
 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)@comp31.ch.
                 Created on  5/28/12 at 12:36:16 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=    -386.9767568     RMS force=    0.9921892817E-06
 OPTIM> Final energy  =    -389.7291031     RMS force=    0.9744787676E-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=     6187.4    
 decide> The unconnected minima in the chain and their distances are:
     2       18.36     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 175 RMS= 0.3105 Dev= 2.20% S= 21.04 time= 1.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.79

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     961 steps. Energy=    -384.4966744       time=       2.28
 Minus side of path:                     976 steps. Energy=    -386.9655190       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4966744  1.4184         -383.0783032  3.8872         -386.9655190   9.503   8.715  26.837   5.403
        *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=     5721.9    
 decide> The unconnected minima in the chain and their distances are:
     2       17.78     3     4        4.70     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1491 Dev= 0.94% S= 19.71 time= 1.21
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=   8.61

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1048 steps. Energy=    -383.8334909       time=       2.66
 Minus side of path:                     967 steps. Energy=    -382.5302715       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8334909  1.4571         -382.3763824 0.15389         -382.5302715  24.725  23.682   2.725  53.220
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3015 Dev= 0.00% S= 4.70 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.14

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     914 steps. Energy=    -386.9655190       time=       2.15
 Minus side of path:                     906 steps. Energy=    -386.9767568       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9655190 0.24829E-02     -386.9630361 0.13721E-01     -386.9767568   4.726   4.704   3.447  42.070
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2696.0    
 decide> The unconnected minima in the chain and their distances are:
     2       11.31     5     5       10.77     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= 0.1701 Dev= 0.36% S= 11.72 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.00

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     968 steps. Energy=    -383.8334909       time=       2.30
 Minus side of path:                     961 steps. Energy=    -385.5361690       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8334909  1.8848         -381.9487099  3.5875         -385.5361690  15.336  11.880   5.151  28.152
        Known (#5)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6961 Dev= 0.16% S= 11.76 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.84

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     977 steps. Energy=    -383.8334909       time=       2.59
 Minus side of path:                     986 steps. Energy=    -384.4966744       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8334909  2.5772         -381.2563290  3.2403         -384.4966744  12.017  10.781  22.711   6.384
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     251.55    
 decide> The unconnected minima in the chain and their distances are:
     2        6.31     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2697 Dev= 0.20% S= 6.60 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     983 steps. Energy=    -385.5361690       time=       2.62
 Minus side of path:                     975 steps. Energy=    -385.4420532       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5361690 0.26570         -385.2704673 0.17159         -385.4420532   5.812   5.627   2.513  57.699
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     430.48    
 decide> The unconnected minima in the chain and their distances are:
     2        7.55     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2113 Dev= 0.34% S= 7.75 time= 0.19
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.37
 isnewts> transition state is the same as number        6 energy=     -385.2704672570
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1001 steps. Energy=    -385.5361690       time=       2.69
 Minus side of path:                     965 steps. Energy=    -385.4420532       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5361690 0.26570         -385.2704673 0.17159         -385.4420532   5.812   5.627   2.513  57.700
        Known (#7)                                              Known (#8)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     503.10    
 decide> The unconnected minima in the chain and their distances are:
     2        6.31     7 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 7_S using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 490 RMS= 0.0737 Dev= 12.24% S= 10.62 time= 9.43
 Following    2 images are candidates for TS:    8   13  
 Converged to TS (number of iterations):         21
 Converged to TS (number of iterations):         21
 DNEB run yielded 2 true transition state(s) time=   8.93
 isnewts> transition state is the same as number        6 energy=     -385.2704672568
 tryconnect> Will not repeat search for TS      2 same as TS      6

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     940 steps. Energy=    -385.4420532       time=       2.36
 Minus side of path:                     969 steps. Energy=    -389.7291031       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4420532  2.5376         -382.9045023  6.8246         -389.7291031   8.669   7.551   4.110  35.276
        Known (#8)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -386.9767568 0.13721E-01    -386.9630361 0.24829E-02    -386.9655190   4.726   4.704   3.447  42.070
   1     -386.9655190  3.8872        -383.0783032  1.4184        -384.4966744   9.503   8.715  26.837   5.403
   5     -384.4966744  3.2403        -381.2563290  2.5772        -383.8334909  12.017  10.781  22.711   6.384
   4     -383.8334909  1.8848        -381.9487099  3.5875        -385.5361690  15.336  11.880   5.151  28.152
   6     -385.5361690 0.26570        -385.2704673 0.17159        -385.4420532   5.812   5.627   2.513  57.699
   8     -385.4420532  2.5376        -382.9045023  6.8246        -389.7291031   8.669   7.551   4.110  35.276

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

 Elapsed time=                                95.07
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             33976 time=          45.05 %= 47.4
 OPTIM> # of energy+gradient+Hessian calls=       349 time=           1.50 %=  1.6
