
 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)@comp31.ch.
                 Created on  5/28/12 at 12:52:22 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=    -379.9078830     RMS force=    0.9982737733E-06
 OPTIM> Final energy  =    -379.7128734     RMS force=    0.9533959835E-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=     5149.7    
 decide> The unconnected minima in the chain and their distances are:
     2       17.27     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 175 RMS= 1.0508 Dev= 2.47% S= 22.74 time= 0.95
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   6.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1015 steps. Energy=    -380.9263577       time=       2.47
 Minus side of path:                     964 steps. Energy=    -380.6973297       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.9263577 0.42612         -380.5002342 0.19710         -380.6973297   5.081   4.286   3.587  40.422
        *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=     5173.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.69     3     4       12.61     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.3277 Dev= 0.90% S= 17.63 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.80

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1028 steps. Energy=    -380.1934631       time=       2.34
 Minus side of path:                    1011 steps. Energy=    -379.7128734       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631  2.5640         -377.6294833  2.0834         -379.7128734  12.004  10.013   5.792  25.034
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 1.3112 Dev= 1.91% S= 16.00 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   5.99

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1011 steps. Energy=    -382.4120776       time=       2.37
 Minus side of path:                    1022 steps. Energy=    -380.6973297       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4120776  2.5362         -379.8758854 0.82144         -380.6973297  22.220  21.483   3.154  45.973
        *NEW* (Placed in 6)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4031.1    
 decide> The unconnected minima in the chain and their distances are:
     5       11.56     3     3       13.55     1 
 

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 0.5607 Dev= 1.05% S= 14.76 time= 0.34
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1003 steps. Energy=    -380.1934631       time=       3.22
 Minus side of path:                    1031 steps. Energy=    -380.9263577       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.1934631  4.5475         -375.6459544  5.2804         -380.9263577  17.356  11.566  20.072   7.224
        Known (#5)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 4.0229 Dev= 15.15% S= 19.84 time= 0.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        238
 DNEB run yielded 1 true transition state(s) time=  18.41

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1064 steps. Energy=    -382.6084653       time=       2.64
 Minus side of path:                    1359 steps. Energy=    -380.9263577       time=       5.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6084653  3.4381         -379.1703200  1.7560         -380.9263577  49.845  45.476   2.559  56.672
        *NEW* (Placed in 7)                                     Known (#3)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     4009.8    
 decide> The unconnected minima in the chain and their distances are:
     4       12.61     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 805 RMS= 0.1136 Dev= 6.01% S= 26.82 time= 20.48
 Following    3 images are candidates for TS:    2   12   16  
 Converged to TS (number of iterations):         25
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         41
 DNEB run yielded 3 true transition state(s) time=  14.87
 isnewts> transition state is the same as number        3 energy=     -379.8758853946
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     949 steps. Energy=    -379.9078830       time=       3.10
 Minus side of path:                    1158 steps. Energy=    -383.8079168       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.9078830 0.18517E-01     -379.8893662  3.9186         -383.8079168  25.160  22.724   1.683  86.146
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1134 steps. Energy=    -383.8079168       time=       2.91
 Minus side of path:                    1207 steps. Energy=    -382.6431096       time=       3.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8079168  4.4200         -379.3879301  3.2552         -382.6431096  39.555  18.644  16.775   8.644
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1028 steps. Energy=    -382.4120776       time=       2.82
 Minus side of path:                    1002 steps. Energy=    -380.6973297       time=       2.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4120776  2.5362         -379.8758854 0.82144         -380.6973297  22.220  21.483   3.153  45.989
        Known (#6)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     36.018    
 decide> The unconnected minima in the chain and their distances are:
     6        3.30     9 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1284 Dev= 0.06% S= 3.32 time= 0.16
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.66

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     983 steps. Energy=    -382.4120776       time=       2.84
 Minus side of path:                     989 steps. Energy=    -382.6431096       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4120776 0.47742E-02     -382.4073034 0.23581         -382.6431096   3.325   3.302   4.556  31.828
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -379.9078830 0.18517E-01    -379.8893662  3.9186        -383.8079168  25.160  22.724   1.683  86.146
   7     -383.8079168  4.4200        -379.3879301  3.2552        -382.6431096  39.555  18.644  16.775   8.644
   9     -382.6431096 0.23581        -382.4073034 0.47742E-02    -382.4120776   3.325   3.302   4.556  31.828
   3     -382.4120776  2.5362        -379.8758854 0.82144        -380.6973297  22.220  21.483   3.154  45.973
   1     -380.6973297 0.19710        -380.5002342 0.42612        -380.9263577   5.081   4.286   3.587  40.422
   4     -380.9263577  5.2804        -375.6459544  4.5475        -380.1934631  17.356  11.566  20.072   7.224
   2     -380.1934631  2.5640        -377.6294833  2.0834        -379.7128734  12.004  10.013   5.792  25.034

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                               132.38
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             50375 time=          53.56 %= 40.5
 OPTIM> # of energy+gradient+Hessian calls=       549 time=           2.26 %=  1.7
