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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: 16:02:45 


 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 1.90     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--- weight matrix 0.0600
  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  - poli_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_R00_1-90A.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       0.0554
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  1.9000
  Estimated number of reflections :      45570
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0600
  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  1.9000

  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 :poli_R00_2-00A.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       1724
Number of   all  reflections      35468
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          35468

   Current auto weighting coefficient =    7.2500257    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   5.99999987E-02
 Actual weight    22.724367      is applied to the X-ray term
Norm of X_ray positional gradient                35.4
Norm of Geom. positional gradient                77.7
Norm of X_ray B-factor gradient                  36.3
Norm of Geom. B-factor gradient                  32.7
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.386
Product of X_ray and Geom B-fact gradients     -0.424E+07
 Cosine of angle between them                      -0.795


Residuals: XRAY=     0.2995E+07 GEOM=     0.1886E+05 TOTAL=     0.3014E+07
 function value    3013736.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.987     1.648
Bond angles  : others                          5121     2.287     1.582
Torsion angles, period  1. refined              265     7.688     5.000
Torsion angles, period  2. refined              135    32.913    22.370
Torsion angles, period  3. refined              475    20.796    15.000
Torsion angles, period  4. refined               19    21.096    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.015     0.020
VDW repulsions: refined_atoms                   548     0.234     0.200
VDW repulsions.others                          1999     0.228     0.200
VDW; torsion: refined_atoms                    1098     0.175     0.200
VDW; torsion.others                            1053     0.083     0.200
HBOND: refined_atoms                             58     0.197     0.200
HBOND.others                                      1     0.043     0.200
VDW repulsions: symmetry: refined_atoms          11     0.219     0.200
VDW repulsions: symmetry: others                 32     0.244     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     7.972     6.870
M. chain bond B values: others                 1074     7.959     6.862
M. chain angle B values: refined atoms         1335    10.146    10.250
M. chain angle B values: others                1336    10.145    10.258
S. chain bond B values: refined atoms          1209     9.352     7.701
S. chain bond B values: others                 1207     9.351     7.694
S. chain angle B values: refined atoms         1719    12.952    11.198
S. chain angle B values: others                1719    12.945    11.199
Long range B values: refined atoms             2628    14.940    78.889
Long range B values: others                    2628    14.953    78.928
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4904, B  =   -1.2339
Partial structure    1: scale =     0.3831, B  =   55.7946
Overall anisotropic scale factors
   B11 =   4.91 B22 =  -1.58 B33 =  -3.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   271.2   268.5  0.20  0.20     153   258.4   253.3  0.29  0.29
 0.083    5552  99.88   134.4   123.3  0.20  0.19     305   133.9   124.0  0.28  0.26
 0.139    7124  99.77    44.8    45.9  0.28  0.24     364    46.4    49.3  0.36  0.33
 0.194    8355  99.91    24.3    21.4  0.39  0.38     424    24.2    21.5  0.41  0.40
 0.249    8476  89.91    19.3     9.5  0.56  0.56     428    19.9     9.9  0.55  0.55
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.821    698   0.753   3240   0.806  0.933  0.9117  0.9444  0.8534  0.9282
  0.0834   4838   0.802    714   0.708   5552   0.790  0.995  0.9029  0.9278  0.8569  0.9346
  0.1387   6411   0.656    713   0.609   7124   0.651  0.792  0.8092  0.8339  0.7194  0.8714
  0.1940   7643   0.409    712   0.357   8355   0.404  0.555  0.5169  0.5125  0.7059  0.7081
  0.2493   7833   0.298    643   0.292   8476   0.298  0.678  0.3229  0.3028  0.4164  0.4677
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2546
Free R factor                        =     0.3268
Average Fourier shell correlation    =     0.6413
AverageFree Fourier shell correlation=     0.6373
Overall weighted R factor            =     0.2203
Free weighted R factor               =     0.2950
Overall weighted R2 factor           =     0.2279
Free weighted R2 factor              =     0.3127
Average correlation coefficient      =     0.7416
Overall correlation coefficient      =     0.9617
Free correlation coefficient         =     0.9219
Cruickshanks DPI for coordinate error=     0.1546
DPI based on free R factor           =     0.1685
Overall figure of merit              =     0.5356
ML based su of positional parameters =     0.2720
ML based su of thermal parameters    =    11.3775
-----------------------------------------------------------------------------
 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    131791.55       18856.781       3013736.3      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   5.99999987E-02
 Actual weight    21.003998      is applied to the X-ray term


 function value    2776731.0    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4877, B  =   -0.3286
Partial structure    1: scale =     0.3850, B  =   55.5157
Overall anisotropic scale factors
   B11 =   4.86 B22 =  -1.56 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3255
Average Fourier shell correlation    =     0.6441
AverageFree Fourier shell correlation=     0.6409
Average correlation coefficient      =     0.7423
Overall figure of merit              =     0.5387
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    131600.33       12597.975       2776731.0       3013736.3    


     CGMAT cycle number =      3

 Weight matrix   5.99999949E-02
 Actual weight    21.027077      is applied to the X-ray term


 function value    2780721.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4857, B  =   -0.1803
Partial structure    1: scale =     0.3852, B  =   55.0582
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.55 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2548
Free R factor                        =     0.3265
Average Fourier shell correlation    =     0.6446
AverageFree Fourier shell correlation=     0.6410
Average correlation coefficient      =     0.7422
Overall figure of merit              =     0.5394
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02


 fvalues    131666.55       12665.878       2780800.0       2776731.0    
 fvalues    131666.55       12665.878       2780800.0       2781228.5    


     CGMAT cycle number =      4

 Weight matrix   6.00000024E-02
 Actual weight    21.131660      is applied to the X-ray term


 function value    2794320.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4864, B  =   -0.1463
Partial structure    1: scale =     0.3853, B  =   54.6644
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.56 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3263
Average Fourier shell correlation    =     0.6434
AverageFree Fourier shell correlation=     0.6399
Average correlation coefficient      =     0.7424
Overall figure of merit              =     0.5378
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02


 fvalues    131622.89       12622.247       2794519.8       2781228.5    

 fvalues    131622.89       12622.247       2794327.3       2794032.5    
 fvalues    131622.89       12622.247       2794327.3       2794032.5    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    21.216824      is applied to the X-ray term


 function value    2805422.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4865, B  =   -0.1309
Partial structure    1: scale =     0.3852, B  =   54.6320
Overall anisotropic scale factors
   B11 =   4.87 B22 =  -1.55 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3264
Average Fourier shell correlation    =     0.6430
AverageFree Fourier shell correlation=     0.6394
Average correlation coefficient      =     0.7424
Overall figure of merit              =     0.5372
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    131638.34       12635.826       2805478.8       2794032.5    
 fvalues    131638.34       12635.826       2805478.8       2805583.3    


     CGMAT cycle number =      6

 Weight matrix   5.99999987E-02
 Actual weight    21.073265      is applied to the X-ray term


 function value    2786466.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4865, B  =   -0.1494
Partial structure    1: scale =     0.3852, B  =   54.6111
Overall anisotropic scale factors
   B11 =   4.86 B22 =  -1.56 B33 =  -3.31 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3265
Average Fourier shell correlation    =     0.6440
AverageFree Fourier shell correlation=     0.6404
Average correlation coefficient      =     0.7423
Overall figure of merit              =     0.5384
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Not converging with gamma equal   8.71641375E-03
 Trying gamma equal   4.29446921E-02
 Gamma decreased to   3.60990353E-02
 fvalues    131626.77       12660.814       2786466.5       2805583.3    


     CGMAT cycle number =      7

 Weight matrix   5.99999987E-02
 Actual weight    21.103664      is applied to the X-ray term


 function value    2790800.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4858, B  =   -0.1652
Partial structure    1: scale =     0.3853, B  =   54.5763
Overall anisotropic scale factors
   B11 =   4.86 B22 =  -1.55 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3265
Average Fourier shell correlation    =     0.6439
AverageFree Fourier shell correlation=     0.6404
Average correlation coefficient      =     0.7422
Overall figure of merit              =     0.5382
-----------------------------------------------------------------------------
 Trying gamma equal   3.60990353E-02
 Gamma decreased to   2.98757106E-02


 fvalues    131645.78       12661.896       2790779.5       2786466.5    
 fvalues    131645.78       12661.896       2790779.5       2790870.5    


     CGMAT cycle number =      8

 Weight matrix   5.99999987E-02
 Actual weight    21.166828      is applied to the X-ray term


 function value    2799011.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4860, B  =   -0.1264
Partial structure    1: scale =     0.3853, B  =   54.5292
Overall anisotropic scale factors
   B11 =   4.86 B22 =  -1.55 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3263
Average Fourier shell correlation    =     0.6436
AverageFree Fourier shell correlation=     0.6400
Average correlation coefficient      =     0.7422
Overall figure of merit              =     0.5378
-----------------------------------------------------------------------------
 Trying gamma equal   2.98757106E-02
 Gamma decreased to   2.42181439E-02


 fvalues    131633.88       12668.839       2799010.0       2790870.5    

 fvalues    131633.88       12668.839       2798966.8       2798940.3    
 fvalues    131633.88       12668.839       2798966.8       2798940.3    


     CGMAT cycle number =      9

 Weight matrix   5.99999987E-02
 Actual weight    21.166506      is applied to the X-ray term


 function value    2798915.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4860, B  =   -0.1262
Partial structure    1: scale =     0.3853, B  =   54.5641
Overall anisotropic scale factors
   B11 =   4.86 B22 =  -1.55 B33 =  -3.30 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2547
Free R factor                        =     0.3262
Average Fourier shell correlation    =     0.6435
AverageFree Fourier shell correlation=     0.6400
Average correlation coefficient      =     0.7423
Overall figure of merit              =     0.5377
-----------------------------------------------------------------------------
 Trying gamma equal   2.42181439E-02
 Gamma decreased to   1.90749019E-02
 fvalues    131634.53       12672.478       2798915.5       2798940.3    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   5.99999987E-02
 Actual weight    21.160702      is applied to the X-ray term
Norm of X_ray positional gradient                34.7
Norm of Geom. positional gradient                34.6
Norm of X_ray B-factor gradient                  34.9
Norm of Geom. B-factor gradient                  35.9
Product of X_ray and Geom posit. gradients     -0.161E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.557E+07
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.2786E+07 GEOM=     0.1268E+05 TOTAL=     0.2798E+07
 function value    2798329.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     2.022     1.648
Bond angles  : others                          5121     1.412     1.582
Torsion angles, period  1. refined              265     7.784     5.000
Torsion angles, period  2. refined              135    33.109    22.370
Torsion angles, period  3. refined              475    21.130    15.000
Torsion angles, period  4. refined               19    20.122    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   553     0.238     0.200
VDW repulsions.others                          2047     0.205     0.200
VDW; torsion: refined_atoms                    1102     0.175     0.200
VDW; torsion.others                            1101     0.094     0.200
HBOND: refined_atoms                             60     0.201     0.200
HBOND.others                                      1     0.135     0.200
VDW repulsions: symmetry: refined_atoms           9     0.232     0.200
VDW repulsions: symmetry: others                 37     0.217     0.200
HBOND: symmetry: refined_atoms                    2     0.133     0.200
M. chain bond B values: refined atoms          1075     7.966     6.756
M. chain bond B values: others                 1074     7.958     6.747
M. chain angle B values: refined atoms         1335    10.118    10.078
M. chain angle B values: others                1336    10.117    10.086
S. chain bond B values: refined atoms          1209     9.349     7.578
S. chain bond B values: others                 1207     9.351     7.571
S. chain angle B values: refined atoms         1719    12.838    11.016
S. chain angle B values: others                1719    12.834    11.016
Long range B values: refined atoms             2639    14.831    77.938
Long range B values: others                    2638    14.839    77.961
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4857, B  =   -0.1365
Partial structure    1: scale =     0.3855, B  =   54.6450
Overall anisotropic scale factors
   B11 =   4.85 B22 =  -1.55 B33 =  -3.30 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   272.1   268.3  0.20  0.20     153   259.2   252.3  0.29  0.29
 0.083    5552  99.88   134.8   123.6  0.21  0.19     305   134.3   124.5  0.28  0.26
 0.139    7124  99.77    44.9    46.1  0.28  0.24     364    46.6    49.4  0.36  0.32
 0.194    8355  99.91    24.4    21.4  0.39  0.38     424    24.2    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.5  0.56  0.56     428    20.0     9.9  0.55  0.55
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.831    698   0.761   3240   0.816  0.936  0.9123  0.9462  0.8511  0.9291
  0.0834   4838   0.804    714   0.709   5552   0.791  0.995  0.9028  0.9270  0.8562  0.9322
  0.1387   6411   0.684    713   0.635   7124   0.679  0.806  0.8262  0.8502  0.7205  0.8723
  0.1940   7643   0.380    712   0.333   8355   0.376  0.527  0.5028  0.4957  0.7071  0.7107
  0.2493   7833   0.306    643   0.296   8476   0.306  0.693  0.3336  0.3147  0.4139  0.4680
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2547
Free R factor                        =     0.3264
Average Fourier shell correlation    =     0.6437
AverageFree Fourier shell correlation=     0.6402
Overall weighted R factor            =     0.2205
Free weighted R factor               =     0.2947
Overall weighted R2 factor           =     0.2282
Free weighted R2 factor              =     0.3136
Average correlation coefficient      =     0.7422
Overall correlation coefficient      =     0.9617
Free correlation coefficient         =     0.9210
Cruickshanks DPI for coordinate error=     0.1547
DPI based on free R factor           =     0.1683
Overall figure of merit              =     0.5378
ML based su of positional parameters =     0.2622
ML based su of thermal parameters    =    10.9920
-----------------------------------------------------------------------------
 Trying gamma equal   1.90749019E-02
 Gamma decreased to   1.43992268E-02
 fvalues    131642.63       12678.994       2798329.3       2798915.5    

 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: poli_R00_1-90A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     2.023     1.648
Bond angles  : others                          5121     1.412     1.582
Torsion angles, period  1. refined              265     7.788     5.000
Torsion angles, period  2. refined              135    33.097    22.370
Torsion angles, period  3. refined              475    21.155    15.000
Torsion angles, period  4. refined               19    20.070    15.000
Chiral centres: refined atoms                   284     0.088     0.200
Planar groups: refined atoms                   2462     0.011     0.020
Planar groups: others                           467     0.002     0.020
VDW repulsions: refined_atoms                   555     0.238     0.200
VDW repulsions.others                          2048     0.204     0.200
VDW; torsion: refined_atoms                    1102     0.176     0.200
VDW; torsion.others                            1101     0.094     0.200
HBOND: refined_atoms                             61     0.200     0.200
HBOND.others                                      1     0.147     0.200
VDW repulsions: symmetry: refined_atoms           9     0.232     0.200
VDW repulsions: symmetry: others                 37     0.217     0.200
HBOND: symmetry: refined_atoms                    2     0.133     0.200
M. chain bond B values: refined atoms          1075     7.968     6.755
M. chain bond B values: others                 1074     7.960     6.747
M. chain angle B values: refined atoms         1335    10.119    10.077
M. chain angle B values: others                1336    10.118    10.086
S. chain bond B values: refined atoms          1209     9.353     7.578
S. chain bond B values: others                 1207     9.355     7.571
S. chain angle B values: refined atoms         1719    12.840    11.015
S. chain angle B values: others                1719    12.836    11.016
Long range B values: refined atoms             2642    14.853    77.976
Long range B values: others                    2641    14.861    77.999
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4853, B  =   -0.1374
Partial structure    1: scale =     0.3854, B  =   54.7144
Overall anisotropic scale factors
   B11 =   4.85 B22 =  -1.55 B33 =  -3.30 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   272.1   268.3  0.20  0.20     153   259.3   252.3  0.29  0.29
 0.083    5552  99.88   134.9   123.7  0.21  0.19     305   134.3   124.4  0.28  0.26
 0.139    7124  99.77    44.9    46.1  0.28  0.24     364    46.6    49.4  0.36  0.32
 0.194    8355  99.91    24.4    21.4  0.39  0.38     424    24.3    21.6  0.41  0.40
 0.249    8476  89.91    19.4     9.5  0.56  0.56     428    20.0     9.9  0.55  0.55
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.831    698   0.761   3240   0.816  0.936  0.9124  0.9462  0.8514  0.9291
  0.0834   4838   0.804    714   0.709   5552   0.792  0.995  0.9028  0.9270  0.8563  0.9322
  0.1387   6411   0.684    713   0.635   7124   0.679  0.806  0.8261  0.8501  0.7201  0.8724
  0.1940   7643   0.382    712   0.335   8355   0.378  0.531  0.5042  0.4972  0.7070  0.7108
  0.2493   7833   0.307    643   0.297   8476   0.306  0.693  0.3338  0.3150  0.4141  0.4681
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2547
Free R factor                        =     0.3264
Average Fourier shell correlation    =     0.6441
AverageFree Fourier shell correlation=     0.6406
Overall weighted R factor            =     0.2205
Free weighted R factor               =     0.2948
Overall weighted R2 factor           =     0.2281
Free weighted R2 factor              =     0.3138
Average correlation coefficient      =     0.7423
Overall correlation coefficient      =     0.9617
Free correlation coefficient         =     0.9211
Cruickshanks DPI for coordinate error=     0.1546
DPI based on free R factor           =     0.1683
Overall figure of merit              =     0.5383
ML based su of positional parameters =     0.2622
ML based su of thermal parameters    =    10.9920
-----------------------------------------------------------------------------
  Time in seconds: CPU =        42.99
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2546   0.3268   0.536      131792.    6876.6   0.0131  0.908   1.987  1.178   0.088
       1   0.2547   0.3255   0.539      131600.    6876.1   0.0133  0.927   1.998  1.184   0.088
       2   0.2548   0.3265   0.539      131642.    6879.9   0.0133  0.924   2.012  1.192   0.088
       3   0.2547   0.3263   0.538      131637.    6879.6   0.0134  0.923   2.015  1.194   0.088
       4   0.2547   0.3264   0.537      131631.    6879.4   0.0134  0.924   2.016  1.194   0.088
       5   0.2547   0.3265   0.538      131627.    6879.3   0.0134  0.926   2.019  1.196   0.088
       6   0.2547   0.3265   0.538      131642.    6880.1   0.0134  0.926   2.020  1.196   0.088
       7   0.2547   0.3263   0.538      131637.    6879.6   0.0134  0.927   2.021  1.197   0.088
       8   0.2547   0.3262   0.538      131635.    6879.5   0.0134  0.927   2.021  1.197   0.088
       9   0.2547   0.3264   0.538      131643.    6880.1   0.0134  0.928   2.022  1.198   0.088
      10   0.2547   0.3264   0.538      131653.    6880.5   0.0134  0.928   2.023  1.198   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2546   0.2547
             R free    0.3268   0.3264
     Rms BondLength    0.0131   0.0134
      Rms BondAngle    1.9873   2.0232
     Rms ChirVolume    0.0880   0.0883
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      84.3s System:    0.3s Elapsed:     1:27  
</pre>
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