
 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)@comp32.ch.
                 Created on  5/28/12 at 10:36: 9 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=    -391.2758247     RMS force=    0.9963919870E-06
 OPTIM> Final energy  =    -389.1369071     RMS force=    0.9916125561E-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      24.56344210    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     14582.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.41     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=    32
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    160 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    185 steps, energy/image=    -353.4957209     RMS=10.07663237     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   31.92     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 315 RMS= 0.0589 Dev= 0.46% S= 25.53 time= 3.68
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.74

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     944 steps. Energy=    -391.4943003       time=       2.76
 Minus side of path:                     955 steps. Energy=    -391.1623981       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4943003 0.58140         -390.9129025 0.24950         -391.1623981  10.365   9.301   2.192  66.150
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    57   59 from     0.44244E-02 to     0.50765E-02 ref=     1.2333    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     11981.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.66     3     4        6.79     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    103 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -330.1186021     RMS=13.03542199     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   28.82     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0457 Dev= 0.63% S= 23.60 time= 2.91
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.08

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     955 steps. Energy=    -389.1345980       time=       2.28
 Minus side of path:                     956 steps. Energy=    -389.1369071       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1345980 0.42189E-01     -389.0924085 0.44499E-01     -389.1369071   1.717   1.708   2.235  64.869
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F 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=   139
 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=    -384.9827416     RMS=3.476846548     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   13.82     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.0400 Dev= 0.69% S= 6.82 time= 0.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   5.30

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     983 steps. Energy=    -391.2758247       time=       3.23
 Minus side of path:                     984 steps. Energy=    -391.1623981       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.2758247 0.20710         -391.0687210 0.93677E-01     -391.1623981   7.914   6.786   2.336  62.073
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     12403.    
 decide> The unconnected minima in the chain and their distances are:
     5       23.12     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=    42
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    230 fraction=    0.990000 images=     4 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    255 steps, energy/image=    -381.0442134     RMS=.5291227546     images=   4
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   38.00     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 385 RMS= 0.0323 Dev= 1.29% S= 24.08 time= 5.45
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.82

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     966 steps. Energy=    -391.4943003       time=       2.99
 Minus side of path:                     995 steps. Energy=    -389.1345980       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4943003  3.5996         -387.8946736  1.2399         -389.1345980  23.822  23.127   2.677  54.155
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -391.2758247 0.20710        -391.0687210 0.93677E-01    -391.1623981   7.914   6.786   2.336  62.073
   1     -391.1623981 0.24950        -390.9129025 0.58140        -391.4943003  10.365   9.301   2.192  66.150
   4     -391.4943003  3.5996        -387.8946736  1.2399        -389.1345980  23.822  23.127   2.677  54.155
   2     -389.1345980 0.42189E-01    -389.0924085 0.44499E-01    -389.1369071   1.717   1.708   2.235  64.869

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

 Elapsed time=                                55.40
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             21941 time=          27.63 %= 49.9
 OPTIM> # of energy+gradient+Hessian calls=       122 time=           0.59 %=  1.1
