
 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)@comp34.ch.
                 Created on  5/28/12 at 12:46:14 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=    -382.6517516     RMS force=    0.9790532668E-06
 OPTIM> Final energy  =    -384.3413309     RMS force=    0.9878865331E-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=     3530.5    
 decide> The unconnected minima in the chain and their distances are:
     2       15.23     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1048 Dev= 0.43% S= 15.82 time= 0.68
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=  10.84

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     994 steps. Energy=    -387.1746544       time=       2.79
 Minus side of path:                     990 steps. Energy=    -388.1413271       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  2.0572         -385.1174077  3.0239         -388.1413271   7.220   6.143  23.928   6.060
        *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      1 steps with      1 missing connections, weight=     7061.0    
 decide> The unconnected minima in the chain and their distances are:
     2       15.23     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.6358 Dev= 4.82% S= 21.15 time= 21.66
 Following    3 images are candidates for TS:    2   11   18  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         51
 Converged to TS (number of iterations):         63
 DNEB run yielded 3 true transition state(s) time=  19.61
 isnewts> transition state is the same as number        1 energy=     -385.1174076651
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1003 steps. Energy=    -384.0989856       time=       2.31
 Minus side of path:                     998 steps. Energy=    -382.6517516       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856  1.8185         -382.2804784 0.37127         -382.6517516  12.146  11.826   1.975  73.406
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     995 steps. Energy=    -387.1746544       time=       2.34
 Minus side of path:                     995 steps. Energy=    -388.1413271       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  2.0572         -385.1174077  3.0239         -388.1413271   7.220   6.143  23.911   6.064
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1207 steps. Energy=    -388.1413271       time=       3.32
 Minus side of path:                     978 steps. Energy=    -384.2712460       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1413271  3.9040         -384.2373332 0.33913E-01     -384.2712460  14.988  13.986   5.277  27.479
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     4907.3    
 decide> The unconnected minima in the chain and their distances are:
     2       16.99     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0890 Dev= 0.35% S= 17.66 time= 1.01
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1659 steps. Energy=    -387.1746544       time=       8.13
 Minus side of path:                    1002 steps. Energy=    -384.0989856       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  4.8234         -382.3512452  1.7477         -384.0989856  35.560  27.056   2.070  70.038
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2562.7    
 decide> The unconnected minima in the chain and their distances are:
     2       13.68     6 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 6_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0682 Dev= 0.00% S= 13.70 time= 0.67
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     992 steps. Energy=    -384.3413309       time=       3.11
 Minus side of path:                    1002 steps. Energy=    -384.2712460       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3413309 0.14978         -384.1915528 0.79693E-01     -384.2712460  13.731  13.685   2.475  58.574
        Known (#2)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -382.6517516 0.37127        -382.2804784  1.8185        -384.0989856  12.146  11.826   1.975  73.406
   5     -384.0989856  1.7477        -382.3512452  4.8234        -387.1746544  35.560  27.056   2.070  70.038
   1     -387.1746544  2.0572        -385.1174077  3.0239        -388.1413271   7.220   6.143  23.928   6.060
   4     -388.1413271  3.9040        -384.2373332 0.33913E-01    -384.2712460  14.988  13.986   5.277  27.479
   6     -384.2712460 0.79693E-01    -384.1915528 0.14978        -384.3413309  13.731  13.685   2.475  58.574

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                               100.82
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             40812 time=          46.75 %= 46.4
 OPTIM> # of energy+gradient+Hessian calls=       259 time=           1.14 %=  1.1
