
 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)@comp30.ch.
                 Created on  5/28/12 at 10:32:53 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=    -381.6110679     RMS force=    0.8935358918E-06
 OPTIM> Final energy  =    -385.8804130     RMS force=    0.7992771015E-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      15.36833949    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3639.7    
 decide> The unconnected minima in the chain and their distances are:
     2       15.37     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=    88
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     66 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     91 steps, energy/image=    -323.8388026     RMS=20.31836403     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   22.26     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 210 RMS= 0.3127 Dev= 0.87% S= 15.98 time= 1.61
 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 1 ...
 Plus  side of path:                    1351 steps. Energy=    -382.0774484       time=       4.30
 Minus side of path:                     998 steps. Energy=    -385.8845121       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.89015         -381.1872984  4.6972         -385.8845121  31.091  27.295   2.034  71.279
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   116  117 from     0.54679E-02 to     0.55543E-02 ref=    0.98098    
 checkperc> Increasing con cutoff atoms   116  130 from     0.10200     to     0.10213     ref=     2.5096    
 checkperc> Increasing con cutoff atoms   119  130 from     0.58204E-01 to     0.59427E-01 ref=     2.5283    
 checkperc> Increasing con cutoff atoms   130  134 from     0.17283E-01 to     0.17357E-01 ref=     2.4471    
 checkperc> Increasing con cutoff atoms   132  143 from     0.55411E-01 to     0.55464E-01 ref=     2.4908    
 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=     2602.2    
 decide> The unconnected minima in the chain and their distances are:
     2        3.45     4     4       13.67     1 
 

 tryconnect> Interpolation for minima 2_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=   145
 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=    -381.9662342     RMS=.9985979401E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   3.727     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0220 Dev= 0.33% S= 3.46 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.97

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     954 steps. Energy=    -385.8804130       time=       2.57
 Minus side of path:                     976 steps. Energy=    -385.8845121       time=       2.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8804130 0.90967E-01     -385.7894459 0.95066E-01     -385.8845121   3.488   3.454   2.133  67.973
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 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=    97
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     50 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     75 steps, energy/image=    -315.8219597     RMS=18.53481459     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   20.82     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 210 RMS= 0.1662 Dev= 1.14% S= 14.07 time= 1.60
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.52
 isnewts> transition state is the same as number        1 energy=     -381.1872983662
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1334 steps. Energy=    -382.0774484       time=       5.12
 Minus side of path:                     964 steps. Energy=    -385.8845121       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.89015         -381.1872984  4.6972         -385.8845121  31.091  27.296   2.034  71.289
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5121.8    
 decide> The unconnected minima in the chain and their distances are:
     4       13.67     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=    97
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     61 fraction=    0.990000 images=    15 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     86 steps, energy/image=    -325.3449875     RMS=17.20254120     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   24.96     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 805 RMS= 0.0601 Dev= 2.35% S= 18.26 time= 23.88
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.21
 isnewts> transition state is the same as number        1 energy=     -381.1872983662
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7279.4    
 decide> The unconnected minima in the chain and their distances are:
     2       15.37     1 
 

 tryconnect> Interpolation for minima 1_S and 2_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=    88
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    128 fraction=    0.990000 images=    15 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    153 steps, energy/image=    -120.4128661     RMS=995.6125514     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   31.07     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.7242371427E-01
 Double-ended search iterations= 805 RMS= 0.0094 Dev= 2.60% S= 21.72 time= 24.10
 Following    2 images are candidates for TS:    4   21  
 Converged to TS (number of iterations):         22
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=   7.95
 isnewts> transition state is the same as number        1 energy=     -381.1872983662
 tryconnect> Will not repeat search for TS      1 same as TS      1
 isnewts> transition state is the same as number        2 energy=     -385.7894459238
 tryconnect> Try the path again for ts      2 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:                     939 steps. Energy=    -385.8845121       time=       2.10
 Minus side of path:                     978 steps. Energy=    -385.8804130       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8845121 0.95066E-01     -385.7894459 0.90967E-01     -385.8804130   3.488   3.454   2.133  67.972
        Known (#4)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13797.    
 decide> The unconnected minima in the chain and their distances are:
     3       23.96     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=    43
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    105 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    130 steps, energy/image=    -360.8944031     RMS=11.95832423     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   28.94     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0182 Dev= 0.42% S= 24.32 time= 2.84
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.06

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1133 steps. Energy=    -382.0774484       time=       3.69
 Minus side of path:                     926 steps. Energy=    -381.6110679       time=       3.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.0774484 0.50451         -381.5729368 0.38131E-01     -381.6110679  24.461  23.965   2.223  65.219
        Known (#3)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -381.6110679 0.38131E-01    -381.5729368 0.50451        -382.0774484  24.461  23.965   2.223  65.219
   1     -382.0774484 0.89015        -381.1872984  4.6972        -385.8845121  31.091  27.295   2.034  71.279
   2     -385.8845121 0.95066E-01    -385.7894459 0.90967E-01    -385.8804130   3.488   3.454   2.133  67.973

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               116.64
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             60488 time=          74.82 %= 64.1
 OPTIM> # of energy+gradient+Hessian calls=       198 time=           0.82 %=  0.7
