
 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 13: 8: 8 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=    -381.4115420     RMS force=    0.9091137211E-06
 OPTIM> Final energy  =    -384.3809262     RMS force=    0.9953443816E-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=    0.20578E+06
 decide> The unconnected minima in the chain and their distances are:
     2       59.04     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4032823407E-01
 Double-ended search iterations= 595 RMS= 0.0665 Dev= 5.30% S= 69.69 time= 11.58
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        201
 DNEB run yielded 1 true transition state(s) time=  19.07

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1992 steps. Energy=    -389.6448428       time=      10.93
 Minus side of path:                    1061 steps. Energy=    -380.6105130       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6448428  9.2912         -380.3536532 0.25686         -380.6105130  69.951  65.941   1.720  84.306
        *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      2 steps with      2 missing connections, weight=    0.16271E+06
 decide> The unconnected minima in the chain and their distances are:
     2       54.04     4     4       16.97     1 
 

 tryconnect> 560-iteration DNEB run for minima 2_F and 4_U using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0306 Dev= 2.73% S= 60.65 time= 10.33
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   5.99

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1066 steps. Energy=    -380.6105130       time=       4.56
 Minus side of path:                    1047 steps. Energy=    -380.6818344       time=       4.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6105130 0.32242         -380.2880910 0.39374         -380.6818344  26.521  25.960   2.048  70.805
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0279 Dev= 0.08% S= 17.18 time= 1.03
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.08

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1068 steps. Energy=    -381.2770161       time=       4.09
 Minus side of path:                    1002 steps. Energy=    -380.6105130       time=       3.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.70640         -380.5706150 0.39898E-01     -380.6105130  21.688  21.547   1.864  77.789
        *NEW* (Placed in 6)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     59909.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.87     5     4       16.97     1 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 5_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0426 Dev= 0.71% S= 38.40 time= 4.96
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.54

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1122 steps. Energy=    -384.3395678       time=       3.66
 Minus side of path:                     992 steps. Energy=    -380.6818344       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678  3.6781         -380.6614622 0.20372E-01     -380.6818344  36.354  35.681   1.639  88.471
        *NEW* (Placed in 7)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 805 RMS= 0.0404 Dev= 11.79% S= 21.61 time= 20.22
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   5.73
 isnewts> transition state is the same as number        3 energy=     -380.5706150299
 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:                    1067 steps. Energy=    -381.2770161       time=       3.46
 Minus side of path:                    1013 steps. Energy=    -380.6105130       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.70640         -380.5706150 0.39898E-01     -380.6105130  21.688  21.547   1.864  77.790
        Known (#6)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     11503.    
 decide> The unconnected minima in the chain and their distances are:
     2        3.67     7     6       22.54     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0669 Dev= 0.02% S= 3.67 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     940 steps. Energy=    -384.3395678       time=       2.89
 Minus side of path:                     953 steps. Energy=    -384.3809262       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678 0.17609E-01     -384.3219585 0.58968E-01     -384.3809262   3.686   3.668   1.703  85.121
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0620 Dev= 0.12% S= 22.93 time= 1.46
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.54

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1020 steps. Energy=    -381.3057367       time=       2.83
 Minus side of path:                    1036 steps. Energy=    -381.4115420       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.3057367 0.31476         -380.9909805 0.42056         -381.4115420  24.115  22.175   2.649  54.731
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 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=    0.94425    
 decide> The unconnected minima in the chain and their distances are:
     6        0.98     8 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0202 Dev= 0.13% S= 0.98 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.88

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1002 steps. Energy=    -381.2770161       time=       3.69
 Minus side of path:                     972 steps. Energy=    -381.3057367       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.19207E-01     -381.2578087 0.47928E-01     -381.3057367   1.034   0.981  12.024  12.059
        Known (#6)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -381.4115420 0.42056        -380.9909805 0.31476        -381.3057367  24.115  22.175   2.649  54.731
   8     -381.3057367 0.47928E-01    -381.2578087 0.19207E-01    -381.2770161   1.034   0.981  12.024  12.059
   3     -381.2770161 0.70640        -380.5706150 0.39898E-01    -380.6105130  21.688  21.547   1.864  77.789
   2     -380.6105130 0.32242        -380.2880910 0.39374        -380.6818344  26.521  25.960   2.048  70.805
   4     -380.6818344 0.20372E-01    -380.6614622  3.6781        -384.3395678  36.354  35.681   1.639  88.471
   6     -384.3395678 0.17609E-01    -384.3219585 0.58968E-01    -384.3809262   3.686   3.668   1.703  85.121

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                               167.38
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             70597 time=          76.03 %= 45.4
 OPTIM> # of energy+gradient+Hessian calls=       491 time=           2.23 %=  1.3
