
 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)@comp24.ch.
                 Created on  5/28/12 at 13:10: 8 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=    -379.2028400     RMS force=    0.9034979018E-06
 OPTIM> Final energy  =    -384.6819565     RMS force=    0.8757164468E-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=     87261.    
 decide> The unconnected minima in the chain and their distances are:
     2       44.35     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0896 Dev= 4.11% S= 51.04 time= 7.15
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=  10.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1623 steps. Energy=    -384.5540878       time=       7.71
 Minus side of path:                    1015 steps. Energy=    -379.3011875       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.5540878  5.5792         -378.9748767 0.32631         -379.3011875  51.475  46.968   2.010  72.140
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     403.49    
 decide> The unconnected minima in the chain and their distances are:
     2        7.38     3     4        1.03     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.8667 Dev= 0.18% S= 7.47 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.52

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     950 steps. Energy=    -385.1178926       time=       2.74
 Minus side of path:                     907 steps. Energy=    -384.5540878       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1178926 0.58265         -384.5352389 0.18849E-01     -384.5540878   5.093   4.831   5.437  26.668
        *NEW* (Placed in 5)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0158 Dev= 0.26% S= 1.04 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.52

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1004 steps. Energy=    -379.3011876       time=       3.82
 Minus side of path:                    1000 steps. Energy=    -379.2028400       time=       2.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.3011876 0.11316         -379.1880258 0.14814E-01     -379.2028400   1.030   1.027  38.511   3.765
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     328.30    
 decide> The unconnected minima in the chain and their distances are:
     2        6.90     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0589 Dev= 0.01% S= 6.91 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.53

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     884 steps. Energy=    -384.6819565       time=       2.59
 Minus side of path:                     942 steps. Energy=    -385.1178926       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6819565 0.25883         -384.4231299 0.69476         -385.1178926   7.066   6.899   2.421  59.897
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -379.2028400 0.14814E-01    -379.1880258 0.11316        -379.3011875   1.030   1.027  38.511   3.765
   1     -379.3011875 0.32631        -378.9748767  5.5792        -384.5540878  51.475  46.968   2.010  72.140
   2     -384.5540878 0.18849E-01    -384.5352389 0.58265        -385.1178926   5.093   4.831   5.437  26.668
   4     -385.1178926 0.69476        -384.4231299 0.25883        -384.6819565   7.066   6.899   2.421  59.897

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

 Elapsed time=                                59.28
 OPTIM> # of energy calls=                         38 time=           0.04 %=  0.1
 OPTIM> # of energy+gradient calls=             18695 time=          22.45 %= 37.9
 OPTIM> # of energy+gradient+Hessian calls=       186 time=           0.89 %=  1.5
