
 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)@comp35.ch.
                 Created on  5/28/12 at 12: 3:35 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=    -288.2209615     RMS force=    0.9317922052E-06
 OPTIM> Final energy  =    -293.0566499     RMS force=    0.8703029428E-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=     7546.2    
 decide> The unconnected minima in the chain and their distances are:
     2       19.61     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= 522 RMS= 5.1677 Dev= 0.31% S= 19.99 time= 1.35
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   0.96

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     562 steps. Energy=    -293.0566499       time=       0.45
 Minus side of path:                     603 steps. Energy=    -291.2446723       time=       0.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.0566499  4.3486         -288.7080619  2.5366         -291.2446723  10.234   8.389  10.651   7.417
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     7652.5    
 decide> The unconnected minima in the chain and their distances are:
     3       19.71     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 363 RMS= 7.0035 Dev= 4.94% S= 20.25 time= 0.92
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   1.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     788 steps. Energy=    -294.0186317       time=       0.71
 Minus side of path:                     574 steps. Energy=    -291.2446723       time=       0.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.0186317  3.5930         -290.4256549 0.81902         -291.2446723  23.783  21.471   2.043  38.667
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     15092.    
 decide> The unconnected minima in the chain and their distances are:
     2       19.61     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1252.392932    
 Double-ended search iterations= 805 RMS= 2.4148 Dev= 0.09% S= 21.68 time= 9.37
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   1.08
 isnewts> transition state is the same as number        2 energy=     -290.4256548754
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     582 steps. Energy=    -291.2446723       time=       0.46
 Minus side of path:                     808 steps. Energy=    -294.0186317       time=       0.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.2446723 0.81902         -290.4256549  3.5930         -294.0186317  23.784  21.472   2.042  38.692
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     15305.    
 decide> The unconnected minima in the chain and their distances are:
     3       19.71     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      73.91988148    
 Double-ended search iterations= 805 RMS= 0.8523 Dev= 0.70% S= 22.50 time= 9.29
 Following    2 images are candidates for TS:    8   16  
 Converged to TS (number of iterations):        102
 Converged to TS (number of iterations):         82
 DNEB run yielded 2 true transition state(s) time=   3.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     553 steps. Energy=    -288.2209615       time=       0.41
 Minus side of path:                     550 steps. Energy=    -289.3452117       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.2209615 0.28315E-01     -288.1926460  1.1526         -289.3452117   6.477   6.326  14.166   5.577
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     586 steps. Energy=    -296.3741598       time=       0.47
 Minus side of path:                     591 steps. Energy=    -291.4422075       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.3741598  10.371         -286.0029476  5.4393         -291.4422075  17.469   9.122   6.581  12.005
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     4004.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.49     6     6       14.18     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 161 RMS= 74.6529 Dev= 38.44% S= 104.68 time= 0.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   1.37
 isnewts> transition state is the same as number        5 energy=     -286.0029475707
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     584 steps. Energy=    -296.3741598       time=       0.49
 Minus side of path:                     588 steps. Energy=    -291.4422075       time=       0.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.3741598  10.371         -286.0029476  5.4393         -291.4422075  17.470   9.122   6.578  12.010
        Known (#6)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.1132 Dev= 0.14% S= 14.49 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.73

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     562 steps. Energy=    -288.2209615       time=       0.43
 Minus side of path:                     547 steps. Energy=    -296.3741598       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.2209615 0.41328         -287.8076846  8.5665         -296.3741598  14.635  14.191   5.868  13.462
        Known (#1)                                              Known (#6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1437.4    
 decide> The unconnected minima in the chain and their distances are:
     3       11.29     6 
 

 tryconnect> 105-iteration DNEB run for minima 3_F and 6_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 353 RMS= 31.7029 Dev= 57.96% S= 13.03 time= 0.56
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   0.87
 isnewts> transition state is the same as number        2 energy=     -290.4256548753
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1520.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.50     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 409 RMS= 13.0325 Dev= 5.08% S= 11.73 time= 0.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   0.84
 isnewts> transition state is the same as number        2 energy=     -290.4256548753
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1851.6    
 decide> The unconnected minima in the chain and their distances are:
     3       12.28     7 
 

 tryconnect> 105-iteration DNEB run for minima 3_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 154 RMS= 17.4762 Dev= 15.60% S= 26.65 time= 0.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   0.96

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     760 steps. Energy=    -294.0186317       time=       0.68
 Minus side of path:                     556 steps. Energy=    -291.4422075       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.0186317  4.0924         -289.9262368  1.5160         -291.4422075  30.355  28.496   2.294  34.439
        Known (#4)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -288.2209615 0.41328        -287.8076846  8.5665        -296.3741598  14.635  14.191   5.868  13.462
   5     -296.3741598  10.371        -286.0029476  5.4393        -291.4422075  17.469   9.122   6.581  12.005
   8     -291.4422075  1.5160        -289.9262368  4.0924        -294.0186317  30.355  28.496   2.294  34.439
   2     -294.0186317  3.5930        -290.4256549 0.81902        -291.2446723  23.783  21.471   2.043  38.667
   1     -291.2446723  2.5366        -288.7080619  4.3486        -293.0566499  10.234   8.389  10.651   7.417

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                                42.42
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             61850 time=          29.51 %= 69.6
 OPTIM> # of energy+gradient+Hessian calls=       559 time=           0.55 %=  1.3
