
 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 10:33:33 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=    -384.8788257     RMS force=    0.9427911224E-06
 OPTIM> Final energy  =    -389.2285387     RMS force=    0.8524536618E-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      14.48156056    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2929.8    
 decide> The unconnected minima in the chain and their distances are:
     2       14.29     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=   134
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     41 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     66 steps, energy/image=    -377.5467146     RMS=.7681715987     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   16.40     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 140 RMS= 1.3442 Dev= 1.20% S= 15.18 time= 0.77
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         61
 Converged to TS (number of iterations):         30
 DNEB run yielded 2 true transition state(s) time=   9.59

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     906 steps. Energy=    -384.8788257       time=       2.36
 Minus side of path:                     914 steps. Energy=    -384.7878273       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8788257 0.92136E-01     -384.7866899 0.11374E-02     -384.7878273   1.644   1.641   3.172  45.712
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   137  138 from     0.95575E-02 to     0.95645E-02 ref=     1.5258    
 checkperc> Increasing con cutoff atoms   137  139 from     0.50023E-01 to     0.50050E-01 ref=     2.4704    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     963 steps. Energy=    -390.1699385       time=       2.90
 Minus side of path:                     943 steps. Energy=    -389.0734643       time=       2.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1699385  1.2031         -388.9668579 0.10661         -389.0734643   3.674   3.509  22.719   6.382
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms   130  134 from     0.30207E-01 to     0.32511E-01 ref=     2.4656    
 checkperc> Increasing con cutoff atoms   131  134 from     0.63963E-01 to     0.65487E-01 ref=     2.7969    
 checkperc> Increasing con cutoff atoms   132  135 from     0.46211E-01 to     0.50023E-01 ref=     2.4437    
 checkperc> Increasing con cutoff atoms   107  109 from     0.68555E-02 to     0.74854E-02 ref=     1.4557    
 checkperc> Increasing con cutoff atoms   132  135 from     0.50023E-01 to     0.52814E-01 ref=     2.4437    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     748.84    
 decide> The unconnected minima in the chain and their distances are:
     2        4.80     5     4        8.60     1 
 

 tryconnect> Interpolation for minima 2_F and 5_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=   138
 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=    -383.3955407     RMS=.7275356689     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   12.17     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 105 RMS= 0.0710 Dev= 0.69% S= 4.82 time= 0.45
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.84

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     914 steps. Energy=    -389.2285387       time=       2.30
 Minus side of path:                     939 steps. Energy=    -389.0734643       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.2285387 0.49627         -388.7322696 0.34119         -389.0734643   5.006   4.803   6.877  21.086
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 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=   136
 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=    -376.8304186     RMS=5.161133523     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   16.53     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 0.2584 Dev= 1.06% S= 9.04 time= 0.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        169
 DNEB run yielded 1 true transition state(s) time=  15.76

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1098 steps. Energy=    -390.0897162       time=       2.88
 Minus side of path:                    1059 steps. Energy=    -384.7878273       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.0897162  6.5711         -383.5186416  1.2692         -384.7878273  47.444  43.253   2.175  66.658
        *NEW* (Placed in 6)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    64   65 from     0.56828E-02 to     0.64299E-02 ref=     1.5338    
 checkperc> Increasing con cutoff atoms    89   92 from     0.16087E-01 to     0.18677E-01 ref=     1.9994    
 checkperc> Increasing con cutoff atoms   105  107 from     0.65917E-02 to     0.70926E-02 ref=     1.3330    
 checkperc> Increasing con cutoff atoms   132  133 from     0.45404E-02 to     0.58058E-02 ref=    0.97906    
 checkperc> Increasing con cutoff atoms   132  145 from     0.11879     to     0.15689     ref=     3.4928    
 checkperc> Increasing con cutoff atoms   137  138 from     0.95645E-02 to     0.10296E-01 ref=     1.5258    
 checkperc> Increasing con cutoff atoms   137  139 from     0.50050E-01 to     0.51943E-01 ref=     2.4704    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     799.99    
 decide> The unconnected minima in the chain and their distances are:
     4        9.27     3 
 

 tryconnect> Interpolation for minima 3_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=   135
 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=    -375.3212179     RMS=5.034150299     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   17.01     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 0.2004 Dev= 2.33% S= 9.88 time= 1.18
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     917 steps. Energy=    -384.8788257       time=       3.19
 Minus side of path:                     908 steps. Energy=    -390.1699385       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8788257  3.3989         -381.4799028  8.6900         -390.1699385  12.262   8.614  20.080   7.221
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -384.8788257  3.3989        -381.4799028  8.6900        -390.1699385  12.262   8.614  20.080   7.221
   2     -390.1699385  1.2031        -388.9668579 0.10661        -389.0734643   3.674   3.509  22.719   6.382
   3     -389.0734643 0.34119        -388.7322696 0.49627        -389.2285387   5.006   4.803   6.877  21.086

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

 Elapsed time=                                64.88
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             17690 time=          23.63 %= 36.4
 OPTIM> # of energy+gradient+Hessian calls=       312 time=           1.39 %=  2.1
