
 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)@comp32.ch.
                 Created on  5/28/12 at 13:10: 4 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.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -381.8415109     RMS force=    0.9664367083E-06
 OPTIM> Final energy  =    -377.2153963     RMS force=    0.9844289940E-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=    0.11469E+06
 decide> The unconnected minima in the chain and their distances are:
     2       48.59     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 490 RMS= 0.0932 Dev= 1.82% S= 58.52 time= 7.77
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        167
 DNEB run yielded 1 true transition state(s) time=  14.68

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1110 steps. Energy=    -377.2153963       time=       2.82
 Minus side of path:                    1200 steps. Energy=    -379.4875075       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.2153963  3.2917         -373.9237051  5.5638         -379.4875075  43.353  31.971   3.679  39.412
        Known (#2)                                              *NEW* (Placed in 3)
 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=     39050.    
 decide> The unconnected minima in the chain and their distances are:
     3       33.93     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 3_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0578 Dev= 0.94% S= 36.73 time= 3.94
 Following    2 images are candidates for TS:    4    9  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         55
 DNEB run yielded 2 true transition state(s) time=   9.97

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     995 steps. Energy=    -380.1934631       time=       2.22
 Minus side of path:                     999 steps. Energy=    -379.8939722       time=       2.19

         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  78.560
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1000 steps. Energy=    -379.5093502       time=       2.15
 Minus side of path:                    1034 steps. Energy=    -380.1934631       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5093502 0.11595         -379.3933954 0.80007         -380.1934631  21.475  20.831   2.589  55.997
        *NEW* (Placed in 6)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     5753.5    
 decide> The unconnected minima in the chain and their distances are:
     3        0.85     6     4       17.92     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0104 Dev= 0.12% S= 0.86 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.84

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     984 steps. Energy=    -379.4875075       time=       2.16
 Minus side of path:                     998 steps. Energy=    -379.5093502       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.4875075 0.28448E-01     -379.4590599 0.50290E-01     -379.5093502   0.891   0.855   7.884  18.391
        Known (#3)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2690 Dev= 0.27% S= 18.22 time= 1.05
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1026 steps. Energy=    -380.1934631       time=       4.10
 Minus side of path:                    1017 steps. Energy=    -381.8415109       time=       4.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631 0.91911         -379.2743536  2.5672         -381.8415109  19.523  17.965   3.059  47.403
        Known (#4)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -381.8415109  2.5672        -379.2743536 0.91911        -380.1934631  19.523  17.965   3.059  47.403
   3     -380.1934631 0.80007        -379.3933954 0.11595        -379.5093502  21.475  20.831   2.589  55.997
   4     -379.5093502 0.50290E-01    -379.4590599 0.28448E-01    -379.4875075   0.891   0.855   7.884  18.391
   1     -379.4875075  5.5638        -373.9237051  3.2917        -377.2153963  43.353  31.971   3.679  39.412

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

 Elapsed time=                                72.10
 OPTIM> # of energy calls=                         62 time=           0.06 %=  0.1
 OPTIM> # of energy+gradient calls=             27297 time=          28.80 %= 39.9
 OPTIM> # of energy+gradient+Hessian calls=       300 time=           1.32 %=  1.8
