# Date 2008-01-16 Time 05:16:50 PST -0800 (1200489410.29 s)
#phil __OFF__

Command line arguments: "../665.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17807
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 665

-------------------------------------------------------------------------------
  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, 86.39, 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: 2.76, per 1000 atoms: 0.98


================================== 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, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0000

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, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2786 [2087/2110]  1878   209  10.0%
  bin  2:  4.2786 -  3.4092 [2015/2035]  1813   202  10.0%
  bin  3:  3.4092 -  2.9821 [1978/1997]  1781   197  10.0%
  bin  4:  2.9821 -  2.7112 [1933/1963]  1740   193  10.0%
  bin  5:  2.7112 -  2.5179 [1963/1982]  1766   197  10.0%
  bin  6:  2.5179 -  2.3700 [1940/1965]  1747   193   9.9%
  bin  7:  2.3700 -  2.2517 [1926/1954]  1733   193  10.0%
  bin  8:  2.2517 -  2.1540 [1926/1962]  1734   192  10.0%
  bin  9:  2.1540 -  2.0713 [1921/1963]  1728   193  10.0%
  bin 10:  2.0713 -  2.0000 [1900/1948]  1710   190  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/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: 0.12 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:
        1.81 -     2.42: 8
        2.42 -     3.04: 2210
        3.04 -     3.66: 4624
        3.66 -     4.28: 9065
        4.28 -     4.90: 12352
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.343 3.040 -x+1/2,-y+1,z+1/2
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28254 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_665/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/model_refine_001.geo

CPU time processing inputs: 8.04


============================ 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 86.39 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1569   r_free= 0.1569   ksol= 0.00   Bsol= 0.00   scale= 1.021    |
|                                                                             |
| 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:   0.10 A                  |
| x-ray target function (ml) for work reflections: 5.264030                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.2345 0.2296      6.2034      6.1507|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.1271 0.1195      5.8116      5.7822|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.1262 0.1262      5.5911      5.6789|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.1256 0.1390      5.4267       5.474|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.1441 0.1268      5.3381      5.2668|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.1354 0.1422      5.2179      5.2281|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.1460 0.1440      5.2157      5.2176|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.1376 0.1318      5.1391      5.1258|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.1393 0.1437      5.0692      5.0546|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.1396 0.1457      5.0392      5.0381|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.1330 0.1292      4.9341      4.9618|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.1342 0.1301      4.9033      4.9528|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.1379 0.1371       4.851      4.8172|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.1399 0.1294      4.8138      4.6663|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.83  22.24   0.88     0.83      31511.81|
|  2:  4.7717 -  3.8079  1299   144  0.92  12.94   1.01     0.96      17674.48|
|  3:  3.8079 -  3.3326  1272   141  0.94  10.22   1.03     1.03       9332.89|
|  4:  3.3326 -  3.0306  1277   142  0.94  10.01   1.04     1.04       6780.53|
|  5:  3.0306 -  2.8149  1255   140  0.94  11.47   1.05     1.03       5248.62|
|  6:  2.8149 -  2.6499  1266   140  0.94  11.45   1.06     1.04       4390.91|
|  7:  2.6499 -  2.5179  1246   139  0.94  11.39   1.07     1.06       3844.95|
|  8:  2.5179 -  2.4087  1249   138  0.94  11.11   1.09     1.08       3500.83|
|  9:  2.4087 -  2.3163  1233   137  0.94  11.06   1.11     1.09       3095.76|
| 10:  2.3163 -  2.2367  1237   138  0.94  11.27   1.13     1.10       2800.96|
| 11:  2.2367 -  2.1669  1250   139  0.94  10.93   1.13     1.12       2505.36|
| 12:  2.1669 -  2.1052  1224   136  0.95  10.00   1.14     1.15       2228.02|
| 13:  2.1052 -  2.0499  1229   136  0.95   9.84   1.14     1.15       1832.90|
| 14:  2.0499 -  2.0000  1230   137  0.95   9.06   1.14     1.12       1375.66|
|alpha:            min =        0.83 max =            1.15 mean =         1.06|
|beta:             min =     1375.66 max =        31511.81 mean =      7080.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.93|
|phase err.(work): min =        0.00 max =           89.57 mean =        11.72|
|phase err.(test): min =        0.00 max =           89.96 mean =        11.86|
|-----------------------------------------------------------------------------|

============================== 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 = 1.866433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.231724              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.641   (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 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      183 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2027 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1818 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2806 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4679 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4386 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5623 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6729 |
|-----------------------------------------------------------------------------|
|-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 |        0.159 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.130 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1569   r_free= 0.1569   ksol= 0.00   Bsol= 0.00   scale= 1.021    |
|                                                                             |
| 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:   0.10 A                  |
| x-ray target function (ml) for work reflections: 5.264030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1309   ksol= 0.33   Bsol= 50.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.76,-1.68,-0.00,-0.00,-0.00); trace/3= -2.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.11 A                  |
| x-ray target function (ml) for work reflections: 5.199598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.758948              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.734   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.123505              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.568   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1309      final r-factor (free) = 0.1464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9900 = 1.76 * 0.50 * 5.4926 + 1.00 * 0.1593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5770 = 1.76 * 0.50 * 5.1183 + 1.00 * 0.0756                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1464      final r-factor (free) = 0.1465          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6381 = 0.12 * 1.00 * 5.1183 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6456 = 0.12 * 1.00 * 5.0986 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.66   16.27    None  None   None       |
|    all(noH): 2823   0      0.00    62.66   16.27    None  None   None       |
|    Sol.    : 438    0      4.19    62.66   36.52    None  None   None       |
|    Mac.    : 2385   0      0.00    51.77   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:     0.000 -   6.266:  124   |   5:    31.331 -  37.598:   91        |
|      1:     6.266 -  12.533: 1395   |   6:    37.598 -  43.864:  104        |
|      2:    12.533 -  18.799:  649   |   7:    43.864 -  50.130:   73        |
|      3:    18.799 -  25.065:  198   |   8:    50.130 -  56.396:   53        |
|      4:    25.065 -  31.331:  117   |   9:    56.396 -  62.662:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1465             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1462             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1462   ksol= 0.33   Bsol= 50.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.76,-1.68,-0.00,-0.00,-0.00); trace/3= -2.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101091                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1463   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.57,-1.48,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.780905              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.119893              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1463      final r-factor (free) = 0.1463          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6154 = 1.78 * 0.50 * 5.0983 + 1.00 * 0.0756                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6032 = 1.78 * 0.50 * 5.0987 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1463      final r-factor (free) = 0.1472          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7941 = 0.12 * 1.00 * 5.0987 + 1.00 * 0.1828                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6166 = 0.12 * 1.00 * 5.0910 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.27    63.83   16.28    None  None   None       |
|    all(noH): 2823   0      2.27    63.83   16.28    None  None   None       |
|    Sol.    : 438    0      5.75    63.83   35.88    None  None   None       |
|    Mac.    : 2385   0      2.27    60.01   12.68    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:     2.270 -   8.426:  564   |   5:    33.050 -  39.206:  121        |
|      1:     8.426 -  14.582: 1267   |   6:    39.206 -  45.362:   85        |
|      2:    14.582 -  20.738:  404   |   7:    45.362 -  51.518:   84        |
|      3:    20.738 -  26.894:  153   |   8:    51.518 -  57.673:   39        |
|      4:    26.894 -  33.050:  100   |   9:    57.673 -  63.829:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1472             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1473             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1473   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.57,-1.48,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.095738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1473   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.39,-1.31,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.102655              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.876  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.707779              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.857  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1473      final r-factor (free) = 0.1505          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4165 = 2.10 * 0.50 * 5.0921 + 1.00 * 0.0631                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4160 = 2.10 * 0.50 * 5.0890 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1057          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6971 = 1.71 * 1.00 * 5.0890 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6979 = 1.71 * 1.00 * 5.0880 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.64    76.32   16.81    None  None   None       |
|    all(noH): 2823   0      0.64    76.32   16.81    None  None   None       |
|    Sol.    : 438    0      6.53    69.33   38.68    None  None   None       |
|    Mac.    : 2385   0      0.64    76.32   12.79    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:     0.639 -   8.208:  595   |   5:    38.481 -  46.049:  115        |
|      1:     8.208 -  15.776: 1336   |   6:    46.049 -  53.617:   81        |
|      2:    15.776 -  23.344:  365   |   7:    53.617 -  61.186:   68        |
|      3:    23.344 -  30.913:  134   |   8:    61.186 -  68.754:   27        |
|      4:    30.913 -  38.481:   96   |   9:    68.754 -  76.322:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1057 r_free = 0.1524             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1056 r_free = 0.1525             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1525   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.39,-1.31,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1524   ksol= 0.32   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.12,-1.06,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.037667              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.126  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.101572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.784  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2509 = 2.04 * 0.50 * 5.0897 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2550 = 2.04 * 0.50 * 5.0985 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5266 = 0.10 * 1.00 * 5.0985 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5256 = 0.10 * 1.00 * 5.1131 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    72.14   15.96    None  None   None       |
|    all(noH): 2823   0      1.94    72.14   15.96    None  None   None       |
|    Sol.    : 438    0      6.24    65.99   35.16    None  None   None       |
|    Mac.    : 2385   0      1.94    72.14   12.44    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:     1.943 -   8.963:  774   |   5:    37.042 -  44.062:  107        |
|      1:     8.963 -  15.983: 1211   |   6:    44.062 -  51.082:   80        |
|      2:    15.983 -  23.003:  334   |   7:    51.082 -  58.102:   39        |
|      3:    23.003 -  30.022:  125   |   8:    58.102 -  65.122:   11        |
|      4:    30.022 -  37.042:  138   |   9:    65.122 -  72.141:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1522             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1522             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1522   ksol= 0.32   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.12,-1.06,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1523   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.04,-0.96,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.417347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.293  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.879714              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.042  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6843 = 1.42 * 0.50 * 5.1135 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6794 = 1.42 * 0.50 * 5.1155 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5064 = 0.88 * 1.00 * 5.1155 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5030 = 0.88 * 1.00 * 5.1090 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.41    80.46   16.44    None  None   None       |
|    all(noH): 2823   0      0.41    80.46   16.44    None  None   None       |
|    Sol.    : 438    0      6.15    68.68   38.09    None  None   None       |
|    Mac.    : 2385   0      0.41    80.46   12.47    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:     0.411 -   8.416:  713   |   5:    40.434 -  48.439:  109        |
|      1:     8.416 -  16.420: 1295   |   6:    48.439 -  56.444:   85        |
|      2:    16.420 -  24.425:  322   |   7:    56.444 -  64.448:   41        |
|      3:    24.425 -  32.430:  135   |   8:    64.448 -  72.453:   14        |
|      4:    32.430 -  40.434:  106   |   9:    72.453 -  80.458:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1541             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1541             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1541   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.04,-0.96,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114072                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.1002 0.1306      5.3991      5.5264|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.0860 0.1144      5.4465      5.6528|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.1041 0.1433      5.4731      5.8141|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.1171 0.1541       5.435      5.6004|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.1273 0.1723      5.3057      5.5338|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.1154 0.1679      5.1864      5.4007|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.1208 0.1670      5.1246      5.3738|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.1108 0.1680      5.0413      5.3172|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.1107 0.1597      4.9912      5.1983|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.1064 0.1804       4.939      5.2831|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.1094 0.1531       4.906       5.167|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.1073 0.1733      4.8541      5.2403|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.1036 0.1661      4.7757      5.0402|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.0996 0.1731      4.6435      4.9455|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.94   9.39   0.98     0.95       7422.88|
|  2:  4.7717 -  3.8079  1299   144  0.95   8.06   1.01     0.99       9206.32|
|  3:  3.8079 -  3.3326  1272   141  0.94  10.85   1.02     1.01      10177.51|
|  4:  3.3326 -  3.0306  1277   142  0.92  12.99   1.00     0.99       9857.54|
|  5:  3.0306 -  2.8149  1255   140  0.91  15.01   0.99     0.96       7897.48|
|  6:  2.8149 -  2.6499  1266   140  0.91  15.18   0.98     0.96       6722.41|
|  7:  2.6499 -  2.5179  1246   139  0.91  14.77   0.98     0.96       5639.71|
|  8:  2.5179 -  2.4087  1249   138  0.92  13.83   0.99     0.97       4926.29|
|  9:  2.4087 -  2.3163  1233   137  0.92  14.56   1.00     0.97       4637.56|
| 10:  2.3163 -  2.2367  1237   138  0.91  14.54   0.99     0.95       4062.33|
| 11:  2.2367 -  2.1669  1250   139  0.91  15.29   0.99     0.96       4076.38|
| 12:  2.1669 -  2.1052  1224   136  0.92  14.46   0.99     0.97       3701.10|
| 13:  2.1052 -  2.0499  1229   136  0.91  14.93   1.00     0.99       3303.97|
| 14:  2.0499 -  2.0000  1230   137  0.92  14.20   0.97     0.93       2461.09|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2461.09 max =        10177.51 mean =      6050.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.87 mean =        13.38|
|phase err.(test): min =        0.00 max =           88.71 mean =        12.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1540   ksol= 0.32   Bsol= 49.99   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.84,-0.78,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.113846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1540   ksol= 0.32   Bsol= 49.99   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.84,-0.78,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.113846                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7717 0.99   1363  152 0.1001 0.1305      5.3967      5.5239|
|  2:  4.7717 -  3.8079 0.99   1299  144 0.0861 0.1145       5.447      5.6533|
|  3:  3.8079 -  3.3326 0.99   1272  141 0.1042 0.1433      5.4733      5.8141|
|  4:  3.3326 -  3.0306 0.99   1277  142 0.1171 0.1541      5.4347      5.6002|
|  5:  3.0306 -  2.8149 0.99   1255  140 0.1272 0.1722      5.3053      5.5333|
|  6:  2.8149 -  2.6499 0.99   1266  140 0.1154 0.1680      5.1861      5.4006|
|  7:  2.6499 -  2.5179 0.99   1246  139 0.1208 0.1670      5.1245      5.3738|
|  8:  2.5179 -  2.4087 0.98   1249  138 0.1108 0.1679      5.0413       5.317|
|  9:  2.4087 -  2.3163 0.98   1233  137 0.1107 0.1597      4.9911      5.1983|
| 10:  2.3163 -  2.2367 1.00   1237  138 0.1064 0.1804      4.9389      5.2831|
| 11:  2.2367 -  2.1669 0.97   1250  139 0.1094 0.1530      4.9059      5.1668|
| 12:  2.1669 -  2.1052 0.97   1224  136 0.1073 0.1732       4.854      5.2402|
| 13:  2.1052 -  2.0499 0.99   1229  136 0.1036 0.1660      4.7756      5.0401|
| 14:  2.0499 -  2.0000 0.97   1230  137 0.0996 0.1731      4.6435      4.9456|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7717  1363   152  0.94   9.36   0.98     0.95       7371.93|
|  2:  4.7717 -  3.8079  1299   144  0.95   8.05   1.01     1.00       9187.73|
|  3:  3.8079 -  3.3326  1272   141  0.94  10.85   1.02     1.01      10179.68|
|  4:  3.3326 -  3.0306  1277   142  0.92  12.98   1.01     0.99       9849.62|
|  5:  3.0306 -  2.8149  1255   140  0.91  15.01   1.00     0.97       7892.26|
|  6:  2.8149 -  2.6499  1266   140  0.91  15.17   0.99     0.96       6717.90|
|  7:  2.6499 -  2.5179  1246   139  0.91  14.77   0.99     0.96       5638.14|
|  8:  2.5179 -  2.4087  1249   138  0.92  13.83   0.99     0.97       4925.25|
|  9:  2.4087 -  2.3163  1233   137  0.92  14.56   1.01     0.98       4637.63|
| 10:  2.3163 -  2.2367  1237   138  0.91  14.53   1.00     0.95       4061.29|
| 11:  2.2367 -  2.1669  1250   139  0.91  15.28   1.00     0.97       4074.79|
| 12:  2.1669 -  2.1052  1224   136  0.92  14.46   1.00     0.98       3699.43|
| 13:  2.1052 -  2.0499  1229   136  0.91  14.93   1.01     1.00       3303.22|
| 14:  2.0499 -  2.0000  1230   137  0.92  14.20   0.98     0.94       2461.66|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2461.66 max =        10179.68 mean =      6043.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.38|
|phase err.(test): min =        0.00 max =           88.74 mean =        12.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.40    80.45   16.43    None  None   None       |
|    all(noH): 2823   0      0.40    80.45   16.43    None  None   None       |
|    Sol.    : 438    0      6.14    68.66   38.07    None  None   None       |
|    Mac.    : 2385   0      0.40    80.45   12.45    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:     0.399 -   8.403:  713   |   5:    40.422 -  48.427:  109        |
|      1:     8.403 -  16.408: 1295   |   6:    48.427 -  56.431:   85        |
|      2:    16.408 -  24.413:  322   |   7:    56.431 -  64.436:   41        |
|      3:    24.413 -  32.417:  135   |   8:    64.436 -  72.441:   14        |
|      4:    32.417 -  40.422:  106   |   9:    72.441 -  80.445:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.504 - 5.474
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 275 from: 281
   mapped sites are within: 0.715 - 5.474

peak=    5.608 closest distance to " NH2 ARG A  56 " =    2.233
peak=    5.508 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.353 closest distance to " CB  GLN A 223 " =    1.385
peak=    5.205 closest distance to " O   HOH Z 126 " =    1.834
peak=    5.016 closest distance to " O   HOH Z 232 " =    2.371
peak=    5.002 closest distance to " CB  SER A  63 " =    1.193
peak=    4.688 closest distance to " CB  GLN A 183 " =    1.207
peak=    4.674 closest distance to " O   HOH Z 142 " =    1.690
peak=    4.665 closest distance to " CA  TYR A  30 " =    0.935
peak=    4.647 closest distance to " CG  PRO A 198 " =    1.292
peak=    4.631 closest distance to " O   HOH Z 236 " =    1.976
peak=    4.528 closest distance to " NE2 GLN A  11 " =    1.032
peak=    4.527 closest distance to " CB  GLU A 152 " =    1.180
peak=    4.510 closest distance to " O   HOH Z  78 " =    1.748
peak=    4.459 closest distance to " C   PRO A 198 " =    1.451
peak=    4.429 closest distance to " CG2 VAL A 257 " =    0.919
peak=    4.414 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.400 closest distance to " O   HOH Z 298 " =    1.890
peak=    4.389 closest distance to " O   HOH Z 369 " =    2.180
peak=    4.370 closest distance to " O   HOH Z  15 " =    2.222
peak=    4.366 closest distance to " CB  ARG A 190 " =    1.681
peak=    4.308 closest distance to " CZ  PHE A 218 " =    1.046
peak=    4.297 closest distance to " O   HOH Z 427 " =    2.950
peak=    4.239 closest distance to " OD1 ASN A  69 " =    2.599
peak=    4.228 closest distance to " O   HOH Z 234 " =    3.666
peak=    4.225 closest distance to " O   HOH Z 250 " =    1.480
peak=    4.195 closest distance to " O   HOH Z 158 " =    3.041
peak=    4.184 closest distance to " ND2 ASN A 187 " =    1.435
peak=    4.171 closest distance to " O   HOH Z 189 " =    2.320
peak=    4.155 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.151 closest distance to " CG  PRO A 243 " =    1.015
peak=    4.145 closest distance to " O   HOH Z  40 " =    1.710
peak=    4.140 closest distance to " O   HOH Z 203 " =    1.733
peak=    4.138 closest distance to " CB  LEU A 228 " =    1.071
peak=    4.127 closest distance to " CB  ARG A  79 " =    1.312
peak=    4.120 closest distance to " O   HOH Z 303 " =    2.030
peak=    4.106 closest distance to " CA  ASN A 215 " =    1.140
peak=    4.097 closest distance to " O   HOH Z 316 " =    3.122
peak=    4.089 closest distance to " O   HOH Z 389 " =    1.894
peak=    4.068 closest distance to " O   HOH Z 209 " =    2.371
peak=    4.026 closest distance to " O   HOH Z 392 " =    3.171
peak=    4.001 closest distance to " CD  ARG A 159 " =    0.715
peak=    3.992 closest distance to " CA  TYR A  30 " =    1.054
peak=    3.991 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.988 closest distance to " CB  TRP A 266 " =    0.985
peak=    3.967 closest distance to " O   HOH Z 193 " =    1.870
peak=    3.963 closest distance to " CB  SER A   3 " =    1.299
peak=    3.952 closest distance to " CB  ASP A 140 " =    0.908
peak=    3.951 closest distance to " CB  VAL A 265 " =    1.233
peak=    3.949 closest distance to " O   HOH Z 261 " =    2.116
peak=    3.930 closest distance to " CA  ARG A  36 " =    1.016
peak=    3.925 closest distance to " O   HOH Z 346 " =    1.674
peak=    3.923 closest distance to " O   HOH Z  66 " =    2.165
peak=    3.888 closest distance to " O   HOH Z  43 " =    1.878
peak=    3.886 closest distance to " O   HOH Z  19 " =    2.426
peak=    3.855 closest distance to " O   HOH Z 402 " =    1.415
peak=    3.837 closest distance to " O   HOH Z 245 " =    1.276
peak=    3.832 closest distance to " CB  ALA A 291 " =    1.334
peak=    3.816 closest distance to " CB  ASN A  39 " =    0.888
peak=    3.813 closest distance to " O   SER A  87 " =    2.203
peak=    3.807 closest distance to " CB  VAL A 202 " =    1.518
peak=    3.806 closest distance to " CG1 ILE A  33 " =    1.273
peak=    3.802 closest distance to " O   HOH Z 403 " =    1.658
peak=    3.796 closest distance to " O   HOH Z  61 " =    1.586
peak=    3.770 closest distance to " O   HOH Z 280 " =    2.990
peak=    3.769 closest distance to " CD2 TRP A 179 " =    1.377
peak=    3.763 closest distance to " NH1AARG A 145 " =    1.215
peak=    3.763 closest distance to " O   HOH Z 368 " =    2.014
peak=    3.760 closest distance to " O   HOH Z 423 " =    1.838
peak=    3.756 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.751 closest distance to " NZ  LYS A 117 " =    3.252
peak=    3.728 closest distance to " N   ARG A 156 " =    1.342
peak=    3.698 closest distance to " CG2 ILE A 120 " =    1.237
peak=    3.697 closest distance to " CA  ARG A 195 " =    1.160
peak=    3.680 closest distance to " CG  ARG A  66 " =    2.650
peak=    3.680 closest distance to " O   HOH Z 344 " =    3.216
peak=    3.674 closest distance to " CB  GLU A 277 " =    3.563
peak=    3.668 closest distance to " O   HOH Z  97 " =    1.983
peak=    3.665 closest distance to " O   HOH Z 148 " =    3.360
peak=    3.651 closest distance to " CD1 LEU A 300 " =    1.230
peak=    3.648 closest distance to " O   HOH Z 272 " =    1.850
peak=    3.648 closest distance to " CA  SER A  87 " =    1.025
peak=    3.647 closest distance to " O   HOH Z 291 " =    1.553
peak=    3.627 closest distance to " O   HOH Z 248 " =    1.631
peak=    3.625 closest distance to " CG1 VAL A 153 " =    0.977
peak=    3.619 closest distance to " CB  SER A 216 " =    0.830
peak=    3.617 closest distance to " CB  ILE A 120 " =    1.210
peak=    3.615 closest distance to " O   HOH Z 172 " =    3.442
peak=    3.612 closest distance to " NH2BARG A 145 " =    2.069
peak=    3.604 closest distance to " O   HOH Z 147 " =    1.782
peak=    3.601 closest distance to " CG1BVAL A  72 " =    1.644
peak=    3.593 closest distance to " CB  ARG A 139 " =    0.927
peak=    3.591 closest distance to " O   HOH Z 214 " =    2.108
peak=    3.587 closest distance to " O   HOH Z 371 " =    3.217
peak=    3.582 closest distance to " OD2 ASP A 286 " =    2.831
peak=    3.580 closest distance to " O   HOH Z 265 " =    2.446
peak=    3.576 closest distance to " CA  THR A 221 " =    1.007
peak=    3.574 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.570 closest distance to " CB  PRO A  54 " =    0.758
peak=    3.569 closest distance to " CB  MET A  47 " =    0.984
peak=    3.555 closest distance to " CA  MET A  40 " =    1.077
peak=    3.555 closest distance to " CD BLYS A 290 " =    1.031
peak=    3.554 closest distance to " O   HOH Z 213 " =    1.839
peak=    3.551 closest distance to " O   HOH Z 305 " =    3.645
peak=    3.549 closest distance to " O   HOH Z  97 " =    2.615
peak=    3.538 closest distance to " O   HOH Z   9 " =    2.117
peak=    3.530 closest distance to " CD1 ILE A 106 " =    0.783
peak=    3.528 closest distance to " CB  MET A  40 " =    0.828
peak=    3.523 closest distance to " O   HOH Z 425 " =    1.948
peak=    3.519 closest distance to " O   HOH Z 132 " =    2.509
peak=    3.519 closest distance to " CA  ALA A  21 " =    1.158
peak=    3.515 closest distance to " O   HOH Z  44 " =    1.793
peak=    3.512 closest distance to " O   HOH Z 403 " =    1.381
peak=    3.511 closest distance to " O   HOH Z 173 " =    1.930
peak=    3.510 closest distance to " CB  TRP A 179 " =    1.315
peak=    3.500 closest distance to " O   HOH Z 219 " =    2.034
peak=    3.495 closest distance to " O   HOH Z 126 " =    2.115
peak=    3.491 closest distance to " N   ASN A  39 " =    1.201
peak=    3.491 closest distance to " CD1 LEU A  96 " =    0.750
peak=    3.489 closest distance to " CB  HIS A 108 " =    0.841
peak=    3.487 closest distance to " O   HOH Z 383 " =    1.769
peak=    3.479 closest distance to " CB  GLU A  46 " =    0.992
peak=    3.477 closest distance to " O   HOH Z 141 " =    1.729
peak=    3.473 closest distance to " O   THR A 220 " =    1.252
peak=    3.471 closest distance to " O   HOH Z 407 " =    2.497
peak=    3.467 closest distance to " O   HOH Z   1 " =    2.076
peak=    3.462 closest distance to " CA  ALA A  43 " =    1.219
peak=    3.460 closest distance to " O   HOH Z  59 " =    1.969
peak=    3.459 closest distance to " C   ILE A 106 " =    1.871
peak=    3.458 closest distance to " O   HOH Z 417 " =    3.087
peak=    3.458 closest distance to " CA  THR A 264 " =    0.882
peak=    3.446 closest distance to " CG2 THR A 221 " =    1.199
peak=    3.445 closest distance to " NH2 ARG A 156 " =    1.109
peak=    3.435 closest distance to " CB  ASN A 110 " =    1.123
peak=    3.433 closest distance to " O   HOH Z 368 " =    3.558
peak=    3.424 closest distance to " O   HOH Z 421 " =    1.767
peak=    3.423 closest distance to " CD  ARG A 269 " =    0.918
peak=    3.422 closest distance to " O   THR A 251 " =    1.161
peak=    3.420 closest distance to " O   HOH Z 185 " =    1.757
peak=    3.419 closest distance to " CA  ALA A 291 " =    0.826
peak=    3.417 closest distance to " CA  ILE A 234 " =    0.926
peak=    3.417 closest distance to " CB  SER A 212 " =    1.151
peak=    3.414 closest distance to " CA  GLY A  80 " =    0.900
peak=    3.413 closest distance to " CB  THR A 157 " =    1.092
peak=    3.410 closest distance to " O   HOH Z 433 " =    1.784
peak=    3.410 closest distance to " CB  TYR A 116 " =    0.760
peak=    3.410 closest distance to " O   HOH Z 285 " =    2.913
peak=    3.409 closest distance to " OE1 GLU A   2 " =    2.194
peak=    3.407 closest distance to " CZ2 TRP A 179 " =    1.753
peak=    3.407 closest distance to " CD1AILE A 234 " =    0.922
peak=    3.406 closest distance to " O   HOH Z 261 " =    1.560
peak=    3.404 closest distance to " ND2 ASN A 110 " =    1.698
peak=    3.401 closest distance to " O   HOH Z 180 " =    2.182
peak=    3.398 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.393 closest distance to " CA  ALA A 158 " =    1.271
peak=    3.392 closest distance to " O   HOH Z 193 " =    2.017
peak=    3.389 closest distance to " NE2 GLN A  73 " =    3.857
peak=    3.385 closest distance to " OG BSER A 164 " =    2.331
peak=    3.384 closest distance to " O   HOH Z 426 " =    1.651
peak=    3.384 closest distance to " CB  ALA A 114 " =    0.852
peak=    3.384 closest distance to " O   HOH Z 435 " =    1.939
peak=    3.372 closest distance to " O   HOH Z  88 " =    3.073
peak=    3.371 closest distance to " CD2 LEU A 297 " =    0.860
peak=    3.371 closest distance to " CB  ALA A 248 " =    1.327
peak=    3.364 closest distance to " CG  LEU A 167 " =    1.250
peak=    3.364 closest distance to " O   HOH Z 234 " =    1.919
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.359 closest distance to " O   HOH Z 133 " =    2.529
peak=    3.355 closest distance to " O   HOH Z  21 " =    1.770
peak=    3.354 closest distance to " O   ALA A 165 " =    1.537
peak=    3.354 closest distance to " NH2AARG A 190 " =    1.951
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.632
peak=    3.345 closest distance to " O   TRP A 274 " =    1.854
peak=    3.341 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.331 closest distance to " CA  ILE A  33 " =    1.465
peak=    3.322 closest distance to " O   HOH Z 187 " =    2.248
peak=    3.320 closest distance to " CB  ALA A 242 " =    0.873
peak=    3.320 closest distance to " CD  LYS A 166 " =    1.198
peak=    3.316 closest distance to " O   HOH Z 365 " =    3.066
peak=    3.315 closest distance to " CB  SER A  26 " =    1.670
peak=    3.312 closest distance to " N   ASN A 127 " =    1.212
peak=    3.309 closest distance to " O   HOH Z 359 " =    1.411
peak=    3.308 closest distance to " NE2 GLN A  77 " =    3.185
peak=    3.296 closest distance to " O   HOH Z 345 " =    3.386
peak=    3.294 closest distance to " CG  GLN A  77 " =    2.084
peak=    3.294 closest distance to " O   HOH Z 128 " =    2.255
peak=    3.294 closest distance to " CB  SER A 141 " =    1.053
peak=    3.292 closest distance to " CD  ARG A  36 " =    0.976
peak=    3.291 closest distance to " CB  THR A  31 " =    1.641
peak=    3.288 closest distance to " CB  LEU A 255 " =    0.804
peak=    3.287 closest distance to " CD2 LEU A 255 " =    1.380
peak=    3.287 closest distance to " O   HOH Z 298 " =    2.499
peak=    3.277 closest distance to " O   HOH Z 411 " =    3.898
peak=    3.273 closest distance to " O   HOH Z 365 " =    3.226
peak=    3.270 closest distance to " CB  LYS A 290 " =    0.987
peak=    3.270 closest distance to " NH1 ARG A  14 " =    1.091
peak=    3.264 closest distance to " CB  PRO A 198 " =    1.119
peak=    3.261 closest distance to " CA  ASP A 140 " =    1.136
peak=    3.257 closest distance to " O   HOH Z  44 " =    3.216
peak=    3.256 closest distance to " CD  LYS A 119 " =    1.349
peak=    3.253 closest distance to " CG2 ILE A  20 " =    1.365
peak=    3.251 closest distance to " CD  ARG A  66 " =    2.461
peak=    3.247 closest distance to " O   HOH Z 329 " =    3.856
peak=    3.247 closest distance to " O   HOH Z 175 " =    2.165
peak=    3.242 closest distance to " O  BHOH Z 338 " =    2.322
peak=    3.236 closest distance to " CB  ALA A  34 " =    1.038
peak=    3.236 closest distance to " CA  ASN A 217 " =    1.201
peak=    3.235 closest distance to " CB  ASN A 224 " =    1.026
peak=    3.234 closest distance to " O   HOH Z 273 " =    2.715
peak=    3.230 closest distance to " CA  ASP A 162 " =    1.083
peak=    3.227 closest distance to " OD1 ASP A 171 " =    1.305
peak=    3.218 closest distance to " O   ALA A   1 " =    1.703
peak=    3.213 closest distance to " OG1 THR A 294 " =    2.346
peak=    3.212 closest distance to " O   HOH Z 337 " =    3.663
peak=    3.203 closest distance to " CB  SER A 273 " =    0.872
peak=    3.203 closest distance to " CG  GLU A 277 " =    2.103
peak=    3.199 closest distance to " CD  ARG A 219 " =    1.125
peak=    3.197 closest distance to " CB  ALA A   9 " =    1.511
peak=    3.197 closest distance to " CB  GLN A  88 " =    1.176
peak=    3.191 closest distance to " N   SER A 135 " =    1.211
peak=    3.189 closest distance to " OG  SER A 206 " =    1.265
peak=    3.188 closest distance to " O   HOH Z 357 " =    1.853
peak=    3.186 closest distance to " O   HOH Z 437 " =    1.331
peak=    3.184 closest distance to " CB  ASN A 215 " =    1.125
peak=    3.183 closest distance to " CB  GLN A 278 " =    0.867
peak=    3.182 closest distance to " CG  LYS A  76 " =    0.985
peak=    3.174 closest distance to " O   HOH Z  88 " =    1.906
peak=    3.173 closest distance to " ND1 HIS A  86 " =    1.769
peak=    3.171 closest distance to " N   GLN A 278 " =    1.130
peak=    3.170 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.168 closest distance to " CD  ARG A 156 " =    1.524
peak=    3.166 closest distance to " O   HOH Z 171 " =    2.178
peak=    3.164 closest distance to " NZ  LYS A  76 " =    1.578
peak=    3.155 closest distance to " O   HOH Z 423 " =    3.016
peak=    3.155 closest distance to " CA  TYR A 116 " =    1.361
peak=    3.153 closest distance to " CG  MET A 113 " =    1.123
peak=    3.153 closest distance to " O   HOH Z  61 " =    1.467
peak=    3.153 closest distance to " CE  LYS A  48 " =    1.087
peak=    3.152 closest distance to " CB  ALA A   1 " =    4.745
peak=    3.151 closest distance to " O   HOH Z 419 " =    2.005
peak=    3.149 closest distance to " CD2 HIS A  81 " =    1.079
peak=    3.147 closest distance to " O   HOH Z  62 " =    2.071
peak=    3.143 closest distance to " CG  GLN A  11 " =    1.569
peak=    3.142 closest distance to " ND1 HIS A  81 " =    1.669
peak=    3.140 closest distance to " CG2 VAL A 197 " =    1.064
peak=    3.137 closest distance to " CE AMET A  47 " =    1.369
peak=    3.136 closest distance to " O   HOH Z  49 " =    2.852
peak=    3.136 closest distance to " CB  SER A  62 " =    1.258
peak=    3.136 closest distance to " CG1 ILE A  49 " =    1.447
peak=    3.131 closest distance to " CA  MET A 105 " =    1.014
peak=    3.127 closest distance to " OG1 THR A 294 " =    1.645
peak=    3.126 closest distance to " NH1BARG A 145 " =    1.135
peak=    3.124 closest distance to " CB  VAL A 126 " =    1.033
peak=    3.119 closest distance to " O   HOH Z 430 " =    5.474
peak=    3.115 closest distance to " O   HOH Z 201 " =    3.135
peak=    3.115 closest distance to " O   HOH Z 163 " =    1.744
peak=    3.110 closest distance to " O   HOH Z 374 " =    2.622
peak=    3.110 closest distance to " CA  ALA A 248 " =    1.204
peak=    3.107 closest distance to " O   HOH Z 116 " =    1.737
peak=    3.106 closest distance to " O   HOH Z 391 " =    2.921
peak=    3.106 closest distance to " O   HOH Z 371 " =    1.760
peak=    3.104 closest distance to " CA  VAL A 125 " =    1.030
peak=    3.103 closest distance to " O   HOH Z 271 " =    2.425
peak=    3.100 closest distance to " O   HOH Z  85 " =    2.274
peak=    3.091 closest distance to " O   HOH Z 392 " =    1.980
peak=    3.084 closest distance to " O   HOH Z 258 " =    1.872
peak=    3.082 closest distance to " CG  ARG A 159 " =    0.878
peak=    3.078 closest distance to " N   TYR A  15 " =    0.719
peak=    3.074 closest distance to " O   HOH Z 327 " =    1.690
peak=    3.071 closest distance to " OD1BASN A 224 " =    2.355
peak=    3.058 closest distance to " CB  VAL A 265 " =    1.962
peak=    3.049 closest distance to " O   HOH Z 406 " =    1.533
peak=    3.042 closest distance to " CG2 ILE A 234 " =    0.737
peak=    3.041 closest distance to " N   GLY A  98 " =    1.051
peak=    3.039 closest distance to " O   HOH Z  49 " =    2.237

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 187         
Filter by distance & map next to the model:
   mapped sites are within: 0.801 - 5.243
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 187
   mapped sites are within: 0.801 - 5.243

peak=   -4.696 closest distance to " CD  ARG A 156 " =    2.014
peak=   -4.530 closest distance to " O   HOH Z 266 " =    5.083
peak=   -4.437 closest distance to " CD  GLN A  58 " =    0.996
peak=   -4.391 closest distance to " SG  CYS A 254 " =    3.528
peak=   -4.303 closest distance to " CB  PRO A 243 " =    2.659
peak=   -4.300 closest distance to " O   VAL A  67 " =    2.734
peak=   -4.249 closest distance to " CG  GLN A 223 " =    1.864
peak=   -4.232 closest distance to " OG BSER A 134 " =    1.209
peak=   -4.168 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -4.156 closest distance to " C   HIS A 108 " =    1.054
peak=   -4.110 closest distance to " CD2 PHE A 192 " =    2.045
peak=   -4.089 closest distance to " O   ILE A 109 " =    2.542
peak=   -4.083 closest distance to " CZ3 TRP A 179 " =    1.160
peak=   -4.077 closest distance to " O   HOH Z 372 " =    2.319
peak=   -4.044 closest distance to " O   HOH Z 377 " =    2.089
peak=   -4.027 closest distance to " CE  MET A 105 " =    2.334
peak=   -4.019 closest distance to " O   HOH Z 231 " =    2.216
peak=   -4.006 closest distance to " CG2 ILE A 263 " =    2.323
peak=   -3.977 closest distance to " O   HOH Z 389 " =    1.907
peak=   -3.975 closest distance to " O   HOH Z  10 " =    1.530
peak=   -3.962 closest distance to " ND2 ASN A  45 " =    1.615
peak=   -3.957 closest distance to " O   HOH Z 198 " =    1.989
peak=   -3.956 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.955 closest distance to " O   HOH Z 114 " =    3.085
peak=   -3.908 closest distance to " CB  ALA A 291 " =    2.281
peak=   -3.880 closest distance to " O   HOH Z 185 " =    2.311
peak=   -3.855 closest distance to " CB  ASN A  39 " =    2.308
peak=   -3.854 closest distance to " O   HOH Z 290 " =    1.236
peak=   -3.847 closest distance to " CG1 VAL A 112 " =    2.854
peak=   -3.844 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.836 closest distance to " CD  ARG A 139 " =    1.516
peak=   -3.824 closest distance to " N   ALA A  43 " =    2.568
peak=   -3.821 closest distance to " O   VAL A  67 " =    2.838
peak=   -3.751 closest distance to " CG  PHE A 283 " =    2.606
peak=   -3.738 closest distance to " O   HOH Z 435 " =    2.849
peak=   -3.728 closest distance to " OD1 ASN A 187 " =    1.564
peak=   -3.708 closest distance to " CG  ASP A 132 " =    2.278
peak=   -3.699 closest distance to " O   PRO A 163 " =    2.032
peak=   -3.697 closest distance to " O   HOH Z  43 " =    1.616
peak=   -3.688 closest distance to " CB  ALA A  43 " =    2.515
peak=   -3.686 closest distance to " OG  SER A  97 " =    2.204
peak=   -3.683 closest distance to " CG  ARG A 269 " =    2.369
peak=   -3.680 closest distance to " O   HOH Z 407 " =    3.021
peak=   -3.679 closest distance to " O   HOH Z 351 " =    1.469
peak=   -3.678 closest distance to " ND2 ASN A  45 " =    1.041
peak=   -3.676 closest distance to " O   HOH Z 313 " =    1.887
peak=   -3.674 closest distance to " O   HOH Z 211 " =    1.722
peak=   -3.665 closest distance to " O   HOH Z 196 " =    1.990
peak=   -3.659 closest distance to " O   HOH Z 353 " =    2.110
peak=   -3.655 closest distance to " CE2 PHE A 218 " =    2.478
peak=   -3.654 closest distance to " O   HOH Z 126 " =    1.871
peak=   -3.612 closest distance to " OXT GLY A 302 " =    2.807
peak=   -3.606 closest distance to " CA  GLY A 203 " =    2.341
peak=   -3.603 closest distance to " NH2AARG A 275 " =    5.243
peak=   -3.600 closest distance to " CD1 PHE A  59 " =    1.873
peak=   -3.598 closest distance to " CG1 VAL A 112 " =    2.596
peak=   -3.596 closest distance to " CZ  PHE A  59 " =    1.551
peak=   -3.562 closest distance to " O   HOH Z  52 " =    1.370
peak=   -3.557 closest distance to " CD2 PHE A  61 " =    2.537
peak=   -3.555 closest distance to " O   HOH Z 311 " =    3.598
peak=   -3.551 closest distance to " OD1 ASP A 171 " =    1.598
peak=   -3.546 closest distance to " O   HOH Z  60 " =    2.361
peak=   -3.518 closest distance to " O   HOH Z  73 " =    2.189
peak=   -3.510 closest distance to " CD  ARG A 195 " =    5.155
peak=   -3.487 closest distance to " O   HOH Z 394 " =    1.508
peak=   -3.486 closest distance to " O   HOH Z 166 " =    2.019
peak=   -3.476 closest distance to " CB  ALA A 291 " =    2.358
peak=   -3.474 closest distance to " NE2 GLN A 278 " =    1.791
peak=   -3.465 closest distance to " OG  SER A  62 " =    1.678
peak=   -3.464 closest distance to " NH1 ARG A 195 " =    2.561
peak=   -3.464 closest distance to " C   ALA A 158 " =    1.308
peak=   -3.463 closest distance to " C   LEU A 143 " =    1.003
peak=   -3.462 closest distance to " OD2 ASP A 191 " =    1.465
peak=   -3.451 closest distance to " CA  GLY A 241 " =    3.047
peak=   -3.449 closest distance to " N   ASP A 286 " =    2.409
peak=   -3.448 closest distance to " CZ  TYR A 169 " =    1.745
peak=   -3.437 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.423 closest distance to " NH2 ARG A  79 " =    1.543
peak=   -3.421 closest distance to " CA  GLY A 133 " =    1.990
peak=   -3.418 closest distance to " C   ASP A 231 " =    2.671
peak=   -3.418 closest distance to " CD1 LEU A 101 " =    2.318
peak=   -3.414 closest distance to " N   SER A 212 " =    1.943
peak=   -3.400 closest distance to " CG  GLN A  11 " =    1.634
peak=   -3.396 closest distance to " O   HOH Z 292 " =    4.557
peak=   -3.396 closest distance to " N   ALA A 248 " =    1.602
peak=   -3.393 closest distance to " O   ALA A 161 " =    1.639
peak=   -3.391 closest distance to " O   HOH Z 198 " =    1.354
peak=   -3.388 closest distance to " O   ARG A 145 " =    1.518
peak=   -3.383 closest distance to " CD1 LEU A 228 " =    2.217
peak=   -3.378 closest distance to " O   HOH Z 322 " =    1.616
peak=   -3.375 closest distance to " O   HOH Z  11 " =    1.738
peak=   -3.374 closest distance to " CD1 LEU A 297 " =    2.403
peak=   -3.373 closest distance to " C   MET A 188 " =    1.339
peak=   -3.370 closest distance to " O   HOH Z 102 " =    1.567
peak=   -3.370 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.362 closest distance to " CB  ALA A 248 " =    2.168
peak=   -3.360 closest distance to " CB  ALA A 248 " =    2.345
peak=   -3.359 closest distance to " N   ALA A 226 " =    2.012
peak=   -3.357 closest distance to " O   HOH Z 193 " =    2.034
peak=   -3.351 closest distance to " O   SER A  95 " =    1.586
peak=   -3.341 closest distance to " OE1 GLN A  88 " =    1.150
peak=   -3.337 closest distance to " O   HOH Z 243 " =    2.047
peak=   -3.327 closest distance to " O   HOH Z 298 " =    1.274
peak=   -3.327 closest distance to " N   THR A 157 " =    1.576
peak=   -3.327 closest distance to " CD1 LEU A  83 " =    2.661
peak=   -3.326 closest distance to " CG1 VAL A 250 " =    2.655
peak=   -3.324 closest distance to " CD1 LEU A   5 " =    2.545
peak=   -3.311 closest distance to " O   ALA A  10 " =    1.660
peak=   -3.309 closest distance to " CB  PHE A 208 " =    2.249
peak=   -3.304 closest distance to " O   HOH Z  51 " =    1.567
peak=   -3.299 closest distance to " OD2 ASP A 171 " =    2.405
peak=   -3.296 closest distance to " N   ASP A 171 " =    2.344
peak=   -3.294 closest distance to " CZ  PHE A 155 " =    1.247
peak=   -3.291 closest distance to " O   HOH Z 295 " =    1.623
peak=   -3.289 closest distance to " NE2 GLN A  88 " =    1.906
peak=   -3.286 closest distance to " O   HOH Z  13 " =    1.551
peak=   -3.280 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.279 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.279 closest distance to " OD1 ASP A 191 " =    1.565
peak=   -3.278 closest distance to " CD2 LEU A 237 " =    2.804
peak=   -3.272 closest distance to " O   PHE A 218 " =    1.562
peak=   -3.269 closest distance to " O   HOH Z  37 " =    1.769
peak=   -3.258 closest distance to " O   HOH Z  44 " =    2.185
peak=   -3.256 closest distance to " O   ALA A  51 " =    1.374
peak=   -3.256 closest distance to " O   HOH Z   6 " =    1.436
peak=   -3.256 closest distance to " O   HOH Z 123 " =    2.270
peak=   -3.248 closest distance to " O   HOH Z 253 " =    3.900
peak=   -3.244 closest distance to " CB  PRO A 163 " =    2.486
peak=   -3.239 closest distance to " CB  ASP A 286 " =    1.783
peak=   -3.237 closest distance to " CD1 ILE A 239 " =    2.241
peak=   -3.236 closest distance to " O   HOH Z 244 " =    2.044
peak=   -3.232 closest distance to " OG  SER A 206 " =    1.761
peak=   -3.231 closest distance to " SG ACYS A 201 " =    1.872
peak=   -3.226 closest distance to " O   SER A 135 " =    1.476
peak=   -3.224 closest distance to " O   GLY A  17 " =    1.151
peak=   -3.222 closest distance to " O   GLY A 211 " =    1.326
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    1.868
peak=   -3.215 closest distance to " O   HOH Z  38 " =    1.529
peak=   -3.212 closest distance to " O   HOH Z 309 " =    2.606
peak=   -3.207 closest distance to " O   HOH Z 134 " =    2.975
peak=   -3.207 closest distance to " CD  GLU A 236 " =    1.055
peak=   -3.198 closest distance to " CG  ARG A  66 " =    2.394
peak=   -3.197 closest distance to " O   LYS A 117 " =    1.686
peak=   -3.192 closest distance to " CG1 VAL A 125 " =    2.009
peak=   -3.190 closest distance to " CG2 THR A 221 " =    2.265
peak=   -3.184 closest distance to " CB  TYR A 172 " =    2.441
peak=   -3.180 closest distance to " CE3 TRP A 150 " =    2.143
peak=   -3.178 closest distance to " O   VAL A 189 " =    2.604
peak=   -3.175 closest distance to " CZ  PHE A 192 " =    2.916
peak=   -3.172 closest distance to " ND2 ASN A 187 " =    1.528
peak=   -3.169 closest distance to " CG1 VAL A 197 " =    2.341
peak=   -3.169 closest distance to " CA  GLY A 241 " =    2.791
peak=   -3.166 closest distance to " NH2BARG A 275 " =    1.927
peak=   -3.165 closest distance to " OG BSER A 134 " =    1.795
peak=   -3.165 closest distance to " O   HOH Z 165 " =    1.955
peak=   -3.163 closest distance to " O   HOH Z 377 " =    1.688
peak=   -3.163 closest distance to " NH2 ARG A  79 " =    2.050
peak=   -3.162 closest distance to " N   TYR A  68 " =    3.224
peak=   -3.160 closest distance to " O   HOH Z 417 " =    2.519
peak=   -3.148 closest distance to " CB  TRP A  85 " =    2.410
peak=   -3.148 closest distance to " O   HOH Z  93 " =    2.335
peak=   -3.147 closest distance to " CG  GLU A 152 " =    1.311
peak=   -3.146 closest distance to " OXT GLY A 302 " =    3.325
peak=   -3.146 closest distance to " OG BSER A 210 " =    2.359
peak=   -3.143 closest distance to " CD2 TYR A 293 " =    1.995
peak=   -3.143 closest distance to " O   HOH Z 175 " =    4.279
peak=   -3.141 closest distance to " O   ALA A 180 " =    1.241
peak=   -3.137 closest distance to " O   HOH Z  41 " =    2.498
peak=   -3.134 closest distance to " CA  GLY A  98 " =    1.950
peak=   -3.134 closest distance to " CG  LEU A  83 " =    1.860
peak=   -3.132 closest distance to " CG  TRP A 266 " =    1.923
peak=   -3.128 closest distance to " CB  ASP A 286 " =    2.089
peak=   -3.113 closest distance to " OE2 GLU A   2 " =    1.850
peak=   -3.111 closest distance to " O   HOH Z 298 " =    2.425
peak=   -3.099 closest distance to " O   HOH Z 166 " =    1.675
peak=   -3.095 closest distance to " O   HOH Z   6 " =    2.021
peak=   -3.083 closest distance to " OD1 ASP A 200 " =    1.413
peak=   -3.081 closest distance to " CG2 ILE A  20 " =    2.971
peak=   -3.080 closest distance to " CD2 LEU A 300 " =    2.906
peak=   -3.079 closest distance to " O   TRP A  70 " =    1.464
peak=   -3.073 closest distance to " O   HOH Z 211 " =    1.794
peak=   -3.066 closest distance to " O   HOH Z 137 " =    1.550
peak=   -3.062 closest distance to " O   ALA A 180 " =    1.016
peak=   -3.054 closest distance to " O   HOH Z  90 " =    1.766
peak=   -3.033 closest distance to " OD2 ASP A  50 " =    2.244
peak=   -3.014 closest distance to " N   GLN A  58 " =    2.051

================= 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    :  0.1569 0.1569   5.264030e+00   5.254157e+00
   1_bss:  0.1313 0.1309   5.199598e+00   5.183534e+00
   1_xyz:  0.1209 0.1464   5.152075e+00   5.308639e+00
   1_adp:  0.1116 0.1465   5.103514e+00   5.315790e+00
   1_occ:  0.1111 0.1462   5.101091e+00   5.314091e+00
   2_bss:  0.1111 0.1463   5.101134e+00   5.314129e+00
   2_xyz:  0.1107 0.1463   5.098826e+00   5.315939e+00
   2_adp:  0.1093 0.1472   5.095965e+00   5.324274e+00
   2_occ:  0.1092 0.1473   5.095738e+00   5.324437e+00
   3_bss:  0.1091 0.1473   5.095880e+00   5.324626e+00
   3_xyz:  0.1077 0.1505   5.098919e+00   5.344849e+00
   3_adp:  0.1057 0.1524   5.096460e+00   5.354940e+00
   3_occ:  0.1056 0.1525   5.096494e+00   5.355128e+00
   4_bss:  0.1055 0.1524   5.096261e+00   5.354853e+00
   4_xyz:  0.1061 0.1533   5.102145e+00   5.361093e+00
   4_adp:  0.1087 0.1522   5.109168e+00   5.355852e+00
   4_occ:  0.1086 0.1522   5.109336e+00   5.356302e+00
   5_bss:  0.1086 0.1523   5.109568e+00   5.356574e+00
   5_xyz:  0.1100 0.1529   5.119276e+00   5.362659e+00
   5_adp:  0.1081 0.1541   5.114113e+00   5.367936e+00
   5_occ:  0.1081 0.1541   5.114072e+00   5.367930e+00
   5_bss:  0.1080 0.1540   5.113846e+00   5.367660e+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:  0.328  50.000  -3.154  -2.763  -1.676  -0.000  -0.000  -0.000
   1_xyz:  0.328  50.000  -3.154  -2.763  -1.676  -0.000  -0.000  -0.000
   1_adp:  0.328  50.000  -3.154  -2.763  -1.676  -0.000  -0.000  -0.000
   1_occ:  0.328  50.000  -3.154  -2.763  -1.676  -0.000  -0.000  -0.000
   2_bss:  0.328  50.000  -2.942  -2.570  -1.483  -0.000  -0.000  -0.000
   2_xyz:  0.328  50.000  -2.942  -2.570  -1.483  -0.000  -0.000  -0.000
   2_adp:  0.328  50.000  -2.942  -2.570  -1.483  -0.000  -0.000  -0.000
   2_occ:  0.328  50.000  -2.942  -2.570  -1.483  -0.000  -0.000  -0.000
   3_bss:  0.331  50.000  -2.745  -2.393  -1.311  -0.000  -0.000  -0.000
   3_xyz:  0.331  50.000  -2.745  -2.393  -1.311  -0.000  -0.000  -0.000
   3_adp:  0.331  50.000  -2.745  -2.393  -1.311  -0.000  -0.000  -0.000
   3_occ:  0.331  50.000  -2.745  -2.393  -1.311  -0.000  -0.000  -0.000
   4_bss:  0.325  50.000  -2.447  -2.121  -1.058  -0.000  -0.000  -0.000
   4_xyz:  0.325  50.000  -2.447  -2.121  -1.058  -0.000  -0.000  -0.000
   4_adp:  0.325  50.000  -2.447  -2.121  -1.058  -0.000  -0.000  -0.000
   4_occ:  0.325  50.000  -2.447  -2.121  -1.058  -0.000  -0.000  -0.000
   5_bss:  0.330  50.000  -2.381  -2.045  -0.960  -0.000  -0.000  -0.000
   5_xyz:  0.330  50.000  -2.381  -2.045  -0.960  -0.000  -0.000  -0.000
   5_adp:  0.330  50.000  -2.381  -2.045  -0.960  -0.000  -0.000  -0.000
   5_occ:  0.330  50.000  -2.381  -2.045  -0.960  -0.000  -0.000  -0.000
   5_bss:  0.325  49.987  -2.167  -1.844  -0.776  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  11.733 0.9316  1.0552     7081.269
   1_bss:  10.101 0.9444  0.9759     4298.903
   1_xyz:  12.077 0.9310  0.9696     5446.689
   1_adp:  12.334 0.9285  0.9666     5488.751
   1_occ:  12.305 0.9287  0.9663     5449.385
   2_bss:  12.306 0.9287  0.9734     5450.792
   2_xyz:  12.372 0.9280  0.9730     5507.978
   2_adp:  12.506 0.9270  0.9685     5551.992
   2_occ:  12.513 0.9270  0.9684     5551.865
   3_bss:  12.517 0.9269  0.9749     5556.421
   3_xyz:  12.849 0.9245  0.9741     5822.137
   3_adp:  13.093 0.9226  0.9666     5889.531
   3_occ:  13.097 0.9226  0.9665     5892.340
   4_bss:  13.089 0.9226  0.9763     5885.294
   4_xyz:  13.212 0.9217  0.9757     5968.938
   4_adp:  13.069 0.9227  0.9719     5945.919
   4_occ:  13.077 0.9226  0.9718     5951.181
   5_bss:  13.082 0.9226  0.9747     5958.190
   5_xyz:  13.181 0.9219  0.9743     6025.602
   5_adp:  13.340 0.9207  0.9675     6049.232
   5_occ:  13.341 0.9207  0.9674     6050.359
   5_bss:  13.336 0.9207  0.9741     6043.441
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5934e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5934e-01
   1_xyz:   1.082  0.010  0.086 15.677  0.005  4.113   7.5585e-02
   1_adp:   1.082  0.010  0.086 15.677  0.005  4.113   7.5585e-02
   1_occ:   1.082  0.010  0.086 15.677  0.005  4.113   7.5585e-02
   2_bss:   1.082  0.010  0.086 15.677  0.005  4.113   7.5585e-02
   2_xyz:   0.996  0.008  0.079 15.474  0.004  4.113   6.3051e-02
   2_adp:   0.996  0.008  0.079 15.474  0.004  4.113   6.3051e-02
   2_occ:   0.996  0.008  0.079 15.474  0.004  4.113   6.3051e-02
   3_bss:   0.996  0.008  0.079 15.474  0.004  4.113   6.3051e-02
   3_xyz:   1.014  0.008  0.080 15.487  0.004  4.115   6.5744e-02
   3_adp:   1.014  0.008  0.080 15.487  0.004  4.115   6.5744e-02
   3_occ:   1.014  0.008  0.080 15.487  0.004  4.115   6.5744e-02
   4_bss:   1.014  0.008  0.080 15.487  0.004  4.115   6.5744e-02
   4_xyz:   0.972  0.007  0.076 15.411  0.004  4.119   6.0461e-02
   4_adp:   0.972  0.007  0.076 15.411  0.004  4.119   6.0461e-02
   4_occ:   0.972  0.007  0.076 15.411  0.004  4.119   6.0461e-02
   5_bss:   0.972  0.007  0.076 15.411  0.004  4.119   6.0461e-02
   5_xyz:   0.908  0.006  0.072 15.278  0.003  4.118   5.4136e-02
   5_adp:   0.908  0.006  0.072 15.278  0.003  4.118   5.4136e-02
   5_occ:   0.908  0.006  0.072 15.278  0.003  4.118   5.4136e-02
   5_bss:   0.908  0.006  0.072 15.278  0.003  4.118   5.4136e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4111e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4111e-01
   1_xyz:   7.471  0.045  0.268 84.127  0.039  2.278   6.9349e-02
   1_adp:   7.471  0.045  0.268 84.127  0.039  2.278   6.9349e-02
   1_occ:   7.471  0.045  0.268 84.127  0.039  2.278   6.9349e-02
   2_bss:   7.471  0.045  0.268 84.127  0.039  2.278   6.9349e-02
   2_xyz:   6.761  0.042  0.248 84.370  0.035  2.326   4.3311e-02
   2_adp:   6.761  0.042  0.248 84.370  0.035  2.326   4.3311e-02
   2_occ:   6.761  0.042  0.248 84.370  0.035  2.326   4.3311e-02
   3_bss:   6.761  0.042  0.248 84.370  0.035  2.326   4.3311e-02
   3_xyz:   6.896  0.044  0.259 83.805  0.035  2.294   4.6918e-02
   3_adp:   6.896  0.044  0.259 83.805  0.035  2.294   4.6918e-02
   3_occ:   6.896  0.044  0.259 83.805  0.035  2.294   4.6918e-02
   4_bss:   6.896  0.044  0.259 83.805  0.035  2.294   4.6918e-02
   4_xyz:   6.480  0.044  0.239 83.234  0.034  2.357   4.0984e-02
   4_adp:   6.480  0.044  0.239 83.234  0.034  2.357   4.0984e-02
   4_occ:   6.480  0.044  0.239 83.234  0.034  2.357   4.0984e-02
   5_bss:   6.480  0.044  0.239 83.234  0.034  2.357   4.0984e-02
   5_xyz:   6.448  0.040  0.219 83.445  0.031  2.345   3.1534e-02
   5_adp:   6.448  0.040  0.219 83.445  0.031  2.345   3.1534e-02
   5_occ:   6.448  0.040  0.219 83.445  0.031  2.345   3.1534e-02
   5_bss:   6.448  0.040  0.219 83.445  0.031  2.345   3.1534e-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:  62.66   0.00  16.27  51.77   0.00  12.55  62.66   4.19  36.52
   1_occ:  62.66   0.00  16.27  51.77   0.00  12.55  62.66   4.19  36.52
   2_bss:  62.66   0.00  16.27  51.77   0.00  12.55  62.66   4.19  36.52
   2_xyz:  62.66   0.00  16.27  51.77   0.00  12.55  62.66   4.19  36.52
   2_adp:  63.83   2.27  16.28  60.01   2.27  12.68  63.83   5.75  35.88
   2_occ:  63.83   2.27  16.28  60.01   2.27  12.68  63.83   5.75  35.88
   3_bss:  63.83   2.27  16.28  60.01   2.27  12.68  63.83   5.75  35.88
   3_xyz:  63.83   2.27  16.28  60.01   2.27  12.68  63.83   5.75  35.88
   3_adp:  76.32   0.64  16.81  76.32   0.64  12.79  69.33   6.53  38.68
   3_occ:  76.32   0.64  16.81  76.32   0.64  12.79  69.33   6.53  38.68
   4_bss:  76.32   0.64  16.81  76.32   0.64  12.79  69.33   6.53  38.68
   4_xyz:  76.32   0.64  16.81  76.32   0.64  12.79  69.33   6.53  38.68
   4_adp:  72.14   1.94  15.96  72.14   1.94  12.44  65.99   6.24  35.16
   4_occ:  72.14   1.94  15.96  72.14   1.94  12.44  65.99   6.24  35.16
   5_bss:  72.14   1.94  15.96  72.14   1.94  12.44  65.99   6.24  35.16
   5_xyz:  72.14   1.94  15.96  72.14   1.94  12.44  65.99   6.24  35.16
   5_adp:  80.46   0.41  16.44  80.46   0.41  12.47  68.68   6.15  38.09
   5_occ:  80.46   0.41  16.44  80.46   0.41  12.47  68.68   6.15  38.09
   5_bss:  80.45   0.40  16.43  80.45   0.40  12.45  68.66   6.14  38.07
------------------------------------------------------------------------
 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:    0.497    0.002    0.066
   1_adp:    0.497    0.002    0.066
   1_occ:    0.497    0.002    0.066
   2_bss:    0.497    0.002    0.066
   2_xyz:    0.686    0.003    0.069
   2_adp:    0.686    0.003    0.069
   2_occ:    0.686    0.003    0.069
   3_bss:    0.686    0.003    0.069
   3_xyz:    0.898    0.003    0.081
   3_adp:    0.898    0.003    0.081
   3_occ:    0.898    0.003    0.081
   4_bss:    0.898    0.003    0.081
   4_xyz:    0.956    0.002    0.084
   4_adp:    0.956    0.002    0.084
   4_occ:    0.956    0.002    0.084
   5_bss:    0.956    0.002    0.084
   5_xyz:    1.004    0.003    0.085
   5_adp:    1.004    0.003    0.085
   5_occ:    1.004    0.003    0.085
   5_bss:    1.004    0.003    0.085
------------------------------------------------------------------------

CPU time actual refinement: 256.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/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_665/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_665/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 256.25 
  Macro-tasks:
    bulk solvent and scale       = 30.11  
    individual site refinement   = 102.18 
    weights calculation          = 24.23  
    collect and process          = 5.33   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 161.93 
  Micro-tasks:
    mask                            = 0.01   
    f_calc                          = 81.26  
    alpha_beta                      = 6.52   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 88.62  
    fmodel                         = 5.48   
    r_factors                      = 0.13   
    phase_errors                   = 8.94   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 192.23 
NUMBER OF MASK CALCS=  1
Time per interpreted Python bytecode instruction: 3.715 micro seconds
Total CPU time: 4.46 minutes
from_scatterers_fft:    629 calls, 80.98 s
gradients_fft:          574 calls, 77.54 s

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

# Date 2008-01-16 Time 05:21:16 PST -0800 (1200489676.80 s)
Start R-work = 0.1569, R-free = 0.1569 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1720 (no bulk solvent and anisotropic scale)

Start R-work = 0.1313, R-free = 0.1309
Final R-work = 0.1080, R-free = 0.1540