
 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     79
 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=     8
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)@comp28.ch.
                 Created on  5/28/12 at 10:32:26 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 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>  237 Cartesian coordinates will be optimised for   79 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=    -292.6953475     RMS force=    0.7586990566E-06
 OPTIM> Final energy  =    -288.7793570     RMS force=    0.8048701049E-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      30.11500703    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     21148.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.62     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=     5
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    229 fraction=    0.990000 images=     5 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    254 steps, energy/image=    -272.8163343     RMS=.8419702334     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   49.37     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 490 RMS= 0.1879 Dev= 4.90% S= 35.68 time= 3.80
 Following    3 images are candidates for TS:    6    9   14  
 Converged to TS (number of iterations):         35
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         12
 DNEB run yielded 3 true transition state(s) time=   2.14

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     540 steps. Energy=    -289.3773078       time=       0.44
 Minus side of path:                     533 steps. Energy=    -292.7248527       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.3773078  3.9559         -285.4214206  7.3034         -292.7248527  10.285   6.899   9.020   8.758
        *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:                     663 steps. Energy=    -291.6986588       time=       0.60
 Minus side of path:                     508 steps. Energy=    -289.3773078       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.6986588  2.5304         -289.1682650 0.20904         -289.3773078  14.232  12.662   2.363  33.429
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     475 steps. Energy=    -288.7793570       time=       0.37
 Minus side of path:                     521 steps. Energy=    -289.8724012       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7793570 0.67306         -288.1062926  1.7661         -289.8724012   5.876   4.184   5.662  13.953
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     12413.    
 decide> The unconnected minima in the chain and their distances are:
     7       22.69     6     6        4.79     3     4        8.36     1 
 

 tryconnect> Interpolation for minima 6_U and 7_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=     9
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    101 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    126 steps, energy/image=    -275.5967178     RMS=2.366034553     images=   3
 intlbfgs> First  minimum number      6
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      6     7 dist=   27.69     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 280 RMS= 0.2658 Dev= 0.28% S= 23.50 time= 1.24
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   0.67

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     532 steps. Energy=    -289.8724012       time=       0.42
 Minus side of path:                     714 steps. Energy=    -291.6986588       time=       0.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.8724012  2.1237         -287.7486540  3.9500         -291.6986588  29.623  27.788   1.937  40.789
        Known (#7)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 checkpair> Energies of the minima in the pair     3    6 are the same - checking distance ...

 tryconnect> Interpolation for minima 3_U and 6_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=    75
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> Backtracking      1 steps, current active atoms=    72
 intlbfgs> switch on true potential at step    312 fraction=    0.990000 images=     2 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    337 steps, energy/image=    -244.5252093     RMS=20.25833711     images=   2
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      3     6 dist=   13.96     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 0.5323 Dev= 2.37% S= 7.75 time= 0.32
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   0.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     522 steps. Energy=    -292.7248527       time=       0.42
 Minus side of path:                     536 steps. Energy=    -289.3773078       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.7248527  7.3034         -285.4214206  3.9559         -289.3773078  10.285   6.899   9.014   8.764
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_U 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=    65
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     88 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    113 steps, energy/image=    -286.2577701     RMS=.5089222330     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   11.21     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5300 Dev= 3.30% S= 10.46 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.75

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     531 steps. Energy=    -291.3102729       time=       0.43
 Minus side of path:                     536 steps. Energy=    -292.6953475       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.3102729  2.7952         -288.5150476  4.1803         -292.6953475  11.061   8.422   9.574   8.251
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     322.52    
 decide> The unconnected minima in the chain and their distances are:
     8        6.85     1 
 

 tryconnect> Interpolation for minima 1_S and 8_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=    69
 intlbfgs> Freezing     64 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=    -289.5361127     RMS=.1072530587     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      1     8 dist=   11.76     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 105 RMS= 0.1670 Dev= 0.56% S= 6.91 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   0.66

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     479 steps. Energy=    -292.7248527       time=       0.38
 Minus side of path:                     518 steps. Energy=    -292.6953475       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.7248527 0.78602E-01     -292.6462509 0.49097E-01     -292.6953475   6.979   6.851   6.448  12.253
        Known (#8)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -292.6953475 0.49097E-01    -292.6462509 0.78602E-01    -292.7248527   6.979   6.851   6.448  12.253
   5     -292.7248527  7.3034        -285.4214206  3.9559        -289.3773078  10.285   6.899   9.014   8.764
   2     -289.3773078 0.20904        -289.1682650  2.5304        -291.6986588  14.232  12.662   2.363  33.429
   4     -291.6986588  3.9500        -287.7486540  2.1237        -289.8724012  29.623  27.788   1.937  40.789
   3     -289.8724012  1.7661        -288.1062926 0.67306        -288.7793570   5.876   4.184   5.662  13.953

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                                18.33
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             22169 time=          11.66 %= 63.6
 OPTIM> # of energy+gradient+Hessian calls=       178 time=           0.19 %=  1.0
