XPLOR-NIH version 2.11-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: darwin/ppc at: 01-Jun-05 09:58:57 X-PLOR>! X-PLOR>! a quick test of the proton chemical shift calculation, based X-PLOR>! on the first 30 residues of reduced human thioredoxin X-PLOR>! X-PLOR> X-PLOR> X-PLOR>struct STRUcture>PSF REMARKS FILENAME="temp.psf" REMARKS =============================================================== REMARKS overall,bonds,angles,improper,vdw,cdih,noe,coup REMARKS energies: 251.79, 25.9778, 117.317, 8.17386, 81.7713, 0.430726, 7.1554, REMARKS =============================================================== REMARKS bonds,angles,impropers,cdih,noe,coup REMARKS 3.964484E-03,0.50798,0.253063,0.158058,1.055106E-02,0.352969 REMARKS =============================================================== REMARKS cdih end_coup noe REMARKS violations : 0 0 0 REMARKS =============================================================== REMARKS jcoup stats: end_rms REMARKS rms-d: 0.352969 REMARKS =============================================================== REMARKS DATE:25-Feb-04 18:37:30 created by user: [unknown] XPLOR: current counts (number in parenthesis is maximum) NATOM= 453(MAXA= 800) NBOND= 454(MAXB= 800) NTHETA= 825(MAXT= 1600) NGRP= 186(MAXGRP= 200) NPHI= 51(MAXP= 100) NIMPHI= 219(MAXIMP= 400) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 174(MAXNB= 200) STRUcture> STRUcture> STRUcture> STRUcture> STRUcture>end X-PLOR>coor COOR>REMARK FILENAME="temp.pdb" COOR>REMARK =============================================================== COOR>REMARK overall,bonds,angles,improper,vdw,cdih,noe,coup COOR>REMARK energies: 251.79, 25.9778, 117.317, 8.17386, 81.7713, 0.430726, 7.1554, COOR>REMARK =============================================================== COOR>REMARK bonds,angles,impropers,cdih,noe,coup COOR>REMARK 3.964484E-03,0.50798,0.253063,0.158058,1.055106E-02,0.352969 COOR>REMARK =============================================================== COOR>REMARK cdih end_coup noe COOR>REMARK violations : 0 0 0 COOR>REMARK =============================================================== COOR>REMARK jcoup stats: end_rms COOR>REMARK rms-d: 0.352969 COOR>REMARK =============================================================== COOR>REMARK DATE:25-Feb-04 18:37:30 created by user: [unknown] COOR>ATOM 1 N MET 1 -7.982 -2.780 9.499 1.00 0.19 COOR>ATOM 2 HT1 MET 1 -8.097 -2.706 8.467 1.00 1.10 X-PLOR> X-PLOR> X-PLOR> X-PLOR>@PROTSHIFTS:protons_setup.tbl ASSFIL: file /home/schwitrs/xplor/databases/protshifts/protons_setup.tbl opened. X-PLOR>! X-PLOR>! Protons_setup.tbl X-PLOR>! X-PLOR>! Setup for proton chemical shift refinement X-PLOR>! X-PLOR>! starts by doing selections for electric field stuff, X-PLOR>! then magnetic anisotropy, X-PLOR>! then ring currents, X-PLOR>! and finally random coil shifts. X-PLOR>! X-PLOR>! Random coil shifts are from Williamson's file random.dat X-PLOR>! X-PLOR>! by John Kuszewski Dec 1994 X-PLOR>! X-PLOR> X-PLOR>set message off echo off end VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: sum over selected elements = 1.000000 VECTOR: zero atoms selected X-PLOR> X-PLOR>protons PROTONSHIFTS> potential harmonic using harmonic potential. PROTONSHIFTS> class alpha PROTONSHIFTS> force 10.0 Setting force consts for class ALPH to 10.000 PROTONSHIFTS> error 0.3 Setting error for class ALPH to 0.300 PROTONSHIFTS> PROTONSHIFTS>OBSEerved (resid 1 and name HA ) 4.01 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 2 and name HA ) 4.36 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 3 and name HA ) 4.56 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 4 and name HA ) 4.75 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 5 and name HA ) 4.37 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 6 and name HA ) 4.57 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 7 and name HA ) 5.00 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 8 and name HA ) 3.95 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 9 and name HA ) 4.01 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 10 and name HA ) 4.23 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 11 and name HA ) 4.10 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 12 and name HA ) 3.58 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 13 and name HA ) 3.99 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 14 and name HA ) 4.06 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 15 and name HA ) 3.72 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 16 and name HA ) 4.31 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 17 and name HA ) 4.19 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 18 and name HA ) 3.92 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 20 and name HA ) 4.65 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 21 and name HA ) 4.28 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 22 and name HA ) 4.42 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 23 and name HA ) 4.85 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 24 and name HA ) 4.47 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 25 and name HA ) 4.69 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 26 and name HA ) 4.30 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 27 and name HA ) 4.95 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 28 and name HA ) 4.76 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 29 and name HA ) 4.81 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS>OBSEerved (resid 30 and name HA ) 3.77 SELRPN: 1 atoms have been selected out of 453 PROTONSHIFTS> PROTONSHIFTS> PROTONSHIFTS> class nspec PROTONSHIFTS> force 10.0 Setting force consts for class NSPE to 10.000 PROTONSHIFTS> degeneracy 2 Setting degeneracy for class NSPE to 2 PROTONSHIFTS> PROTONSHIFTS> OBSEerved (resid 25 and name HG1# ) (resid 25 and name HG2# ) 0.04 0.90 SELRPN: 3 atoms have been selected out of 453 SELRPN: 3 atoms have been selected out of 453 PROTONSHIFTS> PROTONSHIFTS>end X-PLOR> X-PLOR>prot print threshold 0.0 all norm end The following proton delta shifts are greater than the cutoff: (proton)(delta)(calc)(obs)(rcoil)(magn anis)(elec) class ALPH 1 MET HA -0.065 3.945 4.010 3.860 0.122 -0.037 0.000 2 VAL HA -0.124 4.236 4.360 3.530 0.726 -0.007 -0.013 3 LYS HA -0.074 4.486 4.560 3.710 0.797 -0.009 -0.012 4 GLN HA -0.284 4.466 4.750 3.720 0.778 -0.005 -0.027 5 ILE HA 0.045 4.415 4.370 3.570 0.783 0.033 0.030 6 GLU HA -0.369 4.201 4.570 3.650 0.580 -0.033 0.004 7 SER HA -0.584 4.416 5.000 3.850 0.547 0.001 0.018 8 LYS HA 0.508 4.458 3.950 3.710 0.608 0.020 0.120 9 THR HA 0.125 4.135 4.010 3.700 0.401 -0.019 0.053 10 ALA HA -0.105 4.125 4.230 3.700 0.379 0.020 0.026 11 PHE HA 0.896 4.996 4.100 4.450 0.386 -0.018 0.178 12 GLN HA 0.575 4.155 3.580 3.720 0.548 -0.019 -0.094 13 GLU HA 0.080 4.070 3.990 3.650 0.471 -0.015 -0.035 14 ALA HA 0.029 4.089 4.060 3.700 0.479 -0.019 -0.072 15 LEU HA 0.296 4.016 3.720 3.740 0.451 -0.016 -0.158 16 ASP HA 0.259 4.569 4.310 4.120 0.467 0.028 -0.046 17 ALA HA -0.073 4.117 4.190 3.700 0.458 -0.015 -0.026 18 ALA HA 0.108 4.028 3.920 3.700 0.372 -0.012 -0.032 20 ASP HA 0.102 4.752 4.650 4.120 0.658 -0.009 -0.016 21 LYS HA 0.000 4.280 4.280 3.710 0.612 -0.042 0.000 22 LEU HA -0.230 4.190 4.420 3.740 0.455 0.000 -0.005 23 VAL HA -0.588 4.262 4.850 3.530 0.738 -0.002 -0.004 24 VAL HA -0.194 4.276 4.470 3.530 0.694 -0.007 0.059 25 VAL HA -0.329 4.361 4.690 3.530 0.831 -0.003 0.003 26 ASP HA 0.765 5.065 4.300 4.120 0.889 0.004 0.052 27 PHE HA 0.221 5.171 4.950 4.450 0.795 0.008 -0.082 28 SER HA -0.207 4.553 4.760 3.850 0.662 -0.017 0.058 29 ALA HA -0.216 4.594 4.810 3.700 0.887 -0.018 0.025 30 THR HA 0.298 4.068 3.770 3.700 0.375 -0.010 0.003 class NSPE 25 VAL HG11 25 VAL HG12 25 VAL HG13 0.423 0.463 0.040 0.960 -0.169 0.013 -0.341 25 VAL HG21 25 VAL HG22 25 VAL HG23 -0.071 0.829 0.900 0.960 -0.370 -0.008 0.247 RMS error = 0.347 Number of violations: 30.000 X-PLOR> X-PLOR>stop HEAP: maximum use= 1304660 current use= 1158977 X-PLOR: total CPU time= 0.8100 s X-PLOR: entry time at 09:58:57 01-Jun-05 X-PLOR: exit time at 09:58:57 01-Jun-05