
 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> 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)@comp28.ch.
                 Created on  5/28/12 at 13:12:54 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
 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> 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -403.5800679     RMS force=    0.9529659474E-06
 OPTIM> Final energy  =    -405.7749793     RMS force=    0.9272023861E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     291.71    
 decide> The unconnected minima in the chain and their distances are:
     2        6.63     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 3.2883 Dev= 3.03% S= 7.37 time= 0.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     741 steps. Energy=    -405.2459444       time=       2.24
 Minus side of path:                     821 steps. Energy=    -405.7749793       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -405.2459444 0.19373E-01     -405.2265713 0.54841         -405.7749793   3.200   3.035   9.944  14.581
        *NEW* (Placed in 3)                                     Known (#2)
 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=     284.83    
 decide> The unconnected minima in the chain and their distances are:
     3        6.58     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.9259 Dev= 1.04% S= 7.13 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.74

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     847 steps. Energy=    -403.5800679       time=       2.00
 Minus side of path:                    1018 steps. Energy=    -404.1805934       time=       3.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -403.5800679  1.3703         -402.2098156  1.9708         -404.1805934   7.590   5.893   4.439  32.666
        Known (#1)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     442.86    
 decide> The unconnected minima in the chain and their distances are:
     2        7.62     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.3368 Dev= 0.62% S= 8.03 time= 0.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.39

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     900 steps. Energy=    -404.8629184       time=       2.38
 Minus side of path:                    1026 steps. Energy=    -404.1805934       time=       2.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -404.8629184  1.7342         -403.1287415  1.0519         -404.1805934  11.057   7.245  10.180  14.243
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     78.769    
 decide> The unconnected minima in the chain and their distances are:
     3        4.29     5 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4428 Dev= 0.98% S= 4.53 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.95
 isnewts> transition state is the same as number        1 energy=     -405.2265713320
 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:                     835 steps. Energy=    -405.7749793       time=       2.27
 Minus side of path:                     730 steps. Energy=    -405.2459444       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -405.7749793 0.54841         -405.2265713 0.19373E-01     -405.2459444   3.200   3.035   9.945  14.580
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     152.50    
 decide> The unconnected minima in the chain and their distances are:
     2        5.34     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.2542 Dev= 0.47% S= 5.66 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.46
 isnewts> transition state is the same as number        1 energy=     -405.2265713318
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     157.54    
 decide> The unconnected minima in the chain and their distances are:
     3        4.29     5 
 

 tryconnect> 315-iteration DNEB run for minima 3_F and 5_S using 9 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 315 RMS= 0.2291 Dev= 7.16% S= 6.28 time= 4.27
 Following    2 images are candidates for TS:    3    9  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=   6.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     837 steps. Energy=    -407.0715524       time=       2.12
 Minus side of path:                     856 steps. Energy=    -405.7749793       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -407.0715524  3.9795         -403.0920283  2.6830         -405.7749793   3.726   3.207   4.675  31.013
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     824 steps. Energy=    -404.8629184       time=       1.92
 Minus side of path:                     857 steps. Energy=    -407.0715524       time=       2.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -404.8629184 0.97453E-01     -404.7654653  2.3061         -407.0715524   4.431   4.114   4.391  33.019
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -403.5800679  1.3703        -402.2098156  1.9708        -404.1805934   7.590   5.893   4.439  32.666
   3     -404.1805934  1.0519        -403.1287415  1.7342        -404.8629184  11.057   7.245  10.180  14.243
   6     -404.8629184 0.97453E-01    -404.7654653  2.3061        -407.0715524   4.431   4.114   4.391  33.019
   5     -407.0715524  3.9795        -403.0920283  2.6830        -405.7749793   3.726   3.207   4.675  31.013

 Number of TS in the path       =      4
 Number of cycles               =      6

 Elapsed time=                                60.61
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             19727 time=          28.87 %= 47.6
 OPTIM> # of energy+gradient+Hessian calls=       194 time=           1.01 %=  1.7
