Compositions of hepatitis C virus NS5B polymerase and methods for crystallizing same

Information

  • Patent Grant
  • 6434489
  • Patent Number
    6,434,489
  • Date Filed
    Monday, April 3, 2000
    24 years ago
  • Date Issued
    Tuesday, August 13, 2002
    21 years ago
Abstract
The invention relates to the purification, crystallization of and structure of hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase. Also, crystallization conditions for NS5B are provided. Further, the atomic coordinates for the NS5B protein are disclosed. Examples of its use for the determination of the three-dimensional atomic structures of HCV NS5B or HCV NS5B in complex with substrates or substrate analogs or inhibitors are also provided.
Description




FIELD OF THE INVENTION




The present invention relates to compositions and crystals of a hepatitis C virus RNA dependent RNA polymerase called NS5B and to methods of producing such crystals. This invention relates to methods of using the structure coordinates of hepatitis C virus NS5B to solve the structure of homologous NS5B proteins or complexes containing the NS5B protein.




BACKGROUND OF THE INVENTION




Infection by hepatitis C virus (HCV) is a compelling human medical problem. HCV is recognized as the causative agent for most cases of non-A and non-B hepatitis, with an estimated human seroprevalence of 1% globally [Choo, et al.,


Science,


244:359-362 (1989); Kuo, et al.,


Science,


244:362-364 (1989); Purcell,


FEMS Microbiology Reviews;


14:181-191 (1994); Van der Poel.


Current Studies in Hematology and Blood Transfusion


, H. W. Reesink, Ed., (Basel: Karger), pp. 137-163 (1994)]. Four million individuals may be infected in the United States alone [Alter, and Mast,


Gastroenterol. Clin. North Am.,


23:437-455 (1994)].




Upon first exposure to HCV, only about 20% of infected individuals develop acute hepatitis and appear to resolve the infection spontaneously. In the most instances (˜80%), however, the virus establishes a chronic infection that persists for decades [Iwarson,


FEMS Microbiology Reviews,


14: 201-204 (1994)]. This usually results in recurrent and progressively worsening liver inflammation, which often leads to more severe disease states such as cirrhosis and hepatocellular carcinoma [Kew,


FEMS Microbiology Reviews,


14: 211-219 (1994); Saito, et al.,


Proc. Natl. Acad. Sci. USA


87: 6547-6549 (1990)].




The HCV genome encodes a polyprotein of approximately 3000 amino acids [Choo, et al.


Proc. Natl. Acad. Sci. USA,


88: 2451-2455 (1991); Kato, et al.,


Proc. Natl. Acad. Sci. USA,


87: 9524-9528 (1990); Takamizawa, et al.,


J. Virol.,


65:1105-113 (1991)]. The HCV non-structural (NS) proteins provide catalytic machinery for viral replication. The NS proteins are derived by proteolytic cleavage of the polyprotein [Bartenschlager, et al.,


J. Virol.,


67: 3835-3844 (1993); Grakoui, et al.,


J. Virol,


67: 2832-2843 (1993); Grakoui, et al.,


J. Virol.,


67:1385-1395 (1993); Tomei, et al.,


J. Virol.,


67:4017-4026 (1993)].




Until recently, the only therapy available for treating chronic HCV infection was interferon-α (IFN-α). However, not all patients are responsive to IFN-α treatment. While combination therapy of IFN-α and ribavirin has significantly improved the clinical outcome, a need exists for more effective methods of treatment.




The NS5B RNA dependent RNA polymerase is considered a valuable target for antiviral agents. However, drug discovery efforts directed towards the NS5B protein have been hampered by the lack of structural information about NS5B. Such structural information would provide valuable information for discovery of HCV NS5B polymerase inhibitors. However, efforts to determine the structure of HCV NS5B polymerase have been hampered by difficulties in obtaining sufficient quantities of pure active enzyme and by poor solubility of the enzyme. There have been no crystals reported of any NS5B polymerase polypeptide. Thus, x-ray crystallographic analysis of such proteins has not previously been available.




SUMMARY OF THE INVENTION




The present invention addresses this need by providing, for the first time, compositions comprising a crystallized hepatitis C virus (HCV) NS5B polypeptide. Methods for obtaining purified and crystallized NS5B polypeptide are also provided. Such methods comprise solubilizing a NS5B polypeptide in a solution containing a protein stabilizing agent, subjecting the NS5B preparation to cation exchange chromatography, and allowing crystals to form in a precipitant solution containing a protein stabilizing agent and polyethylene glycol under conditions in which crystallization occurs.




The invention also provides a machine-readable data storage medium encoded with the structural coordinates of a NS5B polypeptide or a homologue thereof. Such a homologue contains backbone atoms having a root mean square deviation of equivalent Cα atoms of less than 3.0 Å when compared to the NS5B polypeptide.




The invention also provides a method for determining at least a portion of the three-dimensional structure of molecules or molecular complexes which contain at least some structurally similar features to a HCV NS5B polypeptide.




Still another aspect of the present invention comprises a method of selecting or optimizing a potential ligand or inhibitor by performing drug design with a three-dimensional structure determined for the crystal, preferably in conjunction with computer modeling. The potential ligand or inhibitor is then contacted with the NS5B polypeptide and the binding thereof is detected. If the ligand is a potential inhibitor of NS5B activity, the candidate drug may then be contacted with NS5B and the inhibition of its activity can be measured.




In another embodiment of the invention, a method of obtaining structural information concerning a molecular complex of unknown structure by using the structure coordinates set forth in Table 1 is provided. Such a method comprises the steps of: generating x-ray diffraction data from a crystal of said complex, and applying crystallographic phases derived from at least a portion of the structure coordinates set forth in Table 1 to said x-ray diffraction pattern to generate a three-dimensional electron density map of at least a portion of the unknown structure.











BRIEF DESCRIPTION OF THE FIGURE




FIG.


1


(


a


) depicts the motif organization of NS5B.




FIG.


1


(


b


) depicts a schematic diagram of NS5B polymerase.











DETAILED DESCRIPTION OF THE INVENTION




In order that the invention described herein may be more fully understood, the following detailed description is set forth. All references cited herein are incorporated in their entirety by reference.




The present invention provides, for the first time, crystallizable compositions comprising a HCV NS5B polymerase polypeptide. Thus, one embodiment of this invention provides a composition comprising a crystalline hepatitis C virus NS5B polypeptide.




Another embodiment of the invention provides a NS5B protein whose sequence is more similar to various HCV genotypes and subtypes, particularly at amino acid positions 335, 344 and 550 of SEQ ID NO: 1. Preferred amino acids at these positions are valine, alanine and glutamine respectively, while the published sequence (GenBank Accession No. 130458) of the BK isolate has threonine, valine and arginine at the corresponding positions.




Yet another embodiment of this invention provides methods of using NS5B polypeptides to grow a crystal containing such polypeptides. One such method comprises solubilizing a NS5B protein preparation in a solution containing a protein stabilizing agent; subjecting the NS5B protein preparation to cation exchange chromatography in a buffer containing glycine; and allowing crystals to form in the presence of a precipitant containing a protein stabilizing agent, a salt and polyethylene glycol under conditions in which crystallization occurs. Preferably, such a crystal effectively diffracts x-rays for the determination of the atomic coordinates of the protein to a resolution of greater than 4.0 Ångströms. More preferably, the crystal effectively diffracts x-rays for the determination of the atomic coordinates of the protein to a resolution of greater than 2.8 Ångströms. In a most preferred embodiment, the crystal effectively diffracts x-rays for the determination of the atomic coordinates of the protein to a resolution of greater than 2.2 Ångströms.




As used herein, the terms “HCV NS5B” and “NS5B” refers to the hepatitis C virus non-structural 5B protein as defined in Grakoui, et al.,


J. Virol.


67(3):1385-1395 (1993). See also Simons et al.,


Proc. Natl. Acad. Sci. USA


92(8): 3401-3405 (1995).




HCV “NS5B polypeptides” are polypeptides which have RNA dependent RNA polymerase-like domains similar to the naturally-occurring HCV NS5B. It also includes HCV NS5B and polypeptide fragments of NS5B having polymerase functionalities. These polypeptides also include polypeptides that differ from the NS5B polymerase by having amino acid deletions, substitutions, and additions. NS5B polypeptides may be derived from various HCV genotypes and subtypes known in the art.




The NS5B polypeptide may be produced by any well-known method, including synthetic methods, such as solid phase, liquid phase and combination solid/liquid phase syntheses; recombinant DNA methods, including cDNA cloning, optionally combined with site-directed mutagenesis; and/or purification of the natural products, optionally combined with enzymatic or chemical cleavage methods to produce NS5B or fragments thereof.




Various truncated forms of NS5B are within the scope of the invention and may enhance the solubility of the NS5B protein. A preferred truncation comprises a truncation of a stretch of amino acids in the carboxy terminal region of the protein, preferably containing hydrophobic amino acids. Most preferably, such a truncation includes the four leucine residues in the C-terminal region of NS5B. Truncations of 12-70 amino acids are preferred [Ferrari et al.,


J.Virol.


73:1649-1654 (1999)]. Optionally, it may also be desirable to add amino acids onto the NS5B protein or truncated NS5B. One preferred addition is a polyhistidine tag, 5-20 amino acids in length. Most preferred is a 6 amino acid histidine tag added to the amino-terminus of the NS5B protein or truncated NS5B. Preferably, the NS5B protein has a histidine tag at its amino-terminus for use in purifying the protein.




In one embodiment of the invention, the NS5B polymerase polypeptide is tNS5B, a recombinantly-produced truncated hepatitis C virus RNA dependent RNA polymerase polypeptide. The tNS5B protein contains both a 21 amino acid deletion at the carboxy-terminus and a 6 amino acid histidine tag at the amino-terminus [Ferrari, et al.,


J.Virol.


73:1649-1654 (1999)].




One aspect of the present invention relates to a method of purifying the NS5B polypeptides and obtaining NS5B crystals. Preferably, the NS5B polypeptide may be produced recombinantly in


E. coli


and initial purification may be accomplished by nickel chelate chromatography, as previously described [Petty (1996) “Metal chelate affinity chromatography” in: Ausubel, et al., eds.


Current Protocols in Molecular Biol


., Vol.2 New York, John Wiley and Sons]. This NS5B preparation is transferred into a solution containing a protein stabilizing agent and glycine. Next, the preparation is applied to a cation exchange resin and subjected to chromatography, eluting the protein with a salt gradient. The resulting solution preferably contains a protein stabilizing agent, a salt, a buffering agent and optionally a reducing agent or an oxygen scavenger. Examples of suitable reducing agents are dithiothreitol (DTT), dithioerythritol (DET) and β-mercaptoethanol. If necessary, the reducing agent is present in the buffered solution at a concentration of about 5 mM and is preferably DTT. The pH of the buffering agent may range from 4.5 to 8, preferably between pH 7 and 8.




Although other solution components can be substituted for the above described components, the protein stabilizing agent and salt appear to be important for the solubility of the NS5B protein preparation. Protein stabilizing agents include polyols, sugars, as well as amino acids and amino acid analogs. Some examples include erythritol, sorbitol, glycerol, fructose, trehalose, proline, β-alanine, taurine and glycine betaine. These agents are sometimes referred to as cosmotropic agents and are well known in the art. [Jeruzalmi & Steitz,


J. Mol. Biol.


274: 748-756 (1997)]. The concentration of such agents will vary depending upon the type of agent employed. For example, if glycerol is chosen, it is preferably provided in a concentration range from about 2 to about 20% (v/v), preferably about 10% (v/v), while a salt may be provided in a concentration of above about 150 mM. Many salts are routinely used in the art and may be variously used in the method of the present invention.




Glycine in the buffer solution maintains the solubility of the NS5B preparation in the absence of salt and allows further purification by cation exchange chromatography. Various types of cation exchange chromatography may be employed in this purification step. See Scopes,


Protein Purification: Principles and Practice


, Third ed., Springer-Verlag, New York (1994). Glycine can range in concentration from 500-1500 mM, preferably one molar. Glycine is preferably removed after cation exchange chromatography.




Compounds known as “precipitants” are often used to decrease the solubility of the polypeptide in a concentrated solution. Alternatively, “precipitants” can be changes in physical or chemical parameters which decrease polypeptide solubility, including temperature, pH and salt concentrations. Precipitants induce crystallization by forming an energetically unfavorable precipitant-depleted layer around the polypeptide molecules. To minimize the relative amount of this depletion layer, the polypeptides form associations and ultimately crystals as explained in Weber,


Advances in Protein Chemistry


41:1-36 (1991) which is incorporated by reference. In addition to precipitants, other materials are sometimes added to the polypeptide crystallization solution. These include buffers to adjust the pH of the solution (and hence surface charge on the peptide) and salts to reduce the solubility of the polypeptide. Various precipitants are known in the art and include the following: ammonium sulfate, ethanol, 3-ethyl-2,4 pentanediol; and many of the polyglycols, such as polyethylene glycol. A suitable precipitant for crystallization of NS5B polypeptides is polyethylene glycol (PEG), which combines some of the characteristics of the salts and other organic precipitants.




Crystallization may be accomplished by using any of the known methods in the art [Giegé, et al.,


Acta Crystallogr


. D50: 339-350 (1994); McPherson,


Eur. J. Biochem.


189: 1-23 (1990)]. Such techniques include microbatch, hanging drop, seeding and dialysis. Preferably, hanging-drop vapor diffusion [McPherson,


J. Biol. Chem.


251: 6300-6303 (1976)] or microbatch methods [Chayen,


Structure


5: 1269-1274 (1997)] are used. In each of these methods, it is important to promote continued crystal growth after nucleation by maintaining a supersaturated solution. In the microbatch method, polypeptide is mixed with precipitants to achieve supersaturation, the vessel is sealed and set aside until crystals appear. In the dialysis method, polypeptide is retained in a sealed dialysis membrane which is placed into a solution containing precipitant. Equilibration across the membrane increases the precipitant concentration thereby causing the polypeptide to reach supersaturation levels.




It is desirable to use a NS5B protein preparation having a concentration of at least 1 mg/mL and preferably less than 65 mg/mL. Crystallization may be best achieved in a precipitant solution containing polyethylene glycol 1000-20,000 (PEG; average molecular weight ranging from 1000-20,000 Da), preferably 4000-5000 with concentrations ranging from 15-25% (w/v). It is further desirable to avoid the use of extremely high and low molecular weight PEGs. It may also be desirable to include a protein stabilizing agent. If glycerol is chosen as the protein stabilizing agent, it is preferably provided at concentration ranging from 0.5 to 20% (v/v). A suitable salt, such as sodium chloride, may also be desirable in the precipitant solution, preferably in concentration ranging from 1 to 1000 mM. The precipitant is preferably buffered to a pH of about 4.5 to 8.0. Most preferred is a buffer solution at a pH of about 5 to 6. Specific buffers useful in the precipitant solution may vary and are well-known in the art [Scopes,


Protein Purification: Principles and Practice


, Third ed., (1994) Springer-Verlag, New York]. Examples of useful buffers include but are not limited to Tris, MES and acetate. Crystals routinely grow in a wide range of temperature. It is however preferred that crystals form at temperatures between 4° C. and 26° C., and more preferably at 20° C. to 22° C.




The crystals of the present invention have a wide range of uses. For example, high quality crystals are suitable for x-ray or neutron diffraction analysis to determine the three dimensional structure of NS5B polypeptides and in particular to assist in the identification of the protein's active and effector sites. Knowledge of these sites and solvent accessible residues allow rational design and construction of agonists and antagonists for NS5B polypeptides.




In addition, crystallization itself can be used as a purification method. In some instances, a polypeptide or protein crystallizes from a heterogeneous mixture into crystals. Isolation of such crystals by filtration and/or centrifugation, followed by redissolving the polypeptide affords a purified solution suitable for use in growing the high-quality crystals necessary for diffraction analysis.




Once a crystal of the present invention is grown, x-ray diffraction data can be collected. One method for determining structure uses synchrotron radiation, under standard cryogenic conditions for such x-ray diffraction data collection. However alternative methods may also be used. For example, crystals can be characterized by using x-rays produced in a conventional source (such as a sealed tube or a rotating anode), optionally under cryogenic conditions. Methods of characterization include, but are not limited to, precession photography, oscillation photography and diffractometer data collection.




Advantageously, the crystallizable compositions provided by this invention are amenable to x-ray crystallography. Thus, this invention also provides the three-dimensional structure of an HCV NS5B polypeptide at 1.9 Å resolution. Importantly, this has provided for the first time, detailed information about the shape and structure of the NS5B polymerase protein.




The three-dimensional structure of the HCV NS5B polymerase of this invention is defined by a set of structure coordinates as set forth in Table 1. The term “structure coordinates” refers to Cartesian coordinates derived from mathematical equations related to the patterns obtained on diffraction of a beam of x-rays by the atoms (scattering centers) of NS5B polymerase in crystal form. The diffraction data are used to calculate electron density maps and to establish the positions of the individual atoms of the NS5B enzyme.




Those of skill in the art will understand that a set of structure coordinates for an enzyme or an enzyme-complex or a portion thereof, is a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates will have little effect on overall shape.




The variations in coordinates discussed above may be generated because of mathematical manipulations of the structure coordinates. For example, the structure coordinates set forth in Table 1 can be manipulated by crystallographic permutations of the structure coordinates, fractionalization of the structure coordinates, additions, subtractions, rotations or translations to sets of the structure coordinates or any combinations of the above.




Alternatively, modifications in the crystal structure due to mutations, additions, substitutions, and/or deletions of amino acids, or other changes in any of the components that make up the crystal may also account for variations in structure coordinates. If such variations are within an acceptable standard error as compared to the original coordinates, the resulting three-dimensional shape is considered to be the same.




Various computational analyses are therefore necessary to determine whether a molecular complex or a portion thereof is sufficiently similar to all or parts of the NS5B polypeptide structure described above as to be considered the same. Such analyses may be carried out in current software applications, such as the Molecular Similarity application of QUANTA (Molecular Simulations Inc., San Diego, Calif.) version 4.1, and as described in the accompanying User's Guide.




The Molecular Similarity application permits comparisons between different structures, different conformations of the same structure, and different parts of the same structure. The procedure used in Molecular Similarity to compare structures is divided into four steps: 1) input the structures to be compared; 2) define the atom equivalences in these structures; 3) perform a fitting operation; and 4) analyze the results.




Each structure is identified by a name. One structure is identified as the target (i.e., the fixed structure); all remaining structures are working structures (i.e., moving structures). Since atom equivalency within QUANTA (Molecular Simulations Inc., San Diego, Calif.) is defined by user input, for the purpose of this invention, equivalent atoms are defined as protein alpha carbon atoms (Cα). When the Cα atoms of the working structure are superimposed on the relevant reference Cα atoms described by structure coordinates listed in Table 1 with an RMSD of less than 3 Å, the two structures are considered identical. More preferably, the root mean square deviation is less than 2.0 Å.




The term “root mean square deviation” or “RMSD” means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a way to express the deviation or variation from a trend or object. For purposes of this invention, the “root mean square deviation” defines the variation in the alpha carbon of a protein or protein complex from the relevant portion of the alpha carbon of the NS5B polypeptide as defined by the structure coordinates described herein.




Thus, in accordance with the present invention, the structure coordinates of the NS5B polypeptide and portions thereof are stored in a machine-readable storage medium. Such data may be used for a variety of purposes, such as drug discovery and x-ray crystallographic analysis of a protein crystal.




Accordingly, one aspect of this invention provides a machine-readable data storage medium comprising a data storage material encoded with the structure coordinates set forth in Table 1.




A computer system useful in reading the machine readable data storage medium includes a computer comprising a central processing unit (“CPU”) and a memory storage device. In general, the computer system may be any computer with an operating system such as MS-DOS, PC-DOS, Windows, OS/2, Unix, Unix variant or MacOS. Particularly preferred computer systems are the Silicon Graphics Octane workstation or Compaq AlphaServer DS20. Other hardware systems and software packages will be known to those skilled in the art.




Input hardware coupled to the computer system by input lines, may be implemented in a variety of ways. Machine-readable data of this invention may be inputted via the use of a modem or modems connected by a telephone line or a dedicated data line. Alternatively or additionally, the input hardware may comprise CD-ROM drives or disk drives. A keyboard or optical scanner may also be used as an input device.




Output hardware, coupled to the computer system by output lines, may similarly be implemented by conventional devices. By way of example, output hardware may include a display terminal for displaying a graphical representation of a binding pocket of this invention using a program such as INSIGHT (Molecular Simulations Inc., San Diego, Calif.) as described herein. Output hardware might also include a printer, so that hard copy output may be produced, or a disk drive, to store system output for later use.




In operation, the CPU coordinates the use of the various input and output devices, coordinates data accesses from mass storage and accesses to and from working memory, and determines the sequence of data processing steps. A number of programs may be used to process the machine-readable data of this invention. Such programs are discussed in reference to the computational methods of drug discovery as described herein. Specific references to components of the computer system are included as appropriate throughout the following description of the data storage medium.




A magnetic data storage medium can be encoded with a machine-readable data by a computer system as described above. Storage medium may be, for example, a conventional floppy diskette or hard disk, having a suitable substrate, which may be conventional, and a suitable coating, which may be conventional, on one or both sides, containing magnetic domains whose polarity or orientation can be altered magnetically. Storage medium may also have an opening for receiving the spindle of a disk drive or other data storage device. Alternatively, an optically-readable data storage medium can be encoded with such a machine-readable data, or a set of instructions. Medium can be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk which is optically readable and magneto-optically writable.




In the case of CD-ROM, as is well known, a coating is reflective and is impressed with a plurality of pits to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of the coating. A protective coating, which preferably is substantially transparent, is provided on top of the coating.




In the case of a magneto-optical disk, as is well known, the coating has no pits, but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser. The orientation of the domains can be read by measuring the polarization of laser light reflected from the coating. The arrangement of the domains encodes the data as described above.




The present invention permits the use of structure-based drug design techniques to design, select, and optionally optimize the structure of chemical entities, including inhibitory compounds that are capable of binding to HCV NS5B polymerase or any portion thereof. Also, de novo drug design methods with iterative structure-based drug design methods can be used to develop inhibitors from the crystal structure of the present invention.




One particularly useful drug design technique enabled by this invention is structure-based drug design. Structure-based drug design is a method for optimizing associations between a protein and a compound by determining and evaluating the three-dimensional structures of one or more sets of protein/compound complexes.




Those skilled in the art will realize that association of natural ligands or substrates with the binding pockets of their corresponding receptors or enzymes is the basis of many biological mechanisms of action. The term “binding pocket”, as used herein, refers to any region of a molecule or molecular complex, that, as a result of its shape, favorably associates with another chemical entity or compound. Similarly, drugs may exert their biological effects through association with the binding pockets of receptors and enzymes. Such association may occur with all or a subset of the binding pockets. An understanding of such associations will help lead to the design of drugs having more favorable associations with the target enzyme, and thus, improved biological effects. Therefore, this information is valuable in designing enzyme inhibitors, such as inhibitors of HCV NS5B polypeptides.




In iterative structure-based drug design, crystals of a series of protein/compound complexes are obtained and then the three-dimensional structures of each complex are solved. Such an approach provides insight into the association between the proteins and compounds of each complex. This is accomplished by selecting a compound with inhibitory activity, obtaining crystals of the polypeptide in complex with this compound, solving the three-dimensional structure of the complex, and comparing the polypeptide/compound associations between the new structure and previously solved structure(s). By observing how changes in the compound affect the protein/compound associations, these associations may be optimized.




In some cases, iterative structure-based drug design is carried out by forming successive protein-compound complexes and then crystallizing each new complex. Alternatively, a pre-formed protein crystal is soaked in the presence of an inhibitor, thereby forming a protein/compound complex and obviating the need to crystallize each individual protein/compound complex. Advantageously, the HCV NS5B polymerase crystals provided by this invention may be soaked in the presence of a compound or compounds, such as NS5B inhibitors, substrates or other ligands to provide NS5B polypeptide compound crystal complexes. As used herein, the term “soaked” refers to a process in which the crystal is transferred to a solution containing the compound of interest or the compound of interest is added to the solution containing the crystal.




The structure coordinates set forth in Table 1 can also be used to aid in obtaining structural information about another crystallized molecule or molecular complex. This may be achieved by any of a number of well-known techniques, including molecular replacement.




The structure coordinates set forth in Table 1 can also be used for determining at least a portion of the three-dimensional structure of molecules or molecular complexes which contain at least some structurally similar features to HCV NS5B. In particular, structural information about another crystallized molecule or molecular complex may be obtained using well-known techniques, including molecular replacement.




Therefore, another aspect of this invention provides a method of utilizing molecular replacement to obtain structural information about a crystallized molecule or molecular complex whose structure is unknown comprising the steps of:




a) generating an x-ray diffraction pattern from said crystallized molecule or molecular complex; and




b) applying crystallographic phases derived from at least a portion of the structure coordinates set forth in Table 1 to the x-ray diffraction pattern to generate a three-dimensional electron density map of at least a portion of the molecule or molecular complex whose structure is unknown.




Once the structure coordinates of a protein crystal have been determined, they are useful in solving the structures of other crystals. In addition, the structures of NS5B complexes can be determined from the structure coordinates of the present invention. For example, complexes may be crystallized and their structure elucidated using such methods as difference Fourier or molecular replacement. NS5B complexes suitable for such analysis include, for example, NS5B in complex with an oligonucleotide template/primer duplex (i.e. substrate), wherein the duplex may have a single-stranded overhang of one or both strands on either or both ends of the oligonucleotide. Another example complex is NS5B complexed with a nucleotide triphosphate (i.e. substrate) or analog thereof. Most preferred is NS5B complexed with inhibitors such as nucleotide analogs, non-nucleotide inhibitors or inhibitors unrelated to substrate molecules. Yet another NS5B complex suitable for structure determination using the structure coordinates of NS5B is NS5B in complex with other members of the putative replicase complex, such as HCV NS3 protein, NS3 helicase domain, NS3 protease domain or other HCV proteins. A further NS5B complex suitable for structure determination is NS5B in complex with one or more cellular host factors (Cf. thioredoxin and T7 DNA polymerase) [Doublié et al.,


Nature


391: 251-258(1998)]. Suitable complexes of NS5B may contain several other molecules or combinations of the above described complexes.




Preferably, the crystallized molecule or molecular complex comprises a NS5B polypeptide. More preferably, the crystallized molecule or molecular complex is obtained by soaking a crystal of this invention in a solution. By using molecular replacement, all or part of the structure coordinates of the NS5B polymerase provided by this invention (and set forth in Table 1) can be used to determine the structure of a crystallized molecule or molecular complex whose structure is unknown more quickly and efficiently than attempting to determine such information ab initio.




Molecular replacement provides an accurate estimation of the phases for an unknown structure. Phases are a factor, in equations used to solve crystal structures, that can not be measured experimentally. Obtaining accurate values for the phases, by methods other than molecular replacement, is a time-consuming process. However, when the crystal structure of a protein containing at least a homologous portion has been solved, the phases from the known structure may provide a satisfactory initial estimate of the phases for the unknown structure.




Thus, this method involves generating a preliminary model of a molecule or molecular complex whose structure coordinates are unknown, by orienting and positioning the relevant portion of the NS5B polymerase according to Table 1 within the unit cell of the crystal of the unknown molecule or molecular complex so as best to account for the observed x-ray diffraction pattern amplitudes to generate an electron density map of the structure whose coordinates are unknown. This, in turn, can be subjected to any well-known model building and structure refinement technique to provide a final, accurate structure of the unknown crystallized molecule or molecular complex [Lattman, “Use of the Rotation and Translation Functions”, in


Meth. Enzymol.,


115: 55-77 (1985); Rossman, ed., “The Molecular Replacement Method”,


Int. Sci. Rev. Ser


., No. 13, Gordon & Breach, New York (1972)].




Phase information from the structure coordinates of the present invention may be used to elucidate the structure of other crystals. For example, NS5B molecules in complex with other atoms or molecules, as described above, including complexes containing a heavy atom substructure from which useful phasing information may be extracted. Such complexes include, for example, those containing sulfur atoms of the endogenous cysteine and methionine amino acids as well as any atoms incorporated into, soaked into or cocrystallized within the crystal lattice. Other structures which can be elucidated using the phase information of the present invention include for example other RNA-dependent RNA polymerases (RdRps) of sufficient three-dimensional structure similarity to HCV NS5B as to be solved using molecular replacement. Examples of such RdRps include but are not limited to RdRp from bovine viral diarrhea virus, RdRp from yellow fever virus and RdRp from Dengue virus. Also, RdRps in a complex with a small molecule substrate, inhibitor, intermediate, transition state analog, product or analog of any of these may also be solved using phase information contained in the present invention. Other complexes whose structure can be elucidated from the phase information of the present invention include an RdRp in a complex with a macromolecule such as a template/primer substrate or host elongation factor, such as T7 DdDp/thioredoxin, or with a transcription inhibitor, such as T7 DdRp/T7 lysozyme, or with another HCV protein, such as NS3 protein, NS3 helicase or NS3 protease for example. Complexes containing a combination of the above molecules may also be solved using phase information of the present invention.




The structure of any portion of any crystallized molecule or molecular complex that is sufficiently homologous to any portion of the NS5B polymerase can be solved by this method. The difference Fourier method simply calculates an electron density map using phases calculated from the structure coordinates and observed diffraction amplitudes from a crystal of an unknown structure. This well-known method is often used to solve structures of protein/ligand complexes where the ligand is small and does not affect the crystal form significantly.




In a preferred embodiment, the method of molecular replacement is utilized to obtain structural information about a molecule wherein the molecule comprises a NS5B polypeptide or variant or complex thereof. Preferably the NS5B polypeptide comprises tNS5B or homologues thereof.




The structure coordinates of NS5B polymerase provided by this invention are particularly useful in solving the structure of other crystal forms of NS5B polypeptides.




The structure coordinates are also particularly useful to solve the structure of crystals of NS5B polypeptides, particularly tNS5B and polypeptides related in structure to NS5B. This approach enables the determination of the optimal sites for interaction between chemical entities, including interaction of candidate NS5B inhibitors with NS5B.




All of the complexes referred to above may be studied using well-known x-ray diffraction techniques may be refined versus x-ray data to 3 Å resolution or better, to an R


free


value of about 0.40 or less using computer software, such as X-PLOR [Yale University, ©1992, distributed by Molecular Simulations, Inc.; see e.g., Blundell & Johnson, supra;


Meth, Enzymol


., vol. 114 & 115, H. W. Wyckoff et al., eds., Academic Press (1985)]. This information may thus be used to optimize known NS5B inhibitors, and to design new NS5B inhibitors.




In order that this invention be more fully understood, the following examples are set forth. These examples are for the illustrative purposes only and are not to be construed as limiting the scope of this invention in any way.




EXAMPLE 1




Construction of tNS5B




The amino acid sequence of NS5B (BK) was compared to 16 NS5B proteins from different genotypes and subtypes. Four isolates represent genotype 1 subtype a (HCV-1a) and five are from HCV-1b. The rest are from HCV-2a, 2b, 3a, 3b, 4a, 5a and 6a. Two substitutions were made to the NS5B (BK) sequence, one “T” to “V” at position 335, the other “V” to “A” at position 344 numbered according to SEQ ID NO: 1. The NS5B protein contains an additional change from the published NS5B (BK) sequence (GenBank Accession No. 130458), namely, an “R” to “Q” at position 550 numbered according to SEQ ID NO:1. This NS5B protein has an amino acid sequence more similar than the published NS5B sequence to the other genotypes analyzed.




To make these substitutions, site-directed mutagenesis using the “Quick Change” mutagenesis kit (Stratagene, Calif.) was performed. The resulting clone was verified for correctness by direct sequencing. This NS5B construct was subcloned into pET-21b (Novagen, Wis.) between NheI and BamHI sites. Additional codons were engineered at the N-terminus (coding for a polyhistidine tag, MASHHHHHH, and replacing the native amino acids “SM” at the N-terminus of NS5B) to facilitate the cloning and purification. The C-terminal 21 amino acids were deleted to improve the solubility of NS5B. The sequence of the modified NS5B (designated as His-NS5BΔCT21) is set forth as SEQ ID NO: 1.




EXAMPLE 2




Expression and Purification of tNS5B




Hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) was cloned, transformed into


E. coli


and purified as previously described using nickel chelate chromatography. The particular construct used in this Example is described above and incorporated a six-histidine tag at the N-terminus and a 21-residue truncation from the C-terminus. See also Ferrari, et al.,


J. Virol.


73:1649-1654 (1999). HCV NS5B RdRp was further purified using cation exchange resin (Mono-S HR 16/10, (Amersham Pharmacia Biotech AB, Uppsala, Sweden)) after overnight dialysis into 10% (v/v) glycerol, and 1 M glycine pH 7.0. After gel filtration chromatography (HiPrep 16/60 Sephacryl S100 High Resolution (Amersham Pharmacia AB, Uppsala, Sweden)) into 10% (v/v) glycerol, 600 mM NaCl, 5 mM DTT and 10 mM Tris pH 7.5, recombinant HCV NS5B was concentrated to between 10 and 40 mg/mL. At this stage, the concentrated protein was stored at −80° C. until needed.




EXAMPLE 3




Crystallization and Data Collection




Crystallization experiments were conducted using both hanging-drop vapor diffusion and microbatch methods using newly prepared or freshly-thawed protein. For vapor-diffusion experiments, 2 μL of protein was mixed with an equal volume of precipitant solution, placed on the underside of a siliconized glass coverslip, and sealed in close proximity to 1 mL of the precipitant solution. For the microbatch experiments, 2 μL of protein was mixed thoroughly with an equal volume of precipitant solution and dispensed beneath a layer of paraffin oil. The precipitant solution contained poly(ethylene)glycol 1000 to 20,000 (PEG; average MW ranging from 1000 to 20,000 Da) with concentrations ranging from 15 to 25% [(v/v) or (w/v)]. The precipitant solution also contained 10% (v/v) glycerol and concentrations of NaCl ranging from 0 to 600 mM NaCl, using various buffers between pH 4.5 and 7.0. These buffers included acetate, MES, and Tris. After incubation at temperatures between 4° C. and 26° C. for 24 h, small plate-like crystals formed. Crystals grew to terminal size within two weeks with dimensions up to 300×300×50 μm. After transfer of the crystals to cryoprotectant containing a few percent more PEG than the crystallization medium and up to 30% (v/v) glycerol, the crystals could be either frozen directly in liquid propane for storage prior to diffraction data collection or frozen in a gaseous nitrogen stream immediately before diffraction data collection.




EXAMPLE 4




Protein Preparation. MAD Experiment and Phasing




In preparation for a multiwavelength anomalous diffraction (MAD) experiment for the purpose of obtaining experimental crystallographic phases, a suitable atom or set of atoms must be incorporated into the crystal lattice. It is essential that this atom have an absorption edge within the practical range of x-ray wavelengths used for diffraction data collection. Rather than absorption, fluorescence is conventionally measured. This atom or set of atoms may be added exogenously to the native protein molecule (by soaking or cocrystallization methods), incorporated synthetically or incorporated biosynthetically into the protein itself. We chose the last method by substituting selenomethionine into the protein for the native methionine. This was accomplished by inhibiting the expression system's pathway for methionine biosynthesis and adding a suitable amount of selenomethionine to the growth medium for incorporation into the overexpressed protein. One may also use an expression system which is auxotrophic for methionine and similarly provide selenomethionine in the growth medium. This process is described in Doublié [Doublié,


Meth. Enz.


276: 523-530 (1997)].




The selenomethionine-incorporated HCV NS5B protein was purified and crystallized in the same manner as the wild-type (sulfur-containing methionine) enzyme.




A MAD experiment was performed at beamline 17-ID-B at the Advanced Photon Source at Argonne National Laboratory as described in Hendrickson and Ogata [Hendrickson & Ogata,


Meth. Enz.


276: 494-523 (1997)]. Briefly, an x-ray fluorescence energy scan was collected from a Se met NS5B crystal. Data from this scan were used to assign the fluorescence edge and peak to determine the precise wavelengths of x-ray radiation required for the experiment. Complete x-ray diffraction data sets were collected, using the inverse-beam method [Hendrickson & Ogata,


Meth. Enz.


276: 494-523 (1997)], at the peak fluorescence (wavelength=0.979 Å), at the fluorescence edge (0.980 Å) and at a low-energy remote wavelength (1.032 Å).




Unprocessed diffraction images were indexed and the diffraction intensities integrated using the HKL computer program package [Otwinowski & Minor,


Meth. Enzymol.


276: 307-326 (1997)]. Integrated intensities were reduced to unique data (as amplitides) using the programs of the CCP4 package including SCALA and TRUNCATE [Evans,


Joint CP


4


and ESF


-


EACBM Newsletter


33: 22-24 (1997); French & Wilson,


Acta Crystallogr


. A34: 517-525 (1978)].




The selenium atom substructure was deduced using the direct methods structure solution software Shake-and-Bake version 2.0 beta [Miller et al.,


J. Appl. Crystallogr.


27: 613-621 (1994)] using the reduced, unique data from the peak fluorescence wavelength only.




The calculated sites for the 22 expected (based on amino acid sequence of the NS5B monomer and the anticipation of two NS5B monomers per asymmetric unit, which is based on calculation of the Matthews coefficient and other crystallographic analyses [Matthews,


J. Mol. Biol.


33: 491-497 (1968)]) were then refined and experimental MAD phases calculated using the software SHARP [de La Fortelle & Bricogne,


Meth. Enzymol.


276: 472-494 (1996)]. Subsequent density modification using the program SOLOMON [Abrahams & Leslie,


Acta Crystallogr


. D52: 30-42 (1996)] resulted in an interpretable electron density map.




EXAMPLE 5




Model Building and Refinement




After the polypeptide backbone was fit into the experimental electron density using the software O [Jones et al.,


Acta Crystallogr


. A47: 110-119 (1991)], amino acid side chains were fit into electron density and the HCV NS5B primary sequence was registered onto the three dimensional polypeptide trace. After an initial cycle of manual fitting, the three dimensional coordinates were subjected to coordinate and B-factor refinement using simulated-annealing techniques implemented in the program X-PLOR [Brünger et al.,


Acta Crystallogr


A 46: 585-93 (1990); Karplus et al.,


Cold Spring Harb Symp Quant Biol


52: 381-90 (1987)]. Iterative cycles of manual rebuilding, placement of solvent molecules, and refinement followed until convergence of the free R-factor to 0.30 [Kleywegt & Brunger,


Structure


4:897-904 (1996); Kleywegt & Jones,


Structure


3: 535-40 (1995)]. The stereochemical quality of the model was checked and verified at each cycle with the aid of the programs PROCHECK [Laskowski et al.,


J. Appl. Crystallogr.


26: 283-291 (1993)] and WHATIF [Hooft et al.,


Nature


381: 272 (1996)].




Crystals contain two HCV NS5B monomers per asymmetric unit and belong to space group P2


1


2


1


2


1


with unit cell dimensions 86×105×126 Å. These crystals diffract to at least 1.9 Å resolution. A refined model of HCV NS5B RdRp was produced using data collected from a selenomethionine-incorporated protein. This three-dimensional atomic model contains greater than 95% of the expected scattering matter in the crystal and may be used to solve, using difference Fourier or molecular replacement techniques, the crystal structures of HCV NS5B:ligand complexes where the ligand is a small-molecule inhibitor or substrate of this enzyme. This crystal form is suitable for structure-based drug design due to: (a) only modest concentrations of NaCl and PEG used for crystallization and (b) exposure of the active site to solvent channels. A schematic-representation of the HCV NS5B RdRp structure is shown in FIG.


1


(


b


).




FIG.


1


(


b


) contains schematic representations of the HCV NS5B RdRp monomer in a single large image, showing the location of the structural motifs in the three dimensional structure. The conserved structural motifs found in polymerases [Hansen et al.,


Structure,


5:1109-1122 (1997)] are denoted as lettered dark gray regions; the remainder of the molecule is lighter. The amino acid sequence of these motifs is shown (FIG.


1


(


a


)), above FIG.


1


(


b


) and are:




Motif A: This region forms one strand of the central beta-sheet and contributes an aspartate (D) to the active site;




Motif B: This region determines specificity between a NTP and dNTP substrate;




Motif C: This motif contains the sequence motif GDD and is directly implicated in divalent metal binding and nucleotidyl transferase activity;




Motif D: Buttresses the central beta-sheet; and




Motif E: Determines specificity between DNA and RNA template.




These motifs have all individually been shown to be required for catalytic activity [Hansen et al.,


Structure,


5:1109-1122 (1997); Joyce & Steitz,


Ann. Rev. Biochem.


63:777-822 (1994); Poch et al.,


EMBO J.


8:3867-3874 (1989); Sousa,


Trends Biochem Sci.


21:186-190 (1996)]. The three-dimensional colocalization of the motifs (in the ‘palm’ subdomain) defines the position of the catalytic active site. Additionally, the ‘thumb’ and ‘fingers’ regions (denoted on the Figure), have been shown to bind to the primer strand substrate and template strand substrate, respectively, in other members of the greater polymerase family [Doublié et al.,


Nature


391:251-258 (1998); Huang et al.,


Science


282:1669-1675 (1998); Jacobo-Molina et al.,


Proc. Natl. Acad. Sci


. USA 90:6320-6324 (1993); Kiefer et al.,


Nature


391:304-307 (1998), Pelletier et al.,


Science


264:1891-1903 (1994)].




FIG.


1


(


b


) was created using Molscript and Raster3D [Kraulis,


J. Appl. Crystallogr.


24:946-950 (1991); Merritt & Bacon,


Meth. Enzymol.


277:505-524 (1997)].




Table 1 lists the atomic structure coordinates for hepatitis C virus recombinant tNS5B polymerase, as derived by x-ray diffraction from crystals. The specific columns in Table 1 are defined as follows:
















Column




Description











1




Residue number (using numbering scheme of Table 1)






2




Residue name, using one-letter code (X = solvent)






3




Atom name, conventional PDB nomenclature (OW = solvent)






4




X-coordinate in orthogonal Ångströms, multiplied by 10






5




Y-coordinate in orthogonal Ångströms, multiplied by 10






6




Z-coordinate in orthogonal Ångströms, multiplied by 10






7




B-factor, in Å


2
















The descriptions of the foregoing embodiments of the invention have been presented for purpose of illustration and description. They are not intended to be exhaustive or to limit the invention to the precise forms disclosed, and obviously many modifications and variations are possible in light of the above teaching. The embodiments were chosen and described in order to best explain the principles of the invention to thereby enable others skilled in the art to utilize the invention in various embodiments and with various modifications as are suited to the particular use contemplated. It is intended that the scope of the invention be defined by the claims appended hereto.












TABLE 1











The following table contains one line for each atom in one HCV NS5B






monomer as well as solvent molecules. The columns are: 1) residue






number, 2) 1-letter amino acid code, 3) atom name, 4) x-coordinate






multiplied by 10, 5) y-coordinate multiplied by 10, 6) z-coordinate






multiplied by 10, and 7) B-factor. The coordinates of the second monomer






(x


2


, y


2


, z


2


) are related to the coordinates of the first monomer (x


1


, y


1


, z


1


)






listed below according to the following operation:













x


2


= x


1


· a


11


+ y


1


· a


12


+ z


1


· a


13


+ t


1








y


2


= x


1


· a


21


+ y


1


· a


22


+ z


1


· a


23


+ t


2








z


2


= x


1


· a


31


+ y


1


· a


32


+ z


1


· a


33


+ t


3


  where













a


11


a


12


a


13


  −0.99978  0.01956  0.00754






a


21


a


22


a


23


=  0.01940  0.99961 −0.01986






a


31


a


32


a


33


  −0.00793 −0.01971  0.99977   and













t


1


 t


2


 t


3  


= −1.37838  0.34470 41.27925













The noncrystallographic operation described above should only be






applied to the HCV NS5B protein atoms (i.e. residues 7 through 569).






Following the protein atoms are listed all discrete solvent molecules






(residue X, atom OW) which were modeled into the asymmetric unit.






















7




H




N




161




376




196




40







7




H




CA




152




378




208




40







7




H




C




159




374




222




36







7




H




O




152




369




231




32







7




H




CB




138




371




207




42







7




H




CG




129




376




196




44







7




H




ND1




124




368




187




43







7




H




CD2




125




389




193




42







7




H




CE1




117




375




178




46







7




H




NE2




117




388




182




43







8




H




N




172




376




223




33







8




H




CA




178




373




235




31







8




H




C




178




384




245




24







8




H




O




178




395




241




19







8




H




CB




193




369




232




38







8




H




CG




195




356




225




45







8




H




ND1




201




354




213




44







8




H




CD2




190




343




229




45







8




H




CE1




200




342




209




48







8




H




NE2




194




335




219




50







9




S




N




177




380




258




22







9




S




CA




177




391




268




20







9




S




C




189




399




268




18







9




S




O




189




411




271




17







9




S




CB




175




384




282




18







9




S




OG




183




372




283




19







10




Y




N




201




393




265




18







10




Y




CA




214




400




265




21







10




Y




C




223




394




255




20







10




Y




O




222




383




251




20







10




Y




CB




221




399




278




17







10




Y




CG




214




405




291




17







10




Y




CD1




216




419




294




16







10




Y




CD2




206




397




299




19







10




Y




CE1




209




424




305




19







10




Y




CE2




200




403




310




19







10




Y




CZ




201




416




313




17







10




Y




OH




195




421




323




25







11




T




N




233




403




250




22







11




T




CA




243




398




241




25







11




T




C




256




404




248




25







11




T




O




256




415




253




26







11




T




CB




243




404




226




25







11




T




OG1




240




418




226




28







11




T




CG2




232




396




218




26







12




W




N




266




396




249




25







12




W




CA




279




400




256




26







12




W




C




291




401




247




27







12




W




O




293




393




238




28







12




W




CB




281




390




267




20







12




W




CG




269




388




276




20







12




W




CD1




261




378




277




19







12




W




CD2




265




398




286




19







12




W




NE1




252




380




287




19







12




W




CE2




254




392




293




19







12




W




CE3




269




410




291




17







12




W




CZ2




247




398




303




16







12




W




CZ3




262




416




301




21







12




W




CH2




251




410




307




14







13




T




N




299




411




250




28







13




T




CA




312




413




242




28







13




T




C




323




405




248




31







13




T




O




332




400




241




35







13




T




CB




317




428




242




26







13




T




OG1




319




432




256




27







13




T




CG2




307




437




235




26







14




G




N




323




403




261




31







14




G




CA




333




395




267




30







14




G




C




341




404




277




30







14




G




O




350




399




284




31







15




A




N




339




417




277




27







15




A




CA




345




426




286




26







15




A




C




339




422




300




29







15




A




O




327




419




301




29







15




A




CB




343




441




283




22







16




L




N




347




423




310




31







16




L




CA




342




419




324




30







16




L




C




334




429




331




24







16




L




O




336




441




329




25







16




L




CB




354




415




332




30







16




L




CG




363




404




328




33







16




L




CD1




375




403




337




35







16




L




CD2




356




391




328




32







17




I




N




325




425




339




26







17




I




CA




316




433




347




25







17




I




C




326




436




359




25







17




I




O




330




426




366




26







17




I




CB




303




427




353




21







17




I




CG1




294




423




341




19







17




I




CG2




296




436




362




18







17




I




CD1




281




418




344




21







18




T




N




331




448




360




25







18




T




CA




341




451




370




27







18




T




C




336




459




382




28







18




T




O




326




466




382




26







18




T




CB




352




459




363




22







18




T




OG1




347




471




357




23







18




T




CG2




359




451




353




20







19




P




N




343




457




393




30







19




P




CA




339




463




406




33







19




P




C




344




478




406




38







19




P




O




352




482




398




37







19




P




CB




346




455




417




32







19




P




CG




358




450




410




33







19




P




CD




354




447




396




30







20




C




N




339




485




416




43







20




C




CA




343




499




418




46







20




C




C




355




498




428




48







20




C




O




366




497




424




52







20




C




CB




332




508




423




48







20




C




SG




334




525




417




65







21




A




N




351




498




441




47







21




A




CA




361




497




451




45







21




A




C




364




482




454




44







21




A




O




359




474




447




46







21




A




CB




357




504




464




46







22




A




N




372




479




464




44







22




A




CA




375




466




468




42







22




A




C




362




460




473




40







22




A




O




353




467




479




38







22




A




CB




386




465




479




44







23




E




N




361




446




472




37







23




E




CA




349




439




476




35







23




E




C




353




428




486




33







23




E




O




362




421




484




35







23




E




CB




342




433




464




32







23




E




CG




337




442




453




30







23




E




CD




332




435




441




33







23




E




OE1




339




427




435




33







23




E




OE2




320




437




437




33







24




E




N




345




427




497




32







24




E




CA




346




417




507




29







24




E




C




336




406




505




27







24




E




O




324




410




502




28







24




E




CB




344




423




521




30







24




E




CG




354




434




525




39







24




E




CD




351




437




540




41







24




E




OE1




342




445




542




40







24




E




OE2




359




432




548




43







25




S




N




339




394




506




28







25




S




CA




329




383




505




28







25




S




C




327




377




519




26







25




S




O




316




372




522




26







25




S




CB




334




373




495




30







25




S




OG




345




365




500




34







26




K




N




338




377




527




26







26




K




CA




337




370




540




28







26




K




C




332




380




551




20







26




K




O




336




392




551




20







26




K




CB




351




365




544




29







26




K




CG




363




375




544




41







26




K




CD




367




378




529




43







26




K




CE




372




392




528




40







26




K




NZ




370




396




514




41







27




L




N




324




375




560




23







27




L




CA




318




383




571




22







27




L




C




329




390




579




21







27




L




O




337




384




585




23







27




L




CB




310




374




580




23







27




L




CG




302




380




592




16







27




L




CD1




293




391




588




14







27




L




CD2




295




369




599




16







28




P




N




329




404




579




22







28




P




CA




338




411




587




23







28




P




C




335




408




601




23







28




P




O




324




407




605




22







28




P




CB




335




426




583




23







28




P




CG




327




425




571




25







28




P




CD




319




412




572




22







29




I




N




346




407




609




20







29




I




CA




344




403




623




19







29




I




C




350




414




633




23







29




I




O




362




417




632




24







29




I




CB




350




390




627




17







29




I




CG1




342




379




619




20







29




I




CG2




349




387




641




20







29




I




CD1




328




377




622




12







30




N




N




342




419




642




22







30




N




CA




347




429




652




20







30




N




C




344




423




666




16







30




N




O




342




411




667




18







30




N




CB




341




443




650




18







30




N




CG




327




445




653




17







30




N




OD1




320




435




657




20







30




N




ND2




322




457




652




18







31




A




N




345




431




676




19







31




A




CA




342




426




690




20







31




A




C




328




423




693




22







31




A




O




325




415




702




23







31




A




CB




348




436




700




19







32




I




N




318




429




686




23







32




I




CA




304




427




688




23







32




I




C




298




415




681




23







32




I




O




288




410




685




26







32




I




CB




296




440




683




20







32




I




CG




301




453




689




23







32




I




CD1




294




465




683




21







32




I




CD2




298




453




704




29







33




S




N




305




411




670




23







33




S




CA




301




399




662




22







33




S




C




295




387




669




24







33




S




O




284




383




667




24







33




S




CB




312




395




653




18







33




S




OG




316




406




645




17







34




N




N




303




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34




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34




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287




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281




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362




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29







34




N




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322




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34




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318




351




672




37







34




N




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334




358




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35




S




N




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381




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35




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272




382




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35




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259




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35




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35




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270




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36




L




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36




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250




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36




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36




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668




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36




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237




390




656




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36




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223




389




662




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36




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238




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647




19







37




L




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37




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352




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37




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277




345




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37




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37




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247




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38




R




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332




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38




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31







38




R




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294




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647




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38




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315




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38




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38




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286




313




696




57







38




R




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708




68







38




R




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296




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38




R




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291




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38




R




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39




H




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39




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39




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273




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280




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273




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H




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40




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320




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40




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329




348




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40




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316




349




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32







41




N




N




311




313




589




29







41




N




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312




308




576




33







41




N




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299




305




569




34







41




N




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299




301




557




37







41




N




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320




295




577




38







41




N




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335




297




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45







41




N




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340




308




581




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41




N




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342




286




584




48







42




M




N




288




308




575




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42




M




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307




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33







42




M




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320




561




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42




M




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M




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42




M




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43




V




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43




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368




565




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43




V




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262




351




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44




Y




N




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354




538




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44




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288




359




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44




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281




370




520




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44




Y




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372




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Y




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292




347




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44




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280




343




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Y




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334




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44




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278




348




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44




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260




330




507




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44




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267




344




489




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44




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258




335




494




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44




Y




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246




331




487




27







45




A




N




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378




513




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45




A




CA




284




389




504




23







45




A




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490




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45




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289




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462




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N




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CA




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400




446




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308




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47




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396




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47




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CG2




327




384




446




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S




N




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408




424




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CA




315




407




409




26







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29







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S




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320




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336




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R




N




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R




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336




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357




380




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367




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52







49




R




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364




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54







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R




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369




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55







49




R




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361




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469




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50




S




N




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366




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50




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50




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50




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50




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287




360




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29







51




A




N




298




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A




CA




290




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376




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A




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288




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A




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A




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296




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373




18







52




G




N




299




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360




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52




G




CA




299




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349




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52




G




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287




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350




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52




G




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280




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340




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53




L




N




286




339




362




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53




L




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276




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364




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53




L




C




262




335




363




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53




L




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358




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53




L




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324




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53




L




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287




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53




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53




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281




300




373




35







54




R




N




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348




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54




R




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248




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367




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54




R




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244




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54




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357




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54




R




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353




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54




R




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215




353




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55




Q




N




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55




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55




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247




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315




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55




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326




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55




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285




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321




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55




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312




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55




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294




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327




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56




K




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232




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319




320




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279




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293




309




317




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K




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291




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302




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57




K




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217




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54







58




V




N




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348




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58




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CA




199




358




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58




V




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199




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313




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58




V




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58




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58




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V




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216




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330




22







59




T




N




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352




306




25







59




T




CA




208




353




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59




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201




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284




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59




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59




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286




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59




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59




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223




356




271




22







60




F




N




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344




278




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60




F




CA




182




334




271




25







60




F




C




173




341




260




23







60




F




O




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353




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60




F




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280




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60




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165




333




291




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337




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170




335




303




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60




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144




344




297




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60




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60




F




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149




346




310




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61




D




N




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332




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61




D




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240




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61




D




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145




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D




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D




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D




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D




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D




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62




R




N




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62




R




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62




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113




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62




R




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115




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R




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62




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62




R




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139




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260




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62




R




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62




R




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62




R




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139




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62




R




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63




L




N




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63




L




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63




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63




L




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63




L




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63




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103




319




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63




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101




304




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63




L




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105




327




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31







64




Q




N




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64




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56




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64




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64




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64




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64




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64




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64




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64




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53




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266




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65




V




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65




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65




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65




V




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319




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65




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33




316




212




23







66




L




N




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356




222




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66




L




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66




L




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66




L




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66




L




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66




L




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66




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66




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67




D




N




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232




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67




D




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228




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67




D




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232




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67




D




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67




D




CB




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67




D




CG




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249




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67




D




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349




256




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67




D




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328




255




28







68




D




N




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359




230




19







68




D




CA




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368




233




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68




D




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247




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68




D




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250




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68




D




CB




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228




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68




D




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68




D




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375




208




27







68




D




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354




205




21







69




H




N




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363




257




17







69




H




CA




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366




271




19







69




H




C




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377




274




20







69




H




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282




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69




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CB




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354




280




20







69




H




CG




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344




280




21







69




H




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331




279




20







69




H




CD2




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347




282




19







69




H




CE1




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325




280




21







69




H




NE2




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334




282




22







70




Y




N




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377




268




19







70




Y




CA




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387




270




16







70




Y




C




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400




265




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70




Y




O




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410




273




19







70




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CB




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382




263




18







70




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CG




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392




263




19







70




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CD1




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403




254




20







70




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CD2




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392




273




18







70




Y




CE1




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412




255




19







70




Y




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3




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274




17







70




Y




CZ




3




411




265




17







70




Y




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13




421




266




19







71




R




N




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401




253




18







71




R




CA




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414




248




19







71




R




C




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419




255




16







71




R




O




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256




16







71




R




CB




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414




232




22







71




R




CG




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413




224




21







71




R




CD




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412




209




18







71




R




NE




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400




206




17







71




R




CZ




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388




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18







71




R




NH1




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386




204




20







71




R




NH2




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377




202




19







72




D




N




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410




260




18







72




D




CA




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414




267




18







72




D




C




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421




280




20







72




D




O




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431




284




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72




D




CB




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271




19







72




D




CG




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396




259




21







72




D




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403




249




23







72




D




OD2




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384




260




24







73




V




N




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415




288




18







73




V




CA




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420




301




17







73




V




C




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434




298




17







73




V




O




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444




305




14







73




V




CB




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411




308




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73




V




CG1




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417




320




15







73




V




CG2




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398




313




15







74




L




N




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435




288




14







74




L




CA




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447




285




14







74




L




C




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458




282




15







74




L




O




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470




286




15







74




L




CB




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446




273




16







74




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CG




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458




268




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74




L




CD1




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465




279




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74




L




CD2




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454




257




17







75




K




N




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455




274




17







75




K




CA




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465




271




18







75




K




C




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471




283




13







75




K




O




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482




284




17







75




K




CB




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460




261




19







75




K




CG




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472




255




20







75




K




CD




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467




245




22







75




K




CE




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479




238




27







75




K




NZ




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475




229




30







76




E




N




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462




293




16







76




E




CA




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466




305




20







76




E




C




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475




313




17







76




E




O




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485




319




19







76




E




CB




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454




314




22







76




E




CG




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445




307




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76




E




CD




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432




314




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76




E




OE1




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431




326




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76




E




OE2




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422




307




35







77




M




N




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472




313




16







77




M




CA




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480




321




16







77




M




C




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494




315




16







77




M




O




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503




323




15







77




M




CB




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473




321




17







77




M




CG




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461




330




18







77




M




SD




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449




327




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77




M




CE




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461




335




20







78




K




N




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495




302




17







78




K




CA




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508




296




16







78




K




C




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516




298




18







78




K




O




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529




300




17







78




K




CB




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506




281




17







78




K




CG




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500




277




16







78




K




CD




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503




262




23







78




K




CE




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494




256




30







78




K




NZ




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497




242




33







79




A




N




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510




299




20







79




A




CA




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518




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79




A




C




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525




316




17







79




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183




D




C




27




598




387




22







183




D




O




19




592




394




16







183




D




CB




29




623




388




26







183




D




CG




16




626




396




25







183




D




OD1




14




621




407




27







183




D




OD2




8




635




390




27







184




V




N




31




594




375




22







184




V




CA




25




582




369




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184




V




C




28




569




376




19







184




V




O




19




562




379




16







184




V




CB




29




581




354




16







184




V




CG1




26




567




349




15







184




V




CG2




21




591




346




19







185




V




N




41




566




379




16







185




V




CA




44




554




386




15







185




V




C




39




553




400




16







185




V




O




37




543




406




19







185




V




CB




60




551




386




15







185




V




CG1




66




551




371




12







185




V




CG2




67




561




394




17







186




S




N




36




565




406




18







186




S




CA




30




566




419




19







186




S




C




15




564




419




23







186




S




O




9




558




429




25







186




S




CB




33




579




425




16







186




S




OG




47




582




426




18







187




T




N




8




569




409




23







187




T




CA




−5




569




408




23







187




T




C




−13




558




400




23







187




T




O




−22




552




404




21







187




T




CB




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583




404




25







187




T




OG1




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593




412




28







187




T




CG2




−26




584




406




32







188




L




N




−7




556




388




22







188




L




CA




−13




547




379




21







188




L




C




−15




532




383




20







188




L




O




−26




526




380




20







188




L




CB




−6




547




365




24







188




L




CG




−10




539




352




23







188




L




CD1




−4




545




340




25







188




L




CD2




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525




353




27







189




P




N




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526




390




20







189




P




CA




−8




512




394




18







189




P




C




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509




403




18







189




P




O




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499




401




19







189




P




CB




4




509




402




19







189




P




CG




14




519




397




18







189




P




CD




6




531




396




17







190




Q




N




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518




413




19







190




Q




CA




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515




421




21







190




Q




C




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517




413




21







190




Q




O




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510




415




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190




Q




CB




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523




434




22







190




Q




CG




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520




444




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190




Q




CD




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526




441




31







190




Q




OE1




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538




437




30







190




Q




NE2




−70




518




443




31







191




V




N




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527




404




19







191




V




CA




−60




530




396




21







191




V




C




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518




387




24







191




V




O




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514




386




25







191




V




CB




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543




388




16







191




V




CG1




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545




378




17







191




V




CG2




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555




398




16







192




V




N




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512




381




20







192




V




CA




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501




371




19







192




V




C




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488




377




24







192




V




O




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480




372




19







192




V




CB




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500




362




19







192




V




CG1




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487




354




17







192




V




CG2




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512




353




19







193




M




N




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485




389




25







193




M




CA




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472




395




25







193




M




C




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471




408




22







193




M




O




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461




414




21







193




M




CB




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466




398




26







193




M




CG




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470




387




32







193




M




SD




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462




389




33







193




M




CE




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449




404




19







194




G




N




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483




413




21







194




G




CA




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484




425




23







194




G




C




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478




437




27







194




G




O




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480




439




28







195




S




N




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470




445




25







195




S




CA




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463




457




23







195




S




C




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453




454




21







195




S




O




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448




464




23







195




S




CB




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456




464




24







195




S




OG




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447




456




29







196




S




N




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449




442




21







196




S




CA




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439




438




22







196




S




C




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445




438




20







196




S




O




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438




438




21







196




S




CB




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434




424




19







196




S




OG




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425




425




26







197




Y




N




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459




439




19







197




Y




CA




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465




439




19







197




Y




C




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464




453




19







197




Y




O




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471




462




21







197




Y




CB




−18




480




435




14







197




Y




CG




−4




486




434




13







197




Y




CD1




5




480




427




15







197




Y




CD2




−2




499




440




14







197




Y




CE1




18




487




426




14







197




Y




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9




505




439




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197




Y




CZ




19




499




431




15







197




Y




OH




31




506




430




16







198




G




N




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456




455




21







198




G




CA




4




454




468




21







198




G




C




11




465




475




19







198




G




O




10




467




487




20







199




F




N




18




474




468




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199




F




CA




25




485




474




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199




F




C




16




496




481




21







199




F




O




21




506




486




19







199




F




CB




35




492




464




19







199




F




CG




46




482




460




16







199




F




CD1




55




477




469




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199




F




CD2




47




478




446




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199




F




CE1




66




469




465




17







199




F




CE2




58




470




442




16







199




F




CZ




67




465




451




17







200




Q




N




3




495




480




20







200




Q




CA




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505




486




20







200




Q




C




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502




501




20







200




Q




O




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510




509




21







200




Q




CB




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507




479




20







200




Q




CG




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495




481




21







200




Q




CD




−40




495




473




20







200




Q




OE1




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504




474




18







200




Q




NE2




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486




464




17







201




Y




N




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490




505




21







201




Y




CA




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485




518




19







201




Y




C




6




485




527




23







201




Y




O




17




482




523




22







201




Y




CB




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470




518




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201




Y




CG




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467




509




16







201




Y




CD1




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475




511




18







201




Y




CD2




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457




500




18







201




Y




CE1




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472




504




21







201




Y




CE2




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454




492




22







201




Y




CZ




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462




494




24







201




Y




OH




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459




487




21







202




S




N




4




487




540




25







202




S




CA




14




487




550




21







202




S




C




14




472




554




18







202




S




O




4




465




550




20







202




S




CB




10




495




563




23







202




S




OG




0




489




570




23







203




P




N




24




466




560




20







203




P




CA




23




452




563




20







203




P




C




10




447




570




19







203




P




O




5




436




567




21







203




P




CB




36




450




572




19







203




P




CG




45




460




567




17







203




P




CD




36




472




566




18







204




G




N




4




455




579




22







204




G




CA




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452




586




21







204




G




C




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452




576




23







204




G




O




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443




577




25







205




Q




N




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462




567




23







205




Q




CA




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463




557




22







205




Q




C




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452




547




24







205




Q




O




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448




541




27







205




Q




CB




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476




551




20







205




Q




CG




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488




560




22







205




Q




CD




−30




501




554




24







205




Q




OE1




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503




547




27







205




Q




NE2




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511




557




23







206




R




N




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447




545




24







206




R




CA




−15




436




535




21







206




R




C




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423




541




21







206




R




O




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415




534




19







206




R




CB




0




434




532




21







206




R




CG




3




422




525




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206




R




CD




18




420




523




25







206




R




NE




21




417




510




34







206




R




CZ




21




405




505




32







206




R




NH1




19




394




513




41







206




R




NH2




22




403




492




31







207




V




N




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421




554




23







207




V




CA




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409




561




23







207




V




C




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410




562




20







207




V




O




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400




560




20







207




V




CB




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409




576




24







207




V




CG1




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397




583




24







207




V




CG2




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408




576




22







208




E




N




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421




564




19







208




E




CA




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423




565




23







208




E




C




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420




552




27







208




E




O




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413




551




28







208




E




CB




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438




569




23







208




E




CG




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442




569




30







208




E




CD




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456




574




37







208




E




OE1




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465




568




40







208




E




OE2




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457




585




43







209




F




N




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425




541




26







209




F




CA




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422




528




24







209




F




C




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407




524




24







209




F




O




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401




519




25







209




F




CB




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430




517




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209




F




CG




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427




503




32







209




F




CD1




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432




498




31







209




F




CD2




−52




418




495




30







209




F




CE1




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428




485




34







209




F




CE2




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414




482




31







209




F




CZ




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419




477




33







210




L




N




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400




527




22







210




L




CA




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386




524




21







210




L




C




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377




532




25







210




L




O




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368




527




25







210




L




CB




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381




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22







210




L




CG




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384




517




21







210




L




CD1




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383




524




20







210




L




CD2




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376




505




18







211




V




N




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381




545




27







211




V




CA




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374




554




26







211




V




C




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376




550




23







211




V




O




−94




366




548




21







211




V




CB




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379




569




28







211




V




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375




578




25







211




V




CG2




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375




575




28







212




N




N




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388




547




24







212




N




CA




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391




542




27







212




N




C




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384




529




30







212




N




O




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378




527




34







212




N




CB




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406




541




23







212




N




CG




−108




412




555




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212




N




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405




565




29







212




N




ND2




−106




425




556




24







213




T




N




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384




520




25







213




T




CA




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377




507




24







213




T




C




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362




509




23







213




T




O




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356




503




28







213




T




CB




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379




497




22







213




T




OG1




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393




495




19







213




T




CG2




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372




485




22







214




W




N




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357




518




22







214




W




CA




−93




342




521




25







214




W




C




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339




526




30







214




W




O




−112




328




523




31







214




W




CB




−82




339




531




21







214




W




CG




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324




533




22







214




W




CD1




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316




542




23







214




W




CD2




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316




524




24







214




W




NE1




−80




303




541




23







214




W




CE2




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303




530




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214




W




CE3




−64




318




513




20







214




W




CZ2




−65




292




524




23







214




W




CZ3




−57




307




508




15







214




W




CH2




−57




294




513




20







215




K




N




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348




534




32







215




K




CA




−125




346




541




36







215




K




C




−137




348




531




37







215




K




O




−147




342




533




38







215




K




CB




−127




356




552




33







215




K




CG




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353




565




35







215




K




CD




−125




364




575




39







215




K




CE




−120




361




589




41







215




K




NZ




−123




372




598




44







216




S




N




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355




520




37







216




S




CA




−145




357




510




36







216




S




C




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345




501




33







216




S




O




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345




494




36







216




S




CB




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370




502




34







216




S




OG




−131




368




493




34







217




K




N




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335




502




31







217




K




CA




−141




323




493




34







217




K




C




−148




312




502




39







217




K




O




−144




310




513




39







217




K




CB




−127




318




488




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217




K




CG




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328




483




29







217




K




CD




−123




336




471




24







217




K




CE




−113




347




467




20







217




K




NZ




−119




358




459




20







218




K




N




−158




306




496




40







218




K




CA




−165




295




502




42







218




K




C




−156




284




506




43







218




K




O




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277




517




45







218




K




CB




−176




289




493




46







218




K




CG




−184




300




486




53







218




K




CD




−196




293




478




55







218




K




CE




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302




467




57







218




K




NZ




−194




302




454




57







219




N




N




−146




282




498




43







219




N




CA




−136




271




500




44







219




N




C




−123




277




493




42







219




N




O




−120




273




482




43







219




N




CB




−141




258




494




48







219




N




CG




−131




247




496




57







219




N




OD1




−125




245




507




62







219




N




ND2




−128




239




486




63







220




P




N




−116




286




500




39







220




P




CA




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292




495




36







220




P




C




−92




282




492




31







220




P




O




−90




271




498




32







220




P




CB




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302




505




35







220




P




CG




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296




518




37







220




P




CD




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290




514




37







221




M




N




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286




482




28







221




M




CA




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279




478




26







221




M




C




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291




473




25







221




M




O




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300




468




22







221




M




CB




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269




467




28







221




M




CG




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262




461




32







221




M




SD




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273




448




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221




M




CE




−56




263




430




39







222




G




N




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290




477




22







222




G




CA




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301




473




22







222




G




C




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295




468




20







222




G




O




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283




471




21







223




F




N




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303




460




22







223




F




CA




−7




299




456




21







223




F




C




0




311




452




22







223




F




O




−4




322




450




23







223




F




CB




−8




289




443




22







223




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CG




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296




431




24







223




F




CD1




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301




422




22







223




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CD2




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296




428




25







223




F




CE1




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307




410




26







223




F




CE2




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302




416




27







223




F




CZ




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308




407




23







224




S




N




13




309




453




22







224




S




CA




22




320




450




22







224




S




C




29




316




437




19







224




S




O




29




304




434




19







224




S




CB




33




322




461




18







224




S




OG




40




310




464




19







225




Y




N




32




325




429




20







225




Y




CA




38




322




416




25







225




Y




C




52




329




416




23







225




Y




O




53




341




419




24







225




Y




CB




30




326




404




25







225




Y




CG




35




320




390




25







225




Y




CD1




33




307




387




22







225




Y




CD2




43




328




382




26







225




Y




CE1




38




301




375




23







225




Y




CE2




48




323




370




20







225




Y




CZ




46




309




367




20







225




Y




OH




51




304




355




19







226




D




N




62




321




412




26







226




D




CA




76




327




411




28







226




D




C




81




325




397




24







226




D




O




82




314




392




22







226




D




CB




85




320




421




32







226




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CG




100




323




419




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226




D




OD1




103




335




418




37







226




D




OD2




108




314




418




38







227




T




N




83




336




390




23







227




T




CA




89




336




377




25







227




T




C




104




336




377




25







227




T




O




110




344




384




26







227




T




CB




84




349




369




29







227




T




OG1




70




349




368




23







227




T




CG2




90




349




354




22







228




R




N




110




327




370




27







228




R




CA




124




325




369




32







228




R




C




131




338




362




33







228




R




O




128




340




351




38







228




R




CB




128




313




360




35







228




R




CG




142




313




355




45







228




R




CD




143




303




343




54







228




R




NE




143




289




348




64







228




R




CZ




133




280




344




65







228




R




NH1




123




284




336




65







228




R




NH2




134




268




349




64







229




C




N




138




345




370




31







229




C




CA




145




357




365




31







229




C




C




135




366




357




29







229




C




O




137




369




345




26







229




C




CB




157




353




357




33







229




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SG




167




366




351




47







230




F




N




125




371




364




25







230




F




CA




114




380




358




23







230




F




C




120




391




349




22







230




F




O




115




392




338




21







230




F




CB




105




386




369




21







230




F




CG




93




393




363




17







230




F




CD1




93




406




359




13







230




F




CD2




81




386




363




21







230




F




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81




412




355




15







230




F




CE2




69




392




358




16







230




F




CZ




69




405




354




13







231




D




N




130




398




354




20







231




D




CA




136




409




346




20







231




D




C




140




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332




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231




D




O




138




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322




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D




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148




415




353




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D




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144




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363




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231




D




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132




427




367




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231




D




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153




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367




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232




S




N




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330




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232




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150




388




317




22







232




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138




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309




24







232




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296




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232




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160




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319




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172




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323




28







233




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N




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379




315




25







233




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CA




115




374




307




21







233




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C




108




386




301




19







233




T




O




99




384




292




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106




365




316




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233




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99




374




326




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233




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113




354




323




21







234




V




N




110




398




306




15







234




V




CA




104




410




300




15







234




V




C




109




414




286




19







234




V




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121




417




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V




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105




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310




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234




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100




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V




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98




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N




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277




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17







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254




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96




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259




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E




N




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102




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239




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87




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9







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29







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E




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108




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196




28







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N




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N




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65




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N




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60




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248




17







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N




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N




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59




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N




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N




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D




N




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414




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D




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286




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I




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114




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R




N




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59




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73




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73




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R




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86




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R




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91




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R




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11







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E




N




36




485




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37




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293




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289




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65




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74




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314




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512




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28




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55




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56




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33







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E




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51




559




244




25







244




S




N




21




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263




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7




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258




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249




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21







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I




N




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519




281




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I




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I




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299




18







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I




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301




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245




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303




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496




296




13







245




I




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512




316




14







245




I




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484




304




18







246




Y




N




7




538




300




19







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11




552




306




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5




562




297




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573




301




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26




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306




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34




544




313




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30




536




323




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48




542




309




17







246




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38




527




330




20







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Y




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56




533




315




19







246




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51




525




325




19







246




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59




515




331




19







247




Q




N




5




560




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19







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581




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5




567




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20




569




257




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247




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26




583




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247




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18




593




260




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39




585




257




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248




C




N




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281




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283




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576




292




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C




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291




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248




C




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551




288




19







248




C




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538




276




22







249




C




N




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578




302




20







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C




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589




311




19







249




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603




305




22







249




C




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293




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249




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590




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575




330




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D




N




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312




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307




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323




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D




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315




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D




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311




27







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D




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306




34







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D




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314




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251




L




N




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303




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653




294




22







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L




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284




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4




630




300




18







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3




616




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9




606




296




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11




616




319




22







252




A




N




5




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299




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10




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279




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280




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P




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E




N




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75




705




294




41







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92




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281




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A




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55




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R




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Q




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95




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307




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N




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N




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313




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319




497




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N




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320




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N




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N




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N




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N




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345




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S




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495




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359




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287




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375




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380




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286




49







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N




N




326




486




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N




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314




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266




25







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N




C




313




465




268




25







279




N




O




320




457




262




23







279




N




CB




311




483




251




28







279




N




CG




298




477




246




31







279




N




OD1




298




470




236




36







279




N




ND2




287




479




253




36







280




C




N




304




461




277




21







280




C




CA




302




447




281




22







280




C




C




292




440




272




19







280




C




O




291




427




272




19







280




C




CB




297




445




295




24







280




C




SG




310




451




307




33







281




G




N




283




447




265




21







281




G




CA




273




441




257




20







281




G




C




261




449




254




18







281




G




O




261




462




255




17







282




Y




N




249




442




253




21







282




Y




CA




237




449




250




18







282




Y




C




225




442




257




18







282




Y




O




224




430




257




20







282




Y




CB




234




449




235




19







282




Y




CG




226




461




231




21







282




Y




CD1




231




473




229




16







282




Y




CD2




212




460




228




23







282




Y




CE1




224




484




225




20







282




Y




CE2




204




470




224




15







282




Y




CZ




210




483




222




21







282




Y




OH




202




493




219




26







283




R




N




216




450




263




20







283




R




CA




204




446




270




19







283




R




C




191




448




262




22







283




R




O




190




459




255




24







283




R




CB




204




453




283




22







283




R




CG




190




454




290




22







283




R




CD




191




466




299




21







283




R




NE




178




472




299




29







283




R




CZ




175




485




295




21







283




R




NH1




184




493




291




16







283




R




NH2




162




489




295




27







284




R




N




182




438




262




23







284




R




CA




170




439




255




24







284




R




C




158




434




264




22







284




R




O




149




428




260




25







284




R




CB




170




431




242




21







284




R




CG




180




437




231




28







284




R




CD




179




429




218




35







284




R




NE




192




431




211




45







284




R




CZ




194




441




203




53







284




R




NH1




185




451




201




54







284




R




NH2




206




442




197




55







285




C




N




160




437




277




20







285




C




CA




150




432




287




17







285




C




C




149




443




297




11







285




C




O




155




454




295




13







285




C




CB




154




419




293




20







285




C




SG




170




419




302




16







286




R




N




142




441




308




14







286




R




CA




141




451




318




15







286




R




C




154




455




325




16







286




R




O




161




446




329




17







286




R




CB




131




447




329




17







286




R




CG




131




455




342




14







286




R




CD




120




467




341




17







286




R




NE




107




461




341




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286




R




CZ




97




464




333




18







286




R




NH1




99




474




324




21







286




R




NH2




86




458




333




19







287




A




N




156




468




326




16







287




A




CA




168




474




333




13







287




A




C




163




474




348




18







287




A




O




152




478




351




17







287




A




CB




171




488




329




10







288




S




N




172




469




357




19







288




S




CA




169




469




371




21







288




S




C




170




482




378




20







288




S




O




164




484




389




23







288




S




CB




177




458




378




23







288




S




OG




191




462




377




27







289




G




N




177




492




372




18







289




G




CA




179




505




378




14







289




G




C




172




517




372




16







289




G




O




179




527




370




17







290




V




N




159




516




369




17







290




V




CA




152




527




363




16







290




V




C




139




530




372




16







290




V




O




135




521




379




15







290




V




CB




148




526




348




13







290




V




CG1




161




527




339




13







290




V




CG2




141




513




345




8







291




L




N




134




542




370




17







291




L




CA




122




546




378




18







291




L




C




110




537




375




20







291




L




O




103




533




385




20







291




L




CB




118




560




375




13







291




L




CG




107




566




383




17







291




L




CD1




109




565




398




18







291




L




CD2




105




581




380




19







292




T




N




109




532




363




20







292




T




CA




98




523




360




19







292




T




C




99




508




362




19







292




T




O




90




501




359




19







292




T




CB




94




525




345




18







292




T




OG1




106




524




337




20







292




T




CG2




88




539




342




16







293




T




N




110




504




368




15







293




T




CA




112




490




371




14







293




T




C




101




483




379




14







293




T




O




95




473




376




16







293




T




CB




127




487




377




17







293




T




OG1




137




492




369




21







293




T




CG2




129




472




380




14







294




S




N




97




490




390




14







294




S




CA




86




485




399




15







294




S




C




73




485




392




15







294




S




O




66




475




391




14







294




S




CB




86




493




412




14







294




S




OG




78




487




422




17







295




C




N




69




497




387




15







295




C




CA




56




499




380




17







295




C




C




54




489




368




18







295




C




O




44




482




367




18







295




C




CB




54




513




377




14







295




C




SG




37




517




370




24







296




G




N




64




489




359




18







296




G




CA




63




481




347




14







296




G




C




63




467




351




16







296




G




O




55




459




345




16







297




N




N




71




462




361




16







297




N




CA




70




448




365




15







297




N




C




57




445




371




12







297




N




O




52




434




368




14







297




N




CB




81




445




376




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297




N




CG




95




442




369




25







297




N




OD1




96




441




357




21







297




N




ND2




105




439




378




20







298




T




N




51




454




379




14







298




T




CA




37




451




385




16







298




T




C




27




450




374




15







298




T




O




19




441




373




17







298




T




CB




34




461




396




21







298




T




OG1




45




463




405




23







298




T




CG2




22




456




404




18







299




L




N




26




460




365




16







299




L




CA




17




460




354




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299




L




C




18




448




345




20







299




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O




7




441




342




19







299




L




CB




19




473




345




15







299




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CG




14




486




351




15







299




L




CD1




17




497




341




19







299




L




CD2




0




485




353




17







300




T




N




30




444




342




19







300




T




CA




32




432




333




16







300




T




C




29




419




340




15







300




T




O




24




410




335




15







300




T




CB




47




433




327




21







300




T




OG1




48




443




318




25







300




T




CG2




50




420




320




21







301




C




N




33




418




353




16







301




C




CA




30




406




361




15







301




C




C




14




405




362




11







301




C




O




9




394




359




15







301




C




CB




36




407




375




15







301




C




SG




34




391




384




21







302




Y




N




8




416




365




12







302




Y




CA




−6




416




366




18







302




Y




C




−13




412




353




17







302




Y




O




−23




405




352




17







302




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CB




−11




429




371




18







302




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CG




−26




431




372




20







302




Y




CD1




−33




427




384




23







302




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CD2




−33




437




362




23







302




Y




CE1




−46




429




385




25







302




Y




CE2




−47




439




363




24







302




Y




CZ




−54




435




375




25







302




Y




OH




−67




437




376




25







303




L




N




−8




418




342




17







303




L




CA




−14




416




328




17







303




L




C




−13




401




325




18







303




L




O




−23




395




323




18







303




L




CB




−6




424




318




15







303




L




CG




−9




422




303




18







303




L




CD1




−24




422




300




11







303




L




CD2




−2




433




295




13







304




K




N




−1




395




325




17







304




K




CA




0




381




322




15







304




K




C




−6




372




332




18







304




K




O




−11




361




328




18







304




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CB




15




378




322




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304




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CG




23




386




311




13







304




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CD




38




381




310




11







304




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CE




46




390




301




13







304




K




NZ




60




385




299




15







305




A




N




−6




376




345




16







305




A




CA




−12




367




355




18







305




A




C




−27




367




354




15







305




A




O




−34




356




354




18







305




A




CB




−8




371




369




22







306




S




N




−33




379




352




17







306




S




CA




−48




380




350




19







306




S




C




−53




372




338




20







306




S




O




−62




364




339




15







306




S




CB




−52




394




348




18







306




S




OG




−49




403




359




22







307




A




N




−46




373




327




18







307




A




CA




−49




366




315




15







307




A




C




−47




351




316




17







307




A




O




−55




343




311




21







307




A




CB




−40




371




303




13







308




A




N




−37




346




324




16







308




A




CA




−34




332




326




14







308




A




C




−45




326




335




14







308




A




O




−48




314




334




16







308




A




CB




−21




330




332




15







309




C




N




−51




334




344




19







309




C




CA




−61




329




353




22







309




C




C




−74




326




344




20







309




C




O




−80




315




346




23







309




C




CB




−65




340




363




21







309




C




SG




−54




342




377




27







310




R




N




−77




335




335




24







310




R




CA




−88




332




326




22







310




R




C




−85




320




317




23







310




R




O




−93




311




316




24







310




R




CB




−90




345




317




17







310




R




CG




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357




325




16







310




R




CD




−97




368




316




14







310




R




NE




−99




380




324




18







310




R




CZ




−105




391




320




19







310




R




NH1




−109




393




307




25







310




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NH2




−106




402




328




22







311




A




N




−72




319




312




25







311




A




CA




−68




307




305




25







311




A




C




−69




294




313




27







311




A




O




−73




284




307




27







311




A




CB




−54




309




300




24







312




A




N




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294




325




26







312




A




CA




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282




334




27







312




A




C




−80




280




339




27







312




A




O




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269




346




26







312




A




CB




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284




345




29







313




K




N




−89




289




337




29







313




K




CA




−103




289




342




30







313




K




C




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288




357




30







313




K




O




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280




362




29







313




K




CB




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277




335




33







313




K




CG




−111




278




320




36







313




K




CD




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264




314




39







313




K




CE




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254




315




48







313




K




NZ




−110




241




309




53







314




L




N




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296




363




29







314




L




CA




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297




378




29







314




L




C




−109




304




383




29







314




L




O




−113




314




376




33







314




L




CB




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304




383




28







314




L




CG




−71




296




387




29







314




L




CD1




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285




377




32







314




L




CD2




−58




304




388




26







315




Q




N




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299




393




31







315




Q




CA




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305




398




35







315




Q




C




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317




408




33







315




Q




O




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315




419




33







315




Q




CB




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294




405




42







315




Q




CG




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285




395




50







315




Q




CD




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293




388




56







315




Q




OE1




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297




377




58







315




Q




NE2




−166




295




395




57







316




D




N




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328




406




35







316




D




CA




−133




340




415




37







316




D




C




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342




420




37







316




D




O




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340




432




37







316




D




CB




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338




427




39







316




D




CG




−145




351




435




46







316




D




OD1




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362




431




52







316




D




OD2




−152




351




445




50







317




C




N




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347




411




35







317




C




CA




−96




350




415




30







317




C




C




−94




364




420




28







317




C




O




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373




415




27







317




C




CB




−87




348




403




28







317




C




SG




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332




397




30







318




T




N




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364




431




26







318




T




CA




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377




436




26







318




T




C




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376




437




25







318




T




O




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366




442




26







318




T




CB




−87




379




451




27







318




T




OG1




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376




451




30







318




T




CG2




−85




393




455




21







319




M




N




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386




431




24







319




M




CA




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386




431




26







319




M




C




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397




439




22







319




M




O




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407




442




20







319




M




CB




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386




417




28







319




M




CG




−45




374




409




36







319




M




SD




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377




389




41







319




M




CE




−31




395




390




34







320




L




N




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395




443




23







320




L




CA




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405




450




21







320




L




C




−6




406




443




18







320




L




O




0




395




442




18







320




L




CB




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401




465




20







320




L




CG




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412




474




19







320




L




CD1




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425




472




18







320




L




CD2




−11




407




488




23







321




V




N




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417




437




20







321




V




CA




9




418




430




19







321




V




C




18




429




435




16







321




V




O




14




441




438




16







321




V




CB




6




421




414




18







321




V




CG1




18




419




406




17







321




V




CG2




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412




410




18







322




N




N




31




426




436




17







322




N




CA




42




436




441




19







322




N




C




53




433




431




19







322




N




O




61




425




433




19







322




N




CB




47




432




455




21







322




N




CG




37




435




465




22







322




N




OD1




27




427




467




26







322




N




ND2




39




446




473




23







323




G




N




53




441




420




20







323




G




CA




64




439




410




19







323




G




C




62




425




404




20







323




G




O




52




421




400




20







324




D




N




73




417




405




21







324




D




CA




74




404




400




19







324




D




C




68




393




409




22







324




D




O




69




381




407




23







324




D




CB




88




400




396




25







324




D




CG




97




398




409




29







324




D




OD1




98




407




417




28







324




D




OD2




103




387




410




36







325




D




N




64




398




421




22







325




D




CA




59




388




431




23







325




D




C




43




388




430




19







325




D




O




36




398




430




15







325




D




CB




63




393




445




27







325




D




CG




64




381




455




35







325




D




OD1




54




375




458




39







325




D




OD2




76




378




458




38







326




L




N




39




375




429




17







326




L




CA




24




373




427




21







326




L




C




18




363




436




18







326




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O




24




352




439




19







326




L




CB




22




367




412




22







326




L




CG




8




362




409




23







326




L




CD1




−1




374




409




22







326




L




CD2




8




356




395




24







327




V




N




6




365




441




21







327




V




CA




−1




356




449




22







327




V




C




−15




357




444




21







327




V




O




−21




367




441




18







327




V




CB




0




360




464




20







327




V




CG1




−12




365




470




27







327




V




CG2




5




348




472




21







328




V




N




−21




345




443




23







328




V




CA




−35




343




438




25







328




V




C




−43




335




448




24







328




V




O




−39




324




452




27







328




V




CB




−35




335




424




24







328




V




CG1




−50




334




420




23







328




V




CG2




−28




343




413




26







329




I




N




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341




451




27







329




I




CA




−65




334




460




26







329




I




C




−77




333




452




28







329




I




O




−82




342




445




26







329




I




CB




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342




473




27







329




I




CG1




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343




482




25







329




I




CG2




−79




336




481




21







329




I




CD1




−55




352




493




24







330




C




N




−83




321




452




30







330




C




CA




−95




318




444




32







330




C




C




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308




451




34







330




C




O




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303




462




33







330




C




CB




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312




430




29







330




C




SG




−81




296




432




31







331




E




N




−114




304




444




34







331




E




CA




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294




449




33







331




E




C




−120




281




445




32







331




E




O




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278




433




36







331




E




CB




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298




443




31







331




E




CG




−150




292




449




33







331




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CD




−152




297




463




31







331




E




OE1




−156




309




465




28







331




E




OE2




−151




289




472




31







332




S




N




−118




272




454




32







332




S




CA




−113




258




452




33







332




S




C




−123




249




444




38







332




S




O




−136




251




446




40







332




S




CB




−109




251




464




33







332




S




OG




−105




238




462




30







333




A




N




−119




240




436




38







333




A




CA




−127




231




429




39







333




A




C




−122




216




431




40







333




A




O




−124




208




423




46







333




A




CB




−126




234




414




35







334




G




N




−116




214




443




37







334




G




CA




−111




201




446




36







334




G




C




−96




200




444




37







334




G




O




−91




206




434




39







335




V




N




−89




193




453




37







335




V




CA




−75




191




452




41







335




V




C




−69




187




438




42







335




V




O




−60




193




433




42







335




V




CB




−69




182




464




41







335




V




CG1




−77




169




464




44







335




V




CG2




−54




180




462




44







336




Q




N




−76




177




432




45







336




Q




CA




−71




171




419




45







336




Q




C




−74




181




408




44







336




Q




O




−66




182




398




41







336




Q




CB




−78




158




416




49







336




Q




CG




−74




147




426




53







336




Q




CD




−58




146




428




59







336




Q




OE1




−51




147




418




63







336




Q




NE2




−54




143




440




63







337




E




N




−85




188




409




40







337




E




CA




−88




198




399




39







337




E




C




−79




210




401




41







337




E




O




−74




216




391




40







337




E




CB




−103




202




400




38







337




E




CG




−108




211




388




43







337




E




CD




−105




206




374




46







337




E




OE1




−106




194




371




41







337




E




OE2




−101




214




365




49







338




D




N




−76




214




413




40







338




D




CA




−67




225




417




34







338




D




C




−53




223




411




31







338




D




O




−47




233




407




31







338




D




CB




−67




228




432




30







338




D




CG




−80




234




437




31







338




D




OD1




−89




238




429




34







338




D




OD2




−82




236




449




31







339




A




N




−48




211




411




29







339




A




CA




−35




208




406




30







339




A




C




−35




209




391




33







339




A




O




−26




214




384




35







339




A




CB




−31




194




410




30







340




A




N




−47




206




385




32







340




A




CA




−48




207




370




31







340




A




C




−49




221




366




29







340




A




O




−42




225




356




27







340




A




CB




−61




199




366




28







341




S




N




−56




230




373




28







341




S




CA




−58




244




370




29







341




S




C




−44




251




371




30







341




S




O




−42




261




363




29







341




S




CB




−68




250




379




28







341




S




OG




−80




244




377




34







342




L




N




−36




247




380




31







342




L




CA




−22




253




382




29







342




L




C




−13




250




371




27







342




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O




−5




259




367




28







342




L




CB




−16




249




395




28







342




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CG




−17




259




407




25







342




L




CD1




−7




255




418




22







342




L




CD2




−14




272




402




28







343




R




N




−14




238




366




26







343




R




CA




−5




234




354




29







343




R




C




−10




242




342




27







343




R




O




−1




246




334




26







343




R




CB




−7




219




351




31







343




R




CG




5




210




355




41







343




R




CD




2




195




353




47







343




R




NE




−5




193




341




58







343




R




CZ




−16




187




340




64







343




R




NH1




−22




182




351




67







343




R




NH2




−23




186




328




66







344




A




N




−23




245




341




27







344




A




CA




−28




253




330




24







344




A




C




−24




267




331




24







344




A




O




−20




274




321




24







344




A




CB




−43




252




329




23







345




F




N




−24




272




344




24







345




F




CA




−20




286




346




22







345




F




C




−5




288




343




20







345




F




O




−1




297




336




23







345




F




CB




−22




289




361




16







345




F




CG




−17




303




365




17







345




F




CD1




−4




305




370




17







345




F




CD2




−26




314




365




16







345




F




CE1




0




318




373




19







345




F




CE2




−22




327




368




15







345




F




CZ




−9




329




373




17







346




T




N




3




278




347




20







346




T




CA




17




279




345




23







346




T




C




20




278




330




23







346




T




O




28




286




325




24







346




T




CB




24




267




352




22







346




T




OG1




21




268




366




24







346




T




CG2




39




268




349




21







347




E




N




13




270




323




23







347




E




CA




14




268




308




21







347




E




C




11




281




301




20







347




E




O




17




285




292




22







347




E




CB




5




257




303




21







347




E




CG




11




243




307




26







347




E




CD




1




232




305




35







347




E




OE1




−10




234




301




38







347




E




OE2




5




220




308




40







348




A




N




1




288




307




17







348




A




CA




−2




301




301




17







348




A




C




7




311




303




18







348




A




O




11




318




294




21







348




A




CB




−16




305




306




17







349




M




N




12




311




316




21







349




M




CA




23




321




319




17







349




M




C




35




318




311




16







349




M




O




42




328




307




16







349




M




CB




27




319




334




20







349




M




CG




17




324




344




12







349




M




SD




14




344




343




22







349




M




CE




31




352




352




21







350




T




N




38




306




308




14







350




T




CA




50




302




300




21







350




T




C




48




308




285




24







350




T




O




58




314




280




21







350




T




CB




52




287




299




21







350




T




OG1




53




282




313




25







350




T




CG2




64




284




291




22







351




R




N




36




307




279




22







351




R




CA




34




312




266




20







351




R




C




36




327




265




18







351




R




O




39




332




255




20







351




R




CB




20




309




261




19







351




R




CG




17




295




257




19







351




R




CD




3




294




252




22







351




R




NE




−2




282




258




34







351




R




CZ




−12




281




267




30







351




R




NH1




−17




292




272




30







351




R




NH2




−15




269




272




33







352




Y




N




33




333




276




19







352




Y




CA




34




348




277




16







352




Y




C




48




352




281




16







352




Y




O




51




363




284




20







352




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CB




25




353




288




18







352




Y




CG




10




351




286




22







352




Y




CD1




5




351




273




21







352




Y




CD2




1




349




297




21







352




Y




CE1




−8




349




271




22







352




Y




CE2




−11




347




295




23







352




Y




CZ




−17




348




282




23







352




Y




OH




−30




347




281




24







353




S




N




57




342




281




21







353




S




CA




71




344




284




26







353




S




C




75




345




299




28







353




S




O




85




351




302




35







353




S




CB




78




354




276




21







353




S




OG




79




367




282




28







354




A




N




66




340




308




26







354




A




CA




69




341




322




26







354




A




C




70




327




328




27







354




A




O




62




323




337




26







354




A




CB




59




349




329




23







355




P




N




80




319




324




28







355




P




CA




81




305




330




27







355




P




C




84




306




344




29







355




P




O




89




316




350




27







355




P




CB




93




300




321




23







355




P




CG




101




312




320




26







355




P




CD




92




322




316




29







356




P




N




81




295




352




32







356




P




CA




83




294




366




32







356




P




C




97




289




370




33







356




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O




104




283




363




35







356




P




CB




73




284




370




34







356




P




CG




73




274




359




31







356




P




CD




73




284




347




34







357




G




N




101




294




382




33







357




G




CA




114




289




388




36







357




G




C




110




277




395




40







357




G




O




114




266




392




41







358




D




N




102




279




406




43







358




D




CA




97




268




414




45







358




D




C




83




265




409




42







358




D




O




75




274




407




41







358




D




CB




97




271




429




49







358




D




CG




110




274




435




52







358




D




OD1




119




264




434




56







358




D




OD2




113




285




440




55







359




P




N




80




252




408




41







359




P




CA




66




248




403




41







359




P




C




56




253




413




38







359




P




O




57




251




425




40







359




P




CB




66




233




403




43







359




P




CG




81




230




400




42







359




P




CD




88




240




409




41







360




P




N




46




261




409




36







360




P




CA




35




266




418




33







360




P




C




29




254




426




34







360




P




O




29




243




421




35







360




P




CB




25




272




409




35







360




P




CG




33




276




396




35







360




P




CD




42




264




395




33







361




Q




N




24




257




438




37







361




Q




CA




18




247




446




36







361




Q




C




5




252




452




30







361




Q




O




5




262




459




27







361




Q




CB




28




242




457




43







361




Q




CG




25




230




464




57







361




Q




CD




35




226




474




64







361




Q




OE1




33




227




486




67







361




Q




NE2




47




222




469




67







362




P




N




−5




244




451




29







362




P




CA




−18




248




457




27







362




P




C




−17




247




472




25







362




P




O




−13




237




478




26







362




P




CB




−28




238




451




26







362




P




CG




−21




231




440




25







362




P




CD




−7




231




444




28







363




E




N




−22




258




479




25







363




E




CA




−21




258




493




27







363




E




C




−35




260




499




28







363




E




O




−43




268




494




25







363




E




CB




−11




269




499




28







363




E




CG




2




266




496




29







363




E




CD




8




254




505




33







363




E




OE1




1




249




514




33







363




E




OE2




20




250




503




33







364




Y




N




−38




253




510




31







364




Y




CA




−51




254




516




34







364




Y




C




−51




260




530




34







364




Y




O




−61




260




538




34







364




Y




CB




−59




240




516




35







364




Y




CG




−60




235




502




37







364




Y




CD1




−71




238




494




36







364




Y




CD2




−50




226




497




35







364




Y




CE1




−72




234




481




34







364




Y




CE2




−51




222




483




34







364




Y




CZ




−62




226




476




34







364




Y




OH




−62




222




462




38







365




D




N




−39




264




534




35







365




D




CA




−36




271




547




35







365




D




C




−30




284




544




33







365




D




O




−19




284




538




34







365




D




CB




−27




262




555




40







365




D




CG




−25




267




570




48







365




D




OD1




−28




279




573




50







365




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OD2




−19




259




578




53







366




L




N




−37




295




547




32







366




L




CA




−32




308




544




34







366




L




C




−18




311




549




34







366




L




O




−9




316




542




34







366




L




CB




−41




319




549




32







366




L




CG




−37




333




547




34







366




L




CD1




−34




336




532




35







366




L




CD2




−48




343




552




33







367




E




N




−15




307




562




34







367




E




CA




−2




308




568




35







367




E




C




8




301




561




34







367




E




O




20




304




563




30







367




E




CB




−3




303




583




40







367




E




CG




−13




310




592




45







367




E




CD




−13




305




606




49







367




E




OE1




−2




302




611




51







367




E




OE2




−23




304




612




52







368




L




N




5




292




552




34







368




L




CA




15




284




545




33







368




L




C




19




290




531




32







368




L




O




26




284




524




32







368




L




CB




10




270




543




36







368




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CG




9




263




556




36







368




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CD1




5




248




554




37







368




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CD2




22




263




563




37







369




I




N




13




302




528




31







369




I




CA




16




308




516




28







369




I




C




27




319




518




29







369




I




O




25




329




526




29







369




I




CB




4




314




509




26







369




I




CG1




−5




303




505




22







369




I




CG2




8




323




497




21







369




I




CD1




−18




308




499




21







370




T




N




38




318




511




27







370




T




CA




49




328




511




28







370




T




C




48




337




499




27







370




T




O




50




332




488




30







370




T




CB




63




322




512




29







370




T




OG1




64




314




525




27







370




T




CG2




74




332




512




24







371




S




N




45




350




501




31







371




S




CA




45




360




490




32







371




S




C




52




372




496




34







371




S




O




50




376




507




30







371




S




CB




30




364




487




34







371




S




OG




23




369




499




33







372




C




N




62




377




488




34







372




C




CA




70




388




491




35







372




C




C




80




384




503




33







372




C




O




84




392




511




31







372




C




CB




62




400




496




35







372




C




SG




55




410




482




34







373




S




N




84




371




502




33







373




S




CA




93




365




512




35







373




S




C




86




364




527




35







373




S




O




93




361




536




35







373




S




CB




106




372




513




34







373




S




OG




114




370




501




33







374




S




N




73




367




527




30







374




S




CA




66




368




540




27







374




S




C




55




358




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27







374




S




O




53




350




530




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374




S




CB




61




382




541




28







374




S




OG




71




392




539




36







375




N




N




47




358




551




26







375




N




CA




36




349




553




24







375




N




C




28




355




565




26







375




N




O




33




363




573




25







375




N




CB




40




334




556




25







375




N




CG




46




332




569




28







375




N




OD1




59




333




571




24







375




N




ND2




39




328




579




27







376




V




N




15




351




566




26







376




V




CA




6




355




576




24







376




V




C




8




345




588




23







376




V




O




10




334




585




22







376




V




CB




−8




356




571




27







376




V




CG1




−18




356




583




22







376




V




CG2




−11




368




562




23







377




S




N




7




351




600




23







377




S




CA




8




342




612




21







377




S




C




0




348




623




21







377




S




O




−5




359




621




21







377




S




CB




23




341




617




15







377




S




OG




25




328




624




17







378




V




N




−2




341




634




25







378




V




CA




−11




345




645




27







378




V




C




−4




346




659




24







378




V




O




4




338




662




23







378




V




CB




−23




335




646




25







378




V




CG1




−35




341




654




26







378




V




CG2




−27




330




633




28







379




A




N




−8




356




666




25







379




A




CA




−3




359




680




26







379




A




C




−16




363




687




29







379




A




O




−27




361




682




29







379




A




CB




6




370




680




22







380




H




N




−14




369




699




29







380




H




CA




−26




373




707




27







380




H




C




−22




386




714




28







380




H




O




−11




387




720




31







380




H




CB




−29




363




718




28







380




H




CG




−33




350




712




30







380




H




ND1




−46




345




711




30







380




H




CD2




−25




339




708




30







380




H




CE1




−46




333




706




31







380




H




NE2




−33




329




704




34







381




D




N




−30




396




713




27







381




D




CA




−27




409




720




29







381




D




C




−29




409




735




31







381




D




O




−32




398




740




32







381




D




CB




−36




420




714




32







381




D




CG




−51




419




717




37







381




D




OD1




−55




409




722




31







381




D




OD2




−58




429




714




43







382




A




N




−28




420




742




34







382




A




CA




−30




421




756




37







382




A




C




−43




413




760




38







382




A




O




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29







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1380




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1383




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1387




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OW




345




361




712




50







END










































<160> NUMBER OF SEQ ID NOS:  1













<210> SEQ ID NO 1






<211> LENGTH: 576






<212> TYPE: PRT






<213> ORGANISM: Hepatitis C virus






<220> FEATURE:






<221> NAME/KEY: VARIANT






<222> LOCATION: (335)






<223> OTHER INFORMATION: amino acids at 335, 






#344 and 550 may be






      threonine or valine at 335, vali






#ne or alanine at 344 and arginine






      or glutamine at 550













<400> SEQUENCE: 1













Ala Ser His His His His His His Ser Tyr T






#hr Trp Thr Gly Ala Leu






  1               5 






#                 10 






#                 15













Ile Thr Pro Cys Ala Ala Glu Glu Ser Lys L






#eu Pro Ile Asn Ala Leu






             20     






#             25     






#             30













Ser Asn Ser Leu Leu Arg His His Asn Met V






#al Tyr Ala Thr Thr Ser






         35         






#         40         






#         45













Arg Ser Ala Gly Leu Arg Gln Lys Lys Val T






#hr Phe Asp Arg Leu Gln






     50             






#     55             






#     60













Val Leu Asp Asp His Tyr Arg Asp Val Leu L






#ys Glu Met Lys Ala Lys






 65                 






# 70                 






# 75                 






# 80













Ala Ser Thr Val Lys Ala Lys Leu Leu Ser V






#al Glu Glu Ala Cys Lys






                 85 






#                 90 






#                 95













Leu Thr Pro Pro His Ser Ala Lys Ser Lys P






#he Gly Tyr Gly Ala Lys






            100     






#            105     






#            110













Asp Val Arg Asn Leu Ser Ser Lys Ala Val A






#sn His Ile His Ser Val






        115         






#        120         






#        125













Trp Lys Asp Leu Leu Glu Asp Thr Val Thr P






#ro Ile Asp Thr Thr Ile






    130             






#    135             






#    140













Met Ala Lys Asn Glu Val Phe Cys Val Gln P






#ro Glu Lys Gly Gly Arg






145                 






#150                 






#155                 






#160













Lys Pro Ala Arg Leu Ile Val Phe Pro Asp L






#eu Gly Val Arg Val Cys






                165 






#                170 






#                175













Glu Lys Met Ala Leu Tyr Asp Val Val Ser T






#hr Leu Pro Gln Val Val






            180     






#            185     






#            190













Met Gly Ser Ser Tyr Gly Phe Gln Tyr Ser P






#ro Gly Gln Arg Val Glu






        195         






#        200         






#        205













Phe Leu Val Asn Thr Trp Lys Ser Lys Lys A






#sn Pro Met Gly Phe Ser






    210             






#    215             






#    220













Tyr Asp Thr Arg Cys Phe Asp Ser Thr Val T






#hr Glu Asn Asp Ile Arg






225                 






#230                 






#235                 






#240













Val Glu Glu Ser Ile Tyr Gln Cys Cys Asp L






#eu Ala Pro Glu Ala Arg






                245 






#                250 






#                255













Gln Ala Ile Lys Ser Leu Thr Glu Arg Leu T






#yr Ile Gly Gly Pro Leu






            260     






#            265     






#            270













Thr Asn Ser Lys Gly Gln Asn Cys Gly Tyr A






#rg Arg Cys Arg Ala Ser






        275         






#        280         






#        285













Gly Val Leu Thr Thr Ser Cys Gly Asn Thr L






#eu Thr Cys Tyr Leu Lys






    290             






#    295             






#    300













Ala Ser Ala Ala Cys Arg Ala Ala Lys Leu G






#ln Asp Cys Thr Met Leu






305                 






#310                 






#315                 






#320













Val Asn Gly Asp Asp Leu Val Val Ile Cys G






#lu Ser Ala Gly Xaa Gln






                325 






#                330 






#                335













Glu Asp Ala Ala Ser Leu Arg Xaa Phe Thr G






#lu Ala Met Thr Arg Tyr






            340     






#            345     






#            350













Ser Ala Pro Pro Gly Asp Pro Pro Gln Pro G






#lu Tyr Asp Leu Glu Leu






        355         






#        360         






#        365













Ile Thr Ser Cys Ser Ser Asn Val Ser Val A






#la His Asp Ala Ser Gly






    370             






#    375             






#    380













Lys Arg Val Tyr Tyr Leu Thr Arg Asp Pro T






#hr Thr Pro Leu Ala Arg






385                 






#390                 






#395                 






#400













Ala Ala Trp Glu Thr Ala Arg His Thr Pro V






#al Asn Ser Trp Leu Gly






                405 






#                410 






#                415













Asn Ile Ile Met Tyr Ala Pro Thr Leu Trp A






#la Arg Met Ile Leu Met






            420     






#            425     






#            430













Thr His Phe Phe Ser Ile Leu Leu Ala Gln G






#lu Gln Leu Glu Lys Ala






        435         






#        440         






#        445













Leu Asp Cys Gln Ile Tyr Gly Ala Cys Tyr S






#er Ile Glu Pro Leu Asp






    450             






#    455             






#    460













Leu Pro Gln Ile Ile Glu Arg Leu His Gly L






#eu Ser Ala Phe Ser Leu






465                 






#470                 






#475                 






#480













His Ser Tyr Ser Pro Gly Glu Ile Asn Arg V






#al Ala Ser Cys Leu Arg






                485 






#                490 






#                495













Lys Leu Gly Val Pro Pro Leu Arg Val Trp A






#rg His Arg Ala Arg Ser






            500     






#            505     






#            510













Val Arg Ala Arg Leu Leu Ser Gln Gly Gly A






#rg Ala Ala Thr Cys Gly






        515         






#        520         






#        525













Lys Tyr Leu Phe Asn Trp Ala Val Lys Thr L






#ys Leu Lys Leu Thr Pro






    530             






#    535             






#    540













Ile Pro Ala Ala Ser Xaa Leu Asp Leu Ser G






#ly Trp Phe Val Ala Gly






545                 






#550                 






#555                 






#560













Tyr Ser Gly Gly Asp Ile Tyr His Ser Leu S






#er Arg Ala Arg Pro Arg






                565 






#                570 






#                575













Claims
  • 1. A crystalline composition comprising an HCV NS5B polypeptide, which comprises the amino acid sequence of SEQ ID NO: 1, wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 4.0 Ångströms.
  • 2. The composition of claim 1, wherein the HCV NS5B polypeptide comprises a valine at position 335, an alanine at position 344, and a glutamine at position 550.
  • 3. The crystalline composition of claim 1, wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 2.8 Ångströms.
  • 4. The crystalline composition of claim 1, wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 2.2 Ångströms.
  • 5. A method for preparing a crystalline composition which comprises an HCV NS5B polypeptide, comprising the steps of allowing the formation of a crystal of a purified and stabilized HCV NS5B polypeptide comprising the amino acid sequence of SEQ ID NO: 1 in a crystallization solution which comprises a precipitant, a protein stabilizing agent and a salt under conditions in which crystallization occurs and wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 4.0 Ångströms.
  • 6. The method of claim 5, wherein the HCV NS5B is stabilized with glycerol.
  • 7. The method of claim 5, wherein the HCV NS5B polypeptide is purified from a preparation comprising the HCV NS5B by cation exchange chromatography before the step of allowing the formation of a crystal.
  • 8. The method of claim 7, wherein the preparation comprises glycine.
  • 9. The method of claim 5, wherein the crystal forms from a crystallization method selected from microbatch and vapor diffusion.
  • 10. The method of claim 5, wherein the protein stabilizing agent is glycerol.
  • 11. The method of claim 10, wherein the concentration of the glycerol is about 2 to 20% (volume/volume).
  • 12. The method of claim 10, wherein the concentration of the glycerol is about 10% (volume/volume).
  • 13. The method of claim 5, wherein the precipitant is polyethylene glycol.
  • 14. The method of claim 13, wherein the molecular weight of the polyethylene glycol is 1000 to 20,000 daltons.
  • 15. The method of claim 13, wherein the molecular weight of the polyethylene glycol is 4000 to 5000 daltons.
  • 16. A crystal comprising an HCV NS5B polypeptide which is prepared according to the method of claim 5.
  • 17. A method for preparing a crystalline composition which comprises an HCV NS5B polypeptide, comprising the steps of allowing the formation of a crystal of a purified and stabilized HCV NS5B polypeptide comprising the amino acid sequence of SEQ ID NO: 1 in a crystallization solution which comprises a precipitant, a protein stabilizing agent and a salt under conditions in which crystallization occurs and wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 2.8 Ångströms.
  • 18. The method of claim 17, wherein the HCV NS5B polypeptide is purified from a preparation comprising the HCV NS5B by cation exchange chromatography before the step of allowing the formation of a crystal.
  • 19. The method of claim 18, wherein the preparation comprises glycine.
  • 20. The method of claim 17, wherein the crystal forms from a crystallization method selected from microbatch and vapor diffusion.
  • 21. The method of claim 17, wherein the protein stabilizing agent is glycerol.
  • 22. The method of claim 21, wherein the concentration of the glycerol is about 2 to 20% (volume/volume).
  • 23. The method of claim 21, wherein the concentration of the glycerol is about 10% (volume/volume).
  • 24. The method of claim 17, wherein the precipitant is polyethylene glycol.
  • 25. The method of claim 24, wherein the molecular weight of the polyethylene glycol is 1000 to 20,000 daltons.
  • 26. The method of claim 24, wherein the molecular weight of the polyethylene glycol is 4000 to 5000 daltons.
  • 27. A crystal comprising an HCV NS5B polypeptide which is prepared according to the method of claim 17.
  • 28. A method for preparing a crystalline composition which comprises an HCV NS5B polypeptide, comprising the steps of allowing the formation of a crystal of a purified and stabilized HCV NS5B polypeptide comprising the amino acid sequence of SEQ ID NO: 1 in a crystallization solution which comprises a precipitant, a protein stabilizing agent and a salt under conditions in which crystallization occurs and wherein said crystalline composition effectively diffracts x-rays for the determination of the atomic coordinates of the polypeptide to a resolution of greater than 2.2 Ångströms.
  • 29. The method of claim 28, wherein the HCV NS5B polypeptide is purified from a preparation comprising the HCV NS5B by cation exchange chromatography before the step of allowing the formation of a crystal.
  • 30. The method of claim 29, wherein the preparation comprises glycine.
  • 31. The method of claim 28, wherein the crystal forms from a crystallization method selected from microbatch and vapor diffusion.
  • 32. The method of claim 28, wherein the protein stabilizing agent is glycerol.
  • 33. The method of claim 32, wherein the concentration of the glycerol is about 2 to 20% (volume/volume).
  • 34. The method of claim 32, wherein the concentration of the glycerol is about 10% (volume/volume).
  • 35. The method of claim 28, wherein the precipitant is polyethylene glycol.
  • 36. The method of claim 35, wherein the molecular weight of the polyethylene glycol is 1000 to 20,000 daltons.
  • 37. The method of claim 35, wherein the molecular weight of the polyethylene glycol is 4000 to 5000 daltons.
  • 38. A crystal comprising an HCV NS5B polypeptide which is prepared according to the method of claim 28.
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