
 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)@comp18.ch.
                 Created on  5/28/12 at 13: 9:28 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -386.6011306     RMS force=    0.9919637068E-06
 OPTIM> Final energy  =    -386.6648006     RMS force=    0.9350149324E-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=     8637.4    
 decide> The unconnected minima in the chain and their distances are:
     2       20.52     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1937 Dev= 0.24% S= 21.30 time= 1.81
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         77
 Converged to TS (number of iterations):         63
 DNEB run yielded 2 true transition state(s) time=  11.42

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1212 steps. Energy=    -391.0185085       time=       3.74
 Minus side of path:                     992 steps. Energy=    -387.5455132       time=       3.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.0185085  5.5373         -385.4811743  2.0643         -387.5455132  37.606  32.005   4.843  29.941
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     961 steps. Energy=    -386.6361851       time=       3.42
 Minus side of path:                    1028 steps. Energy=    -387.1179714       time=       4.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6361851 0.18348E-01     -386.6178368 0.50013         -387.1179714  15.160  14.885   1.900  76.327
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     5178.5    
 decide> The unconnected minima in the chain and their distances are:
     2       16.97     5     5        6.65     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0570 Dev= 0.08% S= 17.28 time= 1.38
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=   7.37
 isnewts> transition state is the same as number        2 energy=     -386.6178368482
 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:                     957 steps. Energy=    -386.6361851       time=       2.59
 Minus side of path:                    1032 steps. Energy=    -387.1179714       time=       2.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6361851 0.18348E-01     -386.6178368 0.50013         -387.1179714  15.160  14.885   1.898  76.382
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2057 Dev= 0.22% S= 6.72 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.65

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     980 steps. Energy=    -386.6011306       time=       2.65
 Minus side of path:                     999 steps. Energy=    -386.6361851       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6011306 0.94427         -385.6568568 0.97933         -386.6361851   6.935   6.651   4.770  30.399
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     8767.8    
 decide> The unconnected minima in the chain and their distances are:
     2        9.85     4     3       19.84     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4395 Dev= 0.15% S= 9.93 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     965 steps. Energy=    -387.2934344       time=       3.27
 Minus side of path:                     961 steps. Energy=    -387.5455132       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.2934344 0.44273         -386.8507061 0.69481         -387.5455132   2.694   2.488  16.062   9.027
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 3_U and 6_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1112 Dev= 0.13% S= 20.39 time= 1.34
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   8.59

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1046 steps. Energy=    -391.0185085       time=       3.46
 Minus side of path:                     943 steps. Energy=    -387.1179714       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.0185085  4.0131         -387.0054533 0.11252         -387.1179714  21.613  19.857   3.456  41.954
        Known (#3)                                              Known (#6)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     657.03    
 decide> The unconnected minima in the chain and their distances are:
     2        8.69     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0802 Dev= 0.03% S= 8.73 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.87

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     959 steps. Energy=    -387.2934344       time=       2.76
 Minus side of path:                     958 steps. Energy=    -386.6648006       time=       2.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.2934344  1.0978         -386.1955935 0.46921         -386.6648006   9.172   8.695   5.523  26.252
        Known (#7)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -386.6011306 0.94427        -385.6568568 0.97933        -386.6361851   6.935   6.651   4.770  30.399
   2     -386.6361851 0.18348E-01    -386.6178368 0.50013        -387.1179714  15.160  14.885   1.900  76.327
   6     -387.1179714 0.11252        -387.0054533  4.0131        -391.0185085  21.613  19.857   3.456  41.954
   1     -391.0185085  5.5373        -385.4811743  2.0643        -387.5455132  37.606  32.005   4.843  29.941
   5     -387.5455132 0.69481        -386.8507061 0.44273        -387.2934344   2.694   2.488  16.062   9.027
   7     -387.2934344  1.0978        -386.1955935 0.46921        -386.6648006   9.172   8.695   5.523  26.252

 Number of TS in the path       =      6
 Number of cycles               =      4

 Elapsed time=                                87.13
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             24434 time=          33.84 %= 38.8
 OPTIM> # of energy+gradient+Hessian calls=       375 time=           1.69 %=  1.9
