XPLOR-NIH version 2.9.5 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: 04-Jun-04 10:27:41 X-PLOR>remarks file packing.inp -- test xrefin packing target function X-PLOR>remarks Author: Axel T. Brunger X-PLOR> X-PLOR>topology @TOPPAR:toph19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pro opened. RTFRDR>REMARKS TOPH19.PRO ( protein topology ) RTFRDR>REMARKS =============================== RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>param @TOPPAR:param19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param19.pro opened. PARRDR>remark - parameter file PARAM19 - PARRDR>remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR> PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> chain CHAIN> @TOPPAR:toph19.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pep opened. CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE ASN VAL CYS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = ARG LEU PRO GLY THR PRO GLU ALA ILE CYS ALA THR TYR THR GLY CYS SEQUence-element (terminate with END) = ILE ILE ILE PRO GLY ALA THR CYS PRO GLY ASP TYR ALA ASN SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 46 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 396(MAXA= 400) NBOND= 403(MAXB= 800) NTHETA= 581(MAXT= 800) NGRP= 165(MAXGRP= 200) NPHI= 235(MAXP= 400) NIMPHI= 182(MAXIMP= 200) NDON= 69(MAXPAD= 100) NACC= 64(MAXPAD= 100) NNB= 9(MAXNB= 100) X-PLOR> X-PLOR> X-PLOR>coor COOR>ATOM 1 HT1 THR 1 16.206 14.668 3.850 0.00 0.00 COOR>ATOM 2 HT2 THR 1 17.090 13.935 2.599 0.00 0.00 X-PLOR> X-PLOR>vector do (b=8.0) ( all ) SELRPN: 396 atoms have been selected out of 396 X-PLOR>vector do (q=1.0) ( all ) SELRPN: 396 atoms have been selected out of 396 X-PLOR> X-PLOR>xrefin XREFINE> reset XREFIN: symmetry operators set to P1, all reciprocal and real space data scratched, atom scatter factors scratched. XREFINE> a=40.96 b=18.65 c=22.52 alpha=90.0 beta=90.77 gamma=90.0 XREFINE> XREFINE> nreflections=20000 XREFIN: allocating space for 20000 reflections. XREFINE> reflection REFLection> INDEx 0 2 0 Fobs 4171.8999 XRRR2: 729 new reflections have been added. XREFINE> method=fft XREFINE> resolution 10. 3.0 XREFINE> fwindow 0.1 100000. XREFINE> XREFINE> fft XFFT> grid=0.33333333 prime=5 avoid=2 ! sampling grid of Patterson XFFT> end XREFINE> !! scattering tables, from SCATT input XREFINE> !! XREFINE> SCATter ( chemical C* ) SELRPN: 202 atoms have been selected out of 396 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 55 atoms have been selected out of 396 SCATTER_A1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> XREFINE> SCATter ( chemical O* ) SELRPN: 64 atoms have been selected out of 396 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 6 atoms have been selected out of 396 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> symmetry=(x,y,z) ! Patterson symmetry (no phase shifts) XREFINE> symmetry=(-x,y+1/2,-z) ! XREFINE> XREFINE> asymmetric=(0<=x<1 and 0<=y<=1/2 and 0<=z<1) XREFINE> XREFINE>end X-PLOR> X-PLOR>set timing=on end X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>xrefin XREFINE> target=packing XREFINE> XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=0.0 0.0 0.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=0.0 0.0 0.0 TRANSL> end XMAPASU: using grid [ 40, 18, 24] and sublattice [ 40, 18, 24] Minimum brick that covers asymmetric unit: A= 0,..., 39 B= 0,..., 9 C= 0,..., 23 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 TFSEARC: CPU-Time: translation search= 0.0100 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 1 mean of T-function= 0.589 sigma of T-function= 0.000 maximum of T-function= 0.589 minimum of T-function= 0.589 List of first 1 highest peaks Orthogonal A coordinates Fractional coordinates T=( 0.000 0.000 0.000) TF=( 0.000 0.000 0.000) T= 0.5895 XREFINE>end 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>xrefin XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=2.0 0.0 2.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=0.0 0.0 0.0 TRANSL> end TFSEARC: CPU-Time: translation search= 0.0100 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 1 mean of T-function= 0.567 sigma of T-function= 0.000 maximum of T-function= 0.567 minimum of T-function= 0.567 List of first 1 highest peaks Orthogonal A coordinates Fractional coordinates T=( 2.000 0.000 0.000) TF=( 0.049 0.000 0.000) T= 0.5666 XREFINE>end 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>xrefin XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=2.0 0.0 2.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=4.0 0.0 4.0 TRANSL> end TFSEARC: CPU-Time: translation search= 0.0000 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 1 mean of T-function= 0.581 sigma of T-function= 0.000 maximum of T-function= 0.581 minimum of T-function= 0.581 List of first 1 highest peaks Orthogonal A coordinates Fractional coordinates T=( 2.000 0.000 4.000) TF=( 0.050 0.000 0.178) T= 0.5814 XREFINE>end 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>xrefin XREFINE> fft memory=6000 end XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=2.0 0.0 2.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=4.0 0.0 4.0 TRANSL> end TFSEARC: CPU-Time: translation search= 0.0100 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 1 mean of T-function= 0.581 sigma of T-function= 0.000 maximum of T-function= 0.581 minimum of T-function= 0.581 List of first 1 highest peaks Orthogonal A coordinates Fractional coordinates T=( 2.000 0.000 4.000) TF=( 0.050 0.000 0.178) T= 0.5814 XREFINE>end 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>xrefin XREFINE> fft memory=2000 end XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=2.0 0.0 2.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=4.0 0.0 4.0 TRANSL> end TFSEARC: CPU-Time: translation search= 0.0100 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 1 mean of T-function= 0.581 sigma of T-function= 0.000 maximum of T-function= 0.581 minimum of T-function= 0.581 List of first 1 highest peaks Orthogonal A coordinates Fractional coordinates T=( 2.000 0.000 4.000) TF=( 0.050 0.000 0.178) T= 0.5814 XREFINE>end 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>xrefin XREFINE> fft memory=100000 end XREFINE> search translation TRANSL> mode=orthogonal TRANSL> xgrid=0.0 1.0 2.0 TRANSL> ygrid=0.0 0.0 0.0 TRANSL> zgrid=0.0 1.0 4.0 TRANSL> end TFSEARC: CPU-Time: translation search= 0.0800 TSEARCH: the search is carried out with 1-XREF/wa where XREF is determined by the target "PACK" Summary of translation search: number of grid points= 15 mean of T-function= 0.580 sigma of T-function= 0.007 maximum of T-function= 0.589 minimum of T-function= 0.566 List of first 15 highest peaks Orthogonal A coordinates Fractional coordinates T=( 0.000 0.000 0.000) TF=( 0.000 0.000 0.000) T= 0.5895 T=( 0.000 0.000 1.000) TF=( 0.000 0.000 0.044) T= 0.5866 T=( 1.000 0.000 4.000) TF=( 0.026 0.000 0.178) T= 0.5848 T=( 0.000 0.000 3.000) TF=( 0.001 0.000 0.133) T= 0.5838 T=( 0.000 0.000 2.000) TF=( 0.001 0.000 0.089) T= 0.5830 T=( 1.000 0.000 3.000) TF=( 0.025 0.000 0.133) T= 0.5826 T=( 0.000 0.000 4.000) TF=( 0.001 0.000 0.178) T= 0.5823 T=( 1.000 0.000 2.000) TF=( 0.025 0.000 0.089) T= 0.5822 T=( 1.000 0.000 0.000) TF=( 0.024 0.000 0.000) T= 0.5814 T=( 2.000 0.000 4.000) TF=( 0.050 0.000 0.178) T= 0.5814 T=( 1.000 0.000 1.000) TF=( 0.025 0.000 0.044) T= 0.5808 T=( 2.000 0.000 3.000) TF=( 0.050 0.000 0.133) T= 0.5774 T=( 2.000 0.000 2.000) TF=( 0.049 0.000 0.089) T= 0.5715 T=( 2.000 0.000 0.000) TF=( 0.049 0.000 0.000) T= 0.5666 T=( 2.000 0.000 1.000) TF=( 0.049 0.000 0.044) T= 0.5661 XREFINE>end X-PLOR> X-PLOR>display $result 0.589468 X-PLOR>display $packing 0.589468 X-PLOR>flags exclude * include xref end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.280000 sec. MASKX2: volume inside molecule= 58.9468% MASKX2: volume outside molecule= 41.0532% ENERGY: after XREFIne term CPU= 0.290000 sec. --------------- cycle= 1 -------------------------------------------------- | Etotal =0.411 grad(E)=0.000 E(XREF)=0.411 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 1453793 current use= 901007 X-PLOR: total CPU time= 0.2900 s X-PLOR: entry time at 10:27:41 04-Jun-04 X-PLOR: exit time at 10:27:41 04-Jun-04