
 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)@comp35.ch.
                 Created on  5/28/12 at 10:31:13 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=    -389.6639145     RMS force=    0.9768178271E-06
 OPTIM> Final energy  =    -384.2695727     RMS force=    0.9129670961E-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      66.45792292    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.29113E+06
 decide> The unconnected minima in the chain and their distances are:
     2       66.21     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=     3
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    935 fraction=    0.990000 images=     7 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    960 steps, energy/image=    -324.3012415     RMS=1.253977613     images=   8
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   68.30     Attempts, images and iterations=     0    20   700
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 700 RMS= 0.0594 Dev= 7.34% S= 87.97 time= 16.25
 Following    2 images are candidates for TS:   11   16  
 Converged to TS (number of iterations):        102
 Converged to TS (number of iterations):        133
 DNEB run yielded 2 true transition state(s) time=  18.24

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1929 steps. Energy=    -389.6639145       time=       9.18
 Minus side of path:                    2126 steps. Energy=    -386.4237956       time=      18.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6639145  10.568         -379.0958104  7.3280         -386.4237956 121.017  54.387   1.794  80.814
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    75   76 from     0.71053E-02 to     0.79442E-02 ref=     1.5205    
 checkperc> Increasing con cutoff atoms    75   80 from     0.35113E-01 to     0.40697E-01 ref=     3.8147    
 checkperc> Increasing con cutoff atoms    76   78 from     0.41089E-02 to     0.81550E-02 ref=     1.3335    
 checkperc> Increasing con cutoff atoms    76   80 from     0.30897E-01 to     0.31709E-01 ref=     2.4508    
 checkperc> Increasing con cutoff atoms    79   80 from     0.21003E-01 to     0.21906E-01 ref=     2.1102    
 checkperc> Increasing con cutoff atoms    91   94 from     0.52970E-01 to     0.55875E-01 ref=     2.4524    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1178 steps. Energy=    -384.0892944       time=       5.33
 Minus side of path:                    1382 steps. Energy=    -386.0522745       time=       6.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.0892944 0.74036         -383.3489377  2.7033         -386.0522745  64.220  56.897   1.726  84.021
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    80   81 from     0.11282E-01 to     0.14157E-01 ref=     1.5370    
 checkperc> Increasing con cutoff atoms    81   82 from     0.10275E-01 to     0.11909E-01 ref=     1.5298    
 checkperc> Increasing con cutoff atoms    83   84 from     0.84137E-02 to     0.85851E-02 ref=     1.5279    
 checkperc> Increasing con cutoff atoms    83   85 from     0.40160E-01 to     0.47217E-01 ref=     2.4783    
 checkperc> Increasing con cutoff atoms    62   66 from     0.53930E-01 to     0.61962E-01 ref=     3.7910    
 checkperc> Increasing con cutoff atoms    65   67 from     0.20327E-01 to     0.28187E-01 ref=     2.4054    
 checkperc> Increasing con cutoff atoms    66   67 from     0.31559E-02 to     0.32369E-02 ref=     1.2299    
 checkperc> Increasing con cutoff atoms    77   78 from     0.19067E-01 to     0.22428E-01 ref=     2.2474    
 checkperc> Increasing con cutoff atoms    77   80 from     0.63834E-01 to     0.69577E-01 ref=     2.7965    
 checkperc> Increasing con cutoff atoms    89   92 from     0.16087E-01 to     0.19698E-01 ref=     1.9994    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     13499.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.42     4     5       23.10     3 
 

 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=   106
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     40 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     65 steps, energy/image=    -375.2224884     RMS=6.299508334     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   16.41     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 0.1409 Dev= 0.62% S= 10.47 time= 0.62
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   4.66

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1040 steps. Energy=    -384.3673304       time=       2.86
 Minus side of path:                    1031 steps. Energy=    -384.0892944       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3673304  1.5289         -382.8384160  1.2509         -384.0892944  10.764  10.604   1.890  76.732
        *NEW* (Placed in 6)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    78   81 from     0.68550E-01 to     0.68557E-01 ref=     2.4780    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 3_S and 5_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    177 fraction=    0.990000 images=     4 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    202 steps, energy/image=    -370.3684467     RMS=1.156119839     images=   4
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   31.25     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 315 RMS= 0.2280 Dev= 2.37% S= 26.26 time= 3.69
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=   7.38

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     980 steps. Energy=    -385.1128586       time=       2.40
 Minus side of path:                     984 steps. Energy=    -386.7277073       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1128586  1.8022         -383.3106929  3.4170         -386.7277073  11.795  10.366   6.433  22.539
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 checkperc> Increasing con cutoff atoms    78   81 from     0.68557E-01 to     0.71383E-01 ref=     2.4780    
 checkperc> Increasing con cutoff atoms    87   88 from     0.20299E-01 to     0.21679E-01 ref=     1.6892    
 checkperc> Increasing con cutoff atoms    89   92 from     0.19698E-01 to     0.20230E-01 ref=     1.9994    
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     965 steps. Energy=    -386.7277073       time=       2.33
 Minus side of path:                     941 steps. Energy=    -385.7864973       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.7277073  2.9660         -383.7617525  2.0247         -385.7864973   6.706   5.882  24.202   5.991
        Known (#8)                                              *NEW* (Placed in 9)
 checkperc> Increasing con cutoff atoms    87   88 from     0.21679E-01 to     0.21696E-01 ref=     1.6892    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     1772.6    
 decide> The unconnected minima in the chain and their distances are:
     2        1.02     6     5        6.05     9     7       11.56     3 
 

 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=   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=    -380.4225157     RMS=.4572976522E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   1.807     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0212 Dev= 1.12% S= 1.02 time= 0.15
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.68

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     986 steps. Energy=    -384.3673304       time=       2.56
 Minus side of path:                     995 steps. Energy=    -384.2695727       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3673304 0.11271         -384.2546190 0.14954E-01     -384.2695727   1.023   1.020  38.686   3.748
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> Interpolation for minima 5_F and 9_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=   140
 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=    -381.7819624     RMS=.1401987243     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      9
 intlbfgs> DNEB for minima      5     9 dist=   10.52     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 0.0635 Dev= 0.39% S= 6.07 time= 0.41
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.17

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     987 steps. Energy=    -386.0522745       time=       2.48
 Minus side of path:                     965 steps. Energy=    -385.7864973       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.0522745 0.42742         -385.6248514 0.16165         -385.7864973   6.278   6.052   2.974  48.757
        Known (#5)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> Interpolation for minima 3_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=    98
 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=    -378.4139545     RMS=3.124618989     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   17.21     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.0669 Dev= 1.37% S= 11.71 time= 1.12
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     915 steps. Energy=    -385.1128586       time=       2.04
 Minus side of path:                     984 steps. Energy=    -386.4237956       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1128586 0.20892E-01     -385.0919665  1.3318         -386.4237956  12.427  11.561   1.910  75.916
        Known (#7)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.6639145  10.568        -379.0958104  7.3280        -386.4237956 121.017  54.387   1.794  80.814
   8     -386.4237956  1.3318        -385.0919665 0.20892E-01    -385.1128586  12.427  11.561   1.910  75.916
   4     -385.1128586  1.8022        -383.3106929  3.4170        -386.7277073  11.795  10.366   6.433  22.539
   5     -386.7277073  2.9660        -383.7617525  2.0247        -385.7864973   6.706   5.882  24.202   5.991
   7     -385.7864973 0.16165        -385.6248514 0.42742        -386.0522745   6.278   6.052   2.974  48.757
   2     -386.0522745  2.7033        -383.3489377 0.74036        -384.0892944  64.220  56.897   1.726  84.021
   3     -384.0892944  1.2509        -382.8384160  1.5289        -384.3673304  10.764  10.604   1.890  76.732
   6     -384.3673304 0.11271        -384.2546190 0.14954E-01    -384.2695727   1.023   1.020  38.686   3.748

 Number of TS in the path       =      8
 Number of cycles               =      3

 Elapsed time=                               133.56
 OPTIM> # of energy calls=                         12 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             45820 time=          52.93 %= 39.6
 OPTIM> # of energy+gradient+Hessian calls=       369 time=           1.51 %=  1.1
