
 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)@comp31.ch.
                 Created on  5/28/12 at 12:35:30 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=    -386.6206187     RMS force=    0.9496290450E-06
 OPTIM> Final energy  =    -390.3597304     RMS force=    0.9799319487E-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=     12231.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.04     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2679 Dev= 0.46% S= 25.07 time= 1.83
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         64
 DNEB run yielded 2 true transition state(s) time=  12.25

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     882 steps. Energy=    -389.7581693       time=       2.21
 Minus side of path:                     921 steps. Energy=    -390.9626283       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7581693 0.44328         -389.3148930  1.6477         -390.9626283   3.550   3.190  15.991   9.068
        *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:                     958 steps. Energy=    -390.3597304       time=       2.82
 Minus side of path:                     919 steps. Energy=    -387.3417043       time=       2.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3597304  3.1459         -387.2138617 0.12784         -387.3417043  23.314  22.581   8.143  17.806
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     279.62    
 decide> The unconnected minima in the chain and their distances are:
     5        6.54     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2471 Dev= 0.40% S= 6.94 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     809 steps. Energy=    -386.6206187       time=       3.19
 Minus side of path:                     927 steps. Energy=    -387.9483688       time=       3.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6206187 0.45576         -386.1648635  1.7835         -387.9483688   3.371   3.002  19.652   7.379
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     147.62    
 decide> The unconnected minima in the chain and their distances are:
     5        5.29     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.3593 Dev= 1.04% S= 5.72 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.79
 isnewts> transition state is the same as number        2 energy=     -387.2138616711
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     976 steps. Energy=    -390.3597304       time=       3.08
 Minus side of path:                     949 steps. Energy=    -387.3417043       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3597304  3.1459         -387.2138617 0.12784         -387.3417043  23.320  22.589   8.049  18.016
        Known (#2)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     295.25    
 decide> The unconnected minima in the chain and their distances are:
     5        5.29     6 
 

 tryconnect> 420-iteration DNEB run for minima 5_F and 6_S using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 420 RMS= 0.0097 Dev= 3.62% S= 7.42 time= 7.25
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     897 steps. Energy=    -387.3417043       time=       3.41
 Minus side of path:                     945 steps. Energy=    -387.9483688       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3417043  2.4751         -384.8665593  3.0818         -387.9483688   5.962   5.288  32.188   4.505
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -386.6206187 0.45576        -386.1648635  1.7835        -387.9483688   3.371   3.002  19.652   7.379
   5     -387.9483688  3.0818        -384.8665593  2.4751        -387.3417043   5.962   5.288  32.188   4.505
   2     -387.3417043 0.12784        -387.2138617  3.1459        -390.3597304  23.314  22.581   8.143  17.806

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                                65.20
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20686 time=          29.36 %= 45.0
 OPTIM> # of energy+gradient+Hessian calls=       166 time=           0.84 %=  1.3
