
 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)@comp29.ch.
                 Created on  5/28/12 at 12:59:31 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=    -379.5013770     RMS force=    0.9305824270E-06
 OPTIM> Final energy  =    -388.3561027     RMS force=    0.9821302649E-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=    0.25434E+06
 decide> The unconnected minima in the chain and their distances are:
     2       63.36     1 
 

 tryconnect> 665-iteration DNEB run for minima 1_S and 2_F using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1519928728E-01
 Double-ended search iterations= 665 RMS= 0.0267 Dev= 4.65% S= 79.55 time= 14.85
 Following    3 images are candidates for TS:    1    4   10  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         66
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        138
 Converged to TS (number of iterations):        101
 DNEB run yielded 3 true transition state(s) time=  28.14

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1028 steps. Energy=    -381.5005310       time=       3.38
 Minus side of path:                    1019 steps. Energy=    -379.5013770       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5005310  2.3634         -379.1371665 0.36421         -379.5013770  22.622  22.357   2.495  58.115
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1021 steps. Energy=    -379.7128734       time=       2.37
 Minus side of path:                    1011 steps. Energy=    -379.7549175       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.7128734 0.21718         -379.4956946 0.25922         -379.7549175  17.748  17.337   2.510  57.777
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1692 steps. Energy=    -387.8615748       time=       9.46
 Minus side of path:                    1158 steps. Energy=    -380.2155834       time=       4.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8615748  8.6110         -379.2505819 0.96500         -380.2155834  67.946  64.049   1.764  82.188
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     15059.    
 decide> The unconnected minima in the chain and their distances are:
     2        8.40     6     7       24.37     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0346 Dev= 0.01% S= 8.40 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.85

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     994 steps. Energy=    -388.3561027       time=       3.16
 Minus side of path:                     958 steps. Energy=    -387.8615748       time=       3.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3561027 0.67420         -387.6819043 0.17967         -387.8615748   8.436   8.397   2.071  70.002
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 3_S and 7_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2529 Dev= 0.92% S= 25.69 time= 1.97
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   6.69

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1022 steps. Energy=    -381.7644736       time=       4.07
 Minus side of path:                    1025 steps. Energy=    -380.2155834       time=       3.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7644736  2.4603         -379.3041634 0.91142         -380.2155834  14.441  13.904   2.915  49.743
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     6444.8    
 decide> The unconnected minima in the chain and their distances are:
     8       18.61     3 
 

 tryconnect> 175-iteration DNEB run for minima 3_S and 8_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 2.3630 Dev= 0.79% S= 19.08 time= 1.00
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   5.91

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1004 steps. Energy=    -381.8415109       time=       2.79
 Minus side of path:                    1017 steps. Energy=    -381.7653890       time=       3.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.8415109 0.13005         -381.7114658 0.53923E-01     -381.7653890  17.551  17.362   1.821  79.610
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1140.8    
 decide> The unconnected minima in the chain and their distances are:
     8        7.06    10     9        9.24     3 
 

 tryconnect> 70-iteration DNEB run for minima 8_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0157 Dev= 0.01% S= 7.06 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   4.38

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     968 steps. Energy=    -381.7653890       time=       3.51
 Minus side of path:                    1010 steps. Energy=    -381.7644736       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7653890 0.65272E-02     -381.7588617 0.56119E-02     -381.7644736   7.087   7.059   1.826  79.417
        Known (#10)                                             Known (#8)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5541 Dev= 0.43% S= 9.50 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=   7.37

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1037 steps. Energy=    -381.5005310       time=       4.04
 Minus side of path:                    1172 steps. Energy=    -386.0055417       time=       4.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5005310 0.45173         -381.0487972  4.9567         -386.0055417  23.336  19.924   2.515  57.656
        Known (#3)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1578.0    
 decide> The unconnected minima in the chain and their distances are:
     9        9.24     3 
 

 tryconnect> 735-iteration DNEB run for minima 3_S and 9_F using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1675721423E-01
 Double-ended search iterations= 735 RMS= 0.0052 Dev= 4.72% S= 13.28 time= 17.31
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   4.38

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1035 steps. Energy=    -381.8415109       time=       4.36
 Minus side of path:                     976 steps. Energy=    -381.5005310       time=       3.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.8415109  2.3817         -379.4597675  2.0408         -381.5005310  11.472   9.252   7.029  20.630
        Known (#9)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -379.5013770 0.36421        -379.1371665  2.3634        -381.5005310  22.622  22.357   2.495  58.115
   9     -381.5005310  2.0408        -379.4597675  2.3817        -381.8415109  11.472   9.252   7.029  20.630
   6     -381.8415109 0.13005        -381.7114658 0.53923E-01    -381.7653890  17.551  17.362   1.821  79.610
   7     -381.7653890 0.65272E-02    -381.7588617 0.56119E-02    -381.7644736   7.087   7.059   1.826  79.417
   5     -381.7644736  2.4603        -379.3041634 0.91142        -380.2155834  14.441  13.904   2.915  49.743
   3     -380.2155834 0.96500        -379.2505819  8.6110        -387.8615748  67.946  64.049   1.764  82.188
   4     -387.8615748 0.17967        -387.6819043 0.67420        -388.3561027   8.436   8.397   2.071  70.002

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

 Elapsed time=                               166.85
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             59702 time=          66.90 %= 40.1
 OPTIM> # of energy+gradient+Hessian calls=       550 time=           2.62 %=  1.6
