
 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 13:13:25 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  =    -379.3011876     RMS force=    0.9720334003E-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=     55230.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.08     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0757 Dev= 1.92% S= 44.26 time= 5.00
 Following    2 images are candidates for TS:    3    9  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         43
 DNEB run yielded 2 true transition state(s) time=  11.83

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1001 steps. Energy=    -383.4104804       time=       4.24
 Minus side of path:                    1009 steps. Energy=    -384.0989856       time=       4.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4104804 0.89431E-01     -383.3210495 0.77794         -384.0989856   8.020   7.981   2.069  70.077
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1044 steps. Energy=    -380.2155834       time=       3.05
 Minus side of path:                    1019 steps. Energy=    -381.7644736       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.91142         -379.3041634  2.4603         -381.7644736  14.441  13.904   2.914  49.756
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     42119.    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     6     5       34.16     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1649 Dev= 0.07% S= 13.18 time= 0.37
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.82
 isnewts> transition state is the same as number        2 energy=     -379.3041634428
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1033 steps. Energy=    -380.2155834       time=       3.73
 Minus side of path:                    1028 steps. Energy=    -381.7644736       time=       4.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.91142         -379.3041634  2.4603         -381.7644736  14.441  13.903   2.917  49.710
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 5_U using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0622 Dev= 0.97% S= 37.25 time= 4.08
 Following    3 images are candidates for TS:    2    4    9  
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         59
 Converged to TS (number of iterations):         57
 DNEB run yielded 3 true transition state(s) time=  17.49

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     988 steps. Energy=    -384.0989856       time=       3.08
 Minus side of path:                    1007 steps. Energy=    -382.6517516       time=       3.49

         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  73.399
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1100 steps. Energy=    -387.1746544       time=       4.71
 Minus side of path:                     957 steps. Energy=    -383.3551822       time=       3.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  3.8532         -383.3214602 0.33722E-01     -383.3551822  14.700  13.699   5.338  27.163
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1146 steps. Energy=    -383.4268737       time=       2.96
 Minus side of path:                    1005 steps. Energy=    -380.2155834       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4268737  3.2179         -380.2089945 0.65889E-02     -380.2155834  29.557  28.786   2.249  64.484
        *NEW* (Placed in 9)                                     Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     5643.8    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     6     9       10.49     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_U using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.0576 Dev= 3.33% S= 14.40 time= 21.15
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.64
 isnewts> transition state is the same as number        2 energy=     -379.3041634428
 tryconnect> Will not repeat search for TS      1 same as TS      2

 tryconnect> 105-iteration DNEB run for minima 3_S and 9_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0653 Dev= 0.14% S= 10.56 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.45

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     993 steps. Energy=    -383.4104804       time=       2.36
 Minus side of path:                    1021 steps. Energy=    -383.2580438       time=       2.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4104804  1.8782         -381.5323112  1.7257         -383.2580438  10.739   9.553   2.559  56.659
        Known (#3)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     6681.7    
 decide> The unconnected minima in the chain and their distances are:
     2       18.82     5     9        2.45    10 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0893 Dev= 0.02% S= 19.02 time= 1.02
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.31

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     999 steps. Energy=    -379.3011876       time=       2.35
 Minus side of path:                    1080 steps. Energy=    -380.2155834       time=       2.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.3011876 0.16393E-01     -379.2847946 0.93079         -380.2155834  20.327  18.830   2.181  66.498
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 9_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0688 Dev= 0.02% S= 2.46 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     999 steps. Energy=    -383.2580438       time=       2.34
 Minus side of path:                     987 steps. Energy=    -383.4268737       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2580438 0.17363E-01     -383.2406806 0.18619         -383.4268737   2.567   2.449   5.575  26.010
        Known (#10)                                             Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -382.6517516 0.37127        -382.2804784  1.8185        -384.0989856  12.146  11.826   1.975  73.399
   1     -384.0989856 0.77794        -383.3210495 0.89431E-01    -383.4104804   8.020   7.981   2.069  70.077
   7     -383.4104804  1.8782        -381.5323112  1.7257        -383.2580438  10.739   9.553   2.559  56.659
   9     -383.2580438 0.17363E-01    -383.2406806 0.18619        -383.4268737   2.567   2.449   5.575  26.010
   6     -383.4268737  3.2179        -380.2089945 0.65889E-02    -380.2155834  29.557  28.786   2.249  64.484
   8     -380.2155834 0.93079        -379.2847946 0.16393E-01    -379.3011876  20.327  18.830   2.181  66.498

 Number of TS in the path       =      6
 Number of cycles               =      4

 Elapsed time=                               142.92
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             56985 time=          64.12 %= 44.9
 OPTIM> # of energy+gradient+Hessian calls=       412 time=           1.83 %=  1.3
