
 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)@comp24.ch.
                 Created on  5/28/12 at 12:43:18 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=    -394.7678708     RMS force=    0.9471894182E-06
 OPTIM> Final energy  =    -383.8645237     RMS force=    0.8773833883E-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=    0.60964E+06
 decide> The unconnected minima in the chain and their distances are:
     2       84.79     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 805 RMS= 0.0868 Dev= 6.08% S= 104.73 time= 23.76
 Following    2 images are candidates for TS:    6   16  
 Converged to TS (number of iterations):         97
 Converged to TS (number of iterations):         94
 DNEB run yielded 2 true transition state(s) time=  15.55

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1044 steps. Energy=    -387.6397579       time=       2.60
 Minus side of path:                    1464 steps. Energy=    -395.4417387       time=       4.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6397579 0.60808         -387.0316829  8.4101         -395.4417387  44.409  29.794   2.769  52.358
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1206 steps. Energy=    -389.4906948       time=       3.17
 Minus side of path:                    1657 steps. Energy=    -386.9871926       time=       5.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4906948  6.2271         -383.2635758  3.7236         -386.9871926  60.015  42.918   1.741  83.293
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     68455.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.61     6     5       36.15     3     4        5.50     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= 0.0368 Dev= 0.90% S= 28.71 time= 2.61
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   4.93

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1145 steps. Energy=    -386.9871926       time=       2.77
 Minus side of path:                     993 steps. Energy=    -383.8645237       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9871926  3.1382         -383.8489683 0.15555E-01     -383.8645237  28.697  27.615   2.372  61.118
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 3_U and 5_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1583 Dev= 2.82% S= 46.35 time= 4.52
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         74
 Converged to TS (number of iterations):         46
 DNEB run yielded 2 true transition state(s) time=  10.48

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1029 steps. Energy=    -393.3006789       time=       3.72
 Minus side of path:                     970 steps. Energy=    -390.2502440       time=       3.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3006789  5.2858         -388.0149237  2.2353         -390.2502440  35.531  34.466   3.042  47.668
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     977 steps. Energy=    -390.3031596       time=       2.77
 Minus side of path:                     997 steps. Energy=    -389.3867328       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3031596  4.6242         -385.6789724  3.7078         -389.3867328  15.797  11.271  28.631   5.064
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0657 Dev= 0.07% S= 5.53 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.49

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     944 steps. Energy=    -395.4417387       time=       2.58
 Minus side of path:                     945 steps. Energy=    -394.7678708       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.4417387 0.90701         -394.5347249 0.23315         -394.7678708   7.095   5.501   5.437  26.668
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      3 missing connections, weight=     2407.9    
 decide> The unconnected minima in the chain and their distances are:
     5        1.05    10     9        1.05     8     7       13.40     3 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0195 Dev= 0.19% S= 1.06 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     937 steps. Energy=    -389.4906948       time=       2.62
 Minus side of path:                     933 steps. Energy=    -389.3867328       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4906948 0.11656         -389.3741329 0.12600E-01     -389.3867328   1.056   1.053  42.210   3.435
        Known (#5)                                              Known (#10)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0619 Dev= 0.58% S= 1.07 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     954 steps. Energy=    -390.3031596       time=       3.04
 Minus side of path:                     924 steps. Energy=    -390.2502440       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3031596 0.78526E-01     -390.2246333 0.25611E-01     -390.2502440   1.057   1.054  18.312   7.918
        Known (#9)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 3_S and 7_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2536 Dev= 0.29% S= 14.89 time= 0.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.51

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1224 steps. Energy=    -395.0083085       time=       4.97
 Minus side of path:                    1046 steps. Energy=    -387.6397579       time=       4.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0083085  8.9142         -386.0941396  1.5456         -387.6397579  34.552  22.355   3.385  42.836
        *NEW* (Placed in 11)                                    Known (#3)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     4811.2    
 decide> The unconnected minima in the chain and their distances are:
     7       13.40     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 7_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 805 RMS= 0.0477 Dev= 4.03% S= 18.44 time= 25.78
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   5.68
 isnewts> transition state is the same as number        9 energy=     -386.0941396249
 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:                    1047 steps. Energy=    -387.6397579       time=       4.18
 Minus side of path:                    1226 steps. Energy=    -395.0083085       time=       5.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6397579  1.5456         -386.0941396  8.9142         -395.0083085  34.547  22.350   3.389  42.787
        Known (#3)                                              Known (#11)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     8116.3    
 decide> The unconnected minima in the chain and their distances are:
     7       20.10    11 
 

 tryconnect> 210-iteration DNEB run for minima 7_F and 11_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0482 Dev= 0.25% S= 20.62 time= 1.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.61

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     959 steps. Energy=    -393.3217389       time=       2.33
 Minus side of path:                    1102 steps. Energy=    -395.0083085       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3217389  1.6214         -391.7003422  3.3080         -395.0083085  21.902  19.354   2.314  62.667
        *NEW* (Placed in 12)                                    Known (#11)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      1 missing connections, weight=     3.4979    
 decide> The unconnected minima in the chain and their distances are:
     7        1.52    12 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0279 Dev= 0.03% S= 1.52 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     940 steps. Energy=    -393.3217389       time=       3.39
 Minus side of path:                     956 steps. Energy=    -393.3006789       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3217389 0.65813E-01     -393.2559260 0.44753E-01     -393.3006789   1.524   1.518   3.041  47.687
        Known (#12)                                             Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -394.7678708 0.23315        -394.5347249 0.90701        -395.4417387   7.095   5.501   5.437  26.668
   1     -395.4417387  8.4101        -387.0316829 0.60808        -387.6397579  44.409  29.794   2.769  52.358
   9     -387.6397579  1.5456        -386.0941396  8.9142        -395.0083085  34.552  22.355   3.385  42.836
  11     -395.0083085  3.3080        -391.7003422  1.6214        -393.3217389  21.902  19.354   2.314  62.667
  12     -393.3217389 0.65813E-01    -393.2559260 0.44753E-01    -393.3006789   1.524   1.518   3.041  47.687
   4     -393.3006789  5.2858        -388.0149237  2.2353        -390.2502440  35.531  34.466   3.042  47.668
   8     -390.2502440 0.25611E-01    -390.2246333 0.78526E-01    -390.3031596   1.057   1.054  18.312   7.918
   5     -390.3031596  4.6242        -385.6789724  3.7078        -389.3867328  15.797  11.271  28.631   5.064
   7     -389.3867328 0.12600E-01    -389.3741329 0.11656        -389.4906948   1.056   1.053  42.210   3.435
   2     -389.4906948  6.2271        -383.2635758  3.7236        -386.9871926  60.015  42.918   1.741  83.293
   3     -386.9871926  3.1382        -383.8489683 0.15555E-01    -383.8645237  28.697  27.615   2.372  61.118

 Number of TS in the path       =     11
 Number of cycles               =      6

 Elapsed time=                               202.99
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             82389 time=         104.66 %= 51.6
 OPTIM> # of energy+gradient+Hessian calls=       497 time=           2.25 %=  1.1
