
 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)@comp27.ch.
                 Created on  5/28/12 at 12:59:49 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=    -389.1268325     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      1.227044011    
 Double-ended search iterations= 245 RMS= 0.2572 Dev= 1.12% S= 28.91 time= 2.49
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.65

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     938 steps. Energy=    -388.9251328       time=       2.46
 Minus side of path:                     909 steps. Energy=    -389.1268325       time=       2.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9251328 0.14893         -388.7762058 0.35063         -389.1268325   3.316   3.180   6.804  21.311
        *NEW* (Placed in 3)                                     Known (#1)
 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      1.112965089    
 Double-ended search iterations= 245 RMS= 0.2506 Dev= 1.11% S= 27.61 time= 2.54
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.12

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1065 steps. Energy=    -392.1280303       time=       3.63
 Minus side of path:                     924 steps. Energy=    -388.9251328       time=       2.87

         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  35.974
        *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      1.566053647    
 Double-ended search iterations= 210 RMS= 4.8342 Dev= 0.79% S= 23.50 time= 1.84
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.37

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     877 steps. Energy=    -392.1280303       time=       2.05
 Minus side of path:                     911 steps. Energy=    -392.6910093       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.1280303 0.31097         -391.8170643 0.87395         -392.6910093   3.677   3.446   8.009  18.105
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     11625.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.65     5 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 5_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 210 RMS= 0.1697 Dev= 0.42% S= 23.30 time= 1.81
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.62

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     960 steps. Energy=    -393.4402301       time=       2.73
 Minus side of path:                     931 steps. Energy=    -392.6910093       time=       2.64

         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 6)                                     Known (#5)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 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     6 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0898 Dev= 0.28% S= 23.27 time= 1.82
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   9.72

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     927 steps. Energy=    -394.0488006       time=       2.51
 Minus side of path:                     935 steps. Energy=    -393.4721885       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.0488006 0.65024         -393.3985625 0.73626E-01     -393.4721885  13.582  13.296   1.988  72.928
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 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     7     8        4.54     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0866 Dev= 0.15% S= 11.73 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   5.08

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     962 steps. Energy=    -394.0488006       time=       4.06
 Minus side of path:                     889 steps. Energy=    -393.8368296       time=       2.41

         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 (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2210 Dev= 0.97% S= 4.63 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.77

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     940 steps. Energy=    -393.4721885       time=       3.49
 Minus side of path:                     918 steps. Energy=    -393.4402301       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.4721885 0.74364E-01     -393.3978247 0.42405E-01     -393.4402301   4.713   4.539  24.167   6.000
        Known (#8)                                              Known (#6)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 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= 0.0451 Dev= 0.32% S= 11.03 time= 0.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.36

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     932 steps. Energy=    -393.8368296       time=       3.04
 Minus side of path:                     917 steps. Energy=    -393.7895183       time=       2.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.8368296 0.86306E-01     -393.7505234 0.38995E-01     -393.7895183   8.683   8.365   4.397  32.979
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 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      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0280 Dev= 0.32% S= 3.48 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.00

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     922 steps. Energy=    -393.7903615       time=       2.86
 Minus side of path:                     907 steps. Energy=    -393.7895183       time=       2.81

         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  35.974
   3     -392.1280303 0.31097        -391.8170643 0.87395        -392.6910093   3.677   3.446   8.009  18.105
   4     -392.6910093 0.52966        -392.1613484  1.2789        -393.4402301   5.499   5.311  14.316  10.129
   7     -393.4402301 0.42405E-01    -393.3978247 0.74364E-01    -393.4721885   4.713   4.539  24.167   6.000
   5     -393.4721885 0.73626E-01    -393.3985625 0.65024        -394.0488006  13.582  13.296   1.988  72.928
   6     -394.0488006 0.21232        -393.8364773 0.35233E-03    -393.8368296   1.721   1.716   2.805  51.700
   8     -393.8368296 0.86306E-01    -393.7505234 0.38995E-01    -393.7895183   8.683   8.365   4.397  32.979
   9     -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=                               108.33
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             33637 time=          47.19 %= 43.6
 OPTIM> # of energy+gradient+Hessian calls=       356 time=           1.72 %=  1.6
