
 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)@comp27.ch.
                 Created on  5/28/12 at 12:51:14 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.3551822     RMS force=    0.9284769086E-06
 OPTIM> Final energy  =    -388.4876847     RMS force=    0.8902345791E-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=     73156.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.82     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0617 Dev= 1.77% S= 48.31 time= 6.62
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   7.11

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1077 steps. Energy=    -388.4876847       time=       3.88
 Minus side of path:                    1521 steps. Energy=    -386.9854348       time=       5.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4876847  10.501         -377.9864211  8.9990         -386.9854348  43.907  32.757   2.375  61.049
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     91966.    
 decide> The unconnected minima in the chain and their distances are:
     3       45.14     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 3_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.1007 Dev= 2.61% S= 50.71 time= 7.56
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        215
 DNEB run yielded 1 true transition state(s) time=  22.24

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1101 steps. Energy=    -386.0729061       time=       3.59
 Minus side of path:                     987 steps. Energy=    -386.2584867       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0729061 0.18046         -385.8924457 0.36604         -386.2584867  17.385  14.279   3.222  44.998
        *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=     39151.    
 decide> The unconnected minima in the chain and their distances are:
     3       15.71     4     5       32.79     1 
 

 tryconnect> 140-iteration DNEB run for minima 3_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0908 Dev= 0.07% S= 16.04 time= 0.86
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     950 steps. Energy=    -386.0729061       time=       3.01
 Minus side of path:                     989 steps. Energy=    -386.5483014       time=       3.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0729061 0.13505         -385.9378595 0.61044         -386.5483014   7.840   7.253   1.557  93.149
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 5_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1012 Dev= 0.20% S= 35.55 time= 3.68
 Following    2 images are candidates for TS:    1    5  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         83
 DNEB run yielded 2 true transition state(s) time=  11.69

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1103 steps. Energy=    -387.1746544       time=       2.85
 Minus side of path:                     970 steps. Energy=    -383.3551822       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  3.8532         -383.3214602 0.33722E-01     -383.3551822  14.701  13.700   5.338  27.162
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1066 steps. Energy=    -387.1034948       time=       3.27
 Minus side of path:                     987 steps. Energy=    -385.6168522       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1034948  1.5364         -385.5671127 0.49740E-01     -385.6168522  22.422  20.340   2.456  59.047
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     11017.    
 decide> The unconnected minima in the chain and their distances are:
     3       14.59     6     4       19.92     9     8        1.87     7 
 

 tryconnect> 140-iteration DNEB run for minima 3_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 1.1511 Dev= 0.11% S= 15.15 time= 0.84
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.98

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     992 steps. Energy=    -386.5483014       time=       2.90
 Minus side of path:                    1047 steps. Energy=    -386.9854348       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5483014 0.25724         -386.2910631 0.69437         -386.9854348  16.583  14.599   7.350  19.729
        Known (#6)                                              Known (#3)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 4_F and 9_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0333 Dev= 0.03% S= 20.04 time= 1.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=   9.27

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     886 steps. Energy=    -386.0729061       time=       2.34
 Minus side of path:                     965 steps. Energy=    -386.1180353       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0729061 0.13584E-03     -386.0727702 0.45265E-01     -386.1180353   2.593   2.591   5.692  25.475
        Known (#4)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0116 Dev= 0.01% S= 1.87 time= 0.21
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.62

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     989 steps. Energy=    -387.1034948       time=       2.28
 Minus side of path:                     980 steps. Energy=    -387.1746544       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1034948 0.18851E-02     -387.1016098 0.73045E-01     -387.1746544   1.869   1.868   2.389  60.700
        Known (#8)                                              Known (#7)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     7830.0    
 decide> The unconnected minima in the chain and their distances are:
    10       19.86     9 
 

 tryconnect> 175-iteration DNEB run for minima 9_S and 10_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 2.5134 Dev= 0.12% S= 20.02 time= 1.21
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.25
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     10897.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.17     8 
 

 tryconnect> 210-iteration DNEB run for minima 5_F and 8_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0578 Dev= 0.12% S= 23.15 time= 1.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   7.14

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     982 steps. Energy=    -386.2297062       time=       4.40
 Minus side of path:                    1167 steps. Energy=    -387.1034948       time=       3.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2297062 0.82789         -385.4018158  1.7017         -387.1034948  32.387  18.521   4.186  34.642
        *NEW* (Placed in 11)                                    Known (#8)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2648.8    
 decide> The unconnected minima in the chain and their distances are:
     5       13.84    11 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0203 Dev= 0.01% S= 13.88 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.18

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     946 steps. Energy=    -386.2297062       time=       2.23
 Minus side of path:                     979 steps. Energy=    -386.4322608       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2297062 0.89723E-01     -386.1399829 0.29228         -386.4322608   9.064   8.900   8.817  16.445
        Known (#11)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     679.64    
 decide> The unconnected minima in the chain and their distances are:
     5        8.79    12 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0427 Dev= 0.01% S= 8.80 time= 0.25
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     964 steps. Energy=    -386.4322608       time=       2.73
 Minus side of path:                     918 steps. Energy=    -386.2584867       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.4322608 0.21025         -386.2220138 0.36473E-01     -386.2584867   8.948   8.792   3.151  46.012
        Known (#12)                                             Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -383.3551822 0.33722E-01    -383.3214602  3.8532        -387.1746544  14.701  13.700   5.338  27.162
   8     -387.1746544 0.73045E-01    -387.1016098 0.18851E-02    -387.1034948   1.869   1.868   2.389  60.700
   9     -387.1034948  1.7017        -385.4018158 0.82789        -386.2297062  32.387  18.521   4.186  34.642
  10     -386.2297062 0.89723E-01    -386.1399829 0.29228        -386.4322608   9.064   8.900   8.817  16.445
  11     -386.4322608 0.21025        -386.2220138 0.36473E-01    -386.2584867   8.948   8.792   3.151  46.012
   2     -386.2584867 0.36604        -385.8924457 0.18046        -386.0729061  17.385  14.279   3.222  44.998
   3     -386.0729061 0.13505        -385.9378595 0.61044        -386.5483014   7.840   7.253   1.557  93.149
   6     -386.5483014 0.25724        -386.2910631 0.69437        -386.9854348  16.583  14.599   7.350  19.729
   1     -386.9854348  8.9990        -377.9864211  10.501        -388.4876847  43.907  32.757   2.375  61.049

 Number of TS in the path       =      9
 Number of cycles               =      8

 Elapsed time=                               195.14
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             55466 time=          71.35 %= 36.6
 OPTIM> # of energy+gradient+Hessian calls=       970 time=           4.82 %=  2.5
