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.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
259 BE7 ( 600-) A - Atom types 260 TRU ( 300-) A - OK
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.
235 GLU ( 239-) A -
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.
235 GLU ( 239-) 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: 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'.
6 LYS ( 9-) A CG 6 LYS ( 9-) A CD 6 LYS ( 9-) A CE 6 LYS ( 9-) A NZ 249 ASN ( 253-) A CG 249 ASN ( 253-) A OD1 249 ASN ( 253-) A ND2
251 GLN ( 255-) A High
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :103.000
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 : 1.661 over 1837 bonds
Average difference in B over a bond : 4.14
RMS difference in B over a bond : 5.96
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: 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-) A
16 ASP ( 19-) A 126 ASP ( 130-) A 161 ASP ( 165-) A
11 GLU ( 14-) A 23 GLU ( 26-) A 217 GLU ( 221-) A 232 GLU ( 236-) A
RMS Z-score for bond lengths: 0.335
RMS-deviation in bond distances: 0.007
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 109.90 4.3 12 HIS ( 15-) A CG ND1 CE1 112.07 6.5 12 HIS ( 15-) A ND1 CE1 NE2 106.48 -4.0 16 ASP ( 19-) A CA CB CG 108.56 -4.0 55 ARG ( 58-) A CD NE CZ 129.06 4.1 69 ASP ( 72-) A CA CB CG 117.56 5.0 72 ASP ( 75-) A CA CB CG 118.21 5.6 90 PHE ( 93-) A CA CB CG 121.53 7.7 104 HIS ( 107-) A CG ND1 CE1 109.64 4.0 108 LYS ( 111-) A -C N CA 129.59 4.4 116 HIS ( 119-) A CG ND1 CE1 109.97 4.4 119 HIS ( 122-) A CA CB CG 119.42 5.6 121 ASN ( 124-) A ND2 CG OD1 127.38 4.8 123 LYS ( 127-) A -O -C N 116.56 -4.0 126 ASP ( 130-) A CA CB CG 117.17 4.6 163 ILE ( 167-) A CA CB CG1 117.57 4.2 167 GLY ( 171-) A -C N CA 127.65 4.1 222 PHE ( 226-) A CA CB CG 119.52 5.7 226 ASN ( 230-) A CA CB CG 117.66 5.1 227 PHE ( 231-) A CA CB CG 118.03 4.2 245 GLN ( 249-) A -C N CA 130.09 4.7 249 ASN ( 253-) A -C N CA 129.48 4.3
11 GLU ( 14-) A 16 ASP ( 19-) A 23 GLU ( 26-) A 126 ASP ( 130-) A 161 ASP ( 165-) A 217 GLU ( 221-) A 232 GLU ( 236-) 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.
172 PHE ( 176-) A -2.5 163 ILE ( 167-) A -2.4 198 PRO ( 202-) A -2.4 248 LYS ( 252-) A -2.3 27 PRO ( 30-) A -2.2 159 VAL ( 163-) A -2.1 89 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.
26 SER ( 29-) A PRO omega poor 61 HIS ( 64-) A Poor phi/psi 62 ALA ( 65-) A Poor phi/psi 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 231 GLY ( 235-) A Poor phi/psi 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.861
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 12 HIS ( 15-) A 0 13 TRP ( 16-) 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 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 50 GLN ( 53-) A 0 59 ASN ( 62-) A 0 61 HIS ( 64-) A 0 62 ALA ( 65-) 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 89 GLN ( 92-) A 0 96 SER ( 99-) A 0And so on for a total of 118 lines.
18 PRO ( 21-) A 0.13 LOW 80 PRO ( 83-) A 0.48 HIGH
198 PRO ( 202-) A -39.2 envelop C-alpha (-36 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.
15 LYS ( 18-) A NZ <-> 261 HOH (2045 ) A O 0.20 2.50 INTRA 42 LYS ( 45-) A NZ <-> 261 HOH (2120 ) A O 0.20 2.50 INTRA BF 33 HIS ( 36-) A ND1 <-> 261 HOH (2166 ) A O 0.20 2.50 INTRA 6 LYS ( 9-) A O <-> 12 HIS ( 15-) A NE2 0.20 2.50 INTRA 68 ASP ( 71-) A OD2 <-> 73 LYS ( 76-) A NZ 0.20 2.50 INTRA BF 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.16 2.54 INTRA BL 260 TRU ( 300-) A CL19 <-> 261 HOH (2043 ) A O 0.10 2.70 INTRA 204 THR ( 208-) A OG1 <-> 261 HOH (2123 ) A O 0.10 2.30 INTRA 7 HIS ( 10-) A O <-> 261 HOH (2173 ) A O 0.10 2.30 INTRA 171 ASP ( 175-) A OD1 <-> 261 HOH (2156 ) A O 0.10 2.30 INTRA 234 GLU ( 238-) A OE1 <-> 261 HOH (2131 ) A O 0.07 2.33 INTRA BF 69 ASP ( 72-) A OD2 <-> 120 TRP ( 123-) A NE1 0.05 2.65 INTRA BL 52 THR ( 55-) A N <-> 261 HOH (2026 ) A O 0.04 2.66 INTRA 154 GLN ( 158-) A NE2 <-> 158 ASP ( 162-) A CG 0.01 3.09 INTRA 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 0.01 2.69 INTRA BL 126 ASP ( 130-) A OD1 <-> 129 LYS ( 133-) A N 0.01 2.69 INTRA
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 -6.51 97 LEU ( 100-) A -5.11
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.
261 HOH (2109 ) A O -6.45 -6.29 25.98
100 GLN ( 103-) A 174 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.
28 VAL ( 31-) A N 59 ASN ( 62-) A ND2 71 GLN ( 74-) A N 89 GLN ( 92-) A NE2 97 LEU ( 100-) A N 200 LEU ( 204-) A N 226 ASN ( 230-) A ND2 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N Only metal coordination for 61 HIS ( 64-) A ND1 Only metal coordination for 91 HIS ( 94-) A NE2 Only metal coordination for 93 HIS ( 96-) A NE2 Only metal coordination for 116 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 : 0.174 2nd generation packing quality : 0.802 Ramachandran plot appearance : -1.390 chi-1/chi-2 rotamer normality : -1.861 Backbone conformation : -0.780
Bond lengths : 0.335 (tight) Bond angles : 1.143 Omega angle restraints : 1.064 Side chain planarity : 0.391 (tight) Improper dihedral distribution : 0.606 B-factor distribution : 1.661 (loose) 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 : 1.75
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.4 2nd generation packing quality : -0.1 Ramachandran plot appearance : -2.4 chi-1/chi-2 rotamer normality : -2.6 Backbone conformation : -1.9
Bond lengths : 0.335 (tight) Bond angles : 1.143 Omega angle restraints : 1.064 Side chain planarity : 0.391 (tight) Improper dihedral distribution : 0.606 B-factor distribution : 1.661 (loose) 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.