
 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)@comp21.ch.
                 Created on  5/28/12 at 13:11: 6 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.1678282     RMS force=    0.9687152806E-06
 OPTIM> Final energy  =    -388.7845356     RMS force=    0.9784241277E-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=     20781.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.49     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0927 Dev= 0.46% S= 32.26 time= 2.83
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        131
 DNEB run yielded 1 true transition state(s) time=  10.29

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     993 steps. Energy=    -383.5508335       time=       2.32
 Minus side of path:                     964 steps. Energy=    -387.6877387       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5508335 0.96367         -382.5871638  5.1006         -387.6877387  15.663  13.801   1.886  76.876
        *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=     10775.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.95     4     3       21.39     1 
 

 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= 0.8509 Dev= 0.12% S= 12.15 time= 0.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        111
 DNEB run yielded 1 true transition state(s) time=  10.55

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     974 steps. Energy=    -389.5564792       time=       4.00
 Minus side of path:                     983 steps. Energy=    -387.6877387       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5564792  2.8692         -386.6872932  1.0004         -387.6877387  23.429  22.288   2.857  50.757
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0934 Dev= 0.07% S= 21.84 time= 1.68
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         91
 DNEB run yielded 1 true transition state(s) time=   8.33

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1171 steps. Energy=    -383.5508335       time=       4.93
 Minus side of path:                     977 steps. Energy=    -383.1761707       time=       3.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5508335 0.43250         -383.1183294 0.57841E-01     -383.1761707  24.877  21.776   3.091  46.911
        Known (#3)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1968.5    
 decide> The unconnected minima in the chain and their distances are:
     2        9.95     4     6        0.90     1 
 

 tryconnect> 770-iteration DNEB run for minima 2_F and 4_U using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 770 RMS= 0.0370 Dev= 4.83% S= 24.39 time= 21.24
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.67

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     936 steps. Energy=    -385.3387044       time=       2.13
 Minus side of path:                     951 steps. Energy=    -385.2909508       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3387044 0.66913E-01     -385.2717915 0.19159E-01     -385.2909508   1.054   1.050  19.903   7.285
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0413 Dev= 0.15% S= 0.90 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   5.02

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     967 steps. Energy=    -383.1761707       time=       3.67
 Minus side of path:                     918 steps. Energy=    -383.1678282       time=       4.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1761707 0.32391E-01     -383.1437792 0.24049E-01     -383.1678282   0.913   0.899   8.087  17.929
        Known (#6)                                              Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2951.6    
 decide> The unconnected minima in the chain and their distances are:
     2        9.95     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 805 RMS= 0.0617 Dev= 3.74% S= 18.59 time= 23.14
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):        150
 DNEB run yielded 1 true transition state(s) time=  13.06

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1002 steps. Energy=    -385.3802147       time=       2.47
 Minus side of path:                    1114 steps. Energy=    -388.7845356       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.3802147 0.26948         -385.1107366  3.6738         -388.7845356  35.986  34.488   4.126  35.143
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     3024.3    
 decide> The unconnected minima in the chain and their distances are:
     2        9.96     8     7       12.68     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1649 Dev= 0.04% S= 10.03 time= 0.25
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   5.04

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     896 steps. Energy=    -385.2909508       time=       2.32
 Minus side of path:                     940 steps. Energy=    -388.7845356       time=       3.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2909508 0.15009E-01     -385.2759416  3.5086         -388.7845356  10.323   9.957   3.472  41.759
        Known (#8)                                              Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1952 Dev= 0.16% S= 13.29 time= 0.46
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     969 steps. Energy=    -385.2909508       time=       2.51
 Minus side of path:                    1008 steps. Energy=    -387.6877387       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2909508 0.16222         -385.1287336  2.5590         -387.6877387  18.502  12.943   4.976  29.137
        Known (#8)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -383.1678282 0.24049E-01    -383.1437792 0.32391E-01    -383.1761707   0.913   0.899   8.087  17.929
   3     -383.1761707 0.57841E-01    -383.1183294 0.43250        -383.5508335  24.877  21.776   3.091  46.911
   1     -383.5508335 0.96367        -382.5871638  5.1006        -387.6877387  15.663  13.801   1.886  76.876
   8     -387.6877387  2.5590        -385.1287336 0.16222        -385.2909508  18.502  12.943   4.976  29.137
   7     -385.2909508 0.15009E-01    -385.2759416  3.5086        -388.7845356  10.323   9.957   3.472  41.759

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

 Elapsed time=                               163.02
 OPTIM> # of energy calls=                        136 time=           0.16 %=  0.1
 OPTIM> # of energy+gradient calls=             64322 time=          76.74 %= 47.1
 OPTIM> # of energy+gradient+Hessian calls=       626 time=           2.92 %=  1.8
