
 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 10:36:15 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=    -394.8998583     RMS force=    0.9636479586E-06
 OPTIM> Final energy  =    -399.0858357     RMS force=    0.9402460512E-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      25.84769710    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     14213.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.20     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=    85
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     93 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    118 steps, energy/image=    -387.8487775     RMS=.8680693188     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   29.93     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 280 RMS= 0.1122 Dev= 2.73% S= 26.08 time= 3.23
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   6.91

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     936 steps. Energy=    -404.2039388       time=       2.53
 Minus side of path:                     816 steps. Energy=    -398.4860646       time=       2.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -404.2039388  6.7627         -397.4412710  1.0448         -398.4860646  13.510  11.801   5.028  28.838
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms     3    6 from     0.29296E-01 to     0.35427E-01 ref=     2.3821    
 checkperc> Increasing con cutoff atoms     5    6 from     0.29081E-02 to     0.35964E-02 ref=     1.5204    
 checkperc> Increasing con cutoff atoms     5    9 from     0.27177E-02 to     0.47596E-02 ref=     1.5246    
 checkperc> Increasing con cutoff atoms     7    8 from     0.37301E-02 to     0.40306E-02 ref=    0.96529    
 checkperc> Increasing con cutoff atoms     3    5 from     0.72373E-02 to     0.75199E-02 ref=     1.4495    
 checkperc> Increasing con cutoff atoms     3    6 from     0.35427E-01 to     0.41051E-01 ref=     2.3821    
 checkperc> Increasing con cutoff atoms     5    6 from     0.35964E-02 to     0.53807E-02 ref=     1.5204    
 checkperc> Increasing con cutoff atoms     5    9 from     0.47596E-02 to     0.57115E-02 ref=     1.5246    
 checkperc> Increasing con cutoff atoms     9   13 from     0.16120E-01 to     0.16659E-01 ref=     2.4463    
 checkperc> Increasing con cutoff atoms    11   12 from     0.37998E-02 to     0.43168E-02 ref=    0.98079    
 checkperc> Increasing con cutoff atoms    13   25 from     0.48743E-02 to     0.65142E-02 ref=     1.5255    
 checkperc> Increasing con cutoff atoms    25   26 from     0.17493E-02 to     0.19665E-02 ref=     1.2335    
 checkperc> Increasing con cutoff atoms    60   63 from     0.19913E-01 to     0.20328E-01 ref=     1.9974    
 checkperc> Increasing con cutoff atoms    87   88 from     0.94897E-01 to     0.95406E-01 ref=     1.7610    
 checkperc> Increasing con cutoff atoms   131  132 from     0.14117E-01 to     0.15887E-01 ref=     2.2436    
 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=     9893.9    
 decide> The unconnected minima in the chain and their distances are:
     2       13.11     4     4       19.67     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=   102
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     44 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     69 steps, energy/image=    -388.5190453     RMS=3.687399020     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   20.66     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 210 RMS= 0.0626 Dev= 1.36% S= 13.49 time= 1.87
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.64

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     947 steps. Energy=    -398.9183504       time=       3.73
 Minus side of path:                     854 steps. Energy=    -398.4860646       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.9183504  1.9044         -397.0139515  1.4721         -398.4860646  13.026  10.242  14.236  10.185
        *NEW* (Placed in 5)                                     Known (#4)
 checkperc> Increasing con cutoff atoms     9   13 from     0.16659E-01 to     0.17554E-01 ref=     2.4463    
 checkperc> Increasing con cutoff atoms    10   12 from     0.15806E-01 to     0.17047E-01 ref=     3.1153    
 checkperc> Increasing con cutoff atoms    11   12 from     0.43168E-02 to     0.47103E-02 ref=    0.98079    
 checkperc> Increasing con cutoff atoms    25   26 from     0.19665E-02 to     0.21305E-02 ref=     1.2335    
 checkperc> Increasing con cutoff atoms    26   28 from     0.14340E-01 to     0.14603E-01 ref=     3.1149    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S 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=    97
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     78 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    103 steps, energy/image=    -382.4780270     RMS=.8979359122     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   22.61     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0399 Dev= 0.51% S= 20.16 time= 1.77
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1023 steps. Energy=    -404.2039388       time=       2.81
 Minus side of path:                     939 steps. Energy=    -394.8998583       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -404.2039388  9.6169         -394.5870748 0.31278         -394.8998583  24.890  22.755   3.126  46.389
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     470.13    
 decide> The unconnected minima in the chain and their distances are:
     2        7.77     5 
 

 tryconnect> Interpolation for minima 2_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=   126
 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=    -393.2614694     RMS=1.727409752     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   14.69     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.0364 Dev= 0.56% S= 7.79 time= 0.81
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.30

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     833 steps. Energy=    -398.9183504       time=       2.03
 Minus side of path:                     844 steps. Energy=    -399.0858357       time=       2.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.9183504 0.34437E-01     -398.8839132 0.20192         -399.0858357   8.547   7.768   3.239  44.770
        Known (#5)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -394.8998583 0.31278        -394.5870748  9.6169        -404.2039388  24.890  22.755   3.126  46.389
   1     -404.2039388  6.7627        -397.4412710  1.0448        -398.4860646  13.510  11.801   5.028  28.838
   2     -398.4860646  1.4721        -397.0139515  1.9044        -398.9183504  13.026  10.242  14.236  10.185
   4     -398.9183504 0.34437E-01    -398.8839132 0.20192        -399.0858357   8.547   7.768   3.239  44.770

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                47.80
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             16509 time=          23.11 %= 48.3
 OPTIM> # of energy+gradient+Hessian calls=       164 time=           0.75 %=  1.6
