
 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 12:41:45 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -384.7663572     RMS force=    0.9884221069E-06
 OPTIM> Final energy  =    -388.4533193     RMS force=    0.9003213522E-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=     24240.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.94     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1574 Dev= 2.80% S= 31.91 time= 3.30
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   6.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     931 steps. Energy=    -384.7663572       time=       2.71
 Minus side of path:                     961 steps. Energy=    -385.4505590       time=       3.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.7663572 0.71980E-01     -384.6943775 0.75618         -385.4505590   4.634   4.353   9.096  15.942
        Known (#1)                                              *NEW* (Placed in 3)
 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=     23053.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.46     3 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0924 Dev= 1.75% S= 30.92 time= 3.11
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   7.42

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     959 steps. Energy=    -386.4501057       time=       3.35
 Minus side of path:                     953 steps. Energy=    -385.4398123       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.4501057  1.1968         -385.2533423 0.18647         -385.4398123  12.386  12.228   2.040  71.092
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     21526.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.81     4     5        2.02     3 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 4_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.2028 Dev= 1.28% S= 31.74 time= 3.10
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   6.82

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     935 steps. Energy=    -387.6407704       time=       2.67
 Minus side of path:                     939 steps. Energy=    -386.8408060       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6407704  1.6216         -386.0192194 0.82159         -386.8408060  15.483  14.290   2.079  69.754
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0188 Dev= 0.01% S= 2.02 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     916 steps. Energy=    -385.4505590       time=       3.10
 Minus side of path:                     933 steps. Energy=    -385.4398123       time=       3.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4505590 0.18651E-01     -385.4319080 0.79042E-02     -385.4398123   2.027   2.021   2.869  50.539
        Known (#3)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     7579.6    
 decide> The unconnected minima in the chain and their distances are:
     2       16.53     7     6       14.52     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2173 Dev= 0.23% S= 17.20 time= 0.90
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   6.33

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     970 steps. Energy=    -387.8182390       time=       4.11
 Minus side of path:                     974 steps. Energy=    -386.8408060       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8182390  3.2137         -384.6045684  2.2362         -386.8408060   6.001   5.178  39.682   3.654
        *NEW* (Placed in 8)                                     Known (#7)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 3_S and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1786 Dev= 0.10% S= 14.66 time= 0.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.72
 isnewts> transition state is the same as number        2 energy=     -385.2533423423
 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:                     949 steps. Energy=    -385.4398123       time=       2.27
 Minus side of path:                     956 steps. Energy=    -386.4501057       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4398123 0.18647         -385.2533423  1.1968         -386.4501057  12.386  12.228   2.039  71.123
        Known (#5)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     7708.3    
 decide> The unconnected minima in the chain and their distances are:
     2       16.10     8     6       15.23     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 8_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3235 Dev= 0.10% S= 16.47 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.44

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     939 steps. Energy=    -387.8310675       time=       2.28
 Minus side of path:                     937 steps. Energy=    -388.4533193       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8310675 0.18637         -387.6447009 0.80862         -388.4533193  14.227  13.733   7.689  18.859
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 5_S and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1424 Dev= 0.14% S= 15.36 time= 0.83
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   5.45
 isnewts> transition state is the same as number        2 energy=     -385.2533423424
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     3941.5    
 decide> The unconnected minima in the chain and their distances are:
     9        4.54     8     6       15.67     4 
 

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0173 Dev= 0.00% S= 4.54 time= 0.25
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.73

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     960 steps. Energy=    -387.8310675       time=       2.84
 Minus side of path:                     990 steps. Energy=    -387.8182390       time=       3.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8310675 0.51873E-01     -387.7791947 0.39044E-01     -387.8182390   6.571   4.543   3.122  46.444
        Known (#9)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 4_S and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3372 Dev= 0.36% S= 16.57 time= 0.83
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.99

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     947 steps. Energy=    -386.8007159       time=       4.19
 Minus side of path:                     927 steps. Energy=    -386.4501057       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8007159 0.98710         -385.8136200 0.63649         -386.4501057  13.426  11.939   4.584  31.634
        *NEW* (Placed in 10)                                    Known (#4)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     252.63    
 decide> The unconnected minima in the chain and their distances are:
     6        6.32    10 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3441 Dev= 0.37% S= 7.30 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.65

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     898 steps. Energy=    -386.8007159       time=       3.18
 Minus side of path:                     955 steps. Energy=    -387.6407704       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8007159 0.57134E-02     -386.7950025 0.84577         -387.6407704   5.606   5.569   4.043  35.867
        Known (#10)                                             Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -384.7663572 0.71980E-01    -384.6943775 0.75618        -385.4505590   4.634   4.353   9.096  15.942
   4     -385.4505590 0.18651E-01    -385.4319080 0.79042E-02    -385.4398123   2.027   2.021   2.869  50.539
   2     -385.4398123 0.18647        -385.2533423  1.1968        -386.4501057  12.386  12.228   2.040  71.092
   9     -386.4501057 0.63649        -385.8136200 0.98710        -386.8007159  13.426  11.939   4.584  31.634
  10     -386.8007159 0.57134E-02    -386.7950025 0.84577        -387.6407704   5.606   5.569   4.043  35.867
   3     -387.6407704  1.6216        -386.0192194 0.82159        -386.8408060  15.483  14.290   2.079  69.754
   5     -386.8408060  2.2362        -384.6045684  3.2137        -387.8182390   6.001   5.178  39.682   3.654
   8     -387.8182390 0.39044E-01    -387.7791947 0.51873E-01    -387.8310675   6.571   4.543   3.122  46.444
   7     -387.8310675 0.18637        -387.6447009 0.80862        -388.4533193  14.227  13.733   7.689  18.859

 Number of TS in the path       =      9
 Number of cycles               =      7

 Elapsed time=                               133.34
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39686 time=          53.80 %= 40.3
 OPTIM> # of energy+gradient+Hessian calls=       432 time=           2.21 %=  1.7
