
 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 12:41:32 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -389.6639145     RMS force=    0.9768178271E-06
 OPTIM> Final energy  =    -384.2695727     RMS force=    0.9129670961E-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=    0.29026E+06
 decide> The unconnected minima in the chain and their distances are:
     2       66.21     1 
 

 tryconnect> 665-iteration DNEB run for minima 1_S and 2_F using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 665 RMS= 0.0697 Dev= 2.96% S= 77.35 time= 14.51
 Following    3 images are candidates for TS:   10   16   19  
 Converged to TS (number of iterations):        113
 Converged to TS (number of iterations):        138
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        118
 DNEB run yielded 3 true transition state(s) time=  44.39

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1963 steps. Energy=    -389.6639145       time=      13.02
 Minus side of path:                    2102 steps. Energy=    -386.4237956       time=      17.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6639145  10.568         -379.0958104  7.3280         -386.4237956 121.096  54.544   1.818  79.763
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1072 steps. Energy=    -385.2992767       time=       2.64
 Minus side of path:                     980 steps. Energy=    -384.6480922       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2992767 0.92630         -384.3729749 0.27512         -384.6480922  33.697  33.099   1.791  80.981
        *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:                    1088 steps. Energy=    -384.3673304       time=       3.59
 Minus side of path:                     971 steps. Energy=    -383.7136642       time=       3.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3673304 0.92726         -383.4400742 0.27359         -383.7136642  33.904  33.323   1.757  82.539
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     42590.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.02     6     6        5.78     4     5       34.87     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0149 Dev= 0.21% S= 1.03 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1004 steps. Energy=    -384.2695727       time=       2.33
 Minus side of path:                     985 steps. Energy=    -384.3673304       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2695727 0.14954E-01     -384.2546190 0.11271         -384.3673304   1.023   1.020  38.684   3.748
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 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= 0.2260 Dev= 0.65% S= 6.16 time= 0.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.63

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1007 steps. Energy=    -384.3673304       time=       2.24
 Minus side of path:                     992 steps. Energy=    -385.2992767       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3673304  2.0150         -382.3523005  2.9470         -385.2992767   6.563   5.779  23.845   6.081
        Known (#6)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 3_S and 5_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1004 Dev= 2.62% S= 37.86 time= 4.33
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   5.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1010 steps. Energy=    -384.5587592       time=       2.71
 Minus side of path:                    1172 steps. Energy=    -386.4237956       time=       3.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.5587592  2.8191         -381.7396658  4.6841         -386.4237956  20.361  19.799   3.449  42.041
        *NEW* (Placed in 8)                                     Known (#3)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     8164.0    
 decide> The unconnected minima in the chain and their distances are:
     5       20.14     8 
 

 tryconnect> 210-iteration DNEB run for minima 5_F and 8_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0173 Dev= 0.01% S= 20.18 time= 1.58
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.41

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     962 steps. Energy=    -384.6480922       time=       2.07
 Minus side of path:                     959 steps. Energy=    -384.5587592       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6480922 0.15731         -384.4907820 0.67977E-01     -384.5587592  20.357  20.136   2.335  62.102
        Known (#5)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -389.6639145  10.568        -379.0958104  7.3280        -386.4237956 121.096  54.544   1.818  79.763
   6     -386.4237956  4.6841        -381.7396658  2.8191        -384.5587592  20.361  19.799   3.449  42.041
   7     -384.5587592 0.67977E-01    -384.4907820 0.15731        -384.6480922  20.357  20.136   2.335  62.102
   2     -384.6480922 0.27512        -384.3729749 0.92630        -385.2992767  33.697  33.099   1.791  80.981
   5     -385.2992767  2.9470        -382.3523005  2.0150        -384.3673304   6.563   5.779  23.845   6.081
   4     -384.3673304 0.11271        -384.2546190 0.14954E-01    -384.2695727   1.023   1.020  38.684   3.748

 Number of TS in the path       =      6
 Number of cycles               =      3

 Elapsed time=                               142.85
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42907 time=          48.57 %= 34.0
 OPTIM> # of energy+gradient+Hessian calls=       461 time=           2.09 %=  1.5
