
 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)@comp25.ch.
                 Created on  5/28/12 at 13:12: 2 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=    -378.2543928     RMS force=    0.9482239899E-06
 OPTIM> Final energy  =    -382.1851430     RMS force=    0.9692575181E-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=     43885.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.27     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1583 Dev= 3.26% S= 45.72 time= 3.76
 Following    2 images are candidates for TS:    3    7  
 Converged to TS (number of iterations):         87
 Converged to TS (number of iterations):         90
 DNEB run yielded 2 true transition state(s) time=  15.89
 isnewts> transition state is the same as number        1 energy=     -379.3945994877
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1078 steps. Energy=    -380.7727545       time=       3.85
 Minus side of path:                    1076 steps. Energy=    -380.8184152       time=       3.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545  1.3782         -379.3945995  1.4238         -380.8184152  34.420  32.201   3.306  43.853
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1058 steps. Energy=    -380.8184152       time=       2.96
 Minus side of path:                    1054 steps. Energy=    -380.7727545       time=       4.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.8184152  1.4238         -379.3945995  1.3782         -380.7727545  34.422  32.219   3.275  44.268
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4292.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.33     3     4       14.72     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 0.6382 Dev= 2.18% S= 16.61 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   5.62

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1040 steps. Energy=    -380.7321663       time=       3.77
 Minus side of path:                    1059 steps. Energy=    -382.1851430       time=       3.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7321663  3.9337         -376.7984675  5.3867         -382.1851430  18.012  10.423  20.802   6.970
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2504 Dev= 0.41% S= 15.72 time= 0.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.57

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1003 steps. Energy=    -378.2543928       time=       3.40
 Minus side of path:                    1069 steps. Energy=    -380.8184152       time=       4.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.2543928  2.3854         -375.8690199  4.9494         -380.8184152  18.192  14.724  13.156  11.022
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     34.098    
 decide> The unconnected minima in the chain and their distances are:
     5        3.24     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0373 Dev= 0.16% S= 3.25 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   4.34

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1012 steps. Energy=    -380.7879935       time=       3.48
 Minus side of path:                    1023 steps. Energy=    -380.7321663       time=       2.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7879935 0.98516E-01     -380.6894778 0.42689E-01     -380.7321663   2.483   2.456  23.090   6.280
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3.9007    
 decide> The unconnected minima in the chain and their distances are:
     6        1.57     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0059 Dev= 0.03% S= 1.57 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.46

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1019 steps. Energy=    -380.7727545       time=       2.81
 Minus side of path:                    1019 steps. Energy=    -380.7879935       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.10401E-01     -380.7623536 0.25640E-01     -380.7879935   1.577   1.574   2.911  49.815
        Known (#3)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -378.2543928  2.3854        -375.8690199  4.9494        -380.8184152  18.192  14.724  13.156  11.022
   1     -380.8184152  1.4238        -379.3945995  1.3782        -380.7727545  34.420  32.201   3.306  43.853
   6     -380.7727545 0.10401E-01    -380.7623536 0.25640E-01    -380.7879935   1.577   1.574   2.911  49.815
   5     -380.7879935 0.98516E-01    -380.6894778 0.42689E-01    -380.7321663   2.483   2.456  23.090   6.280
   3     -380.7321663  3.9337        -376.7984675  5.3867        -382.1851430  18.012  10.423  20.802   6.970

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                                81.29
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23373 time=          25.54 %= 31.4
 OPTIM> # of energy+gradient+Hessian calls=       259 time=           1.15 %=  1.4
