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 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.
260 RYX ( 1-) B - Atom types
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: 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'.
1 HIS ( 3-) B CG 1 HIS ( 3-) B ND1 1 HIS ( 3-) B CD2 1 HIS ( 3-) B CE1 1 HIS ( 3-) B NE2 2 HIS ( 4-) B CG 2 HIS ( 4-) B ND1 2 HIS ( 4-) B CD2 2 HIS ( 4-) B CE1 2 HIS ( 4-) B NE2 258 LYS ( 261-) B CG 258 LYS ( 261-) B CD 258 LYS ( 261-) B CE 258 LYS ( 261-) B NZ
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
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
56 ARG ( 58-) B
5 TYR ( 7-) B
64 PHE ( 66-) B
73 ASP ( 75-) B 172 ASP ( 175-) B
24 GLU ( 26-) B 67 GLU ( 69-) B
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.
124 LYS ( 127-) B N -C 1.55 11.2
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 0.994602 0.000134 -0.000473| | 0.000134 0.994401 0.000149| | -0.000473 0.000149 0.992464|Proposed new scale matrix
| 0.023615 -0.000004 0.005726| | -0.000003 0.024069 -0.000004| | 0.000007 -0.000002 0.014328|With corresponding cell
A = 42.351 B = 41.548 C = 71.824 Alpha= 89.987 Beta= 103.657 Gamma= 89.985
The CRYST1 cell dimensions
A = 42.580 B = 41.781 C = 72.348 Alpha= 90.000 Beta= 103.580 Gamma= 90.000
(Under-)estimated Z-score: 13.608
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.
105 HIS ( 107-) B CG ND1 CE1 109.68 4.1 124 LYS ( 127-) B -C N CA 113.98 -4.3 138 LEU ( 141-) B CB CG CD2 123.04 4.1
24 GLU ( 26-) B 56 ARG ( 58-) B 67 GLU ( 69-) B 73 ASP ( 75-) B 172 ASP ( 175-) B
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.
138 LEU ( 141-) B CG 7.2 -20.26 -33.01 The average deviation= 1.503
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.
199 PRO ( 202-) B -2.5 173 PHE ( 176-) B -2.2 160 VAL ( 163-) B -2.2 81 PRO ( 83-) B -2.1 164 ILE ( 167-) B -2.1 148 GLY ( 151-) B -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.
2 HIS ( 4-) B Poor phi/psi 27 SER ( 29-) B PRO omega poor 55 LEU ( 57-) B omega poor 63 ALA ( 65-) B omega poor 73 ASP ( 75-) B Poor phi/psi 74 LYS ( 76-) B Poor phi/psi 82 LEU ( 84-) B omega poor 84 GLY ( 86-) B omega poor 90 GLN ( 92-) B omega poor 109 LYS ( 111-) B Poor phi/psi 175 ASN ( 178-) B Poor phi/psi 194 SER ( 197-) B omega poor 198 PRO ( 201-) B PRO omega poor 200 LEU ( 203-) B Poor phi/psi 204 VAL ( 207-) B omega poor 240 ASP ( 243-) B Poor phi/psi 249 LYS ( 252-) B Poor phi/psi chi-1/chi-2 correlation Z-score : -0.379
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 TRP ( 5-) B 0 5 TYR ( 7-) B 0 8 HIS ( 10-) B 0 17 ASP ( 19-) B 0 18 PHE ( 20-) B 0 22 LYS ( 24-) B 0 25 ARG ( 27-) B 0 27 SER ( 29-) B 0 48 SER ( 50-) B 0 51 GLN ( 53-) B 0 52 ALA ( 54-) B 0 60 ASN ( 62-) B 0 62 HIS ( 64-) B 0 70 ASP ( 72-) B 0 71 SER ( 73-) B 0 73 ASP ( 75-) B 0 75 ALA ( 77-) B 0 78 LYS ( 80-) B 0 81 PRO ( 83-) B 0 83 ASP ( 85-) B 0 90 GLN ( 92-) B 0 101 GLN ( 103-) B 0 105 HIS ( 107-) B 0 109 LYS ( 111-) B 0 113 ALA ( 115-) B 0And so on for a total of 122 lines.
234 PRO ( 237-) B 0.46 HIGH 244 PRO ( 247-) B 0.08 LOW 247 PRO ( 250-) B 0.18 LOW
19 PRO ( 21-) B -116.8 envelop C-gamma (-108 degrees) 44 PRO ( 46-) B 109.2 envelop C-beta (108 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.
1 HIS ( 3-) B CA <-> 261 HOH ( 311 ) B O 0.32 2.48 INTRA BF 210 LYS ( 213-) B NZ <-> 261 HOH ( 373 ) B O 0.32 2.38 INTRA BF 22 LYS ( 24-) B NZ <-> 261 HOH ( 333 ) B O 0.31 2.39 INTRA BF 199 PRO ( 202-) B CD <-> 260 RYX ( 1-) B F2'1 0.23 2.97 INTRA 155 GLN ( 158-) B NE2 <-> 158 VAL ( 161-) B CG2 0.22 2.88 INTRA 159 ASP ( 162-) B OD2 <-> 261 HOH ( 461 ) B O 0.20 2.20 INTRA 13 HIS ( 15-) B ND1 <-> 16 LYS ( 18-) B NZ 0.17 2.83 INTRA 155 GLN ( 158-) B CD <-> 158 VAL ( 161-) B CG2 0.16 3.04 INTRA 254 LYS ( 257-) B NZ <-> 261 HOH ( 408 ) B O 0.16 2.54 INTRA BF 50 ASP ( 52-) B CB <-> 261 HOH ( 381 ) B O 0.12 2.68 INTRA BF 105 HIS ( 107-) B NE2 <-> 191 TYR ( 194-) B OH 0.10 2.60 INTRA BL 195 LEU ( 198-) B CD1 <-> 260 RYX ( 1-) B F2'2 0.09 3.11 INTRA 62 HIS ( 64-) B A CE1 <-> 261 HOH ( 289 ) B O 0.07 2.73 INTRA 73 ASP ( 75-) B OD1 <-> 87 ARG ( 89-) B NE 0.04 2.66 INTRA 148 GLY ( 151-) B N <-> 215 VAL ( 218-) B O 0.03 2.67 INTRA 49 TYR ( 51-) B OH <-> 120 HIS ( 122-) B NE2 0.03 2.67 INTRA BL 167 LYS ( 170-) B NZ <-> 261 HOH ( 265 ) B O 0.02 2.68 INTRA BF 155 GLN ( 158-) B O <-> 158 VAL ( 161-) B CG2 0.01 2.79 INTRA 249 LYS ( 252-) B N <-> 261 HOH ( 277 ) B O 0.01 2.69 INTRA BF 62 HIS ( 64-) B A ND1 <-> 261 HOH ( 303 ) B O 0.01 2.69 INTRA
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.
8 HIS ( 10-) B -6.19 98 LEU ( 100-) B -5.10
Chain identifier: B
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.
2 HIS ( 4-) B -2.91 252 GLN ( 255-) B -2.54
Chain identifier: B
Water, ion, and hydrogenbond related checks
Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem. The last number on each line is
the identifier of the water molecule in the input file.
261 HOH ( 279 ) B O 261 HOH ( 339 ) B O 261 HOH ( 343 ) B O 261 HOH ( 383 ) B O 261 HOH ( 399 ) B O 261 HOH ( 401 ) B O 261 HOH ( 411 ) B O Marked this atom as acceptor 260 RYX ( 1-) B F2'1 Marked this atom as acceptor 260 RYX ( 1-) B F3'1 Marked this atom as acceptor 260 RYX ( 1-) B F2'2 Marked this atom as acceptor 260 RYX ( 1-) B F3'2 Marked this atom as acceptor 260 RYX ( 1-) B F3'3 Metal-coordinating Histidine residue 92 fixed to 1 Metal-coordinating Histidine residue 94 fixed to 1 Metal-coordinating Histidine residue 117 fixed to 1
51 GLN ( 53-) B 175 ASN ( 178-) B
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.
29 VAL ( 31-) B N 43 LYS ( 45-) B N 72 GLN ( 74-) B N 98 LEU ( 100-) B N 174 THR ( 177-) B OG1 197 THR ( 200-) B N 201 LEU ( 204-) B N 227 ASN ( 230-) B ND2 241 ASN ( 244-) B ND2 242 TRP ( 245-) B N 257 PHE ( 260-) B N Only metal coordination for 94 HIS ( 96-) B NE2 Only metal coordination for 117 HIS ( 119-) B 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 : 0.188 2nd generation packing quality : 0.647 Ramachandran plot appearance : -1.313 chi-1/chi-2 rotamer normality : -0.379 Backbone conformation : -1.140
Bond lengths : 0.984 Bond angles : 0.951 Omega angle restraints : 1.235 Side chain planarity : 1.149 Improper dihedral distribution : 1.217 B-factor distribution : 0.624 Inside/Outside distribution : 0.952
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 : 0.5 2nd generation packing quality : -0.4 Ramachandran plot appearance : -1.7 chi-1/chi-2 rotamer normality : -0.7 Backbone conformation : -1.6
Bond lengths : 0.984 Bond angles : 0.951 Omega angle restraints : 1.235 Side chain planarity : 1.149 Improper dihedral distribution : 1.217 B-factor distribution : 0.624 Inside/Outside distribution : 0.952 ==============
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.