
 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)@comp34.ch.
                 Created on  5/28/12 at 12:41:19 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -378.2543928     RMS force=    0.9482239899E-06
 OPTIM> Final energy  =    -382.1851430     RMS force=    0.9692575181E-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=     43885.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.27     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= 0.3359 Dev= 3.62% S= 45.31 time= 3.92
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):        113
 Converged to TS (number of iterations):         83
 DNEB run yielded 2 true transition state(s) time=  17.82

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1074 steps. Energy=    -380.7727545       time=       2.47
 Minus side of path:                    1071 steps. Energy=    -380.8184152       time=       2.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545  1.3782         -379.3945995  1.4238         -380.8184152  34.422  32.220   3.274  44.286
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     979 steps. Energy=    -382.1663989       time=       2.65
 Minus side of path:                    1010 steps. Energy=    -382.2034186       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1663989 0.23477E-01     -382.1429222 0.60496E-01     -382.2034186   1.105   1.090  16.194   8.954
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4292.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.33     3     4       14.72     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 2.8476 Dev= 4.01% S= 16.71 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   7.06

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1008 steps. Energy=    -380.7181380       time=       2.18
 Minus side of path:                    1023 steps. Energy=    -380.7321663       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7181380 0.10783E-01     -380.7073551 0.24811E-01     -380.7321663   1.488   1.485   3.046  47.598
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U 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= 0.1117 Dev= 0.67% S= 15.70 time= 0.68
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.58

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1053 steps. Energy=    -380.8184152       time=       3.71
 Minus side of path:                    1011 steps. Energy=    -378.2543928       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.8184152  4.9494         -375.8690199  2.3854         -378.2543928  18.192  14.724  13.147  11.029
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     1074.5    
 decide> The unconnected minima in the chain and their distances are:
     2        1.74     5     5       10.18     8     7        2.48     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0125 Dev= 0.03% S= 1.74 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.58

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1028 steps. Energy=    -382.1851430       time=       2.30
 Minus side of path:                    1033 steps. Energy=    -382.1663989       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1851430 0.33047E-01     -382.1520962 0.14303E-01     -382.1663989   1.745   1.740   2.843  51.010
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 5_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 105 RMS= 0.9037 Dev= 3.71% S= 15.74 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        158
 DNEB run yielded 1 true transition state(s) time=  13.54

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1366 steps. Energy=    -382.7543847       time=       5.37
 Minus side of path:                    1053 steps. Energy=    -382.2034186       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7543847  1.1904         -381.5639427 0.63948         -382.2034186  44.752  40.440   1.846  78.532
        *NEW* (Placed in 9)                                     Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0330 Dev= 0.07% S= 2.49 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   4.33

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1002 steps. Energy=    -380.7727545       time=       3.31
 Minus side of path:                    1001 steps. Energy=    -380.7181380       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.97806E-01     -380.6749486 0.43189E-01     -380.7181380   2.513   2.484  21.956   6.604
        Known (#3)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1062.6    
 decide> The unconnected minima in the chain and their distances are:
     2       10.20     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 0.9639 Dev= 2.88% S= 15.62 time= 0.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   6.15
 isnewts> transition state is the same as number        5 energy=     -382.1520962070
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     992 steps. Energy=    -382.1851430       time=       2.12
 Minus side of path:                    1017 steps. Energy=    -382.1663989       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1851430 0.33047E-01     -382.1520962 0.14303E-01     -382.1663989   1.745   1.740   2.843  51.010
        Known (#2)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1072.5    
 decide> The unconnected minima in the chain and their distances are:
     6       10.24     8 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6689 Dev= 0.46% S= 16.40 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.34

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1027 steps. Energy=    -382.1663989       time=       2.61
 Minus side of path:                    1046 steps. Energy=    -380.7879935       time=       2.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1663989  3.8225         -378.3438515  2.4441         -380.7879935  18.490  10.385  22.728   6.380
        Known (#5)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3.9007    
 decide> The unconnected minima in the chain and their distances are:
    10        1.57     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0129 Dev= 0.01% S= 1.57 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1002 steps. Energy=    -380.7727545       time=       2.38
 Minus side of path:                    1011 steps. Energy=    -380.7879935       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.10401E-01     -380.7623536 0.25640E-01     -380.7879935   1.577   1.574   2.911  49.815
        Known (#3)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -378.2543928  2.3854        -375.8690199  4.9494        -380.8184152  18.192  14.724  13.147  11.029
   1     -380.8184152  1.4238        -379.3945995  1.3782        -380.7727545  34.422  32.220   3.274  44.286
  10     -380.7727545 0.10401E-01    -380.7623536 0.25640E-01    -380.7879935   1.577   1.574   2.911  49.815
   9     -380.7879935  2.4441        -378.3438515  3.8225        -382.1663989  18.490  10.385  22.728   6.380
   5     -382.1663989 0.14303E-01    -382.1520962 0.33047E-01    -382.1851430   1.745   1.740   2.843  51.010

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

 Elapsed time=                               127.47
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             37438 time=          40.09 %= 31.4
 OPTIM> # of energy+gradient+Hessian calls=       599 time=           2.62 %=  2.1
