
 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 11:32: 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -293.9113524     RMS force=    0.9712540104E-06
 OPTIM> Final energy  =    -291.0274248     RMS force=    0.9041857054E-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=     710.48    
 decide> The unconnected minima in the chain and their distances are:
     2        8.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8120 Dev= 1.01% S= 9.74 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   1.47

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     661 steps. Energy=    -291.5181879       time=       0.56
 Minus side of path:                     838 steps. Energy=    -295.7090080       time=       0.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.5181879  3.5361         -287.9820839  7.7269         -295.7090080  30.663  25.497   2.772  28.499
        *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=     710.59    
 decide> The unconnected minima in the chain and their distances are:
     2        5.38     3     3        8.22     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= 0.1293 Dev= 0.09% S= 5.51 time= 0.07
 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 2 ...
 Plus  side of path:                     495 steps. Energy=    -291.0274248       time=       0.37
 Minus side of path:                     511 steps. Energy=    -291.5181879       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.0274248 0.60874E-01     -290.9665505 0.55164         -291.5181879   5.574   5.380   7.764  10.175
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 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= 0.4817 Dev= 0.61% S= 8.95 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   1.31
 isnewts> transition state is the same as number        1 energy=     -287.9820838618
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     654 steps. Energy=    -291.5181879       time=       0.55
 Minus side of path:                     845 steps. Energy=    -295.7090080       time=       0.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.5181879  3.5361         -287.9820839  7.7269         -295.7090080  30.649  25.471   2.777  28.449
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1110.0    
 decide> The unconnected minima in the chain and their distances are:
     3        8.22     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 3_F using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2703907739    
 Double-ended search iterations= 630 RMS= 0.0386 Dev= 4.00% S= 15.73 time= 5.98
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.86

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     515 steps. Energy=    -290.5380346       time=       0.40
 Minus side of path:                     546 steps. Energy=    -293.9806322       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5380346  2.8243         -287.7137442  6.2669         -293.9806322  12.249  11.390   2.980  26.514
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1421.0    
 decide> The unconnected minima in the chain and their distances are:
     2        8.92     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 2_F using 20 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 700 RMS= 0.0517 Dev= 4.90% S= 14.82 time= 7.40
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.89
 isnewts> transition state is the same as number        4 energy=     -287.7137441592
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     512 steps. Energy=    -290.5380346       time=       0.39
 Minus side of path:                     537 steps. Energy=    -293.9806322       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5380346  2.8243         -287.7137442  6.2669         -293.9806322  12.255  11.395   2.996  26.372
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1665.0    
 decide> The unconnected minima in the chain and their distances are:
     3        8.22     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.8803147734E-01
 Double-ended search iterations= 805 RMS= 0.0258 Dev= 3.03% S= 17.34 time= 9.72
 Following    1 images are candidates for TS:   15  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   0.71
 isnewts> transition state is the same as number        4 energy=     -287.7137441592
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1918.0    
 decide> The unconnected minima in the chain and their distances are:
     3        9.73     5     6        9.99     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1645 Dev= 0.02% S= 9.78 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.67

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     510 steps. Energy=    -290.5380346       time=       0.39
 Minus side of path:                     541 steps. Energy=    -291.5181879       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5380346 0.10291         -290.4351259  1.0831         -291.5181879   9.922   9.726   2.166  36.478
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 1.5250 Dev= 1.04% S= 11.97 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   1.10

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     516 steps. Energy=    -292.1862109       time=       0.41
 Minus side of path:                     506 steps. Energy=    -293.4844345       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.1862109 0.39478         -291.7914275  1.6930         -293.4844345   4.576   3.774   6.565  12.034
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1400.1    
 decide> The unconnected minima in the chain and their distances are:
     5       11.19     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.3033 Dev= 2.75% S= 13.06 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   0.90
 isnewts> transition state is the same as number        4 energy=     -287.7137441592
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1996.3    
 decide> The unconnected minima in the chain and their distances are:
     6        9.99     1 
 

 tryconnect> 770-iteration DNEB run for minima 1_S and 6_F using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 770 RMS= 0.1718 Dev= 2.51% S= 16.14 time= 9.05
 Following    3 images are candidates for TS:    6   13   17  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         42
 DNEB run yielded 3 true transition state(s) time=   2.41
 isnewts> transition state is the same as number        7 energy=     -291.7914274868
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     497 steps. Energy=    -292.1862109       time=       0.39
 Minus side of path:                     481 steps. Energy=    -293.4844345       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.1862109 0.39478         -291.7914275  1.6930         -293.4844345   4.576   3.774   6.564  12.036
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     559 steps. Energy=    -293.9806322       time=       0.45
 Minus side of path:                     541 steps. Energy=    -293.9113524       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9806322  2.7711         -291.2095322  2.7018         -293.9113524  12.923  10.053   8.650   9.133
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     501 steps. Energy=    -293.4844345       time=       0.39
 Minus side of path:                     517 steps. Energy=    -292.1862109       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.4844345  1.6930         -291.7914275 0.39478         -292.1862109   4.576   3.774   6.573  12.018
        Known (#8)                                              Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     220.57    
 decide> The unconnected minima in the chain and their distances are:
     6        4.80    11    12        4.79     1 
 

 checkpair> Energies of the minima in the pair     6   11 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 6_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 3.4577 Dev= 13.22% S= 7.51 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   1.02
 isnewts> transition state is the same as number        7 energy=     -291.7914274867
 tryconnect> Will not repeat search for TS      1 same as TS      7

 checkpair> Energies of the minima in the pair     1   12 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 1_S and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 2.1953 Dev= 0.91% S= 7.41 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.75

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     594 steps. Energy=    -293.9113524       time=       0.48
 Minus side of path:                     504 steps. Energy=    -293.9113524       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9113524  3.6071         -290.3042345  3.6071         -293.9113524   9.739   4.896  18.335   4.309
        Known (#12)                                             Known (#1)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     220.68    
 decide> The unconnected minima in the chain and their distances are:
     6        4.80    11 
 

 checkpair> Energies of the minima in the pair     6   11 are the same - checking distance ...

 tryconnect> 385-iteration DNEB run for minima 6_F and 11_S using 11 images  (DNEB attempt #2)  ...
 tryconnect> Changing to an even number of images for possible permutational isomer
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 385 RMS= 0.4239 Dev= 1.84% S= 8.80 time= 2.45
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   1.15
 isnewts> transition state is the same as number        7 energy=     -291.7914274868
 tryconnect> Will not repeat search for TS      1 same as TS      7
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     331.02    
 decide> The unconnected minima in the chain and their distances are:
     6        4.80    11 
 

 checkpair> Energies of the minima in the pair     6   11 are the same - checking distance ...

 tryconnect> 700-iteration DNEB run for minima 6_F and 11_S using 20 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      77.61587555    
 Double-ended search iterations= 1901 RMS= 2.6310 Dev= 57.85% S= 35.49 time= 20.21
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   1.21
 tryconnect> Transition state with energy      178.4201377     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     405.79    
 decide> The unconnected minima in the chain and their distances are:
     3        7.40    12 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4010 Dev= 0.25% S= 7.71 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        104
 DNEB run yielded 1 true transition state(s) time=   1.74

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     481 steps. Energy=    -291.8556121       time=       0.37
 Minus side of path:                     499 steps. Energy=    -293.9113524       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.8556121 0.73094         -291.1246737  2.7867         -293.9113524   9.389   8.693   2.822  27.993
        *NEW* (Placed in 13)                                    Known (#12)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 13 minima and 12 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     534.03    
 decide> The unconnected minima in the chain and their distances are:
     2        8.11    12 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4655 Dev= 0.18% S= 8.47 time= 0.07
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):        111
 DNEB run yielded 1 true transition state(s) time=   1.77
 isnewts> transition state is the same as number       12 energy=     -291.1246737317
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 13 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     499 steps. Energy=    -291.8556121       time=       0.39
 Minus side of path:                     501 steps. Energy=    -293.9113524       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.8556121 0.73094         -291.1246737  2.7867         -293.9113524   9.390   8.694   2.827  27.948
        Known (#13)                                             Known (#12)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 13 minima and 13 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     727.85    
 decide> The unconnected minima in the chain and their distances are:
     6        9.00    12 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3705 Dev= 0.55% S= 9.51 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        160
 DNEB run yielded 1 true transition state(s) time=   2.56

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     458 steps. Energy=    -292.1862109       time=       0.35
 Minus side of path:                     564 steps. Energy=    -293.9113524       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.1862109 0.99292E-03     -292.1852180  1.7261         -293.9113524  10.416  10.365   2.634  29.996
        Known (#7)                                              Known (#12)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 15 >>>>>>>>>>>>>>>>>>>>> 13 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     811.58    
 decide> The unconnected minima in the chain and their distances are:
     3        7.40    12 
 

 tryconnect> 595-iteration DNEB run for minima 3_F and 12_S using 17 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 595 RMS= 0.1954 Dev= 4.54% S= 10.70 time= 5.28
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.89
 isnewts> transition state is the same as number        4 energy=     -287.7137441592
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 16 >>>>>>>>>>>>>>>>>>>>> 13 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     978.26    
 decide> The unconnected minima in the chain and their distances are:
     6        9.93     8 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2929 Dev= 0.02% S= 10.01 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=   0.67

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     507 steps. Energy=    -293.4844345       time=       0.40
 Minus side of path:                     519 steps. Energy=    -293.9806322       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.4844345 0.44751         -293.0369278 0.94370         -293.9806322  10.566   9.928   2.008  39.341
        Known (#8)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -293.9113524  3.6071        -290.3042345  3.6071        -293.9113524   9.739   4.896  18.335   4.309
  14     -293.9113524  1.7261        -292.1852180 0.99292E-03    -292.1862109  10.416  10.365   2.634  29.996
   7     -292.1862109 0.39478        -291.7914275  1.6930        -293.4844345   4.576   3.774   6.565  12.034
  15     -293.4844345 0.44751        -293.0369278 0.94370        -293.9806322  10.566   9.928   2.008  39.341
   4     -293.9806322  6.2669        -287.7137442  2.8243        -290.5380346  12.249  11.390   2.980  26.514
   6     -290.5380346 0.10291        -290.4351259  1.0831        -291.5181879   9.922   9.726   2.166  36.478
   2     -291.5181879 0.55164        -290.9665505 0.60874E-01    -291.0274248   5.574   5.380   7.764  10.175

 Number of TS in the path       =      7
 Number of cycles               =     16

 Elapsed time=                                97.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            145461 time=          72.58 %= 74.2
 OPTIM> # of energy+gradient+Hessian calls=      1115 time=           1.14 %=  1.2
