
 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)@comp33.ch.
                 Created on  5/28/12 at 13: 8:43 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -377.6390132     RMS force=    0.9868132303E-06
 OPTIM> Final energy  =    -381.3066617     RMS force=    0.9731877753E-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=     68097.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.84     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0627 Dev= 4.02% S= 54.93 time= 5.56
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=   7.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1078 steps. Energy=    -377.9897253       time=       3.53
 Minus side of path:                    1187 steps. Energy=    -381.3026016       time=       3.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9897253 0.76328         -377.2264469  4.0762         -381.3026016  35.311  31.999   1.856  78.125
        *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=     49881.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.04     4     4       14.51     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.2996 Dev= 2.92% S= 45.00 time= 3.83
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.01

 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= 0.1786 Dev= 0.33% S= 14.97 time= 0.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.54

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1014 steps. Energy=    -377.6390132       time=       2.89
 Minus side of path:                    1123 steps. Energy=    -381.2306911       time=       4.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.6390132 0.63576         -377.0032524  4.2274         -381.2306911  17.590  14.509   5.382  26.941
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     46838.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.05     5 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 5_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1163 Dev= 1.95% S= 45.07 time= 3.96
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  16.72
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     81287.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.31     3     4        3.00     5 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0842 Dev= 2.47% S= 52.19 time= 5.54
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=   9.37

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1047 steps. Energy=    -377.7960816       time=       2.45
 Minus side of path:                    1207 steps. Energy=    -380.1934631       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.7960816  3.2628         -374.5333279  5.6601         -380.1934631  39.872  32.225   3.703  39.156
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0740 Dev= 0.05% S= 3.00 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.27

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1004 steps. Energy=    -381.2306911       time=       2.37
 Minus side of path:                     981 steps. Energy=    -381.3026016       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2306911 0.21165E-01     -381.2095263 0.93075E-01     -381.3026016   3.269   3.001   5.477  26.472
        Known (#5)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     38287.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.63     7     6        6.26     3 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 7_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0453 Dev= 0.68% S= 35.54 time= 4.02
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   5.94

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1187 steps. Energy=    -380.2155834       time=       3.91
 Minus side of path:                    1008 steps. Energy=    -381.3469114       time=       3.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834  1.1260         -379.0895915  2.2573         -381.3469114  45.049  42.515   1.712  84.720
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2816 Dev= 0.93% S= 6.75 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   6.41

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1439 steps. Energy=    -381.4125530       time=       4.75
 Minus side of path:                    1021 steps. Energy=    -377.9897253       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4125530  3.4273         -377.9852841 0.44411E-02     -377.9897253  35.228  35.133   1.638  88.510
        *NEW* (Placed in 10)                                    Known (#3)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     24993.    
 decide> The unconnected minima in the chain and their distances are:
     2        4.95     9     8       29.00     7     6        6.26     3 
 

 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= 0.0335 Dev= 0.00% S= 4.95 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.82

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     982 steps. Energy=    -381.3469114       time=       2.58
 Minus side of path:                     963 steps. Energy=    -381.3066617       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3469114 0.40357E-01     -381.3065543 0.10733E-03     -381.3066617   4.961   4.945   2.063  70.289
        Known (#9)                                              Known (#2)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 7_U and 8_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0198 Dev= 0.06% S= 29.34 time= 2.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.86

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1044 steps. Energy=    -380.2155834       time=       3.73
 Minus side of path:                    1023 steps. Energy=    -380.1934631       time=       3.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.42575         -379.7898383 0.40362         -380.1934631  31.387  29.158   1.945  74.539
        Known (#8)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 490-iteration DNEB run for minima 3_S and 6_F using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0124 Dev= 1.44% S= 9.24 time= 7.51
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.91

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1001 steps. Energy=    -377.9897253       time=       3.26
 Minus side of path:                    1477 steps. Energy=    -381.3109698       time=       6.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9897253  2.9767         -375.0130110  6.2980         -381.3109698  39.508  35.445   1.671  86.798
        Known (#3)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     735.80    
 decide> The unconnected minima in the chain and their distances are:
     6        6.26     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 6_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 805 RMS= 0.0034 Dev= 4.79% S= 9.93 time= 20.45
 Following    2 images are candidates for TS:   13   22  
 Converged to TS (number of iterations):         13
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=   7.70
 isnewts> transition state is the same as number        9 energy=     -375.0130109994
 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:                    1019 steps. Energy=    -377.9897253       time=       3.18
 Minus side of path:                    1544 steps. Energy=    -381.3109698       time=       5.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9897253  2.9767         -375.0130110  6.2980         -381.3109698  39.513  35.452   1.669  86.867
        Known (#3)                                              Known (#11)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1464 steps. Energy=    -381.3109698       time=       4.95
 Minus side of path:                     995 steps. Energy=    -377.7960816       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3109698  3.5270         -377.7839730 0.12109E-01     -377.7960816  36.240  36.003   1.632  88.822
        Known (#11)                                             Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -377.6390132 0.63576        -377.0032524  4.2274        -381.2306911  17.590  14.509   5.382  26.941
   4     -381.2306911 0.21165E-01    -381.2095263 0.93075E-01    -381.3026016   3.269   3.001   5.477  26.472
   1     -381.3026016  4.0762        -377.2264469 0.76328        -377.9897253  35.311  31.999   1.856  78.125
   9     -377.9897253  2.9767        -375.0130110  6.2980        -381.3109698  39.508  35.445   1.671  86.798
  11     -381.3109698  3.5270        -377.7839730 0.12109E-01    -377.7960816  36.240  36.003   1.632  88.822
   3     -377.7960816  3.2628        -374.5333279  5.6601        -380.1934631  39.872  32.225   3.703  39.156
   8     -380.1934631 0.40362        -379.7898383 0.42575        -380.2155834  31.387  29.158   1.945  74.539
   5     -380.2155834  1.1260        -379.0895915  2.2573        -381.3469114  45.049  42.515   1.712  84.720
   7     -381.3469114 0.40357E-01    -381.3065543 0.10733E-03    -381.3066617   4.961   4.945   2.063  70.289

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

 Elapsed time=                               228.71
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             88215 time=          93.79 %= 41.0
 OPTIM> # of energy+gradient+Hessian calls=      1001 time=           4.41 %=  1.9
