
 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)@comp28.ch.
                 Created on  5/28/12 at 13:11:33 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=    -380.0677513     RMS force=    0.9921181688E-06
 OPTIM> Final energy  =    -385.0052262     RMS force=    0.9812633651E-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=     40714.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.40     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1525 Dev= 2.26% S= 39.49 time= 4.96
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         62
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time=  35.38

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     962 steps. Energy=    -381.0004776       time=       2.47
 Minus side of path:                    1551 steps. Energy=    -391.6562364       time=       7.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.0004776 0.72784E-01     -380.9276941  10.729         -391.6562364  46.987  46.050   2.554  56.772
        *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=     3954.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.56     4     3        9.53     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1726 Dev= 1.41% S= 15.52 time= 0.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     993 steps. Energy=    -389.0531689       time=       3.96
 Minus side of path:                     993 steps. Energy=    -385.5492809       time=       4.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0531689  4.7099         -384.3432929  1.2060         -385.5492809  15.481  14.664  13.446  10.784
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1094 Dev= 0.06% S= 9.62 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   7.91

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     976 steps. Energy=    -380.0677513       time=       5.30
 Minus side of path:                    1855 steps. Energy=    -391.6562364       time=      11.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.0677513 0.91644E-02     -380.0585869  11.598         -391.6562364  41.449  40.888   2.731  53.086
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2612.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.71     6     5       11.14     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0414 Dev= 0.03% S= 10.73 time= 0.51
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     925 steps. Energy=    -385.0052262       time=       3.00
 Minus side of path:                    1005 steps. Energy=    -385.5492809       time=       3.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0052262 0.21186E-01     -384.9840403 0.56524         -385.5492809  11.212  10.716   2.231  64.986
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.8067 Dev= 0.38% S= 11.75 time= 0.51
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.59

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     983 steps. Energy=    -392.3683405       time=       3.78
 Minus side of path:                     982 steps. Energy=    -389.0531689       time=       4.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3683405  5.7791         -386.5892836  2.4639         -389.0531689  14.145   5.434   3.804  38.116
        *NEW* (Placed in 7)                                     Known (#5)
 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      3 steps with      1 missing connections, weight=     2290.9    
 decide> The unconnected minima in the chain and their distances are:
     6       13.18     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3669 Dev= 0.29% S= 14.00 time= 0.52
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   7.32

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     898 steps. Energy=    -385.5492809       time=       3.08
 Minus side of path:                     987 steps. Energy=    -385.9013867       time=       3.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5492809 0.17999E-01     -385.5312815 0.37011         -385.9013867  14.789  14.335   2.429  59.684
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2501.7    
 decide> The unconnected minima in the chain and their distances are:
     7       13.58     4 
 

 tryconnect> 140-iteration DNEB run for minima 4_S and 7_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2185 Dev= 0.30% S= 14.18 time= 0.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.65

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     968 steps. Energy=    -392.3683405       time=       3.22
 Minus side of path:                    1002 steps. Energy=    -391.7748680       time=       3.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.3683405  2.7746         -389.5937803  2.1811         -391.7748680  13.594  12.666   2.715  53.409
        Known (#7)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2764.5    
 decide> The unconnected minima in the chain and their distances are:
     5       11.14     4 
 

 tryconnect> 805-iteration DNEB run for minima 4_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0339 Dev= 5.21% S= 17.45 time= 26.60
 Following    2 images are candidates for TS:    9   16  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=   7.90
 isnewts> transition state is the same as number        5 energy=     -386.5892836373
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     965 steps. Energy=    -391.6562364       time=       2.32
 Minus side of path:                     943 steps. Energy=    -390.2626510       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6562364  3.8669         -387.7893769  2.4733         -390.2626510   7.281   6.406  16.298   8.897
        Known (#4)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     984 steps. Energy=    -389.0531689       time=       2.41
 Minus side of path:                     953 steps. Energy=    -390.2626510       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0531689  2.4639         -386.5892836  3.6734         -390.2626510  11.414  10.402   5.701  25.435
        Known (#5)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -380.0677513 0.91644E-02    -380.0585869  11.598        -391.6562364  41.449  40.888   2.731  53.086
   8     -391.6562364  3.8669        -387.7893769  2.4733        -390.2626510   7.281   6.406  16.298   8.897
   9     -390.2626510  3.6734        -386.5892836  2.4639        -389.0531689  11.414  10.402   5.701  25.435
   2     -389.0531689  4.7099        -384.3432929  1.2060        -385.5492809  15.481  14.664  13.446  10.784
   4     -385.5492809 0.56524        -384.9840403 0.21186E-01    -385.0052262  11.212  10.716   2.231  64.986

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               185.48
 OPTIM> # of energy calls=                        104 time=           0.14 %=  0.1
 OPTIM> # of energy+gradient calls=             54209 time=          75.32 %= 40.6
 OPTIM> # of energy+gradient+Hessian calls=       605 time=           3.28 %=  1.8
