#CCP4I VERSION CCP4Interface 7.0.024 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 02 Dec 2016 15:22:13 #CCP4I USER marek #CCP4I PROJECT lyso #CCP4I JOB_ID 4 #CCP4I SCRATCH /tmp/marek #CCP4I HOSTNAME Lenovo #CCP4I PID 7553
 
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 ### CCP4 7.0.024: Refmac          version 5.8.0158 : 03/10/16##
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 User: unknown  Run date:  2/12/2016 Run time: 15:22:21 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make check NONE
  Data line--- make     hydrogen ALL     hout NO     peptide NO     cispeptide YES     ssbridge YES     symmetry YES     sugar YES     connectivity NO     link NO
  Data line--- refi     type REST     resi MLKF     meth CGMAT     bref ISOT
  Data line--- ncyc 10
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- weight     AUTO
  Data line--- monitor MEDIUM     torsion 10.0     distance 10.0     angle 10.0     plane 10.0     chiral 10.0     bfactor 10.0     bsphere 10.0     rbond 10.0     ncsr 10.0
  Data line--- labin  FP=F_XDSdataset SIGFP=SIGF_XDSdataset    FREE=FreeR_flag
  Data line--- labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
  Data line--- PNAME XDSproject
  Data line--- DNAME XDSdataset
  Data line--- RSIZE 80
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac1.mtz 



 !------------------------------------------------!
 !                                                !
 !  Input mtz file seems to be output from refmac !
 !  You should always use original mtz            !
 !                                                !
 !------------------------------------------------!



    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic/arp_5.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/arp_5_refmac1.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac1.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac2.mtz

Cell from mtz :    78.715    78.715    37.084    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/marek/Downloads/destination/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/marek/Downloads/destination/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0208
  Refinement of individual isotropic Bfactors
  Refinement resln        :    55.6599  1.5500
  Estimated number of reflections :      21848
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    55.6599  1.5500

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :/home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic/arp_5.
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 13482
                with complete description    : 13482
  NUMBER OF MODIFICATIONS                    :    63
  NUMBER OF LINKS                            :    73
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/marek/Downloads/destination/ccp4-7.0/lib/data/atomsf.lib


  Number of atoms    :    1146
  Number of residues :     430
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : link:SS       is found dist =     2.063 ideal_dist=     2.031
            ch:AA   res:  30  CYS              at:SG  .->AA   res: 115  CYS              at:SG  .
  WARNING : link:SS       is found dist =     2.082 ideal_dist=     2.031
            ch:AA   res:  64  CYS              at:SG  .->AA   res:  80  CYS              at:SG  .
  WARNING : link:SS       is found dist =     2.050 ideal_dist=     2.031
            ch:AA   res:  76  CYS              at:SG  .->AA   res:  94  CYS              at:SG  .
  INFO:     link is found (not be used) dist=   1.647 ideal_dist=   1.420
            ch:AA   res: 102  ALA              at:O   .->ch:AA   res: 104  GLY              at:CA  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CD1  ILE                 2  AA   is missing in the structure
  ATTENTION: atom:CB   LYS                 4  AA   is missing in the structure
  ATTENTION: atom:CG   LYS                 4  AA   is missing in the structure
  ATTENTION: atom:CD   LYS                 4  AA   is missing in the structure
  ATTENTION: atom:CE   LYS                 4  AA   is missing in the structure
  ATTENTION: atom:NZ   LYS                 4  AA   is missing in the structure
  ATTENTION: atom:CE   LYS                 5  AA   is missing in the structure
  ATTENTION: atom:CG   GLN                 6  AA   is missing in the structure
  ATTENTION: atom:CD   GLN                 6  AA   is missing in the structure
  ATTENTION: atom:OE1  GLN                 6  AA   is missing in the structure
  ATTENTION: atom:SG   CYS                 9  AA   is missing in the structure
  ATTENTION: atom:CG   LYS                10  AA   is missing in the structure
  ATTENTION: atom:CD   LYS                10  AA   is missing in the structure
  ATTENTION: atom:NZ   LYS                10  AA   is missing in the structure
  ATTENTION: atom:CG   ASN                11  AA   is missing in the structure
  ATTENTION: atom:OD1  ASN                11  AA   is missing in the structure
  ATTENTION: atom:ND2  ASN                11  AA   is missing in the structure
  ATTENTION: atom:CG   LEU                12  AA   is missing in the structure
  ATTENTION: atom:CD2  LEU                12  AA   is missing in the structure
  ATTENTION: atom:CG2  VAL                13  AA   is missing in the structure
   ... and more ...
  Number of chains                  :       3
  Total number of monomers          :     430
  Number of atoms                   :    2246
  Number of missing atoms           :     101
  Number of rebuilt atoms           :     729
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   1.1842
  CA     8.6266  10.4421   7.3873   0.6599   1.5899  85.7484   1.0211 178.4370   1.7125


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      1469         0      1469
               Angles:      2557         0      2557
              Chirals:       118         0       118
               Planes:       251         0       251
             Torsions:       571         0       571
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        883
Number of   all  reflections      17455
--------------------------------------------------------------------------------
 Number of reflections in file      17455
 Number of reflections read          17455


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     62 TYR CD2   deviation=   0.22 sigma.=   0.02
Atom: A     62 TYR HD2   deviation=  -0.25 sigma.=   0.02
Atom: A     65 HIS CD2   deviation=  -0.28 sigma.=   0.02
Atom: A     65 HIS HD2   deviation=   0.26 sigma.=   0.02

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.711 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.711 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.580 id.= 1.100 dev= -0.52 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.580 id.= 1.100 dev= -0.52 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.531 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.531 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      6 GLN HB2 . - Z     20 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      6 GLN HB2 . - Z     20 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.679 id.= 1.100 dev= -0.42 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.679 id.= 1.100 dev= -0.42 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     12 LEU HB2 . - Z     80 DUM DUM . mod.= 0.732 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     12 LEU HB2 . - Z     80 DUM DUM . mod.= 0.732 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.898 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.898 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.793 id.= 1.100 dev= -0.31 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.793 id.= 1.100 dev= -0.31 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.530 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.530 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     23 ILE HD12. - Z     91 DUM DUM . mod.= 0.549 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     23 ILE HD12. - Z     91 DUM DUM . mod.= 0.549 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.932 id.= 1.820 dev= -0.89 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.932 id.= 1.820 dev= -0.89 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.295 id.= 1.100 dev= -0.80 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.295 id.= 1.100 dev= -0.80 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     41 ARG HD2 . - Z     27 DUM DUM . mod.= 0.589 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     41 ARG HD2 . - Z     27 DUM DUM . mod.= 0.589 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ1 . - Z    179 DUM DUM . mod.= 0.983 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ1 . - Z    179 DUM DUM . mod.= 0.983 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.591 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.591 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.554 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.554 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.687 id.= 1.100 dev= -0.41 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.687 id.= 1.100 dev= -0.41 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     77 ASN HB2 . - Z    106 DUM DUM . mod.= 0.747 id.= 1.100 dev= -0.35 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     77 ASN HB2 . - Z    106 DUM DUM . mod.= 0.747 id.= 1.100 dev= -0.35 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.533 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.533 id.= 1.100 dev= -0.57 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     85 ASP HA  . - Z     77 DUM DUM . mod.= 0.881 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     85 ASP HA  . - Z     77 DUM DUM . mod.= 0.881 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.658 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.658 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.660 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.660 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.631 id.= 1.100 dev= -0.47 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.631 id.= 1.100 dev= -0.47 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.671 id.= 1.100 dev= -0.43 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.671 id.= 1.100 dev= -0.43 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.524 id.= 1.100 dev= -0.58 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.524 id.= 1.100 dev= -0.58 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    101 GLU H   . - Z    184 DUM DUM . mod.= 0.613 id.= 1.100 dev= -0.49 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    101 GLU H   . - Z    184 DUM DUM . mod.= 0.613 id.= 1.100 dev= -0.49 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.392 id.= 1.100 dev= -0.71 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.392 id.= 1.100 dev= -0.71 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.916 id.= 1.100 dev= -0.18 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.916 id.= 1.100 dev= -0.18 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    113 SER HB2 . - Z    265 DUM DUM . mod.= 0.220 id.= 1.100 dev= -0.88 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    113 SER HB2 . - Z    265 DUM DUM . mod.= 0.220 id.= 1.100 dev= -0.88 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    116 ARG HG2 . - Z     45 DUM DUM . mod.= 0.609 id.= 1.100 dev= -0.49 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    116 ARG HG2 . - Z     45 DUM DUM . mod.= 0.609 id.= 1.100 dev= -0.49 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.553 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.553 id.= 1.100 dev= -0.55 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.934 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.934 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HD21. - Z    142 DUM DUM . mod.= 0.619 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HD21. - Z    142 DUM DUM . mod.= 0.619 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HD22. - Z     53 DUM DUM . mod.= 0.561 id.= 1.100 dev= -0.54 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HD22. - Z     53 DUM DUM . mod.= 0.561 id.= 1.100 dev= -0.54 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    121 SER H   . - Z    114 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    121 SER H   . - Z    114 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.615 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.615 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    123 PHE HE1 . - Z     61 DUM DUM . mod.= 0.992 id.= 1.100 dev= -0.11 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HE1 . - Z     61 DUM DUM . mod.= 0.992 id.= 1.100 dev= -0.11 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    51   51   24
 Minimum acceptable grid spacing:   116  116   55
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    51   51   24
 Minimum acceptable grid spacing:   116  116   55
 Weight matrix   0.84620386    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                69.8
Norm of Geom. positional gradient                54.5
Norm of X_ray B-factor gradient                  632.
Norm of Geom. B-factor gradient                 0.185E+05
Product of X_ray and Geom posit. gradients     -0.465E+07
 Cosine of angle between them                      -0.225
Product of X_ray and Geom B-fact gradients     -0.254E+08
 Cosine of angle between them                      -0.001


Residuals: XRAY=     0.8496E+06 GEOM=     0.4800E+05 TOTAL=     0.8976E+06
 function value    897613.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.020     0.019
Bond distances: others                          661     0.000     0.020
Bond angles  : refined atoms                   1075     1.961     1.909
Bond angles  : others                          1482     4.199     3.000
Torsion angles, period  1. refined              112     7.020     5.000
Torsion angles, period  2. refined               26    30.174    25.000
Torsion angles, period  3. refined              100    13.531    15.000
Chiral centres: refined atoms                   118     0.154     0.200
Planar groups: refined atoms                    932     0.017     0.020
Planar groups: others                           166     0.032     0.020
VDW repulsions: refined_atoms                   466     0.325     0.200
VDW repulsions.others                          1228     0.264     0.200
VDW; torsion: refined_atoms                     820     0.174     0.200
VDW; torsion.others                             674     0.104     0.200
HBOND: refined_atoms                             38     0.340     0.200
HBOND.others                                      2     0.181     0.200
DUMMY_NORMAL: refined_atoms                     110     0.245     0.300
DUMMY_NORMAL.others                              84     0.445     0.300
DUMMY_DUMMY: refined_atoms                       22     0.088     0.300
VDW repulsions: symmetry: refined_atoms           8     0.354     0.200
VDW repulsions: symmetry: others                 16     0.372     0.200
HBOND: symmetry: refined_atoms                    1     0.290     0.200
DUMMY_NORMAL: symmetry: refined_atoms             1     0.013     0.300
DUMMY_NORMAL: symmetry: others                    1     0.007     0.300
M. chain bond B values: refined atoms           461     1.261     1.170
M. chain bond B values: others                  462     1.538     1.169
M. chain angle B values: refined atoms          566     1.684     1.738
M. chain angle B values: others                 566     1.850     1.734
S. chain bond B values: refined atoms           347     2.027     1.252
S. chain bond B values: others                  348     2.024     1.259
S. chain angle B values: refined atoms          509     2.408     1.781
S. chain angle B values: others                 510     2.850     1.780
Long range B values: refined atoms             1030     3.904    14.642
Long range B values: others                    1016     3.897    14.677
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.979, B  =   0.354
Partial structure    1: scale =    0.377, B  =  49.148
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 = -0.00 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011     233  97.22   381.8   385.5  0.26  0.33      12   579.5   494.5  0.29  0.24
 0.032     376 100.00   340.7   352.2  0.27  0.31      13   343.0   298.6  0.33  0.37
 0.052     471  99.80   432.6   426.2  0.20  0.25      25   417.3   387.4  0.22  0.24
 0.073     544  99.48   432.1   391.6  0.20  0.23      25   452.4   383.4  0.22  0.22
 0.094     600  99.06   387.2   351.7  0.21  0.23      29   317.0   315.8  0.27  0.27
 0.115     684 100.00   284.4   275.8  0.22  0.24      26   383.1   335.6  0.23  0.24
 0.135     704  99.33   243.6   235.9  0.23  0.25      36   250.9   221.7  0.26  0.28
 0.156     761  99.26   220.3   218.4  0.23  0.23      45   193.9   199.0  0.35  0.33
 0.177     811  99.88   201.7   197.9  0.24  0.24      39   224.4   209.0  0.28  0.27
 0.198     824  95.44   205.5   190.5  0.23  0.23      35   193.9   173.3  0.29  0.30
 0.219     897  99.90   180.0   166.6  0.23  0.23      60   198.9   167.8  0.29  0.28
 0.239     933  99.49   170.4   151.8  0.25  0.24      42   143.0   130.7  0.25  0.26
 0.260     931  97.26   142.8   130.9  0.25  0.24      62   134.2   128.0  0.28  0.25
 0.281     928  93.07   128.2   115.4  0.27  0.25      53   127.9   108.9  0.37  0.36
 0.302    1036 100.00   105.3    99.9  0.27  0.24      66   114.5   100.3  0.30  0.29
 0.323    1089  99.91    95.8    90.2  0.26  0.23      45    85.6    85.9  0.37  0.33
 0.343    1058  97.57    90.5    87.1  0.26  0.23      68    86.0    84.4  0.30  0.27
 0.364    1129 100.00    81.4    80.1  0.27  0.23      65    80.6    75.0  0.27  0.26
 0.385    1164 100.00    76.1    74.1  0.26  0.22      72    77.3    72.5  0.33  0.28
 0.406    1195  99.36    66.2    66.6  0.29  0.24      55    66.0    63.1  0.32  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0107    118   0.803    115   0.702    233   0.753  0.887  0.9408  0.9224  0.5939  0.8854
  0.0315    260   0.837    116   0.775    376   0.818  0.942  0.9131  0.9204  0.8530  0.8482
  0.0523    348   0.888    123   0.810    471   0.868  0.982  0.9471  0.9582  0.8637  0.9125
  0.0731    422   0.899    122   0.819    544   0.881  1.012  0.9491  0.9525  0.8735  0.9044
  0.0939    490   0.868    110   0.807    600   0.857  1.005  0.9071  0.9416  0.6537  0.8827
  0.1147    555   0.807    129   0.780    684   0.802  0.950  0.9364  0.9213  0.8937  0.8798
  0.1355    586   0.802    118   0.651    704   0.776  0.919  0.8963  0.9051  0.8072  0.8629
  0.1563    642   0.798    119   0.754    761   0.791  0.907  0.8302  0.9066  0.5143  0.8489
  0.1771    686   0.817    125   0.709    811   0.800  0.938  0.8980  0.9128  0.7720  0.8534
  0.1979    721   0.846    103   0.792    824   0.839  0.969  0.9081  0.9246  0.8594  0.8536
  0.2187    768   0.830    129   0.710    897   0.813  0.989  0.9035  0.9160  0.7549  0.8528
  0.2395    810   0.829    123   0.732    933   0.816  0.996  0.9005  0.9044  0.8785  0.8015
  0.2603    832   0.815     99   0.771    931   0.810  0.993  0.8953  0.9071  0.7573  0.8218
  0.2811    830   0.782     98   0.715    928   0.775  0.966  0.8552  0.8862  0.6602  0.7887
  0.3018    915   0.756    121   0.628   1036   0.741  0.946  0.8647  0.8762  0.7022  0.8106
  0.3226    960   0.769    129   0.658   1089   0.756  0.938  0.8322  0.8839  0.6523  0.8199
  0.3434    959   0.797     99   0.724   1058   0.790  0.926  0.8632  0.8899  0.7375  0.7978
  0.3642   1000   0.802    129   0.719   1129   0.793  0.910  0.8811  0.8920  0.7776  0.7969
  0.3850   1041   0.767    123   0.674   1164   0.757  0.885  0.8600  0.8809  0.7345  0.8079
  0.4058   1080   0.707    115   0.621   1195   0.699  0.858  0.8072  0.8444  0.5999  0.7804
 $$
Resolution limits                    =     55.660     1.550
Number of used reflections           =      16368
Percentage observed                  =    98.7740
Percentage of free reflections       =     5.0635
Overall R factor                     =     0.2375
Free R factor                        =     0.2831
Average Fourier shell correlation    =     0.9006
AverageFree Fourier shell correlation=     0.8789
Overall weighted R factor            =     0.2436
Free weighted R factor               =     0.2766
Overall weighted R2 factor           =     0.3022
Free weighted R2 factor              =     0.3191
Average correlation coefficient      =     0.8301
Overall correlation coefficient      =     0.9253
Free correlation coefficient         =     0.8881
Cruickshanks DPI for coordinate error=     0.1173
DPI based on free R factor           =     0.1186
Overall figure of merit              =     0.7896
ML based su of positional parameters =     0.0838
ML based su of thermal parameters    =     2.2884
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02


 fvalues    85005.992       47996.117       849621.00       898056.06    


     CGMAT cycle number =      2

 Weight matrix    1.0278370    
 Actual weight    10.000000      is applied to the X-ray term


 function value    844673.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.016     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.982, B  =  -0.082
Partial structure    1: scale =    0.379, B  =  49.376
Overall anisotropic scale factors
   B11 = -0.00 B22 = -0.00 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2098
Free R factor                        =     0.2651
Average Fourier shell correlation    =     0.9194
AverageFree Fourier shell correlation=     0.8956
Average correlation coefficient      =     0.8757
Overall figure of merit              =     0.8080
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02


 fvalues    83207.742       12633.804       834424.81       844711.25    


     CGMAT cycle number =      3

 Weight matrix    1.0406448    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    756625.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.022     0.019
Bond distances: others                          661     0.005     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.984, B  =  -0.005
Partial structure    1: scale =    0.381, B  =  52.019
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2001
Free R factor                        =     0.2547
Average Fourier shell correlation    =     0.9263
AverageFree Fourier shell correlation=     0.9037
Average correlation coefficient      =     0.8885
Overall figure of merit              =     0.8184
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02


 fvalues    82503.758       6588.8301       753427.00       756622.94    


     CGMAT cycle number =      4

 Weight matrix    1.0019109    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    683720.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.004     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.988, B  =  -0.012
Partial structure    1: scale =    0.381, B  =  54.150
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1956
Free R factor                        =     0.2489
Average Fourier shell correlation    =     0.9295
AverageFree Fourier shell correlation=     0.9076
Average correlation coefficient      =     0.8931
Overall figure of merit              =     0.8244
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02


 fvalues    82135.500       4914.4033       683154.31       683720.13    


     CGMAT cycle number =      5

 Weight matrix    1.0151688    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    682705.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.004     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.989, B  =  -0.003
Partial structure    1: scale =    0.382, B  =  54.715
Overall anisotropic scale factors
   B11 = -0.00 B22 = -0.00 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1944
Free R factor                        =     0.2466
Average Fourier shell correlation    =     0.9303
AverageFree Fourier shell correlation=     0.9086
Average correlation coefficient      =     0.8942
Overall figure of merit              =     0.8260
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    82039.555       4691.4199       682369.13       682704.25    


     CGMAT cycle number =      6

 Weight matrix    1.0299186    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    681683.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.006     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.991, B  =   0.019
Partial structure    1: scale =    0.382, B  =  55.669
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1935
Free R factor                        =     0.2448
Average Fourier shell correlation    =     0.9311
AverageFree Fourier shell correlation=     0.9096
Average correlation coefficient      =     0.8950
Overall figure of merit              =     0.8278
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    81923.930       4622.9971       681304.25       681680.25    


     CGMAT cycle number =      7

 Weight matrix    1.0483378    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    680692.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.010     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.993, B  =   0.009
Partial structure    1: scale =    0.382, B  =  56.102
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2425
Average Fourier shell correlation    =     0.9320
AverageFree Fourier shell correlation=     0.9107
Average correlation coefficient      =     0.8961
Overall figure of merit              =     0.8299
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    81802.148       4637.4658       680507.81       680688.25    


     CGMAT cycle number =      8

 Weight matrix   0.96407145    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    618606.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.014     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.995, B  =   0.009
Partial structure    1: scale =    0.382, B  =  56.886
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1910
Free R factor                        =     0.2410
Average Fourier shell correlation    =     0.9326
AverageFree Fourier shell correlation=     0.9114
Average correlation coefficient      =     0.8969
Overall figure of merit              =     0.8314
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Gamma decreased to   9.99999975E-05


 fvalues    81705.891       4737.0410       618565.63       618605.44    


     CGMAT cycle number =      9

 Weight matrix   0.88198042    
 Actual weight    6.8301339      is applied to the X-ray term


 function value    562590.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.021     0.019
Bond distances: others                          661     0.018     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.995, B  =  -0.002
Partial structure    1: scale =    0.390, B  =  58.536
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1907
Free R factor                        =     0.2392
Average Fourier shell correlation    =     0.9328
AverageFree Fourier shell correlation=     0.9118
Average correlation coefficient      =     0.8969
Overall figure of merit              =     0.8324
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Gamma decreased to   9.99999975E-05


 fvalues    81679.641       4707.3936       562221.25       562590.25    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.886 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.886 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.985 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.985 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.785 id.= 1.100 dev= -0.32 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.785 id.= 1.100 dev= -0.32 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.901 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.901 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.873 id.= 1.100 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.873 id.= 1.100 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.620 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.620 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.726 id.= 1.820 dev= -1.09 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.726 id.= 1.820 dev= -1.09 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.668 id.= 1.100 dev= -0.43 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.668 id.= 1.100 dev= -0.43 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ3 . - Z    179 DUM DUM . mod.= 0.804 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ3 . - Z    179 DUM DUM . mod.= 0.804 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.741 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.741 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.713 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.713 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.874 id.= 1.100 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.874 id.= 1.100 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.620 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.620 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.657 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.657 id.= 1.100 dev= -0.44 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.734 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.734 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.939 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.939 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.935 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.935 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.584 id.= 1.100 dev= -0.52 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.584 id.= 1.100 dev= -0.52 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.537 id.= 1.100 dev= -0.56 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.537 id.= 1.100 dev= -0.56 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.954 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.954 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.590 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.590 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HB2 . - Z     21 DUM DUM . mod.= 0.803 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HB2 . - Z     21 DUM DUM . mod.= 0.803 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.893 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.893 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.885 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.885 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
Z     23 DUM DUM . - Z    289 DUM DUM . mod.= 0.968 id.= 1.200 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  6
Z     23 DUM DUM . - Z    289 DUM DUM . mod.= 0.968 id.= 1.200 dev= -0.23 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  6

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    51   51   24
 Minimum acceptable grid spacing:   116  116   55
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   176  176   88
 Maximuum H,K,L                 :    51   51   24
 Minimum acceptable grid spacing:   116  116   55
 Weight matrix   0.88272715    
 Actual weight    6.8301339      is applied to the X-ray term
Norm of X_ray positional gradient                33.4
Norm of Geom. positional gradient                33.6
Norm of X_ray B-factor gradient                  212.
Norm of Geom. B-factor gradient                  180.
Product of X_ray and Geom posit. gradients     -0.600E+07
 Cosine of angle between them                      -0.986
Product of X_ray and Geom B-fact gradients     -0.607E+08
 Cosine of angle between them                      -0.881


Residuals: XRAY=     0.5579E+06 GEOM=      4270.     TOTAL=     0.5622E+06
 function value    562181.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.020     0.019
Bond distances: others                          661     0.003     0.020
Bond angles  : refined atoms                   1075     1.925     1.909
Bond angles  : others                          1482     1.237     3.000
Torsion angles, period  1. refined              112     7.063     5.000
Torsion angles, period  2. refined               26    29.758    25.000
Torsion angles, period  3. refined              100    13.201    15.000
Chiral centres: refined atoms                   118     0.149     0.200
Planar groups: refined atoms                    932     0.010     0.020
Planar groups: others                           166     0.002     0.020
VDW repulsions: refined_atoms                   472     0.337     0.200
VDW repulsions.others                          1308     0.177     0.200
VDW; torsion: refined_atoms                     836     0.179     0.200
VDW; torsion.others                             708     0.090     0.200
HBOND: refined_atoms                             44     0.327     0.200
HBOND.others                                      2     0.179     0.200
DUMMY_NORMAL: refined_atoms                     100     0.257     0.300
DUMMY_NORMAL.others                              74     0.286     0.300
DUMMY_DUMMY: refined_atoms                       12     0.139     0.300
VDW repulsions: symmetry: refined_atoms           8     0.352     0.200
VDW repulsions: symmetry: others                 13     0.221     0.200
HBOND: symmetry: refined_atoms                    3     0.139     0.200
M. chain bond B values: refined atoms           461     1.109     1.120
M. chain bond B values: others                  462     1.108     1.122
M. chain angle B values: refined atoms          566     1.537     1.667
M. chain angle B values: others                 566     1.537     1.667
S. chain bond B values: refined atoms           347     1.785     1.199
S. chain bond B values: others                  348     1.783     1.205
S. chain angle B values: refined atoms          509     2.226     1.711
S. chain angle B values: others                 510     2.224     1.717
Long range B values: refined atoms             1031     4.004    14.197
Long range B values: others                    1019     3.852    14.209
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.996, B  =  -0.002
Partial structure    1: scale =    0.390, B  =  58.712
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011     233  97.22   375.3   378.9  0.27  0.34      12   569.7   520.6  0.26  0.24
 0.032     376 100.00   335.0   352.3  0.25  0.29      13   337.2   296.2  0.30  0.32
 0.052     471  99.80   425.3   426.3  0.17  0.20      25   410.3   400.4  0.20  0.22
 0.073     544  99.48   424.8   390.7  0.18  0.21      25   444.8   388.3  0.19  0.18
 0.094     600  99.06   380.7   349.5  0.18  0.20      29   311.6   323.0  0.26  0.26
 0.115     684 100.00   279.7   272.2  0.19  0.21      26   376.7   344.5  0.18  0.20
 0.135     704  99.33   239.5   235.6  0.19  0.21      36   246.7   222.9  0.24  0.25
 0.156     761  99.26   216.6   216.9  0.17  0.18      45   190.6   196.4  0.25  0.24
 0.177     811  99.88   198.3   195.7  0.18  0.18      39   220.6   210.1  0.20  0.19
 0.198     824  95.44   202.0   189.5  0.17  0.17      35   190.6   179.0  0.20  0.22
 0.219     897  99.90   177.0   167.6  0.17  0.17      60   195.5   173.3  0.23  0.23
 0.239     933  99.49   167.5   151.3  0.20  0.19      42   140.6   126.6  0.26  0.26
 0.260     931  97.26   140.4   131.8  0.18  0.17      62   131.9   127.9  0.27  0.22
 0.281     928  93.07   126.0   116.7  0.21  0.19      53   125.7   109.3  0.27  0.26
 0.302    1036 100.00   103.6   100.2  0.20  0.17      66   112.5   103.7  0.26  0.25
 0.323    1089  99.91    94.2    91.8  0.19  0.17      45    84.1    86.4  0.28  0.25
 0.343    1058  97.57    89.0    86.6  0.18  0.16      68    84.5    84.8  0.28  0.25
 0.364    1129 100.00    80.1    80.7  0.20  0.17      65    79.2    72.8  0.23  0.20
 0.385    1164 100.00    74.8    75.0  0.20  0.17      72    76.0    78.1  0.27  0.22
 0.406    1195  99.36    65.1    68.2  0.25  0.20      55    64.9    64.6  0.31  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0107    118   0.810    115   0.690    233   0.751  0.888  0.8881  0.9208  0.6891  0.8832
  0.0315    260   0.855    116   0.789    376   0.835  0.942  0.9211  0.9323  0.8554  0.8719
  0.0523    348   0.913    123   0.832    471   0.892  0.982  0.9592  0.9693  0.8874  0.9360
  0.0731    422   0.921    122   0.855    544   0.906  1.011  0.9609  0.9632  0.8958  0.9252
  0.0939    490   0.889    110   0.829    600   0.878  1.004  0.9239  0.9554  0.6940  0.9139
  0.1147    555   0.843    129   0.818    684   0.838  0.949  0.9583  0.9416  0.9281  0.9137
  0.1355    586   0.860    118   0.724    704   0.837  0.933  0.9239  0.9378  0.8436  0.9078
  0.1563    642   0.872    119   0.816    761   0.863  0.938  0.9055  0.9495  0.7293  0.9176
  0.1771    686   0.885    125   0.809    811   0.874  0.964  0.9452  0.9523  0.8813  0.9176
  0.1979    721   0.899    103   0.864    824   0.895  0.985  0.9485  0.9583  0.9083  0.9265
  0.2187    768   0.865    129   0.758    897   0.850  0.993  0.9352  0.9470  0.8388  0.9223
  0.2395    810   0.857    123   0.780    933   0.847  0.996  0.9130  0.9287  0.8713  0.8571
  0.2603    832   0.846     99   0.800    931   0.841  0.994  0.9118  0.9367  0.7862  0.9013
  0.2811    830   0.825     98   0.746    928   0.816  0.976  0.8996  0.9220  0.7824  0.8661
  0.3018    915   0.812    121   0.669   1036   0.795  0.961  0.9033  0.9213  0.7483  0.8993
  0.3226    960   0.827    129   0.742   1089   0.817  0.954  0.8902  0.9268  0.7934  0.8997
  0.3434    959   0.840     99   0.758   1058   0.832  0.936  0.8940  0.9300  0.7829  0.8941
  0.3642   1000   0.840    129   0.719   1129   0.826  0.911  0.9133  0.9289  0.8476  0.8950
  0.3850   1041   0.806    123   0.694   1164   0.795  0.885  0.9017  0.9145  0.8203  0.8847
  0.4058   1080   0.755    115   0.678   1195   0.747  0.858  0.8398  0.8829  0.6670  0.8448
 $$
Resolution limits                    =     55.660     1.550
Number of used reflections           =      16368
Percentage observed                  =    98.7740
Percentage of free reflections       =     5.0635
Overall R factor                     =     0.1907
Free R factor                        =     0.2388
Average Fourier shell correlation    =     0.9328
AverageFree Fourier shell correlation=     0.9118
Overall weighted R factor            =     0.1959
Free weighted R factor               =     0.2337
Overall weighted R2 factor           =     0.2563
Free weighted R2 factor              =     0.2840
Average correlation coefficient      =     0.8964
Overall correlation coefficient      =     0.9471
Free correlation coefficient         =     0.9167
Cruickshanks DPI for coordinate error=     0.0942
DPI based on free R factor           =     0.1001
Overall figure of merit              =     0.8328
ML based su of positional parameters =     0.0677
ML based su of thermal parameters    =     1.8563
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Gamma decreased to   9.99999975E-05


 fvalues    81683.992       4270.4375       562123.63       562183.06    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.814 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      1 LYS HE3 . - Z    248 DUM DUM . mod.= 0.814 id.= 1.100 dev= -0.29 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.891 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      3 LEU HD12. - Z     67 DUM DUM . mod.= 0.891 id.= 1.100 dev= -0.21 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.981 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      3 LEU HD22. - Z    102 DUM DUM . mod.= 0.981 id.= 1.100 dev= -0.12 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      6 GLN HB2 . - Z     20 DUM DUM . mod.= 1.000 id.= 1.100 dev= -0.10 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A      6 GLN HB2 . - Z     20 DUM DUM . mod.= 1.000 id.= 1.100 dev= -0.10 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.795 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A      7 GLU HB2 . - Z    216 DUM DUM . mod.= 0.795 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.901 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     13 VAL HG12. - Z    136 DUM DUM . mod.= 0.901 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.931 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     15 GLN HG2 . - Z     62 DUM DUM . mod.= 0.931 id.= 1.100 dev= -0.17 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.879 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     17 MET HG2 . - Z    112 DUM DUM . mod.= 0.879 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.625 id.= 1.100 dev= -0.47 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     19 GLY HA3 . - Z    120 DUM DUM . mod.= 0.625 id.= 1.100 dev= -0.47 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.722 id.= 1.820 dev= -1.10 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     26 PRO CG  . - Z    164 DUM DUM . mod.= 0.722 id.= 1.820 dev= -1.10 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.680 id.= 1.100 dev= -0.42 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     33 PHE HE1 . - Z    239 DUM DUM . mod.= 0.680 id.= 1.100 dev= -0.42 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ2 . - Z     31 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     68 LYS HZ3 . - Z    179 DUM DUM . mod.= 0.771 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     68 LYS HZ3 . - Z    179 DUM DUM . mod.= 0.771 id.= 1.100 dev= -0.33 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.741 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     74 ASN H   . - Z    235 DUM DUM . mod.= 0.741 id.= 1.100 dev= -0.36 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.712 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     75 ALA HB1 . - Z     37 DUM DUM . mod.= 0.712 id.= 1.100 dev= -0.39 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.879 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER HB2 . - Z    154 DUM DUM . mod.= 0.879 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.621 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     79 SER H   . - Z     68 DUM DUM . mod.= 0.621 id.= 1.100 dev= -0.48 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.655 id.= 1.100 dev= -0.45 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     90 ASP HA  . - Z    125 DUM DUM . mod.= 0.655 id.= 1.100 dev= -0.45 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.735 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     92 LEU HB3 . - Z     76 DUM DUM . mod.= 0.735 id.= 1.100 dev= -0.37 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.947 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB2 . - Z    158 DUM DUM . mod.= 0.947 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.939 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A     99 ALA HB3 . - Z     30 DUM DUM . mod.= 0.939 id.= 1.100 dev= -0.16 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.585 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    100 GLY HA3 . - Z     66 DUM DUM . mod.= 0.585 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.536 id.= 1.100 dev= -0.56 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    106 THR HG21. - Z    177 DUM DUM . mod.= 0.536 id.= 1.100 dev= -0.56 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.953 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    112 LYS HB3 . - Z    205 DUM DUM . mod.= 0.953 id.= 1.100 dev= -0.15 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.592 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    118 HIS HB2 . - Z     25 DUM DUM . mod.= 0.592 id.= 1.100 dev= -0.51 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HB2 . - Z     21 DUM DUM . mod.= 0.804 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HB2 . - Z     21 DUM DUM . mod.= 0.804 id.= 1.100 dev= -0.30 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.876 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
A    120 LEU HG  . - Z     34 DUM DUM . mod.= 0.876 id.= 1.100 dev= -0.22 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.900 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  5
A    123 PHE HD1 . - Z    288 DUM DUM . mod.= 0.900 id.= 1.100 dev= -0.20 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  5
Z     23 DUM DUM . - Z    289 DUM DUM . mod.= 0.952 id.= 1.200 dev= -0.25 sig.= 0.30 sym.=  1  0  0  0 ncs  -1 type =  6
Z     23 DUM DUM . - Z    289 DUM DUM . mod.= 0.952 id.= 1.200 dev= -0.25 sig.= 0.30 sym.=  1  0  0  0 ncs   1 type =  6

 labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac2.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   808     0.020     0.019
Bond distances: others                          661     0.005     0.020
Bond angles  : refined atoms                   1075     1.914     1.909
Bond angles  : others                          1482     1.235     3.000
Torsion angles, period  1. refined              112     7.052     5.000
Torsion angles, period  2. refined               26    29.750    25.000
Torsion angles, period  3. refined              100    13.177    15.000
Chiral centres: refined atoms                   118     0.148     0.200
Planar groups: refined atoms                    932     0.010     0.020
Planar groups: others                           166     0.002     0.020
VDW repulsions: refined_atoms                   474     0.336     0.200
VDW repulsions.others                          1308     0.177     0.200
VDW; torsion: refined_atoms                     838     0.179     0.200
VDW; torsion.others                             712     0.089     0.200
HBOND: refined_atoms                             44     0.325     0.200
HBOND.others                                      2     0.153     0.200
DUMMY_NORMAL: refined_atoms                     100     0.256     0.300
DUMMY_NORMAL.others                              72     0.288     0.300
DUMMY_DUMMY: refined_atoms                       12     0.144     0.300
VDW repulsions: symmetry: refined_atoms           8     0.354     0.200
VDW repulsions: symmetry: others                 11     0.238     0.200
HBOND: symmetry: refined_atoms                    3     0.138     0.200
DUMMY_DUMMY: symmetry: refined_atoms              1     0.000     0.300
M. chain bond B values: refined atoms           461     1.098     1.120
M. chain bond B values: others                  462     1.097     1.122
M. chain angle B values: refined atoms          566     1.525     1.667
M. chain angle B values: others                 566     1.524     1.667
S. chain bond B values: refined atoms           347     1.768     1.198
S. chain bond B values: others                  348     1.766     1.204
S. chain angle B values: refined atoms          509     2.209     1.711
S. chain angle B values: others                 510     2.207     1.717
Long range B values: refined atoms             1033     3.991    14.204
Long range B values: others                    1021     3.840    14.215
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.996, B  =  -0.000
Partial structure    1: scale =    0.390, B  =  58.870
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.01 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011     233  97.22   375.3   379.2  0.27  0.34      12   569.7   520.9  0.26  0.24
 0.032     376 100.00   334.9   352.2  0.25  0.29      13   337.2   295.7  0.30  0.32
 0.052     471  99.80   425.3   426.1  0.17  0.20      25   410.3   400.7  0.20  0.22
 0.073     544  99.48   424.8   390.6  0.18  0.21      25   444.7   388.5  0.19  0.18
 0.094     600  99.06   380.7   349.4  0.18  0.20      29   311.6   323.6  0.26  0.26
 0.115     684 100.00   279.6   272.3  0.19  0.21      26   376.6   345.0  0.18  0.20
 0.135     704  99.33   239.5   235.6  0.19  0.21      36   246.7   223.1  0.24  0.25
 0.156     761  99.26   216.6   216.9  0.17  0.18      45   190.6   196.3  0.25  0.24
 0.177     811  99.88   198.3   195.7  0.18  0.18      39   220.6   210.4  0.20  0.19
 0.198     824  95.44   202.0   189.5  0.17  0.17      35   190.6   179.0  0.20  0.22
 0.219     897  99.90   177.0   167.7  0.17  0.17      60   195.5   173.5  0.23  0.23
 0.239     933  99.49   167.5   151.3  0.20  0.19      42   140.6   126.5  0.26  0.26
 0.260     931  97.26   140.4   131.8  0.18  0.17      62   131.9   128.0  0.26  0.22
 0.281     928  93.07   126.0   116.7  0.21  0.19      53   125.7   109.4  0.26  0.26
 0.302    1036 100.00   103.6   100.2  0.20  0.17      66   112.5   103.7  0.26  0.25
 0.323    1089  99.91    94.2    91.8  0.19  0.17      45    84.1    86.2  0.28  0.25
 0.343    1058  97.57    89.0    86.5  0.18  0.16      68    84.5    84.8  0.28  0.25
 0.364    1129 100.00    80.0    80.7  0.20  0.17      65    79.2    72.8  0.23  0.20
 0.385    1164 100.00    74.8    75.0  0.20  0.17      72    76.0    78.3  0.27  0.22
 0.406    1195  99.36    65.1    68.2  0.25  0.20      55    64.8    64.7  0.31  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0107    118   0.810    115   0.691    233   0.751  0.888  0.8883  0.9211  0.6878  0.8837
  0.0315    260   0.856    116   0.790    376   0.836  0.942  0.9210  0.9327  0.8546  0.8719
  0.0523    348   0.914    123   0.833    471   0.893  0.982  0.9598  0.9696  0.8891  0.9366
  0.0731    422   0.921    122   0.854    544   0.906  1.011  0.9608  0.9632  0.8949  0.9252
  0.0939    490   0.889    110   0.830    600   0.878  1.004  0.9235  0.9554  0.6923  0.9141
  0.1147    555   0.845    129   0.819    684   0.840  0.949  0.9590  0.9421  0.9295  0.9143
  0.1355    586   0.862    118   0.725    704   0.839  0.933  0.9246  0.9385  0.8443  0.9084
  0.1563    642   0.873    119   0.818    761   0.864  0.938  0.9065  0.9499  0.7321  0.9181
  0.1771    686   0.886    125   0.811    811   0.875  0.964  0.9455  0.9527  0.8820  0.9183
  0.1979    721   0.900    103   0.865    824   0.896  0.985  0.9487  0.9586  0.9089  0.9269
  0.2187    768   0.865    129   0.759    897   0.850  0.993  0.9355  0.9471  0.8394  0.9225
  0.2395    810   0.858    123   0.782    933   0.848  0.996  0.9128  0.9288  0.8705  0.8571
  0.2603    832   0.846     99   0.802    931   0.842  0.994  0.9127  0.9370  0.7890  0.9012
  0.2811    830   0.826     98   0.746    928   0.817  0.976  0.9001  0.9222  0.7841  0.8662
  0.3018    915   0.812    121   0.669   1036   0.795  0.961  0.9031  0.9213  0.7479  0.8994
  0.3226    960   0.827    129   0.742   1089   0.817  0.954  0.8901  0.9267  0.7942  0.8995
  0.3434    959   0.839     99   0.756   1058   0.832  0.936  0.8933  0.9299  0.7806  0.8940
  0.3642   1000   0.840    129   0.718   1129   0.826  0.911  0.9136  0.9288  0.8486  0.8945
  0.3850   1041   0.807    123   0.695   1164   0.795  0.885  0.9023  0.9146  0.8214  0.8845
  0.4058   1080   0.756    115   0.679   1195   0.748  0.858  0.8403  0.8834  0.6664  0.8450
 $$
Resolution limits                    =     55.660     1.550
Number of used reflections           =      16368
Percentage observed                  =    98.7740
Percentage of free reflections       =     5.0635
Overall R factor                     =     0.1904
Free R factor                        =     0.2385
Average Fourier shell correlation    =     0.9329
AverageFree Fourier shell correlation=     0.9121
Overall weighted R factor            =     0.1956
Free weighted R factor               =     0.2333
Overall weighted R2 factor           =     0.2557
Free weighted R2 factor              =     0.2838
Average correlation coefficient      =     0.8966
Overall correlation coefficient      =     0.9473
Free correlation coefficient         =     0.9169
Cruickshanks DPI for coordinate error=     0.0940
DPI based on free R factor           =     0.0999
Overall figure of merit              =     0.8333
ML based su of positional parameters =     0.0677
ML based su of thermal parameters    =     1.8563
-----------------------------------------------------------------------------
  Time in seconds: CPU =        42.01
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2375   0.2831   0.790       84962.    4609.4   0.0202  1.015   1.961  0.969   0.154
       1   0.2098   0.2651   0.808       83204.    4556.7   0.0208  1.049   1.941  0.952   0.154
       2   0.2001   0.2547   0.818       82504.    4528.9   0.0218  1.097   1.993  0.975   0.157
       3   0.1956   0.2489   0.824       82136.    4513.1   0.0215  1.082   1.999  0.977   0.156
       4   0.1944   0.2466   0.826       82040.    4507.7   0.0212  1.067   1.990  0.972   0.155
       5   0.1935   0.2448   0.828       81924.    4501.8   0.0211  1.062   1.988  0.970   0.155
       6   0.1920   0.2425   0.830       81803.    4495.5   0.0212  1.065   1.991  0.971   0.156
       7   0.1910   0.2410   0.831       81706.    4491.0   0.0214  1.073   1.999  0.976   0.157
       8   0.1907   0.2392   0.832       81680.    4488.3   0.0206  1.031   1.968  0.958   0.153
       9   0.1907   0.2388   0.833       81684.    4488.0   0.0196  0.985   1.925  0.934   0.149
      10   0.1904   0.2385   0.833       81666.    4486.9   0.0196  0.981   1.914  0.928   0.148
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2375   0.1904
             R free    0.2831   0.2385
     Rms BondLength    0.0202   0.0196
      Rms BondAngle    1.9614   1.9137
     Rms ChirVolume    0.1545   0.1480
 $$

 Refmac:  End of Refmac_5.8.0158  
Times: User:      51.2s System:    0.3s Elapsed:     0:52  
*************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final coordinates (XYZOUT) to /home/marek/Desktop/LYSOZYM-seminar/ccp4/arp_5_refmac1.pdb *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final phases (HKLOUT) to /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac2.mtz *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 02 Dec 2016 15:23:13 #CCP4I TERMINATION OUTPUT_FILES /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso_4_XDSdataset.refmac.cif lyso #CCP4I MESSAGE Task completed successfully