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.
257 BE7 ( 503-) A - Atom types 258 BE9 ( 502-) 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.
215 SER ( 220-) 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.
215 SER ( 220-) 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'.
5 LYS ( 9-) A CG 5 LYS ( 9-) A CD 5 LYS ( 9-) A CE 5 LYS ( 9-) A NZ 41 LYS ( 45-) A CG 41 LYS ( 45-) A CD 41 LYS ( 45-) A CE 41 LYS ( 45-) A NZ 48 ASP ( 52-) A CG 48 ASP ( 52-) A OD1 48 ASP ( 52-) A OD2 49 GLN ( 53-) A CG 49 GLN ( 53-) A CD 49 GLN ( 53-) A OE1 49 GLN ( 53-) A NE2 167 LYS ( 172-) A CG 167 LYS ( 172-) A CD 167 LYS ( 172-) A CE 167 LYS ( 172-) A NZ 234 GLU ( 239-) A CG 234 GLU ( 239-) A CD 234 GLU ( 239-) A OE1 234 GLU ( 239-) A OE2
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :110.000
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 6.03
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
23 ARG ( 27-) A 54 ARG ( 58-) A
126 PHE ( 131-) A
125 ASP ( 130-) A 170 ASP ( 175-) A
216 GLU ( 221-) A 231 GLU ( 236-) 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.
23 ARG ( 27-) A CD NE 1.37 -5.1
RMS Z-score for bond lengths: 0.512
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.
11 HIS ( 15-) A CG ND1 CE1 116.90 11.3 11 HIS ( 15-) A ND1 CE1 NE2 103.34 -6.4 11 HIS ( 15-) A CD2 CG ND1 100.88 -5.2 11 HIS ( 15-) A CB CG CD2 136.81 5.9 23 ARG ( 27-) A N CA CB 100.73 -5.7 23 ARG ( 27-) A C CA CB 121.68 6.1 23 ARG ( 27-) A CG CD NE 123.38 7.6 23 ARG ( 27-) A CD NE CZ 168.43 26.0 23 ARG ( 27-) A NH1 CZ NH2 112.37 -4.1 32 HIS ( 36-) A CG ND1 CE1 111.49 5.9 63 ASN ( 67-) A CA CB CG 104.54 -8.1 63 ASN ( 67-) A ND2 CG OD1 128.60 6.0 70 GLN ( 74-) A -C N CA 129.72 4.5 70 GLN ( 74-) A NE2 CD OE1 126.67 4.1 71 ASP ( 75-) A CA CB CG 117.03 4.4 89 PHE ( 93-) A CA CB CG 118.64 4.8 90 HIS ( 94-) A CA CB CG 109.47 -4.3 90 HIS ( 94-) A CG ND1 CE1 109.81 4.2 103 HIS ( 107-) A CA CB CG 109.53 -4.3 115 HIS ( 119-) A CG ND1 CE1 110.82 5.2 120 ASN ( 124-) A ND2 CG OD1 127.27 4.7 125 ASP ( 130-) A CA CB CG 117.16 4.6 157 ASP ( 162-) A CA CB CG 120.16 7.6 173 ASN ( 178-) A CB CG ND2 109.88 -4.3 185 ASP ( 190-) A -O -C N 112.59 -6.5 185 ASP ( 190-) A -CA -C N 126.14 5.0 185 ASP ( 190-) A -C N CA 136.80 8.4 185 ASP ( 190-) A N CA CB 118.22 4.5 185 ASP ( 190-) A CA CB CG 117.74 5.1 186 TYR ( 191-) A -O -C N 115.36 -4.8 186 TYR ( 191-) A -C N CA 129.79 4.5 221 PHE ( 226-) A CA CB CG 120.45 6.6 225 ASN ( 230-) A CA CB CG 119.74 7.1 226 PHE ( 231-) A CA CB CG 119.19 5.4 248 ASN ( 253-) A CA CB CG 126.89 14.3 250 GLN ( 255-) A CG CD OE1 129.88 4.5 250 GLN ( 255-) A NE2 CD OE1 117.10 -5.5
23 ARG ( 27-) A 54 ARG ( 58-) A 125 ASP ( 130-) A 170 ASP ( 175-) A 216 GLU ( 221-) A 231 GLU ( 236-) A
63 ASN ( 67-) A 5.21
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.
23 ARG ( 27-) A -2.7 88 GLN ( 92-) A -2.2 197 PRO ( 202-) A -2.2 171 PHE ( 176-) A -2.1 158 VAL ( 163-) A -2.1 146 GLY ( 151-) 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.
25 SER ( 29-) A PRO omega poor 88 GLN ( 92-) A omega poor 91 PHE ( 95-) A omega poor 107 LYS ( 111-) A Poor phi/psi 173 ASN ( 178-) A Poor phi/psi 186 TYR ( 191-) A omega poor 192 SER ( 197-) A omega poor 196 PRO ( 201-) A PRO omega poor 198 LEU ( 203-) A Poor phi/psi 201 CYS ( 206-) A omega poor 202 VAL ( 207-) A omega poor 210 PRO ( 215-) A omega poor 238 ASP ( 243-) A Poor phi/psi 247 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : 0.139
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 TYR ( 7-) A 0 6 HIS ( 10-) A 0 15 ASP ( 19-) A 0 16 PHE ( 20-) A 0 20 LYS ( 24-) A 0 23 ARG ( 27-) A 0 24 GLN ( 28-) A 0 25 SER ( 29-) A 0 34 ALA ( 38-) A 0 46 SER ( 50-) A 0 49 GLN ( 53-) A 0 50 ALA ( 54-) A 0 58 ASN ( 62-) A 0 60 HIS ( 64-) A 0 62 PHE ( 66-) A 0 68 ASP ( 72-) A 0 69 SER ( 73-) A 0 71 ASP ( 75-) A 0 72 LYS ( 76-) A 0 73 ALA ( 77-) A 0 76 LYS ( 80-) A 0 79 PRO ( 83-) A 0 81 ASP ( 85-) A 0 88 GLN ( 92-) A 0 95 SER ( 99-) A 0And so on for a total of 115 lines.
232 PRO ( 237-) A 0.48 HIGH 242 PRO ( 247-) A 0.11 LOW
9 PRO ( 13-) A 101.5 envelop C-beta (108 degrees) 17 PRO ( 21-) A -121.7 half-chair C-delta/C-gamma (-126 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.
32 HIS ( 36-) A ND1 <-> 259 HOH (1073 ) A O 0.22 2.48 INTRA 41 LYS ( 45-) A O <-> 259 HOH (1070 ) A O 0.11 2.29 INTRA 22 GLU ( 26-) A OE1 <-> 259 HOH (1059 ) A O 0.10 2.30 INTRA 10 GLU ( 14-) A OE2 <-> 259 HOH (1127 ) A O 0.10 2.30 INTRA 103 HIS ( 107-) A NE2 <-> 189 TYR ( 194-) A OH 0.09 2.61 INTRA BL 42 PRO ( 46-) A O <-> 259 HOH (1080 ) A O 0.09 2.31 INTRA 170 ASP ( 175-) A OD1 <-> 259 HOH (1137 ) A O 0.08 2.32 INTRA 257 BE7 ( 503-) A HG <-> 259 HOH (1028 ) A O 0.06 2.74 INTRA 113 GLU ( 117-) A OE2 <-> 115 HIS ( 119-) A NE2 0.05 2.65 INTRA BL 228 GLY ( 233-) A N <-> 231 GLU ( 236-) A OE1 0.04 2.66 INTRA 54 ARG ( 58-) A NH2 <-> 65 GLU ( 69-) A OE2 0.04 2.66 INTRA 49 GLN ( 53-) A N <-> 259 HOH (1147 ) A O 0.02 2.68 INTRA 30 ASP ( 34-) A OD2 <-> 259 HOH (1139 ) A O 0.02 2.38 INTRA 65 GLU ( 69-) A OE2 <-> 259 HOH (1156 ) A O 0.01 2.39 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.
6 HIS ( 10-) A -6.59 96 LEU ( 100-) A -5.25
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.
41 LYS ( 45-) A -2.92
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.
259 HOH (1229 ) A O 16.91 23.50 14.82
131 GLN ( 136-) A 173 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.
27 VAL ( 31-) A N 36 TYR ( 40-) A N 47 TYR ( 51-) A N 63 ASN ( 67-) A ND2 70 GLN ( 74-) A N 96 LEU ( 100-) A N 199 LEU ( 204-) A N 222 ARG ( 227-) A NH1 225 ASN ( 230-) A ND2 239 ASN ( 244-) A ND2 240 TRP ( 245-) A N Only metal coordination for 90 HIS ( 94-) A NE2 Only metal coordination for 92 HIS ( 96-) A NE2 Only metal coordination for 115 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.
259 HOH (1001 ) A O 1.06 K 4 259 HOH (1057 ) A O 0.97 K 4 259 HOH (1139 ) A O 0.94 NA 6 Ion-B 259 HOH (1208 ) A O 0.90 K 4 Ion-B
157 ASP ( 162-) A H-bonding suggests Asn; but Alt-Rotamer
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 : -0.046 2nd generation packing quality : 0.374 Ramachandran plot appearance : -1.442 chi-1/chi-2 rotamer normality : 0.139 Backbone conformation : -0.937
Bond lengths : 0.512 (tight) Bond angles : 1.265 Omega angle restraints : 1.152 Side chain planarity : 0.812 Improper dihedral distribution : 0.748 Inside/Outside distribution : 0.964
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 : 1.40
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.2 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.8 chi-1/chi-2 rotamer normality : -0.4 Backbone conformation : -1.3
Bond lengths : 0.512 (tight) Bond angles : 1.265 Omega angle restraints : 1.152 Side chain planarity : 0.812 Improper dihedral distribution : 0.748 Inside/Outside distribution : 0.964 ==============
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.