
 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 12:59:22 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=    -379.5545729     RMS force=    0.9317000400E-06
 OPTIM> Final energy  =    -380.7997563     RMS force=    0.9214958779E-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=     5445.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.59     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 175 RMS= 0.1875 Dev= 1.09% S= 18.80 time= 0.98
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   6.84

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     991 steps. Energy=    -381.4981176       time=       3.25
 Minus side of path:                    1008 steps. Energy=    -381.5409329       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4981176 0.99822E-02     -381.4881355 0.52797E-01     -381.5409329   3.077   3.053   2.921  49.637
        *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=     5372.2    
 decide> The unconnected minima in the chain and their distances are:
     2        9.79     4     3       16.43     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.4588 Dev= 0.26% S= 10.06 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   5.11

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     988 steps. Energy=    -380.7997563       time=       4.11
 Minus side of path:                     991 steps. Energy=    -381.5409329       time=       3.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.7997563  2.0710         -378.7287784  2.8122         -381.5409329  10.508   9.796  22.805   6.358
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.5028 Dev= 0.37% S= 17.12 time= 0.66
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   6.57
 isnewts> transition state is the same as number        1 energy=     -381.4881354934
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     995 steps. Energy=    -381.4981176       time=       3.15
 Minus side of path:                     989 steps. Energy=    -381.5409329       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4981176 0.99822E-02     -381.4881355 0.52797E-01     -381.5409329   3.077   3.053   2.921  49.639
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5064.1    
 decide> The unconnected minima in the chain and their distances are:
     4       17.17     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1049 Dev= 0.18% S= 17.91 time= 1.02
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=  11.59

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     973 steps. Energy=    -379.6962273       time=       3.84
 Minus side of path:                    1016 steps. Energy=    -381.6670056       time=       4.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6962273 0.35671         -379.3395135  2.3275         -381.6670056   3.262   3.067  12.278  11.810
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1014 steps. Energy=    -381.6670056       time=       4.29
 Minus side of path:                    1019 steps. Energy=    -381.5409329       time=       3.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.6670056  2.9988         -378.6681652  2.8728         -381.5409329   7.256   6.303  26.206   5.533
        Known (#6)                                              Known (#4)
 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      4 steps with      1 missing connections, weight=     2501.3    
 decide> The unconnected minima in the chain and their distances are:
     5       13.57     1 
 

 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= 0.0474 Dev= 0.22% S= 13.67 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.88

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1064 steps. Energy=    -379.6962273       time=       3.65
 Minus side of path:                    1000 steps. Energy=    -379.5545729       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6962273 0.19640         -379.4998301 0.54743E-01     -379.5545729  13.672  13.577   2.762  52.503
        Known (#5)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -379.5545729 0.54743E-01    -379.4998301 0.19640        -379.6962273  13.672  13.577   2.762  52.503
   4     -379.6962273 0.35671        -379.3395135  2.3275        -381.6670056   3.262   3.067  12.278  11.810
   5     -381.6670056  2.9988        -378.6681652  2.8728        -381.5409329   7.256   6.303  26.206   5.533
   2     -381.5409329  2.8122        -378.7287784  2.0710        -380.7997563  10.508   9.796  22.805   6.358

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

 Elapsed time=                                82.28
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21334 time=          24.52 %= 29.8
 OPTIM> # of energy+gradient+Hessian calls=       233 time=           1.15 %=  1.4
