
 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)@comp29.ch.
                 Created on  5/28/12 at 12:54:45 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=    -386.1053788     RMS force=    0.9501329568E-06
 OPTIM> Final energy  =    -396.8219334     RMS force=    0.7851346602E-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=     52419.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.43     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      428.1303623    
 Double-ended search iterations= 395 RMS= 3.1849 Dev= 4.30% S= 38.35 time= 6.02
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        245
 DNEB run yielded 1 true transition state(s) time=  23.89

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     837 steps. Energy=    -383.4519432       time=       1.98
 Minus side of path:                     922 steps. Energy=    -385.4788081       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4519432 0.22196         -383.2299785  2.2488         -385.4788081  21.131  20.736   5.019  28.893
        *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=     37796.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.77     4     3       27.45     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 12.2899 Dev= 14.88% S= 42.63 time= 2.45
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     948 steps. Energy=    -392.9256429       time=       3.52
 Minus side of path:                     945 steps. Energy=    -393.7085109       time=       3.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.9256429  2.5061         -390.4195384  3.2890         -393.7085109   6.005   5.291  33.902   4.277
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 280 RMS= 0.2041 Dev= 0.63% S= 28.78 time= 3.28
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        109
 DNEB run yielded 1 true transition state(s) time=   9.93

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1032 steps. Energy=    -385.0597909       time=       2.98
 Minus side of path:                     957 steps. Energy=    -383.0771300       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0597909  3.1876         -381.8722373  1.2049         -383.0771300  20.109  18.883   2.762  52.500
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      4 missing connections, weight=     23526.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.00     5     6       10.14     4     3       11.37     8     7       19.30     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 245 RMS= 0.2320 Dev= 1.08% S= 27.57 time= 2.47
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.91

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     942 steps. Energy=    -392.9256429       time=       2.36
 Minus side of path:                     973 steps. Energy=    -395.9970883       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.9256429 0.98302         -391.9426233  4.0545         -395.9970883  23.506  21.034   9.133  15.877
        Known (#5)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 30.6499 Dev= 46.65% S= 55.84 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1126 steps. Energy=    -393.8833304       time=       3.17
 Minus side of path:                     900 steps. Energy=    -394.6595000       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.8833304  10.211         -383.6725612  10.987         -394.6595000  17.872  12.350   5.229  27.732
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 6.2848 Dev= 16.07% S= 17.55 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   6.44

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     885 steps. Energy=    -382.9283796       time=       2.46
 Minus side of path:                     918 steps. Energy=    -383.3562220       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9283796 0.36757         -382.5608117 0.79541         -383.3562220   5.992   5.136   7.215  20.098
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.1457 Dev= 0.34% S= 20.45 time= 1.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     937 steps. Energy=    -385.0597909       time=       3.46
 Minus side of path:                    1022 steps. Energy=    -386.1053788       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0597909  1.3863         -383.6735384  2.4318         -386.1053788  21.859  19.325  13.300  10.902
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 13 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      4 missing connections, weight=     2932.9    
 decide> The unconnected minima in the chain and their distances are:
     2        5.25     9     5       11.52     4     3        1.31    13    12       10.80     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 2.2109 Dev= 0.97% S= 5.81 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     929 steps. Energy=    -396.4007070       time=       3.22
 Minus side of path:                     960 steps. Energy=    -395.9970883       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.4007070  2.1506         -394.2501384  1.7469         -395.9970883  18.214  17.636   3.675  39.456
        *NEW* (Placed in 14)                                    Known (#9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 114 RMS= 29.3274 Dev= 47.45% S= 53.34 time= 0.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   4.93

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     851 steps. Energy=    -395.6950382       time=       2.11
 Minus side of path:                     836 steps. Energy=    -395.3818682       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.6950382  1.2140         -394.4810848 0.90078         -395.3818682   2.168   1.935  67.173   2.159
        *NEW* (Placed in 15)                                    *NEW* (Placed in 16)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 13_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0244 Dev= 0.61% S= 1.32 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.96

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     873 steps. Energy=    -383.4519432       time=       2.75
 Minus side of path:                     856 steps. Energy=    -383.3562220       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4519432 0.13350         -383.3184476 0.37774E-01     -383.3562220   1.335   1.314   5.181  27.986
        Known (#3)                                              Known (#13)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 8_S and 12_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 105 RMS= 0.1846 Dev= 0.46% S= 10.89 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.00

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     936 steps. Energy=    -383.0771300       time=       2.47
 Minus side of path:                     900 steps. Energy=    -382.9989026       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0771300 0.23797         -382.8391565 0.15975         -382.9989026   9.353   9.106   3.303  43.906
        Known (#8)                                              *NEW* (Placed in 17)
 Unconnected minimum 17 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 17 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      3 missing connections, weight=     2481.9    
 decide> The unconnected minima in the chain and their distances are:
     2        5.25     9     6       10.14     4    12        4.72    17 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 9_U using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4855829818    
 Double-ended search iterations= 420 RMS= 0.0162 Dev= 2.37% S= 7.46 time= 7.18
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.05

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     950 steps. Energy=    -396.8219334       time=       2.26
 Minus side of path:                     940 steps. Energy=    -395.9970883       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.8219334  3.3274         -393.4945486  2.5025         -395.9970883   5.959   5.258  34.229   4.236
        Known (#2)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 4_U and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 805 RMS= 0.0554 Dev= 3.87% S= 12.32 time= 25.75
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     997 steps. Energy=    -393.7085109       time=       2.50
 Minus side of path:                     911 steps. Energy=    -385.4788081       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7085109  8.4213         -385.2871903 0.19162         -385.4788081  12.348  10.143   5.765  25.150
        Known (#6)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 12_F and 17_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 0.7374 Dev= 6.11% S= 4.75 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.58

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     906 steps. Energy=    -382.9283796       time=       2.76
 Minus side of path:                     895 steps. Energy=    -382.9989026       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9283796 0.29366         -382.6347193 0.36418         -382.9989026   5.477   4.715   3.862  37.547
        Known (#12)                                             Known (#17)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -386.1053788  2.4318        -383.6735384  1.3863        -385.0597909  21.859  19.325  13.300  10.902
   3     -385.0597909  3.1876        -381.8722373  1.2049        -383.0771300  20.109  18.883   2.762  52.500
  11     -383.0771300 0.23797        -382.8391565 0.15975        -382.9989026   9.353   9.106   3.303  43.906
  14     -382.9989026 0.36418        -382.6347193 0.29366        -382.9283796   5.477   4.715   3.862  37.547
   6     -382.9283796 0.36757        -382.5608117 0.79541        -383.3562220   5.992   5.136   7.215  20.098
  10     -383.3562220 0.37774E-01    -383.3184476 0.13350        -383.4519432   1.335   1.314   5.181  27.986
   1     -383.4519432 0.22196        -383.2299785  2.2488        -385.4788081  21.131  20.736   5.019  28.893
  13     -385.4788081 0.19162        -385.2871903  8.4213        -393.7085109  12.348  10.143   5.765  25.150
   2     -393.7085109  3.2890        -390.4195384  2.5061        -392.9256429   6.005   5.291  33.902   4.277
   4     -392.9256429 0.98302        -391.9426233  4.0545        -395.9970883  23.506  21.034   9.133  15.877
  12     -395.9970883  2.5025        -393.4945486  3.3274        -396.8219334   5.959   5.258  34.229   4.236

 Number of TS in the path       =     11
 Number of cycles               =      5

 Elapsed time=                               217.64
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             76885 time=         105.71 %= 48.6
 OPTIM> # of energy+gradient+Hessian calls=       827 time=           4.09 %=  1.9
