
 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)@comp34.ch.
                 Created on  5/28/12 at 13:12:24 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -377.6390132     RMS force=    0.9868132303E-06
 OPTIM> Final energy  =    -381.3066617     RMS force=    0.9731877753E-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=     68097.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.84     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 420 RMS= 0.0766 Dev= 1.04% S= 51.37 time= 5.44
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1088 steps. Energy=    -381.3026016       time=       3.02
 Minus side of path:                    1025 steps. Energy=    -377.6392480       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3026016  4.3085         -376.9941254 0.64512         -377.6392480  17.904  14.545   5.689  25.489
        *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=     46835.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.04     3     4        2.13     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 3_U using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 350 RMS= 0.1205 Dev= 1.75% S= 43.84 time= 3.83
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   7.68

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1346 steps. Energy=    -389.4250406       time=       6.17
 Minus side of path:                    1013 steps. Energy=    -381.3469114       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4250406  10.408         -379.0168602  2.3301         -381.3469114  29.624  26.954   1.813  79.999
        *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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0159 Dev= 0.04% S= 2.13 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     996 steps. Energy=    -377.6390132       time=       2.61
 Minus side of path:                     994 steps. Energy=    -377.6392480       time=       3.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.6390132 0.52994E-01     -377.5860191 0.53229E-01     -377.6392480   2.264   2.126   9.780  14.826
        Known (#1)                                              Known (#4)
 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=     48010.    
 decide> The unconnected minima in the chain and their distances are:
     2        4.95     6     6       36.31     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0092 Dev= 0.03% S= 4.95 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1003 steps. Energy=    -381.3469114       time=       3.08
 Minus side of path:                     950 steps. Energy=    -381.3066617       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3469114 0.40357E-01     -381.3065543 0.10733E-03     -381.3066617   4.961   4.945   2.063  70.287
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 3_S and 6_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 350 RMS= 0.1118 Dev= 1.78% S= 44.18 time= 3.85
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.03
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     68546.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.93     4 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 4_S using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0563 Dev= 2.66% S= 54.02 time= 5.58
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        103
 DNEB run yielded 1 true transition state(s) time=   7.49

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1078 steps. Energy=    -377.9897253       time=       2.83
 Minus side of path:                    1181 steps. Energy=    -381.3026016       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9897253 0.76328         -377.2264469  4.0762         -381.3026016  35.311  31.999   1.856  78.121
        *NEW* (Placed in 7)                                     Known (#3)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     72647.    
 decide> The unconnected minima in the chain and their distances are:
     6       41.73     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 6_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 420 RMS= 0.0697 Dev= 1.28% S= 53.09 time= 5.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        135
 DNEB run yielded 1 true transition state(s) time=   9.96

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1165 steps. Energy=    -378.2543928       time=       2.93
 Minus side of path:                    1106 steps. Energy=    -379.0771301       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.2543928  1.7153         -376.5390568  2.5381         -379.0771301  43.216  34.340   1.869  77.563
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     73090.    
 decide> The unconnected minima in the chain and their distances are:
     6       41.81     7 
 

 tryconnect> 420-iteration DNEB run for minima 6_F and 7_S using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0555 Dev= 3.24% S= 51.79 time= 5.43
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        209
 DNEB run yielded 1 true transition state(s) time=  17.47

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1016 steps. Energy=    -380.2155834       time=       2.21
 Minus side of path:                    1149 steps. Energy=    -383.4268737       time=       2.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.65889E-02     -380.2089945  3.2179         -383.4268737  29.557  28.786   2.248  64.494
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     73091.    
 decide> The unconnected minima in the chain and their distances are:
     6       41.81     4 
 

 tryconnect> 420-iteration DNEB run for minima 4_S and 6_F using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 420 RMS= 0.0637 Dev= 1.19% S= 53.42 time= 5.37
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=   6.80
 isnewts> transition state is the same as number        5 energy=     -377.2264468656
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1056 steps. Energy=    -377.9897253       time=       2.30
 Minus side of path:                    1181 steps. Energy=    -381.3026016       time=       2.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.9897253 0.76328         -377.2264469  4.0762         -381.3026016  35.311  32.001   1.855  78.153
        Known (#7)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     78096.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.65     9     8        7.93     4 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 9_U using 12 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0600 Dev= 2.55% S= 52.08 time= 5.45
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   5.70

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1116 steps. Energy=    -379.0771301       time=       2.56
 Minus side of path:                    1249 steps. Energy=    -381.3469114       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.0771301  3.2131         -375.8640525  5.4829         -381.3469114  56.281  45.110   3.080  47.082
        Known (#9)                                              Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7789 Dev= 0.57% S= 8.24 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.05

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1000 steps. Energy=    -378.2543928       time=       2.08
 Minus side of path:                    1004 steps. Energy=    -377.6392480       time=       2.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.2543928  2.9599         -375.2944682  2.3448         -377.6392480   9.455   7.937  17.682   8.200
        Known (#8)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -377.6390132 0.52994E-01    -377.5860191 0.53229E-01    -377.6392480   2.264   2.126   9.780  14.826
  10     -377.6392480  2.3448        -375.2944682  2.9599        -378.2543928   9.455   7.937  17.682   8.200
   6     -378.2543928  1.7153        -376.5390568  2.5381        -379.0771301  43.216  34.340   1.869  77.563
   9     -379.0771301  3.2131        -375.8640525  5.4829        -381.3469114  56.281  45.110   3.080  47.082
   4     -381.3469114 0.40357E-01    -381.3065543 0.10733E-03    -381.3066617   4.961   4.945   2.063  70.287

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                               190.07
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             71746 time=          75.80 %= 39.9
 OPTIM> # of energy+gradient+Hessian calls=      1052 time=           4.33 %=  2.3
