
 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)@comp28.ch.
                 Created on  5/28/12 at 13: 4:25 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=    -385.7689833     RMS force=    0.9612589376E-06
 OPTIM> Final energy  =    -379.9260352     RMS force=    0.8718081059E-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=    0.10353E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.96     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      205.9380245    
 Double-ended search iterations= 495 RMS= 1.1851 Dev= 0.59% S= 47.86 time= 8.40
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   6.77

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1032 steps. Energy=    -381.5798872       time=       3.57
 Minus side of path:                    1019 steps. Energy=    -381.1278293       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5798872  3.0753         -378.5045406  2.6233         -381.1278293   7.896   5.402  35.791   4.051
        *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=     62064.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.54     3     4       36.60     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 7.7202 Dev= 27.30% S= 24.70 time= 1.94
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):        101
 Converged to TS (number of iterations):         57
 DNEB run yielded 2 true transition state(s) time=  15.57

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1050 steps. Energy=    -381.5798872       time=       3.23
 Minus side of path:                    1008 steps. Energy=    -381.4571452       time=       3.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5798872 0.17502         -381.4048693 0.52276E-01     -381.4571452  15.701  15.116   2.500  57.994
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1345 steps. Energy=    -385.7689833       time=       5.40
 Minus side of path:                    1056 steps. Energy=    -381.5798872       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7689833  4.3306         -381.4384034 0.14148         -381.5798872  44.100  37.464   1.645  88.170
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 4_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 350 RMS= 1.4080 Dev= 0.87% S= 37.54 time= 3.99
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.38
 isnewts> transition state is the same as number        1 energy=     -378.5045405907
 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:                    1030 steps. Energy=    -381.5798872       time=       2.57
 Minus side of path:                    1026 steps. Energy=    -381.1278293       time=       2.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5798872  3.0753         -378.5045406  2.6233         -381.1278293   7.896   5.403  35.602   4.073
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6699.2    
 decide> The unconnected minima in the chain and their distances are:
     2       18.85     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 260 RMS= 9.0845 Dev= 31.26% S= 29.71 time= 1.48
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1041 steps. Energy=    -381.1278293       time=       2.56
 Minus side of path:                    1033 steps. Energy=    -385.9801886       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1278293 0.61464         -380.5131907  5.4670         -385.9801886  19.236  14.995   3.314  43.749
        Known (#4)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     11414.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.52     6 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      32.25099944    
 Double-ended search iterations= 210 RMS= 0.2682 Dev= 0.45% S= 22.58 time= 1.47
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   6.36
 isnewts> transition state is the same as number        5 energy=     -380.5131906511
 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:                    1050 steps. Energy=    -381.1278293       time=       4.31
 Minus side of path:                    1027 steps. Energy=    -385.9801886       time=       4.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1278293 0.61464         -380.5131907  5.4670         -385.9801886  19.235  14.994   3.322  43.651
        Known (#4)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13398.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.85     5 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.0393 Dev= 1.91% S= 20.23 time= 21.33
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   5.09

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1034 steps. Energy=    -385.9801886       time=       3.28
 Minus side of path:                    1020 steps. Energy=    -381.4571452       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9801886  7.6051         -378.3751164  3.0820         -381.4571452  11.416   9.087  14.474  10.018
        Known (#6)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13648.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.90     4 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 15.3326 Dev= 14.27% S= 48.86 time= 1.96
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         75
 Converged to TS (number of iterations):         80
 DNEB run yielded 2 true transition state(s) time=  14.50
 isnewts> transition state is the same as number        8 energy=     -379.9245213976
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     964 steps. Energy=    -379.9260352       time=       2.79
 Minus side of path:                    1099 steps. Energy=    -381.1278293       time=       5.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.9260352 0.15138E-02     -379.9245214  1.2033         -381.1278293  23.938  23.906   1.832  79.162
        Known (#2)                                              Known (#4)

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     919 steps. Energy=    -379.9260352       time=       3.45
 Minus side of path:                    1051 steps. Energy=    -381.1278293       time=       3.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.9260352 0.15138E-02     -379.9245214  1.2033         -381.1278293  23.942  23.910   1.823  79.528
        Known (#2)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -385.7689833  4.3306        -381.4384034 0.14148        -381.5798872  44.100  37.464   1.645  88.170
   1     -381.5798872  3.0753        -378.5045406  2.6233        -381.1278293   7.896   5.402  35.791   4.051
   8     -381.1278293  1.2033        -379.9245214 0.15138E-02    -379.9260352  23.938  23.906   1.832  79.162

 Number of TS in the path       =      3
 Number of cycles               =      6

 Elapsed time=                               160.71
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             63463 time=          70.28 %= 43.7
 OPTIM> # of energy+gradient+Hessian calls=       504 time=           2.35 %=  1.5
