
 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)@comp20.ch.
                 Created on  5/28/12 at 13:10:25 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


 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -389.1268325     RMS force=    0.9524973494E-06
 OPTIM> Final energy  =    -393.7903615     RMS force=    0.8939806970E-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=     18744.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.56     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.3299 Dev= 1.16% S= 29.22 time= 2.61
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   6.94

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     925 steps. Energy=    -389.1268325       time=       2.21
 Minus side of path:                     903 steps. Energy=    -388.9251328       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1268325 0.35063         -388.7762058 0.14893         -388.9251328   3.316   3.180   6.804  21.311
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     15568.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.97     3 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 3_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2263 Dev= 1.60% S= 27.84 time= 2.51
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.34

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1064 steps. Energy=    -392.1280303       time=       4.11
 Minus side of path:                     918 steps. Energy=    -388.9251328       time=       3.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.1280303  5.6021         -386.5259641  2.3992         -388.9251328  25.573  22.032   4.031  35.969
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     11412.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.51     4 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 4_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 2.2566 Dev= 0.35% S= 23.62 time= 1.87
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     945 steps. Energy=    -393.4402301       time=       3.08
 Minus side of path:                     913 steps. Energy=    -392.6910093       time=       3.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4402301  1.2789         -392.1613484 0.52966         -392.6910093   5.499   5.311  14.316  10.129
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     11666.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.65     6     6        3.45     4 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0712 Dev= 0.09% S= 23.46 time= 1.91
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   4.09
 isnewts> transition state is the same as number        3 energy=     -392.1613484019
 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:                     975 steps. Energy=    -393.4402301       time=       3.85
 Minus side of path:                     926 steps. Energy=    -392.6910093       time=       3.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4402301  1.2789         -392.1613484 0.52966         -392.6910093   5.499   5.311  14.309  10.133
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0684 Dev= 0.15% S= 3.48 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   4.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     916 steps. Energy=    -392.6910093       time=       3.71
 Minus side of path:                     879 steps. Energy=    -392.1280303       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.6910093 0.87395         -391.8170643 0.31097         -392.1280303   3.677   3.446   8.009  18.105
        Known (#6)                                              Known (#4)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     11729.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.72     5 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 5_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0398 Dev= 0.08% S= 23.29 time= 1.97
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=  12.06

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     931 steps. Energy=    -393.4721885       time=       3.83
 Minus side of path:                     957 steps. Energy=    -394.0488006       time=       4.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4721885 0.73626E-01     -393.3985625 0.65024         -394.0488006  13.582  13.296   1.988  72.930
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1687.7    
 decide> The unconnected minima in the chain and their distances are:
     2       11.68     8     7        4.54     5 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0487 Dev= 0.01% S= 11.73 time= 0.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   6.70

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     928 steps. Energy=    -394.0488006       time=       4.03
 Minus side of path:                     904 steps. Energy=    -393.8368296       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.0488006 0.21232         -393.8364773 0.35233E-03     -393.8368296   1.721   1.716   2.805  51.700
        Known (#8)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1021 Dev= 0.06% S= 4.62 time= 0.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.65

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     934 steps. Energy=    -393.4402301       time=       2.73
 Minus side of path:                     954 steps. Energy=    -393.4721885       time=       3.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4402301 0.42405E-01     -393.3978247 0.74364E-01     -393.4721885   4.713   4.539  24.165   6.000
        Known (#5)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     1330.0    
 decide> The unconnected minima in the chain and their distances are:
     2       11.00     9 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 9_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1087 Dev= 0.01% S= 11.03 time= 0.56
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   7.13

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     895 steps. Energy=    -393.7895183       time=       2.72
 Minus side of path:                     919 steps. Energy=    -393.8368296       time=       4.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7895183 0.38995E-01     -393.7505234 0.86306E-01     -393.8368296   8.683   8.365   4.397  32.979
        *NEW* (Placed in 10)                                    Known (#9)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     42.136    
 decide> The unconnected minima in the chain and their distances are:
     2        3.48    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0278 Dev= 0.01% S= 3.48 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   4.09

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     898 steps. Energy=    -393.7903615       time=       3.78
 Minus side of path:                     918 steps. Energy=    -393.7895183       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7903615 0.36557E-01     -393.7538042 0.35714E-01     -393.7895183   3.548   3.480   2.242  64.679
        Known (#2)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.1268325 0.35063        -388.7762058 0.14893        -388.9251328   3.316   3.180   6.804  21.311
   2     -388.9251328  2.3992        -386.5259641  5.6021        -392.1280303  25.573  22.032   4.031  35.969
   5     -392.1280303 0.31097        -391.8170643 0.87395        -392.6910093   3.677   3.446   8.009  18.105
   3     -392.6910093 0.52966        -392.1613484  1.2789        -393.4402301   5.499   5.311  14.316  10.129
   8     -393.4402301 0.42405E-01    -393.3978247 0.74364E-01    -393.4721885   4.713   4.539  24.165   6.000
   6     -393.4721885 0.73626E-01    -393.3985625 0.65024        -394.0488006  13.582  13.296   1.988  72.930
   7     -394.0488006 0.21232        -393.8364773 0.35233E-03    -393.8368296   1.721   1.716   2.805  51.700
   9     -393.8368296 0.86306E-01    -393.7505234 0.38995E-01    -393.7895183   8.683   8.365   4.397  32.979
  10     -393.7895183 0.35714E-01    -393.7538042 0.36557E-01    -393.7903615   3.548   3.480   2.242  64.679

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

 Elapsed time=                               139.21
 OPTIM> # of energy calls=                         88 time=           0.12 %=  0.1
 OPTIM> # of energy+gradient calls=             36624 time=          52.37 %= 37.6
 OPTIM> # of energy+gradient+Hessian calls=       393 time=           2.20 %=  1.6
