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.
259 MZM ( 263-) 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: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
1 HIS ( 4-) A High 251 GLN ( 255-) A High
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
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 : 1.548 over 1847 bonds
Average difference in B over a bond : 3.85
RMS difference in B over a bond : 6.12
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
55 ARG ( 58-) A
4 TYR ( 7-) A
23 GLU ( 26-) A 183 GLU ( 187-) A 235 GLU ( 239-) A
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.
11 GLU ( 14-) A C O 1.12 -5.5 235 GLU ( 239-) A C O 1.14 -4.5
RMS Z-score for bond lengths: 0.479
RMS-deviation in bond distances: 0.010
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.
1 HIS ( 4-) A CG ND1 CE1 109.61 4.0 14 HIS ( 17-) A CA CB CG 109.51 -4.3 17 PHE ( 20-) A CA CB CG 108.84 -5.0 24 ARG ( 27-) A -C N CA 114.36 -4.1 64 ASN ( 67-) A CA CB CG 117.22 4.6 71 GLN ( 74-) A CB CG CD 105.53 -4.2 82 ASP ( 85-) A CA CB CG 103.91 -8.7 83 GLY ( 86-) A -C N CA 112.39 -4.8 90 PHE ( 93-) A CA CB CG 118.72 4.9 91 HIS ( 94-) A CA CB CG 108.50 -5.3 116 HIS ( 119-) A CG ND1 CE1 109.82 4.2 119 HIS ( 122-) A CA CB CG 118.18 4.4 119 HIS ( 122-) A CG ND1 CE1 110.19 4.6 121 ASN ( 124-) A ND2 CG OD1 126.84 4.2 123 LYS ( 127-) A -C N CA 111.95 -5.4 155 LYS ( 159-) A CA CB CG 123.08 4.5 171 ASP ( 175-) A CA CB CG 117.46 4.9 215 SER ( 219-) A -C N CA 113.80 -4.4 227 PHE ( 231-) A CA CB CG 120.76 7.0
23 GLU ( 26-) A 55 ARG ( 58-) A 183 GLU ( 187-) A 235 GLU ( 239-) 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.
233 PRO ( 237-) A N -7.4 -26.80 -2.48 The average deviation= 0.911
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.
80 PRO ( 83-) A -2.7 248 LYS ( 252-) A -2.6 163 ILE ( 167-) A -2.5 42 LYS ( 45-) A -2.2 77 LYS ( 80-) A -2.2 27 PRO ( 30-) A -2.2 89 GLN ( 92-) A -2.1 147 GLY ( 151-) A -2.1 187 TYR ( 191-) A -2.0 235 GLU ( 239-) A -2.0 150 LYS ( 154-) A -2.0 159 VAL ( 163-) 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.
26 SER ( 29-) A PRO omega poor 54 LEU ( 57-) A omega poor 72 ASP ( 75-) A Poor phi/psi 81 LEU ( 84-) A omega poor 108 LYS ( 111-) A Poor phi/psi 174 ASN ( 178-) A Poor phi/psi 187 TYR ( 191-) A omega poor 193 SER ( 197-) A omega poor 197 PRO ( 201-) A PRO omega poor 199 LEU ( 203-) A Poor phi/psi 203 VAL ( 207-) A omega poor 239 ASP ( 243-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.020
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!
4 TYR ( 7-) A 0 7 HIS ( 10-) A 0 16 ASP ( 19-) A 0 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 26 SER ( 29-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 51 ALA ( 54-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 69 ASP ( 72-) A 0 70 SER ( 73-) A 0 72 ASP ( 75-) A 0 73 LYS ( 76-) A 0 74 ALA ( 77-) A 0 77 LYS ( 80-) A 0 80 PRO ( 83-) A 0 82 ASP ( 85-) A 0 88 ILE ( 91-) A 0 89 GLN ( 92-) A 0 100 GLN ( 103-) A 0 104 HIS ( 107-) A 0 108 LYS ( 111-) A 0And so on for a total of 114 lines.
18 PRO ( 21-) A 0.17 LOW 243 PRO ( 247-) A 0.18 LOW
80 PRO ( 83-) A -61.6 half-chair C-beta/C-alpha (-54 degrees) 211 PRO ( 215-) A 47.9 half-chair C-delta/C-gamma (54 degrees) 233 PRO ( 237-) A 141.0 envelop C-alpha (144 degrees)
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.
12 HIS ( 15-) A ND1 <-> 15 LYS ( 18-) A NZ 0.30 2.70 INTRA BL 1 HIS ( 4-) A ND1 <-> 260 HOH ( 411 ) A O 0.29 2.41 INTRA BF 133 GLN ( 137-) A NE2 <-> 260 HOH ( 463 ) A O 0.21 2.49 INTRA BF 186 ASP ( 190-) A OD1 <-> 260 HOH ( 444 ) A O 0.10 2.30 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.08 2.62 INTRA BL 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.07 2.63 INTRA BL 33 HIS ( 36-) A ND1 <-> 260 HOH ( 433 ) A O 0.07 2.63 INTRA 72 ASP ( 75-) A OD1 <-> 86 ARG ( 89-) A NE 0.05 2.65 INTRA 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.05 2.65 INTRA BL 164 LYS ( 168-) A NZ <-> 260 HOH ( 399 ) A O 0.04 2.66 INTRA BF 38 ASP ( 41-) A OD1 <-> 40 SER ( 43-) A OG 0.03 2.37 INTRA BF 248 LYS ( 252-) A CB <-> 249 ASN ( 253-) A N 0.03 2.67 INTRA B3 9 GLY ( 12-) A CA <-> 10 PRO ( 13-) A CD 0.02 2.78 INTRA BL 229 GLY ( 233-) A N <-> 232 GLU ( 236-) A OE1 0.02 2.68 INTRA 171 ASP ( 175-) A OD2 <-> 260 HOH ( 388 ) A O 0.01 2.39 INTRA BF 107 ASP ( 110-) A OD1 <-> 260 HOH ( 433 ) A O 0.01 2.39 INTRA 61 HIS ( 64-) A A CD2 <-> 260 HOH ( 369 ) A O 0.01 2.79 INTRA 132 GLN ( 136-) A CG <-> 260 HOH ( 462 ) A O 0.01 2.79 INTRA 52 THR ( 55-) A OG1 <-> 73 LYS ( 76-) A CE 0.01 2.79 INTRA BF
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.
7 HIS ( 10-) A -6.47 97 LEU ( 100-) A -5.16 132 GLN ( 136-) A -5.06
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 -1.76 3.00 -7.53 260 HOH ( 460 ) A O -14.21 11.32 -0.89
260 HOH ( 443 ) A O 260 HOH ( 471 ) A O Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
33 HIS ( 36-) A 174 ASN ( 178-) A 249 ASN ( 253-) A 251 GLN ( 255-) 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.
2 TRP ( 5-) A N 28 VAL ( 31-) A N 71 GLN ( 74-) A N 97 LEU ( 100-) A N 169 SER ( 173-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 241 TRP ( 245-) A N 256 PHE ( 260-) A N Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 HIS ( 119-) A ND1
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.
260 HOH ( 444 ) A O 0.82 NA 4 *2
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 : -0.291 2nd generation packing quality : 0.462 Ramachandran plot appearance : -1.326 chi-1/chi-2 rotamer normality : -1.020 Backbone conformation : -1.119
Bond lengths : 0.479 (tight) Bond angles : 1.173 Omega angle restraints : 1.065 Side chain planarity : 0.519 (tight) Improper dihedral distribution : 0.766 B-factor distribution : 1.548 (loose) Inside/Outside distribution : 0.944
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 : 1.60
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.0 2nd generation packing quality : -0.5 Ramachandran plot appearance : -1.8 chi-1/chi-2 rotamer normality : -1.4 Backbone conformation : -1.5
Bond lengths : 0.479 (tight) Bond angles : 1.173 Omega angle restraints : 1.065 Side chain planarity : 0.519 (tight) Improper dihedral distribution : 0.766 B-factor distribution : 1.548 (loose) Inside/Outside distribution : 0.944 ==============
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.