
 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 13: 1: 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -379.5945428     RMS force=    0.9416678244E-06
 OPTIM> Final energy  =    -391.4506195     RMS force=    0.9877995184E-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=     33716.    
 decide> The unconnected minima in the chain and their distances are:
     2       32.31     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 315 RMS= 0.1213 Dev= 1.90% S= 35.54 time= 3.68
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.29

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     950 steps. Energy=    -380.1327730       time=       2.14
 Minus side of path:                     989 steps. Energy=    -383.2637982       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1327730 0.57971         -379.5530675  3.7107         -383.2637982   7.596   6.630   6.131  23.649
        *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=     23250.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.54     4     3        1.90     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 4_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0870 Dev= 0.55% S= 30.94 time= 2.88
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.72

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 1.7642 Dev= 4.14% S= 2.01 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   4.29

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     976 steps. Energy=    -379.6893348       time=       3.53
 Minus side of path:                     935 steps. Energy=    -380.1327730       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6893348 0.56335         -379.1259883  1.0068         -380.1327730   1.831   1.604 125.046   1.160
        *NEW* (Placed in 5)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     33632.    
 decide> The unconnected minima in the chain and their distances are:
     2       32.28     5     5        1.02     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 5_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 315 RMS= 0.0969 Dev= 3.26% S= 36.40 time= 3.69
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.33

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     986 steps. Energy=    -379.6893348       time=       3.61
 Minus side of path:                     996 steps. Energy=    -385.1859057       time=       4.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.6893348 0.27641         -379.4129295  5.7730         -385.1859057  25.171  23.910   2.270  63.885
        Known (#5)                                              *NEW* (Placed in 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      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0252 Dev= 1.19% S= 1.03 time= 0.18
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   3.71

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     960 steps. Energy=    -379.5945428       time=       2.72
 Minus side of path:                     993 steps. Energy=    -379.6893348       time=       2.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.5945428 0.16239E-01     -379.5783039 0.11103         -379.6893348   1.027   1.024  39.161   3.703
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     19826.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.07     6 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 6_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0903 Dev= 1.21% S= 28.83 time= 3.08
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   8.62

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1256 steps. Energy=    -385.1859057       time=       5.61
 Minus side of path:                    1020 steps. Energy=    -388.0306024       time=       3.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1859057 0.40945         -384.7764568  3.2541         -388.0306024  32.312  27.454   3.868  37.485
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     274.38    
 decide> The unconnected minima in the chain and their distances are:
     2        6.50     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= 0.4791 Dev= 1.23% S= 7.36 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   5.54

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     959 steps. Energy=    -388.2678662       time=       2.41
 Minus side of path:                     936 steps. Energy=    -388.0306024       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2678662  1.0239         -387.2439797 0.78662         -388.0306024   2.187   2.029  73.377   1.976
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     172.12    
 decide> The unconnected minima in the chain and their distances are:
     2        5.56     8 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2178 Dev= 0.47% S= 5.93 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     958 steps. Energy=    -388.9372050       time=       3.10
 Minus side of path:                     941 steps. Energy=    -388.2678662       time=       3.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9372050  1.1819         -387.7553131 0.51255         -388.2678662   3.480   3.351  36.960   3.923
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     33.385    
 decide> The unconnected minima in the chain and their distances are:
     2        3.22     9 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0720 Dev= 1.01% S= 3.31 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   3.61

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     960 steps. Energy=    -388.9372050       time=       3.08
 Minus side of path:                     960 steps. Energy=    -391.4506195       time=       3.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.9372050 0.24490         -388.6923083  2.7583         -391.4506195   4.019   3.220  26.675   5.436
        Known (#9)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -379.5945428 0.16239E-01    -379.5783039 0.11103        -379.6893348   1.027   1.024  39.161   3.703
   3     -379.6893348 0.27641        -379.4129295  5.7730        -385.1859057  25.171  23.910   2.270  63.885
   5     -385.1859057 0.40945        -384.7764568  3.2541        -388.0306024  32.312  27.454   3.868  37.485
   6     -388.0306024 0.78662        -387.2439797  1.0239        -388.2678662   2.187   2.029  73.377   1.976
   7     -388.2678662 0.51255        -387.7553131  1.1819        -388.9372050   3.480   3.351  36.960   3.923
   8     -388.9372050 0.24490        -388.6923083  2.7583        -391.4506195   4.019   3.220  26.675   5.436

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               126.34
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             36341 time=          46.51 %= 36.8
 OPTIM> # of energy+gradient+Hessian calls=       492 time=           2.47 %=  2.0
