
 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 12:48:16 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=    -387.5301052     RMS force=    0.9527542885E-06
 OPTIM> Final energy  =    -388.8754411     RMS force=    0.9493427248E-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=     272.20    
 decide> The unconnected minima in the chain and their distances are:
     2        6.48     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.6439 Dev= 0.92% S= 7.36 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.56

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     951 steps. Energy=    -387.5301052       time=       2.44
 Minus side of path:                     938 steps. Energy=    -388.7319319       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5301052  2.3638         -385.1662914  3.5656         -388.7319319   6.244   5.179  37.631   3.853
        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=     146.25    
 decide> The unconnected minima in the chain and their distances are:
     2        5.27     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.4243 Dev= 0.77% S= 5.72 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   7.13

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     957 steps. Energy=    -388.7894030       time=       2.54
 Minus side of path:                     905 steps. Energy=    -388.7319319       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7894030 0.73403E-01     -388.7160000 0.15932E-01     -388.7319319   2.165   2.153   5.621  25.797
        *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=     217.43    
 decide> The unconnected minima in the chain and their distances are:
     2        6.01     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4125 Dev= 0.44% S= 6.45 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.74
 isnewts> transition state is the same as number        2 energy=     -388.7159999745
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     923 steps. Energy=    -388.7319319       time=       2.21
 Minus side of path:                     957 steps. Energy=    -388.7894030       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7319319 0.15932E-01     -388.7160000 0.73403E-01     -388.7894030   2.165   2.153   5.621  25.797
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     292.50    
 decide> The unconnected minima in the chain and their distances are:
     2        5.27     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_S using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 420 RMS= 0.0593 Dev= 5.33% S= 8.94 time= 6.91
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     971 steps. Energy=    -389.7275325       time=       3.53
 Minus side of path:                     946 steps. Energy=    -388.7319319       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7275325  5.8738         -383.8537256  4.8782         -388.7319319  10.687   9.929  20.831   6.961
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     190.95    
 decide> The unconnected minima in the chain and their distances are:
     2        5.76     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.1752 Dev= 1.02% S= 6.12 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        109
 DNEB run yielded 1 true transition state(s) time=  10.61

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     972 steps. Energy=    -389.4284378       time=       4.07
 Minus side of path:                     870 steps. Energy=    -388.9285679       time=       2.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.4284378 0.59257         -388.8358722 0.92696E-01     -388.9285679  12.674  12.237   2.446  59.270
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     157.98    
 decide> The unconnected minima in the chain and their distances are:
     2        2.16     7     7        5.29     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0194 Dev= 0.11% S= 2.17 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.33

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     924 steps. Energy=    -388.9285679       time=       3.69
 Minus side of path:                     880 steps. Energy=    -388.8754411       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9285679 0.71418E-01     -388.8571494 0.18292E-01     -388.8754411   2.175   2.163   5.710  25.394
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.6402 Dev= 1.22% S= 5.71 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.67
 isnewts> transition state is the same as number        2 energy=     -388.7159999756
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     155.08    
 decide> The unconnected minima in the chain and their distances are:
     7        5.37     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.3094 Dev= 0.42% S= 5.82 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.82
 isnewts> transition state is the same as number        2 energy=     -388.7159999749
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     255.00    
 decide> The unconnected minima in the chain and their distances are:
     7        6.34     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2055 Dev= 0.46% S= 6.68 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.07
 isnewts> transition state is the same as number        6 energy=     -388.8571494017
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     919 steps. Energy=    -388.9285679       time=       3.06
 Minus side of path:                     910 steps. Energy=    -388.8754411       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9285679 0.71418E-01     -388.8571494 0.18292E-01     -388.8754411   2.175   2.163   5.709  25.399
        Known (#7)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     294.60    
 decide> The unconnected minima in the chain and their distances are:
     7        6.65     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.3469 Dev= 0.68% S= 7.51 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.93
 isnewts> transition state is the same as number        1 energy=     -385.1662913774
 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:                     940 steps. Energy=    -387.5301051       time=       3.24
 Minus side of path:                     954 steps. Energy=    -388.7319319       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5301051  2.3638         -385.1662914  3.5656         -388.7319319   6.247   5.187  37.563   3.860
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     295.73    
 decide> The unconnected minima in the chain and their distances are:
     7        5.29     4 
 

 tryconnect> 420-iteration DNEB run for minima 4_S and 7_F using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 420 RMS= 0.0803 Dev= 6.40% S= 10.31 time= 6.99
 Following    2 images are candidates for TS:    6    9  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         19
 DNEB run yielded 2 true transition state(s) time=   7.99

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     947 steps. Energy=    -388.7894030       time=       3.30
 Minus side of path:                     949 steps. Energy=    -389.7722105       time=       3.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7894030  4.8818         -383.9076180  5.8646         -389.7722105  10.731   9.950  20.812   6.967
        Known (#4)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     954 steps. Energy=    -389.7722105       time=       3.75
 Minus side of path:                     965 steps. Energy=    -388.9285679       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7722105  3.1820         -386.5902296  2.3383         -388.9285679   6.361   5.759  32.173   4.507
        Known (#8)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -387.5301052  2.3638        -385.1662914  3.5656        -388.7319319   6.244   5.179  37.631   3.853
   2     -388.7319319 0.15932E-01    -388.7160000 0.73403E-01    -388.7894030   2.165   2.153   5.621  25.797
   9     -388.7894030  4.8818        -383.9076180  5.8646        -389.7722105  10.731   9.950  20.812   6.967
  10     -389.7722105  3.1820        -386.5902296  2.3383        -388.9285679   6.361   5.759  32.173   4.507
   6     -388.9285679 0.71418E-01    -388.8571494 0.18292E-01    -388.8754411   2.175   2.163   5.710  25.394

 Number of TS in the path       =      5
 Number of cycles               =     10

 Elapsed time=                               136.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41583 time=          57.16 %= 41.8
 OPTIM> # of energy+gradient+Hessian calls=       412 time=           2.12 %=  1.5
