
 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)@comp33.ch.
                 Created on  5/28/12 at 10:36:44 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=    -382.6517516     RMS force=    0.9790532668E-06
 OPTIM> Final energy  =    -384.3413309     RMS force=    0.9878865331E-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      15.34157452    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3541.2    
 decide> The unconnected minima in the chain and their distances are:
     2       15.23     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=    93
 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=    -334.6003254     RMS=17.00381662     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   23.14     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 210 RMS= 0.0917 Dev= 0.32% S= 15.99 time= 1.48
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   8.48

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     978 steps. Energy=    -388.1413271       time=       2.33
 Minus side of path:                     993 steps. Energy=    -387.1746544       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1413271  3.0239         -385.1174077  2.0572         -387.1746544   7.220   6.143  23.929   6.060
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7082.4    
 decide> The unconnected minima in the chain and their distances are:
     2       15.23     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=    93
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     87 fraction=    0.990000 images=    15 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    112 steps, energy/image=    -359.0287206     RMS=19.80617006     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   26.28     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 805 RMS= 0.2978 Dev= 5.12% S= 19.91 time= 21.28
 Following    4 images are candidates for TS:    3    8   14   19  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         36
 Converged to TS (number of iterations):         40
 Converged to TS (number of iterations):         48
 DNEB run yielded 4 true transition state(s) time=  20.12
 isnewts> transition state is the same as number        1 energy=     -385.1174076651
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1001 steps. Energy=    -382.6517516       time=       2.42
 Minus side of path:                     986 steps. Energy=    -384.0989856       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6517516 0.37127         -382.2804784  1.8185         -384.0989856  12.146  11.826   1.975  73.407
        Known (#1)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    66   69 from     0.90757E-02 to     0.92762E-02 ref=     1.9776    
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1654 steps. Energy=    -387.1746544       time=       8.95
 Minus side of path:                    1010 steps. Energy=    -384.0989856       time=       4.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  4.8234         -382.3512452  1.7477         -384.0989856  35.564  27.060   2.071  70.025
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     982 steps. Energy=    -388.1413271       time=       2.93
 Minus side of path:                    1017 steps. Energy=    -387.1746544       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.1413271  3.0239         -385.1174077  2.0572         -387.1746544   7.220   6.143  23.913   6.064
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     965 steps. Energy=    -384.2712460       time=       2.43
 Minus side of path:                    1201 steps. Energy=    -388.1413271       time=       4.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2712460 0.33913E-01     -384.2373332  3.9040         -388.1413271  14.988  13.986   5.279  27.470
        *NEW* (Placed in 6)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    96   97 from     0.49602E-02 to     0.49769E-02 ref=     1.3588    
 checkperc> Increasing con cutoff atoms    97  102 from     0.19089E-02 to     0.19108E-02 ref=     1.3713    
 checkperc> Increasing con cutoff atoms    98   99 from     0.17790E-01 to     0.17825E-01 ref=     3.6015    
 checkperc> Increasing con cutoff atoms    99  102 from     0.20123E-01 to     0.20179E-01 ref=     3.4476    
 checkperc> Increasing con cutoff atoms    99  103 from     0.27595E-01 to     0.27637E-01 ref=     4.4788    
 checkperc> Increasing con cutoff atoms   100  102 from     0.17042E-01 to     0.17050E-01 ref=     2.3759    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2570.4    
 decide> The unconnected minima in the chain and their distances are:
     2       13.68     6 
 

 tryconnect> Interpolation for minima 2_F and 6_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=    99
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     48 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     73 steps, energy/image=    -380.3470374     RMS=.1995810076     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   14.26     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3955 Dev= 0.51% S= 13.71 time= 0.67
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.37

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     990 steps. Energy=    -384.2712460       time=       2.41
 Minus side of path:                     972 steps. Energy=    -384.3413309       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2712460 0.79693E-01     -384.1915528 0.14978         -384.3413309  13.731  13.685   2.475  58.574
        Known (#6)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -382.6517516 0.37127        -382.2804784  1.8185        -384.0989856  12.146  11.826   1.975  73.407
   3     -384.0989856  1.7477        -382.3512452  4.8234        -387.1746544  35.564  27.060   2.071  70.025
   1     -387.1746544  2.0572        -385.1174077  3.0239        -388.1413271   7.220   6.143  23.929   6.060
   5     -388.1413271  3.9040        -384.2373332 0.33913E-01    -384.2712460  14.988  13.986   5.279  27.470
   6     -384.2712460 0.79693E-01    -384.1915528 0.14978        -384.3413309  13.731  13.685   2.475  58.574

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

 Elapsed time=                                96.22
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             40822 time=          46.10 %= 47.9
 OPTIM> # of energy+gradient+Hessian calls=       220 time=           0.90 %=  0.9
