
 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 10:31:19 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=    -386.6466841     RMS force=    0.9886400717E-06
 OPTIM> Final energy  =    -391.7815997     RMS force=    0.9914255053E-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      33.28074286    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     36948.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.27     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=    23
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    131 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    156 steps, energy/image=    -260.1093558     RMS=18.37307643     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   38.22     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0461 Dev= 2.11% S= 37.27 time= 5.45
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.00

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1518 steps. Energy=    -391.1577527       time=       5.58
 Minus side of path:                    1110 steps. Energy=    -386.6466841       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.1577527  6.7530         -384.4047873  2.2419         -386.6466841  48.823  42.681   3.085  47.007
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     9304.9    
 decide> The unconnected minima in the chain and their distances are:
     2       21.01     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S 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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    102 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    127 steps, energy/image=    -385.8377440     RMS=.2607186041     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   24.26     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0648 Dev= 1.59% S= 22.70 time= 2.35
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.80
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     18610.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.01     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S 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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=    16 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -385.5321237     RMS=.5295721224     images=  16
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   29.68     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0815 Dev= 10.04% S= 25.70 time= 25.15
 Following    3 images are candidates for TS:    8   20   22  
 Converged to TS (number of iterations):         70
 Converged to TS (number of iterations):         55
 Converged to TS (number of iterations):         20
 DNEB run yielded 3 true transition state(s) time=  14.41

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     915 steps. Energy=    -391.7815997       time=       2.29
 Minus side of path:                     957 steps. Energy=    -391.9827399       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7815997 0.58247E-01     -391.7233524 0.25939         -391.9827399   5.579   5.133   5.170  28.044
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     910 steps. Energy=    -391.7507267       time=       2.09
 Minus side of path:                     898 steps. Energy=    -391.4967252       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7507267 0.26198         -391.4887450 0.79802E-02     -391.4967252   1.928   1.912  23.598   6.145
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     931 steps. Energy=    -391.4967252       time=       2.26
 Minus side of path:                     914 steps. Energy=    -391.1577527       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4967252 0.44017         -391.0565535 0.10120         -391.1577527   4.582   3.967   5.099  28.436
        Known (#6)                                              Known (#3)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     6419.2    
 decide> The unconnected minima in the chain and their distances are:
     4       18.57     5 
 

 tryconnect> Interpolation for minima 4_F and 5_S 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     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -376.5146141     RMS=9.345073046     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   27.27     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 280 RMS= 0.0694 Dev= 2.06% S= 20.24 time= 3.04
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         52
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time=  39.18

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1146 steps. Energy=    -398.8414606       time=       4.44
 Minus side of path:                     861 steps. Energy=    -391.9827399       time=       1.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.8414606  6.9700         -391.8714114 0.11133         -391.9827399  23.130  21.763  15.569   9.314
        *NEW* (Placed in 7)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    26   28 from     0.13377E-01 to     0.15151E-01 ref=     3.1180    
 checkperc> Increasing con cutoff atoms   139  140 from     0.10584E-01 to     0.10594E-01 ref=     1.0474    
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     543.99    
 decide> The unconnected minima in the chain and their distances are:
     7        8.16     5 
 

 tryconnect> Interpolation for minima 5_S and 7_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=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -385.3414528     RMS=3.736412337     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      5     7 dist=   15.55     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 0.6088 Dev= 3.17% S= 8.55 time= 0.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     907 steps. Energy=    -391.7507267       time=       2.09
 Minus side of path:                     895 steps. Energy=    -395.0814382       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.7507267 0.46470         -391.2860270  3.7954         -395.0814382   8.734   8.431  11.999  12.084
        Known (#5)                                              *NEW* (Placed in 8)
 checkperc> Increasing con cutoff atoms    25   26 from     0.19092E-02 to     0.20231E-02 ref=     1.2337    
 checkperc> Increasing con cutoff atoms    26   28 from     0.15151E-01 to     0.16214E-01 ref=     3.1180    
 checkperc> Increasing con cutoff atoms    56   57 from     0.53752E-02 to     0.55785E-02 ref=     1.5242    
 checkperc> Increasing con cutoff atoms   132  135 from     0.46211E-01 to     0.50220E-01 ref=     2.4437    
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     53.696    
 decide> The unconnected minima in the chain and their distances are:
     7        3.77     8 
 

 tryconnect> Interpolation for minima 7_F and 8_S 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=   143
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     17 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     42 steps, energy/image=    -393.6438616     RMS=.6514680951     images=   3
 intlbfgs> First  minimum number      7
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      7     8 dist=   4.476     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 5.0465 Dev= 1.05% S= 4.32 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     865 steps. Energy=    -398.8414606       time=       1.97
 Minus side of path:                     833 steps. Energy=    -395.0814382       time=       1.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.8414606  6.7836         -392.0578826  3.0236         -395.0814382  10.396   3.769   5.644  25.689
        Known (#7)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.6466841  2.2419        -384.4047873  6.7530        -391.1577527  48.823  42.681   3.085  47.007
   4     -391.1577527 0.10120        -391.0565535 0.44017        -391.4967252   4.582   3.967   5.099  28.436
   3     -391.4967252 0.79802E-02    -391.4887450 0.26198        -391.7507267   1.928   1.912  23.598   6.145
   6     -391.7507267 0.46470        -391.2860270  3.7954        -395.0814382   8.734   8.431  11.999  12.084
   7     -395.0814382  3.0236        -392.0578826  6.7836        -398.8414606  10.396   3.769   5.644  25.689
   5     -398.8414606  6.9700        -391.8714114 0.11133        -391.9827399  23.130  21.763  15.569   9.314
   2     -391.9827399 0.25939        -391.7233524 0.58247E-01    -391.7815997   5.579   5.133   5.170  28.044

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                               160.44
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             53006 time=          68.84 %= 42.9
 OPTIM> # of energy+gradient+Hessian calls=       792 time=           3.61 %=  2.2
