
 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)@comp22.ch.
                 Created on  5/28/12 at 12:54: 5 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=    -376.9383809     RMS force=    0.8037852448E-06
 OPTIM> Final energy  =    -378.7573681     RMS force=    0.8652181729E-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=     17508.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.97     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 245 RMS= 0.2873 Dev= 0.59% S= 26.78 time= 1.97
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.43

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1013 steps. Energy=    -376.9383809       time=       3.14
 Minus side of path:                    1014 steps. Energy=    -379.8939722       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.9383809 0.70473         -376.2336546  3.6603         -379.8939722   5.476   4.711  44.112   3.287
        Known (#1)                                              *NEW* (Placed in 3)
 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=     17052.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.74     3 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 3_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 245 RMS= 1.0398 Dev= 0.43% S= 26.33 time= 1.87
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.17

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1003 steps. Energy=    -380.1934631       time=       2.20
 Minus side of path:                    1018 steps. Energy=    -379.8939722       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631 0.47995         -379.7135094 0.18046         -379.8939722   7.116   6.148   1.846  78.559
        *NEW* (Placed in 4)                                     Known (#3)
 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      3 steps with      1 missing connections, weight=     14407.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.33     4 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 245 RMS= 0.2329 Dev= 0.70% S= 24.73 time= 1.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=   9.63

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     980 steps. Energy=    -378.7573681       time=       2.54
 Minus side of path:                    1091 steps. Energy=    -379.5093502       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.7573681 0.27097E-02     -378.7546584 0.75469         -379.5093502  23.624  23.381   2.075  69.886
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6646.8    
 decide> The unconnected minima in the chain and their distances are:
     5       18.80     3 
 

 tryconnect> 175-iteration DNEB run for minima 3_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 0.1479 Dev= 0.30% S= 19.02 time= 0.97
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   6.53
 isnewts> transition state is the same as number        2 energy=     -379.7135094057
 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:                    1005 steps. Energy=    -380.1934631       time=       3.36
 Minus side of path:                    1007 steps. Energy=    -379.8939722       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631 0.47995         -379.7135094 0.18046         -379.8939722   7.116   6.148   1.846  78.557
        Known (#4)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     7195.8    
 decide> The unconnected minima in the chain and their distances are:
     5       19.31     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 175 RMS= 0.2588 Dev= 0.99% S= 19.79 time= 0.94
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.99
 isnewts> transition state is the same as number        1 energy=     -376.2336545636
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     999 steps. Energy=    -376.9383809       time=       2.13
 Minus side of path:                     983 steps. Energy=    -379.8939722       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.9383809 0.70473         -376.2336546  3.6603         -379.8939722   5.476   4.712  44.091   3.289
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     9027.9    
 decide> The unconnected minima in the chain and their distances are:
     5       20.82     4 
 

 tryconnect> 210-iteration DNEB run for minima 4_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 210 RMS= 0.0858 Dev= 0.15% S= 21.02 time= 1.36
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.54

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1031 steps. Energy=    -380.1934631       time=       3.45
 Minus side of path:                    1005 steps. Energy=    -379.5093502       time=       2.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631 0.80007         -379.3933954 0.11595         -379.5093502  21.475  20.834   2.584  56.118
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -376.9383809 0.70473        -376.2336546  3.6603        -379.8939722   5.476   4.711  44.112   3.287
   2     -379.8939722 0.18046        -379.7135094 0.47995        -380.1934631   7.116   6.148   1.846  78.559
   6     -380.1934631 0.80007        -379.3933954 0.11595        -379.5093502  21.475  20.834   2.584  56.118
   3     -379.5093502 0.75469        -378.7546584 0.27097E-02    -378.7573681  23.624  23.381   2.075  69.886

 Number of TS in the path       =      4
 Number of cycles               =      6

 Elapsed time=                                76.29
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26710 time=          28.61 %= 37.5
 OPTIM> # of energy+gradient+Hessian calls=       267 time=           1.16 %=  1.5
