
 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)@comp27.ch.
                 Created on  5/28/12 at 10:34:57 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=    -382.3049686     RMS force=    0.9850491574E-06
 OPTIM> Final energy  =    -379.1307139     RMS force=    0.9581488249E-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      18.57794196    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     6320.8    
 decide> The unconnected minima in the chain and their distances are:
     2       18.47     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=    39
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    152 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    177 steps, energy/image=    -300.6805613     RMS=25.40087996     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   27.36     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 280 RMS= 1.1385 Dev= 1.27% S= 20.22 time= 2.82
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.56

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     960 steps. Energy=    -384.0625319       time=       2.14
 Minus side of path:                     962 steps. Energy=    -383.1732420       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0625319  2.9590         -381.1035731  2.0697         -383.1732420  10.659  10.004  20.248   7.161
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    38   53 from     0.77078E-01 to     0.77112E-01 ref=     2.4918    
 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=     6057.1    
 decide> The unconnected minima in the chain and their distances are:
     2       18.04     4     4        5.48     1 
 

 tryconnect> Interpolation for minima 2_F 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=    33
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    147 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    172 steps, energy/image=    -275.5139369     RMS=36.26640015     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   25.00     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 245 RMS= 2.6343 Dev= 0.77% S= 18.84 time= 2.14
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.25

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     995 steps. Energy=    -379.1307139       time=       2.27
 Minus side of path:                    1289 steps. Energy=    -383.1732420       time=       3.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.1307139 0.57123E-01     -379.0735905  4.0997         -383.1732420  19.437  18.056   1.946  74.505
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_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=   140
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -377.5306656     RMS=.3346737883     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   6.974     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.2515 Dev= 0.61% S= 5.88 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        248
 DNEB run yielded 1 true transition state(s) time=  28.47

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1086 steps. Energy=    -382.3049686       time=       2.62
 Minus side of path:                    1038 steps. Energy=    -382.2473276       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.3049686  1.6197         -380.6853078  1.5620         -382.2473276  43.645  34.446   2.091  69.337
        Known (#1)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    34   35 from     0.28766E-02 to     0.28872E-02 ref=     1.2338    
 checkperc> Increasing con cutoff atoms    36   38 from     0.34052E-02 to     0.34428E-02 ref=     1.4561    
 checkperc> Increasing con cutoff atoms    38   53 from     0.77112E-01 to     0.81337E-01 ref=     2.4918    
 checkperc> Increasing con cutoff atoms    53   54 from     0.25226E-01 to     0.25259E-01 ref=     2.1152    
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     182.53    
 decide> The unconnected minima in the chain and their distances are:
     3        5.67     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -377.7880921     RMS=.9715758466     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   14.14     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 0.2023 Dev= 1.82% S= 6.06 time= 0.71
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   5.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     968 steps. Energy=    -382.3049686       time=       2.15
 Minus side of path:                     968 steps. Energy=    -382.3821617       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.3049686 0.12100         -382.1839715 0.19819         -382.3821617   7.065   6.706   3.513  41.278
        Known (#1)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    28   29 from     0.13593E-01 to     0.13855E-01 ref=     2.0966    
 checkperc> Increasing con cutoff atoms    36   38 from     0.34428E-02 to     0.36891E-02 ref=     1.4561    
 checkperc> Increasing con cutoff atoms    53   54 from     0.25259E-01 to     0.25739E-01 ref=     2.1152    
 checkperc> Increasing con cutoff atoms    55   56 from     0.91419E-02 to     0.96296E-02 ref=     1.5295    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     330.94    
 decide> The unconnected minima in the chain and their distances are:
     4        5.48     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=   140
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -378.3197342     RMS=.7737388028     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   8.494     Attempts, images and iterations=     1    19   665
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 665 RMS= 0.0077 Dev= 3.24% S= 7.59 time= 15.78
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.77

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     975 steps. Energy=    -382.3049686       time=       2.17
 Minus side of path:                     987 steps. Energy=    -383.1732420       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.3049686  2.3953         -379.9096211  3.2636         -383.1732420   6.113   5.488  33.995   4.265
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -382.3049686  2.3953        -379.9096211  3.2636        -383.1732420   6.113   5.488  33.995   4.265
   2     -383.1732420  4.0997        -379.0735905 0.57123E-01    -379.1307139  19.437  18.056   1.946  74.505

 Number of TS in the path       =      2
 Number of cycles               =      4

 Elapsed time=                                90.90
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             35164 time=          42.49 %= 46.7
 OPTIM> # of energy+gradient+Hessian calls=       383 time=           1.47 %=  1.6
