
 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 13:10:12 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -388.1160328     RMS force=    0.9368442178E-06
 OPTIM> Final energy  =    -387.4135552     RMS force=    0.8265137008E-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=     17562.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.99     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1055 Dev= 0.95% S= 28.24 time= 2.40
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   6.61

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1050 steps. Energy=    -388.1071294       time=       4.39
 Minus side of path:                     890 steps. Energy=    -385.9146793       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1071294  2.3535         -385.7536522 0.16103         -385.9146793  14.607  13.301   9.546  15.189
        *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=     5510.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.43     3     4       14.56     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1302 Dev= 0.05% S= 13.64 time= 0.89
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   6.34

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     918 steps. Energy=    -387.4135552       time=       2.46
 Minus side of path:                     901 steps. Energy=    -387.3860533       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4135552 0.76053E-01     -387.3375019 0.48551E-01     -387.3860533   1.868   1.534   3.561  40.720
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 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= 0.1282 Dev= 0.36% S= 15.20 time= 0.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   7.10

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     874 steps. Energy=    -385.9146793       time=       2.73
 Minus side of path:                     984 steps. Energy=    -386.8959175       time=       3.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9146793 0.71736E-01     -385.8429433  1.0530         -386.8959175  14.216  13.834   4.033  35.950
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2185.4    
 decide> The unconnected minima in the chain and their distances are:
     5       12.73     3     6        4.99     1 
 

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3801 Dev= 0.07% S= 12.84 time= 0.54
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.80

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     881 steps. Energy=    -388.1071294       time=       2.70
 Minus side of path:                     916 steps. Energy=    -387.3860533       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1071294 0.85034         -387.2567862 0.12927         -387.3860533  13.566  12.730   2.377  61.005
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3364 Dev= 1.57% S= 5.48 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   5.36

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     955 steps. Energy=    -386.8977357       time=       2.46
 Minus side of path:                     929 steps. Energy=    -386.8959175       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8977357 0.22175         -386.6759817 0.21994         -386.8959175   4.009   3.809  10.299  14.079
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     235.47    
 decide> The unconnected minima in the chain and their distances are:
     7        6.18     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2163 Dev= 0.82% S= 6.62 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.57
 isnewts> transition state is the same as number        5 energy=     -386.6759817143
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     942 steps. Energy=    -386.8977357       time=       2.25
 Minus side of path:                     911 steps. Energy=    -386.8959175       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8977357 0.22175         -386.6759817 0.21994         -386.8959175   4.009   3.809  10.298  14.081
        Known (#7)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     248.92    
 decide> The unconnected minima in the chain and their distances are:
     6        4.99     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 6_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0069 Dev= 1.83% S= 7.12 time= 5.98
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.06

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     923 steps. Energy=    -388.1160328       time=       2.75
 Minus side of path:                     906 steps. Energy=    -386.8959175       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1160328  3.5143         -384.6017369  2.2942         -386.8959175   5.796   4.994  38.583   3.758
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -388.1160328  3.5143        -384.6017369  2.2942        -386.8959175   5.796   4.994  38.583   3.758
   3     -386.8959175  1.0530        -385.8429433 0.71736E-01    -385.9146793  14.216  13.834   4.033  35.950
   1     -385.9146793 0.16103        -385.7536522  2.3535        -388.1071294  14.607  13.301   9.546  15.189
   4     -388.1071294 0.85034        -387.2567862 0.12927        -387.3860533  13.566  12.730   2.377  61.005
   2     -387.3860533 0.48551E-01    -387.3375019 0.76053E-01    -387.4135552   1.868   1.534   3.561  40.720

 Number of TS in the path       =      5
 Number of cycles               =      5

 Elapsed time=                                87.35
 OPTIM> # of energy calls=                         66 time=           0.09 %=  0.1
 OPTIM> # of energy+gradient calls=             27257 time=          37.01 %= 42.4
 OPTIM> # of energy+gradient+Hessian calls=       323 time=           1.58 %=  1.8
