
 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 13:11:40 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=    -385.7689833     RMS force=    0.9612589376E-06
 OPTIM> Final energy  =    -379.9260352     RMS force=    0.8718081059E-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=    0.10353E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.96     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 490 RMS= 0.0384 Dev= 4.20% S= 53.10 time= 8.18
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        242
 DNEB run yielded 1 true transition state(s) time=  18.44

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     948 steps. Energy=    -379.9260352       time=       2.12
 Minus side of path:                    1062 steps. Energy=    -381.1278293       time=       3.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.9260352 0.15138E-02     -379.9245214  1.2033         -381.1278293  23.939  23.907   1.829  79.264
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     49023.    
 decide> The unconnected minima in the chain and their distances are:
     3       36.60     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 3_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0831 Dev= 3.77% S= 40.29 time= 4.18
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        101
 DNEB run yielded 1 true transition state(s) time=   8.44

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1006 steps. Energy=    -381.1278293       time=       2.22
 Minus side of path:                    1035 steps. Energy=    -381.1466521       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1278293 0.40526         -380.7225717 0.42408         -381.1466521  30.808  28.624   1.893  76.578
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     11382.    
 decide> The unconnected minima in the chain and their distances are:
     4       22.49     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1230 Dev= 0.97% S= 23.90 time= 1.49
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   7.94

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1288 steps. Energy=    -387.5661862       time=       4.85
 Minus side of path:                    1105 steps. Energy=    -381.1466521       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.5661862  7.2358         -380.3303727 0.81628         -381.1466521  48.648  44.796   1.739  83.370
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     22764.    
 decide> The unconnected minima in the chain and their distances are:
     4       22.49     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.1308 Dev= 2.13% S= 24.78 time= 22.11
 Following    1 images are candidates for TS:   20  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1019 steps. Energy=    -381.1466521       time=       2.50
 Minus side of path:                    1437 steps. Energy=    -385.7689833       time=       6.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.1466521  2.5726         -378.5740420  7.1949         -385.7689833  26.133  22.538   1.749  82.882
        Known (#4)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -385.7689833  7.1949        -378.5740420  2.5726        -381.1466521  26.133  22.538   1.749  82.882
   2     -381.1466521 0.42408        -380.7225717 0.40526        -381.1278293  30.808  28.624   1.893  76.578
   1     -381.1278293  1.2033        -379.9245214 0.15138E-02    -379.9260352  23.939  23.907   1.829  79.264

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                               101.32
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             44083 time=          49.43 %= 48.8
 OPTIM> # of energy+gradient+Hessian calls=       440 time=           1.95 %=  1.9
