
 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)@comp29.ch.
                 Created on  5/28/12 at 10:33:15 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=    -385.3808385     RMS force=    0.8077090704E-06
 OPTIM> Final energy  =    -392.4539340     RMS force=    0.8817160462E-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      87.71791175    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.12929E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.48     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=     4
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    388 fraction=    0.990000 images=     4 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    413 steps, energy/image=    -371.2284758     RMS=.7075304860     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   52.67     Attempts, images and iterations=     0    15   525
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 525 RMS= 0.0804 Dev= 5.15% S= 64.97 time= 10.26
 Following    3 images are candidates for TS:    6    8   12  
 Converged to TS (number of iterations):        193
 Converged to TS (number of iterations):        108
 Converged to TS (number of iterations):        122
 DNEB run yielded 3 true transition state(s) time=  42.88

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     993 steps. Energy=    -388.6037785       time=       2.35
 Minus side of path:                     976 steps. Energy=    -388.5939899       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6037785 0.64181E-01     -388.5395976 0.54392E-01     -388.5939899   2.209   2.192   6.903  21.005
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1070 steps. Energy=    -388.5431109       time=       3.06
 Minus side of path:                     983 steps. Energy=    -386.9964442       time=       3.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5431109  1.5943         -386.9487917 0.47653E-01     -386.9964442  22.677  20.738   2.562  56.599
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     989 steps. Energy=    -392.4539340       time=       3.93
 Minus side of path:                    1083 steps. Energy=    -390.8604758       time=       3.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.4539340  4.0055         -388.4483860  2.4121         -390.8604758  35.365  33.206   3.725  38.930
        Known (#2)                                              *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms    38   42 from     0.78441E-01 to     0.11660     ref=     4.4497    
 checkperc> Increasing con cutoff atoms    39   50 from     0.35341E-01 to     0.37747E-01 ref=     2.5131    
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     22362.    
 decide> The unconnected minima in the chain and their distances are:
     7       17.18     3     3       25.82     1 
 

 tryconnect> Interpolation for minima 3_U 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=   120
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    116 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    141 steps, energy/image=    -286.4939121     RMS=71.63664740     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   27.37     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 280 RMS= 0.0871 Dev= 0.39% S= 19.20 time= 2.95
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.02

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1085 steps. Energy=    -388.6037785       time=       3.60
 Minus side of path:                    1016 steps. Energy=    -390.8604758       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.6037785  1.2943         -387.3094451  3.5510         -390.8604758  28.874  17.207  10.774  13.458
        Known (#3)                                              Known (#7)
 Unconnected minimum 3 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=    21
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    186 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    211 steps, energy/image=    -80.92835120     RMS=23.12980082     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   36.04     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant      1.168613344    
 Double-ended search iterations= 350 RMS= 0.0614 Dev= 2.05% S= 27.76 time= 4.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   5.50

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1007 steps. Energy=    -385.5138985       time=       3.32
 Minus side of path:                    1637 steps. Energy=    -388.6037785       time=       7.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5138985  1.7831         -383.7308206  4.8730         -388.6037785  35.996  26.972   2.085  69.557
        *NEW* (Placed in 8)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    66   69 from     0.90757E-02 to     0.92650E-02 ref=     1.9776    
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     35.802    
 decide> The unconnected minima in the chain and their distances are:
     8        3.29     1 
 

 tryconnect> Interpolation for minima 1_S and 8_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=   143
 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=    -381.3186313     RMS=.1926525223     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      1     8 dist=   4.485     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.0552 Dev= 0.65% S= 3.31 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     966 steps. Energy=    -385.5138985       time=       2.75
 Minus side of path:                     990 steps. Energy=    -385.3808385       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.5138985 0.18241         -385.3314907 0.49348E-01     -385.3808385   3.329   3.293  11.041  13.133
        Known (#8)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -385.3808385 0.49348E-01    -385.3314907 0.18241        -385.5138985   3.329   3.293  11.041  13.133
   5     -385.5138985  1.7831        -383.7308206  4.8730        -388.6037785  35.996  26.972   2.085  69.557
   4     -388.6037785  1.2943        -387.3094451  3.5510        -390.8604758  28.874  17.207  10.774  13.458
   3     -390.8604758  2.4121        -388.4483860  4.0055        -392.4539340  35.365  33.206   3.725  38.930

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

 Elapsed time=                               118.89
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             34565 time=          42.31 %= 35.6
 OPTIM> # of energy+gradient+Hessian calls=       532 time=           2.59 %=  2.2
