XPLOR-NIH version 2.18-pre4 C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006). N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger User: schwitrs on: tan (x86_64/Linux ) at: 11-Jun-07 15:29:32 X-PLOR> X-PLOR>remark This protocol allows computer to select dimer noes X-PLOR>REMARKS very slow cooling with increase of vdw X-PLOR> X-PLOR>!this is from ubiquitint refinement X-PLOR>!converting this to refine bax X-PLOR> X-PLOR>!---------------------------------------------------------------------- X-PLOR>! read in the PSF file and initial structure X-PLOR> X-PLOR>structure !@bax_short.psf STRUcture>PSF REMARKS FILENAME="bax_short.psf" REMARKS =============================================================== REMARKS overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa REMARKS energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP,173.138,$DCSA REMARKS =============================================================== REMARKS bonds,angles,impropers,noe REMARKS bonds etc: 3.575818E-03,0.549326,0.385884,3.252691E-02 REMARKS =============================================================== REMARKS noe REMARKS violations : 9 REMARKS =============================================================== REMARKS dipo dnh dnh2 dch dch2 dch3 dcc dcc2 REMARKS RMS dipo: 0 0 5.37589 1.44026 REMARKS 3.33263 1.31729 0.696583 REMARKS dcsa csa REMARKS RMS dcsa :0 REMARKS =============================================================== REMARKS DATE:05-Sep-02 11:39:46 created by user: rlipsitz XPLOR: current counts (number in parenthesis is maximum) NATOM= 175(MAXA= 200) NBOND= 174(MAXB= 200) NTHETA= 313(MAXT= 400) NGRP= 70(MAXGRP= 100) NPHI= 19(MAXP= 100) NIMPHI= 82(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 78(MAXNB= 100) STRUcture> STRUcture>end X-PLOR>param @TOPPAR:parallhdg_new.pro @TOPPAR:par_axis.pro end ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg_new.pro opened. PARRDR>remark file parallhdg_new.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use protein.par. PARRDR>remark geometric energy function parameters for distance geometry and PARRDR>remark simulated annealing. Modified by G.M.C. to have sigma's of Param19x and parafloat PARRDR> PARRDR>set message off echo off end PARRDR> @TOPPAR:par_axis.pro end ASSFIL: file /home/schwitrs/xplor/toppar/par_axis.pro opened. PARRDR>remark para_axis.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use axis.par. PARRDR>remark molecule for anisotropy PARRDR> PARRDR>set message off echo off end PARRDR> end X-PLOR> X-PLOR>coor !@bax_short.pdb COOR>REMARK FILENAME="bax_short.pdb" COOR>REMARK =============================================================== COOR>REMARK overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa COOR>REMARK energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP,173.138,$DCSA %WDSUB-ERR: symbol not found: REMARK energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP, ^^^^^ %WDSUB-ERR: symbol not found: REMARK energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP,173.138,$DCSA ^^^^^ COOR>REMARK =============================================================== COOR>REMARK bonds,angles,impropers,noe COOR>REMARK bonds etc: 3.575818E-03,0.549326,0.385884,3.252691E-02 COOR>REMARK =============================================================== COOR>REMARK noe COOR>REMARK violations : 9 COOR>REMARK =============================================================== COOR>REMARK dipo dnh dnh2 dch dch2 dch3 dcc dcc2 COOR>REMARK RMS dipo: 0 0 5.37589 1.44026 COOR>REMARK 3.33263 1.31729 0.696583 COOR>REMARK dcsa csa COOR>REMARK RMS dcsa :0 COOR>REMARK =============================================================== COOR>REMARK DATE:05-Sep-02 11:39:46 created by user: rlipsitz COOR>ATOM 1 N MET 20 10.802 6.788 -2.757 1.00 0.51 COOR>ATOM 2 HN MET 20 11.734 6.732 -2.459 1.00 0.57 X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>!!delete select (resid 502) end X-PLOR> X-PLOR> X-PLOR>!---------------------------------------------------------------------- X-PLOR>! set the weights for the experimental energy terms X-PLOR> X-PLOR>evaluate ($knoe = 25.0) ! noes EVALUATE: symbol $KNOE set to 25.0000 (real) X-PLOR>evaluate ($khb = 50.0) ! hbond EVALUATE: symbol $KHB set to 50.0000 (real) X-PLOR>evaluate ($asym = 0.2) ! slope of NOE potential EVALUATE: symbol $ASYM set to 0.200000 (real) X-PLOR>evaluate ($kcdi = 10.0) ! torsion angles EVALUATE: symbol $KCDI set to 10.0000 (real) X-PLOR>evaluate ($ksani=0.55) EVALUATE: symbol $KSANI set to 0.550000 (real) X-PLOR>evaluate ($khbda=50.0) ! hbond_angle correlation EVALUATE: symbol $KHBDA set to 50.0000 (real) X-PLOR> X-PLOR>evaluate ($cool_steps = 8000) EVALUATE: symbol $COOL_STEPS set to 8000.00 (real) X-PLOR>evaluate ($init_t = 8000.00) EVALUATE: symbol $INIT_T set to 8000.00 (real) X-PLOR> X-PLOR>!---------------------------------------------------------------------- X-PLOR>! The next statement makes sure the experimental energies are used in the X-PLOR>! calculation, and switches off the unwanted energy terms. X-PLOR>! note that the NMR torsions are only switched on in the cooling stage X-PLOR>! we include the noncrystallographic symmetry right from the start X-PLOR>!--------------------------------------------------------------------------- X-PLOR>! Read experimental restraints X-PLOR> X-PLOR>noe NOE> nres = 16000 NOE: allocating space for 16000 restraints. NOE> NOE> set echo on message on end NOE> NOE> class dist NOE> !@3dnoe_s.tbl NOE>assign ( resid 21 and name HN ) ( resid 22 and name HN ) 2.6 2.6 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HN ) ( resid 23 and name HN ) 2.7 2.7 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 23 and name HN ) ( resid 24 and name HN ) 2.7 2.7 0.9 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HN ) ( resid 25 and name HN ) 2.5 2.5 0.8 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name HN ) ( resid 26 and name HN ) 2.6 2.6 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name HN ) ( resid 27 and name HN ) 2.6 2.6 0.9 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and name HN ) ( resid 28 and name HN ) 2.8 2.8 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 29 and name HN ) ( resid 30 and name HN ) 2.8 2.8 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE> NOE> !@cn4d_s.tbl NOE>assign ( resid 20 and name HA ) ( resid 21 and name HN ) 3.8 3.8 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and name HA ) ( resid 23 and name HN ) 4.2 1.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and name HA ) ( resid 24 and name HN ) 3.9 1.4 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 20 and name HN ) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 21 and name HN ) 3.8 3.8 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HB2 or name HB1 )) ( resid 20 and name HN ) 3.7 3.7 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HB2 or name HB1 )) ( resid 21 and name HN ) 3.8 3.8 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and name HE# ) ( resid 20 and name HN ) 3.9 3.9 1.4 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HG1 or name HG2 )) ( resid 20 and name HN ) 3.7 3.7 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HG2 or name HG1 )) ( resid 20 and name HN ) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and name HN ) ( resid 21 and name HB# ) 4.2 4.2 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 21 and name HA ) ( resid 22 and name HN ) 3.6 3.6 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HA ) ( resid 24 and name HN ) 3.5 1.3 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HB# ) ( resid 21 and name HN ) 2.9 2.9 1.0 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HB# ) ( resid 22 and name HN ) 3.1 3.1 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HB# ) ( resid 23 and name HN ) 4.5 4.5 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HD# ) ( resid 21 and name HN ) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HE# ) ( resid 21 and name HN ) 4.4 4.4 1.5 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and ( name HG1 or name HG2 )) ( resid 21 and name HN ) 3.4 3.4 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and ( name HG2 or name HG1 )) ( resid 21 and name HN ) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HN ) ( resid 22 and name HA ) 4.5 4.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name HN ) ( resid 22 and name HB ) 4.3 4.3 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 23 and name HN ) 4.1 4.1 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 24 and name HN ) 4.3 1.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 25 and name HN ) 3.5 1.3 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 26 and name HN ) 4.2 1.4 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HB ) ( resid 22 and name HN ) 3.1 3.1 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HB ) ( resid 23 and name HN ) 3.6 3.6 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HG2# ) ( resid 22 and name HN ) 3.4 3.4 1.1 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HG2# ) ( resid 26 and name HN ) 4.0 4.0 1.0 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name HN ) ( resid 24 and name HB# ) 4.4 4.4 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 3 atoms have been selected out of 175 NOE>assign ( resid 23 and ( name HA1 or name HA2 )) ( resid 24 and name HN ) 3.5 3.5 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 23 and ( name HA2 or name HA1 )) ( resid 24 and name HN ) 3.8 3.8 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 25 and name HN ) 3.9 3.9 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 27 and name HN ) 3.8 1.3 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 28 and name HN ) 4.6 1.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HB# ) ( resid 24 and name HN ) 2.8 2.8 1.0 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HB# ) ( resid 25 and name HN ) 3.0 3.0 1.0 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HB# ) ( resid 26 and name HN ) 4.3 4.3 1.1 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HN ) ( resid 25 and ( name HB1 or name HB2 )) 4.1 4.1 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 26 and name HN ) 4.1 4.1 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 28 and name HN ) 4.0 1.4 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 29 and name HN ) 4.2 1.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 25 and name HN ) 3.1 3.1 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 26 and name HN ) 3.5 3.5 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HB2 or name HB1 )) ( resid 25 and name HN ) 3.2 3.2 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HD1# or name HD2# )) ( resid 25 and name HN ) 3.3 3.3 1.1 SELRPN: 6 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HD2# or name HD1# )) ( resid 25 and name HN ) 3.3 3.3 1.1 SELRPN: 6 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name HG ) ( resid 25 and name HN ) 3.0 3.0 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name HA ) ( resid 27 and name HN ) 4.1 4.1 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name HA ) ( resid 29 and name HN ) 4.5 1.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 27 and name HN ) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and name HN ) 3.5 3.5 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HD1# or name HD2# )) ( resid 26 and name HN ) 3.7 3.7 1.3 SELRPN: 6 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HD2# or name HD1# )) ( resid 26 and name HN ) 3.4 3.4 1.1 SELRPN: 6 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name HG ) ( resid 26 and name HN ) 3.3 3.3 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and name HA ) ( resid 28 and name HN ) 4.5 4.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and name HA ) ( resid 30 and name HN ) 4.0 1.4 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 27 and name HN ) 3.3 3.3 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 28 and name HN ) 3.9 3.9 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and name HN ) 3.2 3.2 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 28 and name HN ) 4.2 4.2 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HD1# or name HD2# )) ( resid 27 and name HN ) 3.7 3.7 1.3 SELRPN: 6 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and name HG ) ( resid 27 and name HN ) 4.5 4.5 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and name HA ) ( resid 29 and name HN ) 4.2 4.2 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and ( name HB1 or name HB2 )) ( resid 28 and name HN ) 3.3 3.3 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and ( name HB1 or name HB2 )) ( resid 29 and name HN ) 3.5 3.5 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and ( name HB2 or name HB1 )) ( resid 28 and name HN ) 3.3 3.3 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and ( name HB2 or name HB1 )) ( resid 29 and name HN ) 3.5 3.5 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and name HG# ) ( resid 28 and name HN ) 3.3 3.3 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 28 and name HG# ) ( resid 30 and name HN ) 4.6 4.6 1.2 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 29 and ( name HA1 or name HA2 )) ( resid 30 and name HN ) 3.7 3.7 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 29 and ( name HA2 or name HA1 )) ( resid 30 and name HN ) 3.9 3.9 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 30 and name HB# ) ( resid 30 and name HN ) 3.3 3.3 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 30 and name HD# ) ( resid 30 and name HN ) 4.5 4.5 1.5 SELRPN: 2 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE> NOE> !@hchc_s.tbl NOE>assign ( resid 20 and name HA ) ( resid 20 and name HE# ) 3.2 3.2 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 3 atoms have been selected out of 175 NOE>assign ( resid 20 and name HA ) ( resid 20 and name HG# ) 3.8 3.8 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and name HA ) ( resid 20 and ( name HG1 or name HG2 )) 4.0 4.0 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and name HA ) ( resid 20 and ( name HG2 or name HG1 )) 4.2 4.2 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>!(inter)assign ( resid 20 and name HA ) ( resid 21 and name HA ) 4.7 1.6 1.6 NOE>assign ( resid 20 and name HA ) ( resid 23 and ( name HA1 or name HA2 )) 4.7 4.7 1.2 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 20 and name HE# ) 3.9 3.9 1.4 SELRPN: 2 atoms have been selected out of 175 SELRPN: 3 atoms have been selected out of 175 NOE>!(inter)assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 21 and name HE# ) 3.3 3.3 1.1 NOE>assign ( resid 20 and name HE# ) ( resid 20 and name HG# ) 3.1 3.1 1.1 SELRPN: 3 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and name HE# ) ( resid 20 and ( name HG1 or name HG2 )) 3.5 3.5 1.2 SELRPN: 3 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and name HE# ) ( resid 20 and ( name HG2 or name HG1 )) 3.6 3.6 1.3 SELRPN: 3 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 20 and name HE# ) ( resid 24 and name HB# ) 3.8 3.8 1.0 SELRPN: 3 atoms have been selected out of 175 SELRPN: 3 atoms have been selected out of 175 NOE>assign ( resid 21 and name HA ) ( resid 21 and name HE# ) 3.4 3.4 1.2 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 21 and name HA ) ( resid 21 and ( name HG1 or name HG2 )) 3.3 3.3 1.2 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 21 and name HA ) ( resid 24 and name HB# ) 3.1 3.1 0.8 SELRPN: 1 atoms have been selected out of 175 SELRPN: 3 atoms have been selected out of 175 NOE>assign ( resid 21 and name HB# ) ( resid 25 and ( name HD1# or name HD2# )) 3.5 3.5 0.9 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>!(inter)assign ( resid 22 and name HA ) ( resid 22 and name HG2# ) 3.1 3.1 1.1 NOE>assign ( resid 22 and name HA ) ( resid 25 and ( name HB1 or name HB2 )) 3.5 3.5 0.9 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 25 and ( name HB2 or name HB1 )) 3.7 3.7 0.9 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 25 and ( name HD1# or name HD2# )) 3.2 3.2 0.8 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 22 and name HA ) ( resid 25 and name HG ) 3.9 1.4 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>!(inter)assign ( resid 22 and name HG2#) ( resid 23 and ( name HA2 or name HA1 )) 4.4 4.4 1.5 NOE>assign ( resid 22 and name HG2#) ( resid 26 and ( name HB1 or name HB2 )) 4.0 4.0 1.0 SELRPN: 3 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 22 and name HG2#) ( resid 26 and ( name HD1# or name HD2# )) 3.1 3.1 0.8 SELRPN: 3 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 22 and name HG2# ) ( resid 26 and name HG ) 3.6 3.6 0.9 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 27 and ( name HB1 or name HB2 )) 4.3 4.3 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 27 and ( name HB2 or name HB1 )) 4.3 4.3 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 24 and name HA ) ( resid 27 and ( name HD1# or name HD2# )) 4.1 4.1 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 24 and name HB# ) ( resid 25 and name HA ) 3.9 3.9 1.4 SELRPN: 3 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>!(inter)assign ( resid 24 and name HB# ) ( resid 25 and ( name HB1 or name HB2 )) 3.9 3.9 1.4 NOE>assign ( resid 25 and name HA ) ( resid 25 and ( name HD1# or name HD2# )) 3.1 3.1 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 25 and ( name HD2# or name HD1# )) 2.9 2.9 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 25 and name HG ) 3.5 3.5 1.2 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name HA ) ( resid 28 and name HG# ) 4.0 4.0 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 25 and ( name HD2# or name HD1# )) 3.1 3.1 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HB2 or name HB1 )) ( resid 25 and ( name HD1# or name HD2# )) 3.1 3.1 1.1 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 25 and ( name HD2# or name HD1# )) ( resid 28 and ( name HB2 or name HB1 )) 3.9 3.9 1.0 SELRPN: 6 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 26 and name HA ) ( resid 26 and ( name HD1# or name HD2# )) 3.8 3.8 1.3 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 26 and name HA ) ( resid 26 and ( name HD2# or name HD1# )) 3.0 3.0 1.0 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 26 and name HA ) ( resid 26 and name HG ) 3.9 3.9 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 26 and ( name HD1# or name HD2# )) 3.5 3.5 1.2 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 26 and ( name HD2# or name HD1# )) 3.5 3.5 1.2 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and ( name HD1# or name HD2# )) 3.6 3.6 1.2 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and ( name HD2# or name HD1# )) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and name HA ) ( resid 27 and ( name HD1# or name HD2# )) 4.0 4.0 1.4 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and name HA ) ( resid 27 and ( name HD2# or name HD1# )) 3.1 3.1 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and name HA ) ( resid 27 and name HG ) 4.2 4.2 1.5 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 27 and ( name HD2# or name HD1# )) 3.8 3.8 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and ( name HD1# or name HD2# )) 3.5 3.5 1.2 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and ( name HD2# or name HD1# )) 3.6 3.6 1.3 SELRPN: 2 atoms have been selected out of 175 SELRPN: 6 atoms have been selected out of 175 NOE>assign ( resid 27 and ( name HD2# or name HD1# )) ( resid 30 and ( name HB2 or name HB1 )) 4.1 4.1 1.0 SELRPN: 6 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 28 and name HA ) ( resid 28 and name HG# ) 3.1 3.1 1.1 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE>assign ( resid 30 and name HA ) ( resid 30 and name HD# ) 3.5 3.5 1.2 SELRPN: 1 atoms have been selected out of 175 SELRPN: 2 atoms have been selected out of 175 NOE> NOE> NOE> class hb NOE> !@hbond_s.tbl NOE>assign ( resid 20 and name O ) ( resid 24 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 20 and name O ) ( resid 24 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name O ) ( resid 25 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 21 and name O ) ( resid 25 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name O ) ( resid 26 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 22 and name O ) ( resid 26 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 23 and name O ) ( resid 27 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 23 and name O ) ( resid 27 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name O ) ( resid 28 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 24 and name O ) ( resid 28 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name O ) ( resid 29 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 25 and name O ) ( resid 29 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name O ) ( resid 30 and name HN ) 1.9 0.4 0.6 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE>assign ( resid 26 and name O ) ( resid 30 and name N ) 2.9 0.5 0.7 SELRPN: 1 atoms have been selected out of 175 SELRPN: 1 atoms have been selected out of 175 NOE> NOE>end X-PLOR> X-PLOR>noe NOE> ceiling 100 NOE> averaging dist sum NOE> potential dist soft !soft NOE> scale dist $knoe NOE> sqconstant dist 1.0 NOE> sqexponent dist 2 NOE> soexponent dist 1 NOE> rswitch dist 0.6 NOE> sqoffset dist 0.0 NOE> asymptote dist 2.0 NOE> NOE> averaging hb sum NOE> potential hb square NOE> scale hb $khb NOE> sqconstant hb 1.0 NOE> sqexponent hb 2 NOE>end X-PLOR> X-PLOR> X-PLOR>restraints dihed DIHEDRAL> scale $kcdi DIHEDRAL> nass = 400 DIHEDRAL> !@phi_s.tbl DIHEDRAL>assign ( resid 20 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name C ) 5.00 -65.13 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 21 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name C ) 5.00 -64.15 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 22 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name C ) 5.00 -60.36 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 23 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name C ) 5.00 -63.25 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 24 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name C ) 5.00 -62.62 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 25 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name C ) 5.00 -63.73 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 26 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name C ) 5.00 -61.84 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 27 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name C ) 5.00 -62.05 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 28 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name C ) 5.00 -63.37 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 29 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name C ) 5.00 -65.24 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL> !@psi_s.tbl DIHEDRAL>assign ( resid 20 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name N ) 5.00 -36.38 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 21 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name N ) 5.00 -39.46 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 22 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name N ) 5.00 -43.45 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 23 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name N ) 5.00 -39.86 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 24 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name N ) 5.00 -41.68 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 25 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name N ) 5.00 -38.94 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 26 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name N ) 5.00 -40.14 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 27 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name N ) 5.00 -40.45 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 28 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name N ) 5.00 -42.31 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>assign ( resid 29 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name CA ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name N ) 5.00 -38.91 30.00 2 SELRPN: 1 atoms have been selected out of 175 DIHEDRAL> DIHEDRAL>end X-PLOR> X-PLOR> X-PLOR> X-PLOR> X-PLOR> X-PLOR>evaluate ($kdnh = $ksani) EVALUATE: symbol $KDNH set to 0.550000 (real) X-PLOR>evaluate ($kdch = 1.0*$kdnh) EVALUATE: symbol $KDCH set to 0.550000 (real) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) EVALUATE: symbol $KDCH3 set to 0.275000 (real) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) EVALUATE: symbol $KDCC set to 1.10000 (real) X-PLOR> X-PLOR>set echo on message on end X-PLOR> X-PLOR>evaluate ($da=12.0) EVALUATE: symbol $DA set to 12.0000 (real) X-PLOR>evaluate ($rhom=0.5) EVALUATE: symbol $RHOM set to 0.500000 (real) X-PLOR>evaluate ($dac=$da*2.18) EVALUATE: symbol $DAC set to 26.1600 (real) X-PLOR>evaluate ($dacc=$da*0.2) EVALUATE: symbol $DACC set to 2.40000 (real) X-PLOR> X-PLOR>set echo on message on end X-PLOR> X-PLOR>dipo XDIP> nres=1000 XDIP: Allocating space for 1000 number of constraints XDIP> XDIP> XDIP> class dnh XDIP> type fixd using fixed distance. XDIP> scale 1.0 Setting scale for class DNH to 1.000 XDIP> sign on Sign will be used. XDIP> average sum using sum averaging. XDIP> force $kdnh Setting force const for class DNH to 0.550 XDIP> potential harmonic using harmonic potential. XDIP> coef 0.0000 $da $rhom Setting coefficients for class DNH to 0.000 12.000 0.500 XDIP> !@DNH_s.tbl XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name HN ) -7.7310 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name HN ) -13.5980 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name HN ) -19.1190 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name HN ) -7.6530 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name HN ) -5.5790 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name HN ) -20.4920 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name HN ) -14.9360 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name HN ) -5.6340 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name HN ) -8.1150 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name HN ) -18.3580 1.0000 1.0000 SELRPN: 1 atoms have been selected out of 175 XDIP> XDIP> XDIP> XDIP>! class dch XDIP>! type fixd XDIP>! scale 1.0 XDIP>! sign on XDIP>! average sum XDIP>! force $kdch XDIP>! potential harmonic XDIP>! coef 0.0000 $dac $rhom XDIP>! @DCH_s.tbl XDIP> XDIP> XDIP>! class dch3 XDIP>! type fixd XDIP>! scale 1.0 XDIP>! sign on XDIP>! average sum XDIP>! force $kdch3 XDIP>! potential square XDIP>! coef 0.0000 $dac $rhom XDIP>! @DCH3.tbl XDIP> XDIP>end X-PLOR> X-PLOR>set echo on message on end X-PLOR> X-PLOR>evaluate ($kcsa = 0.0001) EVALUATE: symbol $KCSA set to 0.100000E-03 (real) X-PLOR> X-PLOR>evaluate ($dacs = 12.0) EVALUATE: symbol $DACS set to 12.0000 (real) X-PLOR>evaluate ($rhcs = 0.5) EVALUATE: symbol $RHCS set to 0.500000 (real) X-PLOR> X-PLOR>dcsa DCSA> nres=200 DCSA: Allocating space for 200 number of constraints DCSA> class heli DCSA> scale 21652.1 Setting scale for class HELI to 21652.10 DCSA> force $kcsa Setting force const for class HELI to 0.000 DCSA> type carb Using csa definition for 13Carbonyl. DCSA> potential harmonic using harmonic potential. DCSA> coeff 0.0 $dacs $rhcs Setting coefficients for class HELI to 0.000 12.000 0.500 DCSA>! sigma 74.7 11.8 -86.5 DCSA> sigma 71.2 23.3 -94.5 Setting sigmas for class HELI to 71.200 23.300 -94.500 DCSA> !@baxcsa_s.tbl DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name N ) -31.25 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name N ) 65.64 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name N ) -32.09 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name N ) 3.10 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name N ) 35.90 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name N ) -31.21 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name N ) 38.45 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name N ) -63.20 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name N ) 77.41 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>assign ( resid 500 and name OO ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name C ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name O ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name N ) -64.73 5.00 5.00 SELRPN: 1 atoms have been selected out of 175 DCSA> DCSA>end X-PLOR> X-PLOR>hbda HBDA> nres=300 HBDA: Allocating space for 300 number of constraints HBDA> class hbon HBDA> force $khbda Setting force const for class HBON to 50.000 HBDA> !@hbda_s.tbl HBDA>assign ( resid 24 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 20 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 25 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 21 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 26 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 22 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 27 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 27 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 23 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 28 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 28 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 24 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 29 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 29 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 25 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>assign ( resid 30 and name N ) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 30 and name HN) SELRPN: 1 atoms have been selected out of 175 SELRPN> ( resid 26 and name O ) SELRPN: 1 atoms have been selected out of 175 HBDA> HBDA>end X-PLOR> X-PLOR>!!evaluate ($rcon = 0.004) X-PLOR> X-PLOR>!!parameters X-PLOR>!! nbonds X-PLOR>!! atom X-PLOR>!! nbxmod 3 X-PLOR>!! wmin = 0.01 ! warning off X-PLOR>!! cutnb = 4.5 ! nonbonded cutoff X-PLOR>!! tolerance 0.5 X-PLOR>!! repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) X-PLOR>!! rexp = 2 ! exponents in (r^irex - R0^irex)^rexp X-PLOR>!! irex = 2 X-PLOR>!! rcon=$rcon ! actually set the vdW weight X-PLOR>!! end X-PLOR>!!end X-PLOR> X-PLOR> X-PLOR>set message on echo on end X-PLOR> X-PLOR> X-PLOR>! Fixing the axis using harmonic restraint X-PLOR>! leave out, let both rotate X-PLOR> X-PLOR>vector do (refx=x) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR>vector do (refy=y) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR>vector do (refz=z) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR> X-PLOR>vector do (harmonic=20.0) (resid 500 and name OO) SELRPN: 1 atoms have been selected out of 175 X-PLOR>vector do (harmonic=0.0) (resid 500 and name Z ) SELRPN: 1 atoms have been selected out of 175 X-PLOR>vector do (harmonic=0.0) (resid 500 and name X ) SELRPN: 1 atoms have been selected out of 175 X-PLOR>vector do (harmonic=0.0) (resid 500 and name Y ) SELRPN: 1 atoms have been selected out of 175 X-PLOR>vector do (harmonic=0.0) (not (resid 500)) SELRPN: 171 atoms have been selected out of 175 X-PLOR>restraints harmonic exponent=2 end X-PLOR>flags include harm end X-PLOR> X-PLOR>!!constraints fix (resid 500:501 and name OO) end X-PLOR> X-PLOR>!------------------------------------------------------------------- X-PLOR>! Set the Flags X-PLOR> X-PLOR>flags FLAGS> exclude * include bond angle impr vdw noe cdih harm dipo hbda !dcsa FLAGS>end X-PLOR> X-PLOR>!------------------------------------------------------------------ X-PLOR>! Dynamics: CA-CA X-PLOR> X-PLOR>vector do (mass = 100.0) (all) ! uniform mass for all atoms SELRPN: 175 atoms have been selected out of 175 X-PLOR>vector do (fbeta = 10.0) (all) ! coupling to heat bath SELRPN: 175 atoms have been selected out of 175 X-PLOR> X-PLOR> X-PLOR> X-PLOR>evaluate ($count =0) EVALUATE: symbol $COUNT set to 0.00000 (real) X-PLOR>while ($count < 1 ) NEXTCD: condition evaluated as true WHILE-clause= loop structure X-PLOR> evaluate ($count = $count + 1) EVALUATE: symbol $COUNT set to 1.00000 (real) X-PLOR> X-PLOR>coor swap end COOR: selected coordinates swaped (main<->comp) X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR> X-PLOR>evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.80) EVALUATE: symbol $INI_RAD set to 0.900000 (real) EVALUATE: symbol $FIN_RAD set to 0.800000 (real) X-PLOR>evaluate ($ini_con= 0.004) evaluate ($fin_con= 4.0) EVALUATE: symbol $INI_CON set to 0.400000E-02 (real) EVALUATE: symbol $FIN_CON set to 4.00000 (real) X-PLOR>evaluate ($ini_ncs = 0.01) evaluate ($fin_ncs = 10) EVALUATE: symbol $INI_NCS set to 0.100000E-01 (real) EVALUATE: symbol $FIN_NCS set to 10.0000 (real) X-PLOR>evaluate ($ini_ang = 0.4) evaluate ($fin_ang = 1.0) EVALUATE: symbol $INI_ANG set to 0.400000 (real) EVALUATE: symbol $FIN_ANG set to 1.00000 (real) X-PLOR>evaluate ($ini_imp = 0.1) evaluate ($fin_imp = 1.0) EVALUATE: symbol $INI_IMP set to 0.100000 (real) EVALUATE: symbol $FIN_IMP set to 1.00000 (real) X-PLOR> X-PLOR>evaluate ($ini_noe = 2.0) evaluate ($fin_noe = 50.0) EVALUATE: symbol $INI_NOE set to 2.00000 (real) EVALUATE: symbol $FIN_NOE set to 50.0000 (real) X-PLOR>evaluate ($ini_hb = 2.0) evaluate ($fin_hb = 50.0) EVALUATE: symbol $INI_HB set to 2.00000 (real) EVALUATE: symbol $FIN_HB set to 50.0000 (real) X-PLOR>evaluate ($knoe = $ini_noe) ! slope of NOE potential EVALUATE: symbol $KNOE set to 2.00000 (real) X-PLOR>evaluate ($khb = 0.0001) ! slope of NOE potential EVALUATE: symbol $KHB set to 0.100000E-03 (real) X-PLOR> X-PLOR>evaluate ($kcdi = 10.0) ! torsion angles EVALUATE: symbol $KCDI set to 10.0000 (real) X-PLOR> X-PLOR>evaluate ($rcon = 0.004) ! force constant for vdW EVALUATE: symbol $RCON set to 0.400000E-02 (real) X-PLOR> X-PLOR>noe NOE> scale dist $knoe NOE> scale hb $khb NOE>end X-PLOR> X-PLOR>evaluate ($ini_sani = 0.001) evaluate ($fin_sani = 1.00) EVALUATE: symbol $INI_SANI set to 0.100000E-02 (real) EVALUATE: symbol $FIN_SANI set to 1.00000 (real) X-PLOR>evaluate ($ksani = $ini_sani) ! slope of NOE potential EVALUATE: symbol $KSANI set to 0.100000E-02 (real) X-PLOR>evaluate ($ksani = 0.0001) ! dipolar coupling force constant EVALUATE: symbol $KSANI set to 0.100000E-03 (real) X-PLOR>evaluate ($kdnh = $ksani) EVALUATE: symbol $KDNH set to 0.100000E-03 (real) X-PLOR>evaluate ($kdch = 1.0*$kdnh) EVALUATE: symbol $KDCH set to 0.100000E-03 (real) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) EVALUATE: symbol $KDCH3 set to 0.500000E-04 (real) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) EVALUATE: symbol $KDCC set to 0.200000E-03 (real) X-PLOR> X-PLOR> X-PLOR> X-PLOR>dipo XDIP> class dnh force $kdnh Setting force const for class DNH to 0.000 XDIP> class dnh2 force $kdnh Setting force const for class DNH2 to 0.000 XDIP>! class dch force $kdch XDIP>! class dch2 force $kdch XDIP>! class dch3 force $kdch3 XDIP> class dcc force $kdcc Setting force const for class DCC to 0.000 XDIP> class dcc2 force $kdcc Setting force const for class DCC2 to 0.000 XDIP>end X-PLOR> X-PLOR>evaluate ($ini_csa = 0.0001) evaluate ($fin_csa = .0009) EVALUATE: symbol $INI_CSA set to 0.100000E-03 (real) EVALUATE: symbol $FIN_CSA set to 0.900000E-03 (real) X-PLOR>evaluate ($kcsa = $ini_csa) EVALUATE: symbol $KCSA set to 0.100000E-03 (real) X-PLOR> X-PLOR>dcsa DCSA> class heli force $kcsa Setting force const for class HELI to 0.000 DCSA>end X-PLOR> X-PLOR>evaluate ($ini_hbda = 2.0) evaluate ($fin_hbda = 500.0) EVALUATE: symbol $INI_HBDA set to 2.00000 (real) EVALUATE: symbol $FIN_HBDA set to 500.000 (real) X-PLOR>evaluate ($khbda = $ini_hbda) EVALUATE: symbol $KHBDA set to 2.00000 (real) X-PLOR> X-PLOR>hbda HBDA> class hbon force $khbda Setting force const for class HBON to 2.000 HBDA>end X-PLOR> X-PLOR>parameters PARRDR> nbonds NBDSET> atom NBDSET> nbxmod 3 NBDSET> wmin = 0.01 ! warning off NBDSET> cutnb = 100 ! nonbonded cutoff NBDSET> tolerance 45 NBDSET> repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) NBDSET> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp NBDSET> irex = 2 NBDSET> rcon=$rcon ! actually set the vdW weight NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>constraints CONS> CONS> interaction (not name ca) (all) SELRPN: 164 atoms have been selected out of 175 SELRPN: 175 atoms have been selected out of 175 CONS> CONS> weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end CONS> CONS> interaction (name ca) (name ca) SELRPN: 11 atoms have been selected out of 175 SELRPN: 11 atoms have been selected out of 175 CONS> CONS> weights * 1 angl 0.4 impr 0.1 vdw 1.0 end CONS> CONS>end X-PLOR> X-PLOR> X-PLOR>!dynamics verlet X-PLOR>! nstep=1000 ! X-PLOR>! X-PLOR>! timestep=0.001 ! X-PLOR>! X-PLOR>! iasvel=maxwell firsttemp= $init_t X-PLOR>! tcoupling = true X-PLOR>! tbath = $init_t X-PLOR>! X-PLOR>! nprint=25 X-PLOR>! iprfrq=0 X-PLOR>! ntrfr = 99999999 X-PLOR>!end X-PLOR> X-PLOR> X-PLOR>!------------------------------------------------------------------- X-PLOR>!Dynamics: All-All Loop X-PLOR>parameters PARRDR> nbonds NBDSET> atom NBDSET> nbxmod 3 NBDSET> wmin = 0.01 ! warning off NBDSET> cutnb = 4.5 ! nonbonded cutoff NBDSET> tolerance 0.5 NBDSET>!! repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) NBDSET> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp NBDSET> irex = 2 NBDSET>!! rcon =1.0 ! actually set the vdW weight NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>evaluate ($kcdi = 20) EVALUATE: symbol $KCDI set to 20.0000 (real) X-PLOR>restraints dihed DIHEDRAL> DIHEDRAL> scale $kcdi DIHEDRAL> DIHEDRAL>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>evaluate ($final_t = 100) { K } EVALUATE: symbol $FINAL_T set to 100.000 (real) X-PLOR>evaluate ($tempstep = 25) { K } EVALUATE: symbol $TEMPSTEP set to 25.0000 (real) X-PLOR> X-PLOR>evaluate ($ncycle = ($init_t-$final_t)/$tempstep) EVALUATE: symbol $NCYCLE set to 316.000 (real) X-PLOR>evaluate ($nstep = int($cool_steps*4.0/$ncycle)) EVALUATE: symbol $NSTEP set to 101.000 (real) X-PLOR> X-PLOR>evaluate ($bath = $init_t) EVALUATE: symbol $BATH set to 8000.00 (real) X-PLOR>evaluate ($k_vdw = $ini_con) EVALUATE: symbol $K_VDW set to 0.400000E-02 (real) X-PLOR>evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) EVALUATE: symbol $K_VDWFACT set to 1.02210 (real) X-PLOR>evaluate ($radius= $ini_rad) EVALUATE: symbol $RADIUS set to 0.900000 (real) X-PLOR>evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) EVALUATE: symbol $RADFACT set to 0.999627 (real) X-PLOR>evaluate ($k_ang = $ini_ang) EVALUATE: symbol $K_ANG set to 0.400000 (real) X-PLOR>evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) EVALUATE: symbol $ANG_FAC set to 1.00290 (real) X-PLOR>evaluate ($k_imp = $ini_imp) EVALUATE: symbol $K_IMP set to 0.100000 (real) X-PLOR>evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) EVALUATE: symbol $IMP_FAC set to 1.00731 (real) X-PLOR>evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) EVALUATE: symbol $NOE_FAC set to 1.01024 (real) X-PLOR>evaluate ($knoe = $ini_noe) EVALUATE: symbol $KNOE set to 2.00000 (real) X-PLOR> X-PLOR>!!evaluate ($khb = $ini_hb) X-PLOR>!!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$cycle)) X-PLOR> X-PLOR>evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle)) EVALUATE: symbol $SANI_FAC set to 1.02210 (real) X-PLOR>evaluate ($ksani = $ini_sani) EVALUATE: symbol $KSANI set to 0.100000E-02 (real) X-PLOR> X-PLOR>evaluate ($kdnh = $ksani) EVALUATE: symbol $KDNH set to 0.100000E-02 (real) X-PLOR>evaluate ($kdch = 1.0*$kdnh) EVALUATE: symbol $KDCH set to 0.100000E-02 (real) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) EVALUATE: symbol $KDCH3 set to 0.500000E-03 (real) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) EVALUATE: symbol $KDCC set to 0.200000E-02 (real) X-PLOR> X-PLOR>evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) EVALUATE: symbol $CSA_FAC set to 1.00698 (real) X-PLOR>evaluate ($kcsa = $ini_csa) EVALUATE: symbol $KCSA set to 0.100000E-03 (real) X-PLOR> X-PLOR> X-PLOR> X-PLOR>vector do (vx = maxwell($bath)) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR>vector do (vy = maxwell($bath)) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR>vector do (vz = maxwell($bath)) (all) SELRPN: 175 atoms have been selected out of 175 X-PLOR> X-PLOR>!evaluate ($i_cool = 0) X-PLOR>!while ($i_cool < $ncycle) loop cool X-PLOR>! evaluate ($i_cool=$i_cool+1) X-PLOR>! X-PLOR>! evaluate ($bath = $bath - $tempstep) X-PLOR>! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) X-PLOR>! evaluate ($radius=max($fin_rad,$radius*$radfact)) X-PLOR>! evaluate ($k_ang = $k_ang*$ang_fac) X-PLOR>! evaluate ($k_imp = $k_imp*$imp_fac) X-PLOR>! evaluate ($knoe = $knoe*$noe_fac) X-PLOR>!!! evaluate ($khb=$khb*$hb_fac) X-PLOR>! X-PLOR>!evaluate ($ksani = $ksani*$sani_fac) X-PLOR>!evaluate ($kdnh = $ksani) X-PLOR>!evaluate ($kdch = 1.0*$kdnh) X-PLOR>!evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>!evaluate ($kdcc = 2.0*$kdnh) X-PLOR>!evaluate ($kcsa = $kcsa*$csa_fac) X-PLOR>! X-PLOR>! X-PLOR>! !parameter reset @parallhdg_new_db.pro @zn.pro end X-PLOR>! constraints interaction (all) (all) weights X-PLOR>! * 1 angles $k_ang improper $k_imp X-PLOR>! end end X-PLOR>! parameter X-PLOR>! nbonds X-PLOR>! cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius X-PLOR>! end end X-PLOR>! X-PLOR>! noe scale dist $knoe X-PLOR>! scale hb $khb X-PLOR>!end X-PLOR>! X-PLOR>!dipo X-PLOR>! class dnh force $kdnh X-PLOR>! class dnh2 force $kdnh X-PLOR>!! class dch force $kdch X-PLOR>!! class dch2 force $kdch X-PLOR>!! class dch3 force $kdch3 X-PLOR>! class dcc force $kdcc X-PLOR>! class dcc2 force $kdcc X-PLOR>!end X-PLOR>! X-PLOR>!dcsa X-PLOR>! class heli force $kcsa X-PLOR>!end X-PLOR>! X-PLOR>!hbda X-PLOR>! class hbon force $khbda X-PLOR>!end X-PLOR>! X-PLOR>! dynamics verlet X-PLOR>! nstep=$nstep timestep=0.002 iasvel=current firsttemp= $bath X-PLOR>! tcoupling = true tbath = $bath nprint=$nstep iprfrq=0 X-PLOR>! ntrfr = 99999999 X-PLOR>! end X-PLOR>!end loop cool X-PLOR> X-PLOR> X-PLOR>!---------------------------------------------------------------- X-PLOR>!Minimize: All-All X-PLOR> X-PLOR>mini powell nstep= 50 nprint= 50 end POWELL: number of degrees of freedom= 525 MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions --------------- cycle= 50 ------ stepsize= 0.0004 ----------------------- | Etotal =1.476 grad(E)=1.016 E(BOND)=0.102 E(ANGL)=0.492 | | E(IMPR)=0.124 E(VDW )=0.666 E(HARM)=0.067 E(CDIH)=0.000 | | E(NOE )=0.000 E(DIPO)=0.025 E(HBDA)=0.002 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>!-------------------------------------------------------------------- X-PLOR>!Minimize CA-CA X-PLOR> X-PLOR>evaluate ($knoe = 2.0) ! slope of NOE potential EVALUATE: symbol $KNOE set to 2.00000 (real) X-PLOR>evaluate ($khb = 2.0) ! slope of NOE potential EVALUATE: symbol $KHB set to 2.00000 (real) X-PLOR>evaluate ($ksani = 0.0001) ! dipolar force constant EVALUATE: symbol $KSANI set to 0.100000E-03 (real) X-PLOR>evaluate ($kcdi = 10.0) !torsion angles EVALUATE: symbol $KCDI set to 10.0000 (real) X-PLOR>evaluate ($kcsa = 0.001) EVALUATE: symbol $KCSA set to 0.100000E-02 (real) X-PLOR> X-PLOR>noe NOE> scale dist $knoe NOE> scale hb $khb NOE>end X-PLOR> X-PLOR>evaluate ($kdnh = $ksani) EVALUATE: symbol $KDNH set to 0.100000E-03 (real) X-PLOR>evaluate ($kdch = 1.0*$kdnh) EVALUATE: symbol $KDCH set to 0.100000E-03 (real) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) EVALUATE: symbol $KDCH3 set to 0.500000E-04 (real) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) EVALUATE: symbol $KDCC set to 0.200000E-03 (real) X-PLOR> X-PLOR>dipo XDIP> class dnh force $kdnh Setting force const for class DNH to 0.000 XDIP> class dnh2 force $kdnh Setting force const for class DNH2 to 0.000 XDIP>! class dch force $kdch XDIP>! class dch2 force $kdch XDIP>! class dch3 force $kdch3 XDIP> class dcc force $kdcc Setting force const for class DCC to 0.000 XDIP> class dcc2 force $kdcc Setting force const for class DCC2 to 0.000 XDIP>end X-PLOR> X-PLOR>dcsa DCSA> class heli force $kcsa Setting force const for class HELI to 0.001 DCSA>end X-PLOR> X-PLOR>hbda HBDA> class hbon force $khbda Setting force const for class HBON to 2.000 HBDA>end X-PLOR> X-PLOR>restraints dihed DIHEDRAL> scale $kcdi DIHEDRAL>end X-PLOR> X-PLOR>evaluate ($rcon = 1.0) EVALUATE: symbol $RCON set to 1.00000 (real) X-PLOR> X-PLOR>parameters PARRDR> nbonds NBDSET> atom NBDSET> nbxmod 3 NBDSET> wmin = 0.01 ! warning off NBDSET> cutnb = 100 ! nonbonded cutoff NBDSET> tolerance 45 NBDSET> repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) NBDSET> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp NBDSET> irex = 2 NBDSET> rcon=$rcon ! actually set the vdW weight NBDSET> end PARRDR>end X-PLOR> X-PLOR>constraints CONS> CONS> interaction (not name ca) (all) SELRPN: 164 atoms have been selected out of 175 SELRPN: 175 atoms have been selected out of 175 CONS> CONS> weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end CONS> CONS> interaction (name ca) (name ca) SELRPN: 11 atoms have been selected out of 175 SELRPN: 11 atoms have been selected out of 175 CONS> CONS> weights * 1 angl 0.4 impr 0.1 vdw 1.0 end CONS> CONS>end X-PLOR> X-PLOR>!mini powell nstep = 250 nprint = 50 end X-PLOR> X-PLOR>!-------------------------------------------------------------------- X-PLOR>!Minimize all-all loop X-PLOR> X-PLOR>parameters PARRDR> nbonds NBDSET> nbxmod 3 NBDSET> wmin = 0.01 ! warning off NBDSET> cutnb = 4.5 ! nonbonded cutoff NBDSET> tolerance 0.5 NBDSET>! repel= 0.9-0.8 ! scale factor for vdW radii = 1 ( L-J radii) NBDSET> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp NBDSET> irex = 2 NBDSET>! rcon= 0.004-4 ! actually set the vdW weight NBDSET> end PARRDR>end X-PLOR> X-PLOR>evaluate ($kcdi = 20) EVALUATE: symbol $KCDI set to 20.0000 (real) X-PLOR> X-PLOR>restraints dihed DIHEDRAL> scale $kcdi DIHEDRAL>end X-PLOR> X-PLOR>evaluate ($final_t = 100) {K} EVALUATE: symbol $FINAL_T set to 100.000 (real) X-PLOR>evaluate ($tempstep = 50) {K} EVALUATE: symbol $TEMPSTEP set to 50.0000 (real) X-PLOR>evaluate ($bath = $init_t) EVALUATE: symbol $BATH set to 8000.00 (real) X-PLOR> X-PLOR>evaluate ($ncycle = ($init_t-$final_t)/$tempstep) EVALUATE: symbol $NCYCLE set to 158.000 (real) X-PLOR>evaluate ($nstep = int($cool_steps*4.0/$ncycle)) EVALUATE: symbol $NSTEP set to 202.000 (real) X-PLOR> X-PLOR>evaluate ($k_vdw = $ini_con) EVALUATE: symbol $K_VDW set to 0.400000E-02 (real) X-PLOR>evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) EVALUATE: symbol $K_VDWFACT set to 1.04469 (real) X-PLOR> X-PLOR>evaluate ($radius= $ini_rad) EVALUATE: symbol $RADIUS set to 0.900000 (real) X-PLOR>evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) EVALUATE: symbol $RADFACT set to 0.999255 (real) X-PLOR> X-PLOR>evaluate ($k_ncs = $ini_ncs) EVALUATE: symbol $K_NCS set to 0.100000E-01 (real) X-PLOR>evaluate ($ncs_fac = ($fin_ncs/$ini_ncs)^(1/$ncycle)) EVALUATE: symbol $NCS_FAC set to 1.04469 (real) X-PLOR> X-PLOR>evaluate ($k_ang = $ini_ang) EVALUATE: symbol $K_ANG set to 0.400000 (real) X-PLOR>evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) EVALUATE: symbol $ANG_FAC set to 1.00582 (real) X-PLOR> X-PLOR>evaluate ($k_imp = $ini_imp) EVALUATE: symbol $K_IMP set to 0.100000 (real) X-PLOR>evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) EVALUATE: symbol $IMP_FAC set to 1.01468 (real) X-PLOR> X-PLOR>evaluate ($knoe = $ini_noe) EVALUATE: symbol $KNOE set to 2.00000 (real) X-PLOR>evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) EVALUATE: symbol $NOE_FAC set to 1.02058 (real) X-PLOR> X-PLOR>!!evaluate ($khb = $ini_hb) X-PLOR>!!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($ksani = $ini_sani) EVALUATE: symbol $KSANI set to 0.100000E-02 (real) X-PLOR>evaluate ($kcsa = $ini_csa) EVALUATE: symbol $KCSA set to 0.100000E-03 (real) X-PLOR>evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) EVALUATE: symbol $CSA_FAC set to 1.01400 (real) X-PLOR> X-PLOR>evaluate ($khbda = $ini_hbda) EVALUATE: symbol $KHBDA set to 2.00000 (real) X-PLOR>evaluate ($hbda_fac = ($fin_hbda/$ini_hbda)^(1/$ncycle)) EVALUATE: symbol $HBDA_FAC set to 1.03556 (real) X-PLOR> X-PLOR>evaluate ($i_cool = 0) EVALUATE: symbol $I_COOL set to 0.00000 (real) X-PLOR>! while ($i_cool < $ncycle) loop minim X-PLOR>! evaluate ($i_cool=$i_cool+1) X-PLOR>! X-PLOR>! evaluate ($bath = $bath - $tempstep) X-PLOR>! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) X-PLOR>! evaluate ($radius=max($fin_rad,$radius*$radfact)) X-PLOR>! evaluate ($k_ncs = $k_ncs*$ncs_fac) X-PLOR>! evaluate ($k_ang = $k_ang*$ang_fac) X-PLOR>! evaluate ($k_imp = $k_imp*$imp_fac) X-PLOR>! evaluate ($knoe = $knoe*$noe_fac) X-PLOR>! !! evaluate ($khb = $khb*$hb_fac) X-PLOR>! evaluate ($ksani = $ksani*$sani_fac) X-PLOR>! evaluate ($kcsa = $kcsa*$csa_fac) X-PLOR>! evaluate ($khbda = $khbda*$hbda_fac) X-PLOR>! X-PLOR>! evaluate ($kdnh = $ksani) X-PLOR>! evaluate ($kdch = 1.0*$kdnh) X-PLOR>! evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>! evaluate ($kdcc = 2.0*$kdnh) X-PLOR>! X-PLOR>! constraints interaction (all) (all) weights X-PLOR>! * 1 angles $k_ang improper $k_imp X-PLOR>! end end X-PLOR>! X-PLOR>! parameter nbonds rcon=$k_vdw X-PLOR>! repel=$radius X-PLOR>! end end X-PLOR>! X-PLOR>! noe X-PLOR>! scale dist $knoe X-PLOR>! scale hb $khb X-PLOR>! end X-PLOR>! X-PLOR>! dipo X-PLOR>! class dnh force $kdnh X-PLOR>! class dnh2 force $kdnh X-PLOR>! ! class dch force $kdch X-PLOR>! ! class dch2 force $kdch X-PLOR>! ! class dch3 force $kdch3 X-PLOR>! class dcc force $kdcc X-PLOR>! class dcc2 force $kdcc X-PLOR>! end X-PLOR>! X-PLOR>! dcsa X-PLOR>! class heli force $kcsa X-PLOR>! end X-PLOR>! X-PLOR>! hbda X-PLOR>! class hbon force $khbda X-PLOR>! end X-PLOR>! X-PLOR>! mini powell nstep = 100 nprint = 50 end X-PLOR>! end loop minim X-PLOR> X-PLOR> X-PLOR>!----------------------------------------------------- X-PLOR> X-PLOR> print threshold=0.3 noe NOEPRI: RMS diff. = 0.020, #(violat.> 0.3)= 0 of 145 NOEs NOEPRI: RMS diff. class DIST = 0.000, #(viol.> 0.3)= 0 of 131 NOEs NOEPRI: RMS diff. class HB = 0.066, #(viol.> 0.3)= 0 of 14 NOEs X-PLOR> evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.204313E-01 (real) X-PLOR> evaluate ($violations_noe=$violations) EVALUATE: symbol $VIOLATIONS_NOE set to 0.00000 (real) X-PLOR> evaluate ($rms_hb=$result) EVALUATE: symbol $RMS_HB set to 0.204313E-01 (real) X-PLOR> evaluate ($violations_hb=$violations) EVALUATE: symbol $VIOLATIONS_HB set to 0.00000 (real) X-PLOR> X-PLOR> print threshold=5. cdih Total number of dihedral angle restraints= 20 overall scale = 20.0000 Number of dihedral angle restraints= 20 Number of violations greater than 5.000: 0 RMS deviation= 0.000 X-PLOR> evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.00000 (real) X-PLOR> evaluate ($violations_cdih=$violations) EVALUATE: symbol $VIOLATIONS_CDIH set to 0.00000 (real) X-PLOR> X-PLOR> print thres=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.001 X-PLOR> evaluate ($rms_bonds=$result) EVALUATE: symbol $RMS_BONDS set to 0.764718E-03 (real) X-PLOR> X-PLOR> print thres=5. angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.161 X-PLOR> evaluate ($rms_angles=$result) EVALUATE: symbol $RMS_ANGLES set to 0.160555 (real) X-PLOR> X-PLOR> print thres=5. impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.315 X-PLOR> evaluate ($rms_impropers=$result) EVALUATE: symbol $RMS_IMPROPERS set to 0.314634 (real) X-PLOR> couplings print threshold 0.5 class phi end The following couplings have delta J greater than the cutoff: (calculated J) (observed J) (delta J) RMS diff. = 0.000, #(violat.> 0.50)= 0. of 0 J-couplings X-PLOR> evaluate ($rms_coup = $result) EVALUATE: symbol $RMS_COUP set to 0.00000 (real) X-PLOR> evaluate ($end_viols = $violations) EVALUATE: symbol $END_VIOLS set to 0.00000 (real) X-PLOR> X-PLOR> X-PLOR> dipo print threshold=1.0 class dnh end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: class DNH ============================================================== set-m-atoms 20 MET N set-n-atoms 20 MET HN Calc: -12.502 Obs: -7.731 Error: 1.000 1.000 Delta: -4.771 ============================================================== set-m-atoms 21 LYS N set-n-atoms 21 LYS HN Calc: -14.878 Obs: -13.598 Error: 1.000 1.000 Delta: -1.280 ============================================================== set-m-atoms 22 THR N set-n-atoms 22 THR HN Calc: -13.740 Obs: -19.119 Error: 1.000 1.000 Delta: 5.379 ============================================================== set-m-atoms 23 GLY N set-n-atoms 23 GLY HN Calc: -0.118 Obs: -7.653 Error: 1.000 1.000 Delta: 7.535 ============================================================== set-m-atoms 25 LEU N set-n-atoms 25 LEU HN Calc: -15.080 Obs: -20.492 Error: 1.000 1.000 Delta: 5.412 ============================================================== set-m-atoms 26 LEU N set-n-atoms 26 LEU HN Calc: -10.099 Obs: -14.936 Error: 1.000 1.000 Delta: 4.837 ============================================================== set-m-atoms 27 LEU N set-n-atoms 27 LEU HN Calc: 3.309 Obs: -5.634 Error: 1.000 1.000 Delta: 8.943 ============================================================== set-m-atoms 28 GLN N set-n-atoms 28 GLN HN Calc: -10.479 Obs: -8.115 Error: 1.000 1.000 Delta: -2.364 X-PLOR> evaluate ($rms_DNH=$result) EVALUATE: symbol $RMS_DNH set to 4.98920 (real) X-PLOR> evaluate ($viol_DNH=$violations) EVALUATE: symbol $VIOL_DNH set to 8.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dnh2 end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DNH2=$result) EVALUATE: symbol $RMS_DNH2 set to 0.00000 (real) X-PLOR> evaluate ($viol_DNH2=$violations) EVALUATE: symbol $VIOL_DNH2 set to 0.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DCH=$result) EVALUATE: symbol $RMS_DCH set to 0.00000 (real) X-PLOR> evaluate ($viol_DCH=$violations) EVALUATE: symbol $VIOL_DCH set to 0.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch2 end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DCH2=$result) EVALUATE: symbol $RMS_DCH2 set to 0.00000 (real) X-PLOR> evaluate ($viol_DCH2=$violations) EVALUATE: symbol $VIOL_DCH2 set to 0.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch3 end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DCH3=$result) EVALUATE: symbol $RMS_DCH3 set to 0.00000 (real) X-PLOR> evaluate ($viol_DCH3=$violations) EVALUATE: symbol $VIOL_DCH3 set to 0.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dcc end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DCC=$result) EVALUATE: symbol $RMS_DCC set to 0.00000 (real) X-PLOR> evaluate ($viol_DCC=$violations) EVALUATE: symbol $VIOL_DCC set to 0.00000 (real) X-PLOR> X-PLOR> dipo print threshold=1.0 class dcc2 end The following dipolar couplings have delta XDIPlar greater than or equal to the cutoff: X-PLOR> evaluate ($rms_DCC2=$result) EVALUATE: symbol $RMS_DCC2 set to 0.00000 (real) X-PLOR> evaluate ($viol_DCC2=$violations) EVALUATE: symbol $VIOL_DCC2 set to 0.00000 (real) X-PLOR> X-PLOR> dcsa print threshold=1.0 class heli end The following CSA have delta DCSA greater than or equal to the cutoff: class HELI ============================================================== set-atom 20 MET C 20 MET O 21 LYS N Calc: -46.286 Obs: -31.250 Error: 5.000 5.000 Delta: -15.036 ============================================================== set-atom 21 LYS C 21 LYS O 22 THR N Calc: 36.831 Obs: 65.640 Error: 5.000 5.000 Delta: -28.809 ============================================================== set-atom 22 THR C 22 THR O 23 GLY N Calc: 20.306 Obs: -32.090 Error: 5.000 5.000 Delta: 52.396 ============================================================== set-atom 23 GLY C 23 GLY O 24 ALA N Calc: -63.768 Obs: 3.100 Error: 5.000 5.000 Delta: -66.868 ============================================================== set-atom 24 ALA C 24 ALA O 25 LEU N Calc: 26.515 Obs: 35.900 Error: 5.000 5.000 Delta: -9.385 ============================================================== set-atom 25 LEU C 25 LEU O 26 LEU N Calc: -46.726 Obs: -31.210 Error: 5.000 5.000 Delta: -15.516 ============================================================== set-atom 26 LEU C 26 LEU O 27 LEU N Calc: 70.448 Obs: 38.450 Error: 5.000 5.000 Delta: 31.998 ============================================================== set-atom 27 LEU C 27 LEU O 28 GLN N Calc: -110.470 Obs: -63.200 Error: 5.000 5.000 Delta: -47.270 ============================================================== set-atom 28 GLN C 28 GLN O 29 GLY N Calc: 52.922 Obs: 77.410 Error: 5.000 5.000 Delta: -24.488 ============================================================== set-atom 29 GLY C 29 GLY O 30 PHE N Calc: -80.160 Obs: -64.730 Error: 5.000 5.000 Delta: -15.430 X-PLOR> evaluate ($rms_heli=$result) EVALUATE: symbol $RMS_HELI set to 35.6336 (real) X-PLOR> evaluate ($viol_heli=$violations) EVALUATE: symbol $VIOL_HELI set to 10.0000 (real) X-PLOR> X-PLOR> hbda print threshhold=0.0 class hbon end The following HBDA is greater than the cutoff: (calc hbda) (Rho) (Theta) class HBON 29 GLY N 29 GLY HN 25 LEU O 0.029 1.770 154.476 X-PLOR> evaluate ($rms_hbon=$result) EVALUATE: symbol $RMS_HBON set to 0.294410E-01 (real) X-PLOR> evaluate ($viol_hbon=$violations) EVALUATE: symbol $VIOL_HBON set to 1.00000 (real) X-PLOR> X-PLOR> remarks =============================================================== X-PLOR> remarks overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa X-PLOR> remarks energies: $ener,$bond,$angl,$impr,$vdw,$noe,$cdih,$coup,$dipo,$dcsa, %WDSUB-ERR: symbol not found: remarks energies: $ener,$bond,$angl,$impr,$vdw,$noe,$cdih,$coup, ^^^^^ %WDSUB-ERR: symbol not found: remarks energies: $ener,$bond,$angl,$impr,$vdw,$noe,$cdih,$coup,$dipo,$dcsa, ^^^^^ X-PLOR> remarks $hbda X-PLOR> remarks =============================================================== X-PLOR> remarks bonds,angles,impropers,noe X-PLOR> remarks bonds etc: $rms_bonds,$rms_angles,$rms_impropers,$rms_noe X-PLOR> remarks =============================================================== X-PLOR> remarks noe X-PLOR> remarks violations : $violations_noe X-PLOR> remarks =============================================================== X-PLOR> remarks dipo dnh dnh2 dch dch2 dch3 dcc dcc2 X-PLOR> remarks RMS dipo: $rms_DNH $rms_DNH2 $rms_DCH $rms_DCH2 X-PLOR> remarks $rms_DCH3 $rms_DCC $rms_DCC2 X-PLOR> remarks dcsa csa X-PLOR> remarks RMS dcsa :$rms_heli X-PLOR> remarks hbda hbon X-PLOR> remarks RMS hbda :$rms_hbon X-PLOR> remarks =============================================================== X-PLOR> X-PLOR> X-PLOR>{====>} {*Name(s) of the family of final structures.*} X-PLOR>evaluate ($file = "short_" + encode($count) + ".pdb") EVALUATE: symbol $FILE set to "short_1.pdb" (string) X-PLOR>write coor output= $file end ASSFIL: file /home/schwitrs/xplor/test/short_1.pdb opened. X-PLOR> X-PLOR>end loop structure X-PLOR>while ($count < 1 ) NEXTCD: condition evaluated as false WHILE-clause= loop structure X-PLOR> evaluate ($count = $count + 1) X-PLOR> X-PLOR>coor swap end X-PLOR>coor copy end X-PLOR> X-PLOR> X-PLOR>evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.80) X-PLOR>evaluate ($ini_con= 0.004) evaluate ($fin_con= 4.0) X-PLOR>evaluate ($ini_ncs = 0.01) evaluate ($fin_ncs = 10) X-PLOR>evaluate ($ini_ang = 0.4) evaluate ($fin_ang = 1.0) X-PLOR>evaluate ($ini_imp = 0.1) evaluate ($fin_imp = 1.0) X-PLOR> X-PLOR>evaluate ($ini_noe = 2.0) evaluate ($fin_noe = 50.0) X-PLOR>evaluate ($ini_hb = 2.0) evaluate ($fin_hb = 50.0) X-PLOR>evaluate ($knoe = $ini_noe) ! slope of NOE potential X-PLOR>evaluate ($khb = 0.0001) ! slope of NOE potential X-PLOR> X-PLOR>evaluate ($kcdi = 10.0) ! torsion angles X-PLOR> X-PLOR>evaluate ($rcon = 0.004) ! force constant for vdW X-PLOR> X-PLOR>noe X-PLOR> scale dist $knoe X-PLOR> scale hb $khb X-PLOR>end X-PLOR> X-PLOR>evaluate ($ini_sani = 0.001) evaluate ($fin_sani = 1.00) X-PLOR>evaluate ($ksani = $ini_sani) ! slope of NOE potential X-PLOR>evaluate ($ksani = 0.0001) ! dipolar coupling force constant X-PLOR>evaluate ($kdnh = $ksani) X-PLOR>evaluate ($kdch = 1.0*$kdnh) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) X-PLOR> X-PLOR> X-PLOR> X-PLOR>dipo X-PLOR> class dnh force $kdnh X-PLOR> class dnh2 force $kdnh X-PLOR>! class dch force $kdch X-PLOR>! class dch2 force $kdch X-PLOR>! class dch3 force $kdch3 X-PLOR> class dcc force $kdcc X-PLOR> class dcc2 force $kdcc X-PLOR>end X-PLOR> X-PLOR>evaluate ($ini_csa = 0.0001) evaluate ($fin_csa = .0009) X-PLOR>evaluate ($kcsa = $ini_csa) X-PLOR> X-PLOR>dcsa X-PLOR> class heli force $kcsa X-PLOR>end X-PLOR> X-PLOR>evaluate ($ini_hbda = 2.0) evaluate ($fin_hbda = 500.0) X-PLOR>evaluate ($khbda = $ini_hbda) X-PLOR> X-PLOR>hbda X-PLOR> class hbon force $khbda X-PLOR>end X-PLOR> X-PLOR>parameters X-PLOR> nbonds X-PLOR> atom X-PLOR> nbxmod 3 X-PLOR> wmin = 0.01 ! warning off X-PLOR> cutnb = 100 ! nonbonded cutoff X-PLOR> tolerance 45 X-PLOR> repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) X-PLOR> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp X-PLOR> irex = 2 X-PLOR> rcon=$rcon ! actually set the vdW weight X-PLOR> end X-PLOR>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>constraints X-PLOR> X-PLOR> interaction (not name ca) (all) X-PLOR> X-PLOR> weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end X-PLOR> X-PLOR> interaction (name ca) (name ca) X-PLOR> X-PLOR> weights * 1 angl 0.4 impr 0.1 vdw 1.0 end X-PLOR> X-PLOR>end X-PLOR> X-PLOR> X-PLOR>!dynamics verlet X-PLOR>! nstep=1000 ! X-PLOR>! X-PLOR>! timestep=0.001 ! X-PLOR>! X-PLOR>! iasvel=maxwell firsttemp= $init_t X-PLOR>! tcoupling = true X-PLOR>! tbath = $init_t X-PLOR>! X-PLOR>! nprint=25 X-PLOR>! iprfrq=0 X-PLOR>! ntrfr = 99999999 X-PLOR>!end X-PLOR> X-PLOR> X-PLOR>!------------------------------------------------------------------- X-PLOR>!Dynamics: All-All Loop X-PLOR>parameters X-PLOR> nbonds X-PLOR> atom X-PLOR> nbxmod 3 X-PLOR> wmin = 0.01 ! warning off X-PLOR> cutnb = 4.5 ! nonbonded cutoff X-PLOR> tolerance 0.5 X-PLOR>!! repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) X-PLOR> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp X-PLOR> irex = 2 X-PLOR>!! rcon =1.0 ! actually set the vdW weight X-PLOR> end X-PLOR>end X-PLOR> X-PLOR> X-PLOR>evaluate ($kcdi = 20) X-PLOR>restraints dihed X-PLOR> X-PLOR> scale $kcdi X-PLOR> X-PLOR>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>evaluate ($final_t = 100) { K } X-PLOR>evaluate ($tempstep = 25) { K } X-PLOR> X-PLOR>evaluate ($ncycle = ($init_t-$final_t)/$tempstep) X-PLOR>evaluate ($nstep = int($cool_steps*4.0/$ncycle)) X-PLOR> X-PLOR>evaluate ($bath = $init_t) X-PLOR>evaluate ($k_vdw = $ini_con) X-PLOR>evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) X-PLOR>evaluate ($radius= $ini_rad) X-PLOR>evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) X-PLOR>evaluate ($k_ang = $ini_ang) X-PLOR>evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) X-PLOR>evaluate ($k_imp = $ini_imp) X-PLOR>evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) X-PLOR>evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) X-PLOR>evaluate ($knoe = $ini_noe) X-PLOR> X-PLOR>!!evaluate ($khb = $ini_hb) X-PLOR>!!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$cycle)) X-PLOR> X-PLOR>evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle)) X-PLOR>evaluate ($ksani = $ini_sani) X-PLOR> X-PLOR>evaluate ($kdnh = $ksani) X-PLOR>evaluate ($kdch = 1.0*$kdnh) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) X-PLOR> X-PLOR>evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) X-PLOR>evaluate ($kcsa = $ini_csa) X-PLOR> X-PLOR> X-PLOR> X-PLOR>vector do (vx = maxwell($bath)) (all) X-PLOR>vector do (vy = maxwell($bath)) (all) X-PLOR>vector do (vz = maxwell($bath)) (all) X-PLOR> X-PLOR>!evaluate ($i_cool = 0) X-PLOR>!while ($i_cool < $ncycle) loop cool X-PLOR>! evaluate ($i_cool=$i_cool+1) X-PLOR>! X-PLOR>! evaluate ($bath = $bath - $tempstep) X-PLOR>! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) X-PLOR>! evaluate ($radius=max($fin_rad,$radius*$radfact)) X-PLOR>! evaluate ($k_ang = $k_ang*$ang_fac) X-PLOR>! evaluate ($k_imp = $k_imp*$imp_fac) X-PLOR>! evaluate ($knoe = $knoe*$noe_fac) X-PLOR>!!! evaluate ($khb=$khb*$hb_fac) X-PLOR>! X-PLOR>!evaluate ($ksani = $ksani*$sani_fac) X-PLOR>!evaluate ($kdnh = $ksani) X-PLOR>!evaluate ($kdch = 1.0*$kdnh) X-PLOR>!evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>!evaluate ($kdcc = 2.0*$kdnh) X-PLOR>!evaluate ($kcsa = $kcsa*$csa_fac) X-PLOR>! X-PLOR>! X-PLOR>! !parameter reset @parallhdg_new_db.pro @zn.pro end X-PLOR>! constraints interaction (all) (all) weights X-PLOR>! * 1 angles $k_ang improper $k_imp X-PLOR>! end end X-PLOR>! parameter X-PLOR>! nbonds X-PLOR>! cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius X-PLOR>! end end X-PLOR>! X-PLOR>! noe scale dist $knoe X-PLOR>! scale hb $khb X-PLOR>!end X-PLOR>! X-PLOR>!dipo X-PLOR>! class dnh force $kdnh X-PLOR>! class dnh2 force $kdnh X-PLOR>!! class dch force $kdch X-PLOR>!! class dch2 force $kdch X-PLOR>!! class dch3 force $kdch3 X-PLOR>! class dcc force $kdcc X-PLOR>! class dcc2 force $kdcc X-PLOR>!end X-PLOR>! X-PLOR>!dcsa X-PLOR>! class heli force $kcsa X-PLOR>!end X-PLOR>! X-PLOR>!hbda X-PLOR>! class hbon force $khbda X-PLOR>!end X-PLOR>! X-PLOR>! dynamics verlet X-PLOR>! nstep=$nstep timestep=0.002 iasvel=current firsttemp= $bath X-PLOR>! tcoupling = true tbath = $bath nprint=$nstep iprfrq=0 X-PLOR>! ntrfr = 99999999 X-PLOR>! end X-PLOR>!end loop cool X-PLOR> X-PLOR> X-PLOR>!---------------------------------------------------------------- X-PLOR>!Minimize: All-All X-PLOR> X-PLOR>mini powell nstep= 50 nprint= 50 end X-PLOR> X-PLOR>!-------------------------------------------------------------------- X-PLOR>!Minimize CA-CA X-PLOR> X-PLOR>evaluate ($knoe = 2.0) ! slope of NOE potential X-PLOR>evaluate ($khb = 2.0) ! slope of NOE potential X-PLOR>evaluate ($ksani = 0.0001) ! dipolar force constant X-PLOR>evaluate ($kcdi = 10.0) !torsion angles X-PLOR>evaluate ($kcsa = 0.001) X-PLOR> X-PLOR>noe X-PLOR> scale dist $knoe X-PLOR> scale hb $khb X-PLOR>end X-PLOR> X-PLOR>evaluate ($kdnh = $ksani) X-PLOR>evaluate ($kdch = 1.0*$kdnh) X-PLOR>evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>evaluate ($kdcc = 2.0*$kdnh) X-PLOR> X-PLOR>dipo X-PLOR> class dnh force $kdnh X-PLOR> class dnh2 force $kdnh X-PLOR>! class dch force $kdch X-PLOR>! class dch2 force $kdch X-PLOR>! class dch3 force $kdch3 X-PLOR> class dcc force $kdcc X-PLOR> class dcc2 force $kdcc X-PLOR>end X-PLOR> X-PLOR>dcsa X-PLOR> class heli force $kcsa X-PLOR>end X-PLOR> X-PLOR>hbda X-PLOR> class hbon force $khbda X-PLOR>end X-PLOR> X-PLOR>restraints dihed X-PLOR> scale $kcdi X-PLOR>end X-PLOR> X-PLOR>evaluate ($rcon = 1.0) X-PLOR> X-PLOR>parameters X-PLOR> nbonds X-PLOR> atom X-PLOR> nbxmod 3 X-PLOR> wmin = 0.01 ! warning off X-PLOR> cutnb = 100 ! nonbonded cutoff X-PLOR> tolerance 45 X-PLOR> repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) X-PLOR> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp X-PLOR> irex = 2 X-PLOR> rcon=$rcon ! actually set the vdW weight X-PLOR> end X-PLOR>end X-PLOR> X-PLOR>constraints X-PLOR> X-PLOR> interaction (not name ca) (all) X-PLOR> X-PLOR> weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end X-PLOR> X-PLOR> interaction (name ca) (name ca) X-PLOR> X-PLOR> weights * 1 angl 0.4 impr 0.1 vdw 1.0 end X-PLOR> X-PLOR>end X-PLOR> X-PLOR>!mini powell nstep = 250 nprint = 50 end X-PLOR> X-PLOR>!-------------------------------------------------------------------- X-PLOR>!Minimize all-all loop X-PLOR> X-PLOR>parameters X-PLOR> nbonds X-PLOR> nbxmod 3 X-PLOR> wmin = 0.01 ! warning off X-PLOR> cutnb = 4.5 ! nonbonded cutoff X-PLOR> tolerance 0.5 X-PLOR>! repel= 0.9-0.8 ! scale factor for vdW radii = 1 ( L-J radii) X-PLOR> rexp = 2 ! exponents in (r^irex - R0^irex)^rexp X-PLOR> irex = 2 X-PLOR>! rcon= 0.004-4 ! actually set the vdW weight X-PLOR> end X-PLOR>end X-PLOR> X-PLOR>evaluate ($kcdi = 20) X-PLOR> X-PLOR>restraints dihed X-PLOR> scale $kcdi X-PLOR>end X-PLOR> X-PLOR>evaluate ($final_t = 100) {K} X-PLOR>evaluate ($tempstep = 50) {K} X-PLOR>evaluate ($bath = $init_t) X-PLOR> X-PLOR>evaluate ($ncycle = ($init_t-$final_t)/$tempstep) X-PLOR>evaluate ($nstep = int($cool_steps*4.0/$ncycle)) X-PLOR> X-PLOR>evaluate ($k_vdw = $ini_con) X-PLOR>evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($radius= $ini_rad) X-PLOR>evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($k_ncs = $ini_ncs) X-PLOR>evaluate ($ncs_fac = ($fin_ncs/$ini_ncs)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($k_ang = $ini_ang) X-PLOR>evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($k_imp = $ini_imp) X-PLOR>evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($knoe = $ini_noe) X-PLOR>evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) X-PLOR> X-PLOR>!!evaluate ($khb = $ini_hb) X-PLOR>!!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($ksani = $ini_sani) X-PLOR>evaluate ($kcsa = $ini_csa) X-PLOR>evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($khbda = $ini_hbda) X-PLOR>evaluate ($hbda_fac = ($fin_hbda/$ini_hbda)^(1/$ncycle)) X-PLOR> X-PLOR>evaluate ($i_cool = 0) X-PLOR>! while ($i_cool < $ncycle) loop minim X-PLOR>! evaluate ($i_cool=$i_cool+1) X-PLOR>! X-PLOR>! evaluate ($bath = $bath - $tempstep) X-PLOR>! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) X-PLOR>! evaluate ($radius=max($fin_rad,$radius*$radfact)) X-PLOR>! evaluate ($k_ncs = $k_ncs*$ncs_fac) X-PLOR>! evaluate ($k_ang = $k_ang*$ang_fac) X-PLOR>! evaluate ($k_imp = $k_imp*$imp_fac) X-PLOR>! evaluate ($knoe = $knoe*$noe_fac) X-PLOR>! !! evaluate ($khb = $khb*$hb_fac) X-PLOR>! evaluate ($ksani = $ksani*$sani_fac) X-PLOR>! evaluate ($kcsa = $kcsa*$csa_fac) X-PLOR>! evaluate ($khbda = $khbda*$hbda_fac) X-PLOR>! X-PLOR>! evaluate ($kdnh = $ksani) X-PLOR>! evaluate ($kdch = 1.0*$kdnh) X-PLOR>! evaluate ($kdch3 = 0.5*$kdnh) X-PLOR>! evaluate ($kdcc = 2.0*$kdnh) X-PLOR>! X-PLOR>! constraints interaction (all) (all) weights X-PLOR>! * 1 angles $k_ang improper $k_imp X-PLOR>! end end X-PLOR>! X-PLOR>! parameter nbonds rcon=$k_vdw X-PLOR>! repel=$radius X-PLOR>! end end X-PLOR>! X-PLOR>! noe X-PLOR>! scale dist $knoe X-PLOR>! scale hb $khb X-PLOR>! end X-PLOR>! X-PLOR>! dipo X-PLOR>! class dnh force $kdnh X-PLOR>! class dnh2 force $kdnh X-PLOR>! ! class dch force $kdch X-PLOR>! ! class dch2 force $kdch X-PLOR>! ! class dch3 force $kdch3 X-PLOR>! class dcc force $kdcc X-PLOR>! class dcc2 force $kdcc X-PLOR>! end X-PLOR>! X-PLOR>! dcsa X-PLOR>! class heli force $kcsa X-PLOR>! end X-PLOR>! X-PLOR>! hbda X-PLOR>! class hbon force $khbda X-PLOR>! end X-PLOR>! X-PLOR>! mini powell nstep = 100 nprint = 50 end X-PLOR>! end loop minim X-PLOR> X-PLOR> X-PLOR>!----------------------------------------------------- X-PLOR> X-PLOR> print threshold=0.3 noe X-PLOR> evaluate ($rms_noe=$result) X-PLOR> evaluate ($violations_noe=$violations) X-PLOR> evaluate ($rms_hb=$result) X-PLOR> evaluate ($violations_hb=$violations) X-PLOR> X-PLOR> print threshold=5. cdih X-PLOR> evaluate ($rms_cdih=$result) X-PLOR> evaluate ($violations_cdih=$violations) X-PLOR> X-PLOR> print thres=0.05 bonds X-PLOR> evaluate ($rms_bonds=$result) X-PLOR> X-PLOR> print thres=5. angles X-PLOR> evaluate ($rms_angles=$result) X-PLOR> X-PLOR> print thres=5. impropers X-PLOR> evaluate ($rms_impropers=$result) X-PLOR> couplings print threshold 0.5 class phi end X-PLOR> evaluate ($rms_coup = $result) X-PLOR> evaluate ($end_viols = $violations) X-PLOR> X-PLOR> X-PLOR> dipo print threshold=1.0 class dnh end X-PLOR> evaluate ($rms_DNH=$result) X-PLOR> evaluate ($viol_DNH=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dnh2 end X-PLOR> evaluate ($rms_DNH2=$result) X-PLOR> evaluate ($viol_DNH2=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch end X-PLOR> evaluate ($rms_DCH=$result) X-PLOR> evaluate ($viol_DCH=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch2 end X-PLOR> evaluate ($rms_DCH2=$result) X-PLOR> evaluate ($viol_DCH2=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dch3 end X-PLOR> evaluate ($rms_DCH3=$result) X-PLOR> evaluate ($viol_DCH3=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dcc end X-PLOR> evaluate ($rms_DCC=$result) X-PLOR> evaluate ($viol_DCC=$violations) X-PLOR> X-PLOR> dipo print threshold=1.0 class dcc2 end X-PLOR> evaluate ($rms_DCC2=$result) X-PLOR> evaluate ($viol_DCC2=$violations) X-PLOR> X-PLOR> dcsa print threshold=1.0 class heli end X-PLOR> evaluate ($rms_heli=$result) X-PLOR> evaluate ($viol_heli=$violations) X-PLOR> X-PLOR> hbda print threshhold=0.0 class hbon end X-PLOR> evaluate ($rms_hbon=$result) X-PLOR> evaluate ($viol_hbon=$violations) X-PLOR> X-PLOR> remarks =============================================================== X-PLOR> remarks overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa X-PLOR> remarks energies: $ener,$bond,$angl,$impr,$vdw,$noe,$cdih,$coup,$dipo,$dcsa, X-PLOR> remarks $hbda X-PLOR> remarks =============================================================== X-PLOR> remarks bonds,angles,impropers,noe X-PLOR> remarks bonds etc: $rms_bonds,$rms_angles,$rms_impropers,$rms_noe X-PLOR> remarks =============================================================== X-PLOR> remarks noe X-PLOR> remarks violations : $violations_noe X-PLOR> remarks =============================================================== X-PLOR> remarks dipo dnh dnh2 dch dch2 dch3 dcc dcc2 X-PLOR> remarks RMS dipo: $rms_DNH $rms_DNH2 $rms_DCH $rms_DCH2 X-PLOR> remarks $rms_DCH3 $rms_DCC $rms_DCC2 X-PLOR> remarks dcsa csa X-PLOR> remarks RMS dcsa :$rms_heli X-PLOR> remarks hbda hbon X-PLOR> remarks RMS hbda :$rms_hbon X-PLOR> remarks =============================================================== X-PLOR> X-PLOR> X-PLOR>{====>} {*Name(s) of the family of final structures.*} X-PLOR>evaluate ($file = "short_" + encode($count) + ".pdb") X-PLOR>write coor output= $file end X-PLOR> X-PLOR>end loop structure X-PLOR> X-PLOR>stop HEAP: maximum use= 1077830 current use= 626900 X-PLOR: total CPU time= 0.1000 s X-PLOR: entry time at 15:29:32 11-Jun-07 X-PLOR: exit time at 15:29:32 11-Jun-07