
 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)@comp32.ch.
                 Created on  5/28/12 at 12:36:30 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=    -386.7898562     RMS force=    0.9064236420E-06
 OPTIM> Final energy  =    -387.8251225     RMS force=    0.7507619007E-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=     28638.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.59     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1878 Dev= 2.23% S= 36.20 time= 3.96
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):        169
 Converged to TS (number of iterations):         52
 DNEB run yielded 2 true transition state(s) time=  20.30

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     959 steps. Energy=    -394.8035742       time=       2.76
 Minus side of path:                     915 steps. Energy=    -392.0963235       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.8035742  2.7507         -392.0528366 0.43487E-01     -392.0963235  11.302  10.252   4.513  32.130
        *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:                     875 steps. Energy=    -387.8299444       time=       2.00
 Minus side of path:                     888 steps. Energy=    -387.8251225       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8299444 0.32708E-01     -387.7972365 0.27886E-01     -387.8251225   1.510   1.504   3.113  46.573
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     20929.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.01     3     4       14.94     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1196 Dev= 0.61% S= 28.57 time= 2.46
 Following    2 images are candidates for TS:    2    5  
 Converged to TS (number of iterations):         48
 Converged to TS (number of iterations):        184
 DNEB run yielded 2 true transition state(s) time=  20.00

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     934 steps. Energy=    -388.0534299       time=       2.40
 Minus side of path:                     942 steps. Energy=    -387.8251225       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0534299  3.6245         -384.4289796  3.3961         -387.8251225  18.431  18.049   1.717  84.427
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1054 steps. Energy=    -392.5382565       time=       4.17
 Minus side of path:                     984 steps. Energy=    -388.9317856       time=       4.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.5382565  7.6364         -384.9018583  4.0299         -388.9317856  45.822  42.797   1.730  83.832
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1171 Dev= 0.72% S= 15.79 time= 0.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=  11.46

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     947 steps. Energy=    -387.5081588       time=       3.54
 Minus side of path:                    1079 steps. Energy=    -388.4596395       time=       3.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5081588 0.49080         -387.0173543  1.4423         -388.4596395  26.327  24.381   1.820  79.651
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3134.5    
 decide> The unconnected minima in the chain and their distances are:
     6       11.31     9     9       11.91     1 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6186 Dev= 0.28% S= 12.26 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.17

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     940 steps. Energy=    -388.0319619       time=       2.94
 Minus side of path:                     947 steps. Energy=    -392.5382565       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0319619  2.9632         -385.0687146  7.4695         -392.5382565  12.081  10.707   4.769  30.403
        *NEW* (Placed in 11)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0876 Dev= 0.03% S= 12.35 time= 0.43
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.68
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3785.2    
 decide> The unconnected minima in the chain and their distances are:
     6        8.17    11    11       14.80     1 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5916 Dev= 0.80% S= 8.88 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   7.38

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     898 steps. Energy=    -388.0534299       time=       3.06
 Minus side of path:                    1125 steps. Energy=    -390.7695405       time=       4.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0534299 0.54703         -387.5063963  3.2631         -390.7695405  23.564  19.320   2.346  61.819
        Known (#6)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 11_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.1647 Dev= 1.89% S= 16.19 time= 0.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        169
 DNEB run yielded 1 true transition state(s) time=  15.64

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1048 steps. Energy=    -387.5081588       time=       2.94
 Minus side of path:                     960 steps. Energy=    -387.8896974       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5081588 0.97263         -386.5355291  1.3542         -387.8896974  12.410  11.472  10.017  14.475
        Known (#9)                                              *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     4056.8    
 decide> The unconnected minima in the chain and their distances are:
     6        8.17    11    11        7.80     9    13       13.55     1 
 

 tryconnect> 630-iteration DNEB run for minima 6_F and 11_U using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 630 RMS= 0.0644 Dev= 5.66% S= 12.95 time= 15.62
 Following    2 images are candidates for TS:    8   12  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=   6.83
 isnewts> transition state is the same as number        6 energy=     -385.0687146103
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     901 steps. Energy=    -388.0534299       time=       2.19
 Minus side of path:                     926 steps. Energy=    -392.5382565       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0534299  5.2586         -382.7948410  9.7434         -392.5382565  12.173  10.933  12.919  11.224
        Known (#6)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     949 steps. Energy=    -388.0319619       time=       2.30
 Minus side of path:                     936 steps. Energy=    -392.5382565       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0319619  2.9632         -385.0687146  7.4695         -392.5382565  12.081  10.707   4.765  30.428
        Known (#11)                                             Known (#7)
 Alternative path found between members of the F set.

 tryconnect> 70-iteration DNEB run for minima 9_U and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1406 Dev= 0.18% S= 7.92 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.42

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     949 steps. Energy=    -387.5081588       time=       3.02
 Minus side of path:                     941 steps. Energy=    -388.0319619       time=       3.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5081588 0.21811         -387.2900493 0.74191         -388.0319619   8.154   7.801   3.008  48.202
        Known (#9)                                              Known (#11)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 13_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1638 Dev= 0.07% S= 14.05 time= 0.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=  10.85

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     827 steps. Energy=    -388.0136798       time=       2.39
 Minus side of path:                     861 steps. Energy=    -388.0319619       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0136798 0.12014E-01     -388.0016654 0.30297E-01     -388.0319619   6.322   6.308   3.785  38.309
        *NEW* (Placed in 14)                                    Known (#11)
 Unconnected minimum 14 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1667.6    
 decide> The unconnected minima in the chain and their distances are:
    14       11.86     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 14_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.3529 Dev= 0.63% S= 13.28 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   7.27
 isnewts> transition state is the same as number       11 energy=     -387.2900492630
 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:                     952 steps. Energy=    -387.5081588       time=       2.74
 Minus side of path:                     937 steps. Energy=    -388.0319619       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5081588 0.21811         -387.2900493 0.74191         -388.0319619   8.154   7.801   3.008  48.201
        Known (#9)                                              Known (#11)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 13 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3335.3    
 decide> The unconnected minima in the chain and their distances are:
    14       11.86     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 14_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 805 RMS= 0.0425 Dev= 5.50% S= 20.50 time= 25.19
 Following    2 images are candidates for TS:    4   17  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=   8.25
 isnewts> transition state is the same as number       11 energy=     -387.2900492630
 tryconnect> Will not repeat search for TS      2 same as TS     11

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                     911 steps. Energy=    -386.7898562       time=       2.31
 Minus side of path:                    1081 steps. Energy=    -387.5081588       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.7898562 0.23954         -386.5503142 0.95784         -387.5081588  12.546  11.910  10.891  13.314
        Known (#1)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  14     -386.7898562 0.23954        -386.5503142 0.95784        -387.5081588  12.546  11.910  10.891  13.314
  11     -387.5081588 0.21811        -387.2900493 0.74191        -388.0319619   8.154   7.801   3.008  48.202
   6     -388.0319619  2.9632        -385.0687146  7.4695        -392.5382565  12.081  10.707   4.769  30.403
   9     -392.5382565  9.7434        -382.7948410  5.2586        -388.0534299  12.173  10.933  12.919  11.224
   3     -388.0534299  3.6245        -384.4289796  3.3961        -387.8251225  18.431  18.049   1.717  84.427

 Number of TS in the path       =      5
 Number of cycles               =      7

 Elapsed time=                               269.27
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             81741 time=         109.19 %= 40.5
 OPTIM> # of energy+gradient+Hessian calls=      1379 time=           7.01 %=  2.6
