
 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 10:31:16 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=    -384.6548395     RMS force=    0.8971298036E-06
 OPTIM> Final energy  =    -381.4188464     RMS force=    0.9636664462E-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      25.69959396    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     13610.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.85     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    197 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    222 steps, energy/image=    -351.1402694     RMS=4.573757923     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   33.94     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 350 RMS= 0.0931 Dev= 3.98% S= 28.62 time= 4.73
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         41
 Converged to TS (number of iterations):         30
 DNEB run yielded 2 true transition state(s) time=   9.72

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1120 steps. Energy=    -388.4922376       time=       4.34
 Minus side of path:                     909 steps. Energy=    -385.8416558       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4922376  3.4385         -385.0537380 0.78792         -385.8416558  24.824  23.416   2.774  52.266
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    36   37 from     0.32709E-02 to     0.44140E-02 ref=    0.98112    
 checkperc> Increasing con cutoff atoms    37   38 from     0.97472E-02 to     0.10932E-01 ref=     2.1183    
 checkperc> Increasing con cutoff atoms    54   56 from     0.70431E-01 to     0.75921E-01 ref=     2.5937    
 checkperc> Increasing con cutoff atoms    55   56 from     0.91419E-02 to     0.95809E-02 ref=     1.5295    
 checkperc> Increasing con cutoff atoms    61   63 from     0.22086E-01 to     0.24204E-01 ref=     3.1061    
 checkperc> Increasing con cutoff atoms    63   64 from     0.21840E-01 to     0.22255E-01 ref=     2.1097    
 checkperc> Increasing con cutoff atoms    65   67 from     0.20327E-01 to     0.20477E-01 ref=     2.4054    
 checkperc> Increasing con cutoff atoms    84   86 from     0.35522E-01 to     0.36667E-01 ref=     2.0803    
 checkperc> Increasing con cutoff atoms   138  140 from     0.46806E-01 to     0.47926E-01 ref=     2.0881    
 checkperc> Increasing con cutoff atoms    13   26 from     0.22207E-01 to     0.22620E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms    38   39 from     0.39406E-02 to     0.49445E-02 ref=     1.5326    
 checkperc> Increasing con cutoff atoms    54   55 from     0.12762E-01 to     0.13264E-01 ref=     1.5336    
 checkperc> Increasing con cutoff atoms    60   63 from     0.16169E-01 to     0.16888E-01 ref=     2.0013    
 checkperc> Increasing con cutoff atoms    80   93 from     0.31068E-01 to     0.36645E-01 ref=     3.8068    
 checkperc> Increasing con cutoff atoms    85   86 from     0.10915E-01 to     0.11143E-01 ref=     1.0469    
 checkperc> Increasing con cutoff atoms   109  116 from     0.54721E-01 to     0.56566E-01 ref=     2.4525    
 checkperc> Increasing con cutoff atoms   109  117 from     0.98636E-01 to     0.10429     ref=     2.5330    
 checkperc> Increasing con cutoff atoms   114  117 from     0.22915E-01 to     0.24871E-01 ref=     1.9961    
 checkperc> Increasing con cutoff atoms   115  116 from     0.23584E-01 to     0.24970E-01 ref=     2.2545    
 checkperc> Increasing con cutoff atoms   138  139 from     0.62873E-02 to     0.63616E-02 ref=     1.4558    
 checkperc> Increasing con cutoff atoms   138  141 from     0.55225E-01 to     0.56529E-01 ref=     2.0530    
 checkperc> Increasing con cutoff atoms   138  142 from     0.51719E-01 to     0.53441E-01 ref=     2.0971    
 checkperc> Increasing con cutoff atoms   139  142 from     0.13645E-01 to     0.13788E-01 ref=     1.0488    
 checkperc> Increasing con cutoff atoms   140  142 from     0.51789E-01 to     0.54558E-01 ref=     1.6964    
 checkperc> Increasing con cutoff atoms   141  142 from     0.45431E-01 to     0.46355E-01 ref=     1.6865    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     983 steps. Energy=    -381.4188464       time=       2.56
 Minus side of path:                     980 steps. Energy=    -385.8416558       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4188464  4.2474         -377.1714459  8.6702         -385.8416558  24.238  19.557   2.517  57.618
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1184.7    
 decide> The unconnected minima in the chain and their distances are:
     4       10.57     1 
 

 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=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     37 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     62 steps, energy/image=    -379.7339983     RMS=.2443471640     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   11.48     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 0.2333 Dev= 1.13% S= 10.88 time= 0.41
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     953 steps. Energy=    -384.6548395       time=       2.20
 Minus side of path:                    1010 steps. Energy=    -388.4922376       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6548395 0.14249         -384.5123536  3.9799         -388.4922376  21.088  16.543   2.726  53.185
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -384.6548395 0.14249        -384.5123536  3.9799        -388.4922376  21.088  16.543   2.726  53.185
   1     -388.4922376  3.4385        -385.0537380 0.78792        -385.8416558  24.824  23.416   2.774  52.266
   2     -385.8416558  8.6702        -377.1714459  4.2474        -381.4188464  24.238  19.557   2.517  57.618

 Number of TS in the path       =      3
 Number of cycles               =      2

 Elapsed time=                                35.72
 OPTIM> # of energy calls=                          4 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             12891 time=          16.54 %= 46.3
 OPTIM> # of energy+gradient+Hessian calls=       111 time=           0.49 %=  1.4
