
 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)@comp34.ch.
                 Created on  5/28/12 at 12:52:11 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -394.7678708     RMS force=    0.9471894182E-06
 OPTIM> Final energy  =    -383.8645237     RMS force=    0.8773833883E-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=    0.60964E+06
 decide> The unconnected minima in the chain and their distances are:
     2       84.79     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 805 RMS= 0.0598 Dev= 3.92% S= 101.89 time= 23.81
 Following    2 images are candidates for TS:    8   16  
 Converged to TS (number of iterations):        128
 Converged to TS (number of iterations):         98
 DNEB run yielded 2 true transition state(s) time=  21.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     839 steps. Energy=    -397.2569368       time=       3.09
 Minus side of path:                     884 steps. Energy=    -398.5631464       time=       3.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.2569368 0.53812         -396.7188181  1.8443         -398.5631464   8.758   8.517   2.923  49.601
        *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:                    1619 steps. Energy=    -386.9871926       time=       6.33
 Minus side of path:                    1216 steps. Energy=    -389.4906948       time=       3.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9871926  3.7236         -383.2635758  6.2271         -389.4906948  60.036  42.972   1.737  83.477
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=    0.12497E+06
 decide> The unconnected minima in the chain and their distances are:
     2       27.61     5     6       46.46     4     4       15.33     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 5_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0497 Dev= 0.73% S= 28.64 time= 2.59
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.73

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1160 steps. Energy=    -386.9871926       time=       3.06
 Minus side of path:                     996 steps. Energy=    -383.8645237       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9871926  3.1382         -383.8489683 0.15555E-01     -383.8645237  28.697  27.616   2.373  61.109
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 455-iteration DNEB run for minima 4_U and 6_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 455 RMS= 0.0695 Dev= 5.30% S= 54.15 time= 8.00
 Following    2 images are candidates for TS:    4    9  
 Converged to TS (number of iterations):         51
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=  11.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1045 steps. Energy=    -395.6295838       time=       3.82
 Minus side of path:                     922 steps. Energy=    -399.3032471       time=       2.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.6295838 0.78533         -394.8442576  4.4590         -399.3032471  14.758   7.830   3.994  36.300
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1467 steps. Energy=    -395.6295838       time=       5.28
 Minus side of path:                    1002 steps. Energy=    -389.4906948       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.6295838  7.9275         -387.7020449  1.7886         -389.4906948  47.783  43.212   1.999  72.548
        Known (#7)                                              Known (#6)
 Unconnected minimum 7 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      3.768894829    
 Double-ended search iterations= 140 RMS= 0.2883 Dev= 0.78% S= 17.90 time= 0.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   5.62

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     882 steps. Energy=    -394.6610214       time=       2.29
 Minus side of path:                     920 steps. Energy=    -394.7678708       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6610214 0.15206E-01     -394.6458155 0.12206         -394.7678708   1.080   1.076  39.612   3.661
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     4146.4    
 decide> The unconnected minima in the chain and their distances are:
     8        5.68     4     4       15.83     9 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8364 Dev= 0.03% S= 5.70 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     843 steps. Energy=    -398.5631464       time=       2.38
 Minus side of path:                     867 steps. Energy=    -399.3032471       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.5631464 0.27462         -398.2885226  1.0147         -399.3032471   7.970   5.682   5.551  26.119
        Known (#4)                                              Known (#8)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 4_F and 9_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.3533 Dev= 1.48% S= 18.55 time= 0.85
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.04

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1056 steps. Energy=    -398.7257479       time=       4.34
 Minus side of path:                     867 steps. Energy=    -394.7678708       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.7257479  5.5354         -393.1902984  1.5776         -394.7678708  29.199  23.077   7.300  19.864
        *NEW* (Placed in 10)                                    Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     4258.4    
 decide> The unconnected minima in the chain and their distances are:
     8       16.21     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 8_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.8400 Dev= 1.22% S= 18.72 time= 0.86
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.08

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     909 steps. Energy=    -395.4417387       time=       3.14
 Minus side of path:                    1070 steps. Energy=    -399.9957445       time=       4.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.4417387  1.5081         -393.9336673  6.0621         -399.9957445  29.114  23.098   7.292  19.884
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     3988.2    
 decide> The unconnected minima in the chain and their distances are:
     8       15.63    11    11        5.50     1 
 

 tryconnect> 140-iteration DNEB run for minima 8_F and 11_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.2597 Dev= 0.84% S= 18.28 time= 0.81
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.28
 isnewts> transition state is the same as number        9 energy=     -393.9336673033
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     908 steps. Energy=    -395.4417387       time=       2.25
 Minus side of path:                    1076 steps. Energy=    -399.9957445       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.4417387  1.5081         -393.9336673  6.0621         -399.9957445  29.116  23.102   7.284  19.908
        Known (#11)                                             Known (#12)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0658 Dev= 0.07% S= 5.53 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.46

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     967 steps. Energy=    -395.4417387       time=       2.57
 Minus side of path:                     951 steps. Energy=    -394.7678708       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.4417387 0.90701         -394.5347249 0.23315         -394.7678708   7.095   5.501   5.437  26.668
        Known (#11)                                             Known (#1)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     4636.1    
 decide> The unconnected minima in the chain and their distances are:
     8       16.67     9 
 

 tryconnect> 175-iteration DNEB run for minima 8_F and 9_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 175 RMS= 0.2923 Dev= 0.98% S= 19.38 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.46
 isnewts> transition state is the same as number        9 energy=     -393.9336673034
 tryconnect> Will not repeat search for TS      1 same as TS      9
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     4643.5    
 decide> The unconnected minima in the chain and their distances are:
     4       16.68    11 
 

 tryconnect> 175-iteration DNEB run for minima 4_F and 11_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.1608 Dev= 1.45% S= 19.36 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.01

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     861 steps. Energy=    -399.3032471       time=       2.29
 Minus side of path:                     957 steps. Energy=    -399.9957445       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -399.3032471  2.5228         -396.7804500  3.2153         -399.9957445  27.236  26.075   6.289  23.055
        Known (#8)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -394.7678708 0.23315        -394.5347249 0.90701        -395.4417387   7.095   5.501   5.437  26.668
   9     -395.4417387  1.5081        -393.9336673  6.0621        -399.9957445  29.114  23.098   7.292  19.884
  12     -399.9957445  3.2153        -396.7804500  2.5228        -399.3032471  27.236  26.075   6.289  23.055
   4     -399.3032471  4.4590        -394.8442576 0.78533        -395.6295838  14.758   7.830   3.994  36.300
   5     -395.6295838  7.9275        -387.7020449  1.7886        -389.4906948  47.783  43.212   1.999  72.548
   2     -389.4906948  6.2271        -383.2635758  3.7236        -386.9871926  60.036  42.972   1.737  83.477
   3     -386.9871926  3.1382        -383.8489683 0.15555E-01    -383.8645237  28.697  27.616   2.373  61.109

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

 Elapsed time=                               192.05
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             68229 time=          89.78 %= 46.7
 OPTIM> # of energy+gradient+Hessian calls=       678 time=           3.23 %=  1.7
