
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> Number of atoms (or variables)  determined as     79
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     8
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp31.ch.
                 Created on  5/28/12 at 12:17:21 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  237 Cartesian coordinates will be optimised for   79 CHARMM atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 natintsetup, NATOMS           79
 cartres            7
 KeyInt>> Using natural internal coordinates. # of coords =        231
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         44      2388
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -291.9888919     RMS force=    0.8268950613E-06
 OPTIM> Final energy  =    -293.0137940     RMS force=    0.9962870345E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3136.6    
 decide> The unconnected minima in the chain and their distances are:
     2       14.64     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 140 RMS= 1.1231 Dev= 1.50% S= 19.50 time= 0.37
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   0.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     603 steps. Energy=    -295.4782402       time=       0.53
 Minus side of path:                     463 steps. Energy=    -288.1210541       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  7.4548         -288.0234243 0.97630E-01     -288.1210541   7.506   6.053  13.562   5.825
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1338.1    
 decide> The unconnected minima in the chain and their distances are:
     2        8.03     3     4        9.36     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6668 Dev= 1.38% S= 10.37 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   1.42

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     461 steps. Energy=    -293.0137940       time=       0.37
 Minus side of path:                     451 steps. Energy=    -292.9163912       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.0137940 0.47344         -292.5403586 0.37603         -292.9163912   2.602   2.531  26.025   3.035
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6384 Dev= 0.77% S= 10.24 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     504 steps. Energy=    -286.6147584       time=       0.42
 Minus side of path:                     482 steps. Energy=    -291.9888919       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -286.6147584 0.74747         -285.8672920  6.1216         -291.9888919   5.731   4.967  11.750   6.723
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1166.7    
 decide> The unconnected minima in the chain and their distances are:
     5        8.70     3     4        7.98     6 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.1805 Dev= 1.22% S= 11.03 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   0.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     481 steps. Energy=    -292.8974138       time=       0.39
 Minus side of path:                     476 steps. Energy=    -293.0073751       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.8974138 0.90463         -291.9927875  1.0146         -293.0073751   2.875   2.713  28.349   2.787
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.5958 Dev= 1.34% S= 8.49 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   0.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     586 steps. Energy=    -289.5801670       time=       0.51
 Minus side of path:                     507 steps. Energy=    -286.6147584       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.5801670  4.5628         -285.0173220  1.5974         -286.6147584  11.538   9.724   4.427  17.845
        *NEW* (Placed in 9)                                     Known (#6)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     1370.7    
 decide> The unconnected minima in the chain and their distances are:
     5        1.80     7     8        7.03     3     4        7.98     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0163 Dev= 0.00% S= 1.80 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   0.42

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     447 steps. Energy=    -292.9163912       time=       0.36
 Minus side of path:                     472 steps. Energy=    -292.8974138       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.9163912 0.36718E-01     -292.8796729 0.17741E-01     -292.8974138   1.807   1.799  10.058   7.855
        Known (#5)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8992 Dev= 1.33% S= 9.50 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        202
 DNEB run yielded 1 true transition state(s) time=   4.14
 isnewts> transition state is the same as number        2 energy=     -292.5403585597
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     472 steps. Energy=    -292.9163912       time=       0.38
 Minus side of path:                     462 steps. Energy=    -293.0137940       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.9163912 0.37603         -292.5403586 0.47344         -293.0137940   2.602   2.531  25.912   3.049
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> 630-iteration DNEB run for minima 4_U and 6_S using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 630 RMS= 0.4685 Dev= 5.09% S= 13.35 time= 6.66
 Following    4 images are candidates for TS:    2   10   13   15  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         17
 DNEB run yielded 4 true transition state(s) time=   2.53
 isnewts> transition state is the same as number        1 energy=     -288.0234242566
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        5 energy=     -285.0173219810
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        5 energy=     -285.0173219810
 tryconnect> Will not repeat search for TS      4 same as TS      5

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     593 steps. Energy=    -295.4782402       time=       0.52
 Minus side of path:                     508 steps. Energy=    -288.1210541       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  7.4548         -288.0234243 0.97630E-01     -288.1210541   7.508   6.056  13.558   5.827
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     468 steps. Energy=    -296.0213034       time=       0.38
 Minus side of path:                     476 steps. Energy=    -289.7633958       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.0213034  7.8598         -288.1615197  1.6019         -289.7633958   5.494   3.484   2.458  32.142
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     605 steps. Energy=    -289.5801670       time=       0.53
 Minus side of path:                     505 steps. Energy=    -286.6147584       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.5801670  4.5628         -285.0173220  1.5974         -286.6147584  11.538   9.724   4.410  17.915
        Known (#9)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     1039.2    
 decide> The unconnected minima in the chain and their distances are:
     7        7.75     3     4        7.48    10    11        5.38     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.6105 Dev= 1.10% S= 10.08 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   0.71
 isnewts> transition state is the same as number        4 energy=     -291.9927874631
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 11 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     491 steps. Energy=    -292.8974138       time=       0.40
 Minus side of path:                     492 steps. Energy=    -293.0073751       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.8974138 0.90463         -291.9927875  1.0146         -293.0073751   2.875   2.713  28.315   2.790
        Known (#7)                                              Known (#8)
 Alternative path found between members of the F set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5264 Dev= 1.18% S= 8.11 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   0.64
 isnewts> transition state is the same as number        1 energy=     -288.0234242566
 tryconnect> Will not repeat search for TS      1 same as TS      1

 tryconnect> 70-iteration DNEB run for minima 1_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2559 Dev= 0.76% S= 5.65 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   0.52

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     500 steps. Energy=    -291.9888919       time=       0.41
 Minus side of path:                     476 steps. Energy=    -289.7633958       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9888919  3.2764         -288.7124777  1.0509         -289.7633958   7.176   5.378   6.328  12.484
        Known (#1)                                              Known (#11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1193.0    
 decide> The unconnected minima in the chain and their distances are:
     8        7.03     3     4        7.92    11 
 

 tryconnect> 560-iteration DNEB run for minima 3_U and 8_F using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      63.85477290    
 Double-ended search iterations= 560 RMS= 0.6740 Dev= 4.68% S= 11.55 time= 5.25
 Following    2 images are candidates for TS:    6   15  
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=   1.51

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     546 steps. Energy=    -295.4782402       time=       0.46
 Minus side of path:                     471 steps. Energy=    -292.9103502       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  4.1581         -291.3201744  1.5902         -292.9103502   8.216   6.229   4.850  16.290
        Known (#3)                                              *NEW* (Placed in 12)
 Connection established between members of the U set.

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     514 steps. Energy=    -295.4782402       time=       0.43
 Minus side of path:                     451 steps. Energy=    -293.0137940       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  6.4406         -289.0376233  3.9762         -293.0137940   7.281   6.480   5.251  15.045
        *NEW* (Placed in 13)                                    Known (#2)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.1523 Dev= 1.29% S= 8.64 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.70

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     551 steps. Energy=    -295.4782402       time=       0.47
 Minus side of path:                     476 steps. Energy=    -296.0011985       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  7.3149         -288.1633300  7.8379         -296.0011985  10.552   8.662  15.114   5.227
        Known (#3)                                              *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 15 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     133.10    
 decide> The unconnected minima in the chain and their distances are:
    13        4.79     3    14        2.84    10 
 

 checkpair> Energies of the minima in the pair     3   13 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 3_U and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.7739 Dev= 0.77% S= 7.52 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   1.18

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     534 steps. Energy=    -295.4782402       time=       0.45
 Minus side of path:                     488 steps. Energy=    -292.9103502       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  4.1581         -291.3201744  1.5902         -292.9103502   8.215   6.229   4.852  16.283
        Known (#13)                                             *NEW* (Placed in 15)
 Unconnected minimum 15 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 10_S and 14_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0241 Dev= 0.03% S= 2.85 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):          8
 DNEB run yielded 1 true transition state(s) time=   0.41

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     459 steps. Energy=    -296.0213034       time=       0.37
 Minus side of path:                     473 steps. Energy=    -296.0011985       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.0213034 0.25455         -295.7667496 0.23445         -296.0011985   2.880   2.844   2.214  35.687
        Known (#10)                                             Known (#14)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 15 minima and 17 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     110.20    
 decide> The unconnected minima in the chain and their distances are:
    15        4.79    12 
 

 checkpair> Energies of the minima in the pair    12   15 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 12_S and 15_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8094 Dev= 1.02% S= 7.54 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   0.82

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                     550 steps. Energy=    -295.4782402       time=       0.47
 Minus side of path:                     536 steps. Energy=    -292.9103502       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.4782402  4.6833         -290.7949651  2.1154         -292.9103502  13.738   7.745   7.444  10.613
        Known (#3)                                              Known (#15)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -291.9888919  3.2764        -288.7124777  1.0509        -289.7633958   7.176   5.378   6.328  12.484
   9     -289.7633958  1.6019        -288.1615197  7.8598        -296.0213034   5.494   3.484   2.458  32.142
  17     -296.0213034 0.25455        -295.7667496 0.23445        -296.0011985   2.880   2.844   2.214  35.687
  15     -296.0011985  7.8379        -288.1633300  7.3149        -295.4782402  10.552   8.662  15.114   5.227
  18     -295.4782402  4.6833        -290.7949651  2.1154        -292.9103502  13.738   7.745   7.444  10.613
  16     -292.9103502  1.5902        -291.3201744  4.1581        -295.4782402   8.215   6.229   4.852  16.283
  14     -295.4782402  6.4406        -289.0376233  3.9762        -293.0137940   7.281   6.480   5.251  15.045

 Number of TS in the path       =      7
 Number of cycles               =      8

 Elapsed time=                                47.74
 OPTIM> # of energy calls=                        128 time=           0.07 %=  0.2
 OPTIM> # of energy+gradient calls=             52242 time=          29.03 %= 60.8
 OPTIM> # of energy+gradient+Hessian calls=       777 time=           0.85 %=  1.8
