
 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)@comp22.ch.
                 Created on  5/28/12 at 13: 5:52 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=    -398.2660216     RMS force=    0.8096896013E-06
 OPTIM> Final energy  =    -396.5648195     RMS force=    0.9283089660E-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=     1772.7    
 decide> The unconnected minima in the chain and their distances are:
     2       12.10     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 105 RMS= 0.6014 Dev= 1.68% S= 12.46 time= 0.44
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        230
 DNEB run yielded 1 true transition state(s) time=  18.70

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     951 steps. Energy=    -394.9413639       time=       2.30
 Minus side of path:                     987 steps. Energy=    -390.9236450       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9413639  7.7471         -387.1942322  3.7294         -390.9236450  30.808  27.112   1.974  73.447
        *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=     1250.9    
 decide> The unconnected minima in the chain and their distances are:
     2       10.04     3     3        6.19     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 105 RMS= 0.5934 Dev= 0.71% S= 10.12 time= 0.44
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     893 steps. Energy=    -396.5648195       time=       2.11
 Minus side of path:                     791 steps. Energy=    -394.9413639       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.5648195  1.6267         -394.9380729 0.32910E-02     -394.9413639  10.170  10.045   7.072  20.503
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 70 RMS= 1.0317 Dev= 0.88% S= 6.48 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.44
 isnewts> transition state is the same as number        2 energy=     -394.9380728652
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     884 steps. Energy=    -396.5648195       time=       2.27
 Minus side of path:                     799 steps. Energy=    -394.9413639       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.5648195  1.6267         -394.9380729 0.32910E-02     -394.9413639  10.170  10.045   7.075  20.496
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     474.83    
 decide> The unconnected minima in the chain and their distances are:
     3        6.19     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 3_F using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      26.53297705    
 Double-ended search iterations= 490 RMS= 0.3790 Dev= 2.42% S= 7.38 time= 9.44
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        249
 DNEB run yielded 1 true transition state(s) time=  42.73

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     968 steps. Energy=    -395.2364132       time=       2.27
 Minus side of path:                     915 steps. Energy=    -398.2660216       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.2364132  4.6646         -390.5717935  7.6942         -398.2660216  33.373  29.548   1.881  77.105
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     712.25    
 decide> The unconnected minima in the chain and their distances are:
     3        6.19     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      50.03188542    
 Double-ended search iterations= 805 RMS= 0.1577 Dev= 6.38% S= 8.17 time= 25.30
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     868 steps. Energy=    -392.4679100       time=       2.87
 Minus side of path:                     907 steps. Energy=    -398.2660216       time=       3.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4679100  1.3915         -391.0763700  7.1897         -398.2660216   4.611   3.040  18.645   7.777
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     318.19    
 decide> The unconnected minima in the chain and their distances are:
     3        6.83     6 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.3298 Dev= 0.02% S= 6.99 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.79

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     908 steps. Energy=    -392.4679100       time=       3.23
 Minus side of path:                     933 steps. Energy=    -394.9413639       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4679100 0.64894         -391.8189653  3.1224         -394.9413639   7.476   6.828  19.045   7.613
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -398.2660216  7.1897        -391.0763700  1.3915        -392.4679100   4.611   3.040  18.645   7.777
   6     -392.4679100 0.64894        -391.8189653  3.1224        -394.9413639   7.476   6.828  19.045   7.613
   2     -394.9413639 0.32910E-02    -394.9380729  1.6267        -396.5648195  10.170  10.045   7.072  20.503

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               144.39
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45312 time=          60.50 %= 41.9
 OPTIM> # of energy+gradient+Hessian calls=       604 time=           3.17 %=  2.2
