
 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)@comp27.ch.
                 Created on  5/28/12 at 12:58:39 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=    -383.2392925     RMS force=    0.9238762667E-06
 OPTIM> Final energy  =    -388.2781099     RMS force=    0.8985343390E-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=     3514.0    
 decide> The unconnected minima in the chain and their distances are:
     2       15.20     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.2501 Dev= 0.34% S= 15.72 time= 0.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.09

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     992 steps. Energy=    -387.4174888       time=       2.71
 Minus side of path:                     974 steps. Energy=    -388.2781099       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4174888  2.1032         -385.3143069  2.9638         -388.2781099   5.765   4.562  28.671   5.057
        *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=     3642.0    
 decide> The unconnected minima in the chain and their distances are:
     3       15.39     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.1186 Dev= 0.46% S= 15.70 time= 0.74
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.56

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     957 steps. Energy=    -383.2392925       time=       3.00
 Minus side of path:                    1001 steps. Energy=    -386.8773057       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2392925 0.75690         -382.4823886  4.3949         -386.8773057  16.303  14.207   2.614  55.471
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7027.9    
 decide> The unconnected minima in the chain and their distances are:
     2       15.20     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 805 RMS= 0.1278 Dev= 5.59% S= 19.42 time= 24.45
 Following    2 images are candidates for TS:    5   13  
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         29
 DNEB run yielded 2 true transition state(s) time=   8.94
 isnewts> transition state is the same as number        2 energy=     -382.4823885811
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        1 energy=     -385.3143069396
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     952 steps. Energy=    -383.2392925       time=       3.29
 Minus side of path:                     986 steps. Energy=    -386.8773057       time=       3.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2392925 0.75690         -382.4823886  4.3949         -386.8773057  16.303  14.207   2.614  55.462
        Known (#1)                                              Known (#4)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     990 steps. Energy=    -388.2781099       time=       3.48
 Minus side of path:                     979 steps. Energy=    -387.4174888       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2781099  2.9638         -385.3143069  2.1032         -387.4174888   5.775   4.578  27.532   5.267
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     7284.1    
 decide> The unconnected minima in the chain and their distances are:
     3       15.39     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 805 RMS= 0.0318 Dev= 4.36% S= 22.02 time= 24.09
 Following    2 images are candidates for TS:    4   11  
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         18
 DNEB run yielded 2 true transition state(s) time=   7.50
 isnewts> transition state is the same as number        2 energy=     -382.4823885805
 tryconnect> Will not repeat search for TS      1 same as TS      2

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     992 steps. Energy=    -386.8331739       time=       2.92
 Minus side of path:                     993 steps. Energy=    -387.4174888       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8331739  1.5466         -385.2865499  2.1309         -387.4174888  19.090  18.752   2.219  65.349
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     5.6569    
 decide> The unconnected minima in the chain and their distances are:
     5        1.78     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0464 Dev= 0.61% S= 1.79 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   4.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     922 steps. Energy=    -386.8773057       time=       2.98
 Minus side of path:                     934 steps. Energy=    -386.8331739       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8773057 0.92306E-01     -386.7849995 0.48174E-01     -386.8331739   1.810   1.782  13.243  10.949
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -383.2392925 0.75690        -382.4823886  4.3949        -386.8773057  16.303  14.207   2.614  55.471
   6     -386.8773057 0.92306E-01    -386.7849995 0.48174E-01    -386.8331739   1.810   1.782  13.243  10.949
   5     -386.8331739  1.5466        -385.2865499  2.1309        -387.4174888  19.090  18.752   2.219  65.349
   1     -387.4174888  2.1032        -385.3143069  2.9638        -388.2781099   5.765   4.562  28.671   5.057

 Number of TS in the path       =      4
 Number of cycles               =      5

 Elapsed time=                               118.71
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             56816 time=          72.23 %= 60.8
 OPTIM> # of energy+gradient+Hessian calls=       196 time=           0.96 %=  0.8
