
 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)@comp35.ch.
                 Created on  5/28/12 at 13: 9:46 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -391.8645413     RMS force=    0.8849644293E-06
 OPTIM> Final energy  =    -379.0342386     RMS force=    0.8130659390E-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=    0.15540E+06
 decide> The unconnected minima in the chain and their distances are:
     2       53.76     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 2_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 560 RMS= 0.1056 Dev= 7.26% S= 77.08 time= 12.20
 Following    3 images are candidates for TS:    5    7   12  
 Converged to TS (number of iterations):        222
 Converged to TS (number of iterations):        114
 Converged to TS (number of iterations):        102
 DNEB run yielded 3 true transition state(s) time=  38.90

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     934 steps. Energy=    -387.9522305       time=       3.88
 Minus side of path:                     967 steps. Energy=    -391.8645413       time=       3.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9522305 0.14843         -387.8038039  4.0607         -391.8645413  14.758  13.571   2.638  54.974
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1214 steps. Energy=    -382.1830963       time=       5.73
 Minus side of path:                    1032 steps. Energy=    -380.3293306       time=       3.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1830963  3.1628         -379.0203160  1.3090         -380.3293306  35.914  28.849   2.699  53.723
        *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:                    1201 steps. Energy=    -382.6739829       time=       4.04
 Minus side of path:                    1327 steps. Energy=    -379.0342386       time=       4.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6739829  7.4545         -375.2194456  3.8148         -379.0342386  40.750  35.802   2.285  63.466
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     43039.    
 decide> The unconnected minima in the chain and their distances are:
     6       35.04     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 6_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1002 Dev= 4.11% S= 43.50 time= 5.06
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   7.99

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     939 steps. Energy=    -384.4448489       time=       2.26
 Minus side of path:                     959 steps. Energy=    -385.0532120       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489  4.0056         -380.4392870  4.6139         -385.0532120  22.589  17.686  10.046  14.433
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     44472.    
 decide> The unconnected minima in the chain and their distances are:
     6       35.43     3 
 

 tryconnect> 350-iteration DNEB run for minima 3_S and 6_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1597 Dev= 2.41% S= 42.20 time= 4.93
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   6.41
 isnewts> transition state is the same as number        4 energy=     -380.4392869638
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     987 steps. Energy=    -384.4448489       time=       3.20
 Minus side of path:                     968 steps. Energy=    -385.0532120       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489  4.0056         -380.4392870  4.6139         -385.0532120  22.612  17.748   9.594  15.113
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     53279.    
 decide> The unconnected minima in the chain and their distances are:
     6       18.07     7     8       36.18     1 
 

 tryconnect> 175-iteration DNEB run for minima 6_F and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0480 Dev= 0.13% S= 18.31 time= 1.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   5.85

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1069 steps. Energy=    -384.6592017       time=       2.97
 Minus side of path:                     925 steps. Energy=    -382.6739829       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6592017  2.0066         -382.6525984 0.21385E-01     -382.6739829  17.743  17.437   3.067  47.276
        *NEW* (Placed in 9)                                     Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 8_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1937 Dev= 1.33% S= 42.31 time= 4.98
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.04

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1114 steps. Energy=    -385.0532120       time=       4.07
 Minus side of path:                    1134 steps. Energy=    -387.7639469       time=       5.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0532120  3.0541         -381.9990803  5.7649         -387.7639469  34.348  29.258   2.755  52.634
        Known (#8)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     9273.2    
 decide> The unconnected minima in the chain and their distances are:
     9       12.61     7    10       19.37     1 
 

 tryconnect> 105-iteration DNEB run for minima 7_U and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3163 Dev= 0.22% S= 12.70 time= 0.53
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   5.98

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     931 steps. Energy=    -384.4448489       time=       2.78
 Minus side of path:                     991 steps. Energy=    -384.6592017       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4448489 0.90558         -383.5392683  1.1199         -384.6592017  16.168  12.608   2.123  68.306
        Known (#7)                                              Known (#9)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 10_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0593 Dev= 0.06% S= 19.73 time= 1.31
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   5.93

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1058 steps. Energy=    -391.8645413       time=       2.84
 Minus side of path:                     967 steps. Energy=    -387.7639469       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.8645413  4.3497         -387.5148117 0.24914         -387.7639469  21.948  19.372   3.834  37.817
        Known (#1)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -391.8645413  4.3497        -387.5148117 0.24914        -387.7639469  21.948  19.372   3.834  37.817
   7     -387.7639469  5.7649        -381.9990803  3.0541        -385.0532120  34.348  29.258   2.755  52.634
   4     -385.0532120  4.6139        -380.4392870  4.0056        -384.4448489  22.589  17.686  10.046  14.433
   8     -384.4448489 0.90558        -383.5392683  1.1199        -384.6592017  16.168  12.608   2.123  68.306
   6     -384.6592017  2.0066        -382.6525984 0.21385E-01    -382.6739829  17.743  17.437   3.067  47.276
   3     -382.6739829  7.4545        -375.2194456  3.8148        -379.0342386  40.750  35.802   2.285  63.466

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

 Elapsed time=                               169.74
 OPTIM> # of energy calls=                        118 time=           0.16 %=  0.1
 OPTIM> # of energy+gradient calls=             50251 time=          67.79 %= 39.9
 OPTIM> # of energy+gradient+Hessian calls=       782 time=           3.93 %=  2.3
