
 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)@comp33.ch.
                 Created on  5/28/12 at 12:59:52 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=    -389.7163378     RMS force=    0.9842381170E-06
 OPTIM> Final energy  =    -386.2896343     RMS force=    0.8147186892E-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=     82663.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.56     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 455 RMS= 0.1771 Dev= 0.76% S= 47.92 time= 7.95
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        159
 DNEB run yielded 1 true transition state(s) time=  20.15

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     993 steps. Energy=    -390.1452404       time=       3.40
 Minus side of path:                    1054 steps. Energy=    -388.5081389       time=       3.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1452404  2.1710         -387.9742244 0.53391         -388.5081389  23.552  20.784   7.174  20.212
        *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=     52331.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.72     4     3       14.11     1 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 4_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 385 RMS= 0.0734 Dev= 0.71% S= 39.11 time= 5.63
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=   9.08

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     960 steps. Energy=    -385.2565250       time=       3.41
 Minus side of path:                     956 steps. Energy=    -385.1135753       time=       3.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2565250 0.25254         -385.0039875 0.10959         -385.1135753   8.289   8.207   3.597  40.316
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0465 Dev= 0.17% S= 14.21 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   3.49

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     990 steps. Energy=    -390.1452404       time=       2.64
 Minus side of path:                     986 steps. Energy=    -389.6354626       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1452404 0.78846         -389.3567821 0.27868         -389.6354626  11.883  11.708   3.671  39.498
        Known (#3)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     37440.    
 decide> The unconnected minima in the chain and their distances are:
     2        5.63     5     6       33.39     4     7        3.38     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2013 Dev= 0.26% S= 5.76 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.18

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1005 steps. Energy=    -386.2896343       time=       2.89
 Minus side of path:                     939 steps. Energy=    -385.2565250       time=       2.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2896343  1.4451         -384.8445499 0.41198         -385.2565250   6.553   5.627   8.005  18.115
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 4_U and 6_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0745 Dev= 2.24% S= 36.70 time= 4.79
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.32

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     986 steps. Energy=    -385.1135753       time=       3.40
 Minus side of path:                    1037 steps. Energy=    -385.8281028       time=       4.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.1135753  1.0124         -384.1011549  1.7269         -385.8281028  23.366  20.221   4.996  29.025
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 6.6803 Dev= 0.58% S= 3.42 time= 0.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.83

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     944 steps. Energy=    -389.6354626       time=       3.45
 Minus side of path:                     968 steps. Energy=    -389.7163378       time=       3.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6354626 0.25948E-01     -389.6095142 0.10682         -389.7163378   3.401   3.383   2.757  52.594
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     5579.9    
 decide> The unconnected minima in the chain and their distances are:
     8       17.74     4 
 

 tryconnect> 175-iteration DNEB run for minima 4_S and 8_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1214 Dev= 0.49% S= 18.05 time= 1.28
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        127
 DNEB run yielded 1 true transition state(s) time=  12.65

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     998 steps. Energy=    -388.5081389       time=       2.71
 Minus side of path:                    1056 steps. Energy=    -388.5315930       time=       2.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.5081389 0.90965E-01     -388.4171741 0.11442         -388.5315930  14.629  12.216   3.394  42.718
        Known (#4)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     11160.    
 decide> The unconnected minima in the chain and their distances are:
     8       17.74     4 
 

 tryconnect> 805-iteration DNEB run for minima 4_S and 8_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.0355 Dev= 5.22% S= 20.45 time= 24.27
 Following    1 images are candidates for TS:   18  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   4.89

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1149 steps. Energy=    -392.8573233       time=       4.55
 Minus side of path:                     996 steps. Energy=    -385.8281028       time=       3.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8573233  7.3210         -385.5363475 0.29176         -385.8281028  26.396  24.278   2.371  61.148
        *NEW* (Placed in 10)                                    Known (#8)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     4213.9    
 decide> The unconnected minima in the chain and their distances are:
    10       16.15     4 
 

 tryconnect> 140-iteration DNEB run for minima 4_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0561 Dev= 0.14% S= 16.42 time= 0.79
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.41

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     973 steps. Energy=    -392.8573233       time=       2.76
 Minus side of path:                     945 steps. Energy=    -388.5081389       time=       2.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.8573233  4.3627         -388.4945919 0.13547E-01     -388.5081389  16.488  16.161   4.187  34.627
        Known (#10)                                             Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -389.7163378 0.10682        -389.6095142 0.25948E-01    -389.6354626   3.401   3.383   2.757  52.594
   3     -389.6354626 0.27868        -389.3567821 0.78846        -390.1452404  11.883  11.708   3.671  39.498
   1     -390.1452404  2.1710        -387.9742244 0.53391        -388.5081389  23.552  20.784   7.174  20.212
   9     -388.5081389 0.13547E-01    -388.4945919  4.3627        -392.8573233  16.488  16.161   4.187  34.627
   8     -392.8573233  7.3210        -385.5363475 0.29176        -385.8281028  26.396  24.278   2.371  61.148
   5     -385.8281028  1.7269        -384.1011549  1.0124        -385.1135753  23.366  20.221   4.996  29.025
   2     -385.1135753 0.10959        -385.0039875 0.25254        -385.2565250   8.289   8.207   3.597  40.316
   4     -385.2565250 0.41198        -384.8445499  1.4451        -386.2896343   6.553   5.627   8.005  18.115

 Number of TS in the path       =      8
 Number of cycles               =      6

 Elapsed time=                               178.12
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             62373 time=          80.25 %= 45.1
 OPTIM> # of energy+gradient+Hessian calls=       615 time=           3.19 %=  1.8
