
 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)@comp24.ch.
                 Created on  5/28/12 at 12:38: 4 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=    -383.6532076     RMS force=    0.9348643695E-06
 OPTIM> Final energy  =    -403.5431088     RMS force=    0.8746046231E-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=     65885.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.39     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= 0.1512 Dev= 2.86% S= 47.84 time= 7.51
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        119
 DNEB run yielded 1 true transition state(s) time=   8.58

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1050 steps. Energy=    -403.5431088       time=       2.94
 Minus side of path:                     867 steps. Energy=    -397.3729873       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -403.5431088  7.9063         -395.6368232  1.7362         -397.3729873  36.084  33.702   2.116  68.534
        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=     19350.    
 decide> The unconnected minima in the chain and their distances are:
     3       26.85     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0648 Dev= 4.36% S= 29.66 time= 3.25
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   7.21

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     968 steps. Energy=    -396.3870891       time=       2.69
 Minus side of path:                     921 steps. Energy=    -396.0459701       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.3870891  1.0703         -395.3167776 0.72919         -396.0459701  17.287  14.627   3.072  47.194
        *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=     15986.    
 decide> The unconnected minima in the chain and their distances are:
     3        9.46     4     5       24.74     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1144 Dev= 0.04% S= 9.51 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     895 steps. Energy=    -396.3870891       time=       2.20
 Minus side of path:                     908 steps. Energy=    -397.3729873       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.3870891 0.40096E-01     -396.3469929  1.0260         -397.3729873   9.786   9.463   6.370  22.762
        Known (#4)                                              Known (#3)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0650 Dev= 3.09% S= 26.93 time= 2.49
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   5.96

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     974 steps. Energy=    -394.7990352       time=       2.43
 Minus side of path:                     948 steps. Energy=    -394.9197839       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.7990352 0.34855E-02     -394.7955497 0.12423         -394.9197839   3.934   3.902   2.620  55.340
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     12496.    
 decide> The unconnected minima in the chain and their distances are:
     4       23.07     6     6        6.04     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1104 Dev= 0.15% S= 23.67 time= 1.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.99

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1005 steps. Energy=    -394.8263176       time=       2.82
 Minus side of path:                    1065 steps. Energy=    -396.3870891       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.8263176 0.48303         -394.3432917  2.0438         -396.3870891  29.311  27.116   3.513  41.272
        *NEW* (Placed in 8)                                     Known (#4)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7985 Dev= 4.27% S= 6.60 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.87

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     972 steps. Energy=    -394.9197839       time=       2.45
 Minus side of path:                     929 steps. Energy=    -383.6532076       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9197839  11.609         -383.3103390 0.34287         -383.6532076   7.083   6.662   4.562  31.786
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     222.26    
 decide> The unconnected minima in the chain and their distances are:
     8        6.06     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0285 Dev= 0.01% S= 6.07 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   3.92

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     960 steps. Energy=    -394.9197839       time=       2.26
 Minus side of path:                     910 steps. Energy=    -394.8263176       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9197839 0.14058         -394.7792057 0.47112E-01     -394.8263176   6.185   6.057   2.381  60.893
        Known (#7)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -383.6532076 0.34287        -383.3103390  11.609        -394.9197839   7.083   6.662   4.562  31.786
   7     -394.9197839 0.14058        -394.7792057 0.47112E-01    -394.8263176   6.185   6.057   2.381  60.893
   5     -394.8263176 0.48303        -394.3432917  2.0438        -396.3870891  29.311  27.116   3.513  41.272
   3     -396.3870891 0.40096E-01    -396.3469929  1.0260        -397.3729873   9.786   9.463   6.370  22.762
   1     -397.3729873  1.7362        -395.6368232  7.9063        -403.5431088  36.084  33.702   2.116  68.534

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

 Elapsed time=                                89.86
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             30819 time=          42.90 %= 47.7
 OPTIM> # of energy+gradient+Hessian calls=       432 time=           1.95 %=  2.2
