
 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)@comp25.ch.
                 Created on  5/28/12 at 12:58:28 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=    -375.1744094     RMS force=    0.9932691612E-06
 OPTIM> Final energy  =    -371.2775909     RMS force=    0.9258943288E-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=     21296.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.72     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 280 RMS= 0.0925 Dev= 3.36% S= 31.24 time= 2.95
 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=  25.43
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     42592.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.72     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0565 Dev= 4.92% S= 37.88 time= 24.13
 Following    1 images are candidates for TS:   15  
 Converged to TS (number of iterations):        186
 DNEB run yielded 1 true transition state(s) time=  20.58

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1050 steps. Energy=    -371.3854582       time=       4.79
 Minus side of path:                     972 steps. Energy=    -369.8751172       time=       3.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -371.3854582  1.6187         -369.7667497 0.10837         -369.8751172  21.878  19.212   2.933  49.445
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     21321.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.00     3     3       27.73     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 70 RMS= 0.0388 Dev= 0.86% S= 1.01 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.15

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     946 steps. Energy=    -371.3854582       time=       2.84
 Minus side of path:                     907 steps. Energy=    -371.2775909       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -371.3854582 0.11991         -371.2655476 0.12043E-01     -371.2775909   1.006   1.004  39.899   3.634
        Known (#3)                                              Known (#2)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1067 Dev= 1.61% S= 31.13 time= 3.10
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=  22.07

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     856 steps. Energy=    -375.6732872       time=       3.37
 Minus side of path:                     910 steps. Energy=    -375.7716026       time=       3.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.6732872 0.14958E-01     -375.6583294 0.11327         -375.7716026   1.080   1.077  41.280   3.513
        *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      2 steps with      2 missing connections, weight=     21827.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.93     5     5        3.53     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 5_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 280 RMS= 1.0216 Dev= 1.52% S= 31.03 time= 3.06
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  27.40

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0851 Dev= 0.14% S= 3.57 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     908 steps. Energy=    -375.1744094       time=       2.11
 Minus side of path:                     938 steps. Energy=    -375.6732872       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.1744094 0.14058         -375.0338327 0.63945         -375.6732872   3.617   3.533   6.459  22.449
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     21804.    
 decide> The unconnected minima in the chain and their distances are:
     3       27.94     5 
 

 tryconnect> 280-iteration DNEB run for minima 3_F and 5_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 280 RMS= 0.1256 Dev= 1.78% S= 31.13 time= 2.93
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        170
 DNEB run yielded 1 true transition state(s) time=  16.61
 isnewts> transition state is the same as number        1 energy=     -369.7667496997
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1059 steps. Energy=    -371.3854582       time=       3.39
 Minus side of path:                     992 steps. Energy=    -369.8751172       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -371.3854582  1.6187         -369.7667497 0.10837         -369.8751172  21.878  19.213   2.932  49.452
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     22598.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.27     6 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 280 RMS= 0.1125 Dev= 2.71% S= 31.32 time= 3.10
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        149
 DNEB run yielded 1 true transition state(s) time=  16.72

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     920 steps. Energy=    -371.3854582       time=       2.43
 Minus side of path:                     892 steps. Energy=    -371.2669468       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -371.3854582 0.11980         -371.2656586 0.12882E-02     -371.2669468   0.824   0.821  18.122   8.001
        Known (#3)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     20709.    
 decide> The unconnected minima in the chain and their distances are:
     7       27.46     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 7_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.2054 Dev= 2.04% S= 31.09 time= 3.00
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=  16.76

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     874 steps. Energy=    -375.2724866       time=       2.51
 Minus side of path:                     954 steps. Energy=    -375.7716026       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.2724866 0.14196         -375.1305244 0.64108         -375.7716026   3.612   3.526   6.508  22.282
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     21193.    
 decide> The unconnected minima in the chain and their distances are:
     7       27.67     5 
 

 tryconnect> 280-iteration DNEB run for minima 5_S and 7_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.2036 Dev= 1.96% S= 31.04 time= 3.00
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        101
 DNEB run yielded 1 true transition state(s) time=   9.06

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1444 steps. Energy=    -371.3854582       time=       5.91
 Minus side of path:                    1411 steps. Energy=    -375.7716026       time=       6.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -371.3854582  2.7895         -368.5959798  7.1756         -375.7716026  41.976  28.290   2.867  50.575
        Known (#3)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -375.1744094 0.14058        -375.0338327 0.63945        -375.6732872   3.617   3.533   6.459  22.449
   3     -375.6732872 0.14958E-01    -375.6583294 0.11327        -375.7716026   1.080   1.077  41.280   3.513
   8     -375.7716026  7.1756        -368.5959798  2.7895        -371.3854582  41.976  28.290   2.867  50.575
   2     -371.3854582 0.11991        -371.2655476 0.12043E-01    -371.2775909   1.006   1.004  39.899   3.634

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

 Elapsed time=                               259.92
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             66675 time=          85.69 %= 33.0
 OPTIM> # of energy+gradient+Hessian calls=      1339 time=           7.34 %=  2.8
