
 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> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/27/2012 at 22:11:56
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    107
 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=    17
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 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>  321 Cartesian coordinates will be optimised for  107 AMBER 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=    -533.6191208     RMS force=    0.9683795423E-06
 OPTIM> Final energy  =    -532.9906145     RMS force=    0.8336857817E-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      53.41526929    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.10410E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.99     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=     4
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    585 fraction=    0.990000 images=     5 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    610 steps, energy/image=    -496.7628075     RMS=1.827469887     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   50.01     Attempts, images and iterations=     0    15   525
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0368 Dev= 1.81% S= 54.16 time= 15.85
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  11.26

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     722 steps. Energy=    -533.3408020       time=       1.82
 Minus side of path:                     646 steps. Energy=    -533.0309019       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3408020 0.52074         -532.8200583 0.21084         -533.0309019  19.749  18.202   2.630  40.679
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    78   79 from     0.14428E-01 to     0.15082E-01 ref=     2.1424    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     47386.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.34     3     3       18.91     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=    10
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    187 fraction=    0.990000 images=     4 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    212 steps, energy/image=    -422.2290856     RMS=23.47512869     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   37.96     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0346 Dev= 1.36% S= 39.40 time= 8.64
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   9.88

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1345 steps. Energy=    -534.1642174       time=       4.55
 Minus side of path:                     809 steps. Energy=    -533.0826256       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1642174  2.4737         -531.6905526  1.3921         -533.0826256  54.146  49.140   1.917  55.825
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S 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=    55
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     87 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    112 steps, energy/image=    -524.0289149     RMS=1.691740005     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   22.25     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 210 RMS= 0.2371 Dev= 0.83% S= 19.59 time= 2.56
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   8.63

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     625 steps. Energy=    -533.5603891       time=       1.51
 Minus side of path:                     623 steps. Energy=    -533.8931573       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5603891 0.91382E-02     -533.5512509 0.34191         -533.8931573   7.285   7.176   2.965  36.084
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 checkperc> Increasing con cutoff atoms    93  102 from     0.47249E-02 to     0.55744E-02 ref=     3.4224    
 checkperc> Increasing con cutoff atoms   101  102 from     0.18279E-02 to     0.22043E-02 ref=     1.0796    
 checkperc> Increasing con cutoff atoms    89   92 from     0.13232     to     0.13779     ref=     2.4716    
 checkperc> Increasing con cutoff atoms    90   91 from     0.81833E-03 to     0.92180E-03 ref=     1.0906    
 checkperc> Increasing con cutoff atoms    93  104 from     0.58999E-02 to     0.59692E-02 ref=     2.1662    
 checkperc> Increasing con cutoff atoms   101  104 from     0.67225E-02 to     0.71771E-02 ref=     2.1598    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      4 missing connections, weight=     17771.    
 decide> The unconnected minima in the chain and their distances are:
     2        3.77     6     5       24.55     4     3       13.61     7     8        6.99     1 
 

 tryconnect> Interpolation for minima 2_F and 6_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=   104
 intlbfgs> Freezing     92 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=    -527.6454882     RMS=.5916216115E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   3.976     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.0313 Dev= 0.29% S= 3.78 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.86

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     647 steps. Energy=    -532.9906145       time=       1.57
 Minus side of path:                     657 steps. Energy=    -533.0826256       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9906145 0.40390E-02     -532.9865755 0.96050E-01     -533.0826256   3.795   3.771   4.644  23.042
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> Interpolation for minima 4_U 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=    33
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     87 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    112 steps, energy/image=    -444.9286040     RMS=28.43499149     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   29.22     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.2961 Dev= 1.02% S= 26.19 time= 4.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.22

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     668 steps. Energy=    -533.0309019       time=       1.69
 Minus side of path:                     975 steps. Energy=    -534.1642174       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0309019 0.10323         -532.9276755  1.2365         -534.1642174  26.196  24.666   2.692  39.753
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 3_F and 7_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=    69
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     39 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     64 steps, energy/image=    -516.3813131     RMS=8.474554648     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   19.10     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 175 RMS= 0.4257 Dev= 0.64% S= 13.85 time= 1.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.52

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     680 steps. Energy=    -533.3408020       time=       1.68
 Minus side of path:                     666 steps. Energy=    -533.5603891       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3408020 0.77874         -532.5620652 0.99832         -533.5603891  15.158  13.614   3.152  33.951
        Known (#3)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 8_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=   104
 intlbfgs> Freezing     92 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=    -513.7339492     RMS=9.545223683     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      1     8 dist=   14.42     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.1083 Dev= 0.71% S= 7.29 time= 1.14
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     648 steps. Energy=    -533.8931573       time=       1.58
 Minus side of path:                     641 steps. Energy=    -533.6191208       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.8931573 0.58103         -533.3121319 0.30699         -533.6191208   8.641   6.990  14.255   7.506
        Known (#8)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -533.6191208 0.30699        -533.3121319 0.58103        -533.8931573   8.641   6.990  14.255   7.506
   3     -533.8931573 0.34191        -533.5512509 0.91382E-02    -533.5603891   7.285   7.176   2.965  36.084
   6     -533.5603891 0.99832        -532.5620652 0.77874        -533.3408020  15.158  13.614   3.152  33.951
   1     -533.3408020 0.52074        -532.8200583 0.21084        -533.0309019  19.749  18.202   2.630  40.679
   5     -533.0309019 0.10323        -532.9276755  1.2365        -534.1642174  26.196  24.666   2.692  39.753
   2     -534.1642174  2.4737        -531.6905526  1.3921        -533.0826256  54.146  49.140   1.917  55.825
   4     -533.0826256 0.96050E-01    -532.9865755 0.40390E-02    -532.9906145   3.795   3.771   4.644  23.042

 Number of TS in the path       =      7
 Number of cycles               =      3

 Elapsed time=                               112.88
 OPTIM> # of energy calls=                         14 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             33676 time=          66.75 %= 59.1
 OPTIM> # of energy+gradient+Hessian calls=       437 time=          23.81 %= 21.1
