X-PLOR: V3.820 user: dcs on: sgi at: 01-Sep-96 12:46:32 Author: Axel T. Brunger Copyright: 1988-95 (Yale University), 1987 (Harvard University) X-PLOR>! average.inp -- Computes the average structure, RMSDs from the average X-PLOR>! for each original structure and the rms RMSD. X-PLOR>! Dave Schweisguth , 19 Aug 1996 X-PLOR>! Derived from nmr/average.inp X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use 'xplor -s' ASSFIL: file xplor.seed opened. SEED=122450.42477417 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 36000) NBOND= 728(MAXB= 36000) NTHETA= 1299(MAXT= 50000) NGRP= 218(MAXGRP= 36000) NPHI= 0(MAXP= 60000) NIMPHI= 461(MAXIMP= 24000) NDON= 68(MAXPAD= 10000) NACC= 105(MAXPAD= 10000) NNB= 63(MAXNB= 4000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> ctonnb=9.5 NBDSET> ctofnb=10.5 NBDSET> cutnb=11.5 NBDSET> tolerance=0.5 NBDSET> rdie NBDSET> switch NBDSET> vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR>restraints dihedral scale=800 end X-PLOR> X-PLOR>flags exclude * include bond angl dihe impr vdw elec noe cdih plan end X-PLOR> X-PLOR>! Compute the mean structure. X-PLOR> X-PLOR>evaluate ($nfile=9) EVALUATE: symbol $NFILE set to 9.00000 (real) X-PLOR>vector do (store1=0) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (store2=0) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (store3=0) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (store4=0) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>evaluate ($count=0) EVALUATE: symbol $COUNT set to 0.000000E+00 (real) X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 1.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.1.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.1.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 00:15:39 created by user: COOR>ATOM 1 P GUA A 1 6.004 11.158 -1.414 1.00 0.39 A COOR>ATOM 2 O1P GUA A 1 5.064 10.046 -1.710 1.00 0.65 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as true X-PLOR> coordinates copy end ! Store first structure in comparison set. COOR: selected main coordinates copied to comp X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0000 0.0000 0.0000) Rotation matrix = 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 Corresp. Eulerian angles (theta1,theta2,theta3) 0.0000 0.0000 0.0000 Corresp. spherical polar angles (psi,phi,kappa) 0.0000 0.0000 0.0000 Corresp. rotation angle 0.0000 about axis 0.0000 1.0000 0.0000 Corresp. quaternions 1.0000 0.0000 0.0000 0.0000 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0000 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 2.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.2.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.2.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 01:57:34 created by user: COOR>ATOM 1 P GUA A 1 -6.036 10.700 5.130 1.00 1.20 A COOR>ATOM 2 O1P GUA A 1 -4.824 11.531 5.343 1.00 1.26 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0010 -0.0337 0.0147) Rotation matrix = -0.980013 -0.005251 0.198863 0.050144 0.960851 0.272489 -0.192509 0.277014 -0.941384 Corresp. Eulerian angles (theta1,theta2,theta3) 214.7970 160.2853 36.1221 Corresp. spherical polar angles (psi,phi,kappa) 171.9172 94.6705 168.6005 Corresp. rotation angle 168.6005 about axis -0.0114 -0.9901 -0.1401 Corresp. quaternions 0.0993 -0.0114 -0.9852 -0.1394 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.7099 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 3.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.3.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.3.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 07:09:26 created by user: COOR>ATOM 1 P GUA A 1 -7.157 9.354 4.699 1.00 0.60 A COOR>ATOM 2 O1P GUA A 1 -7.616 10.400 3.750 1.00 1.35 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0093 0.0054 0.0531) Rotation matrix = -0.975589 -0.165653 0.144169 -0.129095 0.963696 0.233721 -0.177652 0.209404 -0.961556 Corresp. Eulerian angles (theta1,theta2,theta3) 220.3102 164.0613 31.6681 Corresp. spherical polar angles (psi,phi,kappa) 172.2310 56.3699 170.6537 Corresp. rotation angle 170.6537 about axis 0.0749 -0.9908 -0.1126 Corresp. quaternions 0.0815 0.0746 -0.9875 -0.1122 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.4308 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 4.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.4.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.4.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 09:50:51 created by user: COOR>ATOM 1 P GUA A 1 4.994 -11.353 2.813 1.00 0.56 A COOR>ATOM 2 O1P GUA A 1 3.846 -11.693 3.691 1.00 1.40 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0233 -0.0018 0.0495) Rotation matrix = 0.971563 -0.047075 0.232052 -0.049169 -0.998785 0.003247 0.231618 -0.014564 -0.972698 Corresp. Eulerian angles (theta1,theta2,theta3) 86.4019 166.5807 89.1983 Corresp. spherical polar angles (psi,phi,kappa) 88.6113 173.2933 180.5139 Corresp. rotation angle 179.4861 about axis 0.9929 -0.0242 0.1168 Corresp. quaternions 0.0045 0.9929 -0.0242 0.1168 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3750 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 5.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.5.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.5.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 12:27:07 created by user: COOR>ATOM 1 P GUA A 1 7.102 -9.574 5.244 1.00 0.43 A COOR>ATOM 2 O1P GUA A 1 7.254 -10.978 5.708 1.00 1.25 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0077 0.0131 0.0458) Rotation matrix = 0.993537 0.107351 0.036887 0.085501 -0.921496 0.378860 0.074662 -0.373257 -0.924719 Corresp. Eulerian angles (theta1,theta2,theta3) 11.3116 157.6260 5.5610 Corresp. spherical polar angles (psi,phi,kappa) 92.8741 178.3360 202.1289 Corresp. rotation angle 157.8711 about axis 0.9983 0.0501 0.0290 Corresp. quaternions 0.1919 0.9798 0.0492 0.0285 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9534 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 6.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.6.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.6.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 15:01:53 created by user: COOR>ATOM 1 P GUA A 1 -6.396 10.252 4.365 1.00 0.43 A COOR>ATOM 2 O1P GUA A 1 -6.429 11.714 4.626 1.00 1.52 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0132 -0.0132 0.0173) Rotation matrix = -0.994249 -0.055045 0.091861 -0.031338 0.969788 0.241927 -0.102403 0.237657 -0.965936 Corresp. Eulerian angles (theta1,theta2,theta3) 203.3105 165.0023 20.7921 Corresp. spherical polar angles (psi,phi,kappa) 172.9316 79.7893 174.3831 Corresp. rotation angle 174.3831 about axis 0.0218 -0.9924 -0.1211 Corresp. quaternions 0.0490 0.0218 -0.9912 -0.1210 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3867 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 7.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.7.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.7.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 21:08:17 created by user: COOR>ATOM 1 P GUA A 1 -5.171 11.337 -1.790 1.00 0.45 A COOR>ATOM 2 O1P GUA A 1 -5.055 12.230 -2.972 1.00 0.80 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0073 0.0006 0.0002) Rotation matrix = -0.996531 0.077420 0.030547 0.064440 0.950007 -0.305505 -0.052672 -0.302477 -0.951700 Corresp. Eulerian angles (theta1,theta2,theta3) 350.1218 162.1198 174.2900 Corresp. spherical polar angles (psi,phi,kappa) 9.0988 76.8662 182.4152 Corresp. rotation angle 177.5848 about axis -0.0359 -0.9874 0.1540 Corresp. quaternions 0.0211 -0.0359 -0.9872 0.1540 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.4045 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 8.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.8.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.8.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 21:55:36 created by user: COOR>ATOM 1 P GUA A 1 -5.757 11.170 0.727 1.00 0.37 A COOR>ATOM 2 O1P GUA A 1 -6.108 11.350 -0.705 1.00 0.76 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0014 0.0222 0.0406) Rotation matrix = -0.998853 0.014782 0.045545 0.010919 0.996411 -0.083941 -0.046623 -0.083348 -0.995429 Corresp. Eulerian angles (theta1,theta2,theta3) 330.7783 174.5198 151.5163 Corresp. spherical polar angles (psi,phi,kappa) 2.4285 81.2657 182.6437 Corresp. rotation angle 177.3563 about axis -0.0064 -0.9991 0.0419 Corresp. quaternions 0.0231 -0.0064 -0.9988 0.0419 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.5062 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 9.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.9.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.9.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 22:42:39 created by user: COOR>ATOM 1 P GUA A 1 6.113 10.370 -3.809 1.00 0.44 A COOR>ATOM 2 O1P GUA A 1 5.071 10.431 -4.866 1.00 0.98 A X-PLOR> if ($count=1) then NEXTCD: condition evaluated as false X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0076 -0.0071 0.0147) Rotation matrix = 0.985748 -0.068375 -0.153705 0.050516 0.991819 -0.117234 0.160463 0.107798 0.981138 Corresp. Eulerian angles (theta1,theta2,theta3) 123.8929 11.1460 232.6666 Corresp. spherical polar angles (psi,phi,kappa) 39.0110 152.1512 11.6634 Corresp. rotation angle 11.6634 about axis -0.5566 0.7770 -0.2941 Corresp. quaternions 0.9948 -0.0566 0.0790 -0.0299 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.6706 X-PLOR> vector do (store1=store1+x) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store2=store2+y) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store3=store3+z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as false X-PLOR> evaluate ($count=$count+1) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") X-PLOR> coordinates initialize end X-PLOR> coordinates @@$filename X-PLOR> if ($count=1) then X-PLOR> coordinates copy end ! Store first structure in comparison set. X-PLOR> end if X-PLOR> coordinates fit end X-PLOR> vector do (store1=store1+x) (all) X-PLOR> vector do (store2=store2+y) (all) X-PLOR> vector do (store3=store3+z) (all) X-PLOR> vector do (store4=store4+x*x+y*y+z*z) (all) X-PLOR>end loop main X-PLOR> X-PLOR>vector do (x=store1 / $nfile) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (y=store2 / $nfile) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (z=store3 / $nfile) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (b=sqrt(max(0,store4/$nfile-(x**2+y**2+z**2)))) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>! Minimize the averaged structure X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2090 exclusions and 1650 interactions(1-4) NBONDS: found 62126 intra-atom interactions NBONDS: found 62123 intra-atom interactions NBONDS: found 62125 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =-183.376 grad(E)=22.279 E(BOND)=58.557 E(ANGL)=168.593 | | E(DIHE)=0.000 E(IMPR)=16.671 E(VDW )=-294.995 E(ELEC)=-153.233 | | E(CDIH)=0.120 E(NOE )=9.777 E(PLAN)=11.133 | ------------------------------------------------------------------------------- NBONDS: found 62109 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =-316.506 grad(E)=3.759 E(BOND)=8.089 E(ANGL)=94.003 | | E(DIHE)=0.000 E(IMPR)=11.839 E(VDW )=-298.155 E(ELEC)=-153.178 | | E(CDIH)=0.081 E(NOE )=9.666 E(PLAN)=11.149 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =-325.700 grad(E)=2.014 E(BOND)=5.677 E(ANGL)=88.041 | | E(DIHE)=0.000 E(IMPR)=11.493 E(VDW )=-298.302 E(ELEC)=-153.733 | | E(CDIH)=0.075 E(NOE )=9.904 E(PLAN)=11.143 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =-327.411 grad(E)=0.646 E(BOND)=5.646 E(ANGL)=86.817 | | E(DIHE)=0.000 E(IMPR)=11.418 E(VDW )=-298.215 E(ELEC)=-154.236 | | E(CDIH)=0.065 E(NOE )=9.930 E(PLAN)=11.164 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =-328.395 grad(E)=1.189 E(BOND)=5.582 E(ANGL)=86.464 | | E(DIHE)=0.000 E(IMPR)=11.273 E(VDW )=-297.792 E(ELEC)=-155.087 | | E(CDIH)=0.057 E(NOE )=9.914 E(PLAN)=11.195 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =-330.288 grad(E)=1.669 E(BOND)=5.663 E(ANGL)=85.886 | | E(DIHE)=0.000 E(IMPR)=10.929 E(VDW )=-296.708 E(ELEC)=-157.400 | | E(CDIH)=0.050 E(NOE )=10.014 E(PLAN)=11.278 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =-331.748 grad(E)=1.166 E(BOND)=5.822 E(ANGL)=84.940 | | E(DIHE)=0.000 E(IMPR)=11.102 E(VDW )=-296.193 E(ELEC)=-159.032 | | E(CDIH)=0.064 E(NOE )=10.258 E(PLAN)=11.291 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-333.018 grad(E)=1.187 E(BOND)=5.659 E(ANGL)=84.386 | | E(DIHE)=0.000 E(IMPR)=11.279 E(VDW )=-296.033 E(ELEC)=-160.116 | | E(CDIH)=0.106 E(NOE )=10.403 E(PLAN)=11.298 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the averaged structure X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.002 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.190265E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.648 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.648033 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 0.000000E+00 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.332 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.332148 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe NOEPRI: RMS diff. = 0.011, #(violat.> 0.2)= 0 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.011, #(viol.> 0.2)= 0 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.105878E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 0.000000E+00 (real) X-PLOR>print threshold=5 cdih Number of dihedral angle constraints= 203 overall scale = 800.0000 Number of violations greater 5.000: 0 RMS deviation= 0.046 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.461925E-01 (real) X-PLOR>evaluate ($v_cdih=$violations) EVALUATE: symbol $V_CDIH set to 0.000000E+00 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 5.65931, angle 84.386, dihedral 0, improper 11.2793, NOE 10.403, c-dihedral 0.105556, planar 11.298, VdW -296.033, elec -160.116, total -333.018 RMSD: bond 1.902653E-03, angle 0.648033, dihedral 0, improper 0.332148, NOE 1.05878E-02, c-dihedral 4.619248E-02 Violations: bond 0, angle 0, dihedral 0, improper 0, NOE 0, c-dihedral 0 X-PLOR> X-PLOR>! b array (last column) is the rms difference from the mean X-PLOR> X-PLOR>write coordinates output=average.pdb end ASSFIL: file average.pdb opened. X-PLOR> X-PLOR>! Compute an overall rms difference. X-PLOR> X-PLOR>coordinates copy end COOR: selected main coordinates copied to comp X-PLOR>evaluate ($rmsd_rmsd=0) EVALUATE: symbol $RMSD_RMSD set to 0.000000E+00 (real) X-PLOR>evaluate ($rmsd_rmsd_stem=0) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.000000E+00 (real) X-PLOR>evaluate ($rmsd_rmsd_loop=0) EVALUATE: symbol $RMSD_RMSD_LOOP set to 0.000000E+00 (real) X-PLOR> X-PLOR>evaluate ($count=0) EVALUATE: symbol $COUNT set to 0.000000E+00 (real) X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 1.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.1.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.1.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 00:15:39 created by user: COOR>ATOM 1 P GUA A 1 6.004 11.158 -1.414 1.00 0.39 A COOR>ATOM 2 O1P GUA A 1 5.064 10.046 -1.710 1.00 0.65 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0000 0.0000 0.0000) Rotation matrix = 1.000000 0.000016 -0.000020 -0.000016 1.000000 -0.000081 0.000020 0.000081 1.000000 Corresp. Eulerian angles (theta1,theta2,theta3) 0.0009 0.0048 0.0000 Corresp. spherical polar angles (psi,phi,kappa) 0.0000 0.0000 0.0000 Corresp. rotation angle 0.0000 about axis 0.0000 1.0000 0.0000 Corresp. quaternions 1.0000 0.0000 0.0000 0.0000 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3152 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.315156, square sum= 67.2420, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 0.993235E-01 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0475 0.0025 0.0183) Rotation matrix = 0.999989 0.000101 0.004598 -0.000086 0.999995 -0.003276 -0.004599 0.003276 0.999984 Corresp. Eulerian angles (theta1,theta2,theta3) 234.5370 0.3235 125.4684 Corresp. spherical polar angles (psi,phi,kappa) 35.4767 1.6304 359.6765 Corresp. rotation angle 0.3235 about axis -0.5801 -0.8144 0.0165 Corresp. quaternions 1.0000 -0.0016 -0.0023 0.0000 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3126 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.312616, square sum= 44.5644, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.977289E-01 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0630 0.0740 0.2653) Rotation matrix = 0.999628 -0.001069 -0.027247 0.001659 0.999764 0.021667 0.027217 -0.021704 0.999394 Corresp. Eulerian angles (theta1,theta2,theta3) 51.4299 1.9950 308.4920 Corresp. spherical polar angles (psi,phi,kappa) 38.5862 3.5994 1.9965 Corresp. rotation angle 1.9965 about axis 0.6225 0.7817 -0.0392 Corresp. quaternions 0.9998 0.0108 0.0136 -0.0007 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2621 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.262136, square sum= 15.1861, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 0.687153E-01 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 2.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.2.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.2.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 01:57:34 created by user: COOR>ATOM 1 P GUA A 1 -6.036 10.700 5.130 1.00 1.20 A COOR>ATOM 2 O1P GUA A 1 -4.824 11.531 5.343 1.00 1.26 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0010 -0.0337 0.0147) Rotation matrix = -0.980016 -0.004841 0.198860 0.050455 0.960960 0.272049 -0.192413 0.276646 -0.941512 Corresp. Eulerian angles (theta1,theta2,theta3) 214.8195 160.3070 36.1657 Corresp. spherical polar angles (psi,phi,kappa) 171.9285 94.7522 168.6037 Corresp. rotation angle 168.6037 about axis -0.0116 -0.9901 -0.1399 Corresp. quaternions 0.0993 -0.0116 -0.9852 -0.1392 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.7004 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.700449, square sum= 332.1553, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 0.589952 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.1564 0.1092 -0.0021) Rotation matrix = 0.999834 0.017247 0.005885 -0.017165 0.999760 -0.013608 -0.006118 0.013505 0.999890 Corresp. Eulerian angles (theta1,theta2,theta3) 204.3730 0.8495 156.6129 Corresp. spherical polar angles (psi,phi,kappa) 74.6776 51.7660 358.6986 Corresp. rotation angle 1.3014 about axis -0.5969 -0.2642 0.7576 Corresp. quaternions 0.9999 -0.0068 -0.0030 0.0086 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.1923 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.192330, square sum= 16.8678, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.134720 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.3372 0.8762 0.5311) Rotation matrix = 0.995319 -0.084791 -0.046367 0.087280 0.994687 0.054593 0.041491 -0.058384 0.997432 Corresp. Eulerian angles (theta1,theta2,theta3) 35.3997 4.1074 319.6584 Corresp. spherical polar angles (psi,phi,kappa) 66.8865 56.7121 6.4252 Corresp. rotation angle 6.4252 about axis 0.5048 0.3926 -0.7688 Corresp. quaternions 0.9984 0.0283 0.0220 -0.0431 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9777 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.977715, square sum= 211.2598, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.02464 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 3.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.3.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.3.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 07:09:26 created by user: COOR>ATOM 1 P GUA A 1 -7.157 9.354 4.699 1.00 0.60 A COOR>ATOM 2 O1P GUA A 1 -7.616 10.400 3.750 1.00 1.35 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0093 0.0054 0.0531) Rotation matrix = -0.975559 -0.165819 0.144185 -0.129281 0.963704 0.233584 -0.177684 0.209234 -0.961587 Corresp. Eulerian angles (theta1,theta2,theta3) 220.3383 164.0678 31.6859 Corresp. spherical polar angles (psi,phi,kappa) 172.2319 56.3199 170.6523 Corresp. rotation angle 170.6523 about axis 0.0750 -0.9908 -0.1125 Corresp. quaternions 0.0815 0.0747 -0.9875 -0.1121 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3177 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.317678, square sum= 68.3225, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 0.690871 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0017 -0.0562 0.0140) Rotation matrix = 0.999971 -0.007484 0.001289 0.007477 0.999957 0.005511 -0.001330 -0.005501 0.999984 Corresp. Eulerian angles (theta1,theta2,theta3) 346.4036 0.3243 13.1678 Corresp. spherical polar angles (psi,phi,kappa) 98.0268 53.6472 0.5374 Corresp. rotation angle 0.5374 about axis 0.5869 -0.1396 -0.7975 Corresp. quaternions 1.0000 0.0028 -0.0007 -0.0037 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2560 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.256030, square sum= 29.8914, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.200271 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0082 -0.1880 -0.0645) Rotation matrix = 0.999627 0.027271 0.001285 -0.027247 0.999499 -0.016073 -0.001722 0.016032 0.999870 Corresp. Eulerian angles (theta1,theta2,theta3) 186.1313 0.9239 175.4308 Corresp. spherical polar angles (psi,phi,kappa) 87.2792 59.5070 358.1851 Corresp. rotation angle 1.8149 about axis -0.5069 -0.0475 0.8607 Corresp. quaternions 0.9999 -0.0080 -0.0008 0.0136 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3785 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.378526, square sum= 31.6653, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.16792 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 4.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.4.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.4.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 09:50:51 created by user: COOR>ATOM 1 P GUA A 1 4.994 -11.353 2.813 1.00 0.56 A COOR>ATOM 2 O1P GUA A 1 3.846 -11.693 3.691 1.00 1.40 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0233 -0.0018 0.0495) Rotation matrix = 0.971568 -0.047007 0.232046 -0.049225 -0.998781 0.003772 0.231586 -0.015087 -0.972698 Corresp. Eulerian angles (theta1,theta2,theta3) 86.2725 166.5806 89.0687 Corresp. spherical polar angles (psi,phi,kappa) 88.6115 173.2938 180.5442 Corresp. rotation angle 179.4558 about axis 0.9929 -0.0242 0.1167 Corresp. quaternions 0.0047 0.9929 -0.0242 0.1167 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3371 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.337080, square sum= 76.9225, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 0.804494 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0156 -0.0300 0.0841) Rotation matrix = 0.999944 -0.004826 0.009377 0.004774 0.999973 0.005571 -0.009403 -0.005525 0.999941 Corresp. Eulerian angles (theta1,theta2,theta3) 300.4389 0.6249 59.2860 Corresp. spherical polar angles (psi,phi,kappa) 142.0005 40.8646 0.6827 Corresp. rotation angle 0.6827 about axis 0.4656 -0.7880 -0.4028 Corresp. quaternions 1.0000 0.0028 -0.0047 -0.0024 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2801 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.280097, square sum= 35.7753, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.278726 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0086 -0.2580 -0.1385) Rotation matrix = 0.999624 0.024991 -0.011242 -0.025231 0.999446 -0.021719 0.010693 0.021995 0.999701 Corresp. Eulerian angles (theta1,theta2,theta3) 154.0728 1.4014 207.3663 Corresp. spherical polar angles (psi,phi,kappa) 108.2340 48.9635 357.9913 Corresp. rotation angle 2.0087 about axis -0.6236 0.3129 0.7164 Corresp. quaternions 0.9998 -0.0109 0.0055 0.0126 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3629 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.362943, square sum= 29.1118, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.29965 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 5.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.5.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.5.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 12:27:07 created by user: COOR>ATOM 1 P GUA A 1 7.102 -9.574 5.244 1.00 0.43 A COOR>ATOM 2 O1P GUA A 1 7.254 -10.978 5.708 1.00 1.25 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0077 0.0130 0.0458) Rotation matrix = 0.993523 0.107470 0.036907 0.085582 -0.921379 0.379127 0.074750 -0.373512 -0.924608 Corresp. Eulerian angles (theta1,theta2,theta3) 11.3170 157.6094 5.5601 Corresp. spherical polar angles (psi,phi,kappa) 92.8772 178.3342 202.1451 Corresp. rotation angle 157.8549 about axis 0.9983 0.0502 0.0290 Corresp. quaternions 0.1921 0.9797 0.0493 0.0285 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.8040 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.803979, square sum= 437.6011, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 1.45088 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.4160 -0.0765 -0.2108) Rotation matrix = 0.999040 -0.008030 -0.043066 0.008601 0.999877 0.013082 0.042956 -0.013440 0.998987 Corresp. Eulerian angles (theta1,theta2,theta3) 72.6262 2.5797 286.8972 Corresp. spherical polar angles (psi,phi,kappa) 19.9974 32.0898 2.6234 Corresp. rotation angle 2.6234 about axis 0.2897 0.9397 -0.1817 Corresp. quaternions 0.9997 0.0066 0.0215 -0.0042 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2932 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.293175, square sum= 39.1939, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.364677 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.8254 -0.2272 -1.1489) Rotation matrix = 0.985510 0.029796 0.166977 -0.016042 0.996410 -0.083124 -0.168855 0.079241 0.982451 Corresp. Eulerian angles (theta1,theta2,theta3) 244.8600 10.7500 116.4649 Corresp. spherical polar angles (psi,phi,kappa) 26.6735 15.7653 349.1689 Corresp. rotation angle 10.8311 about axis -0.4320 -0.8936 0.1220 Corresp. quaternions 0.9955 -0.0408 -0.0843 0.0115 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.4963 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.496335, square sum= 54.4431, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.54600 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 6.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.6.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.6.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 15:01:53 created by user: COOR>ATOM 1 P GUA A 1 -6.396 10.252 4.365 1.00 0.43 A COOR>ATOM 2 O1P GUA A 1 -6.429 11.714 4.626 1.00 1.52 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0132 -0.0132 0.0173) Rotation matrix = -0.994244 -0.055141 0.091860 -0.031419 0.969754 0.242055 -0.102429 0.237776 -0.965904 Corresp. Eulerian angles (theta1,theta2,theta3) 203.3053 164.9952 20.7817 Corresp. spherical polar angles (psi,phi,kappa) 172.9275 79.7739 174.3824 Corresp. rotation angle 174.3824 about axis 0.0219 -0.9924 -0.1212 Corresp. quaternions 0.0490 0.0218 -0.9912 -0.1210 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2579 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.257937, square sum= 45.0418, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 1.51741 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0419 0.0186 0.0810) Rotation matrix = 0.999936 0.000805 0.011319 -0.000824 0.999998 0.001651 -0.011318 -0.001661 0.999935 Corresp. Eulerian angles (theta1,theta2,theta3) 278.3475 0.6554 81.6992 Corresp. spherical polar angles (psi,phi,kappa) 9.2605 153.8146 359.3429 Corresp. rotation angle 0.6571 about axis 0.1444 -0.9870 0.0710 Corresp. quaternions 1.0000 0.0008 -0.0057 0.0004 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.1794 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.179374, square sum= 14.6718, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.396852 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0319 -0.1880 0.1232) Rotation matrix = 0.999434 0.009658 -0.032235 -0.009857 0.999933 -0.006010 0.032175 0.006324 0.999462 Corresp. Eulerian angles (theta1,theta2,theta3) 101.1206 1.8791 259.4386 Corresp. spherical polar angles (psi,phi,kappa) 160.2813 57.7039 358.0395 Corresp. rotation angle 1.9605 about axis -0.1803 0.9414 0.2852 Corresp. quaternions 0.9999 -0.0031 0.0161 0.0049 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2922 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.292202, square sum= 18.8694, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.63138 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 7.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.7.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.7.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 21:08:17 created by user: COOR>ATOM 1 P GUA A 1 -5.171 11.337 -1.790 1.00 0.45 A COOR>ATOM 2 O1P GUA A 1 -5.055 12.230 -2.972 1.00 0.80 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0073 0.0006 0.0002) Rotation matrix = -0.996537 0.077314 0.030618 0.064317 0.950009 -0.305527 -0.052709 -0.302500 -0.951691 Corresp. Eulerian angles (theta1,theta2,theta3) 350.1157 162.1180 174.2772 Corresp. spherical polar angles (psi,phi,kappa) 9.0987 76.8876 182.4183 Corresp. rotation angle 177.5817 about axis -0.0359 -0.9874 0.1540 Corresp. quaternions 0.0211 -0.0359 -0.9872 0.1540 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3333 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.333336, square sum= 75.2233, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 1.62852 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0196 -0.0129 0.0155) Rotation matrix = 0.999990 -0.003749 0.002505 0.003747 0.999993 0.000820 -0.002508 -0.000811 0.999997 Corresp. Eulerian angles (theta1,theta2,theta3) 287.9151 0.1510 71.8701 Corresp. spherical polar angles (psi,phi,kappa) 123.1624 77.7252 0.2625 Corresp. rotation angle 0.2625 about axis 0.1780 -0.5470 -0.8180 Corresp. quaternions 1.0000 0.0004 -0.0013 -0.0019 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3230 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.322971, square sum= 47.5654, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.501163 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0294 -0.2585 0.0361) Rotation matrix = 0.999647 0.025543 -0.007257 -0.025549 0.999673 -0.000835 0.007234 0.001021 0.999973 Corresp. Eulerian angles (theta1,theta2,theta3) 98.0306 0.4186 263.4332 Corresp. spherical polar angles (psi,phi,kappa) 105.8247 87.9196 358.4775 Corresp. rotation angle 1.5225 about axis -0.0349 0.2727 0.9615 Corresp. quaternions 0.9999 -0.0005 0.0036 0.0128 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3153 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.315324, square sum= 21.9738, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 1.73081 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 8.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.8.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.8.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 21:55:36 created by user: COOR>ATOM 1 P GUA A 1 -5.757 11.170 0.727 1.00 0.37 A COOR>ATOM 2 O1P GUA A 1 -6.108 11.350 -0.705 1.00 0.76 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0014 0.0222 0.0406) Rotation matrix = -0.998853 0.014676 0.045581 0.010796 0.996386 -0.084248 -0.046652 -0.083659 -0.995402 Corresp. Eulerian angles (theta1,theta2,theta3) 330.8538 174.5033 151.5853 Corresp. spherical polar angles (psi,phi,kappa) 2.4368 81.3738 182.6456 Corresp. rotation angle 177.3544 about axis -0.0064 -0.9991 0.0420 Corresp. quaternions 0.0231 -0.0064 -0.9988 0.0420 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.4461 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.446101, square sum= 134.7270, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 1.82753 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0446 0.1118 0.0956) Rotation matrix = 0.999857 0.009566 0.013951 -0.009506 0.999945 -0.004381 -0.013992 0.004248 0.999893 Corresp. Eulerian angles (theta1,theta2,theta3) 253.1106 0.8378 107.4358 Corresp. spherical polar angles (psi,phi,kappa) 36.8386 65.6536 358.9997 Corresp. rotation angle 1.0003 about axis -0.2472 -0.8003 0.5462 Corresp. quaternions 1.0000 -0.0022 -0.0070 0.0048 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3303 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.330275, square sum= 49.7413, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.610244 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.0007 -0.3505 0.2460) Rotation matrix = 0.998932 0.002501 -0.046136 -0.002203 0.999976 0.006519 0.046151 -0.006411 0.998914 Corresp. Eulerian angles (theta1,theta2,theta3) 82.0917 2.6706 278.0431 Corresp. spherical polar angles (psi,phi,kappa) 171.5202 160.0095 357.3260 Corresp. rotation angle 2.6740 about axis 0.1386 0.9891 0.0504 Corresp. quaternions 0.9997 0.0032 0.0231 0.0012 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.5276 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.527611, square sum= 61.5205, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 2.00918 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as true X-PLOR> evaluate ($count=$count+1) EVALUATE: symbol $COUNT set to 9.00000 (real) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") EVALUATE: symbol $FILENAME set to "average.9.pdb" (string) X-PLOR> coordinates initialize end COOR: selected main coordinates initialized X-PLOR> coordinates @@$filename ASSFIL: file average.9.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb" COOR>REMARK 5 DATE:17-Aug-96 22:42:39 created by user: COOR>ATOM 1 P GUA A 1 6.113 10.370 -3.809 1.00 0.44 A COOR>ATOM 2 O1P GUA A 1 5.071 10.431 -4.866 1.00 0.98 A X-PLOR> coordinates fit end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0076 -0.0071 0.0147) Rotation matrix = 0.985785 -0.068079 -0.153598 0.050250 0.991846 -0.117116 0.160319 0.107733 0.981168 Corresp. Eulerian angles (theta1,theta2,theta3) 123.9009 11.1369 232.6750 Corresp. spherical polar angles (psi,phi,kappa) 38.9868 152.2440 11.6499 Corresp. rotation angle 11.6499 about axis -0.5568 0.7773 -0.2930 Corresp. quaternions 0.9948 -0.0565 0.0789 -0.0297 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.6531 X-PLOR> coordinates rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.653130, square sum= 288.7937, denominator= 677.0000 X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) EVALUATE: symbol $RMSD_RMSD set to 2.25411 (real) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0691 0.0131 -0.0691) Rotation matrix = 0.999967 0.004680 -0.006653 -0.004757 0.999921 -0.011601 0.006599 0.011633 0.999911 Corresp. Eulerian angles (theta1,theta2,theta3) 150.4360 0.7663 209.8343 Corresp. spherical polar angles (psi,phi,kappa) 117.8540 22.1053 359.1874 Corresp. rotation angle 0.8126 about axis -0.8192 0.4672 0.3327 Corresp. quaternions 1.0000 -0.0058 0.0033 0.0024 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.2353 X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end SELRPN: 456 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.235313, square sum= 25.2498, denominator= 456.0000 X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.665617 (real) X-PLOR> coordinates fit selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 0.2355 0.6350 0.1136) Rotation matrix = 0.999005 -0.044044 0.007031 0.043622 0.997704 0.051800 -0.009297 -0.051442 0.998633 Corresp. Eulerian angles (theta1,theta2,theta3) 349.7561 2.9965 7.7300 Corresp. spherical polar angles (psi,phi,kappa) 96.8740 40.3356 3.9112 Corresp. rotation angle 3.9112 about axis 0.7568 -0.1197 -0.6426 Corresp. quaternions 0.9994 0.0258 -0.0041 -0.0219 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9958 X-PLOR> coordinates rms selection=(residue 8:14) end SELRPN: 221 atoms have been selected out of 677 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.995832, square sum= 219.1615, denominator= 221.0000 X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) EVALUATE: symbol $RMSD_RMSD_LOOP set to 3.00087 (real) X-PLOR>end loop main X-PLOR>while ($count < $nfile) loop main NEXTCD: condition evaluated as false X-PLOR> evaluate ($count=$count+1) X-PLOR> evaluate ($filename="average."+encode($count)+".pdb") X-PLOR> coordinates initialize end X-PLOR> coordinates @@$filename X-PLOR> coordinates fit end X-PLOR> coordinates rms end X-PLOR> evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2) X-PLOR> coordinates fit selection=(residue 1:7 or residue 15:21) end X-PLOR> coordinates rms selection=(residue 1:7 or residue 15:21) end X-PLOR> evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2) X-PLOR> coordinates fit selection=(residue 8:14) end X-PLOR> coordinates rms selection=(residue 8:14) end X-PLOR> evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2) X-PLOR>end loop main X-PLOR> X-PLOR>! RMS RMSD to the average structure X-PLOR> X-PLOR>evaluate ($rmsd_rmsd=sqrt($rmsd_rmsd / $nfile)) EVALUATE: symbol $RMSD_RMSD set to 0.500456 (real) X-PLOR>evaluate ($rmsd_rmsd_stem=sqrt($rmsd_rmsd_stem / $nfile)) EVALUATE: symbol $RMSD_RMSD_STEM set to 0.271951 (real) X-PLOR>evaluate ($rmsd_rmsd_loop=sqrt($rmsd_rmsd_loop / $nfile)) EVALUATE: symbol $RMSD_RMSD_LOOP set to 0.577434 (real) X-PLOR> X-PLOR>stop CSTACK: size= 40000 used= 227 current= 0 HEAP: maximum use= 196439 current use= 0 X-PLOR: total CPU time= 16.7131 s X-PLOR: entry time at 12:46:32 01-Sep-96 X-PLOR: exit time at 12:46:52 01-Sep-96