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.
258 BE7 ( 700-) A - Atom types 260 SDA ( 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.
61 HIS ( 64-) 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.
61 HIS ( 64-) 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 50 GLN ( 53-) A CG 50 GLN ( 53-) A CD 50 GLN ( 53-) A OE1 50 GLN ( 53-) A NE2 72 ASP ( 75-) A CG 72 ASP ( 75-) A OD1 72 ASP ( 75-) A OD2 73 LYS ( 76-) A CG 73 LYS ( 76-) A CD 73 LYS ( 76-) A CE 73 LYS ( 76-) A NZ 161 ASP ( 165-) A CG 161 ASP ( 165-) A OD1 161 ASP ( 165-) A OD2
61 HIS ( 64-) A Zero
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 : 1.592 over 1825 bonds
Average difference in B over a bond : 3.18
RMS difference in B over a bond : 4.69
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: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
127 PHE ( 131-) A
16 ASP ( 19-) A 31 ASP ( 34-) A 82 ASP ( 85-) A 126 ASP ( 130-) A
23 GLU ( 26-) A 217 GLU ( 221-) A 232 GLU ( 236-) A
RMS Z-score for bond lengths: 0.427
RMS-deviation in bond distances: 0.009
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 CA CB CG 118.34 4.5 12 HIS ( 15-) A CG ND1 CE1 111.98 6.4 25 GLN ( 28-) A NE2 CD OE1 126.99 4.4 33 HIS ( 36-) A CG ND1 CE1 109.75 4.1 55 ARG ( 58-) A CB CG CD 106.00 -4.1 61 HIS ( 64-) A CA CB CG 107.11 -6.7 61 HIS ( 64-) A CG ND1 CE1 109.72 4.1 61 HIS ( 64-) A CB CG CD2 136.44 5.6 63 PHE ( 66-) A CA CB CG 118.20 4.4 82 ASP ( 85-) A CA CB CG 116.60 4.0 90 PHE ( 93-) A CA CB CG 118.88 5.1 92 PHE ( 95-) A CA CB CG 117.90 4.1 93 HIS ( 96-) A CG ND1 CE1 110.13 4.5 98 ASP ( 101-) A CA CB CG 117.26 4.7 108 LYS ( 111-) A -C N CA 129.42 4.3 126 ASP ( 130-) A CA CB CG 120.36 7.8 158 ASP ( 162-) A -C N CA 114.23 -4.2 158 ASP ( 162-) A CA CB CG 107.97 -4.6 174 ASN ( 178-) A CA CB CG 107.99 -4.6 175 PHE ( 179-) A CA CB CG 109.45 -4.3 179 GLY ( 183-) A -C N CA 128.48 4.6 186 ASP ( 190-) A -O -C N 114.32 -5.4 202 CYS ( 206-) A C CA CB 123.39 7.0 202 CYS ( 206-) A CA CB SG 125.37 4.8 203 VAL ( 207-) A -O -C N 113.30 -6.1 222 PHE ( 226-) A CA CB CG 121.92 8.1 223 ARG ( 227-) A CD NE CZ 130.90 5.1 226 ASN ( 230-) A CA CB CG 118.58 6.0 227 PHE ( 231-) A CA CB CG 122.21 8.4
16 ASP ( 19-) A 23 GLU ( 26-) A 31 ASP ( 34-) A 82 ASP ( 85-) A 126 ASP ( 130-) 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 -2.4 198 PRO ( 202-) A -2.3 163 ILE ( 167-) A -2.3 147 GLY ( 151-) A -2.1 52 THR ( 55-) A -2.1 159 VAL ( 163-) A -2.1 108 LYS ( 111-) A -2.1 248 LYS ( 252-) A -2.1 27 PRO ( 30-) 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 62 ALA ( 65-) A Poor phi/psi 73 LYS ( 76-) A Poor phi/psi 83 GLY ( 86-) A omega poor 89 GLN ( 92-) 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 202 CYS ( 206-) A omega poor 248 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.620
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 17 PHE ( 20-) A 0 21 LYS ( 24-) A 0 24 ARG ( 27-) A 0 25 GLN ( 28-) A 0 26 SER ( 29-) A 0 35 ALA ( 38-) A 0 47 SER ( 50-) A 0 49 ASP ( 52-) A 0 50 GLN ( 53-) A 0 51 ALA ( 54-) 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 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 96 SER ( 99-) A 0And so on for a total of 123 lines.
243 PRO ( 247-) A 0.16 LOW
191 PRO ( 195-) A -64.9 envelop C-beta (-72 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.
6 LYS ( 9-) A O <-> 12 HIS ( 15-) A NE2 0.22 2.48 INTRA 33 HIS ( 36-) A ND1 <-> 261 HOH (2221 ) A O 0.20 2.50 INTRA 150 LYS ( 154-) A NZ <-> 261 HOH (2267 ) A O 0.20 2.50 INTRA 164 LYS ( 168-) A NZ <-> 261 HOH (2104 ) A O 0.20 2.50 INTRA BF 83 GLY ( 86-) A N <-> 261 HOH (2127 ) A O 0.16 2.54 INTRA 21 LYS ( 24-) A NZ <-> 261 HOH (2285 ) A O 0.12 2.58 INTRA 221 LYS ( 225-) A NZ <-> 261 HOH (2235 ) A O 0.11 2.59 INTRA 4 TYR ( 7-) A O <-> 261 HOH (2244 ) A O 0.11 2.29 INTRA 34 THR ( 37-) A O <-> 261 HOH (2224 ) A O 0.10 2.30 INTRA 49 ASP ( 52-) A CB <-> 178 ARG ( 182-) A NH1 0.10 3.00 INTRA 186 ASP ( 190-) A OD1 <-> 261 HOH (2175 ) A O 0.10 2.30 INTRA 176 ASP ( 180-) A OD2 <-> 178 ARG ( 182-) A NH2 0.10 2.60 INTRA 77 LYS ( 80-) A NZ <-> 261 HOH (2277 ) A O 0.10 2.60 INTRA BF 104 HIS ( 107-) A NE2 <-> 190 TYR ( 194-) A OH 0.09 2.61 INTRA BL 100 GLN ( 103-) A NE2 <-> 239 ASP ( 243-) A OD1 0.07 2.63 INTRA BL 174 ASN ( 178-) A N <-> 261 HOH (2095 ) A O 0.04 2.66 INTRA 48 TYR ( 51-) A OH <-> 119 HIS ( 122-) A NE2 0.03 2.67 INTRA BL 114 GLU ( 117-) A OE2 <-> 116 HIS ( 119-) A NE2 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.
71 GLN ( 74-) A -6.92 7 HIS ( 10-) A -6.58 97 LEU ( 100-) A -5.23
Chain identifier: A
Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation packing check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the unusual
residues in the structure, so it will be interesting to take a
special look at them.
73 LYS ( 76-) A -3.20 123 LYS ( 127-) A -3.10 248 LYS ( 252-) A -2.59 50 GLN ( 53-) A -2.54
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 (2116 ) A O 6.50 -17.05 18.86 261 HOH (2228 ) A O -6.50 -5.72 26.19 261 HOH (2236 ) A O 7.36 22.11 15.32 261 HOH (2248 ) A O 17.95 2.25 42.38
261 HOH (2172 ) A O 261 HOH (2243 ) A O 261 HOH (2279 ) A O Marked this atom as acceptor 260 SDA ( 300-) A CL8 Marked this atom as acceptor 260 SDA ( 300-) A CL9 Metal-coordinating Histidine residue 91 fixed to 1 Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 116 fixed to 1
174 ASN ( 178-) 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.
28 VAL ( 31-) A N 37 TYR ( 40-) A N 71 GLN ( 74-) A N 86 ARG ( 89-) A NE 97 LEU ( 100-) A N 196 THR ( 200-) A N 200 LEU ( 204-) A N 223 ARG ( 227-) A NH1 226 ASN ( 230-) A ND2 228 ASN ( 232-) A N 240 ASN ( 244-) A ND2 241 TRP ( 245-) A N 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 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.
261 HOH (2117 ) A O 1.03 K 4 261 HOH (2154 ) A O 1.03 K 6 Ion-B 261 HOH (2264 ) A O 0.92 K 5 Ion-B
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 : -0.072 2nd generation packing quality : 0.382 Ramachandran plot appearance : -1.200 chi-1/chi-2 rotamer normality : -0.620 Backbone conformation : -1.251
Bond lengths : 0.427 (tight) Bond angles : 1.239 Omega angle restraints : 1.122 Side chain planarity : 0.661 (tight) Improper dihedral distribution : 0.680 B-factor distribution : 1.592 (loose) Inside/Outside distribution : 0.966
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 : 1.65
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.5 Ramachandran plot appearance : -1.2 chi-1/chi-2 rotamer normality : -0.9 Backbone conformation : -1.5
Bond lengths : 0.427 (tight) Bond angles : 1.239 Omega angle restraints : 1.122 Side chain planarity : 0.661 (tight) Improper dihedral distribution : 0.680 B-factor distribution : 1.592 (loose) Inside/Outside distribution : 0.966 ==============
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.