
 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 11:33:21 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=    -293.7428787     RMS force=    0.8922507917E-06
 OPTIM> Final energy  =    -291.0262394     RMS force=    0.7086740179E-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=     20077.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.18     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 280 RMS= 0.4194 Dev= 1.08% S= 33.61 time= 1.17
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         84
 DNEB run yielded 1 true transition state(s) time=   1.60

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     554 steps. Energy=    -293.2164479       time=       0.47
 Minus side of path:                     550 steps. Energy=    -294.7737219       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.2164479  3.0052         -290.2112212  4.5625         -294.7737219  12.148   9.908   8.309   9.508
        *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      1 steps with      1 missing connections, weight=     40153.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.18     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 805 RMS= 0.3073 Dev= 4.54% S= 44.75 time= 9.61
 Following    5 images are candidates for TS:    5    9   13   17   21  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):         98
 Converged to TS (number of iterations):         44
 Converged to TS (number of iterations):         93
 Converged to TS (number of iterations):         21
 DNEB run yielded 5 true transition state(s) time=   6.20

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     518 steps. Energy=    -293.4462626       time=       0.41
 Minus side of path:                     526 steps. Energy=    -293.4462626       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.4462626  3.9869         -289.4593180  3.9869         -293.4462626  10.270   4.809  19.563   4.038
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     522 steps. Energy=    -287.5782564       time=       0.41
 Minus side of path:                     612 steps. Energy=    -294.4329309       time=       0.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.5782564 0.13919         -287.4390709  6.9939         -294.4329309  15.128  14.597   4.537  17.412
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     574 steps. Energy=    -294.4329309       time=       0.48
 Minus side of path:                     553 steps. Energy=    -294.4329309       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  6.5586         -287.8743468  6.5586         -294.4329309  11.207   0.924   1.538  51.378
        Known (#8)                                              Known (#8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     676 steps. Energy=    -295.5186524       time=       0.58
 Minus side of path:                     528 steps. Energy=    -290.5066486       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5186524  5.2815         -290.2371773 0.26947         -290.5066486  21.534  19.956   2.996  26.370
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     521 steps. Energy=    -291.0753136       time=       0.40
 Minus side of path:                     649 steps. Energy=    -295.5186524       time=       0.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.0753136  1.7638         -289.3115364  6.2071         -295.5186524  14.544  11.309   5.352  14.761
        *NEW* (Placed in 11)                                    Known (#9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     5257.0    
 decide> The unconnected minima in the chain and their distances are:
     2        5.56    11    10       13.90     5     6       13.39     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.3270 Dev= 0.14% S= 5.67 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   0.55

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     510 steps. Energy=    -291.0262394       time=       0.39
 Minus side of path:                     530 steps. Energy=    -291.0753136       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.0262394 0.46536         -290.5608749 0.51444         -291.0753136   6.233   5.557  10.770   7.335
        Known (#2)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 5_U and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.6153 Dev= 1.92% S= 16.04 time= 0.31
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   1.00

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     805 steps. Energy=    -293.3619237       time=       0.75
 Minus side of path:                     557 steps. Energy=    -294.4329309       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.3619237  5.1396         -288.2223166  6.2106         -294.4329309  28.992  25.990   2.025  39.019
        *NEW* (Placed in 12)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1226 Dev= 0.02% S= 13.53 time= 0.31
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   0.56

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     498 steps. Energy=    -293.7428787       time=       0.39
 Minus side of path:                     512 steps. Energy=    -293.4462626       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7428787 0.51680         -293.2260783 0.22018         -293.4462626  13.578  13.388   1.665  47.449
        Known (#1)                                              Known (#6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     2900.3    
 decide> The unconnected minima in the chain and their distances are:
    10       13.34     8     8        8.06     5 
 

 tryconnect> 140-iteration DNEB run for minima 8_U and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.9375 Dev= 0.89% S= 14.18 time= 0.32
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   0.94
 isnewts> transition state is the same as number        8 energy=     -288.2223166266
 tryconnect> Try the path again for ts      1 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:                     814 steps. Energy=    -293.3619237       time=       0.78
 Minus side of path:                     552 steps. Energy=    -294.4329309       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.3619237  5.1396         -288.2223166  6.2106         -294.4329309  29.030  26.017   2.005  39.404
        Known (#12)                                             Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6724 Dev= 0.40% S= 8.47 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   0.66

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     535 steps. Energy=    -293.4462626       time=       0.44
 Minus side of path:                     515 steps. Energy=    -294.4329309       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.4462626  1.6497         -291.7965372  2.6364         -294.4329309  10.407   8.066   4.507  17.528
        Known (#5)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2788.7    
 decide> The unconnected minima in the chain and their distances are:
    10       14.08     7 
 

 tryconnect> 140-iteration DNEB run for minima 7_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2121 Dev= 0.73% S= 15.26 time= 0.30
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   1.11
 isnewts> transition state is the same as number        4 energy=     -287.8743467576
 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:                     556 steps. Energy=    -294.4329309       time=       0.46
 Minus side of path:                     587 steps. Energy=    -294.4329309       time=       0.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.4329309  6.5586         -287.8743468  6.5586         -294.4329309  11.249   1.324   1.665  47.451
        Known (#8)                                              Known (#8)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3176.0    
 decide> The unconnected minima in the chain and their distances are:
    10       14.70     6 
 

 tryconnect> 140-iteration DNEB run for minima 6_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.4421 Dev= 1.21% S= 17.46 time= 0.31
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   0.93

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     577 steps. Energy=    -293.2970251       time=       0.48
 Minus side of path:                     666 steps. Energy=    -293.2970251       time=       0.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.2970251  5.6550         -287.6420228  5.6550         -293.2970251  19.492   4.902  18.191   4.343
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3522.5    
 decide> The unconnected minima in the chain and their distances are:
    11       15.22     7 
 

 tryconnect> 140-iteration DNEB run for minima 7_S and 11_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2511 Dev= 0.24% S= 16.19 time= 0.30
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   1.03

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     517 steps. Energy=    -295.5186524       time=       0.40
 Minus side of path:                     541 steps. Energy=    -292.4736776       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5186524  5.1256         -290.3930946  2.0806         -292.4736776  11.307   7.533   2.494  31.673
        Known (#9)                                              *NEW* (Placed in 15)
 Unconnected minimum 15 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 15 minima and 14 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3774.5    
 decide> The unconnected minima in the chain and their distances are:
     2       15.57     7 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 7_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3907 Dev= 0.37% S= 16.40 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.79
 isnewts> transition state is the same as number        6 energy=     -289.3115363835
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 15 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     667 steps. Energy=    -295.5186524       time=       0.56
 Minus side of path:                     543 steps. Energy=    -291.0753136       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5186524  6.2071         -289.3115364  1.7638         -291.0753136  14.542  11.306   5.380  14.683
        Known (#9)                                              Known (#11)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 15 minima and 15 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     3911.8    
 decide> The unconnected minima in the chain and their distances are:
     9       15.76     7 
 

 tryconnect> 140-iteration DNEB run for minima 7_S and 9_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.9927 Dev= 0.66% S= 16.36 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   0.68

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     549 steps. Energy=    -295.5186524       time=       0.43
 Minus side of path:                     791 steps. Energy=    -293.8576116       time=       0.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5186524  8.5222         -286.9964740  6.8611         -293.8576116  21.739  14.438   1.877  42.082
        Known (#9)                                              *NEW* (Placed in 16)
 Unconnected minimum 16 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 16 minima and 16 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     4346.9    
 decide> The unconnected minima in the chain and their distances are:
    15       16.32     7 
 

 tryconnect> 140-iteration DNEB run for minima 7_S and 15_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2918 Dev= 0.34% S= 17.35 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   0.82
 isnewts> transition state is the same as number       16 energy=     -286.9964740315
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 17 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     805 steps. Energy=    -293.8576116       time=       0.73
 Minus side of path:                     549 steps. Energy=    -295.5186524       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.8576116  6.8611         -286.9964740  8.5222         -295.5186524  21.746  14.440   1.877  42.078
        Known (#16)                                             Known (#9)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 16 minima and 17 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     4752.9    
 decide> The unconnected minima in the chain and their distances are:
    10       13.34     8 
 

 tryconnect> 805-iteration DNEB run for minima 8_S and 10_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 805 RMS= 0.1023 Dev= 3.64% S= 17.67 time= 10.20
 Following    2 images are candidates for TS:   12   18  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=   1.15
 isnewts> transition state is the same as number        8 energy=     -288.2223166266
 tryconnect> Will not repeat search for TS      1 same as TS      8

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                     906 steps. Energy=    -295.5186524       time=       0.89
 Minus side of path:                     522 steps. Energy=    -290.5066486       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5186524  5.1033         -290.4153167 0.91332E-01     -290.5066486  21.912  19.948   3.098  25.501
        Known (#9)                                              Known (#10)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 16 minima and 18 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5372.8    
 decide> The unconnected minima in the chain and their distances are:
    10       13.90     5 
 

 tryconnect> 805-iteration DNEB run for minima 5_S and 10_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 805 RMS= 0.1350 Dev= 5.38% S= 22.52 time= 9.96
 Following    3 images are candidates for TS:    7   11   16  
 Converged to TS (number of iterations):         94
 Converged to TS (number of iterations):         68
 Converged to TS (number of iterations):         22
 DNEB run yielded 3 true transition state(s) time=   3.86
 isnewts> transition state is the same as number        8 energy=     -288.2223166265
 tryconnect> Will not repeat search for TS      3 same as TS      8

 >>>>>  Path run for ts 19 ...
 Plus  side of path:                     641 steps. Energy=    -293.4462626       time=       0.56
 Minus side of path:                     699 steps. Energy=    -292.8082449       time=       0.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.4462626  2.4388         -291.0075006  1.8007         -292.8082449  34.181  27.053   3.688  21.420
        Known (#5)                                              *NEW* (Placed in 17)
 Unconnected minimum 17 found its way to S set.

 >>>>>  Path run for ts 20 ...
 Plus  side of path:                     654 steps. Energy=    -295.8524954       time=       0.58
 Minus side of path:                     809 steps. Energy=    -294.3624436       time=       0.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.8524954  6.8108         -289.0416920  5.3208         -294.3624436  28.733  11.377   5.121  15.426
        *NEW* (Placed in 18)                                    *NEW* (Placed in 19)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 19 minima and 20 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     944.92    
 decide> The unconnected minima in the chain and their distances are:
     9        9.81    17 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 17_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9119 Dev= 0.37% S= 10.54 time= 0.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   1.14

 >>>>>  Path run for ts 21 ...
 Plus  side of path:                     510 steps. Energy=    -293.5968682       time=       0.39
 Minus side of path:                     563 steps. Energy=    -294.7626443       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.5968682 0.80121         -292.7956552  1.9670         -294.7626443  13.365  11.768   3.132  25.227
        *NEW* (Placed in 20)                                    *NEW* (Placed in 21)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 21 minima and 21 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     339.18    
 decide> The unconnected minima in the chain and their distances are:
    16        4.62    21    20        6.22    17 
 

 tryconnect> 70-iteration DNEB run for minima 16_F and 21_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2758 Dev= 0.26% S= 4.97 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        209
 DNEB run yielded 1 true transition state(s) time=   5.16

 >>>>>  Path run for ts 22 ...
 Plus  side of path:                     568 steps. Energy=    -289.2632673       time=       0.45
 Minus side of path:                     591 steps. Energy=    -293.8576116       time=       0.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.2632673  5.1133         -284.1500006  9.7076         -293.8576116  17.856   9.570   2.285  34.569
        *NEW* (Placed in 22)                                    Known (#16)
 Unconnected minimum 22 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 17_S and 20_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0847 Dev= 0.03% S= 6.24 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.56

 >>>>>  Path run for ts 23 ...
 Plus  side of path:                     480 steps. Energy=    -292.8082449       time=       0.37
 Minus side of path:                     518 steps. Energy=    -293.5968682       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.8082449 0.10167E-01     -292.7980781 0.79879         -293.5968682   6.362   6.218   2.381  33.180
        Known (#17)                                             Known (#20)
 Unconnected minimum 20 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 15 >>>>>>>>>>>>>>>>>>>>> 22 minima and 23 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     197.46    
 decide> The unconnected minima in the chain and their distances are:
    16        4.62    21 
 

 tryconnect> 350-iteration DNEB run for minima 16_F and 21_S using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 350 RMS= 0.1091 Dev= 11.05% S= 5.97 time= 1.79
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.53

 >>>>>  Path run for ts 24 ...
 Plus  side of path:                     531 steps. Energy=    -294.7626443       time=       0.42
 Minus side of path:                     510 steps. Energy=    -293.8576116       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.7626443  5.8241         -288.9385152  4.9191         -293.8576116   5.580   4.622   9.423   8.384
        Known (#21)                                             Known (#16)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -293.7428787 0.51680        -293.2260783 0.22018        -293.4462626  13.578  13.388   1.665  47.449
   2     -293.4462626  3.9869        -289.4593180  3.9869        -293.4462626  10.270   4.809  19.563   4.038
  19     -293.4462626  2.4388        -291.0075006  1.8007        -292.8082449  34.181  27.053   3.688  21.420
  23     -292.8082449 0.10167E-01    -292.7980781 0.79879        -293.5968682   6.362   6.218   2.381  33.180
  21     -293.5968682 0.80121        -292.7956552  1.9670        -294.7626443  13.365  11.768   3.132  25.227
  24     -294.7626443  5.8241        -288.9385152  4.9191        -293.8576116   5.580   4.622   9.423   8.384
  16     -293.8576116  6.8611        -286.9964740  8.5222        -295.5186524  21.739  14.438   1.877  42.082
   6     -295.5186524  6.2071        -289.3115364  1.7638        -291.0753136  14.544  11.309   5.352  14.761
   7     -291.0753136 0.51444        -290.5608749 0.46536        -291.0262394   6.233   5.557  10.770   7.335

 Number of TS in the path       =      9
 Number of cycles               =     15

 Elapsed time=                                90.87
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            112780 time=          57.22 %= 63.0
 OPTIM> # of energy+gradient+Hessian calls=      1261 time=           1.33 %=  1.5
