X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 17:20:49 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! dg.inp -- Full metric matrix distance geometry X-PLOR>! Dave Schweisguth , 7 May 1996 X-PLOR>! Derived from nmr/dg_full_embed.inp X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use 'xplor -s' ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/xplor.seed opened. SEED=53787.254699707 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>! Include NOE and dihedral restraints in mmdg X-PLOR> X-PLOR>flags exclude * include bond angle dihe impr vdw noe cdih end X-PLOR>parameter nbonds repel=0.8 end end ! Scale van der Waals radii X-PLOR> X-PLOR>mmdg MMDG>! @groups.inp ! Uncomment to define rigid groups MMDG> ! (which seem to do nothing) MMDG> selection=(all) SELRPN: 677 atoms have been selected out of 677 MMDG> storebounds MMDG>end CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODDIH: dihedral type-based parameters retrieved CODIMP: improper type-based parameters retrieved DGSMOOT: number of connections: 9112 DGSMOOT: using sparse matrix bound smoothing algorithm. DGSMOOT: max. size of network (upper, lower): 154 75 MMDG: storing smoothed bounds matrix in memory. No metrization or embedding performed. X-PLOR> X-PLOR>! Loop until embedding is successful. Once usually suffices. X-PLOR> X-PLOR>evaluate ($embedded="false") EVALUATE: symbol $EMBEDDED set to "false" (string) X-PLOR>while ($embedded="false") loop embed NEXTCD: condition evaluated as true X-PLOR> mmdg recallbounds end MMDG: no atoms will be metrized. NBUPDA: type-based van der Waals parameters retrieved. DGSETNX: found 4054 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR>end loop embed X-PLOR>while ($embedded="false") loop embed NEXTCD: condition evaluated as false X-PLOR> mmdg recallbounds end X-PLOR>end loop embed X-PLOR> X-PLOR>! Scale coordinates by $dgscale (defined by mmdg) X-PLOR> X-PLOR>vector do (x = x * $dgscale) (known) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (y = y * $dgscale) (known) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (z = z * $dgscale) (known) SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>! Regularize X-PLOR> X-PLOR>flags exclude * include dg end X-PLOR>minimize powell nstep=100 drop=10 nprint=25 end POWELL: number of degrees of freedom= 2031 EMMDG-info: vdw bounds are added to stored bounds matrix! DGSETNX: found 4054 exclusions (1--2, 1--3) for repulsive lower bounds. --------------- cycle= 25 ------ stepsize= 0.0021 ----------------------- | Etotal =0.11E+08 grad(E)=20.042 E(DG )=0.11E+08 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0002 ----------------------- | Etotal =0.11E+08 grad(E)=2.034 E(DG )=0.11E+08 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0034 ----------------------- | Etotal =0.11E+08 grad(E)=0.115 E(DG )=0.11E+08 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= -0.0004 ----------------------- | Etotal =0.11E+08 grad(E)=0.025 E(DG )=0.11E+08 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>write coordinates output=dg.pdb end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dg.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 997416 current use= 0 X-PLOR: total CPU time= 65.6321 s X-PLOR: entry time at 17:20:49 17-Aug-96 X-PLOR: exit time at 17:21:56 17-Aug-96