
 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)@comp34.ch.
                 Created on  5/28/12 at 12:16: 8 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=    -289.4554873     RMS force=    0.9176165522E-06
 OPTIM> Final energy  =    -290.4045790     RMS force=    0.9351010250E-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=     1331.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.00     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4958 Dev= 1.15% S= 12.89 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   0.78

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     499 steps. Energy=    -287.5574668       time=       0.39
 Minus side of path:                     577 steps. Energy=    -291.5930512       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.5574668 0.68079         -286.8766732  4.7164         -291.5930512   9.669   5.535   9.134   8.649
        *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      2 steps with      2 missing connections, weight=     1245.9    
 decide> The unconnected minima in the chain and their distances are:
     2        8.32     3     3        8.75     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= 0.4489 Dev= 0.40% S= 8.75 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   0.64

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     496 steps. Energy=    -287.5574668       time=       0.38
 Minus side of path:                     506 steps. Energy=    -287.0470275       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.5574668  1.0525         -286.5049347 0.54209         -287.0470275   3.817   3.694   3.232  24.444
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 6.1963 Dev= 0.13% S= 9.19 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.77

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     505 steps. Energy=    -288.7009795       time=       0.39
 Minus side of path:                     532 steps. Energy=    -289.4554873       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7009795  1.7636         -286.9373485  2.5181         -289.4554873   8.868   7.583   4.612  17.129
        *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      4 steps with      2 missing connections, weight=     735.19    
 decide> The unconnected minima in the chain and their distances are:
     2        8.77     4     3        3.92     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4076 Dev= 0.39% S= 9.16 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   0.72

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     501 steps. Energy=    -288.0325509       time=       0.39
 Minus side of path:                     518 steps. Energy=    -291.5930512       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.0325509 0.42880         -287.6037485  3.9893         -291.5930512   5.255   4.648   3.324  23.766
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2739 Dev= 0.12% S= 4.00 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   0.60

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     492 steps. Energy=    -287.5574668       time=       0.38
 Minus side of path:                     526 steps. Energy=    -289.0613803       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.5574668 0.15408         -287.4033860  1.6580         -289.0613803   5.265   4.457   5.830  13.550
        Known (#3)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     836.35    
 decide> The unconnected minima in the chain and their distances are:
     2        9.13     5     8        4.21     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4731 Dev= 0.34% S= 9.48 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   0.67

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     545 steps. Energy=    -298.7697561       time=       0.49
 Minus side of path:                     520 steps. Energy=    -287.0470275       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -298.7697561  13.231         -285.5383381  1.5087         -287.0470275   9.205   7.697   5.210  15.162
        *NEW* (Placed in 9)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0954 Dev= 0.01% S= 4.23 time= 0.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.57

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     532 steps. Energy=    -289.0613803       time=       0.42
 Minus side of path:                     488 steps. Energy=    -288.7009795       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.0613803 0.39813         -288.6632480 0.37731E-01     -288.7009795   4.296   4.215   2.296  34.401
        Known (#8)                                              Known (#6)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     980.78    
 decide> The unconnected minima in the chain and their distances are:
     2        9.94     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3115 Dev= 0.14% S= 10.37 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   1.13

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     533 steps. Energy=    -292.9542631       time=       0.44
 Minus side of path:                     523 steps. Energy=    -293.0679355       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.9542631  1.2104         -291.7438150  1.3241         -293.0679355   7.558   7.051   2.962  26.671
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1042.3    
 decide> The unconnected minima in the chain and their distances are:
     2       10.14     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2875 Dev= 0.74% S= 10.64 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.76

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     554 steps. Energy=    -290.8184962       time=       0.46
 Minus side of path:                     519 steps. Energy=    -288.0325509       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.8184962  4.1772         -286.6413048  1.3912         -288.0325509  10.293   6.414   6.052  13.055
        *NEW* (Placed in 12)                                    Known (#7)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1096.6    
 decide> The unconnected minima in the chain and their distances are:
     2        9.01    11    10        7.15     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.8973 Dev= 0.40% S= 9.28 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=   0.66

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     462 steps. Energy=    -290.4045790       time=       0.37
 Minus side of path:                     474 steps. Energy=    -291.9988926       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.4045790 0.59078E-01     -290.3455010  1.6534         -291.9988926   3.733   3.628   8.714   9.066
        Known (#2)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3018 Dev= 0.29% S= 7.34 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.75

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     493 steps. Energy=    -287.0470275       time=       0.39
 Minus side of path:                     535 steps. Energy=    -298.7697561       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.0470275 0.64456         -286.4024687  12.367         -298.7697561   9.131   7.957   5.135  15.384
        Known (#5)                                              Known (#9)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 13 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     434.14    
 decide> The unconnected minima in the chain and their distances are:
    13        7.57     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4609 Dev= 0.27% S= 7.85 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     513 steps. Energy=    -290.9350610       time=       0.40
 Minus side of path:                     503 steps. Energy=    -287.1591362       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.9350610  5.7437         -285.1913167  1.9678         -287.1591362   7.227   6.190   3.450  22.900
        *NEW* (Placed in 14)                                    *NEW* (Placed in 15)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 15 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     327.06    
 decide> The unconnected minima in the chain and their distances are:
    13        6.13    15    14        4.58     5 
 

 tryconnect> 70-iteration DNEB run for minima 13_F and 15_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.1516 Dev= 0.42% S= 6.37 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   0.85

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     490 steps. Energy=    -287.1591362       time=       0.38
 Minus side of path:                     532 steps. Energy=    -292.9542631       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.1591362 0.32470         -286.8344410  6.1198         -292.9542631   8.975   8.427   2.042  38.695
        Known (#15)                                             Known (#10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 14_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6525 Dev= 0.47% S= 4.91 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   0.60
 isnewts> transition state is the same as number       11 energy=     -286.4024686590
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 14 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     545 steps. Energy=    -298.7697561       time=       0.45
 Minus side of path:                     489 steps. Energy=    -287.0470275       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -298.7697561  12.367         -286.4024687 0.64456         -287.0470275   9.131   7.957   5.143  15.362
        Known (#9)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 15 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     451.14    
 decide> The unconnected minima in the chain and their distances are:
     2        6.37    15    14        4.58     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 15_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4630 Dev= 0.62% S= 6.71 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     489 steps. Energy=    -288.8534050       time=       0.38
 Minus side of path:                     503 steps. Energy=    -291.9988926       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.8534050  1.8684         -286.9850096  5.0139         -291.9988926   6.359   5.966   3.047  25.924
        *NEW* (Placed in 16)                                    Known (#13)
 Unconnected minimum 16 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 5_S and 14_U using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 350 RMS= 0.0660 Dev= 6.06% S= 7.05 time= 1.94
 Following    2 images are candidates for TS:    3    9  
 Converged to TS (number of iterations):          8
 Converged to TS (number of iterations):         23
 DNEB run yielded 2 true transition state(s) time=   1.13
 isnewts> transition state is the same as number       11 energy=     -286.4024686590
 tryconnect> Will not repeat search for TS      1 same as TS     11

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     507 steps. Energy=    -290.9350610       time=       0.40
 Minus side of path:                     507 steps. Energy=    -298.7697561       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.9350610 0.11508         -290.8199840  7.9498         -298.7697561   7.050   6.671   6.014  13.135
        Known (#14)                                             Known (#9)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 16 minima and 16 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      1 missing connections, weight=     262.48    
 decide> The unconnected minima in the chain and their distances are:
    13        6.40    11 
 

 tryconnect> 70-iteration DNEB run for minima 11_S and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1035 Dev= 0.04% S= 6.47 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   0.66

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     494 steps. Energy=    -293.0679355       time=       0.39
 Minus side of path:                     508 steps. Energy=    -291.9572083       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.0679355  1.3638         -291.7041160 0.25309         -291.9572083   7.415   6.470   3.298  23.956
        Known (#11)                                             *NEW* (Placed in 17)
 Unconnected minimum 17 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 17 minima and 17 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      1 missing connections, weight=     132.65    
 decide> The unconnected minima in the chain and their distances are:
    13        5.10    17 
 

 tryconnect> 70-iteration DNEB run for minima 13_F and 17_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0343 Dev= 0.01% S= 5.11 time= 0.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   0.45

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                     456 steps. Energy=    -291.9988926       time=       0.35
 Minus side of path:                     486 steps. Energy=    -291.9572083       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9988926 0.11442         -291.8844732 0.72735E-01     -291.9572083   5.133   5.100   2.275  34.727
        Known (#13)                                             Known (#17)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -289.4554873  2.5181        -286.9373485  1.7636        -288.7009795   8.868   7.583   4.612  17.129
   7     -288.7009795 0.37731E-01    -288.6632480 0.39813        -289.0613803   4.296   4.215   2.296  34.401
   5     -289.0613803  1.6580        -287.4033860 0.15408        -287.5574668   5.265   4.457   5.830  13.550
   2     -287.5574668  1.0525        -286.5049347 0.54209        -287.0470275   3.817   3.694   3.232  24.444
   6     -287.0470275  1.5087        -285.5383381  13.231        -298.7697561   9.205   7.697   5.210  15.162
  16     -298.7697561  7.9498        -290.8199840 0.11508        -290.9350610   7.050   6.671   6.014  13.135
  12     -290.9350610  5.7437        -285.1913167  1.9678        -287.1591362   7.227   6.190   3.450  22.900
  13     -287.1591362 0.32470        -286.8344410  6.1198        -292.9542631   8.975   8.427   2.042  38.695
   8     -292.9542631  1.2104        -291.7438150  1.3241        -293.0679355   7.558   7.051   2.962  26.671
  17     -293.0679355  1.3638        -291.7041160 0.25309        -291.9572083   7.415   6.470   3.298  23.956
  18     -291.9572083 0.72735E-01    -291.8844732 0.11442        -291.9988926   5.133   5.100   2.275  34.727
  10     -291.9988926  1.6534        -290.3455010 0.59078E-01    -290.4045790   3.733   3.628   8.714   9.066

 Number of TS in the path       =     12
 Number of cycles               =     12

 Elapsed time=                                32.98
 OPTIM> # of energy calls=                         92 time=           0.05 %=  0.1
 OPTIM> # of energy+gradient calls=             34808 time=          17.95 %= 54.4
 OPTIM> # of energy+gradient+Hessian calls=       511 time=           0.52 %=  1.6
