
 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)@comp28.ch.
                 Created on  5/28/12 at 13: 6:58 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=    -376.8434946     RMS force=    0.9352800497E-06
 OPTIM> Final energy  =    -385.2394514     RMS force=    0.9243098185E-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=    0.21942E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.31     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1238691290    
 Double-ended search iterations= 630 RMS= 0.0459 Dev= 1.91% S= 69.73 time= 13.65
 Following    3 images are candidates for TS:    4    8   14  
 Converged to TS (number of iterations):        100
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         59
 DNEB run yielded 2 true transition state(s) time=  37.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1020 steps. Energy=    -376.8434946       time=       4.02
 Minus side of path:                    1020 steps. Energy=    -376.9056308       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.8434946 0.16235E-01     -376.8272595 0.78371E-01     -376.9056308   7.557   7.467  10.740  13.502
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1041 steps. Energy=    -382.9986292       time=       3.86
 Minus side of path:                     977 steps. Energy=    -381.9741642       time=       4.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9986292  1.0446         -381.9539938 0.20170E-01     -381.9741642  19.499  18.654   3.132  46.291
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     63809.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.92     4     5       38.72     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0346 Dev= 0.27% S= 18.16 time= 1.27
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1049 steps. Energy=    -385.2394514       time=       3.70
 Minus side of path:                     957 steps. Energy=    -382.9986292       time=       3.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2394514  2.3023         -382.9371072 0.61522E-01     -382.9986292  18.317  17.924   3.563  40.696
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 3_S and 5_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 385 RMS= 0.0544 Dev= 0.51% S= 41.25 time= 4.94
 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=  19.19
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     68878.    
 decide> The unconnected minima in the chain and their distances are:
     5       40.99     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 5_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 420 RMS= 0.0436 Dev= 0.72% S= 44.04 time= 5.70
 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=  20.03
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.11611E+06
 decide> The unconnected minima in the chain and their distances are:
     5       38.72     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 5_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1742963037    
 Double-ended search iterations= 805 RMS= 0.0342 Dev= 4.79% S= 50.76 time= 21.10
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        182
 DNEB run yielded 1 true transition state(s) time=  17.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1070 steps. Energy=    -382.0757114       time=       3.64
 Minus side of path:                    1067 steps. Energy=    -385.2394514       time=       3.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0757114 0.27970         -381.7960079  3.4434         -385.2394514  22.330  13.606   8.204  17.674
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.13763E+06
 decide> The unconnected minima in the chain and their distances are:
     4       51.63     3 
 

 tryconnect> 525-iteration DNEB run for minima 3_S and 4_F using 15 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 525 RMS= 0.0503 Dev= 1.68% S= 56.80 time= 9.18
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        124
 DNEB run yielded 1 true transition state(s) time=  10.26

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     958 steps. Energy=    -382.0198249       time=       3.79
 Minus side of path:                    1070 steps. Energy=    -382.9986292       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0198249 0.12974E-01     -382.0068513 0.99178         -382.9986292  19.800  18.993   2.987  48.537
        *NEW* (Placed in 7)                                     Known (#4)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     56553.    
 decide> The unconnected minima in the chain and their distances are:
     7       38.38     3 
 

 tryconnect> 385-iteration DNEB run for minima 3_S and 7_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 385 RMS= 0.0570 Dev= 0.76% S= 40.94 time= 4.91
 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=  18.58
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     67516.    
 decide> The unconnected minima in the chain and their distances are:
     7       40.72     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 7_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 420 RMS= 0.0530 Dev= 1.19% S= 43.87 time= 5.77
 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=  20.84
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.11311E+06
 decide> The unconnected minima in the chain and their distances are:
     7       38.38     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 7_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1433940004    
 Double-ended search iterations= 805 RMS= 0.0284 Dev= 4.72% S= 50.41 time= 20.83
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):        184
 DNEB run yielded 1 true transition state(s) time=  18.11

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     995 steps. Energy=    -383.5831698       time=       3.38
 Minus side of path:                     997 steps. Energy=    -382.0757114       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5831698  1.6131         -381.9701194 0.10559         -382.0757114  15.177  14.057   2.012  72.085
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.13503E+06
 decide> The unconnected minima in the chain and their distances are:
     7       40.72     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 7_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4446187806E-01
 Double-ended search iterations= 805 RMS= 0.0548 Dev= 4.27% S= 53.25 time= 21.36
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        229
 DNEB run yielded 1 true transition state(s) time=  24.75
 isnewts> transition state is the same as number        5 energy=     -382.0068512894
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     989 steps. Energy=    -382.0198249       time=       3.83
 Minus side of path:                    1047 steps. Energy=    -382.9986292       time=       5.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0198249 0.12974E-01     -382.0068513 0.99178         -382.9986292  19.800  18.993   2.984  48.594
        Known (#7)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.13776E+06
 decide> The unconnected minima in the chain and their distances are:
     5       40.99     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 805 RMS= 0.0367 Dev= 6.31% S= 54.19 time= 21.12
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        199
 DNEB run yielded 1 true transition state(s) time=  20.81

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1020 steps. Energy=    -382.0757114       time=       2.96
 Minus side of path:                     998 steps. Energy=    -383.1759484       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0757114 0.29740         -381.7783156  1.3976         -383.1759484  14.610  11.957   3.573  40.584
        Known (#6)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.16022E+06
 decide> The unconnected minima in the chain and their distances are:
     4       54.31     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 4_F using 16 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 560 RMS= 0.0445 Dev= 1.79% S= 61.12 time= 10.57
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        184
 DNEB run yielded 1 true transition state(s) time=  14.45
 isnewts> transition state is the same as number        5 energy=     -382.0068512894
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.17291E+06
 decide> The unconnected minima in the chain and their distances are:
     6       55.71     3 
 

 tryconnect> 560-iteration DNEB run for minima 3_S and 6_F using 16 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1505637004    
 Double-ended search iterations= 560 RMS= 0.0757 Dev= 1.47% S= 59.63 time= 10.15
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.59

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1717 steps. Energy=    -382.0757114       time=       6.68
 Minus side of path:                    1036 steps. Energy=    -376.9056308       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0757114  5.2407         -376.8349627 0.70668E-01     -376.9056308  58.702  55.870   1.809  80.158
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -376.8434946 0.16235E-01    -376.8272595 0.78371E-01    -376.9056308   7.557   7.467  10.740  13.502
   9     -376.9056308 0.70668E-01    -376.8349627  5.2407        -382.0757114  58.702  55.870   1.809  80.158
   4     -382.0757114 0.27970        -381.7960079  3.4434        -385.2394514  22.330  13.606   8.204  17.674

 Number of TS in the path       =      3
 Number of cycles               =     12

 Elapsed time=                               450.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            171651 time=         191.48 %= 42.5
 OPTIM> # of energy+gradient+Hessian calls=      2579 time=          12.76 %=  2.8
