
 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)@comp22.ch.
                 Created on  5/28/12 at 13: 1:51 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=    -382.9287207     RMS force=    0.9134004087E-06
 OPTIM> Final energy  =    -384.3999607     RMS force=    0.9408353066E-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=     24867.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.19     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 280 RMS= 1.9169 Dev= 2.15% S= 33.16 time= 2.68
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):        102
 Converged to TS (number of iterations):        142
 DNEB run yielded 2 true transition state(s) time=  34.42
 isnewts> transition state is the same as number        1 energy=     -381.5041574673
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1050 steps. Energy=    -382.9762347       time=       3.58
 Minus side of path:                    1109 steps. Energy=    -384.3618235       time=       3.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9762347  1.4721         -381.5041575  2.8577         -384.3618235  40.625  30.802   6.315  22.960
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1030 steps. Energy=    -382.9762347       time=       2.73
 Minus side of path:                    1091 steps. Energy=    -384.3618235       time=       3.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9762347  1.4721         -381.5041575  2.8577         -384.3618235  40.627  30.818   6.181  23.460
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     285.02    
 decide> The unconnected minima in the chain and their distances are:
     2        6.55     4     3        1.51     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.3270 Dev= 2.26% S= 7.37 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     950 steps. Energy=    -384.4353418       time=       2.67
 Minus side of path:                     952 steps. Energy=    -384.3999607       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4353418 0.67696E-01     -384.3676460 0.32315E-01     -384.3999607   1.560   1.543   4.419  32.816
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0272 Dev= 0.59% S= 1.51 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.65

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     942 steps. Energy=    -382.9762347       time=       2.35
 Minus side of path:                     982 steps. Energy=    -382.9287207       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9762347 0.76905E-01     -382.8993296 0.29391E-01     -382.9287207   1.544   1.505   8.984  16.139
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     260.14    
 decide> The unconnected minima in the chain and their distances are:
     5        6.38     4 
 

 tryconnect> 70-iteration DNEB run for minima 4_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 3.3050 Dev= 0.36% S= 7.25 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.45
 isnewts> transition state is the same as number        3 energy=     -384.3676460136
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     955 steps. Energy=    -384.4353418       time=       2.28
 Minus side of path:                     955 steps. Energy=    -384.3999607       time=       3.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4353418 0.67696E-01     -384.3676460 0.32315E-01     -384.3999607   1.560   1.543   4.418  32.817
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     520.28    
 decide> The unconnected minima in the chain and their distances are:
     5        6.38     4 
 

 tryconnect> 490-iteration DNEB run for minima 4_S and 5_F using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2017697586    
 Double-ended search iterations= 490 RMS= 0.0257 Dev= 3.74% S= 10.15 time= 8.32
 Following    2 images are candidates for TS:    1    8  
 Converged to TS (number of iterations):         12
 Converged to TS (number of iterations):         13
 DNEB run yielded 2 true transition state(s) time=   7.07

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     941 steps. Energy=    -384.3618235       time=       3.10
 Minus side of path:                     949 steps. Energy=    -384.3945167       time=       3.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3618235 0.33166E-01     -384.3286576 0.65859E-01     -384.3945167   1.571   1.554   4.246  34.149
        Known (#4)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     985 steps. Energy=    -384.4353418       time=       2.35
 Minus side of path:                     962 steps. Energy=    -384.3945167       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4353418  5.3201         -379.1152724  5.2792         -384.3945167   7.900   6.587  22.604   6.415
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -382.9287207 0.29391E-01    -382.8993296 0.76905E-01    -382.9762347   1.544   1.505   8.984  16.139
   1     -382.9762347  1.4721        -381.5041575  2.8577        -384.3618235  40.625  30.802   6.315  22.960
   6     -384.3618235 0.33166E-01    -384.3286576 0.65859E-01    -384.3945167   1.571   1.554   4.246  34.149
   7     -384.3945167  5.2792        -379.1152724  5.3201        -384.4353418   7.900   6.587  22.604   6.415
   3     -384.4353418 0.67696E-01    -384.3676460 0.32315E-01    -384.3999607   1.560   1.543   4.419  32.816

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                               107.40
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             31690 time=          37.32 %= 34.7
 OPTIM> # of energy+gradient+Hessian calls=       364 time=           1.78 %=  1.7
