
 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)@comp35.ch.
                 Created on  5/28/12 at 13: 4:29 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=    -384.3093821     RMS force=    0.9664819076E-06
 OPTIM> Final energy  =    -390.8392426     RMS force=    0.9471199411E-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=     67076.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.63     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      227.0466720    
 Double-ended search iterations= 420 RMS= 1.5307 Dev= 0.61% S= 41.20 time= 6.94
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   7.54

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     950 steps. Energy=    -390.2546329       time=       2.34
 Minus side of path:                     924 steps. Energy=    -390.8392426       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2546329  2.3271         -387.9275143  2.9117         -390.8392426   6.246   5.084  24.769   5.854
        *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=     68163.    
 decide> The unconnected minima in the chain and their distances are:
     3       40.85     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 3_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      275.9766488    
 Double-ended search iterations= 420 RMS= 3.6260 Dev= 1.94% S= 41.51 time= 6.85
 Following    2 images are candidates for TS:    6    8  
 Converged to TS (number of iterations):         48
 Converged to TS (number of iterations):         63
 DNEB run yielded 2 true transition state(s) time=  18.46

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     949 steps. Energy=    -387.1704498       time=       3.17
 Minus side of path:                     944 steps. Energy=    -390.2546329       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1704498 0.70896         -386.4614886  3.7931         -390.2546329   5.652   4.691  44.511   3.258
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     935 steps. Energy=    -390.2546329       time=       2.82
 Minus side of path:                     893 steps. Energy=    -390.1447657       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2546329 0.12088         -390.1337555 0.11010E-01     -390.1447657   1.054   1.051  39.802   3.643
        Known (#3)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     66325.    
 decide> The unconnected minima in the chain and their distances are:
     4       40.48     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 4_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      602.4224138    
 Double-ended search iterations= 477 RMS= 4.6502 Dev= 1.01% S= 40.91 time= 8.13
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.83

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     970 steps. Energy=    -386.1793144       time=       3.66
 Minus side of path:                     959 steps. Energy=    -386.0679775       time=       3.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1793144 0.12176         -386.0575501 0.10427E-01     -386.0679775   1.046   1.043  39.519   3.669
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     44678.    
 decide> The unconnected minima in the chain and their distances are:
     4        8.14     6     7       35.34     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 4.4822 Dev= 37.45% S= 8.24 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   4.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     964 steps. Energy=    -387.1704498       time=       2.45
 Minus side of path:                     801 steps. Energy=    -386.1793144       time=       1.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1704498 0.99142         -386.1790281 0.28629E-03     -386.1793144   8.163   8.145   6.811  21.288
        Known (#4)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 7_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      35.55672688    
 Double-ended search iterations= 350 RMS= 3.9675 Dev= 0.19% S= 35.86 time= 4.72
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         69
 Converged to TS (number of iterations):         30
 DNEB run yielded 2 true transition state(s) time=  13.32
 isnewts> transition state is the same as number        4 energy=     -386.0575500915
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     931 steps. Energy=    -384.3093821       time=       3.06
 Minus side of path:                    1297 steps. Energy=    -386.1793144       time=       5.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3093821 0.83756E-01     -384.2256259  1.9537         -386.1793144  36.510  35.653   2.185  66.362
        Known (#1)                                              Known (#6)

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     985 steps. Energy=    -386.1793144       time=       2.53
 Minus side of path:                     965 steps. Energy=    -386.0679775       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1793144 0.12176         -386.0575501 0.10427E-01     -386.0679775   1.046   1.043  39.508   3.670
        Known (#6)                                              Known (#7)
 Alternative path found between members of the F set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -384.3093821 0.83756E-01    -384.2256259  1.9537        -386.1793144  36.510  35.653   2.185  66.362
   5     -386.1793144 0.28629E-03    -386.1790281 0.99142        -387.1704498   8.163   8.145   6.811  21.288
   2     -387.1704498 0.70896        -386.4614886  3.7931        -390.2546329   5.652   4.691  44.511   3.258
   1     -390.2546329  2.3271        -387.9275143  2.9117        -390.8392426   6.246   5.084  24.769   5.854

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

 Elapsed time=                               119.94
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41394 time=          55.43 %= 46.2
 OPTIM> # of energy+gradient+Hessian calls=       363 time=           1.80 %=  1.5
