
 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)@comp34.ch.
                 Created on  5/28/12 at 10:36: 8 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=    -384.3978465     RMS force=    0.8441701754E-06
 OPTIM> Final energy  =    -382.6655446     RMS force=    0.9318835262E-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      62.63580674    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.23417E+06
 decide> The unconnected minima in the chain and their distances are:
     2       61.57     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=     0
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    969 fraction=    0.990000 images=     7 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    994 steps, energy/image=    -349.5366044     RMS=.8993464530     images=   8
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   70.49     Attempts, images and iterations=     0    21   735
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 735 RMS= 0.0875 Dev= 11.57% S= 77.89 time= 18.57
 Following    2 images are candidates for TS:   10   16  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         22
 DNEB run yielded 2 true transition state(s) time=   9.76

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1388 steps. Energy=    -384.3978465       time=       4.45
 Minus side of path:                     966 steps. Energy=    -382.2829759       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3978465  3.5457         -380.8521784  1.4308         -382.2829759  32.829  30.712   1.625  89.214
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    64   65 from     0.53314E-02 to     0.59923E-02 ref=     1.5339    
 checkperc> Increasing con cutoff atoms    65   69 from     0.14305E-01 to     0.16811E-01 ref=     3.3435    
 checkperc> Increasing con cutoff atoms    66   68 from     0.14739E-02 to     0.26481E-02 ref=     1.3254    
 checkperc> Increasing con cutoff atoms    66   69 from     0.17509E-01 to     0.20731E-01 ref=     1.9851    
 checkperc> Increasing con cutoff atoms    67   68 from     0.76076E-02 to     0.77918E-02 ref=     2.2053    
 checkperc> Increasing con cutoff atoms    67   69 from     0.35871E-01 to     0.39588E-01 ref=     2.3962    
 checkperc> Increasing con cutoff atoms    74   75 from     0.18907E-01 to     0.20392E-01 ref=     2.1088    
 checkperc> Increasing con cutoff atoms    90   92 from     0.22249E-01 to     0.25077E-01 ref=     3.1081    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1009 steps. Energy=    -382.4420402       time=       2.67
 Minus side of path:                    1044 steps. Energy=    -382.6655446       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4420402 0.22275         -382.2192905 0.44625         -382.6655446  29.603  29.168   1.915  75.698
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6768.4    
 decide> The unconnected minima in the chain and their distances are:
     4       18.90     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=    50
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     96 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    121 steps, energy/image=    -337.2283837     RMS=12.97429231     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   26.81     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 280 RMS= 0.1844 Dev= 0.41% S= 19.16 time= 2.58
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=   7.99

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1198 steps. Energy=    -382.6442544       time=       4.17
 Minus side of path:                     977 steps. Energy=    -382.2829759       time=       3.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6442544 0.51692         -382.1273297 0.15565         -382.2829759  20.642  19.755   1.876  77.288
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     35.581    
 decide> The unconnected minima in the chain and their distances are:
     4        3.29     5 
 

 tryconnect> Interpolation for minima 4_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=   145
 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=    -378.6722636     RMS=.5403441073E-01 images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   3.750     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0302 Dev= 0.12% S= 3.29 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.32

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1008 steps. Energy=    -382.4420402       time=       2.54
 Minus side of path:                     999 steps. Energy=    -382.6442544       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.4420402 0.17632E-01     -382.4244077 0.21985         -382.6442544   3.312   3.286   3.055  47.471
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -384.3978465  3.5457        -380.8521784  1.4308        -382.2829759  32.829  30.712   1.625  89.214
   3     -382.2829759 0.15565        -382.1273297 0.51692        -382.6442544  20.642  19.755   1.876  77.288
   4     -382.6442544 0.21985        -382.4244077 0.17632E-01    -382.4420402   3.312   3.286   3.055  47.471
   2     -382.4420402 0.22275        -382.2192905 0.44625        -382.6655446  29.603  29.168   1.915  75.698

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                69.21
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             30953 time=          34.93 %= 50.5
 OPTIM> # of energy+gradient+Hessian calls=       178 time=           0.79 %=  1.1
