
 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> Constraint potential parameters read from file congeom.dat
 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)@comp35.ch.
                 Created on  5/28/12 at 10:28:53 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -383.6088508     RMS force=    0.9346328060E-06
 OPTIM> Final energy  =    -382.1773645     RMS force=    0.9946727427E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      6.884313387    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     295.83    
 decide> The unconnected minima in the chain and their distances are:
     2        6.66     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     86 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    111 steps, energy/image=    -374.6209244     RMS=1.081207855     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   12.41     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.6602 Dev= 3.24% S= 9.63 time= 0.40
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         24
 Converged to TS (number of iterations):         23
 DNEB run yielded 2 true transition state(s) time=   7.30

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     998 steps. Energy=    -384.4665363       time=       2.48
 Minus side of path:                     973 steps. Energy=    -383.6088508       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4665363  3.2606         -381.2059480  2.4029         -383.6088508   6.222   5.474  33.562   4.320
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     973 steps. Energy=    -382.1773645       time=       3.10
 Minus side of path:                     979 steps. Energy=    -382.1773645       time=       3.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1773645  3.6200         -378.5573430  3.6200         -382.1773645   3.397   2.943  48.162   3.011
        Known (#2)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     189.01    
 decide> The unconnected minima in the chain and their distances are:
     2        5.73     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -376.3774082     RMS=1.204472467     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   8.372     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.7687 Dev= 1.10% S= 6.54 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.52

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1215 steps. Energy=    -382.9990030       time=       3.46
 Minus side of path:                     951 steps. Energy=    -382.1773645       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.9990030 0.86948         -382.1295216 0.47843E-01     -382.1773645  29.338  28.252   2.614  55.479
        *NEW* (Placed in 4)                                     Known (#2)
 checkperc> Increasing con cutoff atoms     1    6 from     0.60031E-02 to     0.69673E-02 ref=     2.1754    
 checkperc> Increasing con cutoff atoms     2    3 from     0.84330E-02 to     0.86426E-02 ref=     1.0461    
 checkperc> Increasing con cutoff atoms     2    6 from     0.58580E-01 to     0.59448E-01 ref=     2.7759    
 checkperc> Increasing con cutoff atoms     4    7 from     0.70159E-01 to     0.71201E-01 ref=     3.2190    
 checkperc> Increasing con cutoff atoms     9   10 from     0.50203E-02 to     0.51935E-02 ref=     1.2368    
 checkperc> Increasing con cutoff atoms    10   12 from     0.16825E-01 to     0.16899E-01 ref=     3.1154    
 checkperc> Increasing con cutoff atoms    11   12 from     0.28350E-02 to     0.29456E-02 ref=    0.97983    
 checkperc> Increasing con cutoff atoms    29   36 from     0.35130E-01 to     0.39183E-01 ref=     2.4528    
 checkperc> Increasing con cutoff atoms    29   37 from     0.64293E-01 to     0.68033E-01 ref=     2.5588    
 checkperc> Increasing con cutoff atoms    29   38 from     0.26753E-01 to     0.33965E-01 ref=     3.8232    
 checkperc> Increasing con cutoff atoms    39   40 from     0.23498E-02 to     0.31575E-02 ref=     1.5253    
 checkperc> Increasing con cutoff atoms    39   42 from     0.82972E-02 to     0.97075E-02 ref=     3.6261    
 checkperc> Increasing con cutoff atoms    39   47 from     0.15356E-01 to     0.16829E-01 ref=     4.8993    
 checkperc> Increasing con cutoff atoms    39   50 from     0.35341E-01 to     0.36968E-01 ref=     2.5131    
 checkperc> Increasing con cutoff atoms    40   42 from     0.21966E-02 to     0.26098E-02 ref=     2.1257    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     378.03    
 decide> The unconnected minima in the chain and their distances are:
     2        5.73     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     47 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     72 steps, energy/image=    -377.7885461     RMS=.5606391890     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   9.225     Attempts, images and iterations=     1    21   735
 lbfgs> Final DNEB force constant      196.1314519    
 Double-ended search iterations= 735 RMS= 0.3574 Dev= 1.65% S= 7.24 time= 19.68
 Following    2 images are candidates for TS:    5   13  
 Converged to TS (number of iterations):         34
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=   7.75

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     989 steps. Energy=    -383.6088508       time=       2.78
 Minus side of path:                     984 steps. Energy=    -383.5941365       time=       3.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6088508  5.2471         -378.3617382  5.2324         -383.5941365   6.534   5.890  29.996   4.834
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     998 steps. Energy=    -384.4665363       time=       3.18
 Minus side of path:                     967 steps. Energy=    -383.5941365       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4665363  3.2079         -381.2586467  2.3355         -383.5941365   6.154   5.301  34.628   4.187
        Known (#3)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     28.392    
 decide> The unconnected minima in the chain and their distances are:
     2        3.05     5 
 

 tryconnect> Interpolation for minima 2_F and 5_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   143
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     21 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     46 steps, energy/image=    -376.8001296     RMS=3.178720024     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   12.01     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 105 RMS= 0.4056 Dev= 6.39% S= 3.48 time= 0.41
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  18.58
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     56.785    
 decide> The unconnected minima in the chain and their distances are:
     2        3.05     5 
 

 tryconnect> Interpolation for minima 2_F and 5_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   143
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -378.0604340     RMS=.4250461525     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   14.00     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      120.4076978    
 Double-ended search iterations= 805 RMS= 0.1860 Dev= 5.44% S= 5.06 time= 23.96
 Following    1 images are candidates for TS:   16  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.49
 isnewts> transition state is the same as number        4 energy=     -378.3617382317
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     978 steps. Energy=    -383.6088508       time=       3.35
 Minus side of path:                     976 steps. Energy=    -383.5941365       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6088508  5.2471         -378.3617382  5.2324         -383.5941365   6.534   5.890  29.985   4.836
        Known (#1)                                              Known (#5)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     591.66    
 decide> The unconnected minima in the chain and their distances are:
     2        6.66     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   138
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     45 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     70 steps, energy/image=    -379.2247532     RMS=.5923715459     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   12.35     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      60.81406943    
 Double-ended search iterations= 805 RMS= 0.1167 Dev= 0.97% S= 8.18 time= 23.59
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.86

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1002 steps. Energy=    -383.6088508       time=       2.51
 Minus side of path:                     983 steps. Energy=    -382.6086123       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.6088508  3.3976         -380.2112810  2.3973         -382.6086123   6.142   5.098  39.604   3.661
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     558.73    
 decide> The unconnected minima in the chain and their distances are:
     2        8.23     6 
 

 tryconnect> Interpolation for minima 2_F and 6_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   137
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     54 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     79 steps, energy/image=    -377.0564438     RMS=.7339335260     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   13.33     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 0.2401 Dev= 0.48% S= 8.80 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.60

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     962 steps. Energy=    -382.6086123       time=       2.80
 Minus side of path:                     983 steps. Energy=    -382.1773645       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6086123  2.6547         -379.9539486  2.2234         -382.1773645   9.250   8.232  21.546   6.730
        Known (#6)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -383.6088508  3.3976        -380.2112810  2.3973        -382.6086123   6.142   5.098  39.604   3.661
   8     -382.6086123  2.6547        -379.9539486  2.2234        -382.1773645   9.250   8.232  21.546   6.730

 Number of TS in the path       =      2
 Number of cycles               =      7

 Elapsed time=                               167.73
 OPTIM> # of energy calls=                         14 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             80526 time=          98.88 %= 59.0
 OPTIM> # of energy+gradient+Hessian calls=       474 time=           2.08 %=  1.2
