
 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)@comp34.ch.
                 Created on  5/28/12 at 10:36:47 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=    -394.4105553     RMS force=    0.9870129746E-06
 OPTIM> Final energy  =    -399.1231226     RMS force=    0.9752553714E-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      15.14929648    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2840.8    
 decide> The unconnected minima in the chain and their distances are:
     2       14.15     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=    90
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     82 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    107 steps, energy/image=    -383.4630922     RMS=1.112564905     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   17.42     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 175 RMS= 0.6648 Dev= 2.18% S= 16.59 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.10

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     823 steps. Energy=    -394.8134753       time=       1.86
 Minus side of path:                     947 steps. Energy=    -399.1231226       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.8134753 0.54991E-01     -394.7584848  4.3646         -399.1231226  10.525   9.476   3.489  41.563
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    27   28 from     0.35302E-02 to     0.36249E-02 ref=    0.98208    
 checkperc> Increasing con cutoff atoms    76   78 from     0.36853E-02 to     0.37749E-02 ref=     1.3346    
 checkperc> Increasing con cutoff atoms    81   82 from     0.98594E-02 to     0.10526E-01 ref=     1.5299    
 checkperc> Increasing con cutoff atoms    98  103 from     0.15749E-02 to     0.19905E-02 ref=     1.3862    
 checkperc> Increasing con cutoff atoms   102  104 from     0.15144E-02 to     0.26773E-02 ref=     1.3855    
 checkperc> Increasing con cutoff atoms   120  125 from     0.86965E-02 to     0.94320E-02 ref=     2.1598    
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     885.88    
 decide> The unconnected minima in the chain and their distances are:
     3        9.59     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=   118
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     55 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     80 steps, energy/image=    -387.2887915     RMS=1.247508207     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   11.38     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.6367 Dev= 1.33% S= 11.19 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.52

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     965 steps. Energy=    -397.4049495       time=       3.60
 Minus side of path:                     884 steps. Energy=    -396.2382323       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.4049495  5.5319         -391.8730986  4.3651         -396.2382323  15.699   9.538   2.894  50.106
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    16   24 from     0.82423E-02 to     0.85552E-02 ref=     2.7176    
 checkperc> Increasing con cutoff atoms    98  103 from     0.19905E-02 to     0.26639E-02 ref=     1.3862    
 checkperc> Increasing con cutoff atoms   102  104 from     0.26773E-02 to     0.29196E-02 ref=     1.3855    
 checkperc> Increasing con cutoff atoms   120  124 from     0.33553E-02 to     0.41866E-02 ref=     1.3813    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1085.7    
 decide> The unconnected minima in the chain and their distances are:
     3        7.36     4     5        8.81     1 
 

 tryconnect> Interpolation for minima 3_F 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=   133
 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=    -389.3067982     RMS=2.347924161     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   14.21     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.1135 Dev= 0.60% S= 7.45 time= 0.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     892 steps. Energy=    -397.4049495       time=       2.91
 Minus side of path:                     846 steps. Energy=    -394.8134753       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.4049495  2.6139         -394.7910273 0.22448E-01     -394.8134753   7.819   7.359   2.785  52.055
        Known (#4)                                              Known (#3)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 1_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=   123
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     34 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     59 steps, energy/image=    -387.6388532     RMS=2.073029474     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   10.40     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.4782 Dev= 1.59% S= 9.71 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.53
 isnewts> transition state is the same as number        2 energy=     -391.8730985697
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     964 steps. Energy=    -397.4049495       time=       2.37
 Minus side of path:                     898 steps. Energy=    -396.2382323       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.4049495  5.5319         -391.8730986  4.3651         -396.2382323  15.699   9.537   2.891  50.160
        Known (#4)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1372.1    
 decide> The unconnected minima in the chain and their distances are:
     5        8.81     1 
 

 tryconnect> Interpolation for minima 1_S and 5_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   123
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     31 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     56 steps, energy/image=    -389.0218868     RMS=.2355817419     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   10.42     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 805 RMS= 0.0771 Dev= 5.14% S= 14.38 time= 25.76
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.39
 isnewts> transition state is the same as number        2 energy=     -391.8730985699
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1771.8    
 decide> The unconnected minima in the chain and their distances are:
     3        9.59     1 
 

 tryconnect> Interpolation for minima 1_S and 3_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   118
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     57 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     82 steps, energy/image=    -388.9669885     RMS=1.225986726     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   14.24     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      12.76281562    
 Double-ended search iterations= 805 RMS= 0.1636 Dev= 2.74% S= 14.30 time= 25.35
 Following    2 images are candidates for TS:    8   17  
 Converged to TS (number of iterations):         24
 Converged to TS (number of iterations):         23
 DNEB run yielded 2 true transition state(s) time=   6.37
 isnewts> transition state is the same as number        2 energy=     -391.8730985696
 tryconnect> Will not repeat search for TS      2 same as TS      2

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     940 steps. Energy=    -394.4105553       time=       2.17
 Minus side of path:                     882 steps. Energy=    -394.8134753       time=       1.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4105553 0.44372         -393.9668382 0.84664         -394.8134753  10.306   9.594   3.607  40.199
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -394.4105553 0.44372        -393.9668382 0.84664        -394.8134753  10.306   9.594   3.607  40.199
   1     -394.8134753 0.54991E-01    -394.7584848  4.3646        -399.1231226  10.525   9.476   3.489  41.563

 Number of TS in the path       =      2
 Number of cycles               =      5

 Elapsed time=                               112.20
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             55716 time=          74.22 %= 66.1
 OPTIM> # of energy+gradient+Hessian calls=       278 time=           1.28 %=  1.1
