
 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)@comp20.ch.
                 Created on  5/28/12 at 13: 5:27 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=    -379.9078830     RMS force=    0.9982737733E-06
 OPTIM> Final energy  =    -379.7128734     RMS force=    0.9533959835E-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=     5149.7    
 decide> The unconnected minima in the chain and their distances are:
     2       17.27     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 175 RMS= 1.3380 Dev= 1.44% S= 24.53 time= 0.96
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   7.47

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1027 steps. Energy=    -379.9078830       time=       3.90
 Minus side of path:                    1128 steps. Energy=    -380.6973297       time=       4.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.9078830  7.1759         -372.7320018  7.9653         -380.6973297  25.667  12.733   9.412  15.407
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3212.1    
 decide> The unconnected minima in the chain and their distances are:
     2       14.75     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 140 RMS= 0.4436 Dev= 0.55% S= 17.44 time= 0.61
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1030 steps. Energy=    -380.1934631       time=       2.31
 Minus side of path:                     995 steps. Energy=    -379.7128734       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631  2.5640         -377.6294833  2.0834         -379.7128734  12.004  10.013   5.793  25.031
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1667.4    
 decide> The unconnected minima in the chain and their distances are:
     4       11.86     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 4_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 105 RMS= 0.5729 Dev= 2.15% S= 14.82 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        244
 DNEB run yielded 1 true transition state(s) time=  54.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1003 steps. Energy=    -380.5318790       time=       2.64
 Minus side of path:                    1034 steps. Energy=    -380.9263577       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.5318790 0.22838         -380.3035020 0.62286         -380.9263577  28.345  27.899   1.899  76.336
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1622.5    
 decide> The unconnected minima in the chain and their distances are:
     4       11.56     6     6        4.29     3 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 0.3969 Dev= 1.54% S= 14.79 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.58

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1032 steps. Energy=    -380.9263577       time=       2.24
 Minus side of path:                    1004 steps. Energy=    -380.1934631       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9263577  5.2599         -375.6664321  4.5270         -380.1934631  17.287  11.567  20.065   7.227
        Known (#6)                                              Known (#4)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0991 Dev= 0.59% S= 4.31 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.78

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1018 steps. Energy=    -380.9263577       time=       2.16
 Minus side of path:                     999 steps. Energy=    -380.6973297       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9263577 0.42612         -380.5002342 0.19710         -380.6973297   5.081   4.286   3.587  40.422
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -379.9078830  7.1759        -372.7320018  7.9653        -380.6973297  25.667  12.733   9.412  15.407
   5     -380.6973297 0.19710        -380.5002342 0.42612        -380.9263577   5.081   4.286   3.587  40.422
   4     -380.9263577  5.2599        -375.6664321  4.5270        -380.1934631  17.287  11.567  20.065   7.227
   2     -380.1934631  2.5640        -377.6294833  2.0834        -379.7128734  12.004  10.013   5.793  25.031

 Number of TS in the path       =      4
 Number of cycles               =      4

 Elapsed time=                               101.21
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20276 time=          21.93 %= 21.7
 OPTIM> # of energy+gradient+Hessian calls=       386 time=           1.73 %=  1.7
