
 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)@comp31.ch.
                 Created on  5/28/12 at 12:58:20 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=    -384.7510814     RMS force=    0.9752249555E-06
 OPTIM> Final energy  =    -384.2669700     RMS force=    0.9922251644E-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=     23009.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.44     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 280 RMS= 1.0908 Dev= 1.54% S= 34.92 time= 2.95
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.14
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     46019.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.44     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 805 RMS= 0.0934 Dev= 5.52% S= 45.77 time= 24.50
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):        112
 DNEB run yielded 1 true transition state(s) time=  14.77

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     950 steps. Energy=    -393.0920079       time=       2.62
 Minus side of path:                     953 steps. Energy=    -391.5265017       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0920079  1.8620         -391.2300097 0.29649         -391.5265017   9.378   9.044   4.907  29.547
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     42848.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.23     3     3       31.70     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 3_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 210 RMS= 0.1503 Dev= 0.17% S= 23.22 time= 1.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.30

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1446 steps. Energy=    -392.1938277       time=       7.69
 Minus side of path:                     950 steps. Energy=    -384.2669700       time=       3.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.1938277  8.3915         -383.8023118 0.46466         -384.2669700  30.207  26.888   1.972  73.519
        *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 3_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 315 RMS= 0.4001 Dev= 0.94% S= 36.09 time= 3.75
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.21
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     50303.    
 decide> The unconnected minima in the chain and their distances are:
     5       36.91     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 5_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0797 Dev= 2.40% S= 49.88 time= 5.64
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   8.09

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1315 steps. Energy=    -392.2090778       time=       4.00
 Minus side of path:                     948 steps. Energy=    -386.5537864       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2090778  6.0061         -386.2030112 0.35078         -386.5537864  23.435  22.840   2.213  65.527
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     28284.    
 decide> The unconnected minima in the chain and their distances are:
     5        3.80     6     7       30.45     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0321 Dev= 0.02% S= 3.81 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     917 steps. Energy=    -392.2090778       time=       2.15
 Minus side of path:                     902 steps. Energy=    -392.1938277       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2090778 0.93257E-01     -392.1158205 0.78007E-01     -392.1938277   3.813   3.803   3.510  41.309
        Known (#6)                                              Known (#5)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 7_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 315 RMS= 0.1634 Dev= 0.64% S= 33.91 time= 3.72
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.95
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     40105.    
 decide> The unconnected minima in the chain and their distances are:
     7       15.59     4     4       33.12     1 
 

 tryconnect> 140-iteration DNEB run for minima 4_U and 7_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 3.1582 Dev= 0.47% S= 15.94 time= 0.78
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.85

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     965 steps. Energy=    -386.5537864       time=       2.29
 Minus side of path:                     976 steps. Energy=    -386.6359354       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5537864 0.21470E-01     -386.5323166 0.10362         -386.6359354   1.415   1.402   4.732  30.641
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 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      2.953027717    
 Double-ended search iterations= 315 RMS= 0.1512 Dev= 1.53% S= 37.53 time= 3.74
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  18.59
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     28908.    
 decide> The unconnected minima in the chain and their distances are:
     8       30.69     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 8_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 315 RMS= 0.1300 Dev= 0.82% S= 34.51 time= 3.79
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        209
 DNEB run yielded 1 true transition state(s) time=  16.27

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1232 steps. Energy=    -388.3866121       time=       4.80
 Minus side of path:                    1012 steps. Energy=    -387.3417727       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3866121  6.5498         -381.8368601  5.5049         -387.3417727  31.250  21.605   2.668  54.338
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     50520.    
 decide> The unconnected minima in the chain and their distances are:
     6       36.97     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 6_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.1047 Dev= 2.89% S= 49.44 time= 5.66
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        110
 DNEB run yielded 1 true transition state(s) time=   9.86

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     966 steps. Energy=    -388.3718877       time=       3.36
 Minus side of path:                    1149 steps. Energy=    -393.0920079       time=       4.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3718877 0.21313E-01     -388.3505745  4.7414         -393.0920079  20.283  18.464   3.758  38.589
        *NEW* (Placed in 11)                                    Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     23595.    
 decide> The unconnected minima in the chain and their distances are:
     7       14.33    11    11       27.44     1 
 

 tryconnect> 140-iteration DNEB run for minima 7_F and 11_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1125 Dev= 0.17% S= 14.57 time= 0.80
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=  11.91

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1042 steps. Energy=    -393.0920079       time=       3.14
 Minus side of path:                     989 steps. Energy=    -392.2090778       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0920079  3.4834         -389.6086274  2.6005         -392.2090778  29.566  26.190   3.346  43.338
        Known (#3)                                              Known (#6)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 11_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 280 RMS= 0.1368 Dev= 1.04% S= 31.33 time= 2.94
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        191
 DNEB run yielded 1 true transition state(s) time=  21.45

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1326 steps. Energy=    -392.2090778       time=       6.06
 Minus side of path:                     949 steps. Energy=    -386.6359354       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.2090778  5.9158         -386.2932775 0.34266         -386.6359354  23.515  22.913   2.171  66.798
        Known (#6)                                              Known (#8)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     41303.    
 decide> The unconnected minima in the chain and their distances are:
    11       27.44     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 11_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0746 Dev= 5.43% S= 46.20 time= 24.40
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   6.54

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1158 steps. Energy=    -384.7510814       time=       3.34
 Minus side of path:                    1166 steps. Energy=    -386.6359354       time=       4.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.7510814  5.7442         -379.0068907  7.6290         -386.6359354  42.329  30.717   2.722  53.263
        Known (#1)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -384.7510814  5.7442        -379.0068907  7.6290        -386.6359354  42.329  30.717   2.722  53.263
   5     -386.6359354 0.10362        -386.5323166 0.21470E-01    -386.5537864   1.415   1.402   4.732  30.641
   3     -386.5537864 0.35078        -386.2030112  6.0061        -392.2090778  23.435  22.840   2.213  65.527
   4     -392.2090778 0.93257E-01    -392.1158205 0.78007E-01    -392.1938277   3.813   3.803   3.510  41.309
   2     -392.1938277  8.3915        -383.8023118 0.46466        -384.2669700  30.207  26.888   1.972  73.519

 Number of TS in the path       =      5
 Number of cycles               =     10

 Elapsed time=                               333.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            104730 time=         134.98 %= 40.4
 OPTIM> # of energy+gradient+Hessian calls=      1992 time=           9.22 %=  2.8
