
 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)@comp21.ch.
                 Created on  5/28/12 at 12:54:34 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=    -381.6110679     RMS force=    0.8935358918E-06
 OPTIM> Final energy  =    -385.8804130     RMS force=    0.7992771015E-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=     3628.8    
 decide> The unconnected minima in the chain and their distances are:
     2       15.37     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      39.20129138    
 Double-ended search iterations= 162 RMS= 21.6346 Dev= 21.14% S= 42.96 time= 0.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        158
 DNEB run yielded 1 true transition state(s) time=  11.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     942 steps. Energy=    -387.6797690       time=       2.66
 Minus side of path:                     972 steps. Energy=    -386.1900009       time=       3.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6797690  2.5311         -385.1486999  1.0413         -386.1900009  38.663  36.773   2.596  55.851
        *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      1 steps with      1 missing connections, weight=     7257.6    
 decide> The unconnected minima in the chain and their distances are:
     2       15.37     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      146.3563092    
 Double-ended search iterations= 805 RMS= 0.1275 Dev= 0.22% S= 15.59 time= 24.03
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.36

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1336 steps. Energy=    -382.0774484       time=       5.66
 Minus side of path:                     971 steps. Energy=    -385.8845121       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.89015         -381.1872984  4.6972         -385.8845121  31.091  27.296   2.034  71.275
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     2594.4    
 decide> The unconnected minima in the chain and their distances are:
     2        3.45     6     6       13.67     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0350 Dev= 0.30% S= 3.46 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.95

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     966 steps. Energy=    -385.8845121       time=       2.18
 Minus side of path:                     970 steps. Energy=    -385.8804130       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8845121 0.95066E-01     -385.7894459 0.90967E-01     -385.8804130   3.488   3.454   2.133  67.973
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      39.20129138    
 Double-ended search iterations= 147 RMS= 17.2619 Dev= 13.14% S= 43.24 time= 0.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   7.47
 isnewts> transition state is the same as number        2 energy=     -381.1872983663
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1358 steps. Energy=    -382.0774484       time=       4.02
 Minus side of path:                     982 steps. Energy=    -385.8845121       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.89015         -381.1872984  4.6972         -385.8845121  31.091  27.296   2.032  71.355
        Known (#5)                                              Known (#6)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5106.5    
 decide> The unconnected minima in the chain and their distances are:
     6       13.67     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 805 RMS= 0.0481 Dev= 0.94% S= 14.56 time= 23.33
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.74
 isnewts> transition state is the same as number        2 energy=     -381.1872983662
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     8024.9    
 decide> The unconnected minima in the chain and their distances are:
     2        9.25     4     4       19.34     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 3.1558 Dev= 33.43% S= 9.70 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   4.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     970 steps. Energy=    -386.1900009       time=       2.22
 Minus side of path:                     914 steps. Energy=    -385.8804130       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.1900009 0.32165         -385.8683461 0.12067E-01     -385.8804130   9.854   9.248   2.827  51.300
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 175 RMS= 25.1017 Dev= 25.25% S= 68.32 time= 1.16
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        128
 DNEB run yielded 1 true transition state(s) time=   8.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1111 steps. Energy=    -387.6797690       time=       2.89
 Minus side of path:                     953 steps. Energy=    -386.1900009       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.6797690  2.6269         -385.0528954  1.1371         -386.1900009  38.842  36.768   2.605  55.653
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13756.    
 decide> The unconnected minima in the chain and their distances are:
     5       23.96     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 245 RMS= 0.0844 Dev= 0.56% S= 24.12 time= 2.19
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   5.06

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1125 steps. Energy=    -382.0774484       time=       2.80
 Minus side of path:                     928 steps. Energy=    -381.6110679       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.50451         -381.5729368 0.38131E-01     -381.6110679  24.461  23.965   2.223  65.221
        Known (#5)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -381.6110679 0.38131E-01    -381.5729368 0.50451        -382.0774484  24.461  23.965   2.223  65.221
   2     -382.0774484 0.89015        -381.1872984  4.6972        -385.8845121  31.091  27.296   2.034  71.275
   3     -385.8845121 0.95066E-01    -385.7894459 0.90967E-01    -385.8804130   3.488   3.454   2.133  67.973

 Number of TS in the path       =      3
 Number of cycles               =      6

 Elapsed time=                               142.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             63379 time=          79.78 %= 56.1
 OPTIM> # of energy+gradient+Hessian calls=       592 time=           2.28 %=  1.6
