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: 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'.
62 HIS ( 64-) A CG 62 HIS ( 64-) A ND1 62 HIS ( 64-) A CD2 62 HIS ( 64-) A CE1 62 HIS ( 64-) A NE2
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
12 GLU ( 14-) A 24 GLU ( 26-) A 184 GLU ( 187-) A
RMS Z-score for bond lengths: 0.281
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.
93 PHE ( 95-) A CA CB CG 118.76 5.0
RMS Z-score for bond angles: 0.660
RMS-deviation in bond angles: 1.377
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
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.
81 PRO ( 83-) A -2.8 173 PHE ( 176-) A -2.4 2 HIS ( 4-) A -2.3 148 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 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 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 : -0.473
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 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 64 PHE ( 66-) 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 0 105 HIS ( 107-) A 0And so on for a total of 113 lines.
Standard deviation of omega values : 1.883
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.
34 HIS ( 36-) A ND1 <-> 260 HOH ( 354 ) A O 0.18 2.52 INTRA 155 GLN ( 158-) A NE2 <-> 158 VAL ( 161-) A CG2 0.17 2.93 INTRA 25 ARG ( 27-) A CG <-> 202 GLU ( 205-) A CD 0.16 3.04 INTRA BL 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.13 2.87 INTRA BL 25 ARG ( 27-) A NH1 <-> 260 HOH ( 407 ) A O 0.09 2.61 INTRA 78 LYS ( 80-) A NZ <-> 85 THR ( 87-) A CG2 0.09 3.01 INTRA 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.08 2.62 INTRA BL 78 LYS ( 80-) A NZ <-> 85 THR ( 87-) A OG1 0.08 2.62 INTRA 60 ASN ( 62-) A ND2 <-> 65 HIS ( 67-) A CE1 0.08 3.02 INTRA 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.08 2.62 INTRA BL 73 ASP ( 75-) A OD1 <-> 87 ARG ( 89-) A NE 0.07 2.63 INTRA 39 ASP ( 41-) A OD1 <-> 41 SER ( 43-) A OG 0.07 2.33 INTRA 49 TYR ( 51-) A OH <-> 120 HIS ( 122-) A NE2 0.05 2.65 INTRA BL 56 ARG ( 58-) A CG <-> 57 ILE ( 59-) A N 0.03 2.97 INTRA 20 ILE ( 22-) A O <-> 23 GLY ( 25-) A N 0.02 2.68 INTRA BL 226 LEU ( 229-) A O <-> 238 MET ( 241-) A N 0.02 2.68 INTRA BL 109 LYS ( 111-) A NZ <-> 260 HOH ( 429 ) A O 0.02 2.68 INTRA 43 LYS ( 45-) A CG <-> 44 PRO ( 46-) A CD 0.02 3.18 INTRA 111 LYS ( 113-) A NZ <-> 260 HOH ( 321 ) A O 0.01 2.69 INTRA 249 LYS ( 252-) A CB <-> 250 ASN ( 253-) A N 0.01 2.69 INTRA B3
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 -6.37 2 HIS ( 4-) A -5.70 98 LEU ( 100-) A -5.34
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.
260 HOH ( 419 ) A O -13.62 -18.76 15.31
1 HIS ( 3-) A 51 GLN ( 53-) 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 72 GLN ( 74-) A N 98 LEU ( 100-) A N 162 ASP ( 165-) A N 179 ARG ( 182-) A NH1 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 ND1 Only metal coordination for 117 HIS ( 119-) A ND1
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 : -0.365 2nd generation packing quality : 0.418 Ramachandran plot appearance : -1.540 chi-1/chi-2 rotamer normality : -0.473 Backbone conformation : -0.736
Bond lengths : 0.281 (tight) Bond angles : 0.660 (tight) Omega angle restraints : 0.342 (tight) Side chain planarity : 0.222 (tight) Improper dihedral distribution : 0.552 B-factor distribution : 0.591 Inside/Outside distribution : 0.945
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 : 1.80
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.0 2nd generation packing quality : -0.2 Ramachandran plot appearance : -1.5 chi-1/chi-2 rotamer normality : -0.2 Backbone conformation : -1.0
Bond lengths : 0.281 (tight) Bond angles : 0.660 (tight) Omega angle restraints : 0.342 (tight) Side chain planarity : 0.222 (tight) Improper dihedral distribution : 0.552 B-factor distribution : 0.591 Inside/Outside distribution : 0.945 ==============
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.