
 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)@comp32.ch.
                 Created on  5/28/12 at 10:33:42 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=    -382.5427530     RMS force=    0.9973453174E-06
 OPTIM> Final energy  =    -390.5224747     RMS force=    0.9029583014E-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      90.29625131    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     54988.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.94     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=    39
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    281 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    306 steps, energy/image=    -360.2664393     RMS=.6437987437     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   43.13     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1030 Dev= 3.83% S= 51.16 time= 6.96
 Following    2 images are candidates for TS:    4   11  
 Converged to TS (number of iterations):         76
 Converged to TS (number of iterations):         56
 DNEB run yielded 2 true transition state(s) time=  12.87

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     938 steps. Energy=    -390.4787888       time=       2.97
 Minus side of path:                    1074 steps. Energy=    -382.5427530       time=       3.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4787888  13.649         -376.8300957  5.7127         -382.5427530  37.663  26.047   7.913  18.324
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     947 steps. Energy=    -388.2292954       time=       2.19
 Minus side of path:                    1000 steps. Energy=    -390.5224747       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.2292954 0.55595         -387.6733421  2.8491         -390.5224747  17.556  16.599   3.287  44.111
        *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=     3024.1    
 decide> The unconnected minima in the chain and their distances are:
     4       14.45     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=    80
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     66 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     91 steps, energy/image=    -374.0047822     RMS=7.979869964     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   20.04     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 210 RMS= 0.0459 Dev= 0.63% S= 14.71 time= 1.76
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.92

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1110 steps. Energy=    -395.3583493       time=       3.64
 Minus side of path:                     831 steps. Energy=    -388.2292954       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493  7.1575         -388.2008844 0.28411E-01     -388.2292954  17.674  16.960   3.119  46.485
        *NEW* (Placed in 5)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    36   50 from     0.85706E-01 to     0.86489E-01 ref=     2.4730    
 checkperc> Increasing con cutoff atoms    40   46 from     0.53434E-02 to     0.93278E-02 ref=     3.1089    
 checkperc> Increasing con cutoff atoms    42   44 from     0.21060E-02 to     0.21088E-02 ref=     2.1530    
 checkperc> Increasing con cutoff atoms    42   45 from     0.10926E-02 to     0.13738E-02 ref=     1.3375    
 checkperc> Increasing con cutoff atoms    44   46 from     0.32148E-02 to     0.60731E-02 ref=     2.0488    
 checkperc> Increasing con cutoff atoms    94   97 from     0.14296E-01 to     0.14635E-01 ref=     3.6298    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2814.0    
 decide> The unconnected minima in the chain and their distances are:
     5       14.10     3 
 

 tryconnect> Interpolation for minima 3_S and 5_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     58 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     83 steps, energy/image=    -383.6205482     RMS=.4603844718     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   16.81     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 175 RMS= 0.1050 Dev= 0.89% S= 14.73 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     829 steps. Energy=    -390.4787888       time=       1.78
 Minus side of path:                     932 steps. Energy=    -395.3583493       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4787888 0.92242         -389.5563691  5.8020         -395.3583493  16.323  14.107  11.479  12.632
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -382.5427530  5.7127        -376.8300957  13.649        -390.4787888  37.663  26.047   7.913  18.324
   4     -390.4787888 0.92242        -389.5563691  5.8020        -395.3583493  16.323  14.107  11.479  12.632
   3     -395.3583493  7.1575        -388.2008844 0.28411E-01    -388.2292954  17.674  16.960   3.119  46.485
   2     -388.2292954 0.55595        -387.6733421  2.8491        -390.5224747  17.556  16.599   3.287  44.111

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

 Elapsed time=                                53.96
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             18935 time=          25.56 %= 47.4
 OPTIM> # of energy+gradient+Hessian calls=       199 time=           0.96 %=  1.8
