
 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    145
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
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)@comp33.ch.
                 Created on  5/28/12 at 12:49:37 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 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>  435 Cartesian coordinates will be optimised for  145 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=    -391.1712673     RMS force=    0.9838863585E-06
 OPTIM> Final energy  =    -394.7678708     RMS force=    0.9471894182E-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=    0.22041E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.41     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 630 RMS= 0.0873 Dev= 5.66% S= 84.71 time= 16.15
 Following    2 images are candidates for TS:    3   13  
 Converged to TS (number of iterations):         42
 Converged to TS (number of iterations):        134
 DNEB run yielded 2 true transition state(s) time=  14.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     899 steps. Energy=    -392.7449319       time=       2.31
 Minus side of path:                     970 steps. Energy=    -391.1577527       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.7449319  4.6984         -388.0464856  3.1113         -391.1577527  32.628  31.124   1.841  78.769
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     883 steps. Energy=    -390.7995157       time=       2.14
 Minus side of path:                     927 steps. Energy=    -393.0415826       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7995157 0.22798         -390.5715311  2.4701         -393.0415826  17.510  16.445  10.711  13.538
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     58941.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.17     5     6       35.01     4     3        4.56     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.2534 Dev= 1.28% S= 27.07 time= 2.53
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  10.27
 isnewts> transition state is the same as number        2 energy=     -390.5715310688
 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:                     891 steps. Energy=    -390.7995157       time=       3.49
 Minus side of path:                     943 steps. Energy=    -393.0415826       time=       3.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7995157 0.22798         -390.5715311  2.4701         -393.0415826  17.510  16.446  10.696  13.556
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 4_U and 6_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0536 Dev= 2.67% S= 38.61 time= 5.02
 Following    2 images are candidates for TS:    6    9  
 Converged to TS (number of iterations):         59
 Converged to TS (number of iterations):         58
 DNEB run yielded 2 true transition state(s) time=  10.99

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     992 steps. Energy=    -391.7507267       time=       3.29
 Minus side of path:                     963 steps. Energy=    -392.0449973       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7507267  3.5461         -388.2046636  3.8403         -392.0449973  40.257  35.826   2.004  72.351
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     961 steps. Energy=    -399.0761276       time=       3.47
 Minus side of path:                     876 steps. Energy=    -393.0415826       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -399.0761276  6.3180         -392.7580881 0.28349         -393.0415826  12.111  11.535  10.805  13.420
        *NEW* (Placed in 9)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2552 Dev= 1.04% S= 4.81 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   5.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     941 steps. Energy=    -392.7449319       time=       3.26
 Minus side of path:                     932 steps. Energy=    -391.1712673       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.7449319  4.2402         -388.5046940  2.6666         -391.1712673  13.243   4.558  16.259   8.918
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     23508.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.42     6     9        7.99     8     7        3.73     4 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 280 RMS= 0.5671 Dev= 0.89% S= 30.46 time= 3.27
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   5.28

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     989 steps. Energy=    -393.0109403       time=       3.13
 Minus side of path:                    1000 steps. Energy=    -392.8183303       time=       4.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0109403  1.8912         -391.1197043  1.6986         -392.8183303  24.124  22.495   2.499  58.025
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.2497 Dev= 0.96% S= 8.09 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   6.17

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     915 steps. Energy=    -395.9761291       time=       3.51
 Minus side of path:                     832 steps. Energy=    -399.0761276       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.9761291  1.1221         -394.8540576  4.2221         -399.0761276   8.371   5.572  11.214  12.930
        *NEW* (Placed in 12)                                    Known (#9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 1.4894 Dev= 1.51% S= 3.75 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   4.47

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     861 steps. Energy=    -391.1159867       time=       2.84
 Minus side of path:                     873 steps. Energy=    -391.1577527       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1159867 0.32554E-01     -391.0834322 0.74320E-01     -391.1577527   1.180   1.167   5.808  24.967
        *NEW* (Placed in 13)                                    Known (#4)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      4 missing connections, weight=     1257.0    
 decide> The unconnected minima in the chain and their distances are:
     2        9.22    11    10        5.90     6    12        5.98     8     7        3.77    13 
 

 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= 0.4745 Dev= 0.62% S= 9.27 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.72

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     957 steps. Energy=    -392.8183303       time=       3.51
 Minus side of path:                     983 steps. Energy=    -395.4417387       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8183303 0.62939         -392.1889371  3.2528         -395.4417387  11.618  10.428   3.048  47.571
        Known (#11)                                             *NEW* (Placed in 14)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0469 Dev= 0.21% S= 5.91 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.87

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     851 steps. Energy=    -393.0794579       time=       1.95
 Minus side of path:                     815 steps. Energy=    -393.0109403       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0794579 0.94726E-01     -392.9847319 0.26208E-01     -393.0109403   1.668   1.658   9.318  15.562
        *NEW* (Placed in 15)                                    Known (#10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.1422 Dev= 0.44% S= 6.00 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.66

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     918 steps. Energy=    -395.9761291       time=       3.14
 Minus side of path:                     842 steps. Energy=    -392.0449973       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.9761291  3.9745         -392.0016768 0.43321E-01     -392.0449973   6.411   5.979   9.701  14.948
        Known (#12)                                             Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 13_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0444 Dev= 0.58% S= 3.80 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.13

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     881 steps. Energy=    -391.1159867       time=       2.20
 Minus side of path:                     931 steps. Energy=    -391.7507267       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1159867 0.20077E-01     -391.0959095 0.65482         -391.7507267   4.118   3.774   3.497  41.469
        Known (#13)                                             Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 15 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     13 steps with      2 missing connections, weight=     303.36    
 decide> The unconnected minima in the chain and their distances are:
     2        5.50    14    15        5.15     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 14_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0713 Dev= 1.12% S= 5.52 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     928 steps. Energy=    -394.7678708       time=       4.19
 Minus side of path:                     935 steps. Energy=    -395.4417387       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.7678708 0.23315         -394.5347249 0.90701         -395.4417387   7.095   5.501   5.437  26.668
        Known (#2)                                              Known (#14)
 Unconnected minimum 14 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_S and 15_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0885 Dev= 0.31% S= 5.16 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.86

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     848 steps. Energy=    -393.0794579       time=       2.79
 Minus side of path:                     846 steps. Energy=    -393.0415826       time=       2.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0794579 0.12136         -392.9580965 0.83486E-01     -393.0415826   5.646   5.155   8.040  18.035
        Known (#15)                                             Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -391.1712673  2.6666        -388.5046940  4.2402        -392.7449319  13.243   4.558  16.259   8.918
   1     -392.7449319  4.6984        -388.0464856  3.1113        -391.1577527  32.628  31.124   1.841  78.769
   9     -391.1577527 0.74320E-01    -391.0834322 0.32554E-01    -391.1159867   1.180   1.167   5.808  24.967
  13     -391.1159867 0.20077E-01    -391.0959095 0.65482        -391.7507267   4.118   3.774   3.497  41.469
   4     -391.7507267  3.5461        -388.2046636  3.8403        -392.0449973  40.257  35.826   2.004  72.351
  12     -392.0449973 0.43321E-01    -392.0016768  3.9745        -395.9761291   6.411   5.979   9.701  14.948
   8     -395.9761291  1.1221        -394.8540576  4.2221        -399.0761276   8.371   5.572  11.214  12.930
   5     -399.0761276  6.3180        -392.7580881 0.28349        -393.0415826  12.111  11.535  10.805  13.420
  15     -393.0415826 0.83486E-01    -392.9580965 0.12136        -393.0794579   5.646   5.155   8.040  18.035
  11     -393.0794579 0.94726E-01    -392.9847319 0.26208E-01    -393.0109403   1.668   1.658   9.318  15.562
   7     -393.0109403  1.8912        -391.1197043  1.6986        -392.8183303  24.124  22.495   2.499  58.025
  10     -392.8183303 0.62939        -392.1889371  3.2528        -395.4417387  11.618  10.428   3.048  47.571
  14     -395.4417387 0.90701        -394.5347249 0.23315        -394.7678708   7.095   5.501   5.437  26.668

 Number of TS in the path       =     13
 Number of cycles               =      5

 Elapsed time=                               196.42
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             61186 time=          87.26 %= 44.4
 OPTIM> # of energy+gradient+Hessian calls=       653 time=           3.37 %=  1.7
