
 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 10:37:33 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=    -393.3564342     RMS force=    0.9803809862E-06
 OPTIM> Final energy  =    -395.0101498     RMS force=    0.9098875046E-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      9.247715024    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     792.48    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     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=   126
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     20 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     45 steps, energy/image=    -370.6527928     RMS=12.53182740     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   15.63     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.0917 Dev= 0.39% S= 9.46 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     879 steps. Energy=    -393.3564342       time=       2.09
 Minus side of path:                    1101 steps. Energy=    -396.5791634       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3564342 0.21102         -393.1454182  3.4337         -396.5791634  20.925  20.237   3.851  37.651
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    14   24 from     0.35541E-01 to     0.36891E-01 ref=     5.2679    
 checkperc> Increasing con cutoff atoms    15   17 from     0.36495E-02 to     0.37497E-02 ref=     2.1258    
 checkperc> Increasing con cutoff atoms    15   24 from     0.15155E-01 to     0.18230E-01 ref=     4.0148    
 checkperc> Increasing con cutoff atoms    18   23 from     0.15056E-02 to     0.19814E-02 ref=     1.3860    
 checkperc> Increasing con cutoff atoms    18   24 from     0.35405E-02 to     0.55218E-02 ref=     2.4263    
 checkperc> Increasing con cutoff atoms    34   38 from     0.11063E-01 to     0.13811E-01 ref=     2.4487    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1585.0    
 decide> The unconnected minima in the chain and their distances are:
     2        9.24     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=   126
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     20 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     45 steps, energy/image=    -381.7622344     RMS=3.078588915     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   17.76     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 805 RMS= 0.0151 Dev= 4.68% S= 14.06 time= 27.41
 Following    2 images are candidates for TS:    3   22  
 Converged to TS (number of iterations):         10
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   5.16
 isnewts> transition state is the same as number        1 energy=     -393.1454181852
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     832 steps. Energy=    -393.3564342       time=       1.87
 Minus side of path:                    1093 steps. Energy=    -396.5791634       time=       2.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3564342 0.21102         -393.1454182  3.4337         -396.5791634  20.925  20.237   3.854  37.625
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     897 steps. Energy=    -395.0101498       time=       2.34
 Minus side of path:                     879 steps. Energy=    -395.3584522       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0101498 0.17815         -394.8320003 0.52645         -395.3584522   3.801   3.460   2.712  53.463
        Known (#2)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    16   23 from     0.73674E-02 to     0.75883E-02 ref=     2.3381    
 checkperc> Increasing con cutoff atoms    16   24 from     0.94464E-02 to     0.95122E-02 ref=     2.7159    
 checkperc> Increasing con cutoff atoms    17   23 from     0.59518E-02 to     0.61574E-02 ref=     2.7039    
 checkperc> Increasing con cutoff atoms    17   24 from     0.65092E-02 to     0.67624E-02 ref=     2.3308    
 checkperc> Increasing con cutoff atoms    44   46 from     0.31757E-02 to     0.34979E-02 ref=     2.0483    
 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=     443.16    
 decide> The unconnected minima in the chain and their distances are:
     4        7.62     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=   135
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -384.4587820     RMS=5.966773598     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   14.53     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.1042 Dev= 0.84% S= 7.79 time= 0.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.84
 isnewts> transition state is the same as number        1 energy=     -393.1454181851
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     886.33    
 decide> The unconnected minima in the chain and their distances are:
     4        7.62     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=   135
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -386.7534019     RMS=1.311912785     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   16.19     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 805 RMS= 0.1307 Dev= 7.36% S= 10.03 time= 26.94
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   2.79
 isnewts> transition state is the same as number        1 energy=     -393.1454181852
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5012.3    
 decide> The unconnected minima in the chain and their distances are:
     2       17.10     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=    90
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     57 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     82 steps, energy/image=    -376.4796985     RMS=6.094872404     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   24.37     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 245 RMS= 0.7747 Dev= 1.07% S= 17.49 time= 2.49
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.94

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     843 steps. Energy=    -397.2733285       time=       1.91
 Minus side of path:                     880 steps. Energy=    -396.5791634       time=       2.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -397.2733285  1.3253         -395.9480765 0.63109         -396.5791634   5.746   4.551   3.546  40.891
        *NEW* (Placed in 5)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    14   22 from     0.21813E-01 to     0.24727E-01 ref=     4.8960    
 checkperc> Increasing con cutoff atoms    14   24 from     0.36891E-01 to     0.42337E-01 ref=     5.2679    
 checkperc> Increasing con cutoff atoms    15   17 from     0.37497E-02 to     0.41857E-02 ref=     2.1258    
 checkperc> Increasing con cutoff atoms    15   22 from     0.12040E-01 to     0.13208E-01 ref=     3.4418    
 checkperc> Increasing con cutoff atoms    15   23 from     0.16407E-01 to     0.18560E-01 ref=     3.6638    
 checkperc> Increasing con cutoff atoms    15   24 from     0.18230E-01 to     0.19007E-01 ref=     4.0148    
 checkperc> Increasing con cutoff atoms    18   23 from     0.19814E-02 to     0.22496E-02 ref=     1.3860    
 checkperc> Increasing con cutoff atoms    21   22 from     0.27715E-01 to     0.29401E-01 ref=     2.6996    
 checkperc> Increasing con cutoff atoms    22   24 from     0.18114E-02 to     0.18710E-02 ref=     1.3857    
 checkperc> Increasing con cutoff atoms    23   24 from     0.24616E-02 to     0.29898E-02 ref=     1.3920    
 checkperc> Increasing con cutoff atoms    29   39 from     0.11881     to     0.12090     ref=     4.7910    
 checkperc> Increasing con cutoff atoms    40   45 from     0.16331E-02 to     0.23863E-02 ref=     2.1596    
 checkperc> Increasing con cutoff atoms    84   86 from     0.35522E-01 to     0.35712E-01 ref=     2.0803    
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6896.5    
 decide> The unconnected minima in the chain and their distances are:
     4       19.02     3 
 

 tryconnect> Interpolation for minima 3_S and 4_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=    82
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     69 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     94 steps, energy/image=    -337.1025705     RMS=17.15942107     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   25.49     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 245 RMS= 0.0599 Dev= 0.98% S= 19.43 time= 2.49
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.03

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     789 steps. Energy=    -395.3584522       time=       1.71
 Minus side of path:                    1039 steps. Energy=    -396.5791634       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3584522 0.19893E-01     -395.3385587  1.2406         -396.5791634  19.355  19.023   3.565  40.674
        Known (#4)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -393.3564342 0.21102        -393.1454182  3.4337        -396.5791634  20.925  20.237   3.851  37.651
   5     -396.5791634  1.2406        -395.3385587 0.19893E-01    -395.3584522  19.355  19.023   3.565  40.674
   3     -395.3584522 0.52645        -394.8320003 0.17815        -395.0101498   3.801   3.460   2.712  53.463

 Number of TS in the path       =      3
 Number of cycles               =      6

 Elapsed time=                               109.71
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             58108 time=          81.83 %= 74.6
 OPTIM> # of energy+gradient+Hessian calls=       180 time=           0.75 %=  0.7
