
 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 13: 4:32 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=    -381.4115420     RMS force=    0.9091137211E-06
 OPTIM> Final energy  =    -384.3809262     RMS force=    0.9953443816E-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=    0.20578E+06
 decide> The unconnected minima in the chain and their distances are:
     2       59.04     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3322.971292    
 Double-ended search iterations= 1139 RMS= 1.2295 Dev= 0.10% S= 61.22 time= 22.42
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   9.30

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1017 steps. Energy=    -384.3684384       time=       4.00
 Minus side of path:                     962 steps. Energy=    -384.2576339       time=       3.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3684384 0.12422         -384.2442222 0.13412E-01     -384.2576339   2.492   2.410   4.084  35.503
        *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      2 steps with      2 missing connections, weight=    0.21057E+06
 decide> The unconnected minima in the chain and their distances are:
     2        2.26     4     4       59.49     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.4365 Dev= 4.21% S= 2.28 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.63
 isnewts> transition state is the same as number        1 energy=     -384.2442221501
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     967 steps. Energy=    -384.2576339       time=       2.86
 Minus side of path:                    1022 steps. Energy=    -384.3684384       time=       3.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2576339 0.13412E-01     -384.2442222 0.12422         -384.3684384   2.492   2.410   4.084  35.505
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> 595-iteration DNEB run for minima 1_S and 4_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2733.816706    
 Double-ended search iterations= 981 RMS= 0.9299 Dev= 0.08% S= 61.71 time= 19.51
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   9.11

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     970 steps. Energy=    -384.3809262       time=       3.17
 Minus side of path:                     926 steps. Energy=    -384.2740861       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3809262 0.12047         -384.2604565 0.13630E-01     -384.2740861   0.894   0.875  29.221   4.962
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.20478E+06
 decide> The unconnected minima in the chain and their distances are:
     5       58.94     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 5_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      768.8606195    
 Double-ended search iterations= 830 RMS= 0.9768 Dev= 0.07% S= 61.11 time= 16.48
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   7.67

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1006 steps. Energy=    -380.5843132       time=       2.53
 Minus side of path:                    1021 steps. Energy=    -380.6818344       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.5843132 0.15161E-01     -380.5691521 0.11268         -380.6818344   1.024   1.022  38.049   3.811
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     89491.    
 decide> The unconnected minima in the chain and their distances are:
     5       36.62     6     7       34.31     1 
 

 tryconnect> 350-iteration DNEB run for minima 5_F and 6_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      24.06619234    
 Double-ended search iterations= 350 RMS= 0.1863 Dev= 1.15% S= 36.83 time= 4.03
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   6.71

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1157 steps. Energy=    -384.3395678       time=       5.63
 Minus side of path:                    1007 steps. Energy=    -380.5843132       time=       4.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678  3.7763         -380.5632506 0.21063E-01     -380.5843132  36.296  35.606   1.634  88.758
        *NEW* (Placed in 8)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 7_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.77455444    
 Double-ended search iterations= 350 RMS= 0.1671 Dev= 0.54% S= 34.94 time= 4.17
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=   9.25

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1070 steps. Energy=    -380.6105130       time=       2.46
 Minus side of path:                    1062 steps. Energy=    -380.6818344       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6105130 0.32774         -380.2827718 0.39906         -380.6818344  27.250  25.963   2.045  70.912
        *NEW* (Placed in 9)                                     Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     4932.3    
 decide> The unconnected minima in the chain and their distances are:
     5        3.51     8     9       16.97     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0325 Dev= 0.12% S= 3.52 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.01
 isnewts> transition state is the same as number        3 energy=     -384.2604564517
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     936 steps. Energy=    -384.2740861       time=       2.10
 Minus side of path:                     970 steps. Energy=    -384.3809262       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2740861 0.13630E-01     -384.2604565 0.12047         -384.3809262   0.894   0.875  29.222   4.962
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 9_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 0.1256 Dev= 0.31% S= 17.13 time= 0.94
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=   7.86

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     993 steps. Energy=    -380.6105130       time=       3.54
 Minus side of path:                    1050 steps. Energy=    -381.2770161       time=       3.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6105130 0.39898E-01     -380.5706150 0.70640         -381.2770161  21.688  21.547   1.864  77.791
        Known (#9)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     9827.0    
 decide> The unconnected minima in the chain and their distances are:
     2        3.67     8     9       16.97     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0157 Dev= 0.36% S= 3.67 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.85

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     956 steps. Energy=    -384.3395678       time=       2.21
 Minus side of path:                     977 steps. Energy=    -384.3809262       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678 0.17609E-01     -384.3219585 0.58968E-01     -384.3809262   3.686   3.668   1.703  85.122
        Known (#8)                                              Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 9_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2575150228    
 Double-ended search iterations= 805 RMS= 0.0171 Dev= 6.89% S= 20.34 time= 20.25
 Following    1 images are candidates for TS:   16  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.82
 isnewts> transition state is the same as number        8 energy=     -380.5706150292
 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:                    1024 steps. Energy=    -380.6105130       time=       3.45
 Minus side of path:                    1046 steps. Energy=    -381.2770161       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6105130 0.39898E-01     -380.5706150 0.70640         -381.2770161  21.688  21.547   1.864  77.796
        Known (#9)                                              Known (#10)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     11453.    
 decide> The unconnected minima in the chain and their distances are:
    10       22.54     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 10_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 210 RMS= 1.9962 Dev= 1.19% S= 22.86 time= 1.38
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=  10.57

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     995 steps. Energy=    -381.4115420       time=       2.59
 Minus side of path:                    1528 steps. Energy=    -387.0916773       time=       6.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4115420 0.75632E-01     -381.3359099  5.7558         -387.0916773  38.866  35.969   1.932  75.046
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     22907.    
 decide> The unconnected minima in the chain and their distances are:
    10       22.54     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 10_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1070028109    
 Double-ended search iterations= 805 RMS= 0.0117 Dev= 1.37% S= 24.28 time= 20.94
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   4.68

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1015 steps. Energy=    -381.3057367       time=       3.12
 Minus side of path:                    1044 steps. Energy=    -381.4115420       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3057367 0.31476         -380.9909805 0.42056         -381.4115420  24.115  22.175   2.649  54.734
        *NEW* (Placed in 12)                                    Known (#1)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=    0.94423    
 decide> The unconnected minima in the chain and their distances are:
    10        0.98    12 
 

 tryconnect> 70-iteration DNEB run for minima 10_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0772 Dev= 0.28% S= 0.98 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.33

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     963 steps. Energy=    -381.3057367       time=       2.25
 Minus side of path:                     987 steps. Energy=    -381.2770161       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3057367 0.47928E-01     -381.2578087 0.19207E-01     -381.2770161   1.034   0.981  12.024  12.060
        Known (#12)                                             Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -381.4115420 0.42056        -380.9909805 0.31476        -381.3057367  24.115  22.175   2.649  54.734
  13     -381.3057367 0.47928E-01    -381.2578087 0.19207E-01    -381.2770161   1.034   0.981  12.024  12.060
   8     -381.2770161 0.70640        -380.5706150 0.39898E-01    -380.6105130  21.688  21.547   1.864  77.791
   6     -380.6105130 0.32774        -380.2827718 0.39906        -380.6818344  27.250  25.963   2.045  70.912
   4     -380.6818344 0.11268        -380.5691521 0.15161E-01    -380.5843132   1.024   1.022  38.049   3.811
   5     -380.5843132 0.21063E-01    -380.5632506  3.7763        -384.3395678  36.296  35.606   1.634  88.758
   9     -384.3395678 0.17609E-01    -384.3219585 0.58968E-01    -384.3809262   3.686   3.668   1.703  85.122

 Number of TS in the path       =      7
 Number of cycles               =      9

 Elapsed time=                               279.67
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            138290 time=         150.46 %= 53.8
 OPTIM> # of energy+gradient+Hessian calls=       713 time=           3.25 %=  1.2
