
 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: 5:24 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=    -379.5945428     RMS force=    0.9416678244E-06
 OPTIM> Final energy  =    -391.4506195     RMS force=    0.9877995184E-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=     33716.    
 decide> The unconnected minima in the chain and their distances are:
     2       32.31     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 315 RMS= 0.7825 Dev= 0.89% S= 33.15 time= 3.62
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   8.76

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     948 steps. Energy=    -388.9372050       time=       3.08
 Minus side of path:                     933 steps. Energy=    -388.2678662       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9372050  1.1819         -387.7553131 0.51255         -388.2678662   3.480   3.351  36.959   3.923
        *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=     35958.    
 decide> The unconnected minima in the chain and their distances are:
     2        3.22     3     3       33.00     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.2260 Dev= 1.13% S= 3.28 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.82

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     940 steps. Energy=    -388.9372050       time=       2.53
 Minus side of path:                     934 steps. Energy=    -391.4506195       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9372050 0.24490         -388.6923083  2.7583         -391.4506195   4.019   3.220  26.674   5.436
        Known (#3)                                              Known (#2)
 Unconnected minimum 3 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      15.51328216    
 Double-ended search iterations= 315 RMS= 0.2396 Dev= 0.44% S= 33.59 time= 3.65
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   8.08

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     922 steps. Energy=    -385.5701996       time=       2.89
 Minus side of path:                     886 steps. Energy=    -385.4724163       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5701996 0.11291         -385.4572935 0.15123E-01     -385.4724163   1.029   1.026  39.343   3.686
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     32027.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.62     5     5       23.61     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 245 RMS= 0.2342 Dev= 0.24% S= 26.89 time= 2.32
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1028 steps. Energy=    -385.5701996       time=       3.67
 Minus side of path:                    1207 steps. Energy=    -391.4506195       time=       4.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5701996 0.63909         -384.9311079  6.5195         -391.4506195  27.209  26.623   3.420  42.399
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 245 RMS= 6.2970 Dev= 35.83% S= 25.83 time= 2.22
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.80

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     918 steps. Energy=    -385.1859057       time=       2.81
 Minus side of path:                     932 steps. Energy=    -385.5701996       time=       2.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1859057 0.58564         -384.6002688 0.96993         -385.5701996   1.801   1.663 110.232   1.315
        *NEW* (Placed in 7)                                     Known (#5)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13371.    
 decide> The unconnected minima in the chain and their distances are:
     6       23.73     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 6_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      37.33456322    
 Double-ended search iterations= 245 RMS= 0.8155 Dev= 1.12% S= 23.95 time= 2.19
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   5.23

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     900 steps. Energy=    -385.4724163       time=       2.80
 Minus side of path:                     896 steps. Energy=    -385.0880628       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4724163 0.96995         -384.5024631 0.58560         -385.0880628   1.800   1.663 110.323   1.314
        Known (#6)                                              *NEW* (Placed in 8)
 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      3 steps with      1 missing connections, weight=     13465.    
 decide> The unconnected minima in the chain and their distances are:
     7       23.79     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 245 RMS= 0.2711 Dev= 1.04% S= 23.99 time= 2.16
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     906 steps. Energy=    -385.0880628       time=       2.43
 Minus side of path:                     895 steps. Energy=    -385.1859057       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0880628 0.15104E-01     -385.0729590 0.11295         -385.1859057   1.028   1.025  39.318   3.688
        Known (#8)                                              Known (#7)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     13673.    
 decide> The unconnected minima in the chain and their distances are:
     8       23.91     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 8_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      60.81406943    
 Double-ended search iterations= 245 RMS= 1.1960 Dev= 0.66% S= 24.06 time= 2.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   6.09

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     977 steps. Energy=    -379.5945428       time=       3.39
 Minus side of path:                     988 steps. Energy=    -385.1859057       time=       3.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5945428 0.27729         -379.3172558  5.8686         -385.1859057  25.110  23.818   2.277  63.686
        Known (#1)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -379.5945428 0.27729        -379.3172558  5.8686        -385.1859057  25.110  23.818   2.277  63.686
   7     -385.1859057 0.11295        -385.0729590 0.15104E-01    -385.0880628   1.028   1.025  39.318   3.688
   6     -385.0880628 0.58560        -384.5024631 0.96995        -385.4724163   1.800   1.663 110.323   1.314
   3     -385.4724163 0.15123E-01    -385.4572935 0.11291        -385.5701996   1.029   1.026  39.343   3.686
   4     -385.5701996 0.63909        -384.9311079  6.5195        -391.4506195  27.209  26.623   3.420  42.399

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

 Elapsed time=                               111.30
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             38502 time=          49.20 %= 44.2
 OPTIM> # of energy+gradient+Hessian calls=       265 time=           1.26 %=  1.1
