
 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)@comp33.ch.
                 Created on  5/28/12 at 10:33:38 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=    -386.6206187     RMS force=    0.9496290450E-06
 OPTIM> Final energy  =    -390.3597304     RMS force=    0.9799319487E-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      23.15813081    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     12268.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.04     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=    72
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    129 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    154 steps, energy/image=    -376.9685439     RMS=.7000499341     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   28.75     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 280 RMS= 0.0660 Dev= 1.40% S= 25.79 time= 3.20
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=  13.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     935 steps. Energy=    -387.3417043       time=       3.39
 Minus side of path:                     970 steps. Energy=    -390.3597304       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3417043 0.12784         -387.2138617  3.1459         -390.3597304  23.314  22.581   8.145  17.803
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    14   24 from     0.35541E-01 to     0.35884E-01 ref=     5.2679    
 checkperc> Increasing con cutoff atoms   120  125 from     0.91888E-02 to     0.92071E-02 ref=     2.1617    
 checkperc> Increasing con cutoff atoms   120  126 from     0.12102E-01 to     0.12954E-01 ref=     3.1139    
 checkperc> Increasing con cutoff atoms   120  128 from     0.24745E-01 to     0.25271E-01 ref=     3.6710    
 checkperc> Increasing con cutoff atoms   120  129 from     0.23774E-01 to     0.24278E-01 ref=     4.0204    
 checkperc> Increasing con cutoff atoms   122  124 from     0.60793E-02 to     0.61571E-02 ref=     2.1496    
 checkperc> Increasing con cutoff atoms   122  125 from     0.18412E-02 to     0.19132E-02 ref=     1.3371    
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     280.47    
 decide> The unconnected minima in the chain and their distances are:
     3        6.54     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=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     29 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     54 steps, energy/image=    -382.0916184     RMS=.9676449314     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   8.484     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.2468 Dev= 0.60% S= 6.91 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     932 steps. Energy=    -387.9483688       time=       2.90
 Minus side of path:                     812 steps. Energy=    -386.6206187       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.9483688  1.7835         -386.1648635 0.45576         -386.6206187   3.371   3.002  19.651   7.379
        *NEW* (Placed in 4)                                     Known (#1)
 checkperc> Increasing con cutoff atoms   120  125 from     0.92071E-02 to     0.92190E-02 ref=     2.1617    
 checkperc> Increasing con cutoff atoms   120  126 from     0.12954E-01 to     0.12984E-01 ref=     3.1139    
 checkperc> Increasing con cutoff atoms   122  124 from     0.61571E-02 to     0.61582E-02 ref=     2.1496    
 checkperc> Increasing con cutoff atoms   122  125 from     0.19132E-02 to     0.19187E-02 ref=     1.3371    
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     148.07    
 decide> The unconnected minima in the chain and their distances are:
     3        5.29     4 
 

 tryconnect> Interpolation for minima 3_F and 4_S 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     25 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     50 steps, energy/image=    -382.9716596     RMS=.3429271683     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   6.912     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.4254 Dev= 0.32% S= 5.67 time= 0.20
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.81
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     296.15    
 decide> The unconnected minima in the chain and their distances are:
     3        5.29     4 
 

 tryconnect> Interpolation for minima 3_F and 4_S 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     29 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     54 steps, energy/image=    -383.3797006     RMS=.2611688895     images=  15
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   7.842     Attempts, images and iterations=     1    18   630
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 630 RMS= 0.0170 Dev= 1.67% S= 6.92 time= 16.40
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.37

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     905 steps. Energy=    -387.3417043       time=       2.85
 Minus side of path:                     952 steps. Energy=    -387.9483688       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3417043  2.4751         -384.8665593  3.0818         -387.9483688   5.962   5.288  32.187   4.505
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -386.6206187 0.45576        -386.1648635  1.7835        -387.9483688   3.371   3.002  19.651   7.379
   3     -387.9483688  3.0818        -384.8665593  2.4751        -387.3417043   5.962   5.288  32.187   4.505
   1     -387.3417043 0.12784        -387.2138617  3.1459        -390.3597304  23.314  22.581   8.145  17.803

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

 Elapsed time=                                79.52
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             25091 time=          35.14 %= 44.2
 OPTIM> # of energy+gradient+Hessian calls=       366 time=           1.85 %=  2.3
