
 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)@comp32.ch.
                 Created on  5/28/12 at 10:29:16 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=    -397.4484357     RMS force=    0.9301017752E-06
 OPTIM> Final energy  =    -396.6730133     RMS force=    0.9128155356E-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      18.13410572    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     5812.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.96     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=   112
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     52 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     77 steps, energy/image=    -388.8387397     RMS=.3904738696     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   21.02     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 210 RMS= 0.2072 Dev= 0.60% S= 19.23 time= 1.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.33

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     968 steps. Energy=    -398.6490308       time=       3.23
 Minus side of path:                     942 steps. Energy=    -395.3706953       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.6490308  3.9820         -394.6670117 0.70368         -395.3706953  21.132  19.030   5.420  26.753
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms     4    5 from     0.13922E-01 to     0.20712E-01 ref=     2.0888    
 checkperc> Increasing con cutoff atoms     5    6 from     0.58851E-02 to     0.68198E-02 ref=     1.5239    
 checkperc> Increasing con cutoff atoms     9   11 from     0.30632E-02 to     0.39293E-02 ref=     1.3336    
 checkperc> Increasing con cutoff atoms    11   13 from     0.36956E-02 to     0.37091E-02 ref=     1.4555    
 checkperc> Increasing con cutoff atoms    12   13 from     0.19335E-01 to     0.19742E-01 ref=     2.1076    
 checkperc> Increasing con cutoff atoms    14   16 from     0.20851E-01 to     0.23026E-01 ref=     2.5967    
 checkperc> Increasing con cutoff atoms    14   17 from     0.87345E-02 to     0.98739E-02 ref=     3.6231    
 checkperc> Increasing con cutoff atoms    14   18 from     0.47029E-01 to     0.50031E-01 ref=     3.2574    
 checkperc> Increasing con cutoff atoms   130  134 from     0.30207E-01 to     0.37760E-01 ref=     2.4656    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1131.2    
 decide> The unconnected minima in the chain and their distances are:
     2        9.71     4     3        5.96     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=   130
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     35 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     60 steps, energy/image=    -386.3485595     RMS=4.982721600     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   17.44     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 0.2948 Dev= 0.91% S= 10.14 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.89

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     920 steps. Energy=    -396.6730133       time=       2.16
 Minus side of path:                     906 steps. Energy=    -395.6508935       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6730133  3.3133         -393.3596942  2.2912         -395.6508935   5.834   5.163  37.973   3.818
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms     1    2 from     0.40434E-01 to     0.40456E-01 ref=     1.7182    
 checkperc> Increasing con cutoff atoms     6    9 from     0.19050E-01 to     0.19071E-01 ref=     2.5192    
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=    -391.3437849     RMS=.5782999367     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   12.72     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 0.2567 Dev= 0.53% S= 5.16 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     903 steps. Energy=    -397.6360114       time=       2.14
 Minus side of path:                     911 steps. Energy=    -396.7120879       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.6360114  1.2500         -396.3859907 0.32610         -396.7120879   6.773   6.324   2.621  55.328
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms     3    5 from     0.51324E-02 to     0.58031E-02 ref=     1.4465    
 checkperc> Increasing con cutoff atoms     3    6 from     0.15457E-01 to     0.15668E-01 ref=     2.3641    
 checkperc> Increasing con cutoff atoms     3    7 from     0.31056E-01 to     0.34971E-01 ref=     2.4649    
 checkperc> Increasing con cutoff atoms     5    9 from     0.37201E-02 to     0.42056E-02 ref=     1.5231    
 checkperc> Increasing con cutoff atoms    10   12 from     0.16069E-01 to     0.16605E-01 ref=     3.1170    
 checkperc> Increasing con cutoff atoms    10   13 from     0.39753E-01 to     0.45733E-01 ref=     2.7984    
 checkperc> Increasing con cutoff atoms    12   13 from     0.19742E-01 to     0.21678E-01 ref=     2.1076    
 checkperc> Increasing con cutoff atoms    13   14 from     0.60814E-02 to     0.64652E-02 ref=     1.5326    
 checkperc> Increasing con cutoff atoms     1    3 from     0.38780E-02 to     0.44825E-02 ref=     1.0524    
 checkperc> Increasing con cutoff atoms     1    4 from     0.24062E-01 to     0.68098E-01 ref=     1.7418    
 checkperc> Increasing con cutoff atoms     1    5 from     0.43016E-01 to     0.56359E-01 ref=     1.9477    
 checkperc> Increasing con cutoff atoms     1    6 from     0.32168E-01 to     0.54859E-01 ref=     2.1635    
 checkperc> Increasing con cutoff atoms     2    3 from     0.84370E-02 to     0.93648E-02 ref=     1.0461    
 checkperc> Increasing con cutoff atoms     2    4 from     0.20158E-01 to     0.47356E-01 ref=     1.7354    
 checkperc> Increasing con cutoff atoms     2    5 from     0.64589E-01 to     0.10301     ref=     2.0118    
 checkperc> Increasing con cutoff atoms     4    5 from     0.20712E-01 to     0.46755E-01 ref=     2.0888    
 checkperc> Increasing con cutoff atoms     4    6 from     0.14115     to     0.17004     ref=     3.1326    
 checkperc> Increasing con cutoff atoms     5    9 from     0.42056E-02 to     0.53570E-02 ref=     1.5231    
 checkperc> Increasing con cutoff atoms     5   10 from     0.28102E-01 to     0.32609E-01 ref=     2.3994    
 checkperc> Increasing con cutoff atoms     9   10 from     0.38100E-02 to     0.39496E-02 ref=     1.2381    
 checkperc> Increasing con cutoff atoms     9   13 from     0.13584E-01 to     0.13679E-01 ref=     2.4473    
 checkperc> Increasing con cutoff atoms    10   13 from     0.45733E-01 to     0.66747E-01 ref=     2.7984    
 checkperc> Increasing con cutoff atoms    11   25 from     0.65518E-01 to     0.66787E-01 ref=     2.4525    
 checkperc> Increasing con cutoff atoms    13   14 from     0.64652E-02 to     0.81142E-02 ref=     1.5326    
 checkperc> Increasing con cutoff atoms    14   16 from     0.23026E-01 to     0.24343E-01 ref=     2.5967    
 checkperc> Increasing con cutoff atoms    14   17 from     0.98739E-02 to     0.11122E-01 ref=     3.6231    
 checkperc> Increasing con cutoff atoms    14   18 from     0.50031E-01 to     0.51742E-01 ref=     3.2574    
 checkperc> Increasing con cutoff atoms    14   23 from     0.46844E-01 to     0.46981E-01 ref=     4.6010    
 checkperc> Increasing con cutoff atoms    15   16 from     0.33210E-02 to     0.33323E-02 ref=     1.3704    
 checkperc> Increasing con cutoff atoms    16   22 from     0.42186E-02 to     0.44059E-02 ref=     2.4031    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     845.60    
 decide> The unconnected minima in the chain and their distances are:
     5        8.50     4     3        4.01     7     6        5.48     1 
 

 tryconnect> Interpolation for minima 4_U 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=   131
 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=    -391.3416281     RMS=.8022709921E-01 images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   10.24     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 105 RMS= 0.0981 Dev= 0.12% S= 8.53 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     916 steps. Energy=    -395.3706953       time=       2.13
 Minus side of path:                     908 steps. Energy=    -395.6508935       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3706953 0.88418E-01     -395.2822770 0.36862         -395.6508935   9.053   8.504   7.907  18.338
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 3_F and 7_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=   144
 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=    -393.8771283     RMS=.2289938103     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   4.601     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4304 Dev= 2.40% S= 4.06 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     912 steps. Energy=    -398.6490308       time=       2.14
 Minus side of path:                     880 steps. Energy=    -396.7120878       time=       1.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.6490308  2.2788         -396.3702335 0.34185         -396.7120878   4.236   4.005   4.445  32.618
        Known (#3)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 6_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=   142
 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=    -393.2055602     RMS=.2014544502     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   5.803     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0359 Dev= 0.11% S= 4.60 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.62

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     864 steps. Energy=    -397.4484357       time=       1.95
 Minus side of path:                     880 steps. Energy=    -397.6360114       time=       2.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.4484357 0.10307         -397.3453660 0.29065         -397.6360114   4.696   4.593   3.954  36.676
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -397.4484357 0.10307        -397.3453660 0.29065        -397.6360114   4.696   4.593   3.954  36.676
   3     -397.6360114  1.2500        -396.3859907 0.32610        -396.7120879   6.773   6.324   2.621  55.328
   5     -396.7120879 0.34185        -396.3702335  2.2788        -398.6490308   4.236   4.005   4.445  32.618
   1     -398.6490308  3.9820        -394.6670117 0.70368        -395.3706953  21.132  19.030   5.420  26.753
   4     -395.3706953 0.88418E-01    -395.2822770 0.36862        -395.6508935   9.053   8.504   7.907  18.338
   2     -395.6508935  2.2912        -393.3596942  3.3133        -396.6730133   5.834   5.163  37.973   3.818

 Number of TS in the path       =      6
 Number of cycles               =      3

 Elapsed time=                                55.99
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             19847 time=          26.37 %= 47.1
 OPTIM> # of energy+gradient+Hessian calls=       192 time=           0.87 %=  1.5
