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: on: x86_64/Linux at: 11-Mar-05 09:40:15 X-PLOR> X-PLOR>param @TOPPAR:parallhdg_procheck.pro end ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg_procheck.pro opened. PARRDR>remark file parallhdg_procheck.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use protein.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 @iibmtl_deletex.psf end X-PLOR>structure STRUcture>PSF REMARKS FILENAME="iibmtl_deletex.psf" REMARKS corrected proline angles to Engh & Huber, Acta Cryst., A47, 392 (1991) values. REMARKS Needed to define a new atom type, CP, which is equivalent to their REMARKS CH2P atom type. JJK 9/22/95 REMARKS DATE:12-Apr-04 15:53:23 created by user: clore XPLOR: current counts (number in parenthesis is maximum) NATOM= 1521(MAXA= 1600) NBOND= 1529(MAXB= 1600) NTHETA= 2763(MAXT= 3200) NGRP= 629(MAXGRP= 800) NPHI= 166(MAXP= 200) NIMPHI= 761(MAXIMP= 800) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 690(MAXNB= 800) STRUcture>end X-PLOR> X-PLOR>!coor @coor.pdb X-PLOR>coor COOR>ATOM 1 N SER 11 -39.897 -21.068 12.129 1.00 0.00 COOR>ATOM 2 HN SER 11 -40.604 -21.018 12.805 1.00 0.00 %READC-ERR: atom 12 HIS HE2 not found in molecular structure %READC-ERR: atom 66 HIS HE2 not found in molecular structure %READC-ERR: atom 82 HIS HE2 not found in molecular structure %READC-ERR: atom 107 HIS HE2 not found in molecular structure X-PLOR> X-PLOR> X-PLOR>!test fixed mode X-PLOR>!hb database must be read in after psf file X-PLOR>hbdb HBDB> kdir = 0.20 !force constant for directional term HBDB> klin = 0.08 !force constant for linear term (ca. Nico's hbda) HBDB> nseg = 1 ! number of segments that hbdb term is active on HBDB> nmin = 11 !range of residues (1st) HBDB> nmax = 110 !range of residues (last) HBDB> ohcut = 2.60 !cut-off for detection of h-bonds HBDB> coh1cut = 100.0 !cut-off for c-o-h angle in 3-10 helix HBDB> coh2cut = 100.0 !cut-off for c-o-h angle for everything else HBDB> ohncut = 100.0 !cut-off for o-h-n angle HBDB> updfrq = 10 !update frequency usually 1000 HBDB> prnfrq = 10 !print frequency usually 1000 HBDB> freemode = 0 !mode= 1 free search HBDB> fixedmode = 1 !if you want a fixed list, set fixedmode=1, and freemode=0 HBDB> mfdir = 0 ! flag that drives HB's to the minimum of the directional potential HBDB> mflin = 0 ! flag that drives HB's to the minimum of the linearity potential HBDB> kmfd = 10.0 ! corresp force const HBDB> kmfl = 10.0 ! corresp force const HBDB> renf = 2.30 ! forces all found HB's below 2.3 A HBDB> kenf = 30.0 ! corresponding force const HBDB> @HBDB:hbdb_files.inp ASSFIL: file /home/schwitrs/xplor/databases/hbdb/hbdb_files.inp opened. HBDB>file dir 1 HBDB:xyz3_right.dat HBDB>file dir 2 HBDB:xyz3_left.dat HBDB>file dir 3 HBDB:xyz4_centN.dat HBDB>file dir 4 HBDB:xyz4_isolC.dat HBDB>file dir 5 HBDB:xyz5_beta_anti_cent.dat HBDB>file dir 6 HBDB:xyz5_beta_anti_edge.dat HBDB>file dir 7 HBDB:xyz5_beta_para_cent.dat HBDB>file dir 8 HBDB:xyz5_beta_para_edge.dat HBDB>file dir 9 HBDB:xyz5_non_beta.dat HBDB>file dir 10 HBDB:xyz2_right.dat HBDB>file dir 11 HBDB:xyz2_left.dat HBDB> HBDB>file lin 1 HBDB:era_3.dat HBDB>file lin 2 HBDB:era_4.dat HBDB>file lin 3 HBDB:era_5.dat HBDB>file lin 4 HBDB:era_2.dat HBDB>assign ( acc and resid 99 and name O ) ( don and resid 103 and name HN ) HBDB>assign ( acc and resid 97 and name O ) ( don and resid 101 and name HN ) HBDB>assign ( acc and resid 94 and name O ) ( don and resid 98 and name HN ) HBDB>assign ( acc and resid 31 and name O ) ( don and resid 35 and name HN ) HBDB>assign ( acc and resid 29 and name O ) ( don and resid 33 and name HN ) HBDB>assign ( acc and resid 64 and name O ) ( don and resid 19 and name HN ) HBDB>assign ( acc and resid 18 and name O ) ( don and resid 51 and name HN ) HBDB>assign ( acc and resid 20 and name O ) ( don and resid 53 and name HN ) HBDB>assign ( acc and resid 90 and name OD1 ) ( don and resid 93 and name HN ) HBDB>end reading directional HB PMF - 310 right ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz3_right.dat opened. reading directional HB PMF - 310 left ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz3_left.dat opened. reading directional HB PMF - a N-t & cent ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz4_centN.dat opened. reading directional HB PMF - a C-t & isol ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz4_isolC.dat opened. reading directional HB PMF - b anti cent ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz5_beta_anti_cent.dat opened. reading directional HB PMF - b anti long ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz5_beta_anti_edge.dat opened. reading directional HB PMF - b para cent ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz5_beta_para_cent.dat opened. reading directional HB PMF - b para edge ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz5_beta_para_edge.dat opened. reading directional HB PMF - lr isolated ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz5_non_beta.dat opened. reading directional HB PMF - g turn right ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz2_right.dat opened. reading directional HB PMF - g turn left ASSFIL: file /home/schwitrs/xplor/databases/hbdb/xyz2_left.dat opened. calculating directional HB PMF forces i/i+3i/i+4 : directional forces done reading linearity HB PMF - i/i+3 ASSFIL: file /home/schwitrs/xplor/databases/hbdb/era_3.dat opened. reading linearity HB PMF - i/i+4 ASSFIL: file /home/schwitrs/xplor/databases/hbdb/era_4.dat opened. reading linearity HB PMF - lr ASSFIL: file /home/schwitrs/xplor/databases/hbdb/era_5.dat opened. reading linearity HB PMF - i/i+2 ASSFIL: file /home/schwitrs/xplor/databases/hbdb/era_2.dat opened. calculating linearity HB PMF forces linearity HB PMF forces done X-PLOR> X-PLOR>flags exclude * include bonds angles impr hbdb end X-PLOR>mini powell nstep=10 end POWELL: number of degrees of freedom= 4563 Nstep = 1 Fixed HB list: # CO HN dir_type lin_type O-H C-O-H Ca-C-O-H O-H-N Edir Elin 1 99 103 a C-t & isol i/i+4 2.02 142.1 -112.5 162.9 -4.82 0.03 2 97 101 a C-t & isol i/i+4 1.98 164.1 163.4 166.0 -1.78 0.11 3 94 98 a C-t & isol i/i+4 1.97 162.8 -124.5 165.5 -4.39 0.11 4 31 35 a C-t & isol i/i+4 1.82 172.4 -122.1 167.6 -2.71 0.00 5 29 33 a C-t & isol i/i+4 1.98 155.4 -93.0 160.6 -4.75 0.02 6 64 19 lr isolated lr 1.90 165.5 121.9 161.3 -5.47 0.04 7 18 51 lr isolated lr 1.91 160.7 87.6 160.5 -5.75 0.04 8 20 53 lr isolated lr 1.82 141.8 60.9 177.5 -5.34 0.39 9 90 93 310 right i/i+3 2.82 115.3 -91.6 128.6 -0.21 0.00 # of active HBDB terms : 9 Kdir - directional force : 0.200 Klin - linearity force : 0.080 Edir - average energy/HB : -3.913 Elin - average energy/HB : 0.083 --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =464.354 grad(E)=22.963 E(BOND)=219.378 E(ANGL)=255.515 | | E(IMPR)=23.932 E(HBDB)=-34.470 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0000 ----------------------- | Etotal =442.368 grad(E)=21.083 E(BOND)=203.937 E(ANGL)=250.124 | | E(IMPR)=22.777 E(HBDB)=-34.470 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0001 ----------------------- | Etotal =329.791 grad(E)=11.136 E(BOND)=102.440 E(ANGL)=239.814 | | E(IMPR)=22.391 E(HBDB)=-34.853 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0001 ----------------------- | Etotal =282.739 grad(E)=8.527 E(BOND)=86.001 E(ANGL)=211.961 | | E(IMPR)=19.517 E(HBDB)=-34.739 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0002 ----------------------- | Etotal =246.620 grad(E)=14.401 E(BOND)=72.211 E(ANGL)=177.653 | | E(IMPR)=31.598 E(HBDB)=-34.842 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0002 ----------------------- | Etotal =200.402 grad(E)=17.203 E(BOND)=53.422 E(ANGL)=152.214 | | E(IMPR)=30.912 E(HBDB)=-36.147 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= -0.0001 ----------------------- | Etotal =186.523 grad(E)=11.572 E(BOND)=53.921 E(ANGL)=148.511 | | E(IMPR)=20.215 E(HBDB)=-36.123 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0001 ----------------------- | Etotal =155.230 grad(E)=11.855 E(BOND)=18.168 E(ANGL)=144.797 | | E(IMPR)=28.347 E(HBDB)=-36.082 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= 0.0000 ----------------------- | Etotal =152.144 grad(E)=8.736 E(BOND)=22.418 E(ANGL)=142.786 | | E(IMPR)=22.975 E(HBDB)=-36.036 | ------------------------------------------------------------------------------- --------------- cycle= 10 ------ stepsize= 0.0001 ----------------------- | Etotal =135.388 grad(E)=7.221 E(BOND)=13.641 E(ANGL)=136.820 | | E(IMPR)=20.575 E(HBDB)=-35.648 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>stop HEAP: maximum use= 15373353 current use= 15318456 X-PLOR: total CPU time= 2.4900 s X-PLOR: entry time at 09:40:15 11-Mar-05 X-PLOR: exit time at 09:40:18 11-Mar-05