XPLOR-NIH version 2.14-pre2 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: schwitrs on: x86_64/Linux at: 28-Feb-06 16:18:36 X-PLOR> X-PLOR>parameter PARRDR> @TOPPAR:protein.par ASSFIL: file /home/schwitrs/xplor/toppar/protein.par opened. PARRDR>! PARRDR>! xplor-nih protein parameter file, version 1.0 PARRDR>! PARRDR>! This file is intended to work with the topology file protein-1.0.top PARRDR>! PARRDR>! This is a re-named copy of the file parallhdg_procheck.pro PARRDR>! PARRDR>! We've created this new filename in order to eliminate confusion PARRDR>! between the various parameter/topology combinations that ship PARRDR>! with xplor-nih. It has version numbers, and will be updated PARRDR>! along with the rest of the xplor-nih package. PARRDR>! PARRDR>! Its backbone bond lengths and angles are designed to agree with PARRDR>! the Engh & Huber parameter set (reference below), which is used by PARRDR>! PROCHECK, among other structure-validation programs. PARRDR>! PARRDR>! If you find errors, PLEASE let us know. PARRDR>! PARRDR> PARRDR> PARRDR> PARRDR> PARRDR>remark file protein-1.0.par PARRDR>remark Changed version of parallhdg_new.pro so that the bond lengths and angles PARRDR>remark agree with what PROCHECK expects. PARRDR>remark JJK 9/14/98 PARRDR> PARRDR>! file parallhdg_new.pro PARRDR>! geometric energy function parameters for distance geometry and PARRDR>! simulated annealing. Modified by G.M.C. to have sigma's of Param19x and parafloat PARRDR> PARRDR>set message off echo off end PARRDR>end X-PLOR> X-PLOR>structure !@sa_ncs_full_1.psf STRUcture>PSF REMARKS FILENAME="sa_ncs_full_1.psf" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:01-Feb-03 22:09:53 created by user: zhewu XPLOR: current counts (number in parenthesis is maximum) NATOM= 2838(MAXA= 3200) NBOND= 2877(MAXB= 3200) NTHETA= 5138(MAXT= 6400) NGRP= 1245(MAXGRP= 1600) NPHI= 336(MAXP= 400) NIMPHI= 1601(MAXIMP= 3200) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 888(MAXNB= 1600) STRUcture>end X-PLOR> X-PLOR>coor !@gcnd_saxs_init.pdb COOR>REMARK FILENAME="C:\Alex\NIH\SAXS\gc\Justin_final\gcnd_hbdb2_10.pdb" COOR>REMARK =============================================================== COOR>REMARK overall,bonds,angles,improper,vdw,cdih,noe,sani,hbdb,coll COOR>REMARK energies: 1825.58,47.4866,343.531,120.931,134.709,20.0176,303.273,1150.13,-294.497,0 COOR>REMARK =============================================================== COOR>REMARK cdih, noe COOR>REMARK rms: 7.09996,3.386946E-02 COOR>REMARK =============================================================== COOR>REMARK noe, cdih COOR>REMARK violations.: 0, 29 COOR>REMARK =============================================================== COOR>REMARK JNH, JCH, CACO, NCO, CACB, COOR>REMARK violations.: 1.29589,4.39147,0.777258,0.470718,0.672432 COOR>REMARK =============================================================== COOR>REMARK JNH2, JCH2, CAC2, NCO2, CAB2, COOR>REMARK violations.: 1.08337,2.1096,0.652755,0.375391,0.646615 COOR>REMARK =============================================================== COOR>REMARK DATE:14-May-2005 05:39:14 created by user: Alexander COOR>REMARK VERSION:0.9a COOR>ATOM 1 N SER 1 -1.845 1.226 18.369 1.00 4.50 AN1 COOR>ATOM 2 HT1 SER 1 -1.062 1.053 19.029 1.00 0.00 AN1 %READC-ERR: still 4 missing coordinates (in selected subset) X-PLOR> X-PLOR>dele sele (not known) end SELRPN: 4 atoms have been selected out of 2838 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 2834(MAXA= 3200) NBOND= 2873(MAXB= 3200) NTHETA= 5130(MAXT= 6400) NGRP= 1245(MAXGRP= 1600) NPHI= 336(MAXP= 400) NIMPHI= 1597(MAXIMP= 3200) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 888(MAXNB= 1600) X-PLOR> X-PLOR>! **** SAXS data ****** X-PLOR>saxs SAXS> ntyp = 37 ! # of glob types SAXS> ndat = 15 ! # of data points SAXS> kfor = 50.0 ! force const SAXS> prnf = 200 ! printing frequency SAXS> i0 = 5506.0 ! SAXS>file globdef SAXS:glob_def.dat SAXS>file glob_fs TESTDIR:glob_fs_gcnd_tr11.dat SAXS>file is_corr TESTDIR:is_corr_gcnd_tr11.dat SAXS>file saxsdat TESTDIR:jt11_x8.dat SAXS>file h2o_cor TESTDIR:watcorr_jt11.dat SAXS>end reading glob definitions @ /home/schwitrs/xplor/databases/saxs/glob_def.dat reading globbic scattering profiles @ ./glob_fs_gcnd_tr11.dat reading globbic correction function @ ./is_corr_gcnd_tr11.dat 2.694000000000000E-002 1.00040000000000 3.906330000000000E-002 1.00082000000000 5.118670000000000E-002 1.00138000000000 6.331000000000001E-002 1.00206000000000 7.543220000000000E-002 1.00283000000000 8.755560000000000E-002 1.00367000000000 9.968000000000000E-002 1.00454000000000 0.111800000000000 1.00543000000000 0.123922000000000 1.00637000000000 0.136044000000000 1.00741000000000 0.148178000000000 1.00876000000000 0.160289000000000 1.01064000000000 0.172422000000000 1.01334000000000 0.184533000000000 1.01700000000000 0.196678000000000 1.02171000000000 reading experimental SAXS data @ ./jt11_x8.dat 2.694000000000000E-002 5094.00000000000 4.380000000000000E-002 3.906000000000000E-002 4675.00000000000 3.757000000000000E-002 5.119000000000000E-002 4156.00000000000 3.838000000000000E-002 6.331000000000001E-002 3579.00000000000 4.216000000000000E-002 7.543000000000000E-002 2986.00000000000 4.709000000000000E-002 8.756000000000000E-002 2414.00000000000 5.533000000000000E-002 9.968000000000000E-002 1896.00000000000 6.802000000000000E-002 0.111800000000000 1449.00000000000 8.469000000000000E-002 0.123900000000000 1083.00000000000 0.105420000000000 0.136000000000000 798.600000000000 0.134730000000000 0.148200000000000 587.000000000000 0.179170000000000 0.160300000000000 435.900000000000 0.233720000000000 0.172400000000000 331.400000000000 0.302920000000000 0.184500000000000 259.800000000000 0.369880000000000 0.196700000000000 210.200000000000 0.449430000000000 reading surface H2O correction @ ./watcorr_jt11.dat 2.694000000000000E-002 1.00664000000000 3.906000000000000E-002 1.01377000000000 5.119000000000000E-002 1.02375000000000 6.331000000000001E-002 1.03655000000000 7.543000000000000E-002 1.05230000000000 8.756000000000000E-002 1.07126000000000 9.968000000000000E-002 1.09359000000000 0.111800000000000 1.11790000000000 0.123900000000000 1.14423000000000 0.136000000000000 1.17200000000000 0.148200000000000 1.20030000000000 0.160300000000000 1.22697000000000 0.172400000000000 1.24990000000000 0.184500000000000 1.27209000000000 0.196700000000000 1.29571000000000 X-PLOR> X-PLOR> X-PLOR> X-PLOR>flags exclude * include bonds angles impr saxs end X-PLOR>mini powell nstep=10 end POWELL: number of degrees of freedom= 8502 2834 total atoms 0 protein atoms 177 protein residues 469 globs found 355 CYS 22 HG not in globs 378 CYS 24 HG not in globs 401 CYS 26 HG not in globs 564 CYS 36 HG not in globs 879 HIS 57 HD1 not in globs 1290 CYS 82 HG not in globs 1352 HIS 86 HD1 not in globs 1766 CYS 114 HG not in globs 1891 HIS 122 HD1 not in globs 1985 HIS 127 HD1 not in globs 2012 CYS 129 HG not in globs 11 unused atoms 469 globs built 2823 atoms in globs 0.640E+07 Icalc(0) REMARK SAXS =============================================================== REMARK SAXS Chi = 1.12702 REMARK SAXS Force = 50.000 REMARK SAXS Rgyr = 0.0000 REMARK SAXS Dmax = 60.7000 REMARK SAXS REMARK SAXS Fit q Icalc(q) Iexpt(q) Sigma(q) REMARK SAXS Fit 0.269400E-01 0.92203E+00 0.93132E+00 0.40523E-01 REMARK SAXS Fit 0.390600E-01 0.84318E+00 0.86077E+00 0.31900E-01 REMARK SAXS Fit 0.511900E-01 0.74625E+00 0.77274E+00 0.28970E-01 REMARK SAXS Fit 0.633100E-01 0.63960E+00 0.67378E+00 0.27405E-01 REMARK SAXS Fit 0.754300E-01 0.53131E+00 0.57068E+00 0.25538E-01 REMARK SAXS Fit 0.875600E-01 0.42839E+00 0.46967E+00 0.24258E-01 REMARK SAXS Fit 0.996800E-01 0.33637E+00 0.37658E+00 0.23423E-01 REMARK SAXS Fit 0.111800E+00 0.25835E+00 0.29419E+00 0.22288E-01 REMARK SAXS Fit 0.123900E+00 0.19552E+00 0.22506E+00 0.20736E-01 REMARK SAXS Fit 0.136000E+00 0.14704E+00 0.16999E+00 0.19541E-01 REMARK SAXS Fit 0.148200E+00 0.11072E+00 0.12797E+00 0.19101E-01 REMARK SAXS Fit 0.160300E+00 0.84556E-01 0.97137E-01 0.18503E-01 REMARK SAXS Fit 0.172400E+00 0.65553E-01 0.75230E-01 0.18232E-01 REMARK SAXS Fit 0.184500E+00 0.51400E-01 0.60023E-01 0.17453E-01 REMARK SAXS Fit 0.196700E+00 0.40294E-01 0.49466E-01 0.17158E-01 REMARK SAXS =============================================================== --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =2658.870 grad(E)=46.363 E(BOND)=846.981 E(ANGL)=1406.171 | | E(IMPR)=386.666 E(SAXS)=19.053 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0000 ----------------------- | Etotal =2613.015 grad(E)=45.359 E(BOND)=839.601 E(ANGL)=1376.459 | | E(IMPR)=377.903 E(SAXS)=19.052 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0000 ----------------------- | Etotal =2245.205 grad(E)=36.729 E(BOND)=772.320 E(ANGL)=1144.879 | | E(IMPR)=308.955 E(SAXS)=19.051 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0001 ----------------------- | Etotal =1470.509 grad(E)=23.160 E(BOND)=511.840 E(ANGL)=770.372 | | E(IMPR)=169.253 E(SAXS)=19.043 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0001 ----------------------- | Etotal =1097.475 grad(E)=14.789 E(BOND)=353.825 E(ANGL)=548.913 | | E(IMPR)=175.696 E(SAXS)=19.041 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0000 ----------------------- | Etotal =1071.128 grad(E)=18.974 E(BOND)=327.881 E(ANGL)=516.486 | | E(IMPR)=207.721 E(SAXS)=19.041 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= 0.0002 ----------------------- | Etotal =821.940 grad(E)=15.154 E(BOND)=202.009 E(ANGL)=461.837 | | E(IMPR)=139.060 E(SAXS)=19.033 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0000 ----------------------- | Etotal =821.936 grad(E)=15.210 E(BOND)=201.851 E(ANGL)=461.873 | | E(IMPR)=139.179 E(SAXS)=19.033 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= 0.0002 ----------------------- | Etotal =683.487 grad(E)=15.320 E(BOND)=119.162 E(ANGL)=452.892 | | E(IMPR)=92.409 E(SAXS)=19.024 | ------------------------------------------------------------------------------- SAXS: Isaxs = 10 Chi = 1.12619 --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =681.539 grad(E)=13.657 E(BOND)=123.376 E(ANGL)=450.404 | | E(IMPR)=88.734 E(SAXS)=19.025 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>saxs print end REMARK SAXS =============================================================== REMARK SAXS Chi = 1.12619 REMARK SAXS Force = 50.000 REMARK SAXS Rgyr = 0.0000 REMARK SAXS Dmax = 60.7000 REMARK SAXS REMARK SAXS Fit q Icalc(q) Iexpt(q) Sigma(q) REMARK SAXS Fit 0.269400E-01 0.92203E+00 0.93132E+00 0.40523E-01 REMARK SAXS Fit 0.390600E-01 0.84319E+00 0.86077E+00 0.31900E-01 REMARK SAXS Fit 0.511900E-01 0.74626E+00 0.77274E+00 0.28970E-01 REMARK SAXS Fit 0.633100E-01 0.63962E+00 0.67378E+00 0.27405E-01 REMARK SAXS Fit 0.754300E-01 0.53133E+00 0.57068E+00 0.25538E-01 REMARK SAXS Fit 0.875600E-01 0.42842E+00 0.46967E+00 0.24258E-01 REMARK SAXS Fit 0.996800E-01 0.33640E+00 0.37658E+00 0.23423E-01 REMARK SAXS Fit 0.111800E+00 0.25838E+00 0.29419E+00 0.22288E-01 REMARK SAXS Fit 0.123900E+00 0.19554E+00 0.22506E+00 0.20736E-01 REMARK SAXS Fit 0.136000E+00 0.14706E+00 0.16999E+00 0.19541E-01 REMARK SAXS Fit 0.148200E+00 0.11074E+00 0.12797E+00 0.19101E-01 REMARK SAXS Fit 0.160300E+00 0.84571E-01 0.97137E-01 0.18503E-01 REMARK SAXS Fit 0.172400E+00 0.65563E-01 0.75230E-01 0.18232E-01 REMARK SAXS Fit 0.184500E+00 0.51407E-01 0.60023E-01 0.17453E-01 REMARK SAXS Fit 0.196700E+00 0.40298E-01 0.49466E-01 0.17158E-01 REMARK SAXS =============================================================== X-PLOR> X-PLOR>stop HEAP: maximum use= 1010537 current use= 917563 X-PLOR: total CPU time= 2.0100 s X-PLOR: entry time at 16:18:36 28-Feb-06 X-PLOR: exit time at 16:18:38 28-Feb-06