
 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)@comp35.ch.
                 Created on  5/28/12 at 12:20:50 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=    -294.5470669     RMS force=    0.8363359227E-06
 OPTIM> Final energy  =    -296.8912080     RMS force=    0.9536360059E-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=     12058.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.93     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.3711 Dev= 2.12% S= 30.54 time= 0.71
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         73
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time=   2.26

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     540 steps. Energy=    -292.4977479       time=       0.43
 Minus side of path:                     592 steps. Energy=    -297.3730826       time=       0.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.4977479  2.2232         -290.2745236  7.0986         -297.3730826  22.704  17.581   2.154  36.682
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     549 steps. Energy=    -296.4211694       time=       0.43
 Minus side of path:                     523 steps. Energy=    -296.8912080       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.4211694  2.5544         -293.8667956  3.0244         -296.8912080  10.692   8.216   9.705   8.140
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     3511.2    
 decide> The unconnected minima in the chain and their distances are:
     2        4.79     6     6       11.27     3     4       12.53     1 
 

 checkpair> Energies of the minima in the pair     2    6 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4420 Dev= 1.18% S= 7.34 time= 0.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   0.81

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     532 steps. Energy=    -296.4211694       time=       0.41
 Minus side of path:                     534 steps. Energy=    -296.8912080       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.4211694  2.3694         -294.0517830  2.8394         -296.8912080   7.606   6.865   5.609  14.084
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3914 Dev= 1.62% S= 14.37 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   0.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     522 steps. Energy=    -289.5298295       time=       0.39
 Minus side of path:                     577 steps. Energy=    -296.8912080       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.5298295  1.1468         -288.3830094  8.5082         -296.8912080  11.318   9.029   4.844  16.308
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 2.7576 Dev= 0.74% S= 13.14 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   1.32

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     475 steps. Energy=    -297.3730826       time=       0.37
 Minus side of path:                     517 steps. Energy=    -298.0373891       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.3730826  2.7306         -294.6424905  3.3949         -298.0373891  11.383   9.158   6.192  12.758
        Known (#4)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2171.4    
 decide> The unconnected minima in the chain and their distances are:
     5       11.32     3     8        8.97     1 
 

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.5790 Dev= 1.13% S= 15.80 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        126
 DNEB run yielded 1 true transition state(s) time=   2.05

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     807 steps. Energy=    -297.9531561       time=       0.74
 Minus side of path:                     629 steps. Energy=    -296.8042814       time=       0.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.9531561  12.302         -285.6513576  11.153         -296.8042814  32.526  20.278   2.083  37.929
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2887 Dev= 0.22% S= 9.47 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.69

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     498 steps. Energy=    -294.5470669       time=       0.39
 Minus side of path:                     528 steps. Energy=    -298.7697561       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.5470669 0.77845         -293.7686124  5.0011         -298.7697561   6.632   5.872   4.565  17.305
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     2125.8    
 decide> The unconnected minima in the chain and their distances are:
     6        6.02     9     9       11.31     3     8        7.73    11 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1486 Dev= 0.01% S= 6.16 time= 0.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.50

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     534 steps. Energy=    -297.9531561       time=       0.42
 Minus side of path:                     513 steps. Energy=    -296.8912080       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.9531561  1.0866         -296.8665492 0.24659E-01     -296.8912080   6.146   6.024  13.951   5.663
        Known (#9)                                              Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5496 Dev= 1.47% S= 14.24 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   0.80

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     522 steps. Energy=    -290.5381784       time=       0.40
 Minus side of path:                     532 steps. Energy=    -297.9531561       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5381784  1.2288         -289.3094235  8.6437         -297.9531561   9.869   8.082   6.655  11.871
        *NEW* (Placed in 12)                                    Known (#9)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6097 Dev= 0.10% S= 7.95 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   0.73

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     514 steps. Energy=    -299.2840590       time=       0.43
 Minus side of path:                     500 steps. Energy=    -298.0373891       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -299.2840590  1.9736         -297.3104763 0.72691         -298.0373891   8.401   7.357   3.427  23.051
        *NEW* (Placed in 13)                                    Known (#8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     1877.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.18     3    13        4.12    11 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.2536 Dev= 1.39% S= 16.44 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   1.46

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     600 steps. Energy=    -291.5130163       time=       0.48
 Minus side of path:                     576 steps. Energy=    -296.4211694       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.5130163  5.4436         -286.0694157  10.352         -296.4211694  17.455   9.156   6.485  12.182
        *NEW* (Placed in 14)                                    Known (#5)
 Unconnected minimum 14 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 11_S and 13_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2525 Dev= 0.29% S= 4.37 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=   0.60

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     497 steps. Energy=    -299.2840590       time=       0.39
 Minus side of path:                     446 steps. Energy=    -298.7697561       time=       0.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -299.2840590 0.66482         -298.6192385 0.15052         -298.7697561   5.043   4.119  19.162   4.123
        Known (#13)                                             Known (#11)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     2156.2    
 decide> The unconnected minima in the chain and their distances are:
     7       12.92     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.1484 Dev= 0.23% S= 13.48 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   1.10

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     556 steps. Energy=    -289.5298295       time=       0.43
 Minus side of path:                     830 steps. Energy=    -297.5068749       time=       0.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.5298295 0.43333         -289.0965009  8.4104         -297.5068749  26.131  21.054   2.213  35.701
        Known (#7)                                              *NEW* (Placed in 15)
 Unconnected minimum 15 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 15 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     2387.2    
 decide> The unconnected minima in the chain and their distances are:
    12       13.36     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 12_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.9775 Dev= 0.36% S= 14.17 time= 0.33
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   0.94

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     556 steps. Energy=    -290.5381784       time=       0.43
 Minus side of path:                     722 steps. Energy=    -297.5068749       time=       0.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5381784 0.39595         -290.1422331  7.3646         -297.5068749  26.471  21.013   2.274  34.734
        Known (#12)                                             Known (#15)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 15 minima and 14 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2746.9    
 decide> The unconnected minima in the chain and their distances are:
    14       14.00     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 14_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.4403 Dev= 1.97% S= 16.71 time= 0.33
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   0.98

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     550 steps. Energy=    -296.4211694       time=       0.43
 Minus side of path:                     720 steps. Energy=    -292.6822256       time=       0.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.4211694  7.2300         -289.1911437  3.4911         -292.6822256  23.348  20.399   2.336  33.820
        Known (#5)                                              *NEW* (Placed in 16)
 Unconnected minimum 16 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 16 minima and 15 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2864.3    
 decide> The unconnected minima in the chain and their distances are:
     6       11.27     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0620 Dev= 7.73% S= 26.11 time= 9.60
 Following    2 images are candidates for TS:    5   11  
 Converged to TS (number of iterations):         11
 Converged to TS (number of iterations):         84
 DNEB run yielded 2 true transition state(s) time=   2.20

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     588 steps. Energy=    -292.3488456       time=       0.47
 Minus side of path:                     523 steps. Energy=    -292.3554352       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.3488456  1.0429         -291.3059180  1.0495         -292.3554352   6.818   5.901   3.376  23.402
        *NEW* (Placed in 17)                                    *NEW* (Placed in 18)
 Connection established between members of the U set.

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     561 steps. Energy=    -291.9604612       time=       0.45
 Minus side of path:                     550 steps. Energy=    -290.9840374       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9604612  1.5710         -290.3894116 0.59463         -290.9840374  10.693   9.126   2.104  37.549
        *NEW* (Placed in 19)                                    *NEW* (Placed in 20)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 20 minima and 17 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     745.58    
 decide> The unconnected minima in the chain and their distances are:
     5        8.90    18    17        3.42     3 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 18_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.9897 Dev= 0.58% S= 11.29 time= 0.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   0.97
 isnewts> transition state is the same as number       15 energy=     -289.1911437205
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 18 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     569 steps. Energy=    -296.4211694       time=       0.45
 Minus side of path:                     702 steps. Energy=    -292.6822256       time=       0.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.4211694  7.2300         -289.1911437  3.4911         -292.6822256  23.380  20.415   2.301  34.328
        Known (#5)                                              Known (#16)
 Alternative path found between members of the F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 17_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2138 Dev= 0.03% S= 3.47 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=   0.53

 >>>>>  Path run for ts 19 ...
 Plus  side of path:                     513 steps. Energy=    -292.4977479       time=       0.40
 Minus side of path:                     509 steps. Energy=    -292.3488456       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.4977479 0.16205         -292.3356934 0.13152E-01     -292.3488456   3.482   3.423  19.771   3.996
        Known (#3)                                              Known (#17)
 Unconnected minimum 17 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 20 minima and 19 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     714.73    
 decide> The unconnected minima in the chain and their distances are:
     6        8.94    18 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 18_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3855 Dev= 0.22% S= 9.58 time= 0.10
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   0.78

 >>>>>  Path run for ts 20 ...
 Plus  side of path:                     534 steps. Energy=    -290.3650447       time=       0.41
 Minus side of path:                     550 steps. Energy=    -292.3554352       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.3650447  2.2212         -288.1438649  4.2116         -292.3554352   9.301   7.028   4.817  16.401
        *NEW* (Placed in 21)                                    Known (#18)
 Unconnected minimum 21 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 21 minima and 20 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     228.87    
 decide> The unconnected minima in the chain and their distances are:
     5        6.12    21 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 21_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7304 Dev= 0.41% S= 8.04 time= 0.10
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.70

 >>>>>  Path run for ts 21 ...
 Plus  side of path:                     558 steps. Energy=    -296.8912080       time=       0.43
 Minus side of path:                     524 steps. Energy=    -290.3650447       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.8912080  6.8524         -290.0388174 0.32623         -290.3650447  11.360   9.690   4.857  16.266
        Known (#6)                                              Known (#21)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -294.5470669 0.77845        -293.7686124  5.0011        -298.7697561   6.632   5.872   4.565  17.305
  12     -298.7697561 0.15052        -298.6192385 0.66482        -299.2840590   5.043   4.119  19.162   4.123
  10     -299.2840590  1.9736        -297.3104763 0.72691        -298.0373891   8.401   7.357   3.427  23.051
   5     -298.0373891  3.3949        -294.6424905  2.7306        -297.3730826  11.383   9.158   6.192  12.758
   1     -297.3730826  7.0986        -290.2745236  2.2232        -292.4977479  22.704  17.581   2.154  36.682
  19     -292.4977479 0.16205        -292.3356934 0.13152E-01    -292.3488456   3.482   3.423  19.771   3.996
  16     -292.3488456  1.0429        -291.3059180  1.0495        -292.3554352   6.818   5.901   3.376  23.402
  20     -292.3554352  4.2116        -288.1438649  2.2212        -290.3650447   9.301   7.028   4.817  16.401
  21     -290.3650447 0.32623        -290.0388174  6.8524        -296.8912080  11.360   9.690   4.857  16.266
   2     -296.8912080  3.0244        -293.8667956  2.5544        -296.4211694  10.692   8.216   9.705   8.140
   3     -296.4211694  2.3694        -294.0517830  2.8394        -296.8912080   7.606   6.865   5.609  14.084

 Number of TS in the path       =     11
 Number of cycles               =     12

 Elapsed time=                                54.16
 OPTIM> # of energy calls=                        146 time=           0.07 %=  0.1
 OPTIM> # of energy+gradient calls=             60558 time=          29.73 %= 54.9
 OPTIM> # of energy+gradient+Hessian calls=      1003 time=           0.99 %=  1.8
