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 10:28:09 X-PLOR>remarks SURFTEST.INP X-PLOR>remarks TEST OF THE RICHARD'S ACCESSIBLE SURFACE AND CONTACT PROPERTIES USING X-PLOR>remarks A SHORTENED PTI TO SPEED THE RUN. X-PLOR> X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened. RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) 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 DNA/RNA atoms appended . RTFRDR>REMARKS few atoms never referenced switched off. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.wat opened. RTFRDR>remarks TOPH11.WAT RTFRDR>remarks ========== RTFRDR>remarks topology file for water RTFRDR>remarks available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened. PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) PARRDR>REMARKS =========== PARRDR>REMARKS PROTEIN PARAMETERS: PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. PARRDR>REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR>REMARKS PARRDR>set echo=false end PARRDR> @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.wat opened. PARRDR>remarks PARAM11.WAT (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> name=m1 SEGMENT> chain CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> arg pro asp phe cys leu MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 6 residues were inserted into segment "M1 " XPLOR: current counts (number in parenthesis is maximum) NATOM= 64(MAXA= 200) NBOND= 65(MAXB= 100) NTHETA= 93(MAXT= 100) NGRP= 22(MAXGRP= 100) NPHI= 39(MAXP= 100) NIMPHI= 28(MAXIMP= 100) NDON= 12(MAXPAD= 100) NACC= 9(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>segment SEGMENT> name=m2 SEGMENT> chain CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence cys end MAPIC: Atom numbers being modified MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 1 residues were inserted into segment "M2 " XPLOR: current counts (number in parenthesis is maximum) NATOM= 74(MAXA= 200) NBOND= 74(MAXB= 100) NTHETA= 106(MAXT= 200) NGRP= 25(MAXGRP= 100) NPHI= 44(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>patch disu reference 1 ( atom m1 5 * ) reference 2 ( atom m2 1 * ) end SELRPN: 7 atoms have been selected out of 74 SELRPN: 10 atoms have been selected out of 74 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 74(MAXA= 200) NBOND= 75(MAXB= 100) NTHETA= 108(MAXT= 200) NGRP= 25(MAXGRP= 100) NPHI= 47(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>segment SEGMENT> name=solv SEGMENT> molecule MOLECULE> name=TIP3 number=1 MOLECULE> end SEGMENT>end SEGMNT: 1 residues were inserted into segment "SOLV" XPLOR: current counts (number in parenthesis is maximum) NATOM= 77(MAXA= 200) NBOND= 77(MAXB= 100) NTHETA= 109(MAXT= 200) NGRP= 26(MAXGRP= 100) NPHI= 47(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> remarks filename SURFTST.CHR COOR> remarks TEST OF THE RICHARD'S ACCESSIBLE SURFACE AND CONTACT PROPERTIES USING COOR> remarks A SHORTENED PTI TO SPEED THE RUN. COOR> COOR> natoms 77 COOR> 1 1 ARG HT1 26.03323 27.51269 -3.55411 M1 1 0.00000 X-PLOR> X-PLOR>surface SURFAC> mode=access rh2o=1.4 accuracy=0.05 selection=( all ) SELRPN: 77 atoms have been selected out of 77 SURFAC>end SURFAC: half the sigma value being used for atomic radii. SURFAC: ACCEssible surface area SURFAC: ACCUracy= 0.05 RH2O= 1.40 Z-grid= 0.16 number-of-Z-sections= 121 measures-of-arc= 613 and 1284 X-PLOR> X-PLOR>vector show element ( rmsd ) ( attr rmsd > 0 ) SELRPN: 63 atoms have been selected out of 77 ( M1 ARG 1 HT1 ) 5.3492 ( M1 ARG 1 HT2 ) 7.8254 ( M1 ARG 1 N ) 18.712 ( M1 ARG 1 HT3 ) 5.2416 ( M1 ARG 1 CA ) 15.085 ( M1 ARG 1 CB ) 2.5526 ( M1 ARG 1 CG ) 8.8921 ( M1 ARG 1 CD ) 5.6554 ( M1 ARG 1 NE ) 0.38584 ( M1 ARG 1 CZ ) 19.898 ( M1 ARG 1 NH1 ) 21.180 ( M1 ARG 1 HH11 ) 2.1267 ( M1 ARG 1 HH12 ) 9.9103 ( M1 ARG 1 NH2 ) 17.981 ( M1 ARG 1 HH21 ) 9.9710 ( M1 ARG 1 HH22 ) 0.22724 ( M1 ARG 1 C ) 3.7648 ( M1 ARG 1 O ) 16.119 ( M1 PRO 2 CD ) 14.705 ( M1 PRO 2 CA ) 14.739 ( M1 PRO 2 CB ) 11.893 ( M1 PRO 2 CG ) 28.884 ( M1 ASP 3 N ) 0.14226 ( M1 ASP 3 H ) 2.4587 ( M1 ASP 3 CA ) 0.31275 ( M1 ASP 3 CB ) 32.498 ( M1 ASP 3 CG ) 17.924 ( M1 ASP 3 OD1 ) 26.919 ( M1 ASP 3 OD2 ) 36.694 ( M1 ASP 3 C ) 0.59692 ( M1 ASP 3 O ) 6.4636 ( M1 PHE 4 CA ) 14.832 ( M1 PHE 4 CB ) 33.296 ( M1 PHE 4 CG ) 1.5799 ( M1 PHE 4 CD1 ) 12.319 ( M1 PHE 4 CD2 ) 21.784 ( M1 PHE 4 CE1 ) 20.173 ( M1 PHE 4 CE2 ) 23.474 ( M1 PHE 4 CZ ) 24.476 ( M1 PHE 4 O ) 17.123 ( M1 CYS 5 CA ) 7.1348 ( M1 CYS 5 CB ) 1.5945 ( M1 CYS 5 C ) 1.0694 ( M1 CYS 5 O ) 25.960 ( M1 LEU 6 CA ) 6.0465 ( M1 LEU 6 CB ) 15.128 ( M1 LEU 6 CG ) 1.1036 ( M1 LEU 6 CD1 ) 58.067 ( M1 LEU 6 CD2 ) 34.565 ( M1 LEU 6 C ) 14.757 ( M1 LEU 6 OT1 ) 35.304 ( M1 LEU 6 OT2 ) 23.894 ( M2 CYS 1 HT1 ) 5.6977 ( M2 CYS 1 HT2 ) 5.0235 ( M2 CYS 1 N ) 18.643 ( M2 CYS 1 HT3 ) 4.7183 ( M2 CYS 1 CA ) 5.4733 ( M2 CYS 1 CB ) 30.097 ( M2 CYS 1 SG ) 19.575 ( M2 CYS 1 C ) 7.7544 ( M2 CYS 1 OT1 ) 6.3272 ( M2 CYS 1 OT2 ) 25.632 ( SOLV TIP3 1 OH2 ) 69.676 X-PLOR> X-PLOR>surface SURFAC> mode=contact selection= ( all ) SELRPN: 77 atoms have been selected out of 77 SURFAC>end SURFAC: half the sigma value being used for atomic radii. SURFAC: CONTact area SURFAC: ACCUracy= 0.05 RH2O= 1.60 Z-grid= 0.18 number-of-Z-sections= 110 measures-of-arc= 642 and 1471 X-PLOR> X-PLOR>vector show element ( rmsd ) ( attr rmsd > 0 ) SELRPN: 62 atoms have been selected out of 77 ( M1 ARG 1 HT1 ) 0.62892 ( M1 ARG 1 HT2 ) 0.84690 ( M1 ARG 1 N ) 4.5412 ( M1 ARG 1 HT3 ) 0.52883 ( M1 ARG 1 CA ) 4.9326 ( M1 ARG 1 CB ) 0.52548 ( M1 ARG 1 CG ) 2.3736 ( M1 ARG 1 CD ) 1.5867 ( M1 ARG 1 NE ) 0.58503E-01 ( M1 ARG 1 CZ ) 5.6868 ( M1 ARG 1 NH1 ) 4.9625 ( M1 ARG 1 HH11 ) 0.17536 ( M1 ARG 1 HH12 ) 1.0619 ( M1 ARG 1 NH2 ) 4.2275 ( M1 ARG 1 HH21 ) 1.0571 ( M1 ARG 1 HH22 ) 0.80894E-02 ( M1 ARG 1 C ) 1.0924 ( M1 ARG 1 O ) 3.5503 ( M1 PRO 2 CD ) 4.5608 ( M1 PRO 2 CA ) 4.8633 ( M1 PRO 2 CB ) 3.7567 ( M1 PRO 2 CG ) 9.2565 ( M1 ASP 3 H ) 0.21349 ( M1 ASP 3 CA ) 0.20283 ( M1 ASP 3 CB ) 9.7724 ( M1 ASP 3 CG ) 5.2714 ( M1 ASP 3 OD1 ) 5.9876 ( M1 ASP 3 OD2 ) 9.1873 ( M1 ASP 3 C ) 0.12166 ( M1 ASP 3 O ) 1.3416 ( M1 PHE 4 CA ) 4.7427 ( M1 PHE 4 CB ) 10.948 ( M1 PHE 4 CG ) 0.49316 ( M1 PHE 4 CD1 ) 3.5932 ( M1 PHE 4 CD2 ) 6.5951 ( M1 PHE 4 CE1 ) 6.0929 ( M1 PHE 4 CE2 ) 7.3404 ( M1 PHE 4 CZ ) 7.6349 ( M1 PHE 4 O ) 3.9058 ( M1 CYS 5 CA ) 2.1484 ( M1 CYS 5 CB ) 0.19120 ( M1 CYS 5 C ) 0.27991 ( M1 CYS 5 O ) 6.0472 ( M1 LEU 6 CA ) 1.9163 ( M1 LEU 6 CB ) 4.5959 ( M1 LEU 6 CG ) 0.10992 ( M1 LEU 6 CD1 ) 18.373 ( M1 LEU 6 CD2 ) 10.402 ( M1 LEU 6 C ) 4.3729 ( M1 LEU 6 OT1 ) 8.6555 ( M1 LEU 6 OT2 ) 5.4067 ( M2 CYS 1 HT1 ) 0.59719 ( M2 CYS 1 HT2 ) 0.52262 ( M2 CYS 1 N ) 4.6025 ( M2 CYS 1 HT3 ) 0.43902 ( M2 CYS 1 CA ) 1.5887 ( M2 CYS 1 CB ) 9.7713 ( M2 CYS 1 SG ) 5.0860 ( M2 CYS 1 C ) 2.0761 ( M2 CYS 1 OT1 ) 1.3400 ( M2 CYS 1 OT2 ) 5.9950 ( SOLV TIP3 1 OH2 ) 18.551 X-PLOR> X-PLOR>surface SURFAC> mode=access radius=vdw rh2o=1.4 accuracy=0.05 selection=( all ) SELRPN: 77 atoms have been selected out of 77 SURFAC>end SURFAC: half the vdw value being used for atomic radii. SURFAC: ACCEssible surface area SURFAC: ACCUracy= 0.05 RH2O= 1.40 Z-grid= 0.16 number-of-Z-sections= 122 measures-of-arc= 696 and 1602 X-PLOR> X-PLOR>vector show element ( rmsd ) ( attr rmsd > 0 ) SELRPN: 61 atoms have been selected out of 77 ( M1 ARG 1 HT1 ) 3.2464 ( M1 ARG 1 HT2 ) 5.1531 ( M1 ARG 1 N ) 24.247 ( M1 ARG 1 HT3 ) 3.4049 ( M1 ARG 1 CA ) 18.426 ( M1 ARG 1 CB ) 1.7539 ( M1 ARG 1 CG ) 8.7126 ( M1 ARG 1 CD ) 5.2407 ( M1 ARG 1 NE ) 0.73488E-01 ( M1 ARG 1 CZ ) 23.151 ( M1 ARG 1 NH1 ) 24.081 ( M1 ARG 1 HH11 ) 0.70190 ( M1 ARG 1 HH12 ) 7.1467 ( M1 ARG 1 NH2 ) 19.311 ( M1 ARG 1 HH21 ) 7.8744 ( M1 ARG 1 C ) 3.7822 ( M1 ARG 1 O ) 15.258 ( M1 PRO 2 CD ) 14.973 ( M1 PRO 2 CA ) 16.669 ( M1 PRO 2 CB ) 12.230 ( M1 PRO 2 CG ) 30.720 ( M1 ASP 3 H ) 0.74782 ( M1 ASP 3 CA ) 0.28474 ( M1 ASP 3 CB ) 34.922 ( M1 ASP 3 CG ) 21.329 ( M1 ASP 3 OD1 ) 25.768 ( M1 ASP 3 OD2 ) 38.480 ( M1 ASP 3 C ) 0.45873 ( M1 ASP 3 O ) 5.2271 ( M1 PHE 4 CA ) 15.705 ( M1 PHE 4 CB ) 36.314 ( M1 PHE 4 CG ) 1.4448 ( M1 PHE 4 CD1 ) 12.923 ( M1 PHE 4 CD2 ) 22.559 ( M1 PHE 4 CE1 ) 21.413 ( M1 PHE 4 CE2 ) 25.755 ( M1 PHE 4 CZ ) 26.422 ( M1 PHE 4 O ) 16.550 ( M1 CYS 5 CA ) 7.5847 ( M1 CYS 5 CB ) 0.83423 ( M1 CYS 5 C ) 1.1921 ( M1 CYS 5 O ) 26.000 ( M1 LEU 6 CA ) 6.9413 ( M1 LEU 6 CB ) 15.856 ( M1 LEU 6 CG ) 0.32966 ( M1 LEU 6 CD1 ) 62.190 ( M1 LEU 6 CD2 ) 33.503 ( M1 LEU 6 C ) 18.072 ( M1 LEU 6 OT1 ) 35.949 ( M1 LEU 6 OT2 ) 23.550 ( M2 CYS 1 HT1 ) 3.6782 ( M2 CYS 1 HT2 ) 2.9944 ( M2 CYS 1 N ) 23.973 ( M2 CYS 1 HT3 ) 2.7728 ( M2 CYS 1 CA ) 6.6559 ( M2 CYS 1 CB ) 33.640 ( M2 CYS 1 SG ) 18.733 ( M2 CYS 1 C ) 8.0747 ( M2 CYS 1 OT1 ) 5.3947 ( M2 CYS 1 OT2 ) 26.019 ( SOLV TIP3 1 OH2 ) 75.210 X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 893042 current use= 869707 X-PLOR: total CPU time= 0.2200 s X-PLOR: entry time at 10:28:09 04-Jun-04 X-PLOR: exit time at 10:28:09 04-Jun-04