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Database: PDB
Entry: 5DYC
LinkDB: 5DYC
Original site: 5DYC 
HEADER    DNA BINDING PROTEIN                     24-SEP-15   5DYC              
TITLE     CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH SEED6
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PEREGRIN;                                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 625-740;                                      
COMPND   5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1,PROTEIN     
COMPND   6 BR140;                                                               
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: BRPF1, BR140;                                                  
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    DNA BINDING PROTEIN, BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN    
KEYWDS   2 1(BRPF1), MONOCYTIC LEUKEMIA ZINC-FINGER (MOZ), INHIBITOR,           
KEYWDS   3 TRANSCRIPTION                                                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.ZHU,A.CAFLISCH                                                      
REVDAT   2   22-JUN-16 5DYC    1       JRNL                                     
REVDAT   1   25-MAY-16 5DYC    0                                                
JRNL        AUTH   J.ZHU,A.CAFLISCH                                             
JRNL        TITL   TWENTY CRYSTAL STRUCTURES OF BROMODOMAIN AND PHD FINGER      
JRNL        TITL 2 CONTAINING PROTEIN 1 (BRPF1)/LIGAND COMPLEXES REVEAL         
JRNL        TITL 3 CONSERVED BINDING MOTIFS AND RARE INTERACTIONS.              
JRNL        REF    J.MED.CHEM.                   V.  59  5555 2016              
JRNL        REFN                   ISSN 0022-2623                               
JRNL        PMID   27167503                                                     
JRNL        DOI    10.1021/ACS.JMEDCHEM.6B00215                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.65 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (1.10_2155: ???)                              
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 30.40                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 16537                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.200                           
REMARK   3   R VALUE            (WORKING SET) : 0.199                           
REMARK   3   FREE R VALUE                     : 0.235                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.070                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 839                             
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 30.4091 -  2.9975    0.99     2774   110  0.1790 0.2182        
REMARK   3     2  2.9975 -  2.3795    1.00     2659   128  0.2224 0.2377        
REMARK   3     3  2.3795 -  2.0788    0.99     2575   157  0.2000 0.2315        
REMARK   3     4  2.0788 -  1.8887    0.99     2583   141  0.2191 0.2595        
REMARK   3     5  1.8887 -  1.7534    0.99     2548   151  0.2445 0.2929        
REMARK   3     6  1.7534 -  1.6500    0.99     2559   152  0.2376 0.2891        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.170            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.630           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.006            997                                  
REMARK   3   ANGLE     :  0.694           1348                                  
REMARK   3   CHIRALITY :  0.045            143                                  
REMARK   3   PLANARITY :  0.004            179                                  
REMARK   3   DIHEDRAL  : 12.839            622                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    SELECTION: ALL                                                    
REMARK   3    ORIGIN FOR THE GROUP (A):  27.1076   1.6498 -10.0958              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.4615 T22:   0.2106                                     
REMARK   3      T33:   0.2473 T12:   0.1227                                     
REMARK   3      T13:  -0.0143 T23:  -0.0141                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:   5.4630 L22:   2.0704                                     
REMARK   3      L33:   1.8844 L12:   0.1608                                     
REMARK   3      L13:   1.4831 L23:   0.5130                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:  -0.3469 S12:  -0.4994 S13:  -0.0400                       
REMARK   3      S21:   0.4230 S22:   0.1597 S23:  -0.0123                       
REMARK   3      S31:  -0.0129 S32:  -0.1164 S33:   0.1692                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 5DYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-15.                  
REMARK 100 THE DEPOSITION ID IS D_1000214022.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 05-JUL-15                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X06SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.99987                            
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : PSI PILATUS 6M                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16556                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.650                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.440                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.5                               
REMARK 200  DATA REDUNDANCY                : 9.700                              
REMARK 200  R MERGE                    (I) : 0.03900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 28.2000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.74                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 10.00                              
REMARK 200  R MERGE FOR SHELL          (I) : 0.40800                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.400                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 4LC2                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 49.96                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, PH5.5, 0.15 M       
REMARK 280  SODIUM NITRATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP,         
REMARK 280  TEMPERATURE 277K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   Y,X,-Z                                                  
REMARK 290       5555   X-Y,-Y,-Z+1/3                                           
REMARK 290       6555   -X,-X+Y,-Z+2/3                                          
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       42.07733            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       21.03867            
REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       21.03867            
REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       42.07733            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 7060 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375      HOH A 955  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A 977  LIES ON A SPECIAL POSITION.                          
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     SER A   625                                                      
REMARK 465     MET A   626                                                      
REMARK 465     GLY A   740                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     GLU A 627    CG   CD   OE1  OE2                                  
REMARK 470     LYS A 670    NZ                                                  
REMARK 470     GLN A 731    CD   OE1  NE2                                       
REMARK 470     LYS A 738    CE   NZ                                             
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 801                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 5GU A 802                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5C7N   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5C85   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5C87   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5C89   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5D7X   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5DY7   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5DYA   RELATED DB: PDB                                   
DBREF  5DYC A  625   740  UNP    P55201   BRPF1_HUMAN    625    740             
SEQADV 5DYC SER A  625  UNP  P55201    ALA   625 CONFLICT                       
SEQRES   1 A  116  SER MET GLU MET GLN LEU THR PRO PHE LEU ILE LEU LEU          
SEQRES   2 A  116  ARG LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY          
SEQRES   3 A  116  ASN ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO          
SEQRES   4 A  116  ASP TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE          
SEQRES   5 A  116  THR MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN          
SEQRES   6 A  116  PHE ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER          
SEQRES   7 A  116  ASN CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR          
SEQRES   8 A  116  ARG ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL          
SEQRES   9 A  116  LEU ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY              
HET    NO3  A 801       4                                                       
HET    5GU  A 802      12                                                       
HETNAM     NO3 NITRATE ION                                                      
HETNAM     5GU 7-BROMO-3,4-DIHYDROQUINOXALIN-2(1H)-ONE                          
FORMUL   2  NO3    N O3 1-                                                      
FORMUL   3  5GU    C8 H7 BR N2 O                                                
FORMUL   4  HOH   *82(H2 O)                                                     
HELIX    1 AA1 GLN A  629  ASP A  648  1                                  20    
HELIX    2 AA2 ASP A  664  HIS A  668  5                                   5    
HELIX    3 AA3 ASP A  674  ALA A  684  1                                  11    
HELIX    4 AA4 ASN A  689  ASN A  708  1                                  20    
HELIX    5 AA5 THR A  712  MET A  739  1                                  28    
SITE     1 AC1  7 SER A 702  LEU A 705  LYS A 706  TYR A 715                    
SITE     2 AC1  7 ARG A 722  HOH A 929  HOH A 960                               
SITE     1 AC2  8 ILE A 652  VAL A 657  PRO A 658  GLU A 661                    
SITE     2 AC2  8 ASN A 708  PHE A 714  HOH A 908  HOH A 916                    
CRYST1   60.808   60.808   63.116  90.00  90.00 120.00 P 32 2 1      6          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.016445  0.009495  0.000000        0.00000                         
SCALE2      0.000000  0.018989  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.015844        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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