
 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 10:30:37 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=    -383.2392925     RMS force=    0.9238762667E-06
 OPTIM> Final energy  =    -388.2781099     RMS force=    0.8985343390E-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      15.20537286    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3524.5    
 decide> The unconnected minima in the chain and their distances are:
     2       15.20     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=    86
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     61 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     86 steps, energy/image=    -338.3213956     RMS=16.88126538     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   21.69     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 210 RMS= 0.3359 Dev= 1.93% S= 16.22 time= 1.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     984 steps. Energy=    -386.8331739       time=       2.30
 Minus side of path:                     964 steps. Energy=    -383.2392925       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8331739  4.4208         -382.4123907 0.82690         -383.2392925  15.706  13.528   2.820  51.410
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    13   15 from     0.46436E-01 to     0.46830E-01 ref=     2.5792    
 checkperc> Increasing con cutoff atoms    26   27 from     0.17686E-01 to     0.17692E-01 ref=     2.2563    
 checkperc> Increasing con cutoff atoms    64   71 from     0.57758E-02 to     0.67641E-02 ref=     1.5273    
 checkperc> Increasing con cutoff atoms   124  126 from     0.14135E-01 to     0.17313E-01 ref=     2.0489    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7049.0    
 decide> The unconnected minima in the chain and their distances are:
     2       15.20     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    86
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     62 fraction=    0.990000 images=    15 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     87 steps, energy/image=    -356.7939386     RMS=9.713162848     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   24.35     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 805 RMS= 0.0304 Dev= 4.88% S= 21.79 time= 23.98
 Following    2 images are candidates for TS:    4   11  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=   8.11

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     969 steps. Energy=    -386.8773057       time=       3.05
 Minus side of path:                     946 steps. Energy=    -383.2392925       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8773057  4.3949         -382.4823886 0.75690         -383.2392925  16.303  14.207   2.613  55.482
        *NEW* (Placed in 4)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    26   27 from     0.17692E-01 to     0.17722E-01 ref=     2.2563    
 checkperc> Increasing con cutoff atoms    26   29 from     0.53185E-01 to     0.53352E-01 ref=     2.8117    
 checkperc> Increasing con cutoff atoms   120  121 from     0.60051E-02 to     0.60339E-02 ref=     1.3731    
 checkperc> Increasing con cutoff atoms   124  125 from     0.37594E-02 to     0.38550E-02 ref=     1.3171    
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     967 steps. Energy=    -388.2781099       time=       2.72
 Minus side of path:                     969 steps. Energy=    -387.4174888       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2781099  2.9638         -385.3143069  2.1032         -387.4174888   5.765   4.562  28.658   5.060
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    96  104 from     0.11942E-01 to     0.12311E-01 ref=     2.7181    
 checkperc> Increasing con cutoff atoms    97  104 from     0.68084E-02 to     0.68876E-02 ref=     2.3303    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3653.0    
 decide> The unconnected minima in the chain and their distances are:
     5       15.39     1 
 

 tryconnect> Interpolation for minima 1_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=    86
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     76 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    101 steps, energy/image=    -374.7505984     RMS=.9814758813     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   21.68     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 210 RMS= 0.7823 Dev= 1.36% S= 15.81 time= 1.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        159
 DNEB run yielded 1 true transition state(s) time=  12.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     948 steps. Energy=    -387.4174888       time=       3.52
 Minus side of path:                    1071 steps. Energy=    -389.3873024       time=       4.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4174888 0.11205         -387.3054379  2.0819         -389.3873024  29.821  29.097   2.266  64.003
        Known (#5)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    31   34 from     0.98748E-01 to     0.10159     ref=     3.0899    
 checkperc> Increasing con cutoff atoms    33   34 from     0.48388E-01 to     0.56547E-01 ref=     3.8758    
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6610.5    
 decide> The unconnected minima in the chain and their distances are:
     5       18.75     3 
 

 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=    59
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     88 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    113 steps, energy/image=    -332.9396294     RMS=18.96038855     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   24.00     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 245 RMS= 0.0730 Dev= 0.68% S= 19.11 time= 2.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.32

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     993 steps. Energy=    -387.4174888       time=       2.42
 Minus side of path:                     982 steps. Energy=    -386.8331739       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.4174888  2.1309         -385.2865499  1.5466         -386.8331739  19.090  18.752   2.219  65.338
        Known (#5)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -383.2392925 0.82690        -382.4123907  4.4208        -386.8331739  15.706  13.528   2.820  51.410
   5     -386.8331739  1.5466        -385.2865499  2.1309        -387.4174888  19.090  18.752   2.219  65.338
   3     -387.4174888  2.1032        -385.3143069  2.9638        -388.2781099   5.765   4.562  28.658   5.060

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                                88.00
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             38398 time=          48.24 %= 54.8
 OPTIM> # of energy+gradient+Hessian calls=       269 time=           1.18 %=  1.3
