
 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 13:11:17 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=    -391.2758247     RMS force=    0.9963919870E-06
 OPTIM> Final energy  =    -389.1369071     RMS force=    0.9916125561E-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=     14538.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.41     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0529 Dev= 0.28% S= 25.25 time= 2.27
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.83
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     29075.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.41     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0584 Dev= 6.75% S= 29.21 time= 24.29
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.03

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     968 steps. Energy=    -389.1369071       time=       2.67
 Minus side of path:                    1244 steps. Energy=    -391.7888469       time=       5.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1369071  1.2188         -387.9181348  3.8707         -391.7888469  30.012  28.298   2.282  63.542
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2174.7    
 decide> The unconnected minima in the chain and their distances are:
     3       12.96     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 3_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1004 Dev= 0.03% S= 13.08 time= 0.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     942 steps. Energy=    -391.7705351       time=       2.23
 Minus side of path:                     966 steps. Energy=    -391.7888469       time=       2.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7705351 0.82577E-01     -391.6879576 0.10089         -391.7888469   4.389   4.114   3.483  41.632
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2319.2    
 decide> The unconnected minima in the chain and their distances are:
     4       13.24     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0707 Dev= 0.02% S= 13.35 time= 0.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     929 steps. Energy=    -391.2920911       time=       2.43
 Minus side of path:                     965 steps. Energy=    -391.3156991       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2920911 0.44019E-02     -391.2876892 0.28010E-01     -391.3156991   2.026   2.021   1.754  82.684
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2351.2    
 decide> The unconnected minima in the chain and their distances are:
     4       13.05     5     5        5.05     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1341 Dev= 0.04% S= 13.20 time= 0.50
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.19
 isnewts> transition state is the same as number        3 energy=     -391.2876892033
 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:                     957 steps. Energy=    -391.2920911       time=       2.37
 Minus side of path:                     992 steps. Energy=    -391.3156991       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2920911 0.44019E-02     -391.2876892 0.28010E-01     -391.3156991   2.026   2.021   1.754  82.684
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0169 Dev= 0.01% S= 5.05 time= 0.25
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.72

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     947 steps. Energy=    -391.2758247       time=       3.70
 Minus side of path:                     965 steps. Energy=    -391.2920911       time=       4.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2758247 0.24019E-01     -391.2518061 0.40285E-01     -391.2920911   5.064   5.045   2.609  55.574
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2675.3    
 decide> The unconnected minima in the chain and their distances are:
     3       13.88     5 
 

 tryconnect> 140-iteration DNEB run for minima 3_F and 5_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0560 Dev= 0.07% S= 14.08 time= 0.83
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   5.86

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     992 steps. Energy=    -391.3156991       time=       2.65
 Minus side of path:                     956 steps. Energy=    -391.7705351       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.3156991 0.19964         -391.1160577 0.65448         -391.7705351  15.343  14.136   2.856  50.767
        Known (#6)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -391.2758247 0.24019E-01    -391.2518061 0.40285E-01    -391.2920911   5.064   5.045   2.609  55.574
   3     -391.2920911 0.44019E-02    -391.2876892 0.28010E-01    -391.3156991   2.026   2.021   1.754  82.684
   6     -391.3156991 0.19964        -391.1160577 0.65448        -391.7705351  15.343  14.136   2.856  50.767
   2     -391.7705351 0.82577E-01    -391.6879576 0.10089        -391.7888469   4.389   4.114   3.483  41.632
   1     -391.7888469  3.8707        -387.9181348  1.2188        -389.1369071  30.012  28.298   2.282  63.542

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               112.30
 OPTIM> # of energy calls=                         90 time=           0.11 %=  0.1
 OPTIM> # of energy+gradient calls=             41488 time=          53.02 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       407 time=           2.01 %=  1.8
