
 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)@comp24.ch.
                 Created on  5/28/12 at 13: 4:51 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -384.7663572     RMS force=    0.9884221069E-06
 OPTIM> Final energy  =    -388.4533193     RMS force=    0.9003213522E-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=     24240.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.94     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      153.6741246    
 Double-ended search iterations= 449 RMS= 3.3968 Dev= 0.24% S= 29.20 time= 4.98
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.69

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     967 steps. Energy=    -386.8408060       time=       3.26
 Minus side of path:                     947 steps. Energy=    -387.8182390       time=       3.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8408060  2.2362         -384.6045684  3.2137         -387.8182390   6.001   5.178  39.658   3.656
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     9241.5    
 decide> The unconnected minima in the chain and their distances are:
     2       16.10     4     3       17.17     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      39.20129138    
 Double-ended search iterations= 167 RMS= 42.4507 Dev= 37.36% S= 93.34 time= 0.95
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   6.46

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     952 steps. Energy=    -388.4533193       time=       3.19
 Minus side of path:                     952 steps. Energy=    -387.8310675       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.4533193 0.80862         -387.6447009 0.18637         -387.8310675  14.227  13.733   7.689  18.857
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      15.51328216    
 Double-ended search iterations= 175 RMS= 3.0075 Dev= 0.36% S= 17.25 time= 1.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.92

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     952 steps. Energy=    -385.4505590       time=       2.51
 Minus side of path:                     936 steps. Energy=    -384.7663572       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.4505590 0.75618         -384.6943775 0.71980E-01     -384.7663572   4.634   4.353   9.095  15.943
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     4566.3    
 decide> The unconnected minima in the chain and their distances are:
     5        4.54     4     4       16.48     6 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.0335 Dev= 0.22% S= 4.54 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   6.15

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     994 steps. Energy=    -387.8182390       time=       3.24
 Minus side of path:                     991 steps. Energy=    -387.8310675       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8182390 0.39044E-01     -387.7791947 0.51873E-01     -387.8310675   6.571   4.543   3.122  46.448
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 4_F and 6_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 140 RMS= 0.4219 Dev= 1.06% S= 16.69 time= 0.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.39

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     943 steps. Energy=    -386.3396522       time=       2.55
 Minus side of path:                     963 steps. Energy=    -385.4505590       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.3396522  3.2047         -383.1349448  2.3156         -385.4505590   5.949   5.120  22.134   6.551
        *NEW* (Placed in 7)                                     Known (#6)
 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=     4329.7    
 decide> The unconnected minima in the chain and their distances are:
     4       16.30     7 
 

 tryconnect> 140-iteration DNEB run for minima 4_F and 7_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 140 RMS= 0.3006 Dev= 0.77% S= 16.35 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   5.81

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     934 steps. Energy=    -386.3396522       time=       2.16
 Minus side of path:                     959 steps. Energy=    -387.5143372       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.3396522 0.34375E-01     -386.3052769  1.2091         -387.5143372  11.280  11.181   2.217  65.418
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     4330.1    
 decide> The unconnected minima in the chain and their distances are:
     4       16.30     8 
 

 tryconnect> 140-iteration DNEB run for minima 4_F and 8_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 140 RMS= 2.1738 Dev= 2.58% S= 16.97 time= 0.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.85

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     933 steps. Energy=    -387.8182390       time=       2.57
 Minus side of path:                     925 steps. Energy=    -387.5143372       time=       2.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.8182390  1.2293         -386.5889766 0.92536         -387.5143372  18.021  16.049   2.520  57.549
        Known (#4)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -384.7663572 0.71980E-01    -384.6943775 0.75618        -385.4505590   4.634   4.353   9.095  15.943
   5     -385.4505590  2.3156        -383.1349448  3.2047        -386.3396522   5.949   5.120  22.134   6.551
   6     -386.3396522 0.34375E-01    -386.3052769  1.2091        -387.5143372  11.280  11.181   2.217  65.418
   7     -387.5143372 0.92536        -386.5889766  1.2293        -387.8182390  18.021  16.049   2.520  57.549
   4     -387.8182390 0.39044E-01    -387.7791947 0.51873E-01    -387.8310675   6.571   4.543   3.122  46.448
   2     -387.8310675 0.18637        -387.6447009 0.80862        -388.4533193  14.227  13.733   7.689  18.857

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

 Elapsed time=                                86.20
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             27267 time=          36.50 %= 42.3
 OPTIM> # of energy+gradient+Hessian calls=       271 time=           1.36 %=  1.6
