
 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)@comp18.ch.
                 Created on  5/28/12 at 13:11:38 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -397.4484357     RMS force=    0.9301017752E-06
 OPTIM> Final energy  =    -396.6730133     RMS force=    0.9128155356E-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=     5794.5    
 decide> The unconnected minima in the chain and their distances are:
     2       17.96     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1648 Dev= 0.40% S= 18.94 time= 1.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     949 steps. Energy=    -398.6490308       time=       3.80
 Minus side of path:                     942 steps. Energy=    -395.3706953       time=       3.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.6490308  3.9820         -394.6670117 0.70368         -395.3706953  21.133  19.029   5.427  26.718
        *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=     1127.8    
 decide> The unconnected minima in the chain and their distances are:
     2        9.71     4     3        5.96     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.4414 Dev= 0.51% S= 9.97 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   5.28

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     892 steps. Energy=    -395.6508935       time=       2.13
 Minus side of path:                     891 steps. Energy=    -395.3706953       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.6508935 0.36862         -395.2822770 0.88418E-01     -395.3706953   9.053   8.504   7.907  18.339
        *NEW* (Placed in 5)                                     Known (#4)
 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4094 Dev= 0.82% S= 7.29 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   5.67

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     861 steps. Energy=    -397.6360114       time=       1.89
 Minus side of path:                     886 steps. Energy=    -394.9675148       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.6360114  2.9000         -394.7360338 0.23148         -394.9675148   8.881   7.572   2.066  70.196
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     438.08    
 decide> The unconnected minima in the chain and their distances are:
     2        5.16     5     3        5.15     6     6        5.48     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2285 Dev= 1.07% S= 5.61 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   4.85

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     916 steps. Energy=    -396.4052763       time=       2.29
 Minus side of path:                     905 steps. Energy=    -395.6508935       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.4052763  1.1355         -395.2698258 0.38107         -395.6508935  15.210  14.848  14.089  10.292
        *NEW* (Placed in 8)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6938 Dev= 0.60% S= 5.46 time= 0.20
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.67

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.8118 Dev= 1.17% S= 6.85 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   4.96
 isnewts> transition state is the same as number        3 energy=     -394.7360338286
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     845 steps. Energy=    -397.6360114       time=       1.86
 Minus side of path:                     869 steps. Energy=    -394.9675148       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.6360114  2.9000         -394.7360338 0.23148         -394.9675148   8.881   7.572   2.066  70.185
        Known (#6)                                              Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     698.02    
 decide> The unconnected minima in the chain and their distances are:
     2        5.16     5     3        5.96     1 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 5_U using 11 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0209 Dev= 2.35% S= 7.09 time= 5.80
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.47

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     908 steps. Energy=    -396.6730133       time=       2.96
 Minus side of path:                     905 steps. Energy=    -395.6508935       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6730133  3.3133         -393.3596942  2.2912         -395.6508935   5.834   5.163  37.976   3.818
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 455-iteration DNEB run for minima 1_S and 3_F using 13 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 455 RMS= 0.0571 Dev= 7.03% S= 13.46 time= 8.25
 Following    2 images are candidates for TS:    2    9  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=   7.74

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     890 steps. Energy=    -397.4484357       time=       2.52
 Minus side of path:                     931 steps. Energy=    -398.4339524       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.4484357  2.6863         -394.7621397  3.6718         -398.4339524   6.192   5.874   7.741  18.731
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     910 steps. Energy=    -398.6490308       time=       2.76
 Minus side of path:                     895 steps. Energy=    -395.0717139       time=       2.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.6490308  4.5997         -394.0492970  1.0224         -395.0717139  13.425   8.420   4.387  33.051
        Known (#3)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     188.81    
 decide> The unconnected minima in the chain and their distances are:
     3        5.74     9 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 9_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3603 Dev= 0.87% S= 7.01 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.32

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     931 steps. Energy=    -398.4339524       time=       2.38
 Minus side of path:                     874 steps. Energy=    -398.6490308       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.4339524 0.56742E-01     -398.3772103 0.27182         -398.6490308   4.932   4.891   2.614  55.460
        Known (#9)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -397.4484357  2.6863        -394.7621397  3.6718        -398.4339524   6.192   5.874   7.741  18.731
   9     -398.4339524 0.56742E-01    -398.3772103 0.27182        -398.6490308   4.932   4.891   2.614  55.460
   1     -398.6490308  3.9820        -394.6670117 0.70368        -395.3706953  21.133  19.029   5.427  26.718
   2     -395.3706953 0.88418E-01    -395.2822770 0.36862        -395.6508935   9.053   8.504   7.907  18.339
   6     -395.6508935  2.2912        -393.3596942  3.3133        -396.6730133   5.834   5.163  37.976   3.818

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

 Elapsed time=                               123.62
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             37903 time=          50.89 %= 41.2
 OPTIM> # of energy+gradient+Hessian calls=       634 time=           3.15 %=  2.6
