
 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)@comp34.ch.
                 Created on  5/28/12 at 10:33:58 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=    -389.8328792     RMS force=    0.9213414051E-06
 OPTIM> Final energy  =    -394.4192763     RMS force=    0.8976902090E-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      27.33622481    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     20488.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.34     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=    26
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    126 fraction=    0.990000 images=     4 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    151 steps, energy/image=    -349.6884104     RMS=7.045232304     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   34.78     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 350 RMS= 0.0562 Dev= 4.76% S= 30.66 time= 5.05
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):         78
 Converged to TS (number of iterations):         39
 DNEB run yielded 2 true transition state(s) time=  14.27

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     918 steps. Energy=    -392.8445366       time=       2.78
 Minus side of path:                     947 steps. Energy=    -389.8260034       time=       3.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8445366  3.6822         -389.1622948 0.66371         -389.8260034  28.013  26.212   2.599  55.794
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   105  107 from     0.65917E-02 to     0.66239E-02 ref=     1.3330    
 checkperc> Increasing con cutoff atoms   116  117 from     0.51279E-02 to     0.56722E-02 ref=    0.98100    
 checkperc> Increasing con cutoff atoms   118  132 from     0.52835E-01 to     0.61116E-01 ref=     2.4332    
 checkperc> Increasing con cutoff atoms   118  133 from     0.90372E-01 to     0.11470     ref=     2.5245    
 checkperc> Increasing con cutoff atoms   120  127 from     0.16023E-01 to     0.16775E-01 ref=     3.4439    
 checkperc> Increasing con cutoff atoms   122  128 from     0.61825E-02 to     0.65596E-02 ref=     2.7038    
 checkperc> Increasing con cutoff atoms   124  129 from     0.21802E-01 to     0.21906E-01 ref=     4.4240    
 checkperc> Increasing con cutoff atoms   136  137 from     0.84534E-02 to     0.85887E-02 ref=     1.5251    
 checkperc> Increasing con cutoff atoms   121  125 from     0.38108E-02 to     0.40685E-02 ref=     2.2385    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     884 steps. Energy=    -398.5496307       time=       2.84
 Minus side of path:                     886 steps. Energy=    -394.4192763       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -398.5496307  4.7772         -393.7724351 0.64684         -394.4192763   7.229   6.148   8.731  16.608
        *NEW* (Placed in 5)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    89   92 from     0.16087E-01 to     0.16642E-01 ref=     1.9994    
 checkperc> Increasing con cutoff atoms   105  107 from     0.66239E-02 to     0.74346E-02 ref=     1.3330    
 checkperc> Increasing con cutoff atoms   139  140 from     0.10584E-01 to     0.10977E-01 ref=     1.0474    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     288.07    
 decide> The unconnected minima in the chain and their distances are:
     5        6.59     3     4        1.09     1 
 

 tryconnect> Interpolation for minima 3_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=   140
 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=    -363.8540914     RMS=11.42680082     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   14.21     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 0.6403 Dev= 1.10% S= 6.67 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.35

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     917 steps. Energy=    -394.4192763       time=       2.26
 Minus side of path:                     910 steps. Energy=    -392.8681296       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4192763  3.5335         -390.8857681  1.9824         -392.8681296   8.031   7.547  21.269   6.817
        Known (#2)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms   118  132 from     0.61116E-01 to     0.63416E-01 ref=     2.4332    
 checkperc> Increasing con cutoff atoms   118  133 from     0.11470     to     0.11787     ref=     2.5245    
 checkperc> Increasing con cutoff atoms   118  134 from     0.43107E-01 to     0.44397E-01 ref=     3.8206    
 checkperc> Increasing con cutoff atoms   136  137 from     0.85887E-02 to     0.86172E-02 ref=     1.5251    
 Unconnected minimum 6 found its way to F 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=   145
 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=    -385.9218071     RMS=.5808967974E-01 images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   1.458     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0088 Dev= 0.22% S= 1.09 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.96

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     926 steps. Energy=    -389.8328792       time=       2.26
 Minus side of path:                     913 steps. Energy=    -389.8260034       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.8328792 0.13065E-01     -389.8198144 0.61890E-02     -389.8260034   1.090   1.090   2.785  52.073
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1.0849    
 decide> The unconnected minima in the chain and their distances are:
     6        1.03     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=   145
 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=    -388.9029815     RMS=.4092573888E-01 images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      3     6 dist=   1.274     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0164 Dev= 0.47% S= 1.03 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.93

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     850 steps. Energy=    -392.8681296       time=       2.60
 Minus side of path:                     744 steps. Energy=    -392.8445366       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8681296 0.24517E-01     -392.8436128 0.92387E-03     -392.8445366   1.029   1.026   3.274  44.283
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -389.8328792 0.13065E-01    -389.8198144 0.61890E-02    -389.8260034   1.090   1.090   2.785  52.073
   1     -389.8260034 0.66371        -389.1622948  3.6822        -392.8445366  28.013  26.212   2.599  55.794
   5     -392.8445366 0.92387E-03    -392.8436128 0.24517E-01    -392.8681296   1.029   1.026   3.274  44.283
   3     -392.8681296  1.9824        -390.8857681  3.5335        -394.4192763   8.031   7.547  21.269   6.817

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

 Elapsed time=                                57.61
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             18326 time=          26.22 %= 45.5
 OPTIM> # of energy+gradient+Hessian calls=       182 time=           0.90 %=  1.6
