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: [unknown] on: x86/Linux at: 09-Mar-05 12:09:55 X-PLOR>parameter {*Read the parameter file.*} PARRDR>{====>} PARRDR> @TOPPAR:parallhdg.pro ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg.pro opened. PARRDR>remark file parallhdg.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use protein.par. PARRDR>remark geometric energy function parameters for distance geometry and PARRDR>remark simulated annealing. PARRDR> PARRDR>set message off echo off end PARRDR>end X-PLOR> X-PLOR>{====>} X-PLOR>structure STRUcture>PSF REMARKS FILENAME="/Net/newton/u2/xplor/xplor_main/tutorial/nmr/g_protein.psf" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:21-Sep-92 16:38:54 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 855(MAXA= 1600) NBOND= 861(MAXB= 1600) NTHETA= 1551(MAXT= 1600) NGRP= 58(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 439(MAXIMP= 800) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 222(MAXNB= 400) STRUcture>end X-PLOR> X-PLOR>coor COOR>ATOM 1 N MET 1 -14.152 0.961 4.712 1.00 1.26 COOR>ATOM 2 HT1 MET 1 -15.085 0.528 4.868 1.00 1.78 X-PLOR> X-PLOR> X-PLOR>noe NOE>{====>} NOE> nres=3000 {*Estimate greater than the actual number of NOEs.*} NOE: allocating space for 3000 restraints. NOE> class all NOE>{====>} NOE>set message=off echo=off end NOE>end X-PLOR> X-PLOR>flags exclude * include noe end X-PLOR> X-PLOR>noe NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1. NOE> sqexponent * 2 NOE> scale * 50. NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 1 -------------------------------------------------- | Etotal =36.649 grad(E)=2.387 E(NOE )=36.649 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>noe NOE> predict PREDict> mode=assign PREDict> bounds=2.7 PREDict> bounds=3.3 PREDict> bounds=5. PREDict> bounds=6. PREDict> scramble=0. PREDict> unique=true PREDict> end The following bounds will be used: 0.000 2.700 3.300 5.000 6.000 SCRAmbling= 0.000 UNIQue=T BYPAss=F BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> NOE> print thres=0.2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS ALL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 50.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfsets(+/-)= 0.000 0.000 ========== spectrum 1 restraint 166 ========== set-i-atoms 55 THR HG21 55 THR HG22 55 THR HG23 set-j-atoms 8 ASN HN R= 5.247 NOE= 3.00 (- 2.70/+ 2.00) Delta= -0.247 E(NOE)= 3.051 NOEPRI: RMS diff. = 0.012, #(violat.> 0.2)= 1 of 922 NOEs NOEPRI: RMS diff. class ALL = 0.012, #(viol.> 0.2)= 1 of 922 NOEs NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =6.957 grad(E)=0.906 E(NOE )=6.957 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>set seed=123466 end X-PLOR> X-PLOR>noe NOE> NOE> predict PREDict> mode=assign PREDict> bounds=2.7 PREDict> bounds=3.3 PREDict> bounds=5. PREDict> bounds=6. PREDict> scramble=0.5 PREDict> unique=true PREDict> end The following bounds will be used: 0.000 2.700 3.300 5.000 6.000 SCRAmbling= 0.500 UNIQue=T BYPAss=F BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> NOE> print thres=0.3 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS ALL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 50.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfsets(+/-)= 0.000 0.000 ========== spectrum 1 restraint 56 ========== set-i-atoms 54 VAL HB set-j-atoms 8 ASN HN R= 5.420 NOE= 2.50 (- 2.50/+ 2.50) Delta= -0.420 E(NOE)= 8.809 ========== spectrum 1 restraint 69 ========== set-i-atoms 54 VAL HB set-j-atoms 8 ASN HN R= 5.420 NOE= 2.50 (- 2.50/+ 2.50) Delta= -0.420 E(NOE)= 8.809 ========== spectrum 1 restraint 407 ========== set-i-atoms 34 ALA HA set-j-atoms 37 ASN HN R= 3.792 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.492 E(NOE)= 12.118 ========== spectrum 1 restraint 669 ========== set-i-atoms 3 TYR HN set-j-atoms 3 TYR HB1 R= 3.714 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.414 E(NOE)= 8.590 ========== spectrum 1 restraint 719 ========== set-i-atoms 43 TRP HN set-j-atoms 43 TRP HB1 R= 3.678 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.378 E(NOE)= 7.132 ========== spectrum 1 restraint 721 ========== set-i-atoms 44 THR HN set-j-atoms 44 THR HB R= 3.760 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.460 E(NOE)= 10.595 ========== spectrum 1 restraint 780 ========== set-i-atoms 27 GLU HN set-j-atoms 27 GLU HG2 R= 3.668 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.368 E(NOE)= 6.785 NOEPRI: RMS diff. = 0.077, #(violat.> 0.3)= 7 of 922 NOEs NOEPRI: RMS diff. class ALL = 0.077, #(viol.> 0.3)= 7 of 922 NOEs NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 3 -------------------------------------------------- | Etotal =270.232 grad(E)=6.520 E(NOE )=270.232 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>noe NOE> predict PREDict> mode=assign PREDict> bounds=2.7 PREDict> bounds=3.3 PREDict> bounds=5. PREDict> bounds=6. PREDict> scramble=1. PREDict> unique=true PREDict> end The following bounds will be used: 0.000 2.700 3.300 5.000 6.000 SCRAmbling= 1.000 UNIQue=T BYPAss=F BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> NOE> print thres=0.4 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS ALL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 50.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfsets(+/-)= 0.000 0.000 ========== spectrum 1 restraint 35 ========== set-i-atoms 3 TYR HA set-j-atoms 50 LYS HB2 R= 3.866 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.566 E(NOE)= 16.015 ========== spectrum 1 restraint 61 ========== set-i-atoms 53 THR HB set-j-atoms 44 THR HN R= 4.092 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.792 E(NOE)= 31.326 ========== spectrum 1 restraint 178 ========== set-i-atoms 30 PHE HE2 set-j-atoms 3 TYR HB1 R= 3.962 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.662 E(NOE)= 21.883 ========== spectrum 1 restraint 220 ========== set-i-atoms 43 TRP HH2 set-j-atoms 31 LYS HB2 R= 3.832 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.532 E(NOE)= 14.134 ========== spectrum 1 restraint 221 ========== set-i-atoms 43 TRP HZ2 set-j-atoms 31 LYS HB2 R= 3.904 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.604 E(NOE)= 18.219 ========== spectrum 1 restraint 283 ========== set-i-atoms 52 PHE HD1 set-j-atoms 45 TYR HA R= 3.846 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.546 E(NOE)= 14.879 ========== spectrum 1 restraint 355 ========== set-i-atoms 15 GLU HN set-j-atoms 16 THR HN R= 4.042 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.742 E(NOE)= 27.516 ========== spectrum 1 restraint 384 ========== set-i-atoms 55 THR HN set-j-atoms 56 GLU HN R= 4.123 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.823 E(NOE)= 33.854 ========== spectrum 1 restraint 413 ========== set-i-atoms 31 LYS HN set-j-atoms 29 VAL HN R= 4.138 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.838 E(NOE)= 35.136 ========== spectrum 1 restraint 543 ========== set-i-atoms 13 LYS HB1 set-j-atoms 8 ASN HA R= 3.859 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.559 E(NOE)= 15.642 ========== spectrum 1 restraint 683 ========== set-i-atoms 13 LYS HN set-j-atoms 13 LYS HB1 R= 3.829 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.529 E(NOE)= 14.000 ========== spectrum 1 restraint 691 ========== set-i-atoms 22 ASP HN set-j-atoms 22 ASP HB2 R= 3.915 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.615 E(NOE)= 18.938 ========== spectrum 1 restraint 712 ========== set-i-atoms 37 ASN HN set-j-atoms 37 ASN HB1 R= 3.772 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.472 E(NOE)= 11.122 ========== spectrum 1 restraint 716 ========== set-i-atoms 40 ASP HN set-j-atoms 40 ASP HB1 R= 3.812 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.512 E(NOE)= 13.088 ========== spectrum 1 restraint 717 ========== set-i-atoms 42 GLU HN set-j-atoms 42 GLU HB1 R= 3.721 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.421 E(NOE)= 8.881 ========== spectrum 1 restraint 721 ========== set-i-atoms 44 THR HN set-j-atoms 44 THR HB R= 3.760 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.460 E(NOE)= 10.595 NOEPRI: RMS diff. = 0.107, #(violat.> 0.4)= 16 of 922 NOEs NOEPRI: RMS diff. class ALL = 0.107, #(viol.> 0.4)= 16 of 922 NOEs NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 4 -------------------------------------------------- | Etotal =530.524 grad(E)=9.339 E(NOE )=530.524 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>noe NOE> predict PREDict> mode=assign PREDict> bounds=2.7 PREDict> bounds=3.3 PREDict> bounds=5. PREDict> bounds=6. PREDict> scramble=1. PREDict> unique=true PREDict> end The following bounds will be used: 0.000 2.700 3.300 5.000 6.000 SCRAmbling= 1.000 UNIQue=T BYPAss=F BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> NOE> print thres=0.4 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS ALL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 50.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfsets(+/-)= 0.000 0.000 ========== spectrum 1 restraint 35 ========== set-i-atoms 3 TYR HA set-j-atoms 50 LYS HB2 R= 3.866 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.566 E(NOE)= 16.015 ========== spectrum 1 restraint 220 ========== set-i-atoms 43 TRP HH2 set-j-atoms 31 LYS HB2 R= 3.832 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.532 E(NOE)= 14.134 ========== spectrum 1 restraint 221 ========== set-i-atoms 43 TRP HZ2 set-j-atoms 31 LYS HB2 R= 3.904 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.604 E(NOE)= 18.219 ========== spectrum 1 restraint 278 ========== set-i-atoms 52 PHE HD1 set-j-atoms 44 THR HN R= 4.147 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.847 E(NOE)= 35.829 ========== spectrum 1 restraint 355 ========== set-i-atoms 15 GLU HN set-j-atoms 16 THR HN R= 4.042 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.742 E(NOE)= 27.516 ========== spectrum 1 restraint 383 ========== set-i-atoms 51 THR HN set-j-atoms 52 PHE HN R= 4.138 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.838 E(NOE)= 35.112 ========== spectrum 1 restraint 405 ========== set-i-atoms 32 GLN HA set-j-atoms 35 ASN HN R= 3.737 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.437 E(NOE)= 9.549 ========== spectrum 1 restraint 410 ========== set-i-atoms 24 ALA HN set-j-atoms 26 ALA HN R= 3.754 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.454 E(NOE)= 10.326 ========== spectrum 1 restraint 411 ========== set-i-atoms 27 GLU HN set-j-atoms 29 VAL HN R= 4.062 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.762 E(NOE)= 28.995 ========== spectrum 1 restraint 413 ========== set-i-atoms 31 LYS HN set-j-atoms 29 VAL HN R= 4.138 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.838 E(NOE)= 35.136 ========== spectrum 1 restraint 428 ========== set-i-atoms 34 ALA HA set-j-atoms 39 VAL HN R= 3.990 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.690 E(NOE)= 23.812 ========== spectrum 1 restraint 502 ========== set-i-atoms 37 ASN HD21 set-j-atoms 36 ASP HB1 R= 3.769 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.469 E(NOE)= 11.020 ========== spectrum 1 restraint 530 ========== set-i-atoms 5 LEU HG set-j-atoms 7 LEU HA R= 3.915 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.615 E(NOE)= 18.912 ========== spectrum 1 restraint 543 ========== set-i-atoms 13 LYS HB1 set-j-atoms 8 ASN HA R= 3.859 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.559 E(NOE)= 15.642 ========== spectrum 1 restraint 712 ========== set-i-atoms 37 ASN HN set-j-atoms 37 ASN HB1 R= 3.772 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.472 E(NOE)= 11.122 ========== spectrum 1 restraint 716 ========== set-i-atoms 40 ASP HN set-j-atoms 40 ASP HB1 R= 3.812 NOE= 1.65 (- 1.65/+ 1.65) Delta= -0.512 E(NOE)= 13.088 NOEPRI: RMS diff. = 0.110, #(violat.> 0.4)= 16 of 922 NOEs NOEPRI: RMS diff. class ALL = 0.110, #(viol.> 0.4)= 16 of 922 NOEs NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 5 -------------------------------------------------- | Etotal =561.793 grad(E)=9.429 E(NOE )=561.793 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>noe NOE> partition=10 For set 1 there are 85 distance restraints. For set 2 there are 85 distance restraints. For set 3 there are 106 distance restraints. For set 4 there are 83 distance restraints. For set 5 there are 88 distance restraints. For set 6 there are 95 distance restraints. For set 7 there are 98 distance restraints. For set 8 there are 95 distance restraints. For set 9 there are 104 distance restraints. For set 10 there are 83 distance restraints. NOE>end X-PLOR> X-PLOR>noe cv=0 end energy end --------------- cycle= 6 -------------------------------------------------- | Etotal =561.793 grad(E)=9.429 E(NOE )=561.793 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($olde=$noe) EVALUATE: symbol $OLDE set to 561.793 (real) X-PLOR> X-PLOR>evaluate ($tote=0.) EVALUATE: symbol $TOTE set to 0.00000 (real) X-PLOR>noe cv=1 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 7 -------------------------------------------------- | Etotal =526.270 grad(E)=9.096 E(NOE )=526.270 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 526.270 (real) X-PLOR>noe cv=2 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 8 -------------------------------------------------- | Etotal =545.543 grad(E)=9.242 E(NOE )=545.543 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 1071.81 (real) X-PLOR>noe cv=3 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 9 -------------------------------------------------- | Etotal =496.264 grad(E)=8.830 E(NOE )=496.264 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 1568.08 (real) X-PLOR>noe cv=4 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 10 -------------------------------------------------- | Etotal =537.432 grad(E)=9.226 E(NOE )=537.432 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 2105.51 (real) X-PLOR>noe cv=5 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 11 -------------------------------------------------- | Etotal =488.388 grad(E)=8.899 E(NOE )=488.388 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 2593.90 (real) X-PLOR>noe cv=6 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 12 -------------------------------------------------- | Etotal =517.308 grad(E)=9.014 E(NOE )=517.308 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 3111.21 (real) X-PLOR>noe cv=7 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 13 -------------------------------------------------- | Etotal =474.046 grad(E)=8.938 E(NOE )=474.046 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 3585.25 (real) X-PLOR>noe cv=8 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 14 -------------------------------------------------- | Etotal =492.542 grad(E)=8.781 E(NOE )=492.542 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 4077.79 (real) X-PLOR>noe cv=9 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 15 -------------------------------------------------- | Etotal =496.791 grad(E)=8.667 E(NOE )=496.791 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 4574.58 (real) X-PLOR>noe cv=10 end energy end evaluate ($tote=$tote+$noe) --------------- cycle= 16 -------------------------------------------------- | Etotal =481.555 grad(E)=8.549 E(NOE )=481.555 | ------------------------------------------------------------------------------- EVALUATE: symbol $TOTE set to 5056.14 (real) X-PLOR> X-PLOR>evaluate ($tote=$tote/9) EVALUATE: symbol $TOTE set to 561.793 (real) X-PLOR>display $olde $tote 561.793 561.793 X-PLOR> X-PLOR>noe NOE> partition=2 For set 1 there are 449 distance restraints. For set 2 there are 473 distance restraints. NOE> cv=1 NOE> predict PREDict> mode=assign PREDict> bypass=true PREDict> output=noetest41.dat PREDict> end ASSFIL: file noetest41.dat opened. The following bounds will be used: 0.000 SCRAmbling= 0.000 UNIQue=F BYPAss=T BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> close noetest41.dat end NOE> NOE> cv=2 NOE> predict PREDict> mode=assign PREDict> bypass=true PREDict> output=noetest42.dat PREDict> end ASSFIL: file noetest42.dat opened. The following bounds will be used: 0.000 SCRAmbling= 0.000 UNIQue=F BYPAss=T BSYMMetry_error= 0.000 BUNSYMetry_error= 0.000 IREFIne=F NOE> NOE> close noetest42.dat end NOE> NOE> reset NOE> nres=3000 NOE: allocating space for 3000 restraints. NOE> set message=off echo=off end NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1. NOE> sqexponent * 2 NOE> scale * 50. NOE>end X-PLOR> X-PLOR>energy end --------------- cycle= 17 -------------------------------------------------- | Etotal =561.793 grad(E)=9.429 E(NOE )=561.793 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 1379885 current use= 1233917 X-PLOR: total CPU time= 0.7000 s X-PLOR: entry time at 12:09:55 09-Mar-05 X-PLOR: exit time at 12:09:56 09-Mar-05