from __future__ import absolute_import, division, print_function from libtbx import easy_run import time import os from libtbx.test_utils import show_diff def exercise_1(prefix="tst_sort_atoms_1"): """ In an ideal world, this program should preserve everything that was in input pdb file: HEADER, TITLE, REMARKs, CONNECT, etc. Right now it preserves only atoms, CRYST1 and HELIX/SHEET records. """ input_pdb_str = """\ HEADER UNKNOWN FUNCTION 17-FEB-05 1YWF TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PROTEIN TITLE 2 TYROSINE PHOSPHATASE PTPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B+ KEYWDS FOUR STRANDED PARALLEL BETA SHEET WITH FLANKING HELICES, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, TB KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, TBSGC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.GRUNDNER,H.L.NG,T.ALBER,TB STRUCTURAL GENOMICS CONSORTIUM AUTHOR 2 (TBSGC) REVDAT 3 24-FEB-09 1YWF 1 VERSN REVDAT 2 24-OCT-06 1YWF 1 KEYWDS AUTHOR REMARK MASTER REVDAT 1 22-NOV-05 1YWF 0 JRNL AUTH C.GRUNDNER,H.L.NG,T.ALBER JRNL TITL MYCOBACTERIUM TUBERCULOSIS PROTEIN TYROSINE JRNL TITL 2 PHOSPHATASE PTPB STRUCTURE REVEALS A DIVERGED FOLD JRNL TITL 3 AND A BURIED ACTIVE SITE. JRNL REF STRUCTURE V. 13 1625 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16271885 JRNL DOI 10.1016/J.STR.2005.07.017 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 32240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1692 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1609 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1858 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.99000 REMARK 3 B22 (A**2) : -1.99000 REMARK 3 B33 (A**2) : 3.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.244 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1889 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1797 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2561 ; 1.676 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4107 ; 0.915 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 239 ; 5.557 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 295 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2137 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 424 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 444 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2236 ; 0.251 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1177 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 169 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 2 ; 0.260 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 18 ; 0.295 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.205 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1194 ; 0.978 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1910 ; 1.788 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 695 ; 2.805 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 651 ; 4.729 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 1YWF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-05. REMARK 100 THE RCSB ID CODE IS RCSB031997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1157, 0.97949, 0.97973, REMARK 200 0.93927 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33939 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 79.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 66.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M KH2PO4, 20% PEG8000, 10MM REMARK 280 NAACETATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X+1/2,Z+1/4 REMARK 290 3555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -Y+1/2,X,Z+3/4 REMARK 290 7555 -X,-Y,Z REMARK 290 8555 Y,-X+1/2,Z+1/4 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 1.000000 0.000000 0.000000 56.53400 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.32300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 56.53400 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 56.53400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.64600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.53400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.96900 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 56.53400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.53400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.64600 REMARK 290 SMTRY1 6 0.000000 -1.000000 0.000000 56.53400 REMARK 290 SMTRY2 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.96900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 56.53400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 13.32300 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 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 354 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 ASP A 86 REMARK 465 ASP A 87 REMARK 465 ALA A 88 REMARK 465 ASP A 89 REMARK 465 ASP A 90 REMARK 465 SER A 91 REMARK 465 ALA A 92 REMARK 465 PRO A 93 REMARK 465 HIS A 94 REMARK 465 GLU A 95 REMARK 465 THR A 96 REMARK 465 ALA A 97 REMARK 465 PHE A 98 REMARK 465 LYS A 99 REMARK 465 ARG A 100 REMARK 465 LEU A 101 REMARK 465 LEU A 102 REMARK 465 THR A 103 REMARK 465 ASN A 104 REMARK 465 ASP A 105 REMARK 465 GLY A 106 REMARK 465 SER A 107 REMARK 465 ASN A 108 REMARK 465 GLY A 109 REMARK 465 GLU A 110 REMARK 465 SER A 111 REMARK 465 GLY A 112 REMARK 465 GLU A 113 REMARK 465 SER A 114 REMARK 465 SER A 115 REMARK 465 GLN A 116 REMARK 465 GLY A 276 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 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 226 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 466 O HOH A 507 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 164 CD LYS A 164 CE 0.195 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 LYS A 164 CD - CE - NZ ANGL. DEV. = -37.4 DEGREES REMARK 500 ARG A 271 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 119 40.85 -101.39 REMARK 500 CYS A 160 -126.55 -127.33 REMARK 500 PHE A 161 -69.45 -90.71 REMARK 500 ASP A 165 -72.55 -98.47 REMARK 500 LEU A 227 45.01 27.68 REMARK 500 SER A 228 150.03 -45.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 277 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: RV0153C RELATED DB: TARGETDB DBREF 1YWF A 1 276 UNP P96830 P96830_MYCTU 1 276 SEQADV 1YWF MET A -19 UNP P96830 CLONING ARTIFACT SEQADV 1YWF GLY A -18 UNP P96830 CLONING ARTIFACT SEQADV 1YWF SER A -17 UNP P96830 CLONING ARTIFACT SEQADV 1YWF SER A -16 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -15 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -14 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -13 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -12 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -11 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A -10 UNP P96830 CLONING ARTIFACT SEQADV 1YWF SER A -9 UNP P96830 CLONING ARTIFACT SEQADV 1YWF SER A -8 UNP P96830 CLONING ARTIFACT SEQADV 1YWF GLY A -7 UNP P96830 CLONING ARTIFACT SEQADV 1YWF LEU A -6 UNP P96830 CLONING ARTIFACT SEQADV 1YWF VAL A -5 UNP P96830 CLONING ARTIFACT SEQADV 1YWF PRO A -4 UNP P96830 CLONING ARTIFACT SEQADV 1YWF ARG A -3 UNP P96830 CLONING ARTIFACT SEQADV 1YWF GLY A -2 UNP P96830 CLONING ARTIFACT SEQADV 1YWF SER A -1 UNP P96830 CLONING ARTIFACT SEQADV 1YWF HIS A 0 UNP P96830 CLONING ARTIFACT SEQRES 1 A 296 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 296 LEU VAL PRO ARG GLY SER HIS MET ALA VAL ARG GLU LEU SEQRES 3 A 296 PRO GLY ALA TRP ASN PHE ARG ASP VAL ALA ASP THR ALA SEQRES 4 A 296 THR ALA LEU ARG PRO GLY ARG LEU PHE ARG SER SER GLU SEQRES 5 A 296 LEU SER ARG LEU ASP ASP ALA GLY ARG ALA THR LEU ARG SEQRES 6 A 296 ARG LEU GLY ILE THR ASP VAL ALA ASP LEU ARG SER SER SEQRES 7 A 296 ARG GLU VAL ALA ARG ARG GLY PRO GLY ARG VAL PRO ASP SEQRES 8 A 296 GLY ILE ASP VAL HIS LEU LEU PRO PHE PRO ASP LEU ALA SEQRES 9 A 296 ASP ASP ASP ALA ASP ASP SER ALA PRO HIS GLU THR ALA SEQRES 10 A 296 PHE LYS ARG LEU LEU THR ASN ASP GLY SER ASN GLY GLU SEQRES 11 A 296 SER GLY GLU SER SER GLN SER ILE ASN ASP ALA ALA THR SEQRES 12 A 296 ARG TYR MET THR ASP GLU TYR ARG GLN PHE PRO THR ARG SEQRES 13 A 296 ASN GLY ALA GLN ARG ALA LEU HIS ARG VAL VAL THR LEU SEQRES 14 A 296 LEU ALA ALA GLY ARG PRO VAL LEU THR HIS CYS PHE ALA SEQRES 15 A 296 GLY LYS ASP ARG THR GLY PHE VAL VAL ALA LEU VAL LEU SEQRES 16 A 296 GLU ALA VAL GLY LEU ASP ARG ASP VAL ILE VAL ALA ASP SEQRES 17 A 296 TYR LEU ARG SER ASN ASP SER VAL PRO GLN LEU ARG ALA SEQRES 18 A 296 ARG ILE SER GLU MET ILE GLN GLN ARG PHE ASP THR GLU SEQRES 19 A 296 LEU ALA PRO GLU VAL VAL THR PHE THR LYS ALA ARG LEU SEQRES 20 A 296 SER ASP GLY VAL LEU GLY VAL ARG ALA GLU TYR LEU ALA SEQRES 21 A 296 ALA ALA ARG GLN THR ILE ASP GLU THR TYR GLY SER LEU SEQRES 22 A 296 GLY GLY TYR LEU ARG ASP ALA GLY ILE SER GLN ALA THR SEQRES 23 A 296 VAL ASN ARG MET ARG GLY VAL LEU LEU GLY HET PO4 A 277 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *264(H2 O) HELIX 1 1 ALA A 16 THR A 18 5 3 HELIX 2 2 ASP A 37 GLY A 48 1 12 HELIX 3 3 SER A 57 GLY A 65 1 9 HELIX 4 4 ASN A 119 PHE A 133 1 15 HELIX 5 5 PRO A 134 ARG A 136 5 3 HELIX 6 6 GLY A 138 ALA A 152 1 15 HELIX 7 7 ASP A 165 VAL A 178 1 14 HELIX 8 8 ASP A 181 ARG A 191 1 11 HELIX 9 9 SER A 192 ASP A 194 5 3 HELIX 10 10 SER A 195 GLN A 209 1 15 HELIX 11 11 ALA A 216 ALA A 225 1 10 HELIX 12 12 SER A 228 GLY A 233 1 6 HELIX 13 13 ARG A 235 GLY A 251 1 17 HELIX 14 14 SER A 252 ALA A 260 1 9 HELIX 15 15 SER A 263 LEU A 275 1 13 SHEET 1 A 5 ARG A 13 ASP A 14 0 SHEET 2 A 5 LEU A 27 SER A 30 -1 O ARG A 29 N ARG A 13 SHEET 3 A 5 VAL A 156 HIS A 159 1 O VAL A 156 N PHE A 28 SHEET 4 A 5 ASP A 51 ASP A 54 1 N ALA A 51 O LEU A 157 SHEET 5 A 5 ASP A 74 LEU A 77 1 O HIS A 74 N VAL A 52 SITE *** AC1 9 LEU A 83 CYS A 160 PHE A 161 ALA A 162 SITE *** AC1 9 GLY A 163 LYS A 164 ASP A 165 ARG A 166 SITE *** AC1 9 GLU A 218 CRYST1 113.068 113.068 53.292 90.00 90.00 90.00 I 41 8 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 0.008844 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018765 0.00000 ATOM 1 N ARG A 4 7.511 46.981 14.258 1.00 46.91 N ATOM 2 CA ARG A 4 7.057 47.032 12.837 1.00 47.14 C ATOM 3 C ARG A 4 7.149 48.454 12.261 1.00 44.77 C ATOM 4 O ARG A 4 7.798 48.643 11.247 1.00 45.20 O ATOM 5 CB ARG A 4 5.613 46.509 12.682 1.00 47.77 C ATOM 6 CG ARG A 4 5.282 45.235 13.472 1.00 52.79 C ATOM 7 CD ARG A 4 4.921 43.958 12.663 1.00 58.16 C ATOM 8 NE ARG A 4 4.877 44.193 11.216 1.00 63.64 N ATOM 9 CZ ARG A 4 5.947 44.408 10.439 1.00 67.41 C ATOM 10 NH1 ARG A 4 7.176 44.420 10.954 1.00 68.79 N ATOM 11 NH2 ARG A 4 5.785 44.627 9.133 1.00 68.95 N ATOM 0 HA ARG A 4 7.735 46.377 12.271 1.00 47.14 H ATOM 0 HB2 ARG A 4 4.919 47.303 12.994 1.00 47.77 H ATOM 0 HB3 ARG A 4 5.424 46.317 11.615 1.00 47.77 H ATOM 0 HG2 ARG A 4 6.146 44.998 14.111 1.00 52.79 H ATOM 0 HG3 ARG A 4 4.439 45.461 14.142 1.00 52.79 H ATOM 0 HD2 ARG A 4 5.659 43.172 12.879 1.00 58.16 H ATOM 0 HD3 ARG A 4 3.943 43.582 12.998 1.00 58.16 H ATOM 0 HE ARG A 4 3.979 44.193 10.775 1.00 63.64 H ATOM 0 HH11 ARG A 4 7.309 44.267 11.933 1.00 68.79 H ATOM 0 HH12 ARG A 4 7.965 44.582 10.361 1.00 68.79 H ATOM 0 HH21 ARG A 4 4.867 44.630 8.737 1.00 68.95 H ATOM 0 HH22 ARG A 4 6.582 44.788 8.550 1.00 68.95 H ATOM 12 N GLU A 5 6.489 49.425 12.914 1.00 42.64 N ATOM 13 CA GLU A 5 6.285 50.786 12.396 1.00 40.70 C ATOM 14 C GLU A 5 7.010 51.885 13.188 1.00 37.71 C ATOM 15 O GLU A 5 7.249 51.776 14.392 1.00 37.47 O ATOM 16 CB GLU A 5 4.775 51.134 12.383 1.00 41.69 C ATOM 17 CG GLU A 5 3.932 50.296 11.422 1.00 44.73 C ATOM 18 CD GLU A 5 4.140 50.666 9.954 1.00 49.40 C ATOM 19 OE1 GLU A 5 4.507 51.827 9.648 1.00 50.99 O ATOM 20 OE2 GLU A 5 3.938 49.789 9.079 1.00 54.37 O ATOM 0 H GLU A 5 6.083 49.285 13.817 1.00 42.64 H ATOM 0 HA GLU A 5 6.714 50.769 11.383 1.00 40.70 H ATOM 0 HB2 GLU A 5 4.376 51.011 13.401 1.00 41.69 H ATOM 0 HB3 GLU A 5 4.660 52.196 12.119 1.00 41.69 H ATOM 0 HG2 GLU A 5 4.176 49.233 11.563 1.00 44.73 H ATOM 0 HG3 GLU A 5 2.869 50.418 11.676 1.00 44.73 H ATOM 21 N LEU A 6 7.297 52.974 12.490 1.00 34.71 N ATOM 22 CA LEU A 6 7.928 54.158 13.057 1.00 32.83 C ATOM 23 C LEU A 6 7.124 55.354 12.548 1.00 32.42 C ATOM 24 O LEU A 6 7.421 55.925 11.503 1.00 31.01 O ATOM 25 CB LEU A 6 9.391 54.265 12.608 1.00 32.60 C ATOM 26 CG LEU A 6 10.179 55.463 13.111 1.00 30.47 C ATOM 27 CD1 LEU A 6 10.149 55.453 14.651 1.00 33.03 C ATOM 28 CD2 LEU A 6 11.634 55.474 12.576 1.00 30.34 C ATOM 0 H LEU A 6 7.098 53.060 11.514 1.00 34.71 H ATOM 0 HA LEU A 6 7.934 54.115 14.156 1.00 32.83 H ATOM 0 HB2 LEU A 6 9.915 53.352 12.928 1.00 32.60 H ATOM 0 HB3 LEU A 6 9.411 54.279 11.508 1.00 32.60 H ATOM 0 HG LEU A 6 9.711 56.384 12.733 1.00 30.47 H ATOM 0 HD11 LEU A 6 10.715 56.314 15.035 1.00 33.03 H ATOM 0 HD12 LEU A 6 9.107 55.515 14.998 1.00 33.03 H ATOM 0 HD13 LEU A 6 10.603 54.522 15.021 1.00 33.03 H ATOM 0 HD21 LEU A 6 12.162 56.357 12.966 1.00 30.34 H ATOM 0 HD22 LEU A 6 12.153 54.562 12.905 1.00 30.34 H ATOM 0 HD23 LEU A 6 11.621 55.512 11.477 1.00 30.34 H ATOM 29 N PRO A 7 6.021 55.686 13.228 1.00 31.97 N ATOM 30 CA PRO A 7 5.071 56.656 12.662 1.00 31.54 C ATOM 31 C PRO A 7 5.654 58.019 12.286 1.00 29.40 C ATOM 32 O PRO A 7 6.359 58.672 13.062 1.00 31.00 O ATOM 33 CB PRO A 7 3.963 56.730 13.741 1.00 31.52 C ATOM 34 CG PRO A 7 4.012 55.430 14.379 1.00 32.79 C ATOM 35 CD PRO A 7 5.514 55.095 14.483 1.00 32.60 C ATOM 0 HA PRO A 7 4.705 56.327 11.678 1.00 31.54 H ATOM 0 HB2 PRO A 7 4.154 57.540 14.460 1.00 31.52 H ATOM 0 HB3 PRO A 7 2.977 56.923 13.294 1.00 31.52 H ATOM 0 HG2 PRO A 7 3.540 55.455 15.372 1.00 32.79 H ATOM 0 HG3 PRO A 7 3.475 54.675 13.786 1.00 32.79 H ATOM 0 HD2 PRO A 7 5.980 55.544 15.373 1.00 32.60 H ATOM 0 HD3 PRO A 7 5.696 54.012 14.536 1.00 32.60 H ATOM 36 N GLY A 8 5.386 58.417 11.036 1.00 28.81 N ATOM 37 CA GLY A 8 5.916 59.617 10.412 1.00 28.14 C ATOM 38 C GLY A 8 7.143 59.366 9.540 1.00 26.94 C ATOM 39 O GLY A 8 7.557 60.229 8.751 1.00 26.16 O ATOM 0 H GLY A 8 4.784 57.898 10.429 1.00 28.81 H ATOM 0 HA2 GLY A 8 5.129 60.078 9.797 1.00 28.14 H ATOM 0 HA3 GLY A 8 6.177 60.342 11.197 1.00 28.14 H ATOM 40 N ALA A 9 7.683 58.159 9.650 1.00 26.13 N ATOM 41 CA ALA A 9 8.750 57.696 8.757 1.00 25.16 C ATOM 42 C ALA A 9 8.313 56.419 8.034 1.00 25.14 C ATOM 43 O ALA A 9 7.221 55.876 8.276 1.00 25.57 O ATOM 44 CB ALA A 9 10.038 57.470 9.546 1.00 25.41 C ATOM 0 H ALA A 9 7.406 57.489 10.338 1.00 26.13 H ATOM 0 HA ALA A 9 8.947 58.469 7.999 1.00 25.16 H ATOM 0 HB1 ALA A 9 10.830 57.123 8.865 1.00 25.41 H ATOM 0 HB2 ALA A 9 10.349 58.413 10.019 1.00 25.41 H ATOM 0 HB3 ALA A 9 9.864 56.711 10.323 1.00 25.41 H ATOM 45 N TRP A 10 9.132 55.968 7.091 1.00 24.79 N ATOM 46 CA TRP A 10 8.801 54.772 6.341 1.00 23.84 C ATOM 47 C TRP A 10 10.106 53.977 6.084 1.00 23.68 C ATOM 48 O TRP A 10 11.196 54.413 6.461 1.00 21.87 O ATOM 49 CB TRP A 10 8.093 55.130 5.023 1.00 23.84 C ATOM 50 CG TRP A 10 8.914 55.811 3.994 1.00 21.18 C ATOM 51 CD1 TRP A 10 9.502 55.245 2.912 1.00 23.12 C ATOM 52 CD2 TRP A 10 9.276 57.199 3.966 1.00 23.18 C ATOM 53 NE1 TRP A 10 10.195 56.191 2.193 1.00 23.94 N ATOM 54 CE2 TRP A 10 10.049 57.406 2.829 1.00 24.73 C ATOM 55 CE3 TRP A 10 8.976 58.314 4.790 1.00 25.02 C ATOM 56 CZ2 TRP A 10 10.585 58.649 2.506 1.00 24.98 C ATOM 57 CZ3 TRP A 10 9.511 59.554 4.437 1.00 24.23 C ATOM 58 CH2 TRP A 10 10.275 59.704 3.315 1.00 23.25 C ATOM 0 H TRP A 10 9.998 56.399 6.838 1.00 24.79 H ATOM 0 HA TRP A 10 8.103 54.149 6.919 1.00 23.84 H ATOM 0 HB2 TRP A 10 7.692 54.204 4.585 1.00 23.84 H ATOM 0 HB3 TRP A 10 7.233 55.774 5.258 1.00 23.84 H ATOM 0 HD1 TRP A 10 9.435 54.180 2.646 1.00 23.12 H ATOM 0 HE1 TRP A 10 10.715 56.026 1.355 1.00 23.94 H ATOM 0 HE3 TRP A 10 8.340 58.205 5.681 1.00 25.02 H ATOM 0 HZ2 TRP A 10 11.236 58.777 1.629 1.00 24.98 H ATOM 0 HZ3 TRP A 10 9.313 60.428 5.075 1.00 24.23 H ATOM 0 HH2 TRP A 10 10.652 60.704 3.056 1.00 23.25 H TER 1859 HETATM 2117 O HOH A 530 14.129 75.372 1.869 1.00 42.52 O HETATM 2118 O HOH A 531 16.760 75.823 5.378 1.00 55.47 O HETATM 2119 O HOH A 532 17.376 76.181 -1.370 1.00 58.56 O HETATM 2120 O HOH A 533 29.999 39.710 23.377 1.00 65.34 O HETATM 2121 O HOH A 534 5.061 66.928 20.580 1.00 53.64 O HETATM 2122 O HOH A 535 31.453 64.317 11.742 1.00 57.21 O HETATM 2123 O HOH A 536 33.870 40.890 21.690 1.00 49.33 O HETATM 2124 O HOH A 537 12.870 61.651 25.404 1.00 60.53 O HETATM 2125 O HOH A 538 1.073 55.236 2.188 1.00 56.32 O HETATM 2126 O HOH A 539 5.912 53.669 23.394 1.00 76.65 O HETATM 2127 O HOH A 540 15.986 47.456 -16.281 1.00 62.61 O HETATM 2128 O HOH A 541 16.397 56.900 23.573 1.00 58.46 O CONECT 1860 1861 1862 1863 1864 CONECT 1861 1860 CONECT 1862 1860 CONECT 1863 1860 CONECT 1864 1860 END """ result_pdb_str = """\ CRYST1 113.068 113.068 53.292 90.00 90.00 90.00 I 41 SCALE1 0.008844 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018765 0.00000 ATOM 1 N ARG A 4 7.511 46.981 14.258 1.00 46.91 N ATOM 2 CA ARG A 4 7.057 47.032 12.837 1.00 47.14 C ATOM 3 C ARG A 4 7.149 48.454 12.261 1.00 44.77 C ATOM 4 O ARG A 4 7.798 48.643 11.247 1.00 45.20 O ATOM 5 CB ARG A 4 5.613 46.509 12.682 1.00 47.77 C ATOM 6 CG ARG A 4 5.282 45.235 13.472 1.00 52.79 C ATOM 7 CD ARG A 4 4.921 43.958 12.663 1.00 58.16 C ATOM 8 NE ARG A 4 4.877 44.193 11.216 1.00 63.64 N ATOM 9 CZ ARG A 4 5.947 44.408 10.439 1.00 67.41 C ATOM 10 NH1 ARG A 4 7.176 44.420 10.954 1.00 68.79 N ATOM 11 NH2 ARG A 4 5.785 44.627 9.133 1.00 68.95 N ATOM 12 HA ARG A 4 7.735 46.377 12.271 1.00 47.14 H ATOM 13 HB2 ARG A 4 4.919 47.303 12.994 1.00 47.77 H ATOM 14 HB3 ARG A 4 5.424 46.317 11.615 1.00 47.77 H ATOM 15 HG2 ARG A 4 6.146 44.998 14.111 1.00 52.79 H ATOM 16 HG3 ARG A 4 4.439 45.461 14.142 1.00 52.79 H ATOM 17 HD2 ARG A 4 5.659 43.172 12.879 1.00 58.16 H ATOM 18 HD3 ARG A 4 3.943 43.582 12.998 1.00 58.16 H ATOM 19 HE ARG A 4 3.979 44.193 10.775 1.00 63.64 H ATOM 20 HH11 ARG A 4 7.309 44.267 11.933 1.00 68.79 H ATOM 21 HH12 ARG A 4 7.965 44.582 10.361 1.00 68.79 H ATOM 22 HH21 ARG A 4 4.867 44.630 8.737 1.00 68.95 H ATOM 23 HH22 ARG A 4 6.582 44.788 8.550 1.00 68.95 H ATOM 24 N GLU A 5 6.489 49.425 12.914 1.00 42.64 N ATOM 25 CA GLU A 5 6.285 50.786 12.396 1.00 40.70 C ATOM 26 C GLU A 5 7.010 51.885 13.188 1.00 37.71 C ATOM 27 O GLU A 5 7.249 51.776 14.392 1.00 37.47 O ATOM 28 CB GLU A 5 4.775 51.134 12.383 1.00 41.69 C ATOM 29 CG GLU A 5 3.932 50.296 11.422 1.00 44.73 C ATOM 30 CD GLU A 5 4.140 50.666 9.954 1.00 49.40 C ATOM 31 OE1 GLU A 5 4.507 51.827 9.648 1.00 50.99 O ATOM 32 OE2 GLU A 5 3.938 49.789 9.079 1.00 54.37 O ATOM 33 H GLU A 5 6.083 49.285 13.817 1.00 42.64 H ATOM 34 HA GLU A 5 6.714 50.769 11.383 1.00 40.70 H ATOM 35 HB2 GLU A 5 4.376 51.011 13.401 1.00 41.69 H ATOM 36 HB3 GLU A 5 4.660 52.196 12.119 1.00 41.69 H ATOM 37 HG2 GLU A 5 4.176 49.233 11.563 1.00 44.73 H ATOM 38 HG3 GLU A 5 2.869 50.418 11.676 1.00 44.73 H ATOM 39 N LEU A 6 7.297 52.974 12.490 1.00 34.71 N ATOM 40 CA LEU A 6 7.928 54.158 13.057 1.00 32.83 C ATOM 41 C LEU A 6 7.124 55.354 12.548 1.00 32.42 C ATOM 42 O LEU A 6 7.421 55.925 11.503 1.00 31.01 O ATOM 43 CB LEU A 6 9.391 54.265 12.608 1.00 32.60 C ATOM 44 CG LEU A 6 10.179 55.463 13.111 1.00 30.47 C ATOM 45 CD1 LEU A 6 10.149 55.453 14.651 1.00 33.03 C ATOM 46 CD2 LEU A 6 11.634 55.474 12.576 1.00 30.34 C ATOM 47 H LEU A 6 7.098 53.060 11.514 1.00 34.71 H ATOM 48 HA LEU A 6 7.934 54.115 14.156 1.00 32.83 H ATOM 49 HB2 LEU A 6 9.915 53.352 12.928 1.00 32.60 H ATOM 50 HB3 LEU A 6 9.411 54.279 11.508 1.00 32.60 H ATOM 51 HG LEU A 6 9.711 56.384 12.733 1.00 30.47 H ATOM 52 HD11 LEU A 6 10.715 56.314 15.035 1.00 33.03 H ATOM 53 HD12 LEU A 6 9.107 55.515 14.998 1.00 33.03 H ATOM 54 HD13 LEU A 6 10.603 54.522 15.021 1.00 33.03 H ATOM 55 HD21 LEU A 6 12.162 56.357 12.966 1.00 30.34 H ATOM 56 HD22 LEU A 6 12.153 54.562 12.905 1.00 30.34 H ATOM 57 HD23 LEU A 6 11.621 55.512 11.477 1.00 30.34 H ATOM 58 N PRO A 7 6.021 55.686 13.228 1.00 31.97 N ATOM 59 CA PRO A 7 5.071 56.656 12.662 1.00 31.54 C ATOM 60 C PRO A 7 5.654 58.019 12.286 1.00 29.40 C ATOM 61 O PRO A 7 6.359 58.672 13.062 1.00 31.00 O ATOM 62 CB PRO A 7 3.963 56.730 13.741 1.00 31.52 C ATOM 63 CG PRO A 7 4.012 55.430 14.379 1.00 32.79 C ATOM 64 CD PRO A 7 5.514 55.095 14.483 1.00 32.60 C ATOM 65 HA PRO A 7 4.705 56.327 11.678 1.00 31.54 H ATOM 66 HB2 PRO A 7 4.154 57.540 14.460 1.00 31.52 H ATOM 67 HB3 PRO A 7 2.977 56.923 13.294 1.00 31.52 H ATOM 68 HG2 PRO A 7 3.540 55.455 15.372 1.00 32.79 H ATOM 69 HG3 PRO A 7 3.475 54.675 13.786 1.00 32.79 H ATOM 70 HD2 PRO A 7 5.980 55.544 15.373 1.00 32.60 H ATOM 71 HD3 PRO A 7 5.696 54.012 14.536 1.00 32.60 H ATOM 72 N GLY A 8 5.386 58.417 11.036 1.00 28.81 N ATOM 73 CA GLY A 8 5.916 59.617 10.412 1.00 28.14 C ATOM 74 C GLY A 8 7.143 59.366 9.540 1.00 26.94 C ATOM 75 O GLY A 8 7.557 60.229 8.751 1.00 26.16 O ATOM 76 H GLY A 8 4.784 57.898 10.429 1.00 28.81 H ATOM 77 HA2 GLY A 8 5.129 60.078 9.797 1.00 28.14 H ATOM 78 HA3 GLY A 8 6.177 60.342 11.197 1.00 28.14 H ATOM 79 N ALA A 9 7.683 58.159 9.650 1.00 26.13 N ATOM 80 CA ALA A 9 8.750 57.696 8.757 1.00 25.16 C ATOM 81 C ALA A 9 8.313 56.419 8.034 1.00 25.14 C ATOM 82 O ALA A 9 7.221 55.876 8.276 1.00 25.57 O ATOM 83 CB ALA A 9 10.038 57.470 9.546 1.00 25.41 C ATOM 84 H ALA A 9 7.406 57.489 10.338 1.00 26.13 H ATOM 85 HA ALA A 9 8.947 58.469 7.999 1.00 25.16 H ATOM 86 HB1 ALA A 9 10.830 57.123 8.865 1.00 25.41 H ATOM 87 HB2 ALA A 9 10.349 58.413 10.019 1.00 25.41 H ATOM 88 HB3 ALA A 9 9.864 56.711 10.323 1.00 25.41 H ATOM 89 N TRP A 10 9.132 55.968 7.091 1.00 24.79 N ATOM 90 CA TRP A 10 8.801 54.772 6.341 1.00 23.84 C ATOM 91 C TRP A 10 10.106 53.977 6.084 1.00 23.68 C ATOM 92 O TRP A 10 11.196 54.413 6.461 1.00 21.87 O ATOM 93 CB TRP A 10 8.093 55.130 5.023 1.00 23.84 C ATOM 94 CG TRP A 10 8.914 55.811 3.994 1.00 21.18 C ATOM 95 CD1 TRP A 10 9.502 55.245 2.912 1.00 23.12 C ATOM 96 CD2 TRP A 10 9.276 57.199 3.966 1.00 23.18 C ATOM 97 NE1 TRP A 10 10.195 56.191 2.193 1.00 23.94 N ATOM 98 CE2 TRP A 10 10.049 57.406 2.829 1.00 24.73 C ATOM 99 CE3 TRP A 10 8.976 58.314 4.790 1.00 25.02 C ATOM 100 CZ2 TRP A 10 10.585 58.649 2.506 1.00 24.98 C ATOM 101 CZ3 TRP A 10 9.511 59.554 4.437 1.00 24.23 C ATOM 102 CH2 TRP A 10 10.275 59.704 3.315 1.00 23.25 C ATOM 103 H TRP A 10 9.998 56.399 6.838 1.00 24.79 H ATOM 104 HA TRP A 10 8.103 54.149 6.919 1.00 23.84 H ATOM 105 HB2 TRP A 10 7.692 54.204 4.585 1.00 23.84 H ATOM 106 HB3 TRP A 10 7.233 55.774 5.258 1.00 23.84 H ATOM 107 HD1 TRP A 10 9.435 54.180 2.646 1.00 23.12 H ATOM 108 HE1 TRP A 10 10.715 56.026 1.355 1.00 23.94 H ATOM 109 HE3 TRP A 10 8.340 58.205 5.681 1.00 25.02 H ATOM 110 HZ2 TRP A 10 11.236 58.777 1.629 1.00 24.98 H ATOM 111 HZ3 TRP A 10 9.313 60.428 5.075 1.00 24.23 H ATOM 112 HH2 TRP A 10 10.652 60.704 3.056 1.00 23.25 H TER HETATM 113 O HOH A 530 14.129 75.372 1.869 1.00 42.52 O HETATM 114 O HOH A 531 16.760 75.823 5.378 1.00 55.47 O HETATM 115 O HOH A 532 17.376 76.181 -1.370 1.00 58.56 O HETATM 116 O HOH A 533 29.999 39.710 23.377 1.00 65.34 O HETATM 117 O HOH A 534 5.061 66.928 20.580 1.00 53.64 O HETATM 118 O HOH A 535 31.453 64.317 11.742 1.00 57.21 O HETATM 119 O HOH A 536 33.870 40.890 21.690 1.00 49.33 O HETATM 120 O HOH A 537 12.870 61.651 25.404 1.00 60.53 O HETATM 121 O HOH A 538 1.073 55.236 2.188 1.00 56.32 O HETATM 122 O HOH A 539 5.912 53.669 23.394 1.00 76.65 O HETATM 123 O HOH A 540 15.986 47.456 -16.281 1.00 62.61 O HETATM 124 O HOH A 541 16.397 56.900 23.573 1.00 58.46 O END """ in_f = open("%s.pdb" % prefix, 'w') in_f.write(input_pdb_str) in_f.close() cmd = " ".join([ "iotbx.pdb.sort_atoms", "%s.pdb" % prefix, ]) print(cmd) easy_run.call(cmd) assert os.path.isfile("%s_sorted.pdb" % prefix) out_f = open("%s_sorted.pdb" % prefix, 'r') out_str = out_f.read() assert not show_diff(result_pdb_str, out_str) out_f.close() if (__name__ == "__main__"): t0 = time.time() exercise_1() print("Time: %6.4f"%(time.time()-t0)) print("OK")