
 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 11:38: 6 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -290.5270599     RMS force=    0.8739033563E-06
 OPTIM> Final energy  =    -290.7445270     RMS force=    0.9245068781E-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=     500.74    
 decide> The unconnected minima in the chain and their distances are:
     2        7.94     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 106 RMS= 19.7001 Dev= 51.38% S= 16.25 time= 0.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   1.05

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     516 steps. Energy=    -290.5270599       time=       0.42
 Minus side of path:                     513 steps. Energy=    -290.7445270       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5270599 0.18866         -290.3384032 0.40612         -290.7445270   6.608   6.341   6.732  11.735
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     110.20    
 decide> The unconnected minima in the chain and their distances are:
     3        4.79     1 
 

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.1761 Dev= 1.65% S= 7.50 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   1.30

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     573 steps. Energy=    -294.4329309       time=       0.48
 Minus side of path:                     540 steps. Energy=    -290.0198627       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  5.9755         -288.4574618  1.5624         -290.0198627  11.832   9.838   5.948  13.282
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     220.40    
 decide> The unconnected minima in the chain and their distances are:
     3        4.79     1 
 

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> 385-iteration DNEB run for minima 1_S and 3_F using 11 images  (DNEB attempt #2)  ...
 tryconnect> Changing to an even number of images for possible permutational isomer
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 385 RMS= 0.1777 Dev= 2.90% S= 8.84 time= 2.53
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         98
 DNEB run yielded 1 true transition state(s) time=   1.73

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     806 steps. Energy=    -292.6986257       time=       0.76
 Minus side of path:                     626 steps. Energy=    -290.0198627       time=       0.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.6986257  6.8039         -285.8947278  4.1251         -290.0198627  32.026  26.985   1.993  39.629
        *NEW* (Placed in 6)                                     Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     330.59    
 decide> The unconnected minima in the chain and their distances are:
     3        4.79     1 
 

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> 700-iteration DNEB run for minima 1_S and 3_F using 20 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 700 RMS= 0.0926 Dev= 5.00% S= 12.57 time= 7.68
 Following    2 images are candidates for TS:    2   12  
 Converged to TS (number of iterations):         13
 Converged to TS (number of iterations):         58
 DNEB run yielded 2 true transition state(s) time=   1.60
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     516 steps. Energy=    -290.5270599       time=       0.42
 Minus side of path:                     519 steps. Energy=    -291.1944375       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5270599 0.56304         -289.9640195  1.2304         -291.1944375   4.226   3.179   9.261   8.530
        Known (#1)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     579 steps. Energy=    -294.4329309       time=       0.49
 Minus side of path:                     552 steps. Energy=    -290.0198627       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  5.9755         -288.4574618  1.5624         -290.0198627  11.832   9.841   5.926  13.332
        Known (#4)                                              Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     164.58    
 decide> The unconnected minima in the chain and their distances are:
     3        5.48     7 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 1.2779 Dev= 2.17% S= 7.15 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   1.33
 isnewts> transition state is the same as number        3 energy=     -285.8947277944
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     814 steps. Energy=    -292.6507789       time=       0.77
 Minus side of path:                     630 steps. Energy=    -290.0198627       time=       0.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.6507789  6.7561         -285.8947278  4.1251         -290.0198627  29.598  22.988   2.397  32.959
        *NEW* (Placed in 8)                                     Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     329.16    
 decide> The unconnected minima in the chain and their distances are:
     3        5.48     7 
 

 tryconnect> 420-iteration DNEB run for minima 3_F and 7_S using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 420 RMS= 0.0818 Dev= 4.74% S= 12.50 time= 2.76
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   1.08
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     493.75    
 decide> The unconnected minima in the chain and their distances are:
     3        5.48     7 
 

 tryconnect> 805-iteration DNEB run for minima 3_F and 7_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.1380 Dev= 1.87% S= 10.57 time= 10.16
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   0.93
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     595.95    
 decide> The unconnected minima in the chain and their distances are:
     2        8.42     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 160 RMS= 3.6223 Dev= 1.73% S= 9.66 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   1.39
 isnewts> transition state is the same as number        3 energy=     -285.8947277944
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     971.46    
 decide> The unconnected minima in the chain and their distances are:
     2        6.89     5     5        8.64     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 111 RMS= 7.1506 Dev= 43.99% S= 7.15 time= 0.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   0.63

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     499 steps. Energy=    -290.0198627       time=       0.40
 Minus side of path:                     526 steps. Energy=    -290.5270599       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.0198627 0.42698E-01     -289.9771646 0.54990         -290.5270599   7.328   7.279   1.769  44.655
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 1.1075 Dev= 1.97% S= 9.84 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   0.83

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     545 steps. Energy=    -291.1944375       time=       0.45
 Minus side of path:                     532 steps. Energy=    -295.6584236       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.1944375  1.2836         -289.9108777  5.7475         -295.6584236  12.309  10.996   2.422  32.619
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     142.26    
 decide> The unconnected minima in the chain and their distances are:
     3        3.18     9     9        4.79     7 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.2666 Dev= 0.13% S= 3.23 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.52

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     524 steps. Energy=    -290.5270599       time=       0.42
 Minus side of path:                     513 steps. Energy=    -291.1944375       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5270599 0.56304         -289.9640195  1.2304         -291.1944375   4.226   3.179   9.261   8.530
        Known (#3)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 checkpair> Energies of the minima in the pair     7    9 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 7_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.7861 Dev= 1.12% S= 7.66 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   1.36
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     164.58    
 decide> The unconnected minima in the chain and their distances are:
     9        5.48     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 1.0455 Dev= 2.23% S= 7.17 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   1.56

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     629 steps. Energy=    -290.0198627       time=       0.54
 Minus side of path:                     782 steps. Energy=    -292.6986257       time=       0.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.0198627  4.1251         -285.8947278  6.8039         -292.6986257  32.028  26.993   1.989  39.712
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     220.24    
 decide> The unconnected minima in the chain and their distances are:
     9        4.79     7 
 

 checkpair> Energies of the minima in the pair     7    9 are the same - checking distance ...

 tryconnect> 385-iteration DNEB run for minima 7_S and 9_F using 11 images  (DNEB attempt #2)  ...
 tryconnect> Changing to an even number of images for possible permutational isomer
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 385 RMS= 0.0797 Dev= 1.74% S= 13.85 time= 2.54
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):         59
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=   1.68
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Will not repeat search for TS      1 same as TS      2
 isnewts> transition state is the same as number        9 energy=     -289.9640195360
 tryconnect> Try the path again for ts      2 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:                     542 steps. Energy=    -290.5270599       time=       0.44
 Minus side of path:                     507 steps. Energy=    -291.1944375       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5270599 0.56304         -289.9640195  1.2304         -291.1944375   4.226   3.179   9.249   8.541
        Known (#3)                                              Known (#9)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     329.16    
 decide> The unconnected minima in the chain and their distances are:
     9        5.48     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 9_F using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 420 RMS= 0.0466 Dev= 4.77% S= 11.45 time= 2.76
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        110
 DNEB run yielded 1 true transition state(s) time=   1.84
 isnewts> transition state is the same as number       10 energy=     -285.8947277944
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 12 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     657 steps. Energy=    -290.0198627       time=       0.63
 Minus side of path:                     802 steps. Energy=    -292.6986257       time=       0.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.0198627  4.1251         -285.8947278  6.8039         -292.6986257  32.058  26.938   2.013  39.250
        Known (#11)                                             Known (#12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 12 minima and 12 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     330.37    
 decide> The unconnected minima in the chain and their distances are:
     9        4.79     7 
 

 checkpair> Energies of the minima in the pair     7    9 are the same - checking distance ...

 tryconnect> 700-iteration DNEB run for minima 7_S and 9_F using 20 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 700 RMS= 2.5820 Dev= 3.64% S= 12.87 time= 7.70
 Following    2 images are candidates for TS:    8   18  
 Converged to TS (number of iterations):         63
 Converged to TS (number of iterations):         12
 DNEB run yielded 2 true transition state(s) time=   1.64
 isnewts> transition state is the same as number        2 energy=     -288.4574618064
 tryconnect> Will not repeat search for TS      1 same as TS      2
 isnewts> transition state is the same as number        9 energy=     -289.9640195359
 tryconnect> Will not repeat search for TS      2 same as TS      9
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 15 >>>>>>>>>>>>>>>>>>>>> 12 minima and 12 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     493.75    
 decide> The unconnected minima in the chain and their distances are:
     9        5.48     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 9_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.1135 Dev= 6.40% S= 16.78 time= 10.23
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   0.95

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     578 steps. Energy=    -294.4329309       time=       0.49
 Minus side of path:                     542 steps. Energy=    -290.0198627       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  5.9755         -288.4574618  1.5624         -290.0198627  11.833   9.838   5.943  13.293
        *NEW* (Placed in 13)                                    Known (#11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 16 >>>>>>>>>>>>>>>>>>>>> 13 minima and 13 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     496.01    
 decide> The unconnected minima in the chain and their distances are:
     5        4.80    11    11        7.28     1 
 

 checkpair> Energies of the minima in the pair     5   11 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 5_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.2656 Dev= 0.38% S= 7.80 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   0.87

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     534 steps. Energy=    -291.1944375       time=       0.43
 Minus side of path:                     534 steps. Energy=    -295.6584236       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.1944375  1.2836         -289.9108777  5.7475         -295.6584236  12.310  10.996   2.420  32.648
        Known (#7)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to S set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.1875 Dev= 0.18% S= 7.29 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   0.68

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     520 steps. Energy=    -290.5270599       time=       0.42
 Minus side of path:                     481 steps. Energy=    -290.0198627       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5270599 0.54990         -289.9771646 0.42698E-01     -290.0198627   7.328   7.279   1.769  44.657
        Known (#1)                                              Known (#11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 17 >>>>>>>>>>>>>>>>>>>>> 14 minima and 15 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     110.21    
 decide> The unconnected minima in the chain and their distances are:
    10        4.79    14 
 

 checkpair> Energies of the minima in the pair    10   14 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 10_F and 14_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 2.6393 Dev= 1.55% S= 7.30 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   0.70

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     576 steps. Energy=    -294.4329309       time=       0.48
 Minus side of path:                     521 steps. Energy=    -295.6584236       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  3.0955         -291.3373960  4.3210         -295.6584236   9.289   6.454   6.763  11.681
        Known (#13)                                             Known (#14)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 18 >>>>>>>>>>>>>>>>>>>>> 14 minima and 16 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     110.32    
 decide> The unconnected minima in the chain and their distances are:
     4        4.80    13 
 

 checkpair> Energies of the minima in the pair     4   13 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 4_F and 13_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6169 Dev= 0.39% S= 7.21 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.59

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     535 steps. Energy=    -294.4329309       time=       0.44
 Minus side of path:                     527 steps. Energy=    -294.4329309       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  4.8872         -289.5456905  4.8872         -294.4329309   7.607   4.813  19.527   4.046
        Known (#13)                                             Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  15     -290.5270599 0.54990        -289.9771646 0.42698E-01    -290.0198627   7.328   7.279   1.769  44.657
  13     -290.0198627  1.5624        -288.4574618  5.9755        -294.4329309  11.833   9.838   5.943  13.293
  17     -294.4329309  4.8872        -289.5456905  4.8872        -294.4329309   7.607   4.813  19.527   4.046
   2     -294.4329309  5.9755        -288.4574618  1.5624        -290.0198627  11.832   9.838   5.948  13.282
   7     -290.0198627 0.42698E-01    -289.9771646 0.54990        -290.5270599   7.328   7.279   1.769  44.655
   1     -290.5270599 0.18866        -290.3384032 0.40612        -290.7445270   6.608   6.341   6.732  11.735

 Number of TS in the path       =      6
 Number of cycles               =     18

 Elapsed time=                                89.63
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            120580 time=          62.79 %= 70.1
 OPTIM> # of energy+gradient+Hessian calls=      1219 time=           1.30 %=  1.4
