
 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)@comp27.ch.
                 Created on  5/28/12 at 13:10:27 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -387.3512235     RMS force=    0.9649006132E-06
 OPTIM> Final energy  =    -381.1071125     RMS force=    0.9892965902E-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=     71707.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.55     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1054 Dev= 2.83% S= 50.17 time= 6.39
 Following    1 images are candidates for TS:    8  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  28.61
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.14341E+06
 decide> The unconnected minima in the chain and their distances are:
     2       41.55     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 805 RMS= 0.0585 Dev= 4.84% S= 55.07 time= 22.79
 Following    3 images are candidates for TS:    8   15   23  
 Converged to TS (number of iterations):         62
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         15
 DNEB run yielded 3 true transition state(s) time=  13.36

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     991 steps. Energy=    -381.5678225       time=       2.48
 Minus side of path:                    1015 steps. Energy=    -387.3512235       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5678225 0.47244         -381.0953869  6.2558         -387.3512235  26.239  24.007   1.875  77.321
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1191 steps. Energy=    -381.2537041       time=       3.63
 Minus side of path:                    1344 steps. Energy=    -384.5540878       time=       5.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2537041  5.6626         -375.5910803  8.9630         -384.5540878  52.790  41.148   1.650  87.860
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     961 steps. Energy=    -381.1071125       time=       2.66
 Minus side of path:                    1003 steps. Energy=    -381.2003065       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1071125 0.16836E-01     -381.0902763 0.11003         -381.2003065   1.037   1.034  39.542   3.667
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2507.2    
 decide> The unconnected minima in the chain and their distances are:
     6        2.36     4     5       13.56     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0104 Dev= 0.01% S= 2.37 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     989 steps. Energy=    -381.2537041       time=       2.23
 Minus side of path:                     983 steps. Energy=    -381.2003065       time=       2.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2537041 0.56485E-01     -381.1972192 0.30873E-02     -381.2003065   2.379   2.365   2.359  61.460
        Known (#4)                                              Known (#6)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0809 Dev= 0.48% S= 13.99 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.08

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     943 steps. Energy=    -385.1178926       time=       2.19
 Minus side of path:                     967 steps. Energy=    -387.3512235       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1178926 0.84803         -384.2698644  3.0814         -387.3512235  13.576  12.255   5.517  26.284
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     112.72    
 decide> The unconnected minima in the chain and their distances are:
     5        4.83     7 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0654 Dev= 0.38% S= 4.91 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     963 steps. Energy=    -385.1178926       time=       2.29
 Minus side of path:                     906 steps. Energy=    -384.5540878       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1178926 0.58265         -384.5352389 0.18849E-01     -384.5540878   5.093   4.831   5.438  26.666
        Known (#7)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -387.3512235  3.0814        -384.2698644 0.84803        -385.1178926  13.576  12.255   5.517  26.284
   6     -385.1178926 0.58265        -384.5352389 0.18849E-01    -384.5540878   5.093   4.831   5.438  26.666
   2     -384.5540878  8.9630        -375.5910803  5.6626        -381.2537041  52.790  41.148   1.650  87.860
   4     -381.2537041 0.56485E-01    -381.1972192 0.30873E-02    -381.2003065   2.379   2.365   2.359  61.460
   3     -381.2003065 0.11003        -381.0902763 0.16836E-01    -381.1071125   1.037   1.034  39.542   3.667

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

 Elapsed time=                               115.58
 OPTIM> # of energy calls=                         86 time=           0.10 %=  0.1
 OPTIM> # of energy+gradient calls=             45049 time=          53.06 %= 45.9
 OPTIM> # of energy+gradient+Hessian calls=       431 time=           1.95 %=  1.7
