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.
261 667 ( 264-) A -
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) :298.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. 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 lengths: 0.255
RMS-deviation in bond distances: 0.006
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 HIS ( 4-) A CG ND1 CE1 109.72 4.1
RMS Z-score for bond angles: 0.654
RMS-deviation in bond angles: 1.404
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.
204 VAL ( 207-) A 4.17 4 GLY ( 6-) A 4.13
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.
98 LEU ( 100-) A -2.5 81 PRO ( 83-) A -2.3 58 LEU ( 60-) A -2.2 173 PHE ( 176-) A -2.2 65 ASN ( 67-) A -2.1 90 GLN ( 92-) A -2.1 160 VAL ( 163-) A -2.1 28 PRO ( 30-) 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 74 LYS ( 76-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.465
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 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 52 ALA ( 54-) A 0 56 ARG ( 58-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 63 ALA ( 65-) A 0 64 PHE ( 66-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 72 GLN ( 74-) 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 0And so on for a total of 111 lines.
Standard deviation of omega values : 1.386
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!
232 GLY ( 235-) A 1.76 66 126 GLY ( 129-) A 1.61 21
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.
2 HIS ( 4-) A CE1 <-> 3 TRP ( 5-) A O 0.46 2.24 INTRA 2 HIS ( 4-) A ND1 <-> 3 TRP ( 5-) A O 0.38 2.22 INTRA 196 THR ( 199-) A OG1 <-> 261 667 ( 264-) A N1 0.28 2.42 INTRA BL 2 HIS ( 4-) A ND1 <-> 3 TRP ( 5-) A N 0.23 2.67 INTRA BF 165 LYS ( 168-) A NZ <-> 225 LYS ( 228-) A O 0.16 2.54 INTRA 50 ASP ( 52-) A C <-> 51 GLN ( 53-) A NE2 0.15 2.85 INTRA BF 1 HIS ( 3-) A CD2 <-> 2 HIS ( 4-) A N 0.14 2.86 INTRA BF 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.13 2.57 INTRA BL 72 GLN ( 74-) A C <-> 74 LYS ( 76-) A N 0.12 2.78 INTRA BF 99 ASP ( 101-) A OD1 <-> 224 ARG ( 227-) A NH2 0.11 2.59 INTRA 56 ARG ( 58-) A NE <-> 67 GLU ( 69-) A OE1 0.10 2.60 INTRA 4 GLY ( 6-) A N <-> 9 ASN ( 11-) A O 0.08 2.62 INTRA BL 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.06 2.64 INTRA 98 LEU ( 100-) A CD1 <-> 100 GLY ( 102-) A N 0.06 3.04 INTRA 72 GLN ( 74-) A O <-> 74 LYS ( 76-) A N 0.06 2.64 INTRA BF 15 HIS ( 17-) A ND1 <-> 262 HOH ( 336 ) A O 0.06 2.64 INTRA 74 LYS ( 76-) A CB <-> 75 ALA ( 77-) A N 0.05 2.65 INTRA BF 177 ASP ( 180-) A OD2 <-> 179 ARG ( 182-) A NH2 0.04 2.66 INTRA 165 LYS ( 168-) A CE <-> 227 ASN ( 230-) A ND2 0.03 3.07 INTRA 50 ASP ( 52-) A OD2 <-> 51 GLN ( 53-) A NE2 0.03 2.67 INTRA BF 27 SER ( 29-) A O <-> 243 ARG ( 246-) A NH1 0.03 2.67 INTRA BL 34 HIS ( 36-) A CE1 <-> 262 HOH ( 285 ) A O 0.02 2.78 INTRA 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.02 2.68 INTRA BL 20 ILE ( 22-) A C <-> 22 LYS ( 24-) A N 0.01 2.89 INTRA BL 28 PRO ( 30-) A O <-> 246 GLN ( 249-) A N 0.01 2.69 INTRA BL 94 HIS ( 96-) A ND1 <-> 241 ASN ( 244-) A O 0.01 2.69 INTRA BL 20 ILE ( 22-) A O <-> 23 GLY ( 25-) A N 0.01 2.69 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 -6.05 98 LEU ( 100-) A -5.13 2 HIS ( 4-) A -5.10 72 GLN ( 74-) A -5.04 133 GLN ( 136-) A -5.04
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
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
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. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
262 HOH ( 382 ) A O 38.51 25.56 30.73 262 HOH ( 409 ) A O 38.43 22.20 30.15 262 HOH ( 423 ) A O 28.78 13.40 11.89
8 HIS ( 10-) 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 43 LYS ( 45-) A N 51 GLN ( 53-) A N 74 LYS ( 76-) A N 98 LEU ( 100-) A N 165 LYS ( 168-) A N 179 ARG ( 182-) A NE 197 THR ( 200-) A N 201 LEU ( 204-) A N 241 ASN ( 244-) A ND2 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 62 HIS ( 64-) A NE2 Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
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.
227 ASN ( 230-) A OD1
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+.
259 ZN ( 262-) A -.- -.- Too few ligands (2) 260 ZN ( 263-) A -.- -.- Too few ligands (2)
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
262 HOH ( 267 ) A O 1.04 K 4
159 ASP ( 162-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -0.549 2nd generation packing quality : -0.048 Ramachandran plot appearance : -1.590 chi-1/chi-2 rotamer normality : -1.465 Backbone conformation : -1.041
Bond lengths : 0.255 (tight) Bond angles : 0.654 (tight) Omega angle restraints : 0.252 (tight) Side chain planarity : 0.227 (tight) Improper dihedral distribution : 0.573 B-factor distribution : 0.645 Inside/Outside distribution : 0.958
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 : 1.95
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -0.6 Ramachandran plot appearance : -1.6 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : -2.0
Bond lengths : 0.255 (tight) Bond angles : 0.654 (tight) Omega angle restraints : 0.252 (tight) Side chain planarity : 0.227 (tight) Improper dihedral distribution : 0.573 B-factor distribution : 0.645 Inside/Outside distribution : 0.958 ==============
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.