
 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)@comp35.ch.
                 Created on  5/28/12 at 13:11:16 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=    -386.7898562     RMS force=    0.9064236420E-06
 OPTIM> Final energy  =    -387.8251225     RMS force=    0.7507619007E-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=     28638.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.59     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1876 Dev= 4.38% S= 37.39 time= 3.97
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):         57
 Converged to TS (number of iterations):         53
 DNEB run yielded 2 true transition state(s) time=  11.13

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     900 steps. Energy=    -390.1259716       time=       3.99
 Minus side of path:                     951 steps. Energy=    -388.0319619       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1259716  4.3130         -385.8129629  2.2190         -388.0319619  18.679  17.685   3.500  41.427
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     940 steps. Energy=    -388.0534299       time=       2.98
 Minus side of path:                     959 steps. Energy=    -387.8251225       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0534299  3.6345         -384.4189477  3.4062         -387.8251225  18.521  18.048   1.719  84.333
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3785.3    
 decide> The unconnected minima in the chain and their distances are:
     5        8.17     4     4       14.80     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.9112 Dev= 1.38% S= 8.88 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.08

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1120 steps. Energy=    -390.7695405       time=       3.56
 Minus side of path:                     865 steps. Energy=    -388.0534299       time=       2.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7695405  3.2631         -387.5063963 0.54703         -388.0534299  23.564  19.320   2.344  61.851
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0983 Dev= 0.25% S= 16.24 time= 0.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        132
 DNEB run yielded 1 true transition state(s) time=  13.33

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     936 steps. Energy=    -387.8896974       time=       3.08
 Minus side of path:                    1025 steps. Energy=    -387.5081588       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8896974  1.3542         -386.5355291 0.97263         -387.5081588  12.410  11.472  10.017  14.475
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3134.5    
 decide> The unconnected minima in the chain and their distances are:
     5       11.31     8     8       11.91     1 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3056 Dev= 0.27% S= 12.29 time= 0.51
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     910 steps. Energy=    -388.0319619       time=       2.27
 Minus side of path:                     939 steps. Energy=    -392.5382565       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0319619  2.9632         -385.0687146  7.4695         -392.5382565  12.081  10.707   4.770  30.399
        Known (#4)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0924 Dev= 0.09% S= 12.35 time= 0.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   6.96
 isnewts> transition state is the same as number        4 energy=     -386.5355291371
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     957 steps. Energy=    -387.8896974       time=       2.96
 Minus side of path:                    1047 steps. Energy=    -387.5081588       time=       3.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8896974  1.3542         -386.5355291 0.97263         -387.5081588  12.413  11.470  10.051  14.426
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     4056.8    
 decide> The unconnected minima in the chain and their distances are:
     5        8.17     4     4        7.80     8     7       13.55     1 
 

 tryconnect> 630-iteration DNEB run for minima 4_U and 5_F using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 630 RMS= 0.0526 Dev= 4.71% S= 15.20 time= 15.59
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=   6.03
 isnewts> transition state is the same as number        5 energy=     -385.0687146103
 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:                     924 steps. Energy=    -388.0319619       time=       2.27
 Minus side of path:                     939 steps. Energy=    -392.5382565       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0319619  2.9632         -385.0687146  7.4695         -392.5382565  12.081  10.707   4.764  30.434
        Known (#4)                                              Known (#9)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     942 steps. Energy=    -392.5382565       time=       2.54
 Minus side of path:                     895 steps. Energy=    -388.0534299       time=       2.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.5382565  9.7434         -382.7948410  5.2586         -388.0534299  12.173  10.933  12.915  11.227
        Known (#9)                                              Known (#5)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1365 Dev= 0.09% S= 7.93 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.57

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     953 steps. Energy=    -388.0319619       time=       2.92
 Minus side of path:                     948 steps. Energy=    -387.5081588       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.0319619 0.74191         -387.2900493 0.21811         -387.5081588   8.154   7.801   3.008  48.206
        Known (#4)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 7_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0990 Dev= 0.05% S= 14.06 time= 0.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=  10.13
 isnewts> transition state is the same as number        4 energy=     -386.5355291371
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3375.7    
 decide> The unconnected minima in the chain and their distances are:
     8       11.91     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 8_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1921616749    
 Double-ended search iterations= 805 RMS= 0.0190 Dev= 5.36% S= 15.41 time= 25.52
 Following    1 images are candidates for TS:    4  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.16

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     934 steps. Energy=    -386.7898562       time=       2.64
 Minus side of path:                    1092 steps. Energy=    -387.5081588       time=       4.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.7898562 0.23954         -386.5503142 0.95784         -387.5081588  12.547  11.910  10.896  13.308
        Known (#1)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -386.7898562 0.23954        -386.5503142 0.95784        -387.5081588  12.547  11.910  10.896  13.308
   9     -387.5081588 0.21811        -387.2900493 0.74191        -388.0319619   8.154   7.801   3.008  48.206
   5     -388.0319619  2.9632        -385.0687146  7.4695        -392.5382565  12.081  10.707   4.770  30.399
   8     -392.5382565  9.7434        -382.7948410  5.2586        -388.0534299  12.173  10.933  12.915  11.227
   2     -388.0534299  3.6345        -384.4189477  3.4062        -387.8251225  18.521  18.048   1.719  84.333

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

 Elapsed time=                               173.66
 OPTIM> # of energy calls=                        136 time=           0.18 %=  0.1
 OPTIM> # of energy+gradient calls=             64834 time=          85.79 %= 49.4
 OPTIM> # of energy+gradient+Hessian calls=       621 time=           3.03 %=  1.7
