
 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)@comp23.ch.
                 Created on  5/28/12 at 13: 3:29 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -366.7851496     RMS force=    0.8055963618E-06
 OPTIM> Final energy  =    -391.6057956     RMS force=    0.8782856708E-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=    0.12862E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.48     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 525 RMS= 0.2632 Dev= 4.14% S= 69.32 time= 10.56
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):         75
 Converged to TS (number of iterations):        129
 DNEB run yielded 2 true transition state(s) time=  18.20

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     990 steps. Energy=    -366.6768294       time=       2.78
 Minus side of path:                    1001 steps. Energy=    -367.6248705       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -366.6768294  1.1613         -365.5155313  2.1093         -367.6248705  14.467  13.564   3.742  38.747
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1419 steps. Energy=    -390.9884316       time=       4.78
 Minus side of path:                    1240 steps. Energy=    -382.4815302       time=       4.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9884316  11.898         -379.0904227  3.3911         -382.4815302  67.097  49.424   3.154  45.973
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     4537.7    
 decide> The unconnected minima in the chain and their distances are:
     2        5.83     5     6       16.20     3     3        4.41     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1332 Dev= 0.08% S= 5.88 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   4.02

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     955 steps. Energy=    -391.6057956       time=       2.72
 Minus side of path:                     960 steps. Energy=    -390.9884316       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.6057956 0.94679         -390.6590047 0.32943         -390.9884316   6.175   5.833   3.010  48.170
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 3_U and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 0.4759 Dev= 0.39% S= 18.51 time= 0.85
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   6.25
 isnewts> transition state is the same as number        1 energy=     -365.5155313468
 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:                    1007 steps. Energy=    -366.6768294       time=       4.04
 Minus side of path:                     988 steps. Energy=    -367.6248705       time=       3.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -366.6768294  1.1613         -365.5155313  2.1093         -367.6248705  14.467  13.564   3.738  38.788
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0938 Dev= 0.11% S= 4.46 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.83

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     965 steps. Energy=    -366.6768294       time=       3.21
 Minus side of path:                    1147 steps. Energy=    -373.2834960       time=       3.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -366.6768294 0.31802         -366.3588088  6.9247         -373.2834960  28.859  27.197   2.586  56.081
        Known (#3)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4763.7    
 decide> The unconnected minima in the chain and their distances are:
     6       16.83     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.6767 Dev= 3.84% S= 20.34 time= 1.31
 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=  21.21
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     6566.7    
 decide> The unconnected minima in the chain and their distances are:
     6       18.56     4     3        4.41     1 
 

 tryconnect> 175-iteration DNEB run for minima 4_U and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 175 RMS= 0.5748 Dev= 2.40% S= 21.17 time= 1.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   7.26

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     963 steps. Energy=    -367.7898761       time=       3.62
 Minus side of path:                     897 steps. Energy=    -367.6248705       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -367.7898761 0.16527         -367.6246058 0.26467E-03     -367.6248705   2.777   2.771   2.382  60.883
        *NEW* (Placed in 8)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 3_U using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0075 Dev= 1.99% S= 5.31 time= 4.94
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.50

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     961 steps. Energy=    -366.7851496       time=       3.03
 Minus side of path:                     962 steps. Energy=    -366.6768294       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -366.7851496 0.70426         -366.0808933 0.59594         -366.6768294   4.514   4.405   7.487  19.368
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     8465.3    
 decide> The unconnected minima in the chain and their distances are:
     6       20.38     8 
 

 tryconnect> 210-iteration DNEB run for minima 6_F and 8_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 210 RMS= 0.2005 Dev= 3.02% S= 23.68 time= 1.84
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   7.14
 isnewts> transition state is the same as number        6 energy=     -367.6246058053
 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:                     888 steps. Energy=    -367.6248705       time=       3.43
 Minus side of path:                     971 steps. Energy=    -367.7898761       time=       3.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -367.6248705 0.26467E-03     -367.6246058 0.16527         -367.7898761   2.777   2.771   2.381  60.888
        Known (#4)                                              Known (#8)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     8507.5    
 decide> The unconnected minima in the chain and their distances are:
     6       16.20     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 805 RMS= 0.1713 Dev= 5.36% S= 24.60 time= 25.61
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   5.41

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1296 steps. Energy=    -383.0703599       time=       5.90
 Minus side of path:                    1060 steps. Energy=    -366.6768294       time=       3.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0703599  24.166         -358.9043836  7.7724         -366.6768294  42.292  14.271   3.278  44.231
        *NEW* (Placed in 9)                                     Known (#3)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3064.0    
 decide> The unconnected minima in the chain and their distances are:
     6       14.52     9 
 

 tryconnect> 140-iteration DNEB run for minima 6_F and 9_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 0.1535 Dev= 1.11% S= 14.81 time= 0.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.97

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1041 steps. Energy=    -382.4815302       time=       4.04
 Minus side of path:                    1022 steps. Energy=    -383.0703599       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4815302  1.8805         -380.6010207  2.4693         -383.0703599  16.048  14.526   3.483  41.633
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -366.7851496 0.70426        -366.0808933 0.59594        -366.6768294   4.514   4.405   7.487  19.368
   9     -366.6768294  7.7724        -358.9043836  24.166        -383.0703599  42.292  14.271   3.278  44.231
  10     -383.0703599  2.4693        -380.6010207  1.8805        -382.4815302  16.048  14.526   3.483  41.633
   2     -382.4815302  3.3911        -379.0904227  11.898        -390.9884316  67.097  49.424   3.154  45.973
   3     -390.9884316 0.32943        -390.6590047 0.94679        -391.6057956   6.175   5.833   3.010  48.170

 Number of TS in the path       =      5
 Number of cycles               =      7

 Elapsed time=                               203.59
 OPTIM> # of energy calls=                        152 time=           0.22 %=  0.1
 OPTIM> # of energy+gradient calls=             66701 time=          88.67 %= 43.6
 OPTIM> # of energy+gradient+Hessian calls=       775 time=           3.84 %=  1.9
