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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: malyma  Run date: 11/ 3/2021 Run time: 12:30:31 


 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.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

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

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference3:  $$ 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

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 47.32 2.10     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - project_R00_2-30A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - project_R00_2-10A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - project_R00_2-10A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/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
    Standard sugar links 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:     5       0.0454
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.1000
  Estimated number of reflections :      34260
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  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:    47.3245  2.1000

  Damping factors:     1.0000  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
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :project_R00_2-30A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    2286
  Number of residues :     307
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  BBB  is missing in the structure
  ATTENTION: atom:OXT  THR                70  BBB  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  BBB  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 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     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0317


 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:      4485         0      4485
               Angles:      8175         0      8175
              Chirals:       284         0       284
               Planes:       646         0       646
             Torsions:      2321         0      2321
            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       1283
Number of   all  reflections      26407
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          26407

   Current auto weighting coefficient =    7.7495594    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Weight matrix   2.27013063E-02
 Actual weight    7.7495594      is applied to the X-ray term
Norm of X_ray positional gradient                14.0
Norm of Geom. positional gradient                113.
Norm of X_ray B-factor gradient                  18.7
Norm of Geom. B-factor gradient                  19.3
Product of X_ray and Geom posit. gradients     -0.553E+07
 Cosine of angle between them                      -0.259
Product of X_ray and Geom B-fact gradients     -0.130E+07
 Cosine of angle between them                      -0.800


Residuals: XRAY=     0.8207E+06 GEOM=     0.1719E+05 TOTAL=     0.8379E+06
 function value    837866.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.017     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.997     1.648
Bond angles  : others                          5121     2.247     1.582
Torsion angles, period  1. refined              265     6.550     5.000
Torsion angles, period  2. refined              135    33.059    22.370
Torsion angles, period  3. refined              475    19.302    15.000
Torsion angles, period  4. refined               19    18.944    15.000
Chiral centres: refined atoms                   284     0.141     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.010     0.020
VDW repulsions: refined_atoms                   499     0.213     0.200
VDW repulsions.others                          1904     0.191     0.200
VDW; torsion: refined_atoms                    1071     0.174     0.200
VDW; torsion.others                            1144     0.077     0.200
HBOND: refined_atoms                             44     0.158     0.200
VDW repulsions: symmetry: refined_atoms          11     0.183     0.200
VDW repulsions: symmetry: others                 23     0.277     0.200
HBOND: symmetry: refined_atoms                    3     0.116     0.200
M. chain bond B values: refined atoms          1075     5.601     7.097
M. chain bond B values: others                 1074     5.583     7.088
M. chain angle B values: refined atoms         1335     8.154    10.589
M. chain angle B values: others                1336     8.155    10.598
S. chain bond B values: refined atoms          1209     6.266     7.849
S. chain bond B values: others                 1207     6.266     7.840
S. chain angle B values: refined atoms         1719     9.712    11.469
S. chain angle B values: others                1719     9.709    11.470
Long range B values: refined atoms             2570    12.299    79.861
Long range B values: others                    2569    12.302    79.835
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5407, B  =    0.1310
Partial structure    1: scale =     0.3826, B  =   54.8711
Overall anisotropic scale factors
   B11 =   5.69 B22 =  -1.82 B33 =  -3.86 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.7   272.7  0.21  0.22     116   255.3   257.0  0.32  0.33
 0.068    4157  99.86   172.8   162.1  0.20  0.19     220   173.7   162.1  0.25  0.24
 0.114    5265  99.71    67.2    62.4  0.24  0.21     282    65.7    63.2  0.33  0.30
 0.159    6203  99.89    32.6    31.6  0.33  0.29     319    34.4    34.3  0.37  0.33
 0.204    7017  99.95    21.8    16.5  0.43  0.43     344    21.2    15.8  0.44  0.44
$$

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

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.813    567   0.742   2431   0.796  0.913  0.9043  0.9426  0.8431  0.9254
  0.0683   3575   0.837    582   0.743   4157   0.823  0.994  0.9212  0.9380  0.8551  0.9243
  0.1136   4683   0.755    582   0.674   5265   0.746  0.944  0.8520  0.8913  0.7486  0.8924
  0.1589   5624   0.572    579   0.529   6203   0.568  0.737  0.7300  0.7248  0.7399  0.8188
  0.2041   6433   0.340    589   0.294   7022   0.336  0.551  0.3720  0.3750  0.6904  0.6426
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2388
Free R factor                        =     0.3109
Average Fourier shell correlation    =     0.7183
AverageFree Fourier shell correlation=     0.7093
Overall weighted R factor            =     0.2157
Free weighted R factor               =     0.2899
Overall weighted R2 factor           =     0.2334
Free weighted R2 factor              =     0.3170
Average correlation coefficient      =     0.8128
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9154
Cruickshanks DPI for coordinate error=     0.1933
DPI based on free R factor           =     0.2006
Overall figure of merit              =     0.6050
ML based su of positional parameters =     0.2582
ML based su of thermal parameters    =    11.3633
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    105899.73       17190.035       837866.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   2.37039998E-02
 Actual weight    7.7495594      is applied to the X-ray term


 function value    826900.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.007     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5461, B  =    0.0144
Partial structure    1: scale =     0.3841, B  =   52.8591
Overall anisotropic scale factors
   B11 =   5.62 B22 =  -1.79 B33 =  -3.82 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2414
Free R factor                        =     0.3095
Average Fourier shell correlation    =     0.7184
AverageFree Fourier shell correlation=     0.7088
Average correlation coefficient      =     0.8121
Overall figure of merit              =     0.5958
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    105727.97       7555.4849       826900.69       837866.31    


     CGMAT cycle number =      3

 Weight matrix   2.33310889E-02
 Actual weight    7.7495594      is applied to the X-ray term


 function value    826215.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.007     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5495, B  =   -0.1147
Partial structure    1: scale =     0.3842, B  =   53.1983
Overall anisotropic scale factors
   B11 =   5.62 B22 =  -1.81 B33 =  -3.81 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2411
Free R factor                        =     0.3099
Average Fourier shell correlation    =     0.7145
AverageFree Fourier shell correlation=     0.7045
Average correlation coefficient      =     0.8129
Overall figure of merit              =     0.5909
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    105662.13       7380.7813       826215.75       826900.69    


     CGMAT cycle number =      4

 Weight matrix   2.38161050E-02
 Actual weight    7.7495594      is applied to the X-ray term


 function value    825381.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.007     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5533, B  =   -0.0966
Partial structure    1: scale =     0.3849, B  =   52.9903
Overall anisotropic scale factors
   B11 =   5.60 B22 =  -1.80 B33 =  -3.80 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2411
Free R factor                        =     0.3102
Average Fourier shell correlation    =     0.7204
AverageFree Fourier shell correlation=     0.7103
Average correlation coefficient      =     0.8130
Overall figure of merit              =     0.5966
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    105572.30       7242.5806       825381.38       826215.75    


     CGMAT cycle number =      5

 Weight matrix   2.34369021E-02
 Actual weight    7.7495594      is applied to the X-ray term


 function value    825577.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.007     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5531, B  =   -0.2996
Partial structure    1: scale =     0.3851, B  =   53.3507
Overall anisotropic scale factors
   B11 =   5.59 B22 =  -1.81 B33 =  -3.78 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2410
Free R factor                        =     0.3106
Average Fourier shell correlation    =     0.7152
AverageFree Fourier shell correlation=     0.7049
Average correlation coefficient      =     0.8137
Overall figure of merit              =     0.5910
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    105618.17       7171.9282       825315.44       825381.38    
 fvalues    105618.17       7171.9282       825315.44       825666.25    


     CGMAT cycle number =      6

 Weight matrix   3.02196275E-02
 Actual weight    10.074427      is applied to the X-ray term


 function value    1070851.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.007     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5546, B  =   -0.2247
Partial structure    1: scale =     0.3859, B  =   53.4427
Overall anisotropic scale factors
   B11 =   5.59 B22 =  -1.81 B33 =  -3.78 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2409
Free R factor                        =     0.3105
Average Fourier shell correlation    =     0.7129
AverageFree Fourier shell correlation=     0.7026
Average correlation coefficient      =     0.8136
Overall figure of merit              =     0.5887
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    105543.98       7112.7925       1070283.6       825666.25    
 fvalues    105543.98       7112.7925       1070283.6       1070407.8    


     CGMAT cycle number =      7

 Weight matrix   3.98946851E-02
 Actual weight    13.096754      is applied to the X-ray term


 function value    1390601.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.008     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5487, B  =   -0.4654
Partial structure    1: scale =     0.3860, B  =   54.4880
Overall anisotropic scale factors
   B11 =   5.55 B22 =  -1.77 B33 =  -3.77 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2390
Free R factor                        =     0.3106
Average Fourier shell correlation    =     0.7180
AverageFree Fourier shell correlation=     0.7066
Average correlation coefficient      =     0.8155
Overall figure of merit              =     0.5926
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02


 fvalues    105600.38       7850.8179       1391793.8       1070407.8    

 fvalues    105600.38       7850.8179       1391330.1       1390873.0    
 fvalues    105600.38       7850.8179       1391330.1       1390873.0    


     CGMAT cycle number =      8

 Weight matrix   4.02924940E-02
 Actual weight    13.096754      is applied to the X-ray term


 function value    1390574.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.008     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5468, B  =   -0.4584
Partial structure    1: scale =     0.3861, B  =   54.6867
Overall anisotropic scale factors
   B11 =   5.53 B22 =  -1.76 B33 =  -3.77 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2384
Free R factor                        =     0.3109
Average Fourier shell correlation    =     0.7231
AverageFree Fourier shell correlation=     0.7116
Average correlation coefficient      =     0.8160
Overall figure of merit              =     0.5971
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    105562.17       8052.9448       1390574.8       1390873.0    


     CGMAT cycle number =      9

 Weight matrix   3.97236273E-02
 Actual weight    13.096754      is applied to the X-ray term


 function value    1391449.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5438, B  =   -0.4498
Partial structure    1: scale =     0.3862, B  =   54.7471
Overall anisotropic scale factors
   B11 =   5.50 B22 =  -1.74 B33 =  -3.76 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2377
Free R factor                        =     0.3110
Average Fourier shell correlation    =     0.7188
AverageFree Fourier shell correlation=     0.7068
Average correlation coefficient      =     0.8168
Overall figure of merit              =     0.5923
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    105618.78       8331.7520       1391780.5       1390574.8    

 fvalues    105618.78       8331.7520       1391659.9       1391595.0    
 fvalues    105618.78       8331.7520       1391659.9       1391595.0    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Weight matrix   3.95918563E-02
 Actual weight    13.096754      is applied to the X-ray term
Norm of X_ray positional gradient                23.7
Norm of Geom. positional gradient                21.5
Norm of X_ray B-factor gradient                  26.9
Norm of Geom. B-factor gradient                  24.1
Product of X_ray and Geom posit. gradients     -0.681E+07
 Cosine of angle between them                      -0.995
Product of X_ray and Geom B-fact gradients     -0.287E+07
 Cosine of angle between them                      -0.989


Residuals: XRAY=     0.1383E+07 GEOM=      8381.     TOTAL=     0.1392E+07
 function value    1391810.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.577     1.648
Bond angles  : others                          5121     1.276     1.582
Torsion angles, period  1. refined              265     6.973     5.000
Torsion angles, period  2. refined              135    32.253    22.370
Torsion angles, period  3. refined              475    19.700    15.000
Torsion angles, period  4. refined               19    18.955    15.000
Chiral centres: refined atoms                   284     0.071     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   505     0.216     0.200
VDW repulsions.others                          1973     0.182     0.200
VDW; torsion: refined_atoms                    1088     0.164     0.200
VDW; torsion.others                            1105     0.084     0.200
HBOND: refined_atoms                             50     0.197     0.200
VDW repulsions: symmetry: refined_atoms          11     0.193     0.200
VDW repulsions: symmetry: others                 36     0.209     0.200
HBOND: symmetry: refined_atoms                    3     0.109     0.200
M. chain bond B values: refined atoms          1075     6.245     7.061
M. chain bond B values: others                 1074     6.210     7.052
M. chain angle B values: refined atoms         1335     8.564    10.543
M. chain angle B values: others                1336     8.568    10.552
S. chain bond B values: refined atoms          1209     7.108     7.783
S. chain bond B values: others                 1207     7.110     7.775
S. chain angle B values: refined atoms         1719    10.440    11.380
S. chain angle B values: others                1719    10.436    11.381
Long range B values: refined atoms             2581    12.678    80.313
Long range B values: others                    2581    12.687    80.356
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5427, B  =   -0.4178
Partial structure    1: scale =     0.3861, B  =   54.5787
Overall anisotropic scale factors
   B11 =   5.49 B22 =  -1.74 B33 =  -3.75 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.3   270.5  0.21  0.22     116   255.0   253.3  0.33  0.33
 0.068    4157  99.86   172.6   162.2  0.19  0.19     220   173.5   162.1  0.25  0.24
 0.114    5265  99.71    67.1    62.7  0.24  0.21     282    65.6    63.0  0.33  0.30
 0.159    6203  99.89    32.5    31.6  0.33  0.30     319    34.4    34.4  0.37  0.33
 0.204    7017  99.95    21.8    16.4  0.42  0.42     344    21.2    15.6  0.43  0.43
$$

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

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.823    567   0.747   2431   0.805  0.921  0.9009  0.9433  0.8387  0.9249
  0.0683   3575   0.835    582   0.743   4157   0.822  0.992  0.9201  0.9389  0.8542  0.9273
  0.1136   4683   0.772    582   0.690   5265   0.763  0.956  0.8597  0.8977  0.7616  0.8932
  0.1589   5624   0.557    579   0.518   6203   0.554  0.731  0.7298  0.7216  0.7352  0.8175
  0.2041   6433   0.289    589   0.257   7022   0.286  0.451  0.3568  0.3728  0.6994  0.6561
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2376
Free R factor                        =     0.3109
Average Fourier shell correlation    =     0.7184
AverageFree Fourier shell correlation=     0.7064
Overall weighted R factor            =     0.2147
Free weighted R factor               =     0.2892
Overall weighted R2 factor           =     0.2330
Free weighted R2 factor              =     0.3187
Average correlation coefficient      =     0.8169
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9144
Cruickshanks DPI for coordinate error=     0.1923
DPI based on free R factor           =     0.2005
Overall figure of merit              =     0.5916
ML based su of positional parameters =     0.2540
ML based su of thermal parameters    =    11.2784
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    105631.44       8381.3711       1391802.5       1391595.0    
 fvalues    105631.44       8381.3711       1391802.5       1391810.4    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: project_R00_2-10A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.585     1.648
Bond angles  : others                          5121     1.278     1.582
Torsion angles, period  1. refined              265     6.988     5.000
Torsion angles, period  2. refined              135    32.269    22.370
Torsion angles, period  3. refined              475    19.713    15.000
Torsion angles, period  4. refined               19    18.981    15.000
Chiral centres: refined atoms                   284     0.071     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   505     0.217     0.200
VDW repulsions.others                          1976     0.183     0.200
VDW; torsion: refined_atoms                    1089     0.164     0.200
VDW; torsion.others                            1104     0.084     0.200
HBOND: refined_atoms                             50     0.198     0.200
VDW repulsions: symmetry: refined_atoms          11     0.194     0.200
VDW repulsions: symmetry: others                 36     0.209     0.200
HBOND: symmetry: refined_atoms                    3     0.110     0.200
M. chain bond B values: refined atoms          1075     6.287     7.055
M. chain bond B values: others                 1074     6.253     7.045
M. chain angle B values: refined atoms         1335     8.601    10.534
M. chain angle B values: others                1336     8.605    10.542
S. chain bond B values: refined atoms          1209     7.161     7.779
S. chain bond B values: others                 1207     7.163     7.771
S. chain angle B values: refined atoms         1719    10.498    11.373
S. chain angle B values: others                1719    10.494    11.373
Long range B values: refined atoms             2581    12.737    80.202
Long range B values: others                    2581    12.746    80.246
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5427, B  =   -0.3994
Partial structure    1: scale =     0.3861, B  =   54.4725
Overall anisotropic scale factors
   B11 =   5.48 B22 =  -1.73 B33 =  -3.75 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.3   270.6  0.21  0.22     116   255.0   253.4  0.33  0.33
 0.068    4157  99.86   172.6   162.3  0.19  0.19     220   173.5   162.3  0.25  0.24
 0.114    5265  99.71    67.1    62.7  0.24  0.21     282    65.6    63.1  0.33  0.30
 0.159    6203  99.89    32.5    31.6  0.33  0.30     319    34.4    34.4  0.37  0.34
 0.204    7017  99.95    21.8    16.5  0.42  0.42     344    21.2    15.6  0.43  0.43
$$

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

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.823    567   0.747   2431   0.805  0.921  0.9009  0.9434  0.8385  0.9250
  0.0683   3575   0.835    582   0.743   4157   0.822  0.992  0.9201  0.9389  0.8539  0.9275
  0.1136   4683   0.772    582   0.690   5265   0.763  0.956  0.8596  0.8977  0.7616  0.8934
  0.1589   5624   0.558    579   0.519   6203   0.554  0.731  0.7302  0.7222  0.7347  0.8176
  0.2041   6433   0.290    589   0.258   7022   0.287  0.451  0.3577  0.3738  0.6999  0.6561
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2374
Free R factor                        =     0.3111
Average Fourier shell correlation    =     0.7188
AverageFree Fourier shell correlation=     0.7067
Overall weighted R factor            =     0.2145
Free weighted R factor               =     0.2894
Overall weighted R2 factor           =     0.2328
Free weighted R2 factor              =     0.3188
Average correlation coefficient      =     0.8170
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9142
Cruickshanks DPI for coordinate error=     0.1921
DPI based on free R factor           =     0.2007
Overall figure of merit              =     0.5920
ML based su of positional parameters =     0.2540
ML based su of thermal parameters    =    11.2784
-----------------------------------------------------------------------------
  Time in seconds: CPU =        37.00
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2388   0.3109   0.605      105900.    5541.2   0.0168  1.426   1.997  1.251   0.141
       1   0.2414   0.3095   0.596      105728.    5535.7   0.0074  0.551   1.528  0.921   0.073
       2   0.2411   0.3099   0.591      105662.    5535.3   0.0072  0.512   1.501  0.900   0.069
       3   0.2411   0.3102   0.597      105572.    5530.0   0.0069  0.487   1.479  0.884   0.067
       4   0.2410   0.3106   0.591      105607.    5533.6   0.0068  0.478   1.468  0.875   0.066
       5   0.2409   0.3105   0.589      105588.    5532.9   0.0067  0.470   1.457  0.867   0.066
       6   0.2390   0.3106   0.593      105580.    5537.5   0.0080  0.561   1.526  0.908   0.069
       7   0.2384   0.3109   0.597      105562.    5536.8   0.0084  0.584   1.545  0.919   0.069
       8   0.2377   0.3110   0.592      105608.    5541.4   0.0088  0.612   1.572  0.936   0.071
       9   0.2376   0.3109   0.592      105631.    5542.7   0.0089  0.616   1.577  0.939   0.071
      10   0.2374   0.3111   0.592      105622.    5543.0   0.0090  0.623   1.585  0.943   0.071
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2388   0.2374
             R free    0.3109   0.3111
     Rms BondLength    0.0168   0.0090
      Rms BondAngle    1.9973   1.5854
     Rms ChirVolume    0.1409   0.0713
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      78.2s System:    0.3s Elapsed:     1:21  
</pre>
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