
 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)@comp28.ch.
                 Created on  5/28/12 at 10:33:19 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=    -386.2430137     RMS force=    0.9843305590E-06
 OPTIM> Final energy  =    -393.3706425     RMS force=    0.9507813873E-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      24.18079152    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     13947.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.05     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=    23
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    256 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    281 steps, energy/image=    -365.0551442     RMS=.9451171959     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   36.96     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 385 RMS= 0.3695 Dev= 3.08% S= 28.23 time= 5.83
 Following    2 images are candidates for TS:    2    8  
 Converged to TS (number of iterations):         52
 Converged to TS (number of iterations):        212
 DNEB run yielded 2 true transition state(s) time=  37.02

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     955 steps. Energy=    -386.2430137       time=       2.56
 Minus side of path:                    1091 steps. Energy=    -393.7136306       time=       3.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2430137 0.15732         -386.0856936  7.6279         -393.7136306  23.071  21.961   2.318  62.556
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    94   99 from     0.34018E-01 to     0.34494E-01 ref=     2.5460    
 checkperc> Increasing con cutoff atoms    96   98 from     0.23573E-02 to     0.24356E-02 ref=     1.3742    
 checkperc> Increasing con cutoff atoms    96  103 from     0.95100E-02 to     0.97442E-02 ref=     2.3385    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     900 steps. Energy=    -393.0090907       time=       2.97
 Minus side of path:                     926 steps. Energy=    -394.6417674       time=       2.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.0090907 0.26722E-01     -392.9823686  1.6594         -394.6417674   6.529   6.245   3.091  46.906
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    93   94 from     0.15760E-01 to     0.15976E-01 ref=     1.5397    
 checkperc> Increasing con cutoff atoms    94   99 from     0.34494E-01 to     0.36298E-01 ref=     2.5460    
 checkperc> Increasing con cutoff atoms    96   98 from     0.24356E-02 to     0.25124E-02 ref=     1.3742    
 checkperc> Increasing con cutoff atoms    96  102 from     0.61388E-02 to     0.65440E-02 ref=     2.4035    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     629.53    
 decide> The unconnected minima in the chain and their distances are:
     2        8.56     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     28 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     53 steps, energy/image=    -376.8992966     RMS=6.486434308     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   16.80     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.6463 Dev= 1.43% S= 9.83 time= 1.22
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     901 steps. Energy=    -393.3706425       time=       2.24
 Minus side of path:                     923 steps. Energy=    -394.6417674       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3706425  1.9771         -391.3935716  3.2482         -394.6417674   9.009   7.892  24.773   5.853
        Known (#2)                                              Known (#5)
 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      3 steps with      1 missing connections, weight=     219.98    
 decide> The unconnected minima in the chain and their distances are:
     5        6.03     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=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     31 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     56 steps, energy/image=    -388.7913456     RMS=.8317766382     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   7.473     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.4284 Dev= 0.59% S= 6.52 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     899 steps. Energy=    -393.7136306       time=       2.54
 Minus side of path:                     955 steps. Energy=    -394.6417674       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.7136306  2.5247         -391.1889544  3.4528         -394.6417674   6.949   6.033  29.127   4.978
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.2430137 0.15732        -386.0856936  7.6279        -393.7136306  23.071  21.961   2.318  62.556
   4     -393.7136306  2.5247        -391.1889544  3.4528        -394.6417674   6.949   6.033  29.127   4.978
   3     -394.6417674  3.2482        -391.3935716  1.9771        -393.3706425   9.009   7.892  24.773   5.853

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

 Elapsed time=                                74.77
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             18607 time=          25.50 %= 34.1
 OPTIM> # of energy+gradient+Hessian calls=       307 time=           1.50 %=  2.0
