XPLOR-NIH version 2.9.5 
 
 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: 04-Jun-04 10:27:44
 X-PLOR>remarks PLANCONS 
 X-PLOR>remarks TEST CASE FOR PLANAR HARMONIC CONSTRAINTS 
 X-PLOR>remarks 
 X-PLOR> 
 X-PLOR>rtf @TOPPAR:toph11.pro end 
 ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened.
 RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) 
 RTFRDR>REMARKS ============================= 
 RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. 
 RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. 
 RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. 
 RTFRDR>REMARKS DNA/RNA atoms appended . 
 RTFRDR>REMARKS few atoms never referenced switched off. 
 RTFRDR>REMARKS Default for HIStidines is the doubly protonated state 
 RTFRDR> 
 RTFRDR>set echo=false end 
 RTFRDR> end 
 X-PLOR>parameter @TOPPAR:param11.pro end 
 ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened.
 PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) 
 PARRDR>REMARKS =========== 
 PARRDR>REMARKS PROTEIN PARAMETERS: 
 PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) 
 PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) 
 PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 
 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. 
 PARRDR>REMARKS                           JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 
 PARRDR>REMARKS 
 PARRDR>set echo=false end 
 PARRDR> end 
 X-PLOR> 
 X-PLOR>segment 
 SEGMENT>  name=main 
 SEGMENT>  setup=true 
 SEGMENT>  chain 
 CHAIN>     @TOPPAR:toph11.pep 
 ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened.
 CHAIN>REMARKS  TOPH11-MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN>     sequence 
 SEQUENCE>        TRP 
 MAPIC: Atom numbers being modified
 SEQUence-element (terminate with END) =     end 
 MAPIC: Atom numbers being modified
 CHAIN>  end 
 SEGMENT>end 
 SEGMNT:     1 residues were inserted into segment "MAIN"
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=         19(MAXA=         200)  NBOND=         20(MAXB=         100)
 NTHETA=        28(MAXT=         100)  NGRP=           6(MAXGRP=       100)
 NPHI=          10(MAXP=         100)  NIMPHI=        15(MAXIMP=       100)  
 NDON=           4(MAXPAD=       100)  NACC=           2(MAXPAD=       100)
 NNB=           36(MAXNB=        100) 
 X-PLOR> 
 X-PLOR>coor 
 COOR>  remarks TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, 
 COOR>  remarks AND CG 50 STEPS 
 COOR>  remarks EPS=R POTENTIAL 
 COOR>  natoms 19 
 COOR>    1      TRP  HT1    0.10124   0.57409  -1.38529 MAIN 1      0.00000 
 X-PLOR> 
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR>vector do (refx=x) (all) 
 SELRPN:     19 atoms have been selected out of     19
 X-PLOR>vector do (refy=y) (all) 
 SELRPN:     19 atoms have been selected out of     19
 X-PLOR>vector do (refz=z) (all) 
 SELRPN:     19 atoms have been selected out of     19
 X-PLOR> 
 X-PLOR>parameter 
 PARRDR>  hbonds 
 HBDSET>     acce=t don=4.7 doff=5.2 dcut=5.7 aon=50.0 aoff=70.0 acut=90.0 
 HBDSET>  end 
 %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given.  Reset.
 PARRDR>  nbonds 
 NBDSET>     atom cdie shift eps=1.0 
 NBDSET>          cutnb=30.0 ctonnb=99.0 ctofnb=99.0 
 NBDSET>     nbxmod 5 vswitch 
 NBDSET>  end 
 %NBDSET-ERR: inconsistent CTONNB, CTOFNB given. Reset.
 %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given.  Reset.
 PARRDR>end 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test harmonic point constraints *} 
 X-PLOR>{* =============================== *} 
 X-PLOR> 
 X-PLOR>flags exclude * include harm end 
 X-PLOR> 
 X-PLOR>constraints harmonic exponent 2 end 
 Obsolete syntax: please use REStraints HARMonic
 X-PLOR> 
 X-PLOR>vector do ( cons = 40.0 ) ( name ca ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )    40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR> 
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )      40.000000      40.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=     1 --------------------------------------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0014 -----------------------
 | Etotal =71.111     grad(E)=14.128     E(HARM)=71.111                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0111 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       1.472   1.192   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     0.000000, square sum=       0.0000, denominator=       1.0000
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test harmonic planar constraints *} 
 X-PLOR>{* ================================ *} 
 X-PLOR> 
 X-PLOR>flags exclude * include harm end 
 X-PLOR> 
 X-PLOR>{* test constrains parallel to elongation *} 
 X-PLOR>{* energy and gradient should be the same as above *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (1.0 0.5 1.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = -40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )   -40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=     2 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   -90.000    
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )      40.000000      40.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=     3 --------------------------------------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0014 -----------------------
 | Etotal =71.111     grad(E)=14.128     E(HARM)=71.111                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0111 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       1.472   1.192   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     0.000000, square sum=       0.0000, denominator=       1.0000
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test constrains perpenticular to elongation *} 
 X-PLOR>{* energy and gradient should be both zero *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (-0.5 1.0 0.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = -40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )   -40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=     4 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   -90.000    
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=     5 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test constrains parallel to z-direction *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (0.0 0.0 1.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = -40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )   -40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=     6 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   -90.000    
 X-PLOR>vector show (z) (name ca)   evaluate ($z = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    1.0273    
 EVALUATE: symbol $Z set to    1.02727     (real)
 X-PLOR>vector show (refz) (name ca)   evaluate ($zref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $ZREF set to   0.272700E-01 (real)
 X-PLOR>evaluate ($distance = $z - $zref) 
 EVALUATE: symbol $DISTANCE set to    1.00000     (real)
 X-PLOR>display $distance 
1
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=     7 --------------------------------------------------
 | Etotal =40.000     grad(E)=10.596     E(HARM)=40.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =40.000     grad(E)=10.596     E(HARM)=40.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0031 -----------------------
 | Etotal =22.500     grad(E)=7.947      E(HARM)=22.500                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0094 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.118034, square sum=       1.2500, denominator=       1.0000
 X-PLOR> 
 X-PLOR>vector show (z) (name ca)   evaluate ($z = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $Z set to   0.272700E-01 (real)
 X-PLOR>vector show (refz) (name ca)   evaluate ($zref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $ZREF set to   0.272700E-01 (real)
 X-PLOR>evaluate ($distance = $z - $zref) 
 EVALUATE: symbol $DISTANCE set to  -0.728584E-16 (real)
 X-PLOR>display $distance 
-7.285839E-17
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (0.0 0.0 1.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = -40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )   -40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=     8 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(-1.0 -0.5 -1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(    -1.000000   -0.500000   -1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       0.472   0.692  -0.973  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   -90.000    
 X-PLOR>vector show (z) (name ca)   evaluate ($z = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )  -0.97273    
 EVALUATE: symbol $Z set to  -0.972730     (real)
 X-PLOR>vector show (refz) (name ca)   evaluate ($zref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $ZREF set to   0.272700E-01 (real)
 X-PLOR>evaluate ($distance = $z - $zref) 
 EVALUATE: symbol $DISTANCE set to   -1.00000     (real)
 X-PLOR>display $distance 
-1
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )     -80.000000     -80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=     9 --------------------------------------------------
 | Etotal =40.000     grad(E)=10.596     E(HARM)=40.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =40.000     grad(E)=10.596     E(HARM)=40.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0031 -----------------------
 | Etotal =22.500     grad(E)=7.947      E(HARM)=22.500                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0094 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       0.472   0.692   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.118034, square sum=       1.2500, denominator=       1.0000
 X-PLOR> 
 X-PLOR>vector show (z) (name ca)   evaluate ($z = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $Z set to   0.272700E-01 (real)
 X-PLOR>vector show (refz) (name ca)   evaluate ($zref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   0.27270E-01
 EVALUATE: symbol $ZREF set to   0.272700E-01 (real)
 X-PLOR>evaluate ($distance = $z - $zref) 
 EVALUATE: symbol $DISTANCE set to   0.683481E-15 (real)
 X-PLOR>display $distance 
6.83481E-16
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test positive force constant *} 
 X-PLOR>{* energy and gradient should be the same as for point constrains *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (-0.5 1.0 0.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = 40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )    40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=    10 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    90.000    
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )      40.000000      40.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=    11 --------------------------------------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0014 -----------------------
 | Etotal =71.111     grad(E)=14.128     E(HARM)=71.111                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0111 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       1.472   1.192   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     0.000000, square sum=       0.0000, denominator=       1.0000
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* test positive and negative force constant *} 
 X-PLOR>{* energy and gradient should be the same as for point constrains *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (0.0 1.0 0.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = -40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector do ( cons = 40.0 ) ( name CE2 ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )   -40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    40.000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=    12 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca or name ce2 ) end 
 SELRPN:      2 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    9 X ( MAIN 1    TRP  CE2 )       0.000000       0.000000       0.000000
    9 Y ( MAIN 1    TRP  CE2 )       0.000000       0.000000       0.000000
    9 Z ( MAIN 1    TRP  CE2 )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca or name ce2) trans vector=(1.0 0.5 1.0) end 
 SELRPN:      2 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca or name ce2) end 
 SELRPN:      2 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
ATOM      9  CE2 TRP     1       6.424   0.490  -0.601  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ce2) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )   -90.000    
 X-PLOR>vector show (y) (name ca)   evaluate ($y = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    1.6919    
 EVALUATE: symbol $Y set to    1.69190     (real)
 X-PLOR>vector show (refy) (name ca)   evaluate ($yref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    1.1919    
 EVALUATE: symbol $YREF set to    1.19190     (real)
 X-PLOR>evaluate ($distance = $y - $yref) 
 EVALUATE: symbol $DISTANCE set to   0.500000     (real)
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )      40.000000      40.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=    13 --------------------------------------------------
 | Etotal =100.000    grad(E)=16.754     E(HARM)=100.000                       |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =100.000    grad(E)=16.754     E(HARM)=100.000                       |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0013 -----------------------
 | Etotal =81.000     grad(E)=15.079     E(HARM)=81.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0112 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>coor rms sele=(name ce2) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     0.000000, square sum=       0.0000, denominator=       1.0000
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.414214, square sum=       2.0000, denominator=       1.0000
 X-PLOR>vector show (y) (name ca)   evaluate ($y = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    1.1919    
 EVALUATE: symbol $Y set to    1.19190     (real)
 X-PLOR>vector show (refy) (name ca)   evaluate ($yref = $result) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    1.1919    
 EVALUATE: symbol $YREF set to    1.19190     (real)
 X-PLOR>evaluate ($distance = $y - $yref) 
 EVALUATE: symbol $DISTANCE set to    0.00000     (real)
 X-PLOR>display $distance 
0
 X-PLOR>write coor sele=(name ca or name ce2) end 
 SELRPN:      2 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.192   1.027  1.00  0.00      MAIN
ATOM      9  CE2 TRP     1       5.424  -0.010  -1.601  1.00  0.00      MAIN
END
 X-PLOR> 
 X-PLOR>coor swap end 
 COOR: selected coordinates swaped (main<->comp)
 X-PLOR>coor copy end 
 COOR: selected main coordinates copied to comp
 X-PLOR> 
 X-PLOR>vector do ( cons = 0.0 ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{* turn off planar constrains, resulting in point constrains *} 
 X-PLOR>{* energy and gradient should be the same as for point constrains *} 
 X-PLOR>constraints 
 CONS>	harmonic exponent 2 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	normal = (0.0 0.0 0.0) 
 Obsolete syntax: please use REStraints HARMonic
 CONS>	? 

 FIX :    0 atoms fixed
 INTE:   1 active double selections
 --------------- double selection      1 ---------------------------------------
 | WEIGhts :                                                                   |
 | E(HARM)=1.000                                                               |
 -------------------------------------------------------------------------------
 CONS>end 
 X-PLOR> 
 X-PLOR>vector do ( cons = 40.0 ) ( name CA ) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show element ( cons ) ( all ) 
 SELRPN:     19 atoms have been selected out of     19
 ( MAIN TRP  1    HT1  )    0.0000    
 ( MAIN TRP  1    HT2  )    0.0000    
 ( MAIN TRP  1    N    )    0.0000    
 ( MAIN TRP  1    HT3  )    0.0000    
 ( MAIN TRP  1    CA   )    40.000    
 ( MAIN TRP  1    CB   )    0.0000    
 ( MAIN TRP  1    CG   )    0.0000    
 ( MAIN TRP  1    CD2  )    0.0000    
 ( MAIN TRP  1    CE2  )    0.0000    
 ( MAIN TRP  1    CE3  )    0.0000    
 ( MAIN TRP  1    CD1  )    0.0000    
 ( MAIN TRP  1    NE1  )    0.0000    
 ( MAIN TRP  1    HE1  )    0.0000    
 ( MAIN TRP  1    CZ2  )    0.0000    
 ( MAIN TRP  1    CZ3  )    0.0000    
 ( MAIN TRP  1    CH2  )    0.0000    
 ( MAIN TRP  1    C    )    0.0000    
 ( MAIN TRP  1    OT1  )    0.0000    
 ( MAIN TRP  1    OT2  )    0.0000    
 X-PLOR>energy end 
 --------------- cycle=    14 --------------------------------------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )       0.000000       0.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR> 
 X-PLOR>coor sele=(name ca) trans vector=(1.0 0.5 1.0 ) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: translation vector =(     1.000000    0.500000    1.000000 )
 COOR: selected coordinates translated
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       2.472   1.692   1.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     1.500000, square sum=       2.2500, denominator=       1.0000
 X-PLOR>evaluate ($elong=$result) 
 EVALUATE: symbol $ELONG set to    1.50000     (real)
 X-PLOR>vector do (bcomp = cons * $elong * $elong) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 X-PLOR>vector show (bcomp) (name ca) 
 SELRPN:      1 atoms have been selected out of     19
 ( MAIN TRP  1    CA   )    90.000    
 X-PLOR> 
 X-PLOR>test first tol=0.0 sele=( name ca ) end 
 SELRPN:      1 atoms have been selected out of     19
 TESTFD: Parameters: STEP=   0.00500  MASSweighting=F
 TESTFD: The following first derivatives differ by more than TOL=    0.000000

  DIM.         ATOM                 ANALYTIC        FINITE-DIFF     DEVIATION
    5 X ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
    5 Y ( MAIN 1    TRP  CA  )      40.000000      40.000000       0.000000
    5 Z ( MAIN 1    TRP  CA  )      80.000000      80.000000       0.000000
 TESTFD: A total of     0 elements were within the tolerance
 X-PLOR>energy end 
 --------------- cycle=    15 --------------------------------------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 X-PLOR> 
 X-PLOR> 
 X-PLOR>minimize powell nstep=30 step=20 end 
 POWELL: number of degrees of freedom=    57
 --------------- cycle=     1 ------ stepsize=    0.0000 -----------------------
 | Etotal =90.000     grad(E)=15.894     E(HARM)=90.000                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     2 ------ stepsize=    0.0014 -----------------------
 | Etotal =71.111     grad(E)=14.128     E(HARM)=71.111                        |
 -------------------------------------------------------------------------------
 --------------- cycle=     3 ------ stepsize=    0.0111 -----------------------
 | Etotal =0.000      grad(E)=0.000      E(HARM)=0.000                         |
 -------------------------------------------------------------------------------
 POWELL: Gradient converged. Normal termination
 POWELL: Current coordinates set to last minimum
 X-PLOR>write coor sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 CWRITE: using atom subset.
REMARK FILENAME="OUTPUT"
REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP,
REMARK AND CG 50 STEPS
REMARK EPS=R POTENTIAL
REMARK DATE:04-Jun-04  10:27:44       created by user: [unknown]
ATOM      5  CA  TRP     1       1.472   1.192   0.027  1.00  0.00      MAIN
END
 X-PLOR>coor rms sele=(name ca) end 
 SELRPN:      1 atoms have been selected out of     19
 COOR: using atom subset.
 COOR: ATTENTION: atom rms differences copied to RMSD array. 
 COOR: rms=     0.000000, square sum=       0.0000, denominator=       1.0000
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>stop 
 HEAP:   maximum use=   898354 current use=   868147
 X-PLOR: total CPU time=      0.1800 s
 X-PLOR: entry time at 10:27:44 04-Jun-04
 X-PLOR: exit time at 10:27:44 04-Jun-04