
 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> 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)@comp34.ch.
                 Created on  5/28/12 at 12: 9:10 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
 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> 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=    -289.6469053     RMS force=    0.9862018201E-06
 OPTIM> Final energy  =    -295.7090080     RMS force=    0.9240556295E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7012.4    
 decide> The unconnected minima in the chain and their distances are:
     2       19.14     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 182 RMS= 36.1824 Dev= 33.10% S= 49.82 time= 0.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   1.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     505 steps. Energy=    -288.7480032       time=       0.42
 Minus side of path:                     627 steps. Energy=    -296.8276963       time=       0.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7480032 0.39266         -288.3553415  8.4724         -296.8276963  13.353  11.430   2.549  30.998
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2667.8    
 decide> The unconnected minima in the chain and their distances are:
     2        8.70     3     4       12.62     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 108 RMS= 17.3520 Dev= 39.22% S= 14.96 time= 0.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   0.72

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     588 steps. Energy=    -288.7480032       time=       0.51
 Minus side of path:                     545 steps. Energy=    -286.1265511       time=       0.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7480032  6.3067         -282.4412771  3.6853         -286.1265511   9.852   6.645   6.143  12.861
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 105 RMS= 1.6747 Dev= 0.88% S= 15.03 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   1.26

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     657 steps. Energy=    -292.8554469       time=       0.63
 Minus side of path:                     543 steps. Energy=    -290.5603253       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.8554469  6.2216         -286.6338388  3.9265         -290.5603253  16.527  12.941   6.877  11.488
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     2236.3    
 decide> The unconnected minima in the chain and their distances are:
     2        8.70     3     4        9.41     6     7        4.47     1 
 

 tryconnect> 700-iteration DNEB run for minima 2_F and 3_U using 20 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 700 RMS= 0.1611 Dev= 2.98% S= 10.76 time= 8.05
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   0.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     523 steps. Energy=    -288.7480032       time=       0.43
 Minus side of path:                     586 steps. Energy=    -296.8276963       time=       0.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7480032 0.51972         -288.2282822  8.5994         -296.8276963  12.585  11.432   2.539  31.110
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 70 RMS= 1.5384 Dev= 1.67% S= 10.43 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   0.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     421 steps. Energy=    -292.8554469       time=       0.33
 Minus side of path:                     494 steps. Energy=    -295.7404641       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.8554469 0.10529         -292.7501519  2.9903         -295.7404641   8.470   7.484   6.462  12.226
        Known (#6)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 1.3688 Dev= 1.18% S= 4.88 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.48

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     456 steps. Energy=    -289.6469053       time=       0.37
 Minus side of path:                     452 steps. Energy=    -290.3222153       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.6469053 0.45877E-01     -289.6010286 0.72119         -290.3222153   3.707   3.686  10.522   7.508
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     1916.2    
 decide> The unconnected minima in the chain and their distances are:
     2       11.60     5     4        6.99     8     7        2.47     9 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 136 RMS= 24.0067 Dev= 13.12% S= 57.88 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   0.99

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     591 steps. Energy=    -288.7480032       time=       0.51
 Minus side of path:                     550 steps. Energy=    -286.6773926       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7480032  3.5546         -285.1933958  1.4840         -286.6773926  14.046  10.289   2.525  31.286
        Known (#3)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4620 Dev= 2.31% S= 8.28 time= 0.09
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   0.68

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     485 steps. Energy=    -296.8276963       time=       0.40
 Minus side of path:                     520 steps. Energy=    -295.7404641       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.8276963  3.1670         -293.6607035  2.0798         -295.7404641   9.035   7.010  11.772   6.711
        Known (#4)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.5744 Dev= 0.54% S= 3.00 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.47

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     492 steps. Energy=    -290.3222153       time=       0.41
 Minus side of path:                     456 steps. Energy=    -290.5603253       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.3222153  3.3477         -286.9745019  3.5858         -290.5603253   2.974   2.473  48.740   1.621
        Known (#9)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1922.6    
 decide> The unconnected minima in the chain and their distances are:
     2       12.43     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 288 RMS= 39.5558 Dev= 47.46% S= 21.69 time= 0.53
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   0.89

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     581 steps. Energy=    -296.8276963       time=       0.50
 Minus side of path:                     501 steps. Energy=    -295.7090080       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.8276963  1.3959         -295.4317702 0.27724         -295.7090080  12.989  12.439   4.206  18.781
        Known (#4)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -289.6469053 0.45877E-01    -289.6010286 0.72119        -290.3222153   3.707   3.686  10.522   7.508
   9     -290.3222153  3.3477        -286.9745019  3.5858        -290.5603253   2.974   2.473  48.740   1.621
   3     -290.5603253  3.9265        -286.6338388  6.2216        -292.8554469  16.527  12.941   6.877  11.488
   5     -292.8554469 0.10529        -292.7501519  2.9903        -295.7404641   8.470   7.484   6.462  12.226
   8     -295.7404641  2.0798        -293.6607035  3.1670        -296.8276963   9.035   7.010  11.772   6.711
  10     -296.8276963  1.3959        -295.4317702 0.27724        -295.7090080  12.989  12.439   4.206  18.781

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                                27.56
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             33133 time=          18.30 %= 66.4
 OPTIM> # of energy+gradient+Hessian calls=       346 time=           0.39 %=  1.4
