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, Linux aryabhatta 2.4.18-14 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/05/06 17:06:32.559 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 3 3 12 nresn2 I 1 3 3 12 irestypn2 I 1 1 1 3 3 12 invaln2 I 1 1 1 3 3 12 nsegmn2 I 1 3 3 12 iress1n2 I 1 30 1 3 90 360 iress2n2 I 1 30 1 3 90 360 resol2 R 1 3 3 12 rfactr2 R 1 3 3 12 caln2 S 1 1 1 3 3 3 ccaln2 S 1 1 1 3 3 3 alnchn2 S 1 2 1 3 6 6 prottyp2 S 1 3 3 240 source2 S 1 3 3 240 range2 S 1 2 1 3 6 30 name2 S 1 3 3 240 segidn2 S 1 30 1 3 90 1800 codein2 L 1 3 3 12 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 3 1 16 48 192 pdf R 1 3 1 50 150 600 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 3 3 12 nresn I 1 3 3 12 irestypn I 1 1 1 3 3 12 invaln I 1 1 1 3 3 12 nsegmn I 1 3 3 12 iress1n I 1 30 1 3 90 360 iress2n I 1 30 1 3 90 360 resol R 1 3 3 12 rfactr R 1 3 3 12 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 3 3 3 ccaln S 1 1 1 3 3 3 alnchn S 1 2 1 3 6 6 prottyp S 1 3 3 240 source S 1 3 3 240 range S 1 2 1 3 6 30 name S 1 3 3 240 segidn S 1 30 1 3 90 1800 atmfull S 1 3 3 768 codein L 1 3 3 12 iresatmn I 1 1 1 3 3 12 natmn I 1 3 3 12 iatmr1n I 1 1 1 3 3 12 idih I 1 1 1 9 1 3 27 108 idihc I 1 1 1 9 1 3 27 108 iglbsim I 1 3 1 3 9 36 isstruc I 1 1 1 3 3 12 neigh I 1 1 1 3 3 12 ineigh I 1 50 1 1 1 3 150 600 iresol I 1 3 3 12 indats2n I 1 2 1 1 1 3 6 24 imnchw I 1 1 1 3 3 12 iacont I 1 3 3 12 idsta1 I 1 1 1 3 3 12 idsta2 I 1 1 1 3 3 12 fractglsim R 1 3 1 3 9 36 xn R 1 1 1 3 3 12 yn R 1 1 1 3 3 12 zn R 1 1 1 3 3 12 dih R 1 1 1 9 1 3 27 108 acc R 1 1 1 3 3 12 bison R 1 1 1 3 3 12 curvn R 1 1 1 3 3 12 atmnamn S 1 1 1 3 3 12 resnumn S 1 1 1 3 3 15 resnamn S 1 1 1 3 3 12 chainn S 1 1 1 3 3 3 accepts L 1 3 3 12 memrange S 1 2 1 6 1 3 36 36 memalnchn S 1 2 1 6 1 3 36 36 mematmfull S 1 6 1 3 18 4608 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]: 2200483 2148.909 2.099 TOP_________> 2 2 SET STOP_ON_ERROR = 1 TOP_________> 3 3 SET MAXRES = 2000 TOP_________> 4 4 READ_ALIGNMENT FILE = 'str.ali' openf5__224_> Open 11 OLD SEQUENTIAL str.ali 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 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 2000 1 4 8000 32000 nresn2 I 1 4 4 16 irestypn2 I 1 2000 1 4 8000 32000 invaln2 I 1 2000 1 4 8000 32000 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 2000 1 4 8000 8000 ccaln2 S 1 2000 1 4 8000 8000 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 768000 768000 3072000 jentry I 1 768000 768000 3072000 nentries I 1 192000 192000 768000 iar I 1 96000 96000 384000 jar I 1 96000 96000 384000 kar I 1 96000 96000 384000 lar I 1 96000 96000 384000 b1ic R 1 96000 96000 384000 b2ic R 1 96000 96000 384000 t1ic R 1 96000 96000 384000 t2ic R 1 96000 96000 384000 pic R 1 96000 96000 384000 tar L 1 96000 96000 384000 xmin R 1 24000 24000 96000 ymin R 1 24000 24000 96000 zmin R 1 24000 24000 96000 ialn I 1 2000 1 4 8000 32000 nresn I 1 4 4 16 irestypn I 1 2000 1 4 8000 32000 invaln I 1 2000 1 4 8000 32000 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 2000 2000 8000 prof R 1 2000 1 4 8000 32000 gapdst R 1 2002 1 2002 4008004 16032016 caln S 1 2000 1 4 8000 8000 ccaln S 1 2000 1 4 8000 8000 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 24000 1 4 96000 384000 natmn I 1 4 4 16 iatmr1n I 1 2000 1 4 8000 32000 idih I 1 2000 1 9 1 4 72000 288000 idihc I 1 2000 1 9 1 4 72000 288000 iglbsim I 1 4 1 4 16 64 isstruc I 1 2000 1 4 8000 32000 neigh I 1 2000 1 4 8000 32000 ineigh I 1 50 1 2000 1 4 400000 1600000 iresol I 1 4 4 16 indats2n I 1 2 1 24000 1 4 192000 768000 imnchw I 1 2000 1 4 8000 32000 iacont I 1 4 4 16 idsta1 I 1 2000 1 4 8000 32000 idsta2 I 1 2000 1 4 8000 32000 fractglsim R 1 4 1 4 16 64 xn R 1 24000 1 4 96000 384000 yn R 1 24000 1 4 96000 384000 zn R 1 24000 1 4 96000 384000 dih R 1 2000 1 9 1 4 72000 288000 acc R 1 2000 1 4 8000 32000 bison R 1 24000 1 4 96000 384000 curvn R 1 2000 1 4 8000 32000 atmnamn S 1 24000 1 4 96000 384000 resnumn S 1 2000 1 4 8000 40000 resnamn S 1 2000 1 4 8000 32000 chainn S 1 2000 1 4 8000 8000 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 24000 120000 480000 natc I 1 24000 24000 96000 iata I 1 3 1 48000 144000 576000 iatd I 1 4 1 72000 288000 1152000 iatb I 1 2 1 24000 48000 192000 iati I 1 4 1 10000 40000 160000 resseg S 1 2000 2000 8000 iatmr1 I 1 2000 2000 8000 iattyp I 1 24000 24000 96000 iresatm I 1 24000 24000 96000 iatta I 1 24000 24000 96000 indats I 1 24000 1 3 72000 288000 irestyp I 1 2000 2000 8000 idihres I 1 4 1 9 1 2000 72000 288000 natngh I 1 24000 24000 96000 radii R 1 24000 24000 96000 charge R 1 24000 24000 96000 x R 1 24000 24000 96000 y R 1 24000 24000 96000 z R 1 24000 24000 96000 biso R 1 24000 24000 96000 vx R 1 24000 24000 96000 vy R 1 24000 24000 96000 vz R 1 24000 24000 96000 atmacc R 1 24000 24000 96000 resnam S 1 2000 2000 8000 atmnam S 1 24000 24000 96000 resnum S 1 2000 2000 10000 chain S 1 2000 2000 2000 picres L 1 2000 1 3 6000 24000 picatm L 1 24000 1 3 72000 288000 katmr1 I 1 2000 2000 8000 kresatm I 1 24000 24000 96000 krestyp I 1 2000 2000 8000 x2 R 1 24000 24000 96000 y2 R 1 24000 24000 96000 z2 R 1 24000 24000 96000 charg2 R 1 24000 24000 96000 biso2 R 1 24000 24000 96000 radii2 R 1 24000 24000 96000 atm2nam S 1 24000 24000 96000 res2nam S 1 2000 2000 8000 chain2 S 1 2000 2000 2000 res2num S 1 2000 2000 10000 dvx R 1 24000 24000 96000 dvy R 1 24000 24000 96000 dvz R 1 24000 24000 96000 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 24000 24000 96000 iatsym2 I 1 24000 24000 96000 wghsym R 1 24000 24000 96000 Dynamically allocated memory at amaxbnd [B,kB,MB]: 41819089 40838.953 39.882 openf5__224_> Open 11 OLD SEQUENTIAL str.ali Read the alignment from file : str.ali Total number of alignment positions: 405 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1dz8 404 1 1dz8 undefined 2 2cpp 405 1 2cpp undefined TOP_________> 5 5 SEQUENCE_TO_ALI TOP_________> 6 6 SET ALIGN_CODES = '1dz8' '2cpp' TOP_________> 7 7 SET ATOM_FILES = ALIGN_CODES TOP_________> 8 8 SET ATOM_FILES_DIRECTORY = './' TOP_________> 9 9 MALIGN3D openf5__224_> Open 11 OLD SEQUENTIAL ./1dz8.pdb 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: : To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 openf5__224_> Open 11 OLD SEQUENTIAL ./2cpp.pdb malign3_328_> Initial framework positions: 0 malign3_329W> Insufficient overlap; nothing done. TOP_________> 10 10 SET ADD_SEQUENCE = ON TOP_________> 11 11 SET CURRENT_DIRECTORY = ON TOP_________> 12 12 SET OUTPUT = 'LONG' TOP_________> 13 13 SET GAP_PENALTIES_3D = 0.0 1.75 TOP_________> 14 14 SET FIT_ATOMS = 'CA' TOP_________> 15 15 SET WRITE_FIT = ON TOP_________> 16 16 SET WRITE_WHOLE_PDB = ON TOP_________> 17 17 WRITE_ALIGNMENT FILE = 'str_STR.pir' openf5__224_> Open 14 UNKNOWN SEQUENTIAL str_STR.pir TOP_________> 18 18 SET ALIGNMENT_FORMAT = 'PIR' Dynamically allocated memory at finish [B,kB,MB]: 41819089 40838.953 39.882 Starting time : 2003/05/06 17:06:32.559 Closing time : 2003/05/06 17:06:33.879 Total CPU time [seconds] : 1.20