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 09:39:01 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>!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 = 1 !mode= 1 free search HBDB> fixedmode = 0 !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>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> 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 Free HB list: # CO HN dir_type lin_type O-H C-O-H Ca-C-O-H O-H-N Edir Elin 1 15 62 b para edge lr 2.31 174.6 160.7 169.4 -2.69 0.54 2 16 49 b para cent lr 1.94 160.6 -142.2 150.9 -5.84 0.80 3 17 64 b para cent lr 2.08 148.6 127.5 172.7 -4.97 0.61 4 18 51 b para edge lr 1.91 160.7 87.6 160.5 -4.88 0.04 5 20 53 lr isolated lr 1.82 141.8 60.9 177.5 -5.34 0.39 6 25 28 310 right i/i+3 2.03 123.0 -99.5 152.5 -5.36 1.74 7 26 29 310 right i/i+3 1.84 121.4 -90.7 147.3 -4.02 2.60 8 27 31 a N-t & cent i/i+4 2.30 151.0 -134.0 150.8 -3.54 0.17 9 28 32 a N-t & cent i/i+4 2.07 149.5 -99.9 172.0 -3.89 0.99 10 29 33 a N-t & cent i/i+4 1.98 155.4 -93.0 160.6 -4.03 0.02 11 30 34 a N-t & cent i/i+4 2.07 136.1 -103.5 161.7 -2.86 0.00 12 31 35 a N-t & cent i/i+4 1.82 172.4 -122.1 167.6 -2.43 0.00 13 32 36 a N-t & cent i/i+4 2.37 140.1 -118.4 153.6 -2.69 0.00 14 33 37 a C-t & isol i/i+4 2.37 156.1 -160.4 158.3 -1.91 0.02 15 35 38 310 right i/i+3 2.35 104.2 -90.8 126.3 -4.64 3.29 16 36 39 310 right i/i+3 2.57 105.5 -81.1 108.5 -0.94 0.00 17 36 40 a N-t & cent i/i+4 2.48 152.8 -153.8 152.1 -0.51 0.10 18 37 41 a C-t & isol i/i+4 2.13 154.6 -157.8 158.9 -3.68 0.00 19 38 43 lr isolated lr 2.38 119.2 53.6 158.8 -2.36 0.30 20 43 46 310 right i/i+3 2.43 109.1 -85.1 126.2 -3.33 3.69 21 47 16 b para edge lr 2.54 162.5 -91.7 157.1 -1.51 0.00 22 49 18 b para cent lr 2.21 119.7 -141.6 147.4 0.00 0.07 23 52 55 310 right i/i+3 1.79 116.6 -91.4 134.8 -3.21 4.00 24 53 56 310 right i/i+3 2.34 139.5 -103.1 117.0 -0.72 4.00 25 57 60 310 right i/i+3 2.54 135.9 -149.8 105.3 0.00 0.00 26 61 81 b para edge lr 1.95 154.0 -28.8 147.5 -3.41 0.93 27 62 17 b para cent lr 2.42 163.2 159.5 156.0 -1.45 0.25 28 63 83 b para edge lr 2.33 167.2 -136.6 142.2 -3.35 0.34 29 64 19 b para edge lr 1.90 165.5 121.9 161.3 -5.50 0.04 30 66 69 310 right i/i+3 1.72 131.9 -85.3 144.8 0.00 3.46 31 66 70 a C-t & isol i/i+4 1.90 148.9 151.2 131.8 0.00 4.00 32 69 73 a N-t & cent i/i+4 2.25 146.7 -140.0 143.2 -4.68 1.18 33 70 74 a C-t & isol i/i+4 2.06 153.3 -106.4 162.2 -5.01 0.09 34 72 76 a N-t & cent i/i+4 2.19 145.3 -135.1 154.2 -5.38 0.09 35 73 77 a C-t & isol i/i+4 2.08 162.4 -118.6 164.5 -4.43 0.09 36 77 80 310 right i/i+3 2.22 107.6 -100.7 151.7 -5.30 1.30 37 81 63 b para cent lr 1.81 152.0 -132.1 157.5 -4.72 0.65 38 85 67 lr isolated lr 2.12 149.5 14.4 177.2 -5.43 1.51 39 91 95 a N-t & cent i/i+4 2.10 141.7 -109.4 145.8 -4.16 1.40 40 92 96 a N-t & cent i/i+4 2.56 149.1 -140.5 156.6 -1.74 0.00 41 93 97 a N-t & cent i/i+4 2.30 155.5 175.1 162.9 -0.33 0.40 42 94 98 a N-t & cent i/i+4 1.97 162.8 -124.5 165.5 -4.65 0.11 43 95 99 a C-t & isol i/i+4 2.51 147.0 -141.9 148.4 -3.40 0.00 44 96 99 310 right i/i+3 2.32 101.2 -93.5 124.8 -4.58 3.88 45 97 101 a N-t & cent i/i+4 1.98 164.1 163.4 166.0 -0.99 0.11 46 98 102 a N-t & cent i/i+4 1.94 151.0 -104.6 158.2 -4.90 0.29 47 99 103 a N-t & cent i/i+4 2.02 142.1 -112.5 162.9 -4.60 0.03 48 100 104 a C-t & isol i/i+4 1.96 151.2 -111.0 156.2 -5.52 0.18 49 102 105 310 right i/i+3 2.11 107.3 -93.5 135.6 -5.49 3.41 50 103 107 a C-t & isol i/i+4 2.01 162.2 11.0 125.9 0.00 4.00 51 39 42 310 left i/i+3 2.59 86.0 -98.9 149.2 0.00 0.00 # of active HBDB terms : 51 Kdir - directional force : 0.200 Klin - linearity force : 0.080 Edir - average energy/HB : -3.222 Elin - average energy/HB : 1.002 --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =385.603 grad(E)=23.051 E(BOND)=219.378 E(ANGL)=255.515 | | E(IMPR)=23.932 E(HBDB)=-113.222 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0000 ----------------------- | Etotal =364.048 grad(E)=21.184 E(BOND)=203.963 E(ANGL)=250.132 | | E(IMPR)=22.776 E(HBDB)=-112.824 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0001 ----------------------- | Etotal =250.140 grad(E)=11.264 E(BOND)=102.508 E(ANGL)=239.535 | | E(IMPR)=22.348 E(HBDB)=-114.251 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0001 ----------------------- | Etotal =202.513 grad(E)=8.671 E(BOND)=86.061 E(ANGL)=211.794 | | E(IMPR)=19.487 E(HBDB)=-114.829 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0002 ----------------------- | Etotal =167.258 grad(E)=15.861 E(BOND)=72.396 E(ANGL)=175.419 | | E(IMPR)=35.076 E(HBDB)=-115.633 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0002 ----------------------- | Etotal =129.383 grad(E)=16.897 E(BOND)=51.613 E(ANGL)=154.420 | | E(IMPR)=38.379 E(HBDB)=-115.028 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= -0.0001 ----------------------- | Etotal =105.245 grad(E)=10.068 E(BOND)=50.379 E(ANGL)=152.277 | | E(IMPR)=20.787 E(HBDB)=-118.198 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0001 ----------------------- | Etotal =76.395 grad(E)=8.084 E(BOND)=25.506 E(ANGL)=143.911 | | E(IMPR)=22.002 E(HBDB)=-115.023 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= 0.0000 ----------------------- | Etotal =75.984 grad(E)=10.606 E(BOND)=21.209 E(ANGL)=143.752 | | E(IMPR)=26.137 E(HBDB)=-115.114 | ------------------------------------------------------------------------------- --------------- cycle= 10 ------ stepsize= 0.0002 ----------------------- | Etotal =80.135 grad(E)=13.939 E(BOND)=22.054 E(ANGL)=139.411 | | E(IMPR)=29.725 E(HBDB)=-111.055 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! the following doesn't work: strange errors result. This might be fixed by X-PLOR>! adding a reset keyword X-PLOR>!test fixed mode X-PLOR>!hbdb X-PLOR>! freemode = 0 !mode= 1 free search X-PLOR>! fixedmode = 1 !if you want a fixed list, set fixedmode=1, and freemode=0 X-PLOR>!assign ( acc and resid 99 and name O ) ( don and resid 103 and name HN ) X-PLOR>!assign ( acc and resid 97 and name O ) ( don and resid 101 and name HN ) X-PLOR>!assign ( acc and resid 94 and name O ) ( don and resid 98 and name HN ) X-PLOR>!assign ( acc and resid 31 and name O ) ( don and resid 35 and name HN ) X-PLOR>!assign ( acc and resid 29 and name O ) ( don and resid 33 and name HN ) X-PLOR>!assign ( acc and resid 64 and name O ) ( don and resid 19 and name HN ) X-PLOR>!assign ( acc and resid 18 and name O ) ( don and resid 51 and name HN ) X-PLOR>!assign ( acc and resid 20 and name O ) ( don and resid 53 and name HN ) X-PLOR>!assign ( acc and resid 90 and name OD1 ) ( don and resid 93 and name HN ) X-PLOR>!end X-PLOR>! X-PLOR>!flags exclude * include bonds angles impr hbdb end X-PLOR>!mini powell nstep=5 end X-PLOR>! X-PLOR>stop HEAP: maximum use= 15373353 current use= 15318456 X-PLOR: total CPU time= 2.4100 s X-PLOR: entry time at 09:39:01 11-Mar-05 X-PLOR: exit time at 09:39:04 11-Mar-05