
 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)@comp21.ch.
                 Created on  5/28/12 at 12:38:31 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.
 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= 4.20
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         91
 DNEB run yielded 1 true transition state(s) time=   6.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1001 steps. Energy=    -385.7707842       time=       2.31
 Minus side of path:                    1001 steps. Energy=    -385.4437110       time=       2.28

         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= 2.79
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.39

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1162 steps. Energy=    -385.7361205       time=       2.96
 Minus side of path:                    1009 steps. Energy=    -385.2135385       time=       2.27

         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      2.429463211    
 Double-ended search iterations= 245 RMS= 0.2276 Dev= 1.28% S= 29.84 time= 2.19
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        157
 DNEB run yielded 1 true transition state(s) time=  12.39

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     972 steps. Energy=    -384.9060936       time=       2.15
 Minus side of path:                     999 steps. Energy=    -380.7388602       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9060936  4.6323         -380.2737939 0.46507         -380.7388602  12.971  12.684   2.686  53.993
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      3 missing connections, weight=     41747.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.13     6     6       11.81     4     4       26.14     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= 0.1890 Dev= 0.67% S= 29.12 time= 2.76
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.61
 isnewts> transition state is the same as number        2 energy=     -382.8887168997
 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:                    1165 steps. Energy=    -385.7361205       time=       2.98
 Minus side of path:                     996 steps. Energy=    -385.2135385       time=       2.22

         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   1.833  79.086
        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= 0.0851 Dev= 0.04% S= 11.89 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.50

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     986 steps. Energy=    -385.4437110       time=       2.22
 Minus side of path:                     964 steps. Energy=    -385.2135385       time=       2.10

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

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1890 Dev= 0.66% S= 34.88 time= 2.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   5.44

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1049 steps. Energy=    -385.5500505       time=       2.47
 Minus side of path:                    1145 steps. Energy=    -388.3575902       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5500505  4.6283         -380.9217548  7.4358         -388.3575902  36.576  26.884   4.383  33.084
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     27020.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.01     9 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 9_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0324 Dev= 0.83% S= 31.24 time= 3.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.87
 isnewts> transition state is the same as number        2 energy=     -382.8887169000
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     30554.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.26     5     4        2.12     9 
 

 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= 0.1116 Dev= 1.04% S= 32.39 time= 3.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.13

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1000 steps. Energy=    -383.0471519       time=       2.21
 Minus side of path:                    1166 steps. Energy=    -385.7361205       time=       2.97

         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   1.925  75.329
        *NEW* (Placed in 10)                                    Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0577 Dev= 0.01% S= 2.13 time= 0.22
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.91

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     916 steps. Energy=    -385.4437110       time=       1.97
 Minus side of path:                     936 steps. Energy=    -385.5500505       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4437110 0.37855E-02     -385.4399256 0.11012         -385.5500505   2.132   2.121   5.964  24.311
        Known (#4)                                              Known (#9)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=    0.66490    
 decide> The unconnected minima in the chain and their distances are:
     2        0.87    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0110 Dev= 0.02% S= 0.88 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.64

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     982 steps. Energy=    -383.0206471       time=       2.14
 Minus side of path:                     981 steps. Energy=    -383.0471519       time=       2.13

         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 (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -388.3575902  7.4358        -380.9217548  4.6283        -385.5500505  36.576  26.884   4.383  33.084
   8     -385.5500505 0.11012        -385.4399256 0.37855E-02    -385.4437110   2.132   2.121   5.964  24.311
   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   1.925  75.329
   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       =      6
 Number of cycles               =      6

 Elapsed time=                               117.65
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             47193 time=          55.98 %= 47.6
 OPTIM> # of energy+gradient+Hessian calls=       538 time=           1.98 %=  1.7
