
 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> Constraint potential parameters read from file congeom.dat
 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)@comp29.ch.
                 Created on  5/28/12 at 10:35: 5 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -391.4617264     RMS force=    0.9202775967E-06
 OPTIM> Final energy  =    -391.2684032     RMS force=    0.9870640645E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      33.83668703    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     27320.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.08     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    43
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    174 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    199 steps, energy/image=    -378.1972502     RMS=.9945832563     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   34.73     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.2660 Dev= 2.46% S= 37.12 time= 5.33
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         64
 Converged to TS (number of iterations):         90
 DNEB run yielded 2 true transition state(s) time=  13.61

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     966 steps. Energy=    -391.2244416       time=       2.86
 Minus side of path:                     934 steps. Energy=    -389.3839080       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2244416  2.2178         -389.0066100 0.37730         -389.3839080  16.140  13.727   4.698  30.865
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    13   26 from     0.22207E-01 to     0.22504E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms    13   28 from     0.11943     to     0.12037     ref=     2.4983    
 checkperc> Increasing con cutoff atoms    18   24 from     0.35405E-02 to     0.36096E-02 ref=     2.4263    
 checkperc> Increasing con cutoff atoms    54   56 from     0.70431E-01 to     0.77716E-01 ref=     2.5937    
 checkperc> Increasing con cutoff atoms   131  133 from     0.18214E-01 to     0.19145E-01 ref=     3.0973    
 checkperc> Increasing con cutoff atoms   132  144 from     0.12880     to     0.12981     ref=     2.8758    
 checkperc> Increasing con cutoff atoms   135  136 from     0.91077E-02 to     0.95089E-02 ref=     1.5272    
 checkperc> Increasing con cutoff atoms   135  143 from     0.33423E-01 to     0.33572E-01 ref=     2.5262    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     924 steps. Energy=    -391.4356342       time=       2.95
 Minus side of path:                     927 steps. Energy=    -393.6609809       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342  1.3910         -390.0446368  3.6163         -393.6609809  19.228  17.405   3.265  44.413
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms     5    6 from     0.58851E-02 to     0.59019E-02 ref=     1.5239    
 checkperc> Increasing con cutoff atoms     5   10 from     0.28102E-01 to     0.28958E-01 ref=     2.3994    
 checkperc> Increasing con cutoff atoms    11   12 from     0.32189E-02 to     0.37078E-02 ref=    0.98055    
 checkperc> Increasing con cutoff atoms    13   26 from     0.22504E-01 to     0.23379E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms    13   27 from     0.63692E-01 to     0.68061E-01 ref=     2.4042    
 checkperc> Increasing con cutoff atoms    13   28 from     0.12037     to     0.13184     ref=     2.4983    
 checkperc> Increasing con cutoff atoms    15   22 from     0.12040E-01 to     0.12356E-01 ref=     3.4418    
 checkperc> Increasing con cutoff atoms    25   27 from     0.45144E-02 to     0.46456E-02 ref=     1.3315    
 checkperc> Increasing con cutoff atoms    26   27 from     0.17686E-01 to     0.19255E-01 ref=     2.2563    
 checkperc> Increasing con cutoff atoms   107  114 from     0.76446E-01 to     0.10583     ref=     2.4840    
 checkperc> Increasing con cutoff atoms   135  136 from     0.95089E-02 to     0.97328E-02 ref=     1.5272    
 checkperc> Increasing con cutoff atoms    89   90 from     0.39571E-02 to     0.41434E-02 ref=     1.2355    
 checkperc> Increasing con cutoff atoms   111  113 from     0.24108E-01 to     0.27316E-01 ref=     2.4207    
 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=     14523.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.29     3     4        5.23     1 
 

 tryconnect> Interpolation for minima 2_F and 3_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    48
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    114 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    139 steps, energy/image=    -362.8803824     RMS=3.222392919     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   32.15     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 315 RMS= 0.1297 Dev= 0.89% S= 25.93 time= 4.23
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   6.69

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     844 steps. Energy=    -391.4356342       time=       2.00
 Minus side of path:                     871 steps. Energy=    -390.7278775       time=       2.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342 0.74644         -390.6891897 0.38688E-01     -390.7278775   7.625   6.914   5.446  26.624
        Known (#5)                                              *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms     5    6 from     0.59019E-02 to     0.60054E-02 ref=     1.5239    
 checkperc> Increasing con cutoff atoms    11   12 from     0.37078E-02 to     0.37701E-02 ref=    0.98055    
 checkperc> Increasing con cutoff atoms    13   26 from     0.23379E-01 to     0.23976E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms    13   27 from     0.68061E-01 to     0.71077E-01 ref=     2.4042    
 checkperc> Increasing con cutoff atoms    13   28 from     0.13184     to     0.13750     ref=     2.4983    
 checkperc> Increasing con cutoff atoms    25   27 from     0.46456E-02 to     0.47010E-02 ref=     1.3315    
 checkperc> Increasing con cutoff atoms    26   27 from     0.19255E-01 to     0.20812E-01 ref=     2.2563    
 checkperc> Increasing con cutoff atoms    26   29 from     0.53185E-01 to     0.55973E-01 ref=     2.8117    
 checkperc> Increasing con cutoff atoms   118  130 from     0.84047E-02 to     0.87594E-02 ref=     1.5268    
 checkperc> Increasing con cutoff atoms   135  136 from     0.97328E-02 to     0.10072E-01 ref=     1.5272    
 checkperc> Increasing con cutoff atoms   135  143 from     0.33572E-01 to     0.38063E-01 ref=     2.5262    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 4_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   140
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -383.6863124     RMS=3.801787234     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   12.68     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      17.10339358    
 Double-ended search iterations= 105 RMS= 0.1837 Dev= 0.66% S= 5.26 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.94

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     921 steps. Energy=    -391.4617264       time=       2.23
 Minus side of path:                     886 steps. Energy=    -389.3839080       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4617264  2.8110         -388.6506790 0.73323         -389.3839080   5.780   5.229   6.907  20.993
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     17420.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.38     7     5       10.06     3 
 

 tryconnect> Interpolation for minima 2_F and 7_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    40
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    111 fraction=    0.990000 images=     4 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    136 steps, energy/image=    -300.6466855     RMS=15.64641708     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      2     7 dist=   35.21     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 350 RMS= 0.0421 Dev= 0.29% S= 26.18 time= 5.38
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.43

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1237 steps. Energy=    -391.2684032       time=       3.79
 Minus side of path:                     876 steps. Energy=    -391.4356342       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2684032  1.4104         -389.8580234  1.5776         -391.4356342  30.117  26.863   2.352  61.643
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 3_S and 5_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   112
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     34 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     59 steps, energy/image=    -378.2162382     RMS=7.925450150     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   16.39     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 140 RMS= 0.2269 Dev= 1.51% S= 10.15 time= 0.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.36

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     875 steps. Energy=    -391.4356342       time=       2.43
 Minus side of path:                     864 steps. Energy=    -392.0698724       time=       2.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4356342 0.69070         -390.7449373  1.3249         -392.0698724   3.649   3.439  16.448   8.816
        Known (#5)                                              *NEW* (Placed in 8)
 checkperc> Increasing con cutoff atoms     5   10 from     0.28958E-01 to     0.29253E-01 ref=     2.3994    
 checkperc> Increasing con cutoff atoms   109  111 from     0.36462E-01 to     0.37554E-01 ref=     2.3908    
 checkperc> Increasing con cutoff atoms   109  113 from     0.28562E-01 to     0.29720E-01 ref=     2.5642    
 checkperc> Increasing con cutoff atoms   131  133 from     0.19145E-01 to     0.20758E-01 ref=     3.0973    
 checkperc> Increasing con cutoff atoms   134  135 from     0.11706E-01 to     0.11882E-01 ref=     1.5376    
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     777.73    
 decide> The unconnected minima in the chain and their distances are:
     8        9.19     3 
 

 tryconnect> Interpolation for minima 3_S and 8_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     47 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     72 steps, energy/image=    -180.3246555     RMS=77.40071610     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      3     8 dist=   17.00     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 0.1805 Dev= 0.82% S= 9.21 time= 1.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.45

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     884 steps. Energy=    -392.0698724       time=       2.16
 Minus side of path:                     928 steps. Energy=    -391.2244416       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.0698724 0.96404         -391.1058370 0.11860         -391.2244416   9.552   9.188   2.406  60.271
        Known (#8)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -391.4617264  2.8110        -388.6506790 0.73323        -389.3839080   5.780   5.229   6.907  20.993
   1     -389.3839080 0.37730        -389.0066100  2.2178        -391.2244416  16.140  13.727   4.698  30.865
   7     -391.2244416 0.11860        -391.1058370 0.96404        -392.0698724   9.552   9.188   2.406  60.271
   6     -392.0698724  1.3249        -390.7449373 0.69070        -391.4356342   3.649   3.439  16.448   8.816
   5     -391.4356342  1.5776        -389.8580234  1.4104        -391.2684032  30.117  26.863   2.352  61.643

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                                91.88
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             31901 time=          46.85 %= 51.0
 OPTIM> # of energy+gradient+Hessian calls=       353 time=           1.70 %=  1.9
