
 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 12:40:38 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=    -394.8998583     RMS force=    0.9636479586E-06
 OPTIM> Final energy  =    -399.0858357     RMS force=    0.9402460512E-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=     14167.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.20     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= 0.1716 Dev= 1.08% S= 26.23 time= 2.45
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   6.67

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1092 steps. Energy=    -404.2039388       time=       4.37
 Minus side of path:                     933 steps. Energy=    -394.8998583       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -404.2039388  9.6169         -394.5870748 0.31278         -394.8998583  24.947  22.785   3.053  47.499
        *NEW* (Placed in 3)                                     Known (#1)
 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=     8873.3    
 decide> The unconnected minima in the chain and their distances are:
     2       20.70     3 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 3_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.5446 Dev= 0.79% S= 22.13 time= 1.84
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   4.68

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     862 steps. Energy=    -403.7339027       time=       2.08
 Minus side of path:                     915 steps. Energy=    -400.3572578       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -403.7339027  4.0544         -399.6795082 0.67775         -400.3572578  15.806  14.965   3.707  39.120
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     4212.4    
 decide> The unconnected minima in the chain and their distances are:
     2       13.95     5     4       11.45     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0712 Dev= 0.14% S= 14.33 time= 0.81
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.20

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     816 steps. Energy=    -399.0819833       time=       2.47
 Minus side of path:                     835 steps. Energy=    -399.0858357       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -399.0819833 0.27911E-01     -399.0540726 0.31763E-01     -399.0858357   1.034   1.026   4.042  35.869
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2131 Dev= 0.02% S= 11.67 time= 0.48
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.25

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     846 steps. Energy=    -403.7339027       time=       2.50
 Minus side of path:                     823 steps. Energy=    -404.2039388       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -403.7339027 0.92198         -402.8119227  1.3920         -404.2039388  12.791  11.447   7.928  18.290
        Known (#4)                                              Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2574.8    
 decide> The unconnected minima in the chain and their distances are:
     6       13.71     5 
 

 tryconnect> 140-iteration DNEB run for minima 5_S and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.5748 Dev= 0.08% S= 14.08 time= 0.82
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   6.09

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     814 steps. Energy=    -400.4871602       time=       2.47
 Minus side of path:                     847 steps. Energy=    -399.0819833       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -400.4871602  1.7753         -398.7118610 0.37012         -399.0819833  11.057  10.324   4.143  35.001
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     4580.1    
 decide> The unconnected minima in the chain and their distances are:
     7       16.61     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= 0.1514 Dev= 0.54% S= 17.38 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        112
 DNEB run yielded 1 true transition state(s) time=   8.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     866 steps. Energy=    -400.3572578       time=       2.68
 Minus side of path:                     790 steps. Energy=    -398.6660243       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -400.3572578  1.8132         -398.5440203 0.12200         -398.6660243  11.344  10.882   3.108  46.661
        Known (#5)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     560.27    
 decide> The unconnected minima in the chain and their distances are:
     7        8.24     8 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1503 Dev= 0.08% S= 8.28 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.99

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     850 steps. Energy=    -400.4871602       time=       2.26
 Minus side of path:                     876 steps. Energy=    -398.6660243       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -400.4871602  2.7230         -397.7641900 0.90183         -398.6660243   8.443   8.244   2.947  49.203
        Known (#7)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -394.8998583 0.31278        -394.5870748  9.6169        -404.2039388  24.947  22.785   3.053  47.499
   4     -404.2039388  1.3920        -402.8119227 0.92198        -403.7339027  12.791  11.447   7.928  18.290
   2     -403.7339027  4.0544        -399.6795082 0.67775        -400.3572578  15.806  14.965   3.707  39.120
   6     -400.3572578  1.8132        -398.5440203 0.12200        -398.6660243  11.344  10.882   3.108  46.661
   7     -398.6660243 0.90183        -397.7641900  2.7230        -400.4871602   8.443   8.244   2.947  49.203
   5     -400.4871602  1.7753        -398.7118610 0.37012        -399.0819833  11.057  10.324   4.143  35.001
   3     -399.0819833 0.27911E-01    -399.0540726 0.31763E-01    -399.0858357   1.034   1.026   4.042  35.869

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                                82.77
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23496 time=          33.67 %= 40.7
 OPTIM> # of energy+gradient+Hessian calls=       419 time=           2.02 %=  2.4
