[Alisha-Joness-MacBook-Pro:solvethestructure/xplor-nih-2.33/181TAR] jonesy% xplor RNA_anneal.inp 
		       Xplor-NIH version 2.33 
 
 C.D. Schwieters, J.J.  Kuszewski,       Progr. NMR Spectr. 48, 47-62 (2006). 
 N. Tjandra, and G.M. Clore              J. Magn. Res., 160, 66-74 (2003). 
 http://nmr.cit.nih.gov/xplor-nih        based on X-PLOR 3.851 by A.T. Brunger 

 User: jonesy       on: d-128-208-(darwin/x86_64 )  at: 08-May-13 14:22:49
X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR> EVALUATE: symbol $NUMSTRUCTS set to    5.00000     (real)
X-PLOR> EVALUATE: symbol $RANDOMSEED set to    785.000     (real)
X-PLOR> EVALUATE: symbol $USE_GRAPHICS set to FALSE (logical)
X-PLOR> EVALUATE: symbol $MAXRESID set to    56.0000     (real)
X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR> X-PLOR>eval ($proc_num=0) 
 EVALUATE: symbol $PROC_NUM set to    0.00000     (real)
 X-PLOR>end 
 X-PLOR>cpyth "xplor.command('eval ($num_procs=%s)' % env['XPLOR_NUM_PROCESSES'])" 
 X-PLOR>eval ($num_procs=1) 
 EVALUATE: symbol $NUM_PROCS set to    1.00000     (real)
 X-PLOR>end 
 X-PLOR>eval ($num_procs=min($num_procs,$numStructs)) 
 EVALUATE: symbol $NUM_PROCS set to    1.00000     (real)
 X-PLOR>if ( $proc_num >= $num_procs ) then  stop end if 
 NEXTCD: condition evaluated as false
 X-PLOR>eval ($firstStruct = int($proc_num * $numStructs / $num_procs)) 
 EVALUATE: symbol $FIRSTSTRUCT set to    0.00000     (real)
 X-PLOR>eval ($lastStruct  = int(($proc_num+1)  * $numStructs / $num_procs)) 
 EVALUATE: symbol $LASTSTRUCT set to    5.00000     (real)
 X-PLOR>! 
 X-PLOR>! read in the PSF and initial PDB files 
 X-PLOR>! 
 X-PLOR>parameter @TOPPAR:nucleic.par end 
 ASSFIL: file /Users/jonesy/Desktop/solvethestructure/xplor-nih-2.33/toppar/nucleic.par opened.
 PARRDR>! 
 PARRDR>! xplor-nih nucleic acid parameter file, version 1.1 
 PARRDR>! 
 PARRDR>! This file is intended to work with the topology file nucleic-1.1.top 
 PARRDR>! 
 PARRDR>! This is a re-named and fixed copy of the file parnah1er1_mod_new.inp 
 PARRDR>! 
 PARRDR>! We've created this new filename in order to eliminate confusion 
 PARRDR>! between the various parameter/topology combinations that ship 
 PARRDR>! with xplor-nih.  It has version numbers, and will be updated 
 PARRDR>! along with the rest of the xplor-nih package. 
 PARRDR>! 
 PARRDR>! chemical types have been named such that mixed protein/nucleic acid 
 PARRDR>! refinements are possible. 
 PARRDR>! 
 PARRDR>! If you find errors, PLEASE let us know. 
 PARRDR>! 
 PARRDR> 
 PARRDR>remark  NUCLEIC ACID PARAMETER FILE CREATION RUN 
 PARRDR>remark  >>>NO WARRANTY EXPRESSED OR IMPLIED<<< 
 PARRDR>remark 
 PARRDR>remark  ALL HYDROGEN NUCLEIC ACID PARAMETER FILE. 
 PARRDR>remark  DERIVED FROM PARMDNA8. LN and MP 1984 
 PARRDR>remark  H-bond wells made 0.5 kcal deeper to improve basepair energies 8/20/84/ln 
 PARRDR>remark  H stretch & bend constants from URACIL normal mode fit. 
 PARRDR>remark  Magnesium (fudge) and spermine included. 
 PARRDR>remark  all references to water removed, ATB, 3-JAN-85 
 PARRDR>remark  ALL IMPROPERS force constants increased to 500 to 
 PARRDR>remark  ensure perfect planes and chirality: GMC 1987 
 PARRDR>remark  DIHEDRAL force constants that keep purin rings parallel 
 PARRDR>remark  increased to 500 (MN 7-NOV-86) 
 PARRDR>remark  includes parameters for purine GMC 1987 
 PARRDR>remark  included impropers for chirality  from parallhdg.dna (CDS 2005/11/03) 
 PARRDR>set echo=false mess=off end 
 PARRDR> end 
 X-PLOR>parameter @TOPPAR:protein.par end 
 ASSFIL: file /Users/jonesy/Desktop/solvethestructure/xplor-nih-2.33/toppar/protein.par opened.
 PARRDR>! 
 PARRDR>! xplor-nih protein parameter file, version 1.0 
 PARRDR>! 
 PARRDR>! This file is intended to work with the topology file protein-1.0.top 
 PARRDR>! 
 PARRDR>! This is a re-named copy of the file parallhdg_procheck.pro 
 PARRDR>! 
 PARRDR>! We've created this new filename in order to eliminate confusion 
 PARRDR>! between the various parameter/topology combinations that ship 
 PARRDR>! with xplor-nih.  It has version numbers, and will be updated 
 PARRDR>! along with the rest of the xplor-nih package. 
 PARRDR>! 
 PARRDR>! Its backbone bond lengths and angles are designed to agree with 
 PARRDR>! the Engh & Huber parameter set (reference below), which is used by 
 PARRDR>! PROCHECK, among other structure-validation programs. 
 PARRDR>! 
 PARRDR>! If you find errors, PLEASE let us know. 
 PARRDR>! 
 PARRDR> 
 PARRDR> 
 PARRDR> 
 PARRDR> 
 PARRDR>remark file protein-1.0.par 
 PARRDR>remark Changed version of parallhdg_new.pro so that the bond lengths and angles 
 PARRDR>remark agree with what PROCHECK expects. 
 PARRDR>remark JJK 9/14/98 
 PARRDR> 
 PARRDR>!   file parallhdg_new.pro 
 PARRDR>!   geometric energy function parameters for distance geometry and 
 PARRDR>!   simulated annealing.  Modified by G.M.C. to have sigma's of Param19x and parafloat 
 PARRDR> 
 PARRDR>set message off echo off end 
 PARRDR> end 
 X-PLOR>structure @cmplx3.tmplt.pdb end 
 ASSFIL: file cmplx3.tmplt.pdb opened.
 STRUcture>REMARK FILENAME="cmplx3.tmplt.pdb" 
 STRUcture>REMARK produced by nmr/generate_template.inp 
 STRUcture>REMARK DATE:02-May-13  13:17:19       created by user: jonesy 
 STRUcture>ATOM      1  N   DAB     1      13.356  -4.230  -4.022  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N 
              ^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356  -4.230 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356  -4.230  -4.022 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356  -4.230  -4.022  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356  -4.230  -4.022  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      1  N   DAB     1      13.356  -4.230  -4.022  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      2  HT1 DAB     1      13.834  -3.594  -4.693  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 
              ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834  -3.594 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834  -3.594  -4.693 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834  -3.594  -4.693  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834  -3.594  -4.693  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      2  HT1 DAB     1      13.834  -3.594  -4.693  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      3  HT2 DAB     1      12.524  -4.651  -4.483  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 
              ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524  -4.651 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524  -4.651  -4.483 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524  -4.651  -4.483  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524  -4.651  -4.483  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      3  HT2 DAB     1      12.524  -4.651  -4.483  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      4  HT3 DAB     1      14.014  -4.980  -3.737  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 
              ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014  -4.980 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014  -4.980  -3.737 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014  -4.980  -3.737  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014  -4.980  -3.737  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      4  HT3 DAB     1      14.014  -4.980  -3.737  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      5  CA  DAB     1      12.926  -3.441  -2.817  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA 
              ^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926  -3.441 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926  -3.441  -2.817 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926  -3.441  -2.817  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926  -3.441  -2.817  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      5  CA  DAB     1      12.926  -3.441  -2.817  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      6  HA  DAB     1      13.726  -3.353  -2.152  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA 
              ^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726  -3.353 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726  -3.353  -2.152 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726  -3.353  -2.152  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726  -3.353  -2.152  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      6  HA  DAB     1      13.726  -3.353  -2.152  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      7  CB  DAB     1      12.533  -2.034  -3.290  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB 
              ^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533  -2.034 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533  -2.034  -3.290 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533  -2.034  -3.290  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533  -2.034  -3.290  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      7  CB  DAB     1      12.533  -2.034  -3.290  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      8  HB1 DAB     1      13.295  -1.344  -3.020  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 
              ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295  -1.344 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295  -1.344  -3.020 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295  -1.344  -3.020  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295  -1.344  -3.020  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      8  HB1 DAB     1      13.295  -1.344  -3.020  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM      9  HB2 DAB     1      11.612  -1.741  -2.809  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9 
           ^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 
              ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB 
                  ^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1 
                          ^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612 
                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612  -1.741 
                                         ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612  -1.741  -2.809 
                                                 ^^^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612  -1.741  -2.809  1.00 
                                                         ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612  -1.741  -2.809  1.00  0.00 
                                                               ^^^^
 %STRUcture-ERR: unrecognized command:
 ATOM      9  HB2 DAB     1      11.612  -1.741  -2.809  1.00  0.00      JB18 
                                                                         ^^^^
 STRUcture>ATOM     10  CG  DAB     1      12.333  -2.003  -4.812  1.00  0.00      JB18 
 %STRUcture-ERR: unrecognized command:
 ATOM 
 ^^^^
 %PARSER-ERR: Too many parsing errors --> termination
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating