
 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 10:35:33 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=    -383.9810874     RMS force=    0.9967696212E-06
 OPTIM> Final energy  =    -385.8649070     RMS force=    0.9817715371E-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      34.52262078    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     41265.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.52     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=    14
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    182 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    207 steps, energy/image=    -358.9402084     RMS=2.510519731     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   38.39     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0545 Dev= 4.37% S= 37.62 time= 5.23
 Following    3 images are candidates for TS:    5    7    9  
 Converged to TS (number of iterations):        118
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         79
 DNEB run yielded 3 true transition state(s) time=  22.33

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1042 steps. Energy=    -383.9810874       time=       3.52
 Minus side of path:                     969 steps. Energy=    -382.7709519       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.9810874  1.2334         -382.7476810 0.23271E-01     -382.7709519  23.675  23.477   2.300  63.042
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    71   75 from     0.28842E-01 to     0.29527E-01 ref=     2.4627    
 checkperc> Increasing con cutoff atoms   105  108 from     0.25293E-01 to     0.25403E-01 ref=     2.0015    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1029 steps. Energy=    -384.6463498       time=       3.61
 Minus side of path:                     919 steps. Energy=    -384.0549925       time=       2.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6463498 0.68276         -383.9635886 0.91404E-01     -384.0549925  20.094  19.543   2.109  68.764
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    62   66 from     0.53930E-01 to     0.54148E-01 ref=     3.7910    
 checkperc> Increasing con cutoff atoms    67   70 from     0.89094E-02 to     0.10320E-01 ref=     3.0792    
 checkperc> Increasing con cutoff atoms    75   77 from     0.21733E-01 to     0.28538E-01 ref=     2.4002    
 checkperc> Increasing con cutoff atoms    75   79 from     0.77395E-01 to     0.78335E-01 ref=     2.5315    
 checkperc> Increasing con cutoff atoms    94  105 from     0.54442E-01 to     0.56056E-01 ref=     2.5144    
 checkperc> Increasing con cutoff atoms    95  102 from     0.19714E-01 to     0.22341E-01 ref=     3.4382    
 checkperc> Increasing con cutoff atoms    98  103 from     0.16672E-02 to     0.22883E-02 ref=     1.3863    
 checkperc> Increasing con cutoff atoms    98  104 from     0.62713E-02 to     0.74380E-02 ref=     2.4253    
 checkperc> Increasing con cutoff atoms   103  104 from     0.26463E-02 to     0.28344E-02 ref=     1.3921    
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     912 steps. Energy=    -385.8649070       time=       2.08
 Minus side of path:                    1048 steps. Energy=    -384.0550271       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8649070  1.9858         -383.8790580 0.17597         -384.0550271  21.208  18.166   2.261  64.123
        Known (#2)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    62   66 from     0.54148E-01 to     0.54497E-01 ref=     3.7910    
 checkperc> Increasing con cutoff atoms    67   70 from     0.10320E-01 to     0.10480E-01 ref=     3.0792    
 checkperc> Increasing con cutoff atoms    75   77 from     0.28538E-01 to     0.29235E-01 ref=     2.4002    
 checkperc> Increasing con cutoff atoms    75   79 from     0.78335E-01 to     0.83920E-01 ref=     2.5315    
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     5220.6    
 decide> The unconnected minima in the chain and their distances are:
     6       17.33     3 
 

 tryconnect> Interpolation for minima 3_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=    70
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     76 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    101 steps, energy/image=    -368.6299165     RMS=9.603190605     images=   4
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      3     6 dist=   25.45     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 245 RMS= 0.0872 Dev= 0.79% S= 17.50 time= 2.09
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   7.21

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     953 steps. Energy=    -385.8649070       time=       3.00
 Minus side of path:                    1000 steps. Energy=    -382.8545546       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.8649070  3.8257         -382.0391570 0.81540         -382.8545546  26.607  25.711   1.555  93.250
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     175.47    
 decide> The unconnected minima in the chain and their distances are:
     7        5.59     3 
 

 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=   137
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     18 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     43 steps, energy/image=    -375.0510402     RMS=3.716756807     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   14.34     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.0397 Dev= 0.76% S= 5.62 time= 0.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.55

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     966 steps. Energy=    -382.8545546       time=       3.17
 Minus side of path:                     997 steps. Energy=    -382.7709519       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.8545546 0.66531         -382.1892428 0.58171         -382.7709519   5.726   5.593   5.822  24.904
        Known (#7)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -383.9810874  1.2334        -382.7476810 0.23271E-01    -382.7709519  23.675  23.477   2.300  63.042
   5     -382.7709519 0.58171        -382.1892428 0.66531        -382.8545546   5.726   5.593   5.822  24.904
   4     -382.8545546 0.81540        -382.0391570  3.8257        -385.8649070  26.607  25.711   1.555  93.250

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

 Elapsed time=                                71.34
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             21687 time=          26.14 %= 36.6
 OPTIM> # of energy+gradient+Hessian calls=       312 time=           1.43 %=  2.0
