
 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)@comp22.ch.
                 Created on  5/28/12 at 12:53:43 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -392.1126712     RMS force=    0.9748240394E-06
 OPTIM> Final energy  =    -392.6563397     RMS force=    0.9925367704E-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=     1044.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.15     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 108 RMS= 9.6630 Dev= 11.35% S= 26.12 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   5.37

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1508 steps. Energy=    -395.8412271       time=       5.37
 Minus side of path:                     926 steps. Energy=    -392.3677491       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.8412271  3.6518         -392.1894696 0.17828         -392.3677491  18.982  16.765   1.877  77.234
        *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=     743.99    
 decide> The unconnected minima in the chain and their distances are:
     2        8.53     4     4        4.98     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 6.3269 Dev= 67.51% S= 9.40 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     918 steps. Energy=    -392.6563397       time=       2.15
 Minus side of path:                     920 steps. Energy=    -392.3677491       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6563397 0.30376         -392.3525794 0.15170E-01     -392.3677491   8.687   8.530   4.280  33.876
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.1427 Dev= 0.21% S= 4.99 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   6.11
 isnewts> transition state is the same as number        1 energy=     -392.1894695729
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1545 steps. Energy=    -395.7764936       time=       8.30
 Minus side of path:                     959 steps. Energy=    -392.3677491       time=       3.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.7764936  3.5870         -392.1894696 0.17828         -392.3677491  21.201  19.478   1.831  79.209
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     246.58    
 decide> The unconnected minima in the chain and their distances are:
     4        4.98     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 385 RMS= 0.0084 Dev= 0.89% S= 5.27 time= 5.99
 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=  27.10
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     369.87    
 decide> The unconnected minima in the chain and their distances are:
     4        4.98     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 4_F using 21 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 735 RMS= 0.0127 Dev= 4.87% S= 5.60 time= 21.96
 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=  24.36
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2089.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.15     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0139 Dev= 2.32% S= 10.66 time= 25.99
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.88
 isnewts> transition state is the same as number        2 energy=     -392.3525793850
 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:                     925 steps. Energy=    -392.6563397       time=       2.14
 Minus side of path:                     936 steps. Energy=    -392.3677491       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6563397 0.30376         -392.3525794 0.15170E-01     -392.3677491   8.687   8.530   4.288  33.812
        Known (#2)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6174.7    
 decide> The unconnected minima in the chain and their distances are:
     3       18.35     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      50.03188542    
 Double-ended search iterations= 175 RMS= 3.5060 Dev= 2.76% S= 18.43 time= 1.27
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   6.23

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1048 steps. Energy=    -395.9942596       time=       2.72
 Minus side of path:                     906 steps. Energy=    -395.8412271       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.9942596  1.0269         -394.9673907 0.87384         -395.8412271  16.665  13.532   5.673  25.561
        *NEW* (Placed in 6)                                     Known (#3)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     8908.5    
 decide> The unconnected minima in the chain and their distances are:
     5       20.73     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      77.61587555    
 Double-ended search iterations= 314 RMS= 17.1944 Dev= 28.58% S= 24.05 time= 2.75
 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=  18.17
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     10974.    
 decide> The unconnected minima in the chain and their distances are:
     6       22.22     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      17.95856326    
 Double-ended search iterations= 210 RMS= 0.1735 Dev= 0.35% S= 22.37 time= 1.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   5.36

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1563 steps. Energy=    -395.8412271       time=       5.61
 Minus side of path:                     825 steps. Energy=    -392.1126712       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.8412271  3.7290         -392.1121847 0.48645E-03     -392.1126712  18.733  18.352   1.756  82.592
        Known (#3)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -392.1126712 0.48645E-03    -392.1121847  3.7290        -395.8412271  18.733  18.352   1.756  82.592
   1     -395.8412271  3.6518        -392.1894696 0.17828        -392.3677491  18.982  16.765   1.877  77.234
   2     -392.3677491 0.15170E-01    -392.3525794 0.30376        -392.6563397   8.687   8.530   4.280  33.876

 Number of TS in the path       =      3
 Number of cycles               =      8

 Elapsed time=                               202.76
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             67845 time=          93.83 %= 46.3
 OPTIM> # of energy+gradient+Hessian calls=      1090 time=           5.16 %=  2.5
