
 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 12:47: 3 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=    -382.7203188     RMS force=    0.9426126713E-06
 OPTIM> Final energy  =    -387.2743146     RMS force=    0.9606454704E-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=     9588.0    
 decide> The unconnected minima in the chain and their distances are:
     2       21.24     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 210 RMS= 0.5231 Dev= 0.79% S= 21.40 time= 1.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=   8.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     945 steps. Energy=    -387.3621153       time=       2.21
 Minus side of path:                     870 steps. Energy=    -387.2743146       time=       1.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.3621153 0.12675         -387.2353624 0.38952E-01     -387.2743146  13.282  13.196   2.390  60.673
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     15500.    
 decide> The unconnected minima in the chain and their distances are:
     3       24.93     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      41.16135595    
 Double-ended search iterations= 245 RMS= 0.5856 Dev= 0.57% S= 25.05 time= 2.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   6.71

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     964 steps. Energy=    -383.7889800       time=       2.45
 Minus side of path:                     999 steps. Energy=    -387.2743146       time=       3.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7889800 0.74428         -383.0447010  4.2296         -387.2743146  16.517  15.707   3.793  38.224
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3227.0    
 decide> The unconnected minima in the chain and their distances are:
     4       14.78     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 1.0878 Dev= 0.42% S= 14.86 time= 0.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        120
 DNEB run yielded 1 true transition state(s) time=  15.45

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1290 steps. Energy=    -394.6900421       time=       5.79
 Minus side of path:                    1604 steps. Energy=    -388.7357779       time=       9.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6900421  11.615         -383.0752798  5.6605         -388.7357779  49.788  42.748   2.388  60.714
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6453.9    
 decide> The unconnected minima in the chain and their distances are:
     4       14.78     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7984714498E-01
 Double-ended search iterations= 805 RMS= 0.0082 Dev= 4.10% S= 17.12 time= 24.96
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.75

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     925 steps. Energy=    -382.7203188       time=       3.54
 Minus side of path:                    1652 steps. Energy=    -388.7357779       time=       8.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.7203188 0.58451E-01     -382.6618682  6.0739         -388.7357779  32.998  31.675   2.655  54.617
        Known (#1)                                              Known (#6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     11394.    
 decide> The unconnected minima in the chain and their distances are:
     4       22.50     6 
 

 tryconnect> 210-iteration DNEB run for minima 4_F and 6_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 210 RMS= 0.2696 Dev= 0.76% S= 22.97 time= 1.68
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        125
 DNEB run yielded 1 true transition state(s) time=  10.65

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     962 steps. Energy=    -388.7357779       time=       2.99
 Minus side of path:                     953 steps. Energy=    -390.1831633       time=       2.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7357779 0.45076         -388.2850143  1.8981         -390.1831633  19.069  16.378   4.108  35.295
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     16561.    
 decide> The unconnected minima in the chain and their distances are:
     4       25.49     7 
 

 tryconnect> 245-iteration DNEB run for minima 4_F and 7_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 245 RMS= 0.1206 Dev= 0.21% S= 26.26 time= 2.37
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   7.65

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     978 steps. Energy=    -390.1831633       time=       3.42
 Minus side of path:                    1024 steps. Energy=    -390.7237171       time=       3.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.1831633  1.2762         -388.9069546  1.8168         -390.7237171  36.833  34.968   2.573  56.346
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     846.90    
 decide> The unconnected minima in the chain and their distances are:
     3        9.46     8 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 0.6547 Dev= 5.62% S= 9.56 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        103
 DNEB run yielded 1 true transition state(s) time=   9.19

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1289 steps. Energy=    -390.9898259       time=       5.26
 Minus side of path:                     966 steps. Energy=    -387.9538974       time=       2.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9898259  4.0001         -386.9897329 0.96416         -387.9538974  14.181  12.323   3.321  43.663
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1693.8    
 decide> The unconnected minima in the chain and their distances are:
     3        9.46     8 
 

 tryconnect> 735-iteration DNEB run for minima 3_F and 8_S using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 735 RMS= 0.0383 Dev= 6.20% S= 12.86 time= 20.69
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.87

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     982 steps. Energy=    -390.7237171       time=       2.67
 Minus side of path:                     933 steps. Energy=    -387.3621153       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7237171  3.4544         -387.2693214 0.92794E-01     -387.3621153  10.756   9.463   4.589  31.598
        Known (#8)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -382.7203188 0.58451E-01    -382.6618682  6.0739        -388.7357779  32.998  31.675   2.655  54.617
   5     -388.7357779 0.45076        -388.2850143  1.8981        -390.1831633  19.069  16.378   4.108  35.295
   6     -390.1831633  1.2762        -388.9069546  1.8168        -390.7237171  36.833  34.968   2.573  56.346
   8     -390.7237171  3.4544        -387.2693214 0.92794E-01    -387.3621153  10.756   9.463   4.589  31.598
   1     -387.3621153 0.12675        -387.2353624 0.38952E-01    -387.2743146  13.282  13.196   2.390  60.673

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                               185.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             67200 time=          87.54 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       679 time=           3.34 %=  1.8
