.
8 HIS ( 10-) A -6.43 2 HIS ( 4-) A -5.88 133 GLN ( 136-) A -5.20 98 LEU ( 100-) A -5.16 7 LYS ( 9-) A -5.12
Chain identifier: A
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
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.
15 HIS ( 17-) A 175 ASN ( 178-) A
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.
29 VAL ( 31-) A N 62 HIS ( 64-) A N 63 ALA ( 65-) A N 72 GLN ( 74-) A N 98 LEU ( 100-) A N 140 VAL ( 143-) A N 179 ARG ( 182-) A NE 197 THR ( 200-) A N 201 LEU ( 204-) A N 227 ASN ( 230-) A ND2 241 ASN ( 244-) A ND2 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
83 ASP ( 85-) A H-bonding suggests Asn
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 : -0.432 2nd generation packing quality : 0.482 Ramachandran plot appearance : -1.594 chi-1/chi-2 rotamer normality : -0.162 Backbone conformation : -0.874
Bond lengths : 0.239 (tight) Bond angles : 0.608 (tight) Omega angle restraints : 0.682 (tight) Side chain planarity : 0.220 (tight) Improper dihedral distribution : 0.624 B-factor distribution : 0.558 Inside/Outside distribution : 0.950
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 : 1.70
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -0.3 Ramachandran plot appearance : -2.0 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -1.2
Bond lengths : 0.239 (tight) Bond angles : 0.608 (tight) Omega angle restraints : 0.682 (tight) Side chain planarity : 0.220 (tight) Improper dihedral distribution : 0.624 B-factor distribution : 0.558 Inside/Outside distribution : 0.950 ==============
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.