
 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)@comp21.ch.
                 Created on  5/28/12 at 13: 1:53 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=    -392.0964927     RMS force=    0.9815533048E-06
 OPTIM> Final energy  =    -389.4449695     RMS force=    0.9440446519E-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=     91888.    
 decide> The unconnected minima in the chain and their distances are:
     2       45.13     1 
 

 tryconnect> 455-iteration DNEB run for minima 1_S and 2_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 455 RMS= 0.8837 Dev= 0.79% S= 54.50 time= 7.93
 Following    2 images are candidates for TS:    5   11  
 Converged to TS (number of iterations):        165
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=  19.82

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     998 steps. Energy=    -390.9059379       time=       3.78
 Minus side of path:                     903 steps. Energy=    -384.2357417       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9059379  6.7315         -384.1744464 0.61295E-01     -384.2357417  20.733  19.563   5.852  24.776
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     923 steps. Energy=    -389.9449230       time=       2.91
 Minus side of path:                     928 steps. Energy=    -389.4449695       time=       2.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.9449230  5.2436         -384.7013648  4.7436         -389.4449695  18.220  16.884   5.272  27.502
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     12763.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.95     4     3        8.79     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_U and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 210 RMS= 1.3839 Dev= 0.48% S= 23.91 time= 1.71
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   3.64

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     936 steps. Energy=    -384.2357417       time=       2.08
 Minus side of path:                     867 steps. Energy=    -388.0944861       time=       1.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.2357417 0.22472         -384.0110230  4.0835         -388.0944861  12.244  11.676  10.157  14.276
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 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= 0.9724 Dev= 1.55% S= 9.61 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   5.47

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     912 steps. Energy=    -392.5784843       time=       2.19
 Minus side of path:                    1049 steps. Energy=    -396.7935684       time=       2.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.5784843  3.4933         -389.0851800  7.7084         -396.7935684  18.893  15.171   9.485  15.287
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     5117.8    
 decide> The unconnected minima in the chain and their distances are:
     5       16.71     6     3        3.43     7     7        7.43     1 
 

 tryconnect> 175-iteration DNEB run for minima 5_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 1.7791 Dev= 0.63% S= 17.21 time= 1.17
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    5  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   4.99

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     916 steps. Energy=    -389.6380457       time=       2.08
 Minus side of path:                     944 steps. Energy=    -389.9449230       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6380457 0.31254         -389.3255085 0.61941         -389.9449230  14.662  14.495   2.975  48.744
        *NEW* (Placed in 9)                                     Known (#5)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 1.3519 Dev= 0.50% S= 3.76 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        194
 DNEB run yielded 1 true transition state(s) time=  15.42

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1070 steps. Energy=    -390.9059379       time=       4.07
 Minus side of path:                     961 steps. Energy=    -387.8327292       time=       3.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.9059379  5.8918         -385.0141599  2.8186         -387.8327292  39.368  32.687   2.029  71.460
        Known (#3)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4424 Dev= 0.25% S= 7.60 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   5.55

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     941 steps. Energy=    -392.0964927       time=       3.28
 Minus side of path:                     901 steps. Energy=    -392.5784843       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.0964927  1.6402         -390.4563360  2.1221         -392.5784843  10.620   7.443  24.038   6.032
        Known (#1)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     204.05    
 decide> The unconnected minima in the chain and their distances are:
     9        4.98     6     3        3.43     7 
 

 tryconnect> 70-iteration DNEB run for minima 6_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2646 Dev= 0.32% S= 5.02 time= 0.19
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     888 steps. Energy=    -389.6380457       time=       1.97
 Minus side of path:                     835 steps. Energy=    -388.0944861       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.6380457  1.5554         -388.0826043 0.11882E-01     -388.0944861   5.055   4.975   5.184  27.969
        Known (#9)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 3_F and 7_S using 7 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 245 RMS= 0.1043 Dev= 4.59% S= 3.86 time= 2.31
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.49

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     890 steps. Energy=    -392.5784843       time=       1.99
 Minus side of path:                     892 steps. Energy=    -390.9059379       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -392.5784843  4.5058         -388.0727143  2.8332         -390.9059379   3.968   3.433  37.468   3.870
        Known (#7)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -392.0964927  1.6402        -390.4563360  2.1221        -392.5784843  10.620   7.443  24.038   6.032
   9     -392.5784843  4.5058        -388.0727143  2.8332        -390.9059379   3.968   3.433  37.468   3.870
   1     -390.9059379  6.7315        -384.1744464 0.61295E-01    -384.2357417  20.733  19.563   5.852  24.776
   3     -384.2357417 0.22472        -384.0110230  4.0835        -388.0944861  12.244  11.676  10.157  14.276
   8     -388.0944861 0.11882E-01    -388.0826043  1.5554        -389.6380457   5.055   4.975   5.184  27.969
   5     -389.6380457 0.31254        -389.3255085 0.61941        -389.9449230  14.662  14.495   2.975  48.744
   2     -389.9449230  5.2436        -384.7013648  4.7436        -389.4449695  18.220  16.884   5.272  27.502

 Number of TS in the path       =      7
 Number of cycles               =      4

 Elapsed time=                               120.34
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             36304 time=          48.02 %= 39.9
 OPTIM> # of energy+gradient+Hessian calls=       629 time=           2.90 %=  2.4
