
 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)@comp27.ch.
                 Created on  5/28/12 at 12:49:17 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=    -399.4433289     RMS force=    0.8667251535E-06
 OPTIM> Final energy  =    -388.3743583     RMS force=    0.9589739517E-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=     84690.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.91     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0592 Dev= 4.00% S= 55.63 time= 8.10
 Following    2 images are candidates for TS:    7   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  26.86

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     950 steps. Energy=    -388.3743583       time=       2.20
 Minus side of path:                    1201 steps. Energy=    -394.3983805       time=       3.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.3743583 0.35380         -388.0205580  6.3778         -394.3983805  29.211  27.403   1.977  73.349
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     14103.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.16     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1462 Dev= 0.49% S= 25.91 time= 2.37
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         84
 DNEB run yielded 1 true transition state(s) time=   8.65

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     857 steps. Energy=    -396.7931836       time=       2.33
 Minus side of path:                     866 steps. Energy=    -397.5322550       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7931836 0.62676         -396.1664218  1.3658         -397.5322550  11.044  10.906   2.724  53.224
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     6848.0    
 decide> The unconnected minima in the chain and their distances are:
     3       14.40     4     5       15.69     1 
 

 tryconnect> 140-iteration DNEB run for minima 3_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 2.7339 Dev= 0.71% S= 14.82 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   6.83

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     917 steps. Energy=    -396.7931836       time=       2.94
 Minus side of path:                     917 steps. Energy=    -394.3983805       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.7931836  3.4212         -393.3720265  1.0264         -394.3983805  16.418  14.408   4.937  29.370
        Known (#4)                                              Known (#3)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.2328 Dev= 0.82% S= 16.39 time= 0.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   4.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     885 steps. Energy=    -396.1464806       time=       2.04
 Minus side of path:                     937 steps. Energy=    -397.9716366       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806 0.65883         -395.4876487  2.4840         -397.9716366   7.632   7.478   9.142  15.862
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     2697.0    
 decide> The unconnected minima in the chain and their distances are:
     5       13.90     7     6        2.33     1 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.1108 Dev= 0.65% S= 14.05 time= 0.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     880 steps. Energy=    -397.5322550       time=       2.80
 Minus side of path:                    1047 steps. Energy=    -397.9716366       time=       4.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.5322550 0.59115         -396.9411086  1.0305         -397.9716366  15.018  13.898   2.547  56.920
        Known (#5)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 70 RMS= 0.3164 Dev= 1.51% S= 2.61 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     851 steps. Energy=    -395.5808440       time=       2.08
 Minus side of path:                     891 steps. Energy=    -396.1464806       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.5808440 0.60761E-01     -395.5200832 0.62640         -396.1464806  10.397  10.130   5.581  25.981
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     25.240    
 decide> The unconnected minima in the chain and their distances are:
     6        2.33     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_F using 5 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 175 RMS= 0.2112 Dev= 0.99% S= 2.77 time= 1.21
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.48

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     885 steps. Energy=    -396.1464806       time=       2.74
 Minus side of path:                     844 steps. Energy=    -399.4433289       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.1464806  3.7716         -392.3749288  7.0684         -399.4433289   4.422   2.329  35.212   4.118
        Known (#6)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -399.4433289  7.0684        -392.3749288  3.7716        -396.1464806   4.422   2.329  35.212   4.118
   4     -396.1464806 0.65883        -395.4876487  2.4840        -397.9716366   7.632   7.478   9.142  15.862
   5     -397.9716366  1.0305        -396.9411086 0.59115        -397.5322550  15.018  13.898   2.547  56.920
   2     -397.5322550  1.3658        -396.1664218 0.62676        -396.7931836  11.044  10.906   2.724  53.224
   3     -396.7931836  3.4212        -393.3720265  1.0264        -394.3983805  16.418  14.408   4.937  29.370
   1     -394.3983805  6.3778        -388.0205580 0.35380        -388.3743583  29.211  27.403   1.977  73.349

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

 Elapsed time=                               113.45
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             32304 time=          43.77 %= 38.6
 OPTIM> # of energy+gradient+Hessian calls=       622 time=           2.99 %=  2.6
