
 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)@comp25.ch.
                 Created on  5/28/12 at 12:43:57 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -387.3512235     RMS force=    0.9649006132E-06
 OPTIM> Final energy  =    -380.2894341     RMS force=    0.9918613530E-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=     12642.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.30     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2922 Dev= 0.58% S= 26.07 time= 1.80
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.96

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1217 steps. Energy=    -383.6651687       time=       3.48
 Minus side of path:                     992 steps. Energy=    -380.2894341       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6651687  4.1812         -379.4839342 0.80550         -380.2894341  22.485  19.799   2.894  50.102
        *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=     23051.    
 decide> The unconnected minima in the chain and their distances are:
     3       28.46     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.168613344    
 Double-ended search iterations= 280 RMS= 0.1560 Dev= 0.83% S= 34.08 time= 2.92
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=   7.79

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     960 steps. Energy=    -387.3512235       time=       2.18
 Minus side of path:                     972 steps. Energy=    -382.5974758       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3512235  5.4390         -381.9122599 0.68522         -382.5974758  24.701  21.419   1.816  79.833
        Known (#1)                                              *NEW* (Placed in 4)
 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      2 steps with      1 missing connections, weight=     20396.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.32     4 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 4_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.3341 Dev= 0.77% S= 29.45 time= 2.94
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.67
 isnewts> transition state is the same as number        1 energy=     -379.4839341701
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1231 steps. Energy=    -383.6651687       time=       5.37
 Minus side of path:                    1000 steps. Energy=    -380.2894341       time=       3.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6651687  4.1812         -379.4839342 0.80550         -380.2894341  22.485  19.800   2.895  50.084
        Known (#3)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     25283.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.30     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0560 Dev= 8.88% S= 32.62 time= 24.21
 Following    1 images are candidates for TS:   19  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   6.23
 isnewts> transition state is the same as number        1 energy=     -379.4839341711
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     28855.    
 decide> The unconnected minima in the chain and their distances are:
     3       30.67     4 
 

 tryconnect> 315-iteration DNEB run for minima 3_F and 4_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0727 Dev= 0.88% S= 34.20 time= 3.92
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   6.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1155 steps. Energy=    -385.5179524       time=       5.67
 Minus side of path:                     995 steps. Energy=    -382.5974758       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5179524  4.5782         -380.9397188  1.6578         -382.5974758  38.578  34.131   4.776  30.361
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     7881.8    
 decide> The unconnected minima in the chain and their distances are:
     3       19.90     5 
 

 tryconnect> 175-iteration DNEB run for minima 3_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0553 Dev= 0.26% S= 20.15 time= 1.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   6.06

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     936 steps. Energy=    -383.6651687       time=       2.28
 Minus side of path:                    1112 steps. Energy=    -385.1441530       time=       3.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6651687 0.37727E-01     -383.6274419  1.5167         -385.1441530  18.430  17.691   4.458  32.526
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2818.2    
 decide> The unconnected minima in the chain and their distances are:
     6       14.13     5 
 

 tryconnect> 140-iteration DNEB run for minima 5_S and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0271 Dev= 0.02% S= 14.19 time= 0.86
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   6.18

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     966 steps. Energy=    -385.1441530       time=       4.38
 Minus side of path:                     970 steps. Energy=    -385.5179524       time=       3.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1441530 0.50960E-01     -385.0931926 0.42476         -385.5179524  14.445  14.126   1.911  75.863
        Known (#6)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -387.3512235  5.4390        -381.9122599 0.68522        -382.5974758  24.701  21.419   1.816  79.833
   4     -382.5974758  1.6578        -380.9397188  4.5782        -385.5179524  38.578  34.131   4.776  30.361
   6     -385.5179524 0.42476        -385.0931926 0.50960E-01    -385.1441530  14.445  14.126   1.911  75.863
   5     -385.1441530  1.5167        -383.6274419 0.37727E-01    -383.6651687  18.430  17.691   4.458  32.526
   1     -383.6651687  4.1812        -379.4839342 0.80550        -380.2894341  22.485  19.799   2.894  50.102

 Number of TS in the path       =      5
 Number of cycles               =      7

 Elapsed time=                               125.09
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             47993 time=          61.28 %= 49.0
 OPTIM> # of energy+gradient+Hessian calls=       436 time=           1.92 %=  1.5
