# Date 2008-01-16 Time 05:17:29 PST -0800 (1200489449.36 s)
#phil __OFF__

Command line arguments: "../669.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16380
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 669

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00033
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964215

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0003

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00033
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964215

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2798 [2138/2162]  1920   218  10.2%
  bin  2:  4.2798 -  3.4099 [2036/2056]  1838   198   9.7%
  bin  3:  3.4099 -  2.9827 [2020/2039]  1817   203  10.0%
  bin  4:  2.9827 -  2.7117 [1980/2010]  1776   204  10.3%
  bin  5:  2.7117 -  2.5183 [2002/2021]  1806   196   9.8%
  bin  6:  2.5183 -  2.3704 [1975/2000]  1776   199  10.1%
  bin  7:  2.3704 -  2.2521 [1962/1990]  1768   194   9.9%
  bin  8:  2.2521 -  2.1544 [1962/1998]  1766   196  10.0%
  bin  9:  2.1544 -  2.0717 [1947/1989]  1755   192   9.9%
  bin 10:  2.0717 -  2.0003 [1567/1988]  1408   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 10
        2.29 -     2.94: 1596
        2.94 -     3.59: 4414
        3.59 -     4.25: 9091
        4.25 -     4.90: 12900
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.636 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.824 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.830 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.889 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28006 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001.geo

CPU time processing inputs: 9.11


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3205   r_free= 0.3135   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.060011                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.2833 0.2744      6.3611      6.2562|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.2458 0.2578      6.4518       6.496|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.2852 0.2559      6.4013      6.3501|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.2961 0.3245      6.2724      6.2908|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.3297 0.2718      6.1345       6.035|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.3228 0.3760      6.0267      6.0287|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.3324 0.3249      6.0073      5.9958|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.3646 0.3171      6.0244      5.9593|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.3458 0.3303      5.9214      5.8756|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.3784 0.3534      5.9723      5.8984|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.3759 0.3685      5.8794      5.9343|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.3593 0.3566      5.8153      5.8796|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.3718 0.3539      5.7359      5.6997|
| 14:  2.0502 -  2.0003 0.71    903  106 0.3311 0.3691      5.6522      5.6213|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7732  1389   152  0.81  24.33   0.86     0.82      38364.29|
|  2:  4.7732 -  3.8088  1318   152  0.84  21.81   0.96     0.91      46358.58|
|  3:  3.8088 -  3.3333  1300   142  0.81  25.62   0.97     0.93      45057.76|
|  4:  3.3333 -  3.0312  1308   142  0.78  28.48   0.97     0.90      39237.67|
|  5:  3.0312 -  2.8154  1278   144  0.73  33.17   1.00     0.87      31159.19|
|  6:  2.8154 -  2.6504  1286   143  0.71  35.00   0.97     0.85      28955.24|
|  7:  2.6504 -  2.5183  1278   144  0.70  35.56   1.00     0.86      26821.08|
|  8:  2.5183 -  2.4091  1269   138  0.70  35.26   0.97     0.88      24612.74|
|  9:  2.4091 -  2.3167  1268   143  0.71  34.85   1.01     0.90      22569.48|
| 10:  2.3167 -  2.2371  1275   142  0.69  36.47   1.03     0.90      21123.44|
| 11:  2.2371 -  2.1673  1248   134  0.68  37.46   1.00     0.91      21684.46|
| 12:  2.1673 -  2.1055  1245   141  0.68  38.06   1.03     0.91      20480.36|
| 13:  2.1055 -  2.0502  1265   136  0.65  40.46   1.01     0.88      18682.58|
| 14:  2.0502 -  2.0003   903   106  0.66  39.78   1.05     0.82      15786.23|
|alpha:            min =        0.82 max =            0.93 mean =         0.88|
|beta:             min =    15786.23 max =        46358.58 mean =     29089.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.73|
|phase err.(work): min =        0.00 max =           89.97 mean =        33.05|
|phase err.(test): min =        0.00 max =           89.99 mean =        32.86|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.170787              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.344   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.618644              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.215   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.636 -  1.962:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.962 -  2.289:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.289 -  2.615:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.615 -  2.941:     1565 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.941 -  3.268:     1871 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.268 -  3.594:     2543 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.594 -  3.921:     4689 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.921 -  4.247:     4402 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.574:     5890 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     7010 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.636 |       0.211 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3205   r_free= 0.3135   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.060011                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2995   r_free= 0.2973   ksol= 0.32   Bsol= 56.31   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-3.07,4.76,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.026778                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.800347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.109   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.350755              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.907   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2995      final r-factor (work) = 0.2061          |
| start r-factor (free) = 0.2973      final r-factor (free) = 0.2303          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6063 = 2.80 * 0.50 * 6.0280 + 1.00 * 0.1661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1477 = 2.80 * 0.50 * 5.7695 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2061      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.2303      final r-factor (free) = 0.2315          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0312 = 0.35 * 1.00 * 5.7695 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1341 = 0.35 * 1.00 * 5.6004 + 1.00 * 0.1698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.09   16.25    None  None   None       |
|    all(noH): 2823   0      0.00    85.09   16.25    None  None   None       |
|    Sol.    : 438    0      5.06    62.86   37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    85.09   12.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.509:  581   |   5:    42.544 -  51.053:   98        |
|      1:     8.509 -  17.018: 1478   |   6:    51.053 -  59.561:   61        |
|      2:    17.018 -  25.526:  321   |   7:    59.561 -  68.070:    6        |
|      3:    25.526 -  34.035:  146   |   8:    68.070 -  76.579:    0        |
|      4:    34.035 -  42.544:  131   |   9:    76.579 -  85.088:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1938 r_free = 0.2315             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1933 r_free = 0.2314             target_work(ml) = 5.600         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1933   r_free= 0.2314   ksol= 0.32   Bsol= 56.31   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-3.07,4.76,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.600346                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1897   r_free= 0.2283   ksol= 0.33   Bsol= 65.87   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.68,0.73,-0.00,0.00,0.00); trace/3= -1.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.585732                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.800884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.225   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.190461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.437   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2283      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1111 = 1.80 * 0.50 * 5.5991 + 1.00 * 0.0694                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9587 = 1.80 * 0.50 * 5.4459 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1333          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5210 = 1.19 * 1.00 * 5.4459 + 1.00 * 0.0379                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2924 = 1.19 * 1.00 * 5.2764 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.34   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    84.34   17.49    None  None   None       |
|    Sol.    : 438    0      4.58    84.34   42.25    None  None   None       |
|    Mac.    : 2385   0      0.00    80.70   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.434:  709   |   5:    42.168 -  50.601:   82        |
|      1:     8.434 -  16.867: 1295   |   6:    50.601 -  59.035:   90        |
|      2:    16.867 -  25.301:  310   |   7:    59.035 -  67.468:   58        |
|      3:    25.301 -  33.734:  132   |   8:    67.468 -  75.902:   35        |
|      4:    33.734 -  42.168:  104   |   9:    75.902 -  84.335:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1333 r_free = 0.1768             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1332 r_free = 0.1766             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1332   r_free= 0.1766   ksol= 0.33   Bsol= 65.87   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.68,0.73,-0.00,0.00,0.00); trace/3= -1.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.277842                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1764   ksol= 0.34   Bsol= 71.34   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.24,0.07,-0.00,0.00,0.00); trace/3= -1.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.275671                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.219591              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.805  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.221926              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.353  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9095 = 2.22 * 0.50 * 5.2753 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8593 = 2.22 * 0.50 * 5.2254 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1706 = 0.22 * 1.00 * 5.2254 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1595 = 0.22 * 1.00 * 5.1856 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    82.94   16.71    None  None   None       |
|    all(noH): 2823   0      1.04    82.94   16.71    None  None   None       |
|    Sol.    : 438    0      1.89    82.94   39.34    None  None   None       |
|    Mac.    : 2385   0      1.04    80.04   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.042 -   9.231:  931   |   5:    41.989 -  50.178:   83        |
|      1:     9.231 -  17.420: 1150   |   6:    50.178 -  58.367:   79        |
|      2:    17.420 -  25.610:  263   |   7:    58.367 -  66.557:   40        |
|      3:    25.610 -  33.799:  127   |   8:    66.557 -  74.746:   20        |
|      4:    33.799 -  41.989:  126   |   9:    74.746 -  82.935:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1600             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1172 r_free = 0.1598             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1598   ksol= 0.34   Bsol= 71.34   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-2.24,0.07,-0.00,0.00,0.00); trace/3= -1.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.172028                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1597   ksol= 0.33   Bsol= 61.47   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.96,-0.06,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.171681                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.873036              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.145321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.949  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5092 = 2.87 * 0.50 * 5.1855 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4692 = 2.87 * 0.50 * 5.1483 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7568 = 0.15 * 1.00 * 5.1483 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7548 = 0.15 * 1.00 * 5.1411 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    81.48   16.36    None  None   None       |
|    all(noH): 2823   0      0.49    81.48   16.36    None  None   None       |
|    Sol.    : 438    0      0.49    81.48   38.14    None  None   None       |
|    Mac.    : 2385   0      1.64    78.74   12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.494 -   8.593:  765   |   5:    40.988 -  49.087:   87        |
|      1:     8.593 -  16.692: 1296   |   6:    49.087 -  57.186:   73        |
|      2:    16.692 -  24.791:  281   |   7:    57.186 -  65.285:   41        |
|      3:    24.791 -  32.889:  130   |   8:    65.285 -  73.384:   16        |
|      4:    32.889 -  40.988:  129   |   9:    73.384 -  81.483:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1563             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1562             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1562   ksol= 0.33   Bsol= 61.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.96,-0.06,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136392                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1562   ksol= 0.33   Bsol= 61.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.91,-0.14,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136353                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.888287              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.735  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.158080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.872  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9270 = 1.89 * 0.50 * 5.1405 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9181 = 1.89 * 0.50 * 5.1442 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.3976 = 4.16 * 1.00 * 5.1442 + 1.00 * 0.0077                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.3862 = 4.16 * 1.00 * 5.1408 + 1.00 * 0.0105                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.31   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    89.31   16.74    None  None   None       |
|    Sol.    : 438    0      0.00    87.87   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    89.31   12.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.931:  931   |   5:    44.657 -  53.588:   93        |
|      1:     8.931 -  17.863: 1186   |   6:    53.588 -  62.520:   73        |
|      2:    17.863 -  26.794:  244   |   7:    62.520 -  71.451:   34        |
|      3:    26.794 -  35.725:  126   |   8:    71.451 -  80.382:   19        |
|      4:    35.725 -  44.657:  112   |   9:    80.382 -  89.314:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1594             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1594             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1594   ksol= 0.33   Bsol= 61.47   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.91,-0.14,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149862                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.1024 0.1341      5.4226      5.5533|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.0862 0.1127      5.4498      5.6457|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.1049 0.1476      5.4771      5.8356|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.1211 0.1617      5.4462      5.5983|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.1320 0.1667      5.3248      5.5432|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.1217 0.2085      5.2218      5.5369|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.1278 0.1559      5.1805      5.3173|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.1155 0.1688       5.084      5.3433|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.1175 0.1858      5.0425       5.318|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.1120 0.1730      4.9586      5.2126|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.1142 0.1652      4.9438       5.201|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.1131 0.1842      4.8881       5.307|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.1072 0.1753      4.7987      5.0505|
| 14:  2.0502 -  2.0003 0.71    903  106 0.0954 0.1706      4.6499      4.9363|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7732  1389   152  0.94   9.66   0.97     0.94       7756.04|
|  2:  4.7732 -  3.8088  1318   152  0.95   8.06   1.00     0.99       9386.88|
|  3:  3.8088 -  3.3333  1300   142  0.94  10.97   1.02     1.01      10202.27|
|  4:  3.3333 -  3.0312  1308   142  0.92  13.29   1.00     0.99      10031.11|
|  5:  3.0312 -  2.8154  1278   144  0.90  15.43   0.99     0.96       8147.94|
|  6:  2.8154 -  2.6504  1286   143  0.90  16.33   0.98     0.95       7257.71|
|  7:  2.6504 -  2.5183  1278   144  0.90  15.78   0.98     0.95       6376.74|
|  8:  2.5183 -  2.4091  1269   138  0.91  15.23   0.98     0.96       5495.56|
|  9:  2.4091 -  2.3167  1268   143  0.91  15.35   0.99     0.95       5177.36|
| 10:  2.3167 -  2.2371  1275   142  0.90  15.81   0.98     0.94       4323.17|
| 11:  2.2371 -  2.1673  1248   134  0.90  15.86   0.98     0.94       4413.10|
| 12:  2.1673 -  2.1055  1245   141  0.90  15.91   0.99     0.97       4060.84|
| 13:  2.1055 -  2.0502  1265   136  0.90  16.12   0.98     0.95       3526.69|
| 14:  2.0502 -  2.0003   903   106  0.92  14.09   0.95     0.91       2545.85|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2545.85 max =        10202.27 mean =      6454.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.61|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1582   ksol= 0.32   Bsol= 61.47   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.70,0.02,-0.00,0.00,0.00); trace/3= -1.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.147053                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1582   ksol= 0.32   Bsol= 61.47   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.70,0.02,-0.00,0.00,0.00); trace/3= -1.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.147053                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.1027 0.1253      5.4023      5.5029|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.0863 0.1107      5.4389      5.6318|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.1053 0.1455       5.475       5.824|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.1207 0.1631      5.4439      5.6015|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.1320 0.1666      5.3236       5.539|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.1214 0.2085      5.2202      5.5367|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.1278 0.1559      5.1802      5.3167|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.1154 0.1690       5.084      5.3432|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.1174 0.1861      5.0428      5.3189|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.1120 0.1731       4.959      5.2126|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.1143 0.1653      4.9441      5.2015|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.1131 0.1840      4.8883       5.306|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.1071 0.1756      4.7989      5.0514|
| 14:  2.0502 -  2.0003 0.71    903  106 0.0954 0.1706      4.6507      4.9371|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0739 -  4.7732  1389   152  0.94   9.11   0.97     0.94       7042.98|
|  2:  4.7732 -  3.8088  1318   152  0.95   7.75   1.01     0.99       8827.60|
|  3:  3.8088 -  3.3333  1300   142  0.94  10.85   1.02     1.02       9985.03|
|  4:  3.3333 -  3.0312  1308   142  0.92  13.26   1.00     0.99       9979.29|
|  5:  3.0312 -  2.8154  1278   144  0.91  15.40   1.00     0.97       8127.78|
|  6:  2.8154 -  2.6504  1286   143  0.90  16.29   0.98     0.96       7224.73|
|  7:  2.6504 -  2.5183  1278   144  0.90  15.78   0.98     0.96       6369.99|
|  8:  2.5183 -  2.4091  1269   138  0.91  15.24   0.99     0.96       5499.02|
|  9:  2.4091 -  2.3167  1268   143  0.91  15.36   1.00     0.96       5184.14|
| 10:  2.3167 -  2.2371  1275   142  0.90  15.82   0.99     0.95       4326.76|
| 11:  2.2371 -  2.1673  1248   134  0.90  15.86   0.99     0.95       4415.28|
| 12:  2.1673 -  2.1055  1245   141  0.90  15.92   1.00     0.98       4064.68|
| 13:  2.1055 -  2.0502  1265   136  0.90  16.13   0.99     0.96       3530.35|
| 14:  2.0502 -  2.0003   903   106  0.92  14.12   0.96     0.93       2553.50|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2553.50 max =         9985.03 mean =      6334.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.00|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.32   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    89.32   16.74    None  None   None       |
|    Sol.    : 438    0      0.00    87.87   40.36    None  None   None       |
|    Mac.    : 2385   0      0.00    89.32   12.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.934:  931   |   5:    44.660 -  53.591:   93        |
|      1:     8.934 -  17.866: 1186   |   6:    53.591 -  62.522:   73        |
|      2:    17.866 -  26.797:  244   |   7:    62.522 -  71.454:   34        |
|      3:    26.797 -  35.728:  126   |   8:    71.454 -  80.385:   19        |
|      4:    35.728 -  44.660:  112   |   9:    80.385 -  89.317:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 4.730
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 287
   mapped sites are within: 0.702 - 4.730

peak=    5.502 closest distance to " NH2 ARG A  56 " =    2.211
peak=    5.331 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.102 closest distance to " CG  PRO A  54 " =    1.375
peak=    4.952 closest distance to " CB  PRO A  54 " =    0.990
peak=    4.869 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.825 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.812 closest distance to " NE2 GLN A  11 " =    1.068
peak=    4.784 closest distance to " O   HOH Z 126 " =    1.893
peak=    4.775 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.752 closest distance to " O   HOH Z 142 " =    1.755
peak=    4.703 closest distance to " CB  ARG A 190 " =    1.617
peak=    4.699 closest distance to " CB  ARG A  79 " =    1.398
peak=    4.648 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.550 closest distance to " CB  SER A  63 " =    1.145
peak=    4.543 closest distance to " CG  PRO A 213 " =    1.184
peak=    4.520 closest distance to " O   HOH Z 298 " =    1.978
peak=    4.509 closest distance to " CG  PRO A 198 " =    1.298
peak=    4.486 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.448 closest distance to " O   HOH Z  78 " =    1.675
peak=    4.437 closest distance to " CG2 VAL A 257 " =    0.846
peak=    4.284 closest distance to " O   HOH Z  15 " =    2.153
peak=    4.266 closest distance to " O   HOH Z  40 " =    1.821
peak=    4.257 closest distance to " O  BHOH Z  74 " =    1.165
peak=    4.257 closest distance to " CE  LYS A  76 " =    0.858
peak=    4.251 closest distance to " O   HOH Z 369 " =    2.386
peak=    4.246 closest distance to " O   HOH Z 189 " =    2.918
peak=    4.177 closest distance to " CB  ASN A 148 " =    1.456
peak=    4.162 closest distance to " CB  VAL A 265 " =    1.225
peak=    4.142 closest distance to " ND2 ASN A 187 " =    1.414
peak=    4.138 closest distance to " CB  LEU A 228 " =    1.101
peak=    4.124 closest distance to " O   HOH Z 368 " =    2.132
peak=    4.120 closest distance to " O   HOH Z 303 " =    2.095
peak=    4.117 closest distance to " O   HOH Z 427 " =    3.017
peak=    4.079 closest distance to " CB  GLU A 277 " =    3.694
peak=    4.064 closest distance to " C   PRO A 198 " =    1.468
peak=    4.052 closest distance to " NH1AARG A 145 " =    1.328
peak=    4.042 closest distance to " O   HOH Z  53 " =    2.482
peak=    4.031 closest distance to " CD2 TRP A 179 " =    1.337
peak=    4.025 closest distance to " CG  PRO A 243 " =    1.040
peak=    4.022 closest distance to " CA  ARG A 195 " =    1.201
peak=    4.001 closest distance to " CB  GLU A 152 " =    1.257
peak=    3.987 closest distance to " CZ3 TRP A 266 " =    1.159
peak=    3.971 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.970 closest distance to " O   SER A  87 " =    2.294
peak=    3.967 closest distance to " O   HOH Z 287 " =    1.961
peak=    3.964 closest distance to " CB  TYR A 169 " =    0.739
peak=    3.957 closest distance to " O   HOH Z 316 " =    3.173
peak=    3.953 closest distance to " O   HOH Z  63 " =    2.052
peak=    3.944 closest distance to " CB  ASN A 142 " =    1.011
peak=    3.943 closest distance to " O   HOH Z 346 " =    1.741
peak=    3.939 closest distance to " OE1 GLN A  55 " =    1.536
peak=    3.934 closest distance to " O   HOH Z 313 " =    2.029
peak=    3.924 closest distance to " O   HOH Z  61 " =    1.664
peak=    3.923 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.920 closest distance to " CA  ASN A 215 " =    1.087
peak=    3.908 closest distance to " O   HOH Z 158 " =    3.142
peak=    3.891 closest distance to " CD  LYS A 166 " =    1.257
peak=    3.890 closest distance to " O   HOH Z 406 " =    1.651
peak=    3.888 closest distance to " CA  ARG A  36 " =    1.066
peak=    3.886 closest distance to " ND2 ASN A 249 " =    0.880
peak=    3.883 closest distance to " O   HOH Z  43 " =    1.946
peak=    3.872 closest distance to " O   HOH Z 250 " =    1.462
peak=    3.864 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.863 closest distance to " O   HOH Z 234 " =    3.788
peak=    3.863 closest distance to " CB  VAL A 202 " =    1.552
peak=    3.858 closest distance to " O   HOH Z 272 " =    1.841
peak=    3.851 closest distance to " O   HOH Z 214 " =    2.135
peak=    3.846 closest distance to " O  BHOH Z 338 " =    2.372
peak=    3.821 closest distance to " CB  ASP A 124 " =    0.719
peak=    3.815 closest distance to " CA  ALA A  51 " =    0.953
peak=    3.810 closest distance to " O   ASN A  74 " =    1.351
peak=    3.808 closest distance to " CB  GLU A  46 " =    0.967
peak=    3.807 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.804 closest distance to " OD1 ASN A  69 " =    2.609
peak=    3.796 closest distance to " O   HOH Z 203 " =    1.719
peak=    3.785 closest distance to " CA  VAL A 125 " =    1.135
peak=    3.779 closest distance to " OG BSER A 164 " =    2.324
peak=    3.778 closest distance to " CD  ARG A 269 " =    0.937
peak=    3.763 closest distance to " O   THR A 220 " =    1.217
peak=    3.752 closest distance to " CB  TRP A 266 " =    1.028
peak=    3.752 closest distance to " O   HOH Z 180 " =    2.184
peak=    3.744 closest distance to " CB  ASP A 140 " =    1.107
peak=    3.744 closest distance to " CE1 PHE A  38 " =    1.224
peak=    3.729 closest distance to " O   HOH Z 265 " =    2.286
peak=    3.718 closest distance to " CD1 LEU A 300 " =    1.188
peak=    3.712 closest distance to " CB  GLU A 128 " =    0.966
peak=    3.711 closest distance to " CA  SER A  87 " =    1.036
peak=    3.708 closest distance to " CB  SER A 212 " =    1.201
peak=    3.702 closest distance to " O   HOH Z 353 " =    2.629
peak=    3.685 closest distance to " O   HOH Z 423 " =    1.885
peak=    3.685 closest distance to " CG  LEU A 167 " =    1.267
peak=    3.682 closest distance to " O   HOH Z 133 " =    2.652
peak=    3.681 closest distance to " CB  THR A  31 " =    1.556
peak=    3.681 closest distance to " CB  PRO A  90 " =    1.123
peak=    3.677 closest distance to " O   HOH Z 365 " =    2.880
peak=    3.662 closest distance to " O   HOH Z 148 " =    3.467
peak=    3.652 closest distance to " O   HOH Z 368 " =    3.540
peak=    3.641 closest distance to " O   HOH Z 419 " =    2.138
peak=    3.637 closest distance to " O   HOH Z 209 " =    2.285
peak=    3.624 closest distance to " O   HOH Z 402 " =    1.373
peak=    3.620 closest distance to " CG2AVAL A  72 " =    1.760
peak=    3.614 closest distance to " O   HOH Z 392 " =    2.932
peak=    3.612 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.602 closest distance to " O   HOH Z 294 " =    1.552
peak=    3.594 closest distance to " N   ARG A 156 " =    1.369
peak=    3.588 closest distance to " CB  ASN A 110 " =    1.140
peak=    3.585 closest distance to " CA  THR A 264 " =    0.917
peak=    3.581 closest distance to " O   HOH Z 193 " =    1.804
peak=    3.580 closest distance to " CG  GLN A  11 " =    1.771
peak=    3.580 closest distance to " CB  SER A   3 " =    1.300
peak=    3.577 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.572 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.571 closest distance to " CG  MET A 185 " =    1.165
peak=    3.562 closest distance to " CB  LEU A  83 " =    0.767
peak=    3.558 closest distance to " CG2 ILE A 120 " =    1.201
peak=    3.555 closest distance to " O   HOH Z 285 " =    2.335
peak=    3.550 closest distance to " O   HOH Z 261 " =    1.839
peak=    3.541 closest distance to " O   HOH Z 411 " =    3.902
peak=    3.539 closest distance to " O   HOH Z 193 " =    1.895
peak=    3.535 closest distance to " O   HOH Z 291 " =    1.560
peak=    3.526 closest distance to " O   HOH Z   1 " =    2.161
peak=    3.521 closest distance to " O   HOH Z 394 " =    3.996
peak=    3.519 closest distance to " O   HOH Z 248 " =    1.603
peak=    3.510 closest distance to " O   HOH Z 172 " =    3.406
peak=    3.504 closest distance to " O   ALA A 165 " =    1.556
peak=    3.499 closest distance to " CB  SER A 210 " =    0.822
peak=    3.494 closest distance to " CA  MET A 105 " =    1.041
peak=    3.490 closest distance to " CB  ASN A 187 " =    1.063
peak=    3.490 closest distance to " O   HOH Z 389 " =    1.868
peak=    3.488 closest distance to " O   HOH Z  59 " =    2.053
peak=    3.481 closest distance to " O   HOH Z  66 " =    2.217
peak=    3.477 closest distance to " CA  ILE A 234 " =    0.992
peak=    3.473 closest distance to " O   HOH Z 213 " =    2.041
peak=    3.470 closest distance to " CG  GLU A  37 " =    0.899
peak=    3.464 closest distance to " CD  ARG A  66 " =    2.338
peak=    3.463 closest distance to " N   ASN A  39 " =    1.283
peak=    3.452 closest distance to " NE2 HIS A 207 " =    1.183
peak=    3.447 closest distance to " CG2 ILE A 234 " =    0.834
peak=    3.446 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.438 closest distance to " CA  ALA A 160 " =    0.940
peak=    3.434 closest distance to " CA  ALA A 154 " =    1.042
peak=    3.433 closest distance to " CA  ASN A 217 " =    1.214
peak=    3.422 closest distance to " CE1 TYR A 186 " =    1.362
peak=    3.422 closest distance to " N   TYR A 116 " =    1.536
peak=    3.422 closest distance to " NE2 GLN A  73 " =    4.001
peak=    3.422 closest distance to " O   HOH Z 325 " =    2.453
peak=    3.410 closest distance to " O   HOH Z 128 " =    2.104
peak=    3.410 closest distance to " CD2 LEU A 297 " =    0.903
peak=    3.409 closest distance to " O   HOH Z 337 " =    3.611
peak=    3.401 closest distance to " O   THR A 182 " =    1.398
peak=    3.398 closest distance to " CB  ALA A 291 " =    1.235
peak=    3.397 closest distance to " O   HOH Z 128 " =    2.214
peak=    3.397 closest distance to " O   HOH Z 290 " =    0.948
peak=    3.390 closest distance to " CD BLYS A 290 " =    0.932
peak=    3.389 closest distance to " CB  ILE A 120 " =    1.273
peak=    3.388 closest distance to " CA  TYR A 116 " =    1.385
peak=    3.378 closest distance to " O   HOH Z 359 " =    1.524
peak=    3.378 closest distance to " CG AARG A 275 " =    1.130
peak=    3.375 closest distance to " CD1 ILE A 199 " =    0.863
peak=    3.375 closest distance to " O   HOH Z 132 " =    2.651
peak=    3.363 closest distance to " C   ILE A 106 " =    1.950
peak=    3.362 closest distance to " O   HOH Z 421 " =    1.977
peak=    3.359 closest distance to " CB  ALA A 242 " =    0.887
peak=    3.357 closest distance to " O   HOH Z 185 " =    1.809
peak=    3.355 closest distance to " O   ASN A  74 " =    2.091
peak=    3.355 closest distance to " O   HOH Z 371 " =    3.009
peak=    3.345 closest distance to " CB  MET A  47 " =    0.973
peak=    3.345 closest distance to " CB  PHE A 204 " =    0.765
peak=    3.344 closest distance to " CA  THR A 221 " =    1.033
peak=    3.338 closest distance to " CB  SER A 273 " =    0.880
peak=    3.333 closest distance to " O   HOH Z 261 " =    1.755
peak=    3.328 closest distance to " O   HOH Z   9 " =    2.021
peak=    3.326 closest distance to " O   HOH Z 417 " =    3.385
peak=    3.324 closest distance to " CB  TYR A 116 " =    0.763
peak=    3.323 closest distance to " O   HOH Z  88 " =    3.222
peak=    3.323 closest distance to " O   HOH Z 305 " =    3.646
peak=    3.321 closest distance to " O   HOH Z  62 " =    2.042
peak=    3.321 closest distance to " CB  THR A  82 " =    1.460
peak=    3.320 closest distance to " O   HOH Z 126 " =    1.636
peak=    3.319 closest distance to " CB  GLN A  89 " =    1.336
peak=    3.317 closest distance to " CZ2 TRP A 179 " =    1.781
peak=    3.315 closest distance to " CA  ASN A 127 " =    1.131
peak=    3.310 closest distance to " CB  ARG A 139 " =    1.032
peak=    3.308 closest distance to " CA  ALA A 129 " =    1.264
peak=    3.303 closest distance to " CA  ARG A 139 " =    1.007
peak=    3.297 closest distance to " O   HOH Z 106 " =    4.193
peak=    3.290 closest distance to " CB  ASN A 215 " =    1.112
peak=    3.289 closest distance to " CB  TRP A 179 " =    1.417
peak=    3.288 closest distance to " O   HOH Z 258 " =    1.655
peak=    3.284 closest distance to " O   HOH Z  80 " =    2.163
peak=    3.281 closest distance to " O   HOH Z 147 " =    1.850
peak=    3.281 closest distance to " CG2 ILE A 239 " =    0.742
peak=    3.280 closest distance to " CG2AVAL A 121 " =    2.388
peak=    3.277 closest distance to " O   HOH Z 218 " =    4.730
peak=    3.277 closest distance to " CB  GLN A  88 " =    1.215
peak=    3.275 closest distance to " CB  GLN A 103 " =    0.797
peak=    3.274 closest distance to " CB  ALA A 104 " =    0.702
peak=    3.274 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.273 closest distance to " O   HOH Z 407 " =    2.558
peak=    3.273 closest distance to " O   TYR A 116 " =    1.365
peak=    3.273 closest distance to " O   HOH Z 193 " =    2.041
peak=    3.273 closest distance to " OE2 GLU A  53 " =    1.591
peak=    3.273 closest distance to " CB  ALA A 248 " =    1.221
peak=    3.272 closest distance to " O   HOH Z 251 " =    1.592
peak=    3.270 closest distance to " O   HOH Z  88 " =    1.849
peak=    3.269 closest distance to " OE1 GLN A  11 " =    2.143
peak=    3.265 closest distance to " O   HOH Z  97 " =    2.467
peak=    3.263 closest distance to " CA  ASP A 124 " =    0.708
peak=    3.262 closest distance to " OD2 ASP A 286 " =    3.239
peak=    3.259 closest distance to " CD1AILE A 234 " =    1.019
peak=    3.256 closest distance to " CA  ARG A 159 " =    1.258
peak=    3.256 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.251 closest distance to " O   HOH Z 383 " =    2.010
peak=    3.243 closest distance to " O   HOH Z 116 " =    3.152
peak=    3.241 closest distance to " O   HOH Z 234 " =    1.912
peak=    3.237 closest distance to " CB  ALA A 114 " =    1.044
peak=    3.237 closest distance to " O   HOH Z 163 " =    1.832
peak=    3.236 closest distance to " CB  MET A  40 " =    0.798
peak=    3.234 closest distance to " O   HOH Z  44 " =    1.632
peak=    3.233 closest distance to " O   HOH Z 380 " =    1.769
peak=    3.232 closest distance to " CE  LYS A  48 " =    1.083
peak=    3.229 closest distance to " O   HOH Z 422 " =    2.706
peak=    3.225 closest distance to " O   SER A 164 " =    1.420
peak=    3.224 closest distance to " O   HOH Z 426 " =    1.906
peak=    3.222 closest distance to " CA  ALA A 291 " =    0.747
peak=    3.219 closest distance to " CG2 THR A 221 " =    1.131
peak=    3.218 closest distance to " CB  ASP A 298 " =    1.168
peak=    3.217 closest distance to " N   PHE A 130 " =    1.226
peak=    3.217 closest distance to " NZ  LYS A  48 " =    1.206
peak=    3.214 closest distance to " CB  ALA A  43 " =    0.762
peak=    3.211 closest distance to " O   HOH Z 384 " =    3.027
peak=    3.209 closest distance to " CA  GLN A  94 " =    0.748
peak=    3.208 closest distance to " CA  ALA A 158 " =    1.304
peak=    3.207 closest distance to " O   HOH Z   1 " =    1.582
peak=    3.201 closest distance to " CA  LEU A  83 " =    1.207
peak=    3.196 closest distance to " CB  SER A  62 " =    1.105
peak=    3.196 closest distance to " CB  ARG A 138 " =    0.942
peak=    3.195 closest distance to " N   ASN A 127 " =    1.305
peak=    3.194 closest distance to " O   HOH Z  88 " =    2.563
peak=    3.191 closest distance to " CG2 ILE A  20 " =    1.200
peak=    3.188 closest distance to " O   HOH Z 152 " =    2.284
peak=    3.188 closest distance to " CB  PRO A 243 " =    1.375
peak=    3.187 closest distance to " O   HOH Z 183 " =    1.253
peak=    3.185 closest distance to " O   HOH Z  80 " =    1.609
peak=    3.184 closest distance to " OH  TYR A 116 " =    1.091
peak=    3.184 closest distance to " O   THR A 251 " =    1.123
peak=    3.184 closest distance to " O   HOH Z 171 " =    4.045
peak=    3.181 closest distance to " OG BSER A 134 " =    2.902
peak=    3.180 closest distance to " ND1 HIS A  86 " =    1.721
peak=    3.177 closest distance to " O   HOH Z  44 " =    3.012
peak=    3.176 closest distance to " CB  GLN A 205 " =    1.068
peak=    3.169 closest distance to " N   GLY A  98 " =    1.083
peak=    3.168 closest distance to " CB  SER A 141 " =    1.023
peak=    3.168 closest distance to " O   HOH Z 299 " =    4.483
peak=    3.165 closest distance to " NE  ARG A  79 " =    0.989
peak=    3.165 closest distance to " OG  SER A  22 " =    2.708
peak=    3.164 closest distance to " O   HOH Z 391 " =    2.959
peak=    3.161 closest distance to " O   HOH Z 271 " =    2.631
peak=    3.160 closest distance to " CA  ASP A 162 " =    1.004
peak=    3.160 closest distance to " OG BSER A  99 " =    2.317
peak=    3.156 closest distance to " CG2 VAL A 197 " =    1.105
peak=    3.152 closest distance to " O   HOH Z 425 " =    1.318
peak=    3.144 closest distance to " O   PHE A  61 " =    1.389
peak=    3.138 closest distance to " CB  LEU A 300 " =    0.893
peak=    3.137 closest distance to " O   ALA A 158 " =    1.295
peak=    3.137 closest distance to " CB  SER A 216 " =    0.902
peak=    3.134 closest distance to " CG2 THR A 220 " =    0.926
peak=    3.127 closest distance to " CA  ARG A 102 " =    1.112
peak=    3.122 closest distance to " O   HOH Z  97 " =    2.006
peak=    3.114 closest distance to " N   ASP A 162 " =    1.175
peak=    3.104 closest distance to " O   HOH Z 132 " =    3.358
peak=    3.099 closest distance to " CA  GLY A 211 " =    1.329
peak=    3.090 closest distance to " CG2 VAL A 268 " =    0.925
peak=    3.068 closest distance to " CA  ASP A 191 " =    1.266
peak=    3.058 closest distance to " O   HOH Z 417 " =    2.055
peak=    3.049 closest distance to " CA  GLU A  46 " =    1.064
peak=    3.030 closest distance to " CE1 PHE A 218 " =    1.214

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.781 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 188
   mapped sites are within: 0.781 - 5.719

peak=   -4.835 closest distance to " CD  ARG A  14 " =    3.493
peak=   -4.717 closest distance to " CD  GLN A  58 " =    0.964
peak=   -4.518 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.447 closest distance to " O   HOH Z 231 " =    2.234
peak=   -4.366 closest distance to " CG1 VAL A 112 " =    2.656
peak=   -4.364 closest distance to " C   HIS A 108 " =    1.066
peak=   -4.358 closest distance to " O   HOH Z 377 " =    2.115
peak=   -4.341 closest distance to " OG BSER A 134 " =    1.322
peak=   -4.299 closest distance to " O   VAL A  67 " =    2.716
peak=   -4.264 closest distance to " O   PRO A 198 " =    1.300
peak=   -4.176 closest distance to " CB  PRO A 243 " =    2.685
peak=   -4.136 closest distance to " O   HOH Z 198 " =    1.849
peak=   -4.109 closest distance to " CZ3 TRP A 179 " =    1.210
peak=   -4.061 closest distance to " CD2 PHE A 192 " =    2.030
peak=   -4.059 closest distance to " O   HOH Z 266 " =    5.549
peak=   -4.023 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.975 closest distance to " OG  SER A  97 " =    2.265
peak=   -3.969 closest distance to " CE  MET A 105 " =    2.524
peak=   -3.916 closest distance to " CG  GLN A 223 " =    2.074
peak=   -3.894 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.892 closest distance to " CG2 ILE A  49 " =    2.798
peak=   -3.872 closest distance to " O   HOH Z 196 " =    2.046
peak=   -3.861 closest distance to " CA  VAL A  67 " =    2.964
peak=   -3.856 closest distance to " O   HOH Z 372 " =    2.333
peak=   -3.843 closest distance to " CG1 VAL A 112 " =    2.889
peak=   -3.841 closest distance to " CE BMET A  47 " =    1.462
peak=   -3.826 closest distance to " CG  GLN A  11 " =    1.727
peak=   -3.817 closest distance to " OXT GLY A 302 " =    2.965
peak=   -3.805 closest distance to " O   HOH Z 185 " =    2.301
peak=   -3.774 closest distance to " OD2 ASP A 191 " =    1.475
peak=   -3.768 closest distance to " N   ALA A 248 " =    1.629
peak=   -3.767 closest distance to " CE2 PHE A  61 " =    2.669
peak=   -3.765 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.752 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.735 closest distance to " CB  ALA A 161 " =    2.600
peak=   -3.730 closest distance to " CB  ASN A  39 " =    2.321
peak=   -3.724 closest distance to " O   HOH Z 211 " =    1.393
peak=   -3.722 closest distance to " N   ALA A  43 " =    2.498
peak=   -3.721 closest distance to " O   HOH Z  10 " =    1.484
peak=   -3.719 closest distance to " CD1 LEU A 101 " =    2.423
peak=   -3.714 closest distance to " CA  GLY A 241 " =    2.343
peak=   -3.711 closest distance to " NE2 GLN A  88 " =    1.946
peak=   -3.707 closest distance to " O   HOH Z  73 " =    2.342
peak=   -3.704 closest distance to " OD1 ASN A 148 " =    1.444
peak=   -3.682 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.664 closest distance to " CA  GLY A 241 " =    3.344
peak=   -3.658 closest distance to " O   PRO A 163 " =    2.018
peak=   -3.655 closest distance to " CA  GLY A 203 " =    2.436
peak=   -3.641 closest distance to " O   SER A 210 " =    2.009
peak=   -3.625 closest distance to " CG  ARG A 269 " =    2.526
peak=   -3.619 closest distance to " O   ALA A  10 " =    1.680
peak=   -3.609 closest distance to " CG1 VAL A 250 " =    2.647
peak=   -3.602 closest distance to " CB  ALA A  43 " =    2.629
peak=   -3.595 closest distance to " O   HOH Z  51 " =    1.687
peak=   -3.593 closest distance to " O   HOH Z 407 " =    3.131
peak=   -3.590 closest distance to " CG1 VAL A 125 " =    1.851
peak=   -3.586 closest distance to " CE3 TRP A 150 " =    2.244
peak=   -3.583 closest distance to " O   HOH Z  37 " =    1.730
peak=   -3.582 closest distance to " C   LEU A 143 " =    1.033
peak=   -3.579 closest distance to " O   HOH Z 114 " =    3.086
peak=   -3.566 closest distance to " CD1 PHE A  59 " =    1.957
peak=   -3.563 closest distance to " O   HOH Z 290 " =    1.281
peak=   -3.545 closest distance to " CB  ALA A 291 " =    2.277
peak=   -3.544 closest distance to " CB  ASP A 132 " =    2.314
peak=   -3.543 closest distance to " NE2 GLN A 194 " =    1.855
peak=   -3.536 closest distance to " O   PHE A 218 " =    1.493
peak=   -3.535 closest distance to " ND2 ASN A  45 " =    1.855
peak=   -3.535 closest distance to " O   HOH Z 389 " =    2.052
peak=   -3.531 closest distance to " NH2 ARG A  79 " =    1.500
peak=   -3.528 closest distance to " CG  GLU A 277 " =    1.213
peak=   -3.526 closest distance to " O   HOH Z 102 " =    1.605
peak=   -3.525 closest distance to " O   HOH Z 313 " =    1.889
peak=   -3.516 closest distance to " O   HOH Z 106 " =    1.848
peak=   -3.516 closest distance to " OD1 ASP A 171 " =    1.650
peak=   -3.514 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.501 closest distance to " CG2 ILE A 263 " =    2.348
peak=   -3.497 closest distance to " O   GLY A  17 " =    1.158
peak=   -3.496 closest distance to " ND2 ASN A 249 " =    2.414
peak=   -3.496 closest distance to " ND2 ASN A  45 " =    1.116
peak=   -3.495 closest distance to " CD1 LEU A 255 " =    2.912
peak=   -3.493 closest distance to " CG  HIS A  86 " =    1.097
peak=   -3.492 closest distance to " CB  ALA A   7 " =    2.351
peak=   -3.491 closest distance to " O   HOH Z 298 " =    1.288
peak=   -3.483 closest distance to " NH2AARG A 275 " =    5.362
peak=   -3.463 closest distance to " O   HOH Z 166 " =    1.952
peak=   -3.441 closest distance to " O   VAL A 189 " =    2.621
peak=   -3.429 closest distance to " O   HOH Z 348 " =    2.154
peak=   -3.427 closest distance to " CB  ALA A 129 " =    2.404
peak=   -3.426 closest distance to " CB  ALA A 100 " =    2.140
peak=   -3.418 closest distance to " CG2 THR A 178 " =    2.355
peak=   -3.418 closest distance to " O   VAL A 189 " =    1.581
peak=   -3.416 closest distance to " N   THR A  52 " =    1.698
peak=   -3.407 closest distance to " O   ARG A 145 " =    1.613
peak=   -3.396 closest distance to " O   SER A  95 " =    1.723
peak=   -3.385 closest distance to " C   MET A 188 " =    1.343
peak=   -3.381 closest distance to " CG  ARG A  66 " =    2.324
peak=   -3.380 closest distance to " O   HOH Z 134 " =    3.191
peak=   -3.378 closest distance to " O   HOH Z 243 " =    1.945
peak=   -3.360 closest distance to " CA  ILE A 263 " =    1.033
peak=   -3.359 closest distance to " CA  GLY A 133 " =    2.289
peak=   -3.350 closest distance to " CB  ALA A 248 " =    2.349
peak=   -3.340 closest distance to " O   HOH Z 191 " =    5.719
peak=   -3.337 closest distance to " O   ILE A 106 " =    1.955
peak=   -3.337 closest distance to " NE2 GLN A 278 " =    1.675
peak=   -3.337 closest distance to " O   HOH Z  60 " =    1.952
peak=   -3.333 closest distance to " O   HOH Z 174 " =    2.656
peak=   -3.329 closest distance to " C   SER A 206 " =    1.501
peak=   -3.325 closest distance to " C   THR A 264 " =    1.407
peak=   -3.323 closest distance to " CG2 VAL A 189 " =    2.133
peak=   -3.322 closest distance to " CB  TRP A  85 " =    2.467
peak=   -3.319 closest distance to " ND2 ASN A  60 " =    1.384
peak=   -3.319 closest distance to " O   SER A 135 " =    1.455
peak=   -3.316 closest distance to " CZ  PHE A 155 " =    1.295
peak=   -3.315 closest distance to " O   HOH Z 421 " =    3.185
peak=   -3.311 closest distance to " O   HOH Z  11 " =    1.627
peak=   -3.304 closest distance to " CD1 ILE A 239 " =    2.302
peak=   -3.291 closest distance to " O   HOH Z 359 " =    3.075
peak=   -3.290 closest distance to " O   HOH Z   6 " =    1.417
peak=   -3.289 closest distance to " O   GLY A  80 " =    2.453
peak=   -3.286 closest distance to " O   HOH Z 326 " =    5.159
peak=   -3.282 closest distance to " O   HOH Z 311 " =    3.761
peak=   -3.278 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.278 closest distance to " CG1 VAL A  67 " =    3.116
peak=   -3.277 closest distance to " O   TRP A  70 " =    1.446
peak=   -3.274 closest distance to " O   HOH Z 351 " =    1.606
peak=   -3.274 closest distance to " O   HOH Z 429 " =    2.181
peak=   -3.267 closest distance to " N   THR A 157 " =    1.537
peak=   -3.263 closest distance to " CB  ASP A 286 " =    2.078
peak=   -3.257 closest distance to " CD  ARG A  79 " =    1.188
peak=   -3.254 closest distance to " O   TYR A 247 " =    2.834
peak=   -3.249 closest distance to " CA  SER A 135 " =    1.292
peak=   -3.248 closest distance to " O   ALA A  34 " =    2.448
peak=   -3.248 closest distance to " O   HOH Z 393 " =    1.375
peak=   -3.248 closest distance to " CG  LEU A  83 " =    1.990
peak=   -3.241 closest distance to " O   HOH Z  52 " =    1.514
peak=   -3.239 closest distance to " CD  GLU A 236 " =    1.116
peak=   -3.234 closest distance to " O   HOH Z 275 " =    1.503
peak=   -3.233 closest distance to " O   GLY A 211 " =    1.322
peak=   -3.233 closest distance to " CD  GLN A 223 " =    1.467
peak=   -3.233 closest distance to " O   HOH Z 216 " =    1.411
peak=   -3.228 closest distance to " OE1 GLN A  88 " =    1.043
peak=   -3.226 closest distance to " O   HOH Z 111 " =    1.789
peak=   -3.224 closest distance to " OD1 ASN A 187 " =    1.611
peak=   -3.223 closest distance to " O   HOH Z 174 " =    3.872
peak=   -3.220 closest distance to " O   GLN A 240 " =    2.175
peak=   -3.219 closest distance to " CD  ARG A 139 " =    1.645
peak=   -3.214 closest distance to " O   HOH Z 322 " =    1.669
peak=   -3.213 closest distance to " CG1BVAL A  41 " =    2.772
peak=   -3.210 closest distance to " CG  PHE A 283 " =    2.627
peak=   -3.209 closest distance to " O   HOH Z  38 " =    1.558
peak=   -3.202 closest distance to " CD1 TRP A  70 " =    1.128
peak=   -3.199 closest distance to " O   ALA A 180 " =    1.391
peak=   -3.191 closest distance to " CA  GLY A 241 " =    2.869
peak=   -3.190 closest distance to " CG  TRP A 266 " =    1.879
peak=   -3.190 closest distance to " ND2 ASN A 187 " =    1.554
peak=   -3.188 closest distance to " O   ARG A  24 " =    1.768
peak=   -3.188 closest distance to " O   HOH Z 295 " =    1.665
peak=   -3.188 closest distance to " O   HOH Z 357 " =    2.125
peak=   -3.184 closest distance to " O   HOH Z 126 " =    1.869
peak=   -3.184 closest distance to " CG  ASP A 231 " =    0.781
peak=   -3.182 closest distance to " O   GLU A 152 " =    1.376
peak=   -3.177 closest distance to " OG BSER A 134 " =    1.826
peak=   -3.177 closest distance to " O   HOH Z 265 " =    2.341
peak=   -3.171 closest distance to " CD2 HIS A 207 " =    2.317
peak=   -3.165 closest distance to " O   HOH Z 323 " =    1.498
peak=   -3.164 closest distance to " O   ALA A 227 " =    1.659
peak=   -3.161 closest distance to " O   HOH Z  13 " =    1.793
peak=   -3.154 closest distance to " O   ASN A 187 " =    1.708
peak=   -3.151 closest distance to " O   HOH Z  64 " =    1.445
peak=   -3.151 closest distance to " N   ASN A  60 " =    1.337
peak=   -3.147 closest distance to " O   ALA A 292 " =    2.225
peak=   -3.145 closest distance to " C   GLY A 262 " =    2.004
peak=   -3.144 closest distance to " NH2BARG A 275 " =    1.937
peak=   -3.142 closest distance to " CA  GLY A 133 " =    2.068
peak=   -3.137 closest distance to " O   HOH Z 298 " =    2.549
peak=   -3.135 closest distance to " OE2 GLU A 152 " =    1.242
peak=   -3.124 closest distance to " O   HOH Z 353 " =    2.143
peak=   -3.114 closest distance to " O   HOH Z 281 " =    2.719
peak=   -3.104 closest distance to " O   HOH Z  89 " =    2.993
peak=   -3.103 closest distance to " CG1AVAL A  41 " =    2.741
peak=   -3.099 closest distance to " O   HOH Z 128 " =    2.675
peak=   -3.090 closest distance to " CB  TYR A  15 " =    2.233
peak=   -3.080 closest distance to " OD2 ASP A 171 " =    1.810
peak=   -3.078 closest distance to " OH  TYR A 247 " =    1.848
peak=   -3.072 closest distance to " O   HOH Z 283 " =    5.577
peak=   -3.060 closest distance to " OD2 ASP A 171 " =    2.475
peak=   -3.051 closest distance to " OD1AASN A 224 " =    1.804
peak=   -3.024 closest distance to " CZ  TYR A 169 " =    1.758

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3205 0.3135   6.060011e+00   6.035369e+00
   1_bss:  0.2995 0.2973   6.026778e+00   6.001446e+00
   1_xyz:  0.2061 0.2303   5.645239e+00   5.726178e+00
   1_adp:  0.1938 0.2315   5.601449e+00   5.732982e+00
   1_occ:  0.1933 0.2314   5.600346e+00   5.733845e+00
   2_bss:  0.1897 0.2283   5.585732e+00   5.720853e+00
   2_xyz:  0.1429 0.1757   5.319417e+00   5.483814e+00
   2_adp:  0.1333 0.1768   5.278441e+00   5.486487e+00
   2_occ:  0.1332 0.1766   5.277842e+00   5.485958e+00
   3_bss:  0.1327 0.1764   5.275671e+00   5.483339e+00
   3_xyz:  0.1184 0.1646   5.188583e+00   5.420215e+00
   3_adp:  0.1174 0.1600   5.172688e+00   5.397449e+00
   3_occ:  0.1172 0.1598   5.172028e+00   5.397149e+00
   4_bss:  0.1170 0.1597   5.171681e+00   5.397380e+00
   4_xyz:  0.1112 0.1573   5.139160e+00   5.383214e+00
   4_adp:  0.1115 0.1563   5.137007e+00   5.376237e+00
   4_occ:  0.1113 0.1562   5.136392e+00   5.376242e+00
   5_bss:  0.1113 0.1562   5.136353e+00   5.376260e+00
   5_xyz:  0.1132 0.1572   5.149159e+00   5.385588e+00
   5_adp:  0.1120 0.1594   5.149861e+00   5.397956e+00
   5_occ:  0.1119 0.1594   5.149862e+00   5.398118e+00
   5_bss:  0.1118 0.1582   5.147053e+00   5.392278e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.318  56.311  -3.261  -3.072   4.762  -0.000   0.000   0.000
   1_xyz:  0.318  56.311  -3.261  -3.072   4.762  -0.000   0.000   0.000
   1_adp:  0.318  56.311  -3.261  -3.072   4.762  -0.000   0.000   0.000
   1_occ:  0.318  56.311  -3.261  -3.072   4.762  -0.000   0.000   0.000
   2_bss:  0.333  65.868  -3.102  -2.681   0.726  -0.000   0.000   0.000
   2_xyz:  0.333  65.868  -3.102  -2.681   0.726  -0.000   0.000   0.000
   2_adp:  0.333  65.868  -3.102  -2.681   0.726  -0.000   0.000   0.000
   2_occ:  0.333  65.868  -3.102  -2.681   0.726  -0.000   0.000   0.000
   3_bss:  0.335  71.342  -2.638  -2.237   0.074  -0.000   0.000   0.000
   3_xyz:  0.335  71.342  -2.638  -2.237   0.074  -0.000   0.000   0.000
   3_adp:  0.335  71.342  -2.638  -2.237   0.074  -0.000   0.000   0.000
   3_occ:  0.335  71.342  -2.638  -2.237   0.074  -0.000   0.000   0.000
   4_bss:  0.329  61.467  -2.316  -1.963  -0.064  -0.000  -0.000  -0.000
   4_xyz:  0.329  61.467  -2.316  -1.963  -0.064  -0.000  -0.000  -0.000
   4_adp:  0.329  61.467  -2.316  -1.963  -0.064  -0.000  -0.000  -0.000
   4_occ:  0.329  61.467  -2.316  -1.963  -0.064  -0.000  -0.000  -0.000
   5_bss:  0.329  61.467  -2.232  -1.906  -0.139  -0.000  -0.000  -0.000
   5_xyz:  0.329  61.467  -2.232  -1.906  -0.139  -0.000  -0.000  -0.000
   5_adp:  0.329  61.467  -2.232  -1.906  -0.139  -0.000  -0.000  -0.000
   5_occ:  0.329  61.467  -2.232  -1.906  -0.139  -0.000  -0.000  -0.000
   5_bss:  0.324  61.470  -2.026  -1.702   0.023  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.028 0.7275  0.8822    29088.941
   1_bss:  31.604 0.7419  0.8837    25816.189
   1_xyz:  22.027 0.8432  0.9772    13406.680
   1_adp:  22.274 0.8403  0.9699    13604.646
   1_occ:  22.303 0.8400  0.9693    13606.386
   2_bss:  21.642 0.8470  0.9402    13188.925
   2_xyz:  16.076 0.8979  0.9671     7831.516
   2_adp:  16.077 0.8978  0.9594     7796.551
   2_occ:  16.062 0.8980  0.9594     7786.550
   3_bss:  15.981 0.8987  0.9630     7749.914
   3_xyz:  14.652 0.9097  0.9692     6770.621
   3_adp:  14.125 0.9142  0.9642     6474.543
   3_occ:  14.119 0.9142  0.9640     6469.361
   4_bss:  14.119 0.9142  0.9694     6470.085
   4_xyz:  13.802 0.9168  0.9725     6303.081
   4_adp:  13.635 0.9182  0.9689     6228.104
   4_occ:  13.634 0.9182  0.9689     6222.575
   5_bss:  13.633 0.9182  0.9697     6223.606
   5_xyz:  13.773 0.9173  0.9685     6333.488
   5_adp:  14.033 0.9152  0.9599     6453.620
   5_occ:  14.034 0.9152  0.9598     6454.299
   5_bss:  13.954 0.9158  0.9665     6334.124
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6606e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6606e-01
   1_xyz:   1.103  0.008  0.072 15.234  0.004  4.112   6.9409e-02
   1_adp:   1.103  0.008  0.072 15.234  0.004  4.112   6.9409e-02
   1_occ:   1.103  0.008  0.072 15.234  0.004  4.112   6.9409e-02
   2_bss:   1.103  0.008  0.072 15.234  0.004  4.112   6.9409e-02
   2_xyz:   0.970  0.007  0.073 14.952  0.003  4.125   5.5009e-02
   2_adp:   0.970  0.007  0.073 14.952  0.003  4.125   5.5009e-02
   2_occ:   0.970  0.007  0.073 14.952  0.003  4.125   5.5009e-02
   3_bss:   0.970  0.007  0.073 14.952  0.003  4.125   5.5009e-02
   3_xyz:   1.005  0.008  0.076 14.913  0.004  4.131   6.0184e-02
   3_adp:   1.005  0.008  0.076 14.913  0.004  4.131   6.0184e-02
   3_occ:   1.005  0.008  0.076 14.913  0.004  4.131   6.0184e-02
   4_bss:   1.005  0.008  0.076 14.913  0.004  4.131   6.0184e-02
   4_xyz:   1.088  0.010  0.084 14.994  0.004  4.116   7.3570e-02
   4_adp:   1.088  0.010  0.084 14.994  0.004  4.116   7.3570e-02
   4_occ:   1.088  0.010  0.084 14.994  0.004  4.116   7.3570e-02
   5_bss:   1.088  0.010  0.084 14.994  0.004  4.116   7.3570e-02
   5_xyz:   0.995  0.008  0.077 14.766  0.004  4.116   6.1232e-02
   5_adp:   0.995  0.008  0.077 14.766  0.004  4.116   6.1232e-02
   5_occ:   0.995  0.008  0.077 14.766  0.004  4.116   6.1232e-02
   5_bss:   0.995  0.008  0.077 14.766  0.004  4.116   6.1232e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.636   2.4300e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.636   2.4300e-01
   1_xyz:   8.099  0.049  0.290 82.929  0.031  2.208   7.2660e-02
   1_adp:   8.099  0.049  0.290 82.929  0.031  2.208   7.2660e-02
   1_occ:   8.099  0.049  0.290 82.929  0.031  2.208   7.2660e-02
   2_bss:   8.099  0.049  0.290 82.929  0.031  2.208   7.2660e-02
   2_xyz:   6.450  0.034  0.234 83.813  0.035  2.395   4.7003e-02
   2_adp:   6.450  0.034  0.234 83.813  0.035  2.395   4.7003e-02
   2_occ:   6.450  0.034  0.234 83.813  0.035  2.395   4.7003e-02
   3_bss:   6.450  0.034  0.234 83.813  0.035  2.395   4.7003e-02
   3_xyz:   6.964  0.043  0.256 82.750  0.037  2.384   4.1589e-02
   3_adp:   6.964  0.043  0.256 82.750  0.037  2.384   4.1589e-02
   3_occ:   6.964  0.043  0.256 82.750  0.037  2.384   4.1589e-02
   4_bss:   6.964  0.043  0.256 82.750  0.037  2.384   4.1589e-02
   4_xyz:   7.181  0.055  0.287 82.527  0.036  2.282   5.8206e-02
   4_adp:   7.181  0.055  0.287 82.527  0.036  2.282   5.8206e-02
   4_occ:   7.181  0.055  0.287 82.527  0.036  2.282   5.8206e-02
   5_bss:   7.181  0.055  0.287 82.527  0.036  2.282   5.8206e-02
   5_xyz:   6.642  0.050  0.248 82.616  0.034  2.371   4.0004e-02
   5_adp:   6.642  0.050  0.248 82.616  0.034  2.371   4.0004e-02
   5_occ:   6.642  0.050  0.248 82.616  0.034  2.371   4.0004e-02
   5_bss:   6.642  0.050  0.248 82.616  0.034  2.371   4.0004e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  85.09   0.00  16.25  85.09   0.00  12.42  62.86   5.06  37.12
   1_occ:  85.09   0.00  16.25  85.09   0.00  12.42  62.86   5.06  37.12
   2_bss:  85.09   0.00  16.25  85.09   0.00  12.42  62.86   5.06  37.12
   2_xyz:  85.09   0.00  16.25  85.09   0.00  12.42  62.86   5.06  37.12
   2_adp:  84.34   0.00  17.49  80.70   0.00  12.95  84.34   4.58  42.25
   2_occ:  84.34   0.00  17.49  80.70   0.00  12.95  84.34   4.58  42.25
   3_bss:  84.34   0.00  17.49  80.70   0.00  12.95  84.34   4.58  42.25
   3_xyz:  84.34   0.00  17.49  80.70   0.00  12.95  84.34   4.58  42.25
   3_adp:  82.94   1.04  16.71  80.04   1.04  12.55  82.94   1.89  39.34
   3_occ:  82.94   1.04  16.71  80.04   1.04  12.55  82.94   1.89  39.34
   4_bss:  82.94   1.04  16.71  80.04   1.04  12.55  82.94   1.89  39.34
   4_xyz:  82.94   1.04  16.71  80.04   1.04  12.55  82.94   1.89  39.34
   4_adp:  81.48   0.49  16.36  78.74   1.64  12.36  81.48   0.49  38.14
   4_occ:  81.48   0.49  16.36  78.74   1.64  12.36  81.48   0.49  38.14
   5_bss:  81.48   0.49  16.36  78.74   1.64  12.36  81.48   0.49  38.14
   5_xyz:  81.48   0.49  16.36  78.74   1.64  12.36  81.48   0.49  38.14
   5_adp:  89.31   0.00  16.74  89.31   0.00  12.40  87.87   0.00  40.35
   5_occ:  89.31   0.00  16.74  89.31   0.00  12.40  87.87   0.00  40.35
   5_bss:  89.32   0.00  16.74  89.32   0.00  12.40  87.87   0.00  40.36
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.309    0.011    0.260
   1_adp:    1.309    0.011    0.260
   1_occ:    1.309    0.011    0.260
   2_bss:    1.309    0.011    0.260
   2_xyz:    1.060    0.006    0.330
   2_adp:    1.060    0.006    0.330
   2_occ:    1.060    0.006    0.330
   3_bss:    1.060    0.006    0.330
   3_xyz:    1.033    0.010    0.373
   3_adp:    1.033    0.010    0.373
   3_occ:    1.033    0.010    0.373
   4_bss:    1.033    0.010    0.373
   4_xyz:    1.203    0.016    0.388
   4_adp:    1.203    0.016    0.388
   4_occ:    1.203    0.016    0.388
   5_bss:    1.203    0.016    0.388
   5_xyz:    1.420    0.008    0.394
   5_adp:    1.420    0.008    0.394
   5_occ:    1.420    0.008    0.394
   5_bss:    1.420    0.008    0.394
------------------------------------------------------------------------

CPU time actual refinement: 322.29


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_669/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 322.14 
  Macro-tasks:
    bulk solvent and scale       = 37.35  
    individual site refinement   = 134.83 
    weights calculation          = 29.24  
    collect and process          = 6.61   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 208.15 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 101.01 
    alpha_beta                      = 8.40   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 110.93 
    fmodel                         = 6.52   
    r_factors                      = 0.16   
    phase_errors                   = 11.23  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 241.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.551 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    644 calls, 100.65 s
gradients_fft:          589 calls,  97.26 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 05:23:04 PST -0800 (1200489784.07 s)
Start R-work = 0.3205, R-free = 0.3135 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.2995, R-free = 0.2973
Final R-work = 0.1118, R-free = 0.1582