
 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 13:10:53 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=    -381.5798872     RMS force=    0.9084062456E-06
 OPTIM> Final energy  =    -385.6445936     RMS force=    0.8753210849E-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=     1679.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.89     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2306 Dev= 0.75% S= 12.54 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         91
 DNEB run yielded 1 true transition state(s) time=   9.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1069 steps. Energy=    -381.5798872       time=       3.54
 Minus side of path:                    1351 steps. Energy=    -385.7689833       time=       5.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5798872 0.14148         -381.4384034  4.3306         -385.7689833  44.099  37.461   1.644  88.178
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3359.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.89     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.0898 Dev= 4.77% S= 17.94 time= 20.76
 Following    2 images are candidates for TS:    4   19  
 Converged to TS (number of iterations):         79
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=  10.46
 isnewts> transition state is the same as number        1 energy=     -381.4384033524
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1053 steps. Energy=    -381.5798872       time=       2.76
 Minus side of path:                    1352 steps. Energy=    -385.7689833       time=       6.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5798872 0.14148         -381.4384034  4.3306         -385.7689833  44.101  37.464   1.641  88.343
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     997 steps. Energy=    -385.6445936       time=       3.58
 Minus side of path:                     994 steps. Energy=    -386.5783153       time=       2.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.6445936  2.0141         -383.6304813  2.9478         -386.5783153   6.539   5.768  23.993   6.043
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to 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=     1082.5    
 decide> The unconnected minima in the chain and their distances are:
     4       10.27     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2251 Dev= 0.62% S= 10.82 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   8.78
 isnewts> transition state is the same as number        1 energy=     -381.4384033526
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2165.0    
 decide> The unconnected minima in the chain and their distances are:
     4       10.27     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 805 RMS= 0.0617 Dev= 5.31% S= 12.92 time= 20.82
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.57
 isnewts> transition state is the same as number        1 energy=     -381.4384033526
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     72439.    
 decide> The unconnected minima in the chain and their distances are:
     4       41.69     3 
 

 tryconnect> 420-iteration DNEB run for minima 3_S and 4_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.2537 Dev= 2.36% S= 44.42 time= 6.01
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        117
 DNEB run yielded 1 true transition state(s) time=   9.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1008 steps. Energy=    -384.8152122       time=       2.65
 Minus side of path:                    1128 steps. Energy=    -385.7689833       time=       3.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8152122 0.12561         -384.6895980  1.0794         -385.7689833  35.415  34.443   2.218  65.382
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     13378.    
 decide> The unconnected minima in the chain and their distances are:
     4       23.74     5 
 

 tryconnect> 245-iteration DNEB run for minima 4_F and 5_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1870 Dev= 0.53% S= 24.65 time= 1.99
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.53

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1170 steps. Energy=    -385.7689833       time=       3.90
 Minus side of path:                    1038 steps. Energy=    -386.5783153       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.7689833  1.7127         -384.0562763  2.5220         -386.5783153  44.994  41.751   1.691  85.742
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -381.5798872 0.14148        -381.4384034  4.3306        -385.7689833  44.099  37.461   1.644  88.178
   5     -385.7689833  1.7127        -384.0562763  2.5220        -386.5783153  44.994  41.751   1.691  85.742
   3     -386.5783153  2.9478        -383.6304813  2.0141        -385.6445936   6.539   5.768  23.993   6.043

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

 Elapsed time=                               140.70
 OPTIM> # of energy calls=                        142 time=           0.15 %=  0.1
 OPTIM> # of energy+gradient calls=             63555 time=          68.53 %= 48.7
 OPTIM> # of energy+gradient+Hessian calls=       536 time=           2.40 %=  1.7
