
 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 10:33:54 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=    -399.4433289     RMS force=    0.8667251535E-06
 OPTIM> Final energy  =    -388.3743583     RMS force=    0.9589739517E-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      44.23073739    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     84946.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.91     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    440 fraction=    0.990000 images=     4 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    465 steps, energy/image=    -372.4269905     RMS=1.147842269     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   45.10     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0802 Dev= 3.40% S= 54.22 time= 8.51
 Following    2 images are candidates for TS:    7   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=  25.79

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1199 steps. Energy=    -394.3983805       time=       4.72
 Minus side of path:                     943 steps. Energy=    -388.3743583       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  6.3778         -388.0205580 0.35380         -388.3743583  29.211  27.403   1.977  73.344
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    29   30 from     0.73609E-02 to     0.83533E-02 ref=     1.5469    
 checkperc> Increasing con cutoff atoms    29   33 from     0.25888E-01 to     0.31160E-01 ref=     2.5618    
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     14146.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.16     1 
 

 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=    23
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    148 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    173 steps, energy/image=    -378.1264222     RMS=1.895957193     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   27.98     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 280 RMS= 0.2048 Dev= 1.80% S= 26.36 time= 3.09
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):         43
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         56
 DNEB run yielded 2 true transition state(s) time=   9.49

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     934 steps. Energy=    -396.9446441       time=       2.27
 Minus side of path:                    1320 steps. Energy=    -399.4433289       time=       4.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.9446441  2.0188         -394.9258455  4.5175         -399.4433289  26.468  23.249   1.915  75.731
        *NEW* (Placed in 4)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    27   30 from     0.25724E-01 to     0.25764E-01 ref=     2.4574    
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     887 steps. Energy=    -396.6857038       time=       2.11
 Minus side of path:                     922 steps. Energy=    -394.3983805       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6857038  3.1084         -393.5772961 0.82108         -394.3983805  14.167  12.922   6.810  21.293
        *NEW* (Placed in 5)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    27   30 from     0.25764E-01 to     0.25808E-01 ref=     2.4574    
 checkperc> Increasing con cutoff atoms    93  105 from     0.70498E-02 to     0.79427E-02 ref=     1.5257    
 checkperc> Increasing con cutoff atoms    93  108 from     0.13632     to     0.14244     ref=     2.5112    
 checkperc> Increasing con cutoff atoms   105  106 from     0.34315E-02 to     0.39992E-02 ref=     1.2345    
 checkperc> Increasing con cutoff atoms   105  108 from     0.21373E-01 to     0.23475E-01 ref=     2.0042    
 checkperc> Increasing con cutoff atoms   119  126 from     0.29467E-01 to     0.33135E-01 ref=     4.5208    
 checkperc> Increasing con cutoff atoms   120  126 from     0.14891E-01 to     0.15743E-01 ref=     3.1091    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     43.339    
 decide> The unconnected minima in the chain and their distances are:
     3        3.51     4 
 

 tryconnect> Interpolation for minima 3_F and 4_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=   142
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     19 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     44 steps, energy/image=    -390.0458943     RMS=.3812148133     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   4.746     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.7162 Dev= 1.20% S= 3.81 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.96
 isnewts> transition state is the same as number        3 energy=     -393.5772961085
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     901 steps. Energy=    -396.6857038       time=       2.53
 Minus side of path:                     915 steps. Energy=    -394.3983805       time=       2.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.6857038  3.1084         -393.5772961 0.82108         -394.3983805  14.167  12.923   6.799  21.326
        Known (#5)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     86.678    
 decide> The unconnected minima in the chain and their distances are:
     3        3.51     4 
 

 tryconnect> Interpolation for minima 3_F and 4_S using 15 initial images  (interp attempt #2)  ...
 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     18 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     43 steps, energy/image=    -389.9988072     RMS=.3092070646     images=  15
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   5.219     Attempts, images and iterations=     1    12   420
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 420 RMS= 0.0966 Dev= 3.63% S= 4.65 time= 7.13
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     878 steps. Energy=    -394.3983805       time=       2.67
 Minus side of path:                     921 steps. Energy=    -396.9446441       time=       2.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.3983805  3.7105         -390.6878780  6.2568         -396.9446441   6.264   3.510  12.567  11.538
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -399.4433289  4.5175        -394.9258455  2.0188        -396.9446441  26.468  23.249   1.915  75.731
   5     -396.9446441  6.2568        -390.6878780  3.7105        -394.3983805   6.264   3.510  12.567  11.538
   1     -394.3983805  6.3778        -388.0205580 0.35380        -388.3743583  29.211  27.403   1.977  73.344

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

 Elapsed time=                                93.57
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             30075 time=          40.54 %= 43.3
 OPTIM> # of energy+gradient+Hessian calls=       432 time=           2.12 %=  2.3
