
 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)@comp17.ch.
                 Created on  5/28/12 at 13: 9:50 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -385.7689833     RMS force=    0.9612589376E-06
 OPTIM> Final energy  =    -383.7306646     RMS force=    0.9139135387E-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=     37128.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.36     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0641 Dev= 2.32% S= 38.16 time= 4.28
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1097 steps. Energy=    -385.4052762       time=       3.68
 Minus side of path:                    1192 steps. Energy=    -382.9509283       time=       4.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4052762  6.8655         -378.5397571  4.4112         -382.9509283  41.204  37.566   1.688  85.899
        *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=     30269.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.66     3     4       16.10     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0684 Dev= 1.11% S= 31.67 time= 2.72
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=   6.86

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1008 steps. Energy=    -386.1328673       time=       2.69
 Minus side of path:                    1002 steps. Energy=    -383.8195022       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1328673  2.9962         -383.1366870 0.68282         -383.8195022  15.937  15.620   3.287  44.112
        *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:                    1001 steps. Energy=    -386.1328673       time=       3.52
 Minus side of path:                     997 steps. Energy=    -385.4052762       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1328673  1.6015         -384.5314079 0.87387         -385.4052762  19.657  19.474   2.387  60.740
        Known (#5)                                              Known (#3)
 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= 0.1734 Dev= 0.55% S= 17.00 time= 0.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        144
 DNEB run yielded 1 true transition state(s) time=  11.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1032 steps. Energy=    -382.9509283       time=       2.96
 Minus side of path:                    1121 steps. Energy=    -382.9485167       time=       3.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9509283 0.49175         -382.4591785 0.48934         -382.9485167  37.108  34.600   1.582  91.664
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     8361.0    
 decide> The unconnected minima in the chain and their distances are:
     2        2.55     6     4       16.10     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0208 Dev= 0.04% S= 2.56 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   4.19

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     996 steps. Energy=    -383.7306646       time=       3.29
 Minus side of path:                     997 steps. Energy=    -383.8195022       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7306646 0.48158E-01     -383.6825069 0.13700         -383.8195022   2.670   2.551   5.290  27.410
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 805 RMS= 0.0446 Dev= 5.34% S= 19.28 time= 22.43
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  10.60

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1007 steps. Energy=    -386.5783153       time=       2.57
 Minus side of path:                    1023 steps. Energy=    -382.9485167       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5783153  5.5399         -381.0384254  1.9101         -382.9485167  11.294   9.996   4.470  32.439
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     15474.    
 decide> The unconnected minima in the chain and their distances are:
     5       24.92     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2699 Dev= 0.79% S= 28.44 time= 2.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   5.76
 isnewts> transition state is the same as number        1 energy=     -378.5397571274
 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:                    1127 steps. Energy=    -385.4052762       time=       2.93
 Minus side of path:                    1176 steps. Energy=    -382.9509283       time=       3.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4052762  6.8655         -378.5397571  4.4112         -382.9509283  41.200  37.564   1.687  85.955
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     20485.    
 decide> The unconnected minima in the chain and their distances are:
     3       27.36     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1343 Dev= 2.64% S= 31.10 time= 2.73
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        103
 DNEB run yielded 1 true transition state(s) time=  10.00
 isnewts> transition state is the same as number        2 energy=     -383.1366870106
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1016 steps. Energy=    -383.8195022       time=       2.80
 Minus side of path:                    1015 steps. Energy=    -386.1328673       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8195022 0.68282         -383.1366870  2.9962         -386.1328673  15.937  15.620   3.284  44.153
        Known (#6)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     30948.    
 decide> The unconnected minima in the chain and their distances are:
     5       24.92     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0275 Dev= 5.05% S= 36.48 time= 27.35
 Following    2 images are candidates for TS:    8   17  
 Converged to TS (number of iterations):         97
 Converged to TS (number of iterations):         52
 DNEB run yielded 2 true transition state(s) time=  18.01
 isnewts> transition state is the same as number        3 energy=     -384.5314079027
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1148 steps. Energy=    -385.7689833       time=       4.52
 Minus side of path:                    1148 steps. Energy=    -384.7605017       time=       5.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7689833  4.6146         -381.1543956  3.6061         -384.7605017  43.179  33.388   1.925  75.333
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1011 steps. Energy=    -386.1328673       time=       3.82
 Minus side of path:                     989 steps. Energy=    -385.4052762       time=       2.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1328673  1.6015         -384.5314079 0.87387         -385.4052762  19.657  19.474   2.388  60.733
        Known (#5)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 10 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     186.46    
 decide> The unconnected minima in the chain and their distances are:
     6        5.71     9 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2094 Dev= 0.98% S= 6.27 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        115
 DNEB run yielded 1 true transition state(s) time=  10.74

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     987 steps. Energy=    -383.8195022       time=       3.89
 Minus side of path:                     939 steps. Energy=    -383.7273157       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8195022 0.16282         -383.6566826 0.70633E-01     -383.7273157  13.255  13.217   2.548  56.911
        Known (#6)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     225.53    
 decide> The unconnected minima in the chain and their distances are:
     2        6.09     9 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2854 Dev= 0.76% S= 6.61 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.73
 isnewts> transition state is the same as number        5 energy=     -383.6825068921
 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:                    1009 steps. Energy=    -383.8195022       time=       3.69
 Minus side of path:                     986 steps. Energy=    -383.7306646       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8195022 0.13700         -383.6825069 0.48158E-01     -383.7306646   2.670   2.551   5.290  27.410
        Known (#6)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 10 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     372.92    
 decide> The unconnected minima in the chain and their distances are:
     6        5.71     9 
 

 tryconnect> 455-iteration DNEB run for minima 6_F and 9_S using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0111 Dev= 1.44% S= 8.37 time= 7.49
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.80

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     995 steps. Energy=    -384.7605017       time=       2.95
 Minus side of path:                     986 steps. Energy=    -383.8195022       time=       3.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.7605017  3.4508         -381.3096970  2.5098         -383.8195022   6.588   5.715  38.231   3.793
        Known (#9)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -385.7689833  4.6146        -381.1543956  3.6061        -384.7605017  43.179  33.388   1.925  75.333
  13     -384.7605017  3.4508        -381.3096970  2.5098        -383.8195022   6.588   5.715  38.231   3.793
   5     -383.8195022 0.13700        -383.6825069 0.48158E-01    -383.7306646   2.670   2.551   5.290  27.410

 Number of TS in the path       =      3
 Number of cycles               =      9

 Elapsed time=                               249.42
 OPTIM> # of energy calls=                        204 time=           0.23 %=  0.1
 OPTIM> # of energy+gradient calls=             94910 time=         114.31 %= 45.8
 OPTIM> # of energy+gradient+Hessian calls=       755 time=           3.45 %=  1.4
