
 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)@comp32.ch.
                 Created on  5/28/12 at 13: 7:50 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1065 Dev= 0.79% S= 15.84 time= 0.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  11.79

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     990 steps. Energy=    -387.1746544       time=       2.51
 Minus side of path:                     989 steps. Energy=    -388.1413271       time=       3.52

         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  23.930   6.059
        *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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.0841 Dev= 3.84% S= 20.77 time= 21.83
 Following    3 images are candidates for TS:    2    8   14  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         26
 Converged to TS (number of iterations):         28
 DNEB run yielded 3 true transition state(s) time=  14.36

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1014 steps. Energy=    -384.0989856       time=       3.59
 Minus side of path:                     994 steps. Energy=    -382.6517516       time=       2.49

         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  73.404
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     991 steps. Energy=    -384.0989856       time=       3.14
 Minus side of path:                     998 steps. Energy=    -384.9856005       time=       3.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856  2.0300         -382.0690256  2.9166         -384.9856005   6.463   5.580  22.900   6.332
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1002 steps. Energy=    -384.9856005       time=       3.38
 Minus side of path:                    1681 steps. Energy=    -388.1413271       time=       6.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9856005  1.7191         -383.2665300  4.8748         -388.1413271  35.263  27.214   2.021  71.746
        Known (#6)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3608.2    
 decide> The unconnected minima in the chain and their distances are:
     2       15.34     6 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 6_S using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2173 Dev= 0.07% S= 15.43 time= 0.67
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.21
 isnewts> transition state is the same as number        4 energy=     -383.2665299806
 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:                    1618 steps. Energy=    -388.1413271       time=       6.17
 Minus side of path:                    1005 steps. Energy=    -384.9856005       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1413271  4.8748         -383.2665300  1.7191         -384.9856005  35.254  27.200   2.023  71.668
        Known (#4)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1107 Dev= 1.32% S= 17.64 time= 1.05
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.20
 isnewts> transition state is the same as number        3 energy=     -382.0690255668
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     991 steps. Energy=    -384.0989856       time=       2.87
 Minus side of path:                     977 steps. Energy=    -384.9856005       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0989856  2.0300         -382.0690256  2.9166         -384.9856005   6.463   5.580  22.879   6.338
        Known (#5)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     7216.5    
 decide> The unconnected minima in the chain and their distances are:
     2       15.34     6 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 805 RMS= 0.1275 Dev= 5.46% S= 16.98 time= 21.97
 Following    2 images are candidates for TS:    8   14  
 Converged to TS (number of iterations):         44
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=  11.45
 isnewts> transition state is the same as number        4 energy=     -383.2665299806
 tryconnect> Will not repeat search for TS      2 same as TS      4

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     996 steps. Energy=    -384.3413309       time=       2.43
 Minus side of path:                    1009 steps. Energy=    -384.2712460       time=       3.28

         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   2.476  58.574
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     2474.9    
 decide> The unconnected minima in the chain and their distances are:
     7       13.53     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 7_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3201 Dev= 1.43% S= 15.31 time= 0.71
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.35
 isnewts> transition state is the same as number        1 energy=     -385.1174076651
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     995 steps. Energy=    -387.1746544       time=       2.77
 Minus side of path:                     977 steps. Energy=    -388.1413271       time=       3.42

         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  23.914   6.064
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2727.6    
 decide> The unconnected minima in the chain and their distances are:
     7       13.97     4 
 

 tryconnect> 140-iteration DNEB run for minima 4_S and 7_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2281 Dev= 0.28% S= 15.56 time= 0.69
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.40
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     4949.8    
 decide> The unconnected minima in the chain and their distances are:
     7       13.53     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 7_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 805 RMS= 0.0466 Dev= 8.74% S= 26.80 time= 22.24
 Following    3 images are candidates for TS:    3   13   22  
 Converged to TS (number of iterations):         14
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         20
 DNEB run yielded 2 true transition state(s) time=  46.85
 isnewts> transition state is the same as number        1 energy=     -385.1174076651
 tryconnect> Will not repeat search for TS      1 same as TS      1

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1203 steps. Energy=    -388.1413271       time=       4.75
 Minus side of path:                     967 steps. Energy=    -384.2712460       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1413271  3.9040         -384.2373332 0.33913E-01     -384.2712460  14.989  13.986   5.276  27.480
        Known (#4)                                              Known (#7)
 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  73.404
   3     -384.0989856  2.0300        -382.0690256  2.9166        -384.9856005   6.463   5.580  22.900   6.332
   4     -384.9856005  1.7191        -383.2665300  4.8748        -388.1413271  35.263  27.214   2.021  71.746
   9     -388.1413271  3.9040        -384.2373332 0.33913E-01    -384.2712460  14.989  13.986   5.276  27.480
   7     -384.2712460 0.79693E-01    -384.1915528 0.14978        -384.3413309  13.731  13.685   2.476  58.574

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                               252.42
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             94922 time=         109.49 %= 43.4
 OPTIM> # of energy+gradient+Hessian calls=       846 time=           4.11 %=  1.6
