
 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: 9:32 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -385.8079668     RMS force=    0.9722541170E-06
 OPTIM> Final energy  =    -385.2626841     RMS force=    0.9578389499E-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=     1067.2    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 0.6341 Dev= 1.54% S= 14.93 time= 0.41
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   5.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1968 steps. Energy=    -383.9142203       time=      10.76
 Minus side of path:                    1008 steps. Energy=    -385.2626841       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.9142203  5.4533         -378.4609317  6.8018         -385.2626841  65.816  59.045   1.791  80.972
        *NEW* (Placed in 3)                                     Known (#2)
 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      1 steps with      1 missing connections, weight=     2134.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.22     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 805 RMS= 3.9078 Dev= 5.61% S= 24.32 time= 20.31
 Following    4 images are candidates for TS:    2   10   18   22  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):        130
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         57
 DNEB run yielded 4 true transition state(s) time=  22.95
 isnewts> transition state is the same as number        1 energy=     -378.4609316710
 tryconnect> Try the path again for ts      4 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     980 steps. Energy=    -385.8079668       time=       2.65
 Minus side of path:                    1001 steps. Energy=    -386.8129981       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8079668  2.5002         -383.3077684  3.5052         -386.8129981   5.606   5.414   7.465  19.423
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     992 steps. Energy=    -383.7489462       time=       2.55
 Minus side of path:                    1089 steps. Energy=    -384.1587665       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7489462 0.18953E-01     -383.7299930 0.42877         -384.1587665  14.015  12.135   3.314  43.755
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1013 steps. Energy=    -379.6292852       time=       3.42
 Minus side of path:                    1038 steps. Energy=    -381.5270744       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6292852 0.94401         -378.6852711  2.8418         -381.5270744   6.590   6.170  27.821   5.212
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1989 steps. Energy=    -383.9142203       time=      12.09
 Minus side of path:                    1019 steps. Energy=    -385.2626841       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.9142203  5.4533         -378.4609317  6.8018         -385.2626841  65.816  59.048   1.792  80.925
        Known (#3)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     529.10    
 decide> The unconnected minima in the chain and their distances are:
     2        8.09     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 1.0327 Dev= 1.99% S= 8.77 time= 0.22
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.82
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1058.2    
 decide> The unconnected minima in the chain and their distances are:
     2        8.09     4 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 4_S using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 630 RMS= 0.0581 Dev= 4.92% S= 22.77 time= 12.37
 Following    3 images are candidates for TS:    2    8   13  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         68
 DNEB run yielded 3 true transition state(s) time=  16.09
 isnewts> transition state is the same as number        4 energy=     -378.6852711132
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1014 steps. Energy=    -385.2931964       time=       4.47
 Minus side of path:                     997 steps. Energy=    -385.2626841       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2931964  5.0626         -380.2306156  5.0321         -385.2626841  13.322   6.619   3.597  40.313
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1013 steps. Energy=    -379.6292852       time=       2.67
 Minus side of path:                    1001 steps. Energy=    -381.5270744       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6292852 0.94401         -378.6852711  2.8418         -381.5270744   6.591   6.171  27.669   5.241
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1103 steps. Energy=    -383.7749650       time=       3.63
 Minus side of path:                    1209 steps. Energy=    -381.1556837       time=       4.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7749650  3.3590         -380.4160082 0.73968         -381.1556837  37.210  31.954   2.006  72.286
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     200.68    
 decide> The unconnected minima in the chain and their distances are:
     9        5.85     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6576 Dev= 1.14% S= 6.35 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.76

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1005 steps. Energy=    -385.2931964       time=       2.56
 Minus side of path:                    1006 steps. Energy=    -385.1964560       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2931964 0.48591         -384.8072899 0.38917         -385.1964560   8.314   8.199   1.677  86.483
        Known (#9)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     198.27    
 decide> The unconnected minima in the chain and their distances are:
    12        5.83     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 12_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3125 Dev= 1.92% S= 6.30 time= 0.21
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.72
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     341.86    
 decide> The unconnected minima in the chain and their distances are:
    12        6.99     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 12_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.6505 Dev= 0.55% S= 7.53 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     974 steps. Energy=    -385.8079668       time=       2.23
 Minus side of path:                     989 steps. Energy=    -385.9701342       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8079668 0.46882         -385.3391478 0.63099         -385.9701342   8.052   7.911   1.886  76.890
        Known (#1)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     396.55    
 decide> The unconnected minima in the chain and their distances are:
    12        5.83     4 
 

 tryconnect> 455-iteration DNEB run for minima 4_S and 12_F using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 455 RMS= 0.0839 Dev= 4.39% S= 8.11 time= 6.58
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.44

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1010 steps. Energy=    -385.1964560       time=       2.41
 Minus side of path:                     998 steps. Energy=    -386.8129981       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1964560  5.6653         -379.5312026  7.2818         -386.8129981  15.960   5.838   2.318  62.550
        Known (#12)                                             Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -385.8079668  2.5002        -383.3077684  3.5052        -386.8129981   5.606   5.414   7.465  19.423
  11     -386.8129981  7.2818        -379.5312026  5.6653        -385.1964560  15.960   5.838   2.318  62.550
   9     -385.1964560 0.38917        -384.8072899 0.48591        -385.2931964   8.314   8.199   1.677  86.483
   6     -385.2931964  5.0626        -380.2306156  5.0321        -385.2626841  13.322   6.619   3.597  40.313

 Number of TS in the path       =      4
 Number of cycles               =      8

 Elapsed time=                               226.13
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             76075 time=          80.71 %= 35.7
 OPTIM> # of energy+gradient+Hessian calls=       992 time=           4.72 %=  2.1
