XPLOR-NIH version 2.10-pre1 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 09-Mar-05 12:10:11 X-PLOR>remarks file rxfinite.inp X-PLOR>remarks tests for finite difference and selection for NMR relaxation refinement X-PLOR> X-PLOR> X-PLOR>{====>} X-PLOR>evaluate ($init_t = 300) {* initial annealing temperature, in K *} EVALUATE: symbol $INIT_T set to 300.000 (real) X-PLOR> X-PLOR>{====>} X-PLOR>evaluate ($high_steps = 2000 ) {* total number of steps at high temp *} EVALUATE: symbol $HIGH_STEPS set to 2000.00 (real) X-PLOR> X-PLOR> X-PLOR>evaluate ($seed = 12344332124) EVALUATE: symbol $SEED set to 0.123443E+11 (real) X-PLOR> X-PLOR>parameter {* read the parameter file *} PARRDR>{====>} PARRDR> @TOPPAR:parallhdg.pro ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg.pro opened. PARRDR>remark file parallhdg.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. PARRDR> PARRDR>set message off echo off end PARRDR> nbonds NBDSET> atom nbxmod -3 tolerance 0.5 NBDSET> wmin 1.5 repel 0.80 rcon 4.0 rexp 2 cutnb 5.0 NBDSET> end PARRDR>end X-PLOR> X-PLOR>{====>} X-PLOR>structure STRUcture>PSF REMARKS FILENAME="generate.psf" REMARKS CMTI-I, 1st structure REMARKS DATE:28-Feb-93 12:52:14 created by user: brunger XPLOR: current counts (number in parenthesis is maximum) NATOM= 436(MAXA= 800) NBOND= 441(MAXB= 800) NTHETA= 802(MAXT= 1600) NGRP= 37(MAXGRP= 100) NPHI= 53(MAXP= 100) NIMPHI= 151(MAXIMP= 200) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 156(MAXNB= 200) STRUcture> STRUcture>end X-PLOR> X-PLOR>coor COOR>REMARK FILENAME="/usr/steroid4/brunger/cmti/traj_21.pdb" COOR>REMARK c30.sff final structure COOR>REMARK DATE:21-Apr-93 00:33:31 created by user: brunger COOR>ATOM 1 CA ARG 1 -9.899 5.511 -8.800 0.00 0.00 COOR>ATOM 2 HA ARG 1 -10.139 4.459 -8.781 0.00 0.00 X-PLOR> X-PLOR> X-PLOR> X-PLOR>relaxation {* intensity restraints *} RELAx> nrestraints 2500 { expected number of restraints } RELAX: allocating space for 2500 intensities. RELAx> RELAx> RELAx>{ ==================== specify the physical parameters of the system } RELAx> RELAx> group CMTI { a group of spectra, CMTI is defined } RELAx> RELAx> RELAx> unresolved CMTI EQUIvalent> methyl { methyl protons are unresolved } EQUIvalent> end RELAx> RELAx> average 3 { r-3 average to methyl groups } RELAx> RELAx> omega CMTI 500.0e6 { spectrometer frequency in Hz } RELAx> RELAx> taucorrel CMTI isotropic 2.3e-9 end { correlation time ( in s) } RELAx> RELAx> set message off echo off end RELAx> RELAx> clgroup T150 CMTI { which belongs to group CMTI } RELAx> taumix T150 0.15 { mixing time, in s } RELAx> minint T150 0.05 { minimum measurable intensity } RELAx> RELAx> weight * 0.0 RELAx> weight T150 1.0 RELAx> RELAx> cutoff { cutoff used for gradient and relaxation matrix } CUTOff> mode all value 4. CUTOff> end RELAx> RELAx> tolerance 0.05 RELAx> RELAx> potential parabola { error estimates are not used } RELAx> iexp 0.1666666667 { Dev = I_calc^iexp - I_obs^iexp } RELAx> eexp 2 { E = Dev^eexp } RELAx> RELAx> selection CMTI ( hydrogen and resid 10:20 ) SELRPN: 73 atoms have been selected out of 436 RELAx> RELAx> unresolved CMTI EQUIvalent> methyl { methyl protons are unresolved } EQUIvalent> end RELAx> RELAx>end X-PLOR> X-PLOR> X-PLOR>vector do (fbeta=50) (all) {* friction coefficient for MD heatbath, in 1/ps *} SELRPN: 436 atoms have been selected out of 436 X-PLOR>vector do (mass=100) (all) {* uniform heavy masses to speed md *} SELRPN: 436 atoms have been selected out of 436 X-PLOR> X-PLOR> X-PLOR>set seed $seed end X-PLOR> X-PLOR> X-PLOR> {* outer loop over the weights *} X-PLOR>evaluate ($factor=2000.) EVALUATE: symbol $FACTOR set to 2000.00 (real) X-PLOR> X-PLOR> relax RELAx> CUTOff ! use cutoff CUTOff> MODE all ! for energy AND gradient CUTOff> VALUe 4. ! at 4 A CUTOff> end RELAx> RELAx> TOLErance 0.0 ! recalculate if moved > TOLE RELAx> RELAx> POTEntial parabola ! RELAx> EEXP = 2 ! E = Dev^EEXP RELAx> IEXP = 0.1666666667 ! Dev = I_calc^IEXP - I_obs^IEXP RELAx> end X-PLOR> X-PLOR> relax RELAx> weight * 0.0 RELAx> weight T150 $factor RELAx> end X-PLOR> X-PLOR> X-PLOR> relax RELAx> calibrate CALIbrate> automatic off CALIbrate> exclude = 3.0 CALIbrate> reference = all CALIbrate> group = class CALIbrate> end RELAX: intensities updated for calibration class N(reference) N(all) calibration --------------------------------------------- T150 0 83 0.3569E+00 --------------------------------------------- RELAx> tolerance = 0.0 RELAx> end X-PLOR> X-PLOR> X-PLOR>flags excl * incl relax end X-PLOR> X-PLOR>test first selection= ( resid 14 and name HN) step=0.001 tol=0.0 end SELRPN: 1 atoms have been selected out of 436 RELAX: R-factor in spectra-group 1 0.07731 RELAX: R-factor in spectra-group 1 0.07730 RELAX: R-factor in spectra-group 1 0.07732 RELAX: R-factor in spectra-group 1 0.07731 RELAX: R-factor in spectra-group 1 0.07732 RELAX: R-factor in spectra-group 1 0.07732 RELAX: R-factor in spectra-group 1 0.07730 TESTFD: Parameters: STEP= 0.00100 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 228 X ( 14 SER HN ) -40.142924 -40.142917 0.000007 228 Y ( 14 SER HN ) -58.923199 -58.923161 0.000038 228 Z ( 14 SER HN ) 35.608834 35.608790 0.000044 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>stop HEAP: maximum use= 1357299 current use= 1172917 X-PLOR: total CPU time= 0.5900 s X-PLOR: entry time at 12:10:11 09-Mar-05 X-PLOR: exit time at 12:10:12 09-Mar-05