
 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 12:19:43 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -293.7879877     RMS force=    0.8478311649E-06
 OPTIM> Final energy  =    -293.5739354     RMS force=    0.7649488188E-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=     1497.5    
 decide> The unconnected minima in the chain and their distances are:
     2       11.44     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5592 Dev= 0.77% S= 14.56 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   0.90

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     488 steps. Energy=    -293.7879877       time=       0.40
 Minus side of path:                     487 steps. Energy=    -293.9068789       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7879877 0.90487         -292.8831180  1.0238         -293.9068789   2.847   2.684  28.434   2.778
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1207.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.32     4     3        4.79     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3721 Dev= 0.59% S= 12.80 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.77

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     538 steps. Energy=    -293.9068789       time=       0.46
 Minus side of path:                     512 steps. Energy=    -291.0054140       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9068789  4.4829         -289.4240116  1.5814         -291.0054140  11.420   8.570   8.493   9.302
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 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_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.9619 Dev= 1.87% S= 7.54 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   1.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     546 steps. Energy=    -291.4769962       time=       0.46
 Minus side of path:                     496 steps. Energy=    -291.9598361       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4769962  1.1904         -290.2866120  1.6732         -291.9598361  13.706  12.962   2.581  30.612
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     265.66    
 decide> The unconnected minima in the chain and their distances are:
     2        4.64     5     4        5.49     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2185 Dev= 0.20% S= 5.20 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   1.04

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     509 steps. Energy=    -291.0054140       time=       0.42
 Minus side of path:                     513 steps. Energy=    -289.9978466       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.0054140  1.1267         -289.8786905 0.11916         -289.9978466  11.254  10.898   2.748  28.751
        Known (#5)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 5.9537 Dev= 2.23% S= 8.17 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   0.68
 isnewts> transition state is the same as number        1 energy=     -292.8831179588
 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:                     516 steps. Energy=    -293.7879877       time=       0.44
 Minus side of path:                     495 steps. Energy=    -293.9068789       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7879877 0.90487         -292.8831180  1.0238         -293.9068789   2.855   2.689  28.764   2.747
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     420.11    
 decide> The unconnected minima in the chain and their distances are:
     2        4.64     5     3        4.79     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 5_U using 10 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0149 Dev= 3.67% S= 6.57 time= 2.07
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:   10  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   0.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     534 steps. Energy=    -293.5739354       time=       0.45
 Minus side of path:                     429 steps. Energy=    -291.0054140       time=       0.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.5739354  2.5698         -291.0041715 0.12426E-02     -291.0054140   4.900   4.644  22.227   3.554
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 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
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 385 RMS= 0.4979 Dev= 7.30% S= 17.00 time= 2.71
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=   1.59

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     567 steps. Energy=    -291.9598361       time=       0.50
 Minus side of path:                     575 steps. Energy=    -289.4342316       time=       0.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9598361  6.1420         -285.8178610  3.6164         -289.4342316  16.794  15.229   3.157  25.024
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     623 steps. Energy=    -293.7879877       time=       0.59
 Minus side of path:                     498 steps. Energy=    -289.4342316       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7879877  7.7657         -286.0222525  3.4120         -289.4342316  18.014  12.082   2.717  29.080
        Known (#3)                                              Known (#10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     234.35    
 decide> The unconnected minima in the chain and their distances are:
     9        6.17     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3552 Dev= 0.35% S= 6.46 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   0.87

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     553 steps. Energy=    -291.4769962       time=       0.46
 Minus side of path:                     484 steps. Energy=    -291.9598361       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4769962  1.1904         -290.2866120  1.6732         -291.9598361  13.706  12.962   2.580  30.620
        *NEW* (Placed in 11)                                    Known (#9)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     330.32    
 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 700 RMS= 0.1835 Dev= 4.51% S= 20.02 time= 8.17
 Following    2 images are candidates for TS:    7   13  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         44
 DNEB run yielded 2 true transition state(s) time=   1.45
 isnewts> transition state is the same as number        7 energy=     -285.8178610151
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        8 energy=     -286.0222524758
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     579 steps. Energy=    -289.4342316       time=       0.50
 Minus side of path:                     560 steps. Energy=    -291.9598361       time=       0.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.4342316  3.6164         -285.8178610  6.1420         -291.9598361  16.794  15.230   3.153  25.055
        Known (#10)                                             Known (#9)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 11 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     629 steps. Energy=    -293.7879877       time=       0.56
 Minus side of path:                     517 steps. Energy=    -289.4342316       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7879877  7.7657         -286.0222525  3.4120         -289.4342316  18.016  12.086   2.707  29.179
        Known (#3)                                              Known (#10)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     331.42    
 decide> The unconnected minima in the chain and their distances are:
     4        5.49     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 4_F using 12 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 420 RMS= 0.1615 Dev= 3.87% S= 15.85 time= 2.96
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):         47
 DNEB run yielded 2 true transition state(s) time=   2.01
 isnewts> transition state is the same as number        8 energy=     -286.0222524758
 tryconnect> Will not repeat search for TS      2 same as TS      8

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     532 steps. Energy=    -293.7879877       time=       0.45
 Minus side of path:                     516 steps. Energy=    -291.8555557       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7879877  7.5039         -286.2841109  5.5714         -291.8555557  13.459  11.162   6.791  11.634
        Known (#1)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     468.70    
 decide> The unconnected minima in the chain and their distances are:
     9        6.17     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 9_F using 14 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 490 RMS= 0.0589 Dev= 5.08% S= 9.15 time= 4.03
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   0.62
 isnewts> transition state is the same as number        9 energy=     -290.2866119592
 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:                     571 steps. Energy=    -291.4769962       time=       0.49
 Minus side of path:                     493 steps. Energy=    -291.9598361       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4769962  1.1904         -290.2866120  1.6732         -291.9598361  13.707  12.964   2.572  30.710
        Known (#11)                                             Known (#9)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     481.97    
 decide> The unconnected minima in the chain and their distances are:
     9        7.84    12 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 12_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6197 Dev= 0.26% S= 8.31 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        176
 DNEB run yielded 1 true transition state(s) time=   3.03

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     517 steps. Energy=    -290.1813887       time=       0.42
 Minus side of path:                     677 steps. Energy=    -291.4370166       time=       0.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.1813887  2.2757         -287.9056393  3.5314         -291.4370166  16.984  16.066   2.010  39.310
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 14 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     497.13    
 decide> The unconnected minima in the chain and their distances are:
     4        5.49     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #3)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.2333 Dev= 5.51% S= 26.83 time= 10.80
 Following    4 images are candidates for TS:    5    9   15   22  
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         14
 DNEB run yielded 4 true transition state(s) time=   2.72
 isnewts> transition state is the same as number        9 energy=     -290.2866119592
 tryconnect> Will not repeat search for TS      1 same as TS      9
 isnewts> transition state is the same as number        8 energy=     -286.0222524758
 tryconnect> Will not repeat search for TS      3 same as TS      8
 isnewts> transition state is the same as number        1 energy=     -292.8831179588
 tryconnect> Will not repeat search for TS      4 same as TS      1

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     531 steps. Energy=    -288.8993551       time=       0.44
 Minus side of path:                     496 steps. Energy=    -289.4342316       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.8993551  2.5302         -286.3692014  3.0650         -289.4342316  10.643   9.880   5.754  13.729
        *NEW* (Placed in 15)                                    Known (#10)
 Unconnected minimum 15 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 15 minima and 15 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     558.06    
 decide> The unconnected minima in the chain and their distances are:
    11        4.79     6     7        7.65     1 
 

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

 tryconnect> 70-iteration DNEB run for minima 6_U and 11_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 1.0256 Dev= 1.00% S= 7.20 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   0.98
 isnewts> transition state is the same as number        9 energy=     -290.2866119592
 tryconnect> Will not repeat search for TS      1 same as TS      9

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9585 Dev= 1.79% S= 9.82 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   0.90
 isnewts> transition state is the same as number        9 energy=     -290.2866119592
 tryconnect> Will not repeat search for TS      1 same as TS      9
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 15 minima and 15 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     588.15    
 decide> The unconnected minima in the chain and their distances are:
     9        5.75    14    14        7.35    12 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 14_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1913 Dev= 0.17% S= 5.83 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   0.58

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     465 steps. Energy=    -291.3176368       time=       0.37
 Minus side of path:                     485 steps. Energy=    -291.4370166       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3176368 0.43268E-01     -291.2743688 0.16265         -291.4370166   2.717   2.677   6.977  11.323
        *NEW* (Placed in 16)                                    Known (#14)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 12_S and 14_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5569 Dev= 0.39% S= 7.86 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   1.21

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     467 steps. Energy=    -292.7722361       time=       0.38
 Minus side of path:                     480 steps. Energy=    -292.5658815       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.7722361 0.75601         -292.0162296 0.54965         -292.5658815   3.459   3.175   5.002  15.793
        *NEW* (Placed in 17)                                    *NEW* (Placed in 18)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 18 minima and 17 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     511.28    
 decide> The unconnected minima in the chain and their distances are:
     9        4.82    16    16        7.36     1 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 16_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0951 Dev= 0.42% S= 4.91 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.51

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                     491 steps. Energy=    -291.9598361       time=       0.40
 Minus side of path:                     454 steps. Energy=    -291.3176368       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.9598361 0.64842         -291.3114157 0.62211E-02     -291.3176368   4.904   4.826   8.381   9.426
        Known (#9)                                              Known (#16)
 Unconnected minimum 16 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 16_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.0126 Dev= 0.22% S= 7.73 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   0.85
 isnewts> transition state is the same as number        9 energy=     -290.2866119592
 tryconnect> Will not repeat search for TS      1 same as TS      9
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 18 minima and 18 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=     490.34    
 decide> The unconnected minima in the chain and their distances are:
    14        7.64    17    17        3.55    12 
 

 tryconnect> 70-iteration DNEB run for minima 14_F and 17_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5129 Dev= 0.59% S= 8.04 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   1.24

 >>>>>  Path run for ts 19 ...
 Plus  side of path:                     609 steps. Energy=    -291.4769962       time=       0.53
 Minus side of path:                     515 steps. Energy=    -292.7722361       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4769962  3.1466         -288.3304014  4.4418         -292.7722361  17.176  13.045   3.807  20.750
        Known (#11)                                             Known (#17)
 Unconnected minimum 17 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 12_S and 17_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2067 Dev= 0.41% S= 3.60 time= 0.09
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   0.49

 >>>>>  Path run for ts 20 ...
 Plus  side of path:                     485 steps. Energy=    -292.7722361       time=       0.40
 Minus side of path:                     481 steps. Energy=    -291.8555557       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.7722361  1.0961         -291.6761500 0.17941         -291.8555557   3.664   3.552   8.513   9.280
        Known (#17)                                             Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -293.7879877  7.5039        -286.2841109  5.5714        -291.8555557  13.459  11.162   6.791  11.634
  20     -291.8555557 0.17941        -291.6761500  1.0961        -292.7722361   3.664   3.552   8.513   9.280
  19     -292.7722361  4.4418        -288.3304014  3.1466        -291.4769962  17.176  13.045   3.807  20.750
   9     -291.4769962  1.1904        -290.2866120  1.6732        -291.9598361  13.706  12.962   2.580  30.620
   7     -291.9598361  6.1420        -285.8178610  3.6164        -289.4342316  16.794  15.229   3.157  25.024
   8     -289.4342316  3.4120        -286.0222525  7.7657        -293.7879877  18.014  12.082   2.717  29.080
   1     -293.7879877 0.90487        -292.8831180  1.0238        -293.9068789   2.847   2.684  28.434   2.778
   2     -293.9068789  4.4829        -289.4240116  1.5814        -291.0054140  11.420   8.570   8.493   9.302
   6     -291.0054140 0.12426E-02    -291.0041715  2.5698        -293.5739354   4.900   4.644  22.227   3.554

 Number of TS in the path       =      9
 Number of cycles               =     14

 Elapsed time=                                75.50
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             91121 time=          50.37 %= 66.7
 OPTIM> # of energy+gradient+Hessian calls=      1096 time=           1.22 %=  1.6
