
 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 13: 1:10 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -399.4433289     RMS force=    0.8667251535E-06
 OPTIM> Final energy  =    -388.3743583     RMS force=    0.9589739517E-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=     84690.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.91     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 455 RMS= 0.0968 Dev= 1.13% S= 50.92 time= 8.41
 Following    2 images are candidates for TS:    8   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  22.99

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1202 steps. Energy=    -394.3983805       time=       3.30
 Minus side of path:                     935 steps. Energy=    -388.3743583       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  6.3778         -388.0205580 0.35380         -388.3743583  29.210  27.402   1.977  73.327
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     14103.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.16     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1317 Dev= 1.64% S= 26.01 time= 2.42
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   5.78

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     905 steps. Energy=    -396.6857038       time=       2.63
 Minus side of path:                     929 steps. Energy=    -394.3983805       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6857038  3.1084         -393.5772961 0.82108         -394.3983805  14.167  12.922   6.810  21.291
        *NEW* (Placed in 4)                                     Known (#3)
 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=     9892.3    
 decide> The unconnected minima in the chain and their distances are:
     4       21.47     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1183 Dev= 0.94% S= 23.60 time= 1.89
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.67

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1054 steps. Energy=    -396.1464806       time=       4.67
 Minus side of path:                    1076 steps. Energy=    -397.9716366       time=       5.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  1.0069         -395.1395357  2.8321         -397.9716366  23.255   7.485   9.573  15.146
        *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      5 steps with      2 missing connections, weight=     9202.1    
 decide> The unconnected minima in the chain and their distances are:
     4       20.95     6     5        2.33     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2208 Dev= 0.15% S= 22.02 time= 1.94
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.55

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     876 steps. Energy=    -397.5322550       time=       2.90
 Minus side of path:                     909 steps. Energy=    -397.5139278       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.57192E-01     -397.4750629 0.38865E-01     -397.5139278   1.244   1.242   4.239  34.205
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 70 RMS= 2.1289 Dev= 3.80% S= 2.70 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   7.42

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     917 steps. Energy=    -396.1464806       time=       2.51
 Minus side of path:                    1013 steps. Energy=    -397.9156787       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  1.2542         -394.8922531  3.0234         -397.9156787  24.387  18.165   2.400  60.428
        Known (#5)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     4538.4    
 decide> The unconnected minima in the chain and their distances are:
     4       12.23     8     7       13.90     6     5        2.33     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0786 Dev= 0.06% S= 12.30 time= 0.51
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.94

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     851 steps. Energy=    -396.7931836       time=       2.61
 Minus side of path:                     864 steps. Energy=    -397.5322550       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7931836 0.62676         -396.1664218  1.3658         -397.5322550  11.044  10.906   2.724  53.225
        *NEW* (Placed in 10)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 6_U and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0691 Dev= 0.08% S= 14.08 time= 0.89
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.06

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     878 steps. Energy=    -397.5322550       time=       2.34
 Minus side of path:                    1036 steps. Energy=    -397.9716366       time=       3.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.59115         -396.9411086  1.0305         -397.9716366  15.018  13.898   2.547  56.922
        Known (#7)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_U using 5 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 0.1178 Dev= 1.67% S= 2.87 time= 1.28
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.94

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     902 steps. Energy=    -396.1464806       time=       2.33
 Minus side of path:                     821 steps. Energy=    -399.4433289       time=       1.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  3.7716         -392.3749288  7.0684         -399.4433289   4.422   2.329  35.210   4.118
        Known (#5)                                              Known (#1)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     59.885    
 decide> The unconnected minima in the chain and their distances are:
     4        3.91    10 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0304 Dev= 0.01% S= 3.92 time= 0.25
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     876 steps. Energy=    -396.6702512       time=       2.32
 Minus side of path:                     848 steps. Energy=    -396.7931836       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6702512 0.14182E-01     -396.6560690 0.13711         -396.7931836   2.561   2.556   2.724  53.224
        *NEW* (Placed in 11)                                    Known (#10)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     3.8196    
 decide> The unconnected minima in the chain and their distances are:
     4        1.56    11 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0080 Dev= 0.00% S= 1.56 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.16

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     835 steps. Energy=    -396.6702512       time=       2.83
 Minus side of path:                     823 steps. Energy=    -396.6857038       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6702512 0.13214E-01     -396.6570369 0.28667E-01     -396.6857038   1.566   1.563   2.266  63.999
        Known (#11)                                             Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -399.4433289  7.0684        -392.3749288  3.7716        -396.1464806   4.422   2.329  35.210   4.118
   3     -396.1464806  1.0069        -395.1395357  2.8321        -397.9716366  23.255   7.485   9.573  15.146
   7     -397.9716366  1.0305        -396.9411086 0.59115        -397.5322550  15.018  13.898   2.547  56.922
   6     -397.5322550  1.3658        -396.1664218 0.62676        -396.7931836  11.044  10.906   2.724  53.225
   9     -396.7931836 0.13711        -396.6560690 0.14182E-01    -396.6702512   2.561   2.556   2.724  53.224
  10     -396.6702512 0.13214E-01    -396.6570369 0.28667E-01    -396.6857038   1.566   1.563   2.266  63.999
   2     -396.6857038  3.1084        -393.5772961 0.82108        -394.3983805  14.167  12.922   6.810  21.291
   1     -394.3983805  6.3778        -388.0205580 0.35380        -388.3743583  29.210  27.402   1.977  73.327

 Number of TS in the path       =      8
 Number of cycles               =      7

 Elapsed time=                               143.27
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41462 time=          57.47 %= 40.1
 OPTIM> # of energy+gradient+Hessian calls=       625 time=           3.18 %=  2.2
