
 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)@comp26.ch.
                 Created on  5/28/12 at 12:35:58 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -385.8946338     RMS force=    0.8767091115E-06
 OPTIM> Final energy  =    -387.1446599     RMS force=    0.8309702819E-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=     11477.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.56     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1232 Dev= 1.19% S= 25.97 time= 1.72
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   7.31

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     974 steps. Energy=    -385.9119519       time=       3.14
 Minus side of path:                     953 steps. Energy=    -385.8946338       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9119519 0.32534E-01     -385.8794178 0.15216E-01     -385.8946338   4.108   3.935   1.886  76.884
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     9121.2    
 decide> The unconnected minima in the chain and their distances are:
     2       20.89     3 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 3_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2486 Dev= 1.84% S= 24.21 time= 1.73
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=   9.58

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1183 steps. Energy=    -387.7418332       time=       5.01
 Minus side of path:                     945 steps. Energy=    -385.9119519       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.7418332  2.3319         -385.4099322 0.50202         -385.9119519  23.831  19.742   4.589  31.597
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1632.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.78     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4350 Dev= 1.97% S= 15.72 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=  10.42

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1128 steps. Energy=    -390.3109461       time=       4.38
 Minus side of path:                     938 steps. Energy=    -387.7418332       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.3109461  2.6437         -387.6672768 0.74556E-01     -387.7418332  22.791  21.338   1.921  75.468
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3265.8    
 decide> The unconnected minima in the chain and their distances are:
     2       11.78     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 805 RMS= 0.2816 Dev= 6.97% S= 23.41 time= 25.86
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        160
 DNEB run yielded 1 true transition state(s) time=  14.20

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     927 steps. Energy=    -386.9056522       time=       2.28
 Minus side of path:                     967 steps. Energy=    -387.1446599       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9056522  1.2199         -385.6857351  1.4589         -387.1446599  13.355  10.920   2.497  58.060
        *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      4 steps with      1 missing connections, weight=     1819.0    
 decide> The unconnected minima in the chain and their distances are:
     6       12.21     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 1.5966 Dev= 0.10% S= 17.64 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        234
 DNEB run yielded 1 true transition state(s) time=  24.36
 tryconnect> Transition state with energy      104.6394791     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3638.0    
 decide> The unconnected minima in the chain and their distances are:
     6       12.21     4 
 

 tryconnect> 805-iteration DNEB run for minima 4_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 805 RMS= 0.0467 Dev= 5.33% S= 31.85 time= 25.19
 Following    2 images are candidates for TS:   14   21  
 Converged to TS (number of iterations):         52
 Converged to TS (number of iterations):         20
 DNEB run yielded 2 true transition state(s) time=   9.10
 isnewts> transition state is the same as number        4 energy=     -385.6857351391
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1200 steps. Energy=    -389.4535132       time=       4.45
 Minus side of path:                     951 steps. Energy=    -387.1446599       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4535132  8.5329         -380.9205881  6.2241         -387.1446599  33.624  28.015   4.956  29.260
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     957 steps. Energy=    -386.9056522       time=       2.75
 Minus side of path:                     948 steps. Energy=    -387.1446599       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9056522  1.2199         -385.6857351  1.4589         -387.1446599  13.355  10.920   2.498  58.058
        Known (#6)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     7977.5    
 decide> The unconnected minima in the chain and their distances are:
     6       19.98     3 
 

 tryconnect> 175-iteration DNEB run for minima 3_S and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3126 Dev= 0.85% S= 22.77 time= 1.19
 Following    2 images are candidates for TS:    2    5  
 Converged to TS (number of iterations):         98
 Converged to TS (number of iterations):         42
 DNEB run yielded 2 true transition state(s) time=  14.10
 isnewts> transition state is the same as number        2 energy=     -385.4099322184
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        4 energy=     -385.6857351391
 tryconnect> Will not repeat search for TS      2 same as TS      4

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1282 steps. Energy=    -389.0133712       time=       5.99
 Minus side of path:                     965 steps. Energy=    -385.9119519       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.0133712  3.6034         -385.4099322 0.50202         -385.9119519  31.014  27.293   3.447  42.062
        *NEW* (Placed in 8)                                     Known (#3)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     8687.2    
 decide> The unconnected minima in the chain and their distances are:
     6       20.56     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1466 Dev= 1.84% S= 24.58 time= 1.70
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        107
 DNEB run yielded 1 true transition state(s) time=   8.94

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1137 steps. Energy=    -390.1326012       time=       4.59
 Minus side of path:                    1070 steps. Energy=    -385.8946338       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1326012  8.2424         -381.8901695  4.0045         -385.8946338  40.315  31.392   4.618  31.400
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     8176.0    
 decide> The unconnected minima in the chain and their distances are:
     7       20.15     9 
 

 tryconnect> 210-iteration DNEB run for minima 7_F and 9_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0455 Dev= 0.07% S= 20.98 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.16

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     964 steps. Energy=    -390.1326012       time=       3.44
 Minus side of path:                     893 steps. Energy=    -389.4535132       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1326012  1.4289         -388.7036913 0.74982         -389.4535132  20.889  20.162   7.188  20.174
        Known (#9)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -385.8946338  4.0045        -381.8901695  8.2424        -390.1326012  40.315  31.392   4.618  31.400
   9     -390.1326012  1.4289        -388.7036913 0.74982        -389.4535132  20.889  20.162   7.188  20.174
   5     -389.4535132  8.5329        -380.9205881  6.2241        -387.1446599  33.624  28.015   4.956  29.260

 Number of TS in the path       =      3
 Number of cycles               =      9

 Elapsed time=                               223.27
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             73927 time=          99.18 %= 44.4
 OPTIM> # of energy+gradient+Hessian calls=      1003 time=           5.23 %=  2.3
