
 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)@comp25.ch.
                 Created on  5/28/12 at 13:10:58 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>> 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=    -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= 0.1223 Dev= 0.92% S= 25.83 time= 1.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   6.61

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     964 steps. Energy=    -385.9119519       time=       2.72
 Minus side of path:                     981 steps. Energy=    -386.8386492       time=       2.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9119519 0.51570         -385.3962563  1.4424         -386.8386492  20.613  19.371   7.764  18.675
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2158.3    
 decide> The unconnected minima in the chain and their distances are:
     2       12.80     4     3        3.93     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3383 Dev= 0.50% S= 14.29 time= 0.52
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.55

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0120 Dev= 0.00% S= 3.94 time= 0.25
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   5.06

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     986 steps. Energy=    -385.9119519       time=       4.20
 Minus side of path:                     945 steps. Energy=    -385.8946338       time=       3.22

         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  76.883
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 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=     4194.7    
 decide> The unconnected minima in the chain and their distances are:
     2       12.80     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 805 RMS= 0.3336 Dev= 5.21% S= 23.48 time= 25.23
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.00

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1210 steps. Energy=    -389.4535132       time=       5.64
 Minus side of path:                     947 steps. Energy=    -387.1446599       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4535132  8.5329         -380.9205881  6.2241         -387.1446599  33.629  28.022   4.943  29.334
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 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= 0.2033 Dev= 1.38% S= 24.12 time= 1.78
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   7.13
 isnewts> transition state is the same as number        1 energy=     -385.3962562799
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     955 steps. Energy=    -385.9119519       time=       3.37
 Minus side of path:                     973 steps. Energy=    -386.8386492       time=       4.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9119519 0.51570         -385.3962563  1.4424         -386.8386492  20.614  19.372   7.737  18.742
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     18242.    
 decide> The unconnected minima in the chain and their distances are:
     2       20.89     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.3905 Dev= 4.25% S= 32.31 time= 25.09
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   6.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     948 steps. Energy=    -387.9455862       time=       2.66
 Minus side of path:                    1236 steps. Energy=    -390.1326012       time=       5.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9455862  6.4853         -381.4603198  8.6723         -390.1326012  34.534  27.821   5.034  28.805
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     10102.    
 decide> The unconnected minima in the chain and their distances are:
     5       20.15     7     6       12.44     1 
 

 tryconnect> 210-iteration DNEB run for minima 5_F and 7_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0483 Dev= 0.18% S= 20.97 time= 1.92
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   4.45

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     966 steps. Energy=    -390.1326012       time=       2.62
 Minus side of path:                     935 steps. Energy=    -389.4535132       time=       2.73

         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   7.194  20.154
        Known (#7)                                              Known (#5)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6238 Dev= 0.30% S= 13.91 time= 0.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        180
 DNEB run yielded 1 true transition state(s) time=  19.95

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     925 steps. Energy=    -387.1446599       time=       3.08
 Minus side of path:                     948 steps. Energy=    -387.9455862       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1446599 0.67219         -386.4724693  1.4731         -387.9455862  20.939  20.250   7.516  19.293
        Known (#2)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2318.9    
 decide> The unconnected minima in the chain and their distances are:
     6       13.24     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3813 Dev= 0.61% S= 14.63 time= 0.48
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        159
 DNEB run yielded 1 true transition state(s) time=  12.06
 isnewts> transition state is the same as number        7 energy=     -386.4724692818
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     960 steps. Energy=    -387.1446599       time=       2.23
 Minus side of path:                     945 steps. Energy=    -387.9455862       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1446599 0.67219         -386.4724693  1.4731         -387.9455862  20.940  20.252   7.485  19.371
        Known (#2)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3852.9    
 decide> The unconnected minima in the chain and their distances are:
     6       12.44     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 805 RMS= 0.1146 Dev= 6.94% S= 23.90 time= 23.94
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   4.48
 isnewts> transition state is the same as number        5 energy=     -381.4603197873
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     948 steps. Energy=    -387.9455862       time=       2.14
 Minus side of path:                    1256 steps. Energy=    -390.1326012       time=       3.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9455862  6.4853         -381.4603198  8.6723         -390.1326012  34.531  27.814   5.052  28.704
        Known (#6)                                              Known (#7)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 7 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4637.8    
 decide> The unconnected minima in the chain and their distances are:
     6       13.24     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      18.85649142    
 Double-ended search iterations= 805 RMS= 0.1770 Dev= 5.17% S= 22.01 time= 23.95
 Following    1 images are candidates for TS:   12  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.39
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 7 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     16824.    
 decide> The unconnected minima in the chain and their distances are:
     6       25.62     4 
 

 tryconnect> 245-iteration DNEB run for minima 4_S and 6_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2241 Dev= 0.61% S= 29.85 time= 2.37
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   5.42
 isnewts> transition state is the same as number        1 energy=     -385.3962562798
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 7 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     22954.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.56     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 805 RMS= 0.0708 Dev= 6.07% S= 34.93 time= 24.26
 Following    2 images are candidates for TS:   11   20  
 Converged to TS (number of iterations):        110
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=  10.31
 isnewts> transition state is the same as number        7 energy=     -386.4724692817
 tryconnect> Will not repeat search for TS      2 same as TS      7

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1066 steps. Energy=    -385.8946338       time=       2.59
 Minus side of path:                    1138 steps. Energy=    -390.1326012       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8946338  4.0045         -381.8901695  8.2424         -390.1326012  40.314  31.388   4.626  31.347
        Known (#1)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -385.8946338  4.0045        -381.8901695  8.2424        -390.1326012  40.314  31.388   4.626  31.347
   6     -390.1326012  1.4289        -388.7036913 0.74982        -389.4535132  20.889  20.162   7.194  20.154
   3     -389.4535132  8.5329        -380.9205881  6.2241        -387.1446599  33.629  28.022   4.943  29.334

 Number of TS in the path       =      3
 Number of cycles               =     11

 Elapsed time=                               328.26
 OPTIM> # of energy calls=                        302 time=           0.39 %=  0.1
 OPTIM> # of energy+gradient calls=            136432 time=         174.86 %= 53.3
 OPTIM> # of energy+gradient+Hessian calls=      1343 time=           6.31 %=  1.9
