
 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 12:50:59 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=    -389.6639145     RMS force=    0.9768178271E-06
 OPTIM> Final energy  =    -384.2695727     RMS force=    0.9129670961E-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=    0.29026E+06
 decide> The unconnected minima in the chain and their distances are:
     2       66.21     1 
 

 tryconnect> 665-iteration DNEB run for minima 1_S and 2_F using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7984714498E-01
 Double-ended search iterations= 665 RMS= 0.0292 Dev= 4.42% S= 82.22 time= 14.84
 Following    2 images are candidates for TS:   10   15  
 Converged to TS (number of iterations):        135
 Converged to TS (number of iterations):        127
 DNEB run yielded 2 true transition state(s) time=  24.44

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    2124 steps. Energy=    -386.4237956       time=      13.80
 Minus side of path:                    1928 steps. Energy=    -389.6639145       time=       9.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.4237956  7.3280         -379.0958104  10.568         -389.6639145 121.091  54.415   1.809  80.169
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1435 steps. Energy=    -385.9571485       time=       7.17
 Minus side of path:                    1164 steps. Energy=    -383.9913743       time=       4.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9571485  2.7041         -383.2530609 0.73831         -383.9913743  64.159  56.834   1.723  84.164
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     13843.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.65     5     4       23.29     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1133 Dev= 0.06% S= 10.71 time= 0.34
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   4.58

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1027 steps. Energy=    -384.2695727       time=       3.64
 Minus side of path:                    1018 steps. Energy=    -383.9913743       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2695727  1.5291         -382.7404462  1.2509         -383.9913743  10.811  10.649   1.885  76.917
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 3_S and 4_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1781 Dev= 0.66% S= 24.95 time= 1.63
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.38

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     965 steps. Energy=    -386.7277073       time=       2.59
 Minus side of path:                     971 steps. Energy=    -385.1128586       time=       2.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.7277073  3.4170         -383.3106929  1.8022         -385.1128586  11.795  10.366   6.437  22.526
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     2307.8    
 decide> The unconnected minima in the chain and their distances are:
     4        9.14     6     7       11.56     3 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9596 Dev= 0.25% S= 9.40 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     987 steps. Energy=    -386.0522745       time=       2.86
 Minus side of path:                     967 steps. Energy=    -385.9571485       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0522745 0.11119         -385.9410886 0.16060E-01     -385.9571485   1.033   1.030  40.176   3.609
        *NEW* (Placed in 8)                                     Known (#4)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0818 Dev= 0.10% S= 11.66 time= 0.41
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.39

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     932 steps. Energy=    -385.1128586       time=       2.72
 Minus side of path:                     993 steps. Energy=    -386.4237956       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1128586 0.20892E-01     -385.0919665  1.3318         -386.4237956  12.427  11.561   1.911  75.874
        Known (#7)                                              Known (#3)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     740.54    
 decide> The unconnected minima in the chain and their distances are:
     8        9.05     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.0025 Dev= 0.16% S= 9.28 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     969 steps. Energy=    -386.9875125       time=       2.42
 Minus side of path:                     979 steps. Energy=    -386.0522745       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9875125  2.9537         -384.0337884  2.0185         -386.0522745   6.633   5.824  24.327   5.960
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     228.49    
 decide> The unconnected minima in the chain and their distances are:
     9        6.11     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0720 Dev= 0.05% S= 6.13 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.82

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     948 steps. Energy=    -386.7277073       time=       2.26
 Minus side of path:                     972 steps. Energy=    -386.9875125       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.7277073 0.16350         -386.5642110 0.42330         -386.9875125   6.334   6.114   3.006  48.237
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.6639145  10.568        -379.0958104  7.3280        -386.4237956 121.091  54.415   1.809  80.169
   6     -386.4237956  1.3318        -385.0919665 0.20892E-01    -385.1128586  12.427  11.561   1.911  75.874
   4     -385.1128586  1.8022        -383.3106929  3.4170        -386.7277073  11.795  10.366   6.437  22.526
   8     -386.7277073 0.16350        -386.5642110 0.42330        -386.9875125   6.334   6.114   3.006  48.237
   7     -386.9875125  2.9537        -384.0337884  2.0185        -386.0522745   6.633   5.824  24.327   5.960
   5     -386.0522745 0.11119        -385.9410886 0.16060E-01    -385.9571485   1.033   1.030  40.176   3.609
   2     -385.9571485  2.7041        -383.2530609 0.73831        -383.9913743  64.159  56.834   1.723  84.164
   3     -383.9913743  1.2509        -382.7404462  1.5291        -384.2695727  10.811  10.649   1.885  76.917

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                               134.07
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41842 time=          49.75 %= 37.1
 OPTIM> # of energy+gradient+Hessian calls=       410 time=           1.97 %=  1.5
