
 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 12:55:18 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=    -379.4076960     RMS force=    0.9895102542E-06
 OPTIM> Final energy  =    -376.2013730     RMS force=    0.8801950210E-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=     39339.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.01     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      304.2642554    
 Double-ended search iterations= 830 RMS= 2.6564 Dev= 0.11% S= 34.84 time= 10.12
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   5.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     982 steps. Energy=    -376.0998640       time=       2.31
 Minus side of path:                     993 steps. Energy=    -380.2621646       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.0998640 0.20750         -375.8923654  4.3698         -380.2621646   8.797   6.519   5.339  27.159
        *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=     28118.    
 decide> The unconnected minima in the chain and their distances are:
     2        6.74     3     3       30.30     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.1656 Dev= 0.69% S= 6.77 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.42

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     965 steps. Energy=    -376.2013730       time=       2.52
 Minus side of path:                    1015 steps. Energy=    -380.2621646       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.2013730  1.2049         -374.9964402  5.2657         -380.2621646  12.540   9.778   7.824  18.532
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 3_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      216.2349257    
 Double-ended search iterations= 803 RMS= 4.0476 Dev= 0.13% S= 30.86 time= 8.83
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):         68
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=  12.51
 isnewts> transition state is the same as number        1 energy=     -375.8923654231
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number        1 energy=     -375.8923654231
 tryconnect> Will not repeat search for TS      2 same as TS      1

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     986 steps. Energy=    -376.0998640       time=       2.22
 Minus side of path:                     993 steps. Energy=    -380.2621646       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.0998640 0.20750         -375.8923654  4.3698         -380.2621646   8.799   6.519   5.296  27.378
        Known (#3)                                              Known (#4)
 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=     30446.    
 decide> The unconnected minima in the chain and their distances are:
     4       31.23     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 4_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      216.2349257    
 Double-ended search iterations= 692 RMS= 2.6200 Dev= 0.08% S= 31.73 time= 7.60
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.31

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     971 steps. Energy=    -379.4076960       time=       2.77
 Minus side of path:                    1042 steps. Energy=    -380.2621646       time=       3.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.4076960 0.19067         -379.2170298  1.0451         -380.2621646  32.111  31.258   2.089  69.397
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -379.4076960 0.19067        -379.2170298  1.0451        -380.2621646  32.111  31.258   2.089  69.397
   2     -380.2621646  5.2657        -374.9964402  1.2049        -376.2013730  12.540   9.778   7.824  18.532

 Number of TS in the path       =      2
 Number of cycles               =      3

 Elapsed time=                                76.57
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             35178 time=          41.14 %= 53.7
 OPTIM> # of energy+gradient+Hessian calls=       257 time=           1.16 %=  1.5
