MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, OSF1 cancercenter.columbia.edu V5.0 alpha Date and time of compilation : 07/05/2002 17:16:17 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/12 15:50:31.782 TOP_________> 105 705 SET ALNFILE = 'monomer.ali' TOP_________> 106 706 SET KNOWNS = '1ga2' TOP_________> 107 707 SET SEQUENCE = 'prk7' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Status of dynamic memory allocation in routine: amaxseq Variable T L1 U1 L2 U2 L3 U3 Size Bytes --------------------------------------------------------------------------- iseqdb I 1 1 1 4 nseqdb I 1 1 1 4 seqdb S 1 1 1 1 1 4 codep S 1 1 1 20 ialn2 I 1 1 1 4 4 16 nresn2 I 1 4 4 16 irestypn2 I 1 1 1 4 4 16 invaln2 I 1 1 1 4 4 16 nsegmn2 I 1 4 4 16 iress1n2 I 1 30 1 4 120 480 iress2n2 I 1 30 1 4 120 480 resol2 R 1 4 4 16 rfactr2 R 1 4 4 16 caln2 S 1 1 1 4 4 4 ccaln2 S 1 1 1 4 4 4 alnchn2 S 1 2 1 4 8 8 prottyp2 S 1 4 4 320 source2 S 1 4 4 320 range2 S 1 2 1 4 8 40 name2 S 1 4 4 320 segidn2 S 1 30 1 4 120 2400 codein2 L 1 4 4 16 iattmod I 1 50 50 200 iatmgrp I 1 220 220 880 grpatm S 1 50 50 250 attmod S 1 220 220 1980 var R 1 4 1 16 64 256 pdf R 1 4 1 50 200 800 ientry I 1 4 4 16 jentry I 1 4 4 16 nentries I 1 1 1 4 iar I 1 1 1 4 jar I 1 1 1 4 kar I 1 1 1 4 lar I 1 1 1 4 b1ic R 1 1 1 4 b2ic R 1 1 1 4 t1ic R 1 1 1 4 t2ic R 1 1 1 4 pic R 1 1 1 4 tar L 1 1 1 4 xmin R 1 1 1 4 ymin R 1 1 1 4 zmin R 1 1 1 4 ialn I 1 1 1 4 4 16 nresn I 1 4 4 16 irestypn I 1 1 1 4 4 16 invaln I 1 1 1 4 4 16 nsegmn I 1 4 4 16 iress1n I 1 30 1 4 120 480 iress2n I 1 30 1 4 120 480 resol R 1 4 4 16 rfactr R 1 4 4 16 alnacc R 1 1 1 4 prof R 1 1 1 4 4 16 gapdst R 1 3 1 3 9 36 caln S 1 1 1 4 4 4 ccaln S 1 1 1 4 4 4 alnchn S 1 2 1 4 8 8 prottyp S 1 4 4 320 source S 1 4 4 320 range S 1 2 1 4 8 40 name S 1 4 4 320 segidn S 1 30 1 4 120 2400 atmfull S 1 4 4 1024 codein L 1 4 4 16 iresatmn I 1 1 1 4 4 16 natmn I 1 4 4 16 iatmr1n I 1 1 1 4 4 16 idih I 1 1 1 9 1 4 36 144 idihc I 1 1 1 9 1 4 36 144 iglbsim I 1 4 1 4 16 64 isstruc I 1 1 1 4 4 16 neigh I 1 1 1 4 4 16 ineigh I 1 50 1 1 1 4 200 800 iresol I 1 4 4 16 indats2n I 1 2 1 1 1 4 8 32 imnchw I 1 1 1 4 4 16 iacont I 1 4 4 16 idsta1 I 1 1 1 4 4 16 idsta2 I 1 1 1 4 4 16 fractglsim R 1 4 1 4 16 64 xn R 1 1 1 4 4 16 yn R 1 1 1 4 4 16 zn R 1 1 1 4 4 16 dih R 1 1 1 9 1 4 36 144 acc R 1 1 1 4 4 16 bison R 1 1 1 4 4 16 curvn R 1 1 1 4 4 16 atmnamn S 1 1 1 4 4 16 resnumn S 1 1 1 4 4 20 resnamn S 1 1 1 4 4 16 chainn S 1 1 1 4 4 4 accepts L 1 4 4 16 memrange S 1 2 1 6 1 4 48 48 memalnchn S 1 2 1 6 1 4 48 48 mematmfull S 1 6 1 4 24 6144 iatc I 1 5 1 1 5 20 natc I 1 1 1 4 iata I 1 3 1 1 3 12 iatd I 1 4 1 1 4 16 iatb I 1 2 1 1 2 8 iati I 1 4 1 1 4 16 resseg S 1 1 1 4 iatmr1 I 1 1 1 4 iattyp I 1 1 1 4 iresatm I 1 1 1 4 iatta I 1 1 1 4 indats I 1 1 1 3 3 12 irestyp I 1 1 1 4 idihres I 1 4 1 9 1 1 36 144 natngh I 1 1 1 4 radii R 1 1 1 4 charge R 1 1 1 4 x R 1 1 1 4 y R 1 1 1 4 z R 1 1 1 4 biso R 1 1 1 4 vx R 1 1 1 4 vy R 1 1 1 4 vz R 1 1 1 4 atmacc R 1 1 1 4 resnam S 1 1 1 4 atmnam S 1 1 1 4 resnum S 1 1 1 5 chain S 1 1 1 1 picres L 1 1 1 3 3 12 picatm L 1 1 1 3 3 12 katmr1 I 1 1 1 4 kresatm I 1 1 1 4 krestyp I 1 1 1 4 x2 R 1 1 1 4 y2 R 1 1 1 4 z2 R 1 1 1 4 charg2 R 1 1 1 4 biso2 R 1 1 1 4 radii2 R 1 1 1 4 atm2nam S 1 1 1 4 res2nam S 1 1 1 4 chain2 S 1 1 1 1 res2num S 1 1 1 5 dvx R 1 1 1 4 dvy R 1 1 1 4 dvz R 1 1 1 4 pdbfil S 1 16331 16331 2090368 pdblst S 1 16331 16331 81655 indatm I 1 1 1 4 itcsr I 1 7 1 1 7 28 iatm I 1 1 1 4 ipcsr I 1 1 1 4 indatt I 1 1 1 4 itacsr I 1 7 1 1 7 28 iatt I 1 1 1 4 ipacsr I 1 1 1 4 iapairs I 1 2 1 1 2 8 iarsr2 I 1 50 1 50 2500 10000 iarsr I 1 50 50 200 indcsr I 1 1 1 4 pcsr R 1 1 1 4 pacsr R 1 1 1 4 iatsym1 I 1 1 1 4 iatsym2 I 1 1 1 4 wghsym R 1 1 1 4 Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL monomer.ali Status of dynamic memory allocation in routine: amaxbnd Variable T L1 U1 L2 U2 L3 U3 Size Bytes --------------------------------------------------------------------------- iseqdb I 1 1 1 4 nseqdb I 1 1 1 4 seqdb S 1 1 1 1 1 4 codep S 1 1 1 20 ialn2 I 1 220 1 4 880 3520 nresn2 I 1 4 4 16 irestypn2 I 1 220 1 4 880 3520 invaln2 I 1 220 1 4 880 3520 nsegmn2 I 1 4 4 16 iress1n2 I 1 30 1 4 120 480 iress2n2 I 1 30 1 4 120 480 resol2 R 1 4 4 16 rfactr2 R 1 4 4 16 caln2 S 1 220 1 4 880 880 ccaln2 S 1 220 1 4 880 880 alnchn2 S 1 2 1 4 8 8 prottyp2 S 1 4 4 320 source2 S 1 4 4 320 range2 S 1 2 1 4 8 40 name2 S 1 4 4 320 segidn2 S 1 30 1 4 120 2400 codein2 L 1 4 4 16 iattmod I 1 50 50 200 iatmgrp I 1 220 220 880 grpatm S 1 50 50 250 attmod S 1 220 220 1980 var R 1 4 1 16 64 256 pdf R 1 4 1 50 200 800 ientry I 1 84480 84480 337920 jentry I 1 84480 84480 337920 nentries I 1 21120 21120 84480 iar I 1 10560 10560 42240 jar I 1 10560 10560 42240 kar I 1 10560 10560 42240 lar I 1 10560 10560 42240 b1ic R 1 10560 10560 42240 b2ic R 1 10560 10560 42240 t1ic R 1 10560 10560 42240 t2ic R 1 10560 10560 42240 pic R 1 10560 10560 42240 tar L 1 10560 10560 42240 xmin R 1 2640 2640 10560 ymin R 1 2640 2640 10560 zmin R 1 2640 2640 10560 ialn I 1 220 1 4 880 3520 nresn I 1 4 4 16 irestypn I 1 220 1 4 880 3520 invaln I 1 220 1 4 880 3520 nsegmn I 1 4 4 16 iress1n I 1 30 1 4 120 480 iress2n I 1 30 1 4 120 480 resol R 1 4 4 16 rfactr R 1 4 4 16 alnacc R 1 220 220 880 prof R 1 220 1 4 880 3520 gapdst R 1 222 1 222 49284 197136 caln S 1 220 1 4 880 880 ccaln S 1 220 1 4 880 880 alnchn S 1 2 1 4 8 8 prottyp S 1 4 4 320 source S 1 4 4 320 range S 1 2 1 4 8 40 name S 1 4 4 320 segidn S 1 30 1 4 120 2400 atmfull S 1 4 4 1024 codein L 1 4 4 16 iresatmn I 1 2640 1 4 10560 42240 natmn I 1 4 4 16 iatmr1n I 1 220 1 4 880 3520 idih I 1 220 1 9 1 4 7920 31680 idihc I 1 220 1 9 1 4 7920 31680 iglbsim I 1 4 1 4 16 64 isstruc I 1 220 1 4 880 3520 neigh I 1 220 1 4 880 3520 ineigh I 1 50 1 220 1 4 44000 176000 iresol I 1 4 4 16 indats2n I 1 2 1 2640 1 4 21120 84480 imnchw I 1 220 1 4 880 3520 iacont I 1 4 4 16 idsta1 I 1 220 1 4 880 3520 idsta2 I 1 220 1 4 880 3520 fractglsim R 1 4 1 4 16 64 xn R 1 2640 1 4 10560 42240 yn R 1 2640 1 4 10560 42240 zn R 1 2640 1 4 10560 42240 dih R 1 220 1 9 1 4 7920 31680 acc R 1 220 1 4 880 3520 bison R 1 2640 1 4 10560 42240 curvn R 1 220 1 4 880 3520 atmnamn S 1 2640 1 4 10560 42240 resnumn S 1 220 1 4 880 4400 resnamn S 1 220 1 4 880 3520 chainn S 1 220 1 4 880 880 accepts L 1 4 4 16 memrange S 1 2 1 6 1 4 48 48 memalnchn S 1 2 1 6 1 4 48 48 mematmfull S 1 6 1 4 24 6144 iatc I 1 5 1 2640 13200 52800 natc I 1 2640 2640 10560 iata I 1 3 1 5280 15840 63360 iatd I 1 4 1 7920 31680 126720 iatb I 1 2 1 2640 5280 21120 iati I 1 4 1 1100 4400 17600 resseg S 1 220 220 880 iatmr1 I 1 220 220 880 iattyp I 1 2640 2640 10560 iresatm I 1 2640 2640 10560 iatta I 1 2640 2640 10560 indats I 1 2640 1 3 7920 31680 irestyp I 1 220 220 880 idihres I 1 4 1 9 1 220 7920 31680 natngh I 1 2640 2640 10560 radii R 1 2640 2640 10560 charge R 1 2640 2640 10560 x R 1 2640 2640 10560 y R 1 2640 2640 10560 z R 1 2640 2640 10560 biso R 1 2640 2640 10560 vx R 1 2640 2640 10560 vy R 1 2640 2640 10560 vz R 1 2640 2640 10560 atmacc R 1 2640 2640 10560 resnam S 1 220 220 880 atmnam S 1 2640 2640 10560 resnum S 1 220 220 1100 chain S 1 220 220 220 picres L 1 220 1 3 660 2640 picatm L 1 2640 1 3 7920 31680 katmr1 I 1 220 220 880 kresatm I 1 2640 2640 10560 krestyp I 1 220 220 880 x2 R 1 2640 2640 10560 y2 R 1 2640 2640 10560 z2 R 1 2640 2640 10560 charg2 R 1 2640 2640 10560 biso2 R 1 2640 2640 10560 radii2 R 1 2640 2640 10560 atm2nam S 1 2640 2640 10560 res2nam S 1 220 220 880 chain2 S 1 220 220 220 res2num S 1 220 220 1100 dvx R 1 2640 2640 10560 dvy R 1 2640 2640 10560 dvz R 1 2640 2640 10560 pdbfil S 1 16331 16331 2090368 pdblst S 1 16331 16331 81655 indatm I 1 1 1 4 itcsr I 1 7 1 1 7 28 iatm I 1 1 1 4 ipcsr I 1 1 1 4 indatt I 1 1 1 4 itacsr I 1 7 1 1 7 28 iatt I 1 1 1 4 ipacsr I 1 1 1 4 iapairs I 1 2 1 1 2 8 iarsr2 I 1 50 1 50 2500 10000 iarsr I 1 50 50 200 indcsr I 1 1 1 4 pcsr R 1 1 1 4 pacsr R 1 1 1 4 iatsym1 I 1 2640 2640 10560 iatsym2 I 1 2640 2640 10560 wghsym R 1 2640 2640 10560 Dynamically allocated memory at amaxbnd [B,kB,MB]: 4994449 4877.392 4.763 openf5__224_> Open 11 OLD SEQUENTIAL monomer.ali Read the alignment from file : monomer.ali Total number of alignment positions: 190 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ga2 166 1 1ga2 Protease 2 prk7 189 1 prk7 park7 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1ga2.atm rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 166 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 4994449 4877.392 4.763 Starting time : 2003/03/12 15:50:31.782 Closing time : 2003/03/12 15:50:35.448 Total CPU time [seconds] : 0.00