
 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)@comp17.ch.
                 Created on  5/28/12 at 13:11:51 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=    -380.1934631     RMS force=    0.9683759579E-06
 OPTIM> Final energy  =    -379.4775903     RMS force=    0.9014069247E-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=     5371.7    
 decide> The unconnected minima in the chain and their distances are:
     2       17.51     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 1.3586 Dev= 1.75% S= 31.97 time= 1.99
 Following    2 images are candidates for TS:    2    5  
 Converged to TS (number of iterations):         51
 Converged to TS (number of iterations):         38
 DNEB run yielded 2 true transition state(s) time=  14.60

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1066 steps. Energy=    -380.1934631       time=       3.67
 Minus side of path:                    1032 steps. Energy=    -381.6394866       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631  5.5427         -374.6507665  6.9887         -381.6394866  27.541  18.157  10.829  13.391
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1034 steps. Energy=    -379.5530127       time=       3.44
 Minus side of path:                    1060 steps. Energy=    -380.7727545       time=       2.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5530127  5.7670         -373.7860159  6.9867         -380.7727545  20.716  17.193  14.338  10.113
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1542.7    
 decide> The unconnected minima in the chain and their distances are:
     2        2.08     4     4       11.53     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0380 Dev= 0.08% S= 2.09 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   4.12

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     992 steps. Energy=    -379.4775903       time=       3.10
 Minus side of path:                     996 steps. Energy=    -379.5575820       time=       3.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.4775903 0.40489E-01     -379.4371010 0.12048         -379.5575820   1.892   1.882  38.352   3.781
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.8387 Dev= 0.18% S= 18.56 time= 0.36
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  57.52
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1567.1    
 decide> The unconnected minima in the chain and their distances are:
     6       11.62     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 6_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4492 Dev= 0.22% S= 18.50 time= 0.36
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.82
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1619.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.74     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5150 Dev= 0.19% S= 17.35 time= 0.37
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  19.66
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2427.0    
 decide> The unconnected minima in the chain and their distances are:
     6        0.82     4     5       13.44     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U 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= 0.0050 Dev= 0.01% S= 0.82 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=   2.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     995 steps. Energy=    -379.5530127       time=       2.07
 Minus side of path:                     973 steps. Energy=    -379.5575820       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5530127 0.42811E-02     -379.5487316 0.88504E-02     -379.5575820   0.828   0.818   3.587  40.424
        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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.2187 Dev= 0.16% S= 14.26 time= 0.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.36

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1017 steps. Energy=    -380.7181380       time=       2.22
 Minus side of path:                     990 steps. Energy=    -380.1934631       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7181380  5.0523         -375.6658630  4.5276         -380.1934631  14.596  13.161   6.584  22.022
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     15.332    
 decide> The unconnected minima in the chain and their distances are:
     5        2.48     7 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0302 Dev= 0.19% S= 2.49 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.75

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1009 steps. Energy=    -380.7727545       time=       2.14
 Minus side of path:                    1016 steps. Energy=    -380.7181380       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7727545 0.97806E-01     -380.6749486 0.43189E-01     -380.7181380   2.513   2.484  21.956   6.604
        Known (#5)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -380.1934631  4.5276        -375.6658630  5.0523        -380.7181380  14.596  13.161   6.584  22.022
   6     -380.7181380 0.43189E-01    -380.6749486 0.97806E-01    -380.7727545   2.513   2.484  21.956   6.604
   2     -380.7727545  6.9867        -373.7860159  5.7670        -379.5530127  20.716  17.193  14.338  10.113
   4     -379.5530127 0.42811E-02    -379.5487316 0.88504E-02    -379.5575820   0.828   0.818   3.587  40.424
   3     -379.5575820 0.12048        -379.4371010 0.40489E-01    -379.4775903   1.892   1.882  38.352   3.781

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               162.03
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             28733 time=          31.98 %= 19.7
 OPTIM> # of energy+gradient+Hessian calls=       904 time=           4.08 %=  2.5
