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.
Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.
39 PRO ( 42-) B - 66 GLU ( 69-) B - 213 SER ( 217-) B -
In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.
39 PRO ( 42-) B - 40 SER ( 43-) B - 66 GLU ( 69-) B - 213 SER ( 217-) B -
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: B
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.
50 GLN ( 53-) B High 217 GLU ( 221-) B High 231 GLY ( 235-) B High
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
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 : 1.622 over 1848 bonds
Average difference in B over a bond : 4.04
RMS difference in B over a bond : 5.64
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: B
Nomenclature related problems
Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
187 TYR ( 191-) B
4 PHE ( 7-) B 63 PHE ( 66-) B 127 PHE ( 131-) B 256 PHE ( 260-) B
31 ASP ( 34-) B 69 ASP ( 72-) B 72 ASP ( 75-) B
66 GLU ( 69-) B
RMS Z-score for bond lengths: 0.513
RMS-deviation in bond distances: 0.012
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 HIS ( 96-) B CG ND1 CE1 109.66 4.1
31 ASP ( 34-) B 66 GLU ( 69-) B 69 ASP ( 72-) B 72 ASP ( 75-) B
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-) B -2.5 198 PRO ( 202-) B -2.4 172 PHE ( 176-) B -2.3 159 VAL ( 163-) B -2.2 89 GLN ( 92-) B -2.1
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-) B PRO omega poor 28 VAL ( 31-) B omega poor 57 LEU ( 60-) B omega poor 61 HIS ( 64-) B Poor phi/psi 74 ALA ( 77-) B omega poor 108 LYS ( 111-) B Poor phi/psi 153 LEU ( 157-) B omega poor 174 ASN ( 178-) B Poor phi/psi 193 SER ( 197-) B omega poor 195 THR ( 199-) B omega poor 197 PRO ( 201-) B PRO omega poor 199 LEU ( 203-) B Poor phi/psi 203 VAL ( 207-) B omega poor 239 ASP ( 243-) B Poor phi/psi 248 LYS ( 252-) B Poor phi/psi chi-1/chi-2 correlation Z-score : -0.852
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 PHE ( 7-) B 0 12 HIS ( 15-) B 0 13 TRP ( 16-) B 0 16 ASP ( 19-) B 0 17 PHE ( 20-) B 0 21 LYS ( 24-) B 0 23 GLU ( 26-) B 0 24 ARG ( 27-) B 0 25 GLN ( 28-) B 0 26 SER ( 29-) B 0 47 SER ( 50-) B 0 59 ASN ( 62-) B 0 61 HIS ( 64-) B 0 69 ASP ( 72-) B 0 71 GLN ( 74-) B 0 72 ASP ( 75-) B 0 74 ALA ( 77-) B 0 77 LYS ( 80-) B 0 80 PRO ( 83-) B 0 82 ASP ( 85-) B 0 88 ILE ( 91-) B 0 89 GLN ( 92-) B 0 96 SER ( 99-) B 0 97 HIS ( 100-) B 0 98 ASP ( 101-) B 0And so on for a total of 122 lines.
10 PRO ( 13-) B 101.2 envelop C-beta (108 degrees) 18 PRO ( 21-) B -114.3 envelop C-gamma (-108 degrees) 211 PRO ( 215-) B 45.4 half-chair C-delta/C-gamma (54 degrees) 233 PRO ( 237-) B 26.6 half-chair N/C-delta (18 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.
157 VAL ( 161-) B A CG1 <-> 221 LYS ( 225-) B CD 0.46 2.74 INTRA 24 ARG ( 27-) B NE <-> 260 HOH ( 466 ) B O 0.31 2.39 INTRA 155 LYS ( 159-) B NZ <-> 173 THR ( 177-) B O 0.24 2.46 INTRA 37 TYR ( 40-) B CD1 <-> 256 PHE ( 260-) B C 0.17 3.03 INTRA 12 HIS ( 15-) B ND1 <-> 15 LYS ( 18-) B NZ 0.13 2.87 INTRA 228 ASN ( 232-) B OD1 <-> 235 GLU ( 239-) B N 0.11 2.59 INTRA 209 LYS ( 213-) B CD <-> 256 PHE ( 260-) B CE2 0.09 3.11 INTRA 232 GLU ( 236-) B CB <-> 233 PRO ( 237-) B CD 0.08 3.02 INTRA BF 69 ASP ( 72-) B OD2 <-> 120 TRP ( 123-) B NE1 0.06 2.64 INTRA BL 164 LYS ( 168-) B NZ <-> 260 HOH ( 468 ) B O 0.05 2.65 INTRA 176 ASP ( 180-) B OD2 <-> 178 ARG ( 182-) B NH2 0.04 2.66 INTRA 49 ASP ( 52-) B OD2 <-> 50 GLN ( 53-) B NE2 0.04 2.66 INTRA BF 96 SER ( 99-) B N <-> 97 HIS ( 100-) B N 0.02 2.58 INTRA BL 29 ASP ( 32-) B OD1 <-> 108 LYS ( 111-) B N 0.01 2.69 INTRA BL 97 HIS ( 100-) B C <-> 223 ARG ( 227-) B NH2 0.01 3.09 INTRA BL 104 HIS ( 107-) B NE2 <-> 190 TYR ( 194-) B OH 0.01 2.69 INTRA BL 103 GLU ( 106-) B OE2 <-> 242 ARG ( 246-) B N 0.01 2.69 INTRA BL
Chain identifier: B
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-) B -6.26 234 GLU ( 238-) B -5.07
Chain identifier: B
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: B
Water, ion, and hydrogenbond related checks
Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
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.
11 GLU ( 14-) B N 28 VAL ( 31-) B N 97 HIS ( 100-) B N 126 ASP ( 130-) B N 176 ASP ( 180-) B N 200 LEU ( 204-) B N 228 ASN ( 232-) B N 240 ASN ( 244-) B ND2 241 TRP ( 245-) B N 256 PHE ( 260-) B N Only metal coordination for 93 HIS ( 96-) B NE2
232 GLU ( 236-) B H-bonding suggests Gln
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 : -0.047 2nd generation packing quality : 0.364 Ramachandran plot appearance : -1.564 chi-1/chi-2 rotamer normality : -0.852 Backbone conformation : -1.026
Bond lengths : 0.513 (tight) Bond angles : 0.730 Omega angle restraints : 1.243 Side chain planarity : 0.621 (tight) Improper dihedral distribution : 0.765 B-factor distribution : 1.622 (loose) Inside/Outside distribution : 0.915
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 : 1.73
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -0.3 Ramachandran plot appearance : -2.0 chi-1/chi-2 rotamer normality : -1.0 Backbone conformation : -1.4
Bond lengths : 0.513 (tight) Bond angles : 0.730 Omega angle restraints : 1.243 Side chain planarity : 0.621 (tight) Improper dihedral distribution : 0.765 B-factor distribution : 1.622 (loose) Inside/Outside distribution : 0.915 ==============
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.