
 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)@comp18.ch.
                 Created on  5/28/12 at 13: 6:22 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -376.9383809     RMS force=    0.8037852448E-06
 OPTIM> Final energy  =    -380.6469630     RMS force=    0.9849794545E-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=     39029.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.92     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 350 RMS= 0.1468 Dev= 3.55% S= 37.13 time= 3.86
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=  10.19

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1354 steps. Energy=    -380.2155834       time=       4.42
 Minus side of path:                    1014 steps. Energy=    -381.3469114       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834  1.7550         -378.4605445  2.8864         -381.3469114  45.845  42.563   1.777  81.598
        *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      2 steps with      2 missing connections, weight=     39342.    
 decide> The unconnected minima in the chain and their distances are:
     2       15.89     4     4       32.81     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0407 Dev= 0.16% S= 15.95 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.33

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1034 steps. Energy=    -381.3066617       time=       2.97
 Minus side of path:                     990 steps. Energy=    -380.6469630       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3066617 0.81225         -380.4944124 0.15255         -380.6469630  13.815  13.420   1.834  79.049
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 4_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 1.0051 Dev= 3.79% S= 36.56 time= 3.22
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   6.17

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     991 steps. Energy=    -381.3469114       time=       2.11
 Minus side of path:                    1166 steps. Energy=    -380.2155834       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3469114  2.2573         -379.0895915  1.1260         -380.2155834  45.049  42.515   1.712  84.719
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     34596.    
 decide> The unconnected minima in the chain and their distances are:
     5       32.58     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 5_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 315 RMS= 0.3018 Dev= 3.44% S= 35.61 time= 3.14
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   5.92
 isnewts> transition state is the same as number        3 energy=     -379.0895914774
 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:                    1015 steps. Energy=    -381.3469114       time=       2.21
 Minus side of path:                    1183 steps. Energy=    -380.2155834       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3469114  2.2573         -379.0895915  1.1260         -380.2155834  45.049  42.516   1.711  84.727
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     36666.    
 decide> The unconnected minima in the chain and their distances are:
     5        4.94     4     3       33.18     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0141 Dev= 0.02% S= 4.95 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   2.90

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1010 steps. Energy=    -381.3469114       time=       2.18
 Minus side of path:                     969 steps. Energy=    -381.3066617       time=       2.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3469114 0.40357E-01     -381.3065543 0.10733E-03     -381.3066617   4.961   4.945   2.063  70.289
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 3_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.2188 Dev= 2.68% S= 35.31 time= 3.15
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1051 steps. Energy=    -380.2155834       time=       2.34
 Minus side of path:                    1036 steps. Energy=    -380.1934631       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.42575         -379.7898383 0.40362         -380.1934631  31.387  29.159   1.946  74.529
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     379.97    
 decide> The unconnected minima in the chain and their distances are:
     6        7.24     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2593 Dev= 0.25% S= 7.50 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     994 steps. Energy=    -376.9383809       time=       2.08
 Minus side of path:                    1002 steps. Energy=    -379.8939722       time=       2.11

         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 7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     232.30    
 decide> The unconnected minima in the chain and their distances are:
     6        6.15     7 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 7_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.1013 Dev= 0.68% S= 6.20 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.12

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     978 steps. Energy=    -380.1934631       time=       2.03
 Minus side of path:                    1019 steps. Energy=    -379.8939722       time=       2.17

         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
        Known (#6)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -376.9383809 0.70473        -376.2336546  3.6603        -379.8939722   5.476   4.711  44.112   3.287
   8     -379.8939722 0.18046        -379.7135094 0.47995        -380.1934631   7.116   6.148   1.846  78.559
   6     -380.1934631 0.40362        -379.7898383 0.42575        -380.2155834  31.387  29.159   1.946  74.529
   1     -380.2155834  1.7550        -378.4605445  2.8864        -381.3469114  45.845  42.563   1.777  81.598
   5     -381.3469114 0.40357E-01    -381.3065543 0.10733E-03    -381.3066617   4.961   4.945   2.063  70.289
   2     -381.3066617 0.81225        -380.4944124 0.15255        -380.6469630  13.815  13.420   1.834  79.049

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

 Elapsed time=                                93.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             38265 time=          41.01 %= 43.6
 OPTIM> # of energy+gradient+Hessian calls=       372 time=           1.44 %=  1.5
