
 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)@comp23.ch.
                 Created on  5/28/12 at 13: 3:44 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=    -388.3575902     RMS force=    0.9042067956E-06
 OPTIM> Final energy  =    -383.0206471     RMS force=    0.9368276356E-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=     46586.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.98     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 350 RMS= 0.1937 Dev= 1.79% S= 46.14 time= 4.43
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         91
 DNEB run yielded 1 true transition state(s) time=   8.43

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1001 steps. Energy=    -385.7707842       time=       3.48
 Minus side of path:                    1001 steps. Energy=    -385.4437110       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7707842  4.9571         -380.8136678  4.6300         -385.4437110  25.396  19.065   2.731  53.097
        *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=     39195.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.42     4     3       25.32     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 4_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1230 Dev= 0.62% S= 29.20 time= 2.83
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   7.41

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1162 steps. Energy=    -385.7361205       time=       4.69
 Minus side of path:                    1009 steps. Energy=    -385.2135385       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7361205  2.8474         -382.8887169  2.3248         -385.2135385  25.364  20.813   1.834  79.083
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 245 RMS= 0.2293 Dev= 0.80% S= 30.44 time= 2.29
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  11.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1298 steps. Energy=    -385.7707842       time=       5.48
 Minus side of path:                    1005 steps. Energy=    -380.3822920       time=       3.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7707842  5.4824         -380.2884256 0.93866E-01     -380.3822920  30.097  25.599   3.001  48.314
        Known (#3)                                              *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=     39134.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.13     6     6       11.81     4     7       24.79     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0545 Dev= 0.62% S= 29.07 time= 2.90
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   6.01
 isnewts> transition state is the same as number        2 energy=     -382.8887168998
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1195 steps. Energy=    -385.7361205       time=       4.94
 Minus side of path:                     996 steps. Energy=    -385.2135385       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7361205  2.8474         -382.8887169  2.3248         -385.2135385  25.365  20.814   1.833  79.102
        Known (#5)                                              Known (#6)
 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      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0928 Dev= 0.04% S= 11.90 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     972 steps. Energy=    -385.2135385       time=       2.53
 Minus side of path:                     988 steps. Energy=    -385.4437110       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2135385 0.33714         -384.8763999 0.56731         -385.4437110  12.284  11.813   5.956  24.344
        Known (#6)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 245 RMS= 0.2098 Dev= 1.39% S= 30.07 time= 2.26
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   7.14

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1114 steps. Energy=    -387.8615748       time=       3.64
 Minus side of path:                    1228 steps. Energy=    -385.7707842       time=       5.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8615748  9.8751         -377.9864865  7.7843         -385.7707842  46.395  24.151   6.129  23.658
        *NEW* (Placed in 8)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     31067.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.26     5     8        8.05     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 5_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0486 Dev= 1.08% S= 32.48 time= 3.64
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.41

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     991 steps. Energy=    -383.0471519       time=       3.37
 Minus side of path:                    1154 steps. Energy=    -385.7361205       time=       4.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0471519 0.25695         -382.7901993  2.9459         -385.7361205  32.280  31.038   1.926  75.299
        *NEW* (Placed in 9)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0461 Dev= 0.01% S= 8.06 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.98

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     973 steps. Energy=    -387.8615748       time=       2.72
 Minus side of path:                     993 steps. Energy=    -388.3561027       time=       3.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8615748 0.17967         -387.6819043 0.67420         -388.3561027   8.436   8.397   2.071  69.999
        Known (#8)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     1.6797    
 decide> The unconnected minima in the chain and their distances are:
     2        0.87     9    10        1.00     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0125 Dev= 0.02% S= 0.88 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   4.39

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     956 steps. Energy=    -383.0206471       time=       3.20
 Minus side of path:                     955 steps. Energy=    -383.0471519       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0206471 0.22140E-01     -382.9985073 0.48645E-01     -383.0471519   0.884   0.873  30.760   4.714
        Known (#2)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1377 Dev= 0.00% S= 1.01 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.20

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     938 steps. Energy=    -388.3575902       time=       2.80
 Minus side of path:                     899 steps. Energy=    -388.3561027       time=       2.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3575902 0.17809E-01     -388.3397810 0.16322E-01     -388.3561027   1.008   1.005   3.506  41.360
        Known (#1)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -388.3575902 0.17809E-01    -388.3397810 0.16322E-01    -388.3561027   1.008   1.005   3.506  41.360
   8     -388.3561027 0.67420        -387.6819043 0.17967        -387.8615748   8.436   8.397   2.071  69.999
   6     -387.8615748  9.8751        -377.9864865  7.7843        -385.7707842  46.395  24.151   6.129  23.658
   1     -385.7707842  4.9571        -380.8136678  4.6300        -385.4437110  25.396  19.065   2.731  53.097
   5     -385.4437110 0.56731        -384.8763999 0.33714        -385.2135385  12.284  11.813   5.956  24.344
   2     -385.2135385  2.3248        -382.8887169  2.8474        -385.7361205  25.364  20.813   1.834  79.083
   7     -385.7361205  2.9459        -382.7901993 0.25695        -383.0471519  32.280  31.038   1.926  75.299
   9     -383.0471519 0.48645E-01    -382.9985073 0.22140E-01    -383.0206471   0.884   0.873  30.760   4.714

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                               149.43
 OPTIM> # of energy calls=                        116 time=           0.14 %=  0.1
 OPTIM> # of energy+gradient calls=             46295 time=          57.02 %= 38.2
 OPTIM> # of energy+gradient+Hessian calls=       476 time=           2.23 %=  1.5
