
 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)@comp34.ch.
                 Created on  5/28/12 at 12:36: 9 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -382.1773825     RMS force=    0.9268464572E-06
 OPTIM> Final energy  =    -395.0112249     RMS force=    0.9702229703E-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=     89549.    
 decide> The unconnected minima in the chain and their distances are:
     2       44.74     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 455 RMS= 0.1830 Dev= 2.52% S= 54.95 time= 8.18
 Following    2 images are candidates for TS:    6   13  
 Converged to TS (number of iterations):         87
 Converged to TS (number of iterations):         43
 DNEB run yielded 2 true transition state(s) time=  13.47

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     902 steps. Energy=    -390.4787888       time=       2.82
 Minus side of path:                    1086 steps. Energy=    -382.5427530       time=       4.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4787888  13.649         -376.8300957  5.7127         -382.5427530  37.663  26.047   7.910  18.331
        *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:                     931 steps. Energy=    -395.0968200       time=       2.72
 Minus side of path:                     922 steps. Energy=    -394.9216256       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0968200  1.1978         -393.8989985  1.0226         -394.9216256   6.976   5.912   6.210  23.351
        *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      4 steps with      3 missing connections, weight=     9303.4    
 decide> The unconnected minima in the chain and their distances are:
     2        3.77     5     5       19.67     3     4       11.80     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2777 Dev= 0.04% S= 3.77 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     896 steps. Energy=    -395.0968200       time=       2.99
 Minus side of path:                     900 steps. Energy=    -395.0112249       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0968200 0.11704         -394.9797827 0.31442E-01     -395.0112249   3.780   3.767   2.230  65.019
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_U and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3620 Dev= 0.52% S= 20.86 time= 1.28
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.32

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0208 Dev= 0.00% S= 11.81 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.66

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     982 steps. Energy=    -382.5427530       time=       3.15
 Minus side of path:                     921 steps. Energy=    -382.1773825       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5427530 0.45059         -382.0921640 0.85218E-01     -382.1773825  12.375  11.800   2.246  64.568
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     7814.0    
 decide> The unconnected minima in the chain and their distances are:
     6       19.84     3 
 

 tryconnect> 175-iteration DNEB run for minima 3_S and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1819 Dev= 1.17% S= 21.63 time= 1.28
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.90
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     7917.3    
 decide> The unconnected minima in the chain and their distances are:
     2       19.93     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2672 Dev= 0.57% S= 21.10 time= 1.30
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.74
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     15217.    
 decide> The unconnected minima in the chain and their distances are:
     5       19.67     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0787 Dev= 5.03% S= 30.34 time= 27.00
 Following    3 images are candidates for TS:    4   19   22  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):         13
 Converged to TS (number of iterations):         28
 DNEB run yielded 3 true transition state(s) time=  11.80
 isnewts> transition state is the same as number        2 energy=     -393.8989984699
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     936 steps. Energy=    -395.3583493       time=       2.95
 Minus side of path:                     841 steps. Energy=    -390.4787888       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493  5.8020         -389.5563691 0.92242         -390.4787888  16.323  14.107  11.480  12.631
        *NEW* (Placed in 7)                                     Known (#3)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     919 steps. Energy=    -394.9216256       time=       2.91
 Minus side of path:                     929 steps. Energy=    -395.3198837       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9216256  1.2371         -393.6845693  1.6353         -395.3198837  14.738  13.526  14.506   9.996
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     926 steps. Energy=    -395.0968200       time=       2.43
 Minus side of path:                     937 steps. Energy=    -394.9216256       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0968200  1.1978         -393.8989985  1.0226         -394.9216256   6.976   5.913   6.210  23.348
        Known (#5)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     3.1724    
 decide> The unconnected minima in the chain and their distances are:
     8        1.47     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0395 Dev= 0.09% S= 1.47 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=   3.62

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     878 steps. Energy=    -395.3198837       time=       3.20
 Minus side of path:                     832 steps. Energy=    -395.3583493       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3198837 0.23765E-01     -395.2961192 0.62230E-01     -395.3583493   1.472   1.469   3.037  47.743
        Known (#8)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -382.1773825 0.85218E-01    -382.0921640 0.45059        -382.5427530  12.375  11.800   2.246  64.568
   1     -382.5427530  5.7127        -376.8300957  13.649        -390.4787888  37.663  26.047   7.910  18.331
   5     -390.4787888 0.92242        -389.5563691  5.8020        -395.3583493  16.323  14.107  11.480  12.631
   8     -395.3583493 0.62230E-01    -395.2961192 0.23765E-01    -395.3198837   1.472   1.469   3.037  47.743
   6     -395.3198837  1.6353        -393.6845693  1.2371        -394.9216256  14.738  13.526  14.506   9.996
   2     -394.9216256  1.0226        -393.8989985  1.1978        -395.0968200   6.976   5.912   6.210  23.351
   3     -395.0968200 0.11704        -394.9797827 0.31442E-01    -395.0112249   3.780   3.767   2.230  65.019

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                               190.08
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             54843 time=          77.02 %= 40.5
 OPTIM> # of energy+gradient+Hessian calls=      1011 time=           5.31 %=  2.8
