# Date 2008-01-16 Time 05:18:16 PST -0800 (1200489496.28 s)
#phil __OFF__

Command line arguments: "../676.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17484
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 676

-------------------------------------------------------------------------------
  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, 47.1647, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0004

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, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2795 [2093/2118]  1884   209  10.0%
  bin  2:  4.2795 -  3.4099 [2024/2042]  1822   202  10.0%
  bin  3:  3.4099 -  2.9828 [1983/2002]  1784   199  10.0%
  bin  4:  2.9828 -  2.7118 [1956/1986]  1761   195  10.0%
  bin  5:  2.7118 -  2.5184 [1960/1979]  1764   196  10.0%
  bin  6:  2.5184 -  2.3705 [1949/1974]  1751   198  10.2%
  bin  7:  2.3705 -  2.2522 [1944/1972]  1755   189   9.7%
  bin  8:  2.2522 -  2.1545 [1941/1977]  1744   197  10.1%
  bin  9:  2.1545 -  2.0718 [1902/1944]  1711   191  10.0%
  bin 10:  2.0718 -  2.0004 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/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: 0.14 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: 7
        2.42 -     3.04: 2202
        3.04 -     3.66: 4619
        3.66 -     4.28: 9035
        4.28 -     4.90: 12349
  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
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.209 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28207 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_676/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 47.16465 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= 0.1953   r_free= 0.1852   ksol= 0.00   Bsol= 0.00   scale= 1.011    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.566820                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.2411 0.2404      6.2214       6.179|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.1502 0.1372      5.9494      5.9003|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.1539 0.1475      5.8114       5.857|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.1736 0.1590      5.7475      5.6582|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.1829 0.1490      5.5885      5.4357|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.1890 0.1795      5.5339      5.5435|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.1925 0.1676      5.5105      5.3855|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.1942 0.1869      5.4746      5.4695|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.1941 0.1845      5.4068      5.3844|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.2029 0.2014      5.4253       5.338|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.1931 0.1784      5.3427      5.2812|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.2035 0.1816      5.3339      5.3689|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.2055 0.2004      5.2513        5.23|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.2050 0.1728      5.2159      5.0276|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7727  1370   153  0.82  23.15   0.88     0.82      33716.46|
|  2:  4.7727 -  3.8087  1303   145  0.91  14.62   1.00     0.95      20934.73|
|  3:  3.8087 -  3.3333  1280   142  0.93  12.34   1.02     1.01      12973.31|
|  4:  3.3333 -  3.0313  1281   140  0.92  13.43   1.03     1.02      10266.81|
|  5:  3.0313 -  2.8155  1257   142  0.90  15.68   1.04     1.01       8459.27|
|  6:  2.8155 -  2.6505  1273   140  0.90  16.47   1.05     1.02       7487.96|
|  7:  2.6505 -  2.5184  1251   139  0.90  16.05   1.06     1.03       6719.74|
|  8:  2.5184 -  2.4092  1254   140  0.90  16.41   1.07     1.05       6443.90|
|  9:  2.4092 -  2.3168  1240   140  0.90  16.96   1.09     1.06       5967.50|
| 10:  2.3168 -  2.2372  1236   137  0.89  17.45   1.11     1.07       5707.33|
| 11:  2.2372 -  2.1674  1254   137  0.89  17.23   1.11     1.10       5354.73|
| 12:  2.1674 -  2.1056  1236   138  0.90  16.61   1.12     1.12       4860.44|
| 13:  2.1056 -  2.0503  1229   134  0.90  16.46   1.12     1.13       4056.36|
| 14:  2.0503 -  2.0004  1166   132  0.91  15.79   1.11     1.13       3082.68|
|alpha:            min =        0.82 max =            1.13 mean =         1.03|
|beta:             min =     3082.68 max =        33716.46 mean =      9962.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.86 mean =        16.36|
|phase err.(test): min =        0.00 max =           89.84 mean =        16.11|
|-----------------------------------------------------------------------------|

============================== 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 = 2.526583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.412   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286217              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.294   (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:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      186 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2796 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4661 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4374 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5597 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6752 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.131 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    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= 0.1953   r_free= 0.1852   ksol= 0.00   Bsol= 0.00   scale= 1.011    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.566820                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1750   r_free= 0.1633   ksol= 0.32   Bsol= 50.48   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.56,-1.66,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.517618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.392418              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.155998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.319   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1750      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1467          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9089 = 2.39 * 0.50 * 5.6422 + 1.00 * 0.1596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3404 = 2.39 * 0.50 * 5.2427 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1467      final r-factor (free) = 0.1457          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8265 = 0.16 * 1.00 * 5.2427 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0858 = 0.16 * 1.00 * 5.1430 + 1.00 * 0.2835                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.29   16.09    None  None   None       |
|    all(noH): 2823   0      0.00    76.29   16.09    None  None   None       |
|    Sol.    : 438    0      4.81    62.44   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    76.29   12.28    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 -   7.629:  285   |   5:    38.143 -  45.772:  115        |
|      1:     7.629 -  15.257: 1686   |   6:    45.772 -  53.400:   80        |
|      2:    15.257 -  22.886:  358   |   7:    53.400 -  61.029:   40        |
|      3:    22.886 -  30.514:  144   |   8:    61.029 -  68.657:    4        |
|      4:    30.514 -  38.143:  110   |   9:    68.657 -  76.286:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1457             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1450             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1450   ksol= 0.32   Bsol= 50.48   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.20,-1.56,-1.66,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.138287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1449   ksol= 0.33   Bsol= 50.48   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.27,-1.55,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.138310                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.108603              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.253  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.616584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.427   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1449      final r-factor (free) = 0.1463          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 2.9195 = 1.11 * 0.50 * 5.1423 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 2.9020 = 1.11 * 0.50 * 5.1390 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1463      final r-factor (free) = 0.1495          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7782 = 1.62 * 1.00 * 5.1390 + 1.00 * 0.4705                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2639 = 1.62 * 1.00 * 5.1065 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    76.31   16.96    None  None   None       |
|    all(noH): 2823   0      0.87    76.31   16.96    None  None   None       |
|    Sol.    : 438    0      6.10    70.36   39.20    None  None   None       |
|    Mac.    : 2385   0      0.87    76.31   12.87    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:     0.873 -   8.416:  615   |   5:    38.591 -  46.135:  110        |
|      1:     8.416 -  15.960: 1333   |   6:    46.135 -  53.679:   86        |
|      2:    15.960 -  23.504:  354   |   7:    53.679 -  61.222:   70        |
|      3:    23.504 -  31.047:  120   |   8:    61.222 -  68.766:   32        |
|      4:    31.047 -  38.591:   99   |   9:    68.766 -  76.310:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1495             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1496             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1496   ksol= 0.33   Bsol= 50.48   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.27,-1.55,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122110                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1494   ksol= 0.32   Bsol= 50.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.09,-1.28,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.009169              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.184  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.077788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1494      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1849 = 2.01 * 0.50 * 5.1081 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1873 = 2.01 * 0.50 * 5.1015 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7101 = 3.08 * 1.00 * 5.1015 + 1.00 * 0.0088                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7097 = 3.08 * 1.00 * 5.1010 + 1.00 * 0.0098                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.72   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    90.72   16.97    None  None   None       |
|    Sol.    : 438    0      6.14    80.75   39.72    None  None   None       |
|    Mac.    : 2385   0      0.00    90.72   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:     0.000 -   9.072:  849   |   5:    45.362 -  54.434:  103        |
|      1:     9.072 -  18.145: 1257   |   6:    54.434 -  63.507:   71        |
|      2:    18.145 -  27.217:  254   |   7:    63.507 -  72.579:   28        |
|      3:    27.217 -  36.289:  128   |   8:    72.579 -  81.651:    6        |
|      4:    36.289 -  45.362:  123   |   9:    81.651 -  90.724:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1529             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1529             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1529   ksol= 0.32   Bsol= 50.56   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.09,-1.28,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1529   ksol= 0.32   Bsol= 50.92   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.80,-0.95,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106577                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.814477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.818  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.102391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.292  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6924 = 1.81 * 0.50 * 5.1033 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6927 = 1.81 * 0.50 * 5.1103 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5331 = 0.10 * 1.00 * 5.1103 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5318 = 0.10 * 1.00 * 5.1320 + 1.00 * 0.0063                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    78.07   15.84    None  None   None       |
|    all(noH): 2823   0      1.86    78.07   15.84    None  None   None       |
|    Sol.    : 438    0      5.79    65.43   35.08    None  None   None       |
|    Mac.    : 2385   0      1.86    78.07   12.30    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:     1.856 -   9.477:  973   |   5:    39.963 -  47.585:  105        |
|      1:     9.477 -  17.099: 1110   |   6:    47.585 -  55.207:   64        |
|      2:    17.099 -  24.720:  268   |   7:    55.207 -  62.828:   15        |
|      3:    24.720 -  32.342:  129   |   8:    62.828 -  70.450:    6        |
|      4:    32.342 -  39.963:  151   |   9:    70.450 -  78.071:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1534             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1534             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1534   ksol= 0.32   Bsol= 50.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.80,-0.95,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126186                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1535   ksol= 0.33   Bsol= 50.92   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.80,-0.88,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.898828              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.661  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.169468              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.589  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9288 = 1.90 * 0.50 * 5.1320 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9207 = 1.90 * 0.50 * 5.1199 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8740 = 0.17 * 1.00 * 5.1199 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8737 = 0.17 * 1.00 * 5.1150 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.32    77.06   15.81    None  None   None       |
|    all(noH): 2823   0      1.32    77.06   15.81    None  None   None       |
|    Sol.    : 438    0      5.76    64.10   35.55    None  None   None       |
|    Mac.    : 2385   0      1.32    77.06   12.18    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:     1.320 -   8.893:  848   |   5:    39.188 -  46.762:  116        |
|      1:     8.893 -  16.467: 1196   |   6:    46.762 -  54.336:   73        |
|      2:    16.467 -  24.041:  291   |   7:    54.336 -  61.910:   22        |
|      3:    24.041 -  31.615:  135   |   8:    61.910 -  69.483:    6        |
|      4:    31.615 -  39.188:  133   |   9:    69.483 -  77.057:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1534             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1534             target_work(ml) = 5.117         |
| 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= 0.1089   r_free= 0.1534   ksol= 0.33   Bsol= 50.92   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.80,-0.88,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116624                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.1021 0.1280      5.4041      5.5128|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.0878 0.1134      5.4547      5.6493|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.1041 0.1489      5.4709      5.8591|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.1184 0.1467      5.4358      5.5654|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.1284 0.1724      5.3102      5.5222|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.1163 0.1721      5.1851      5.4136|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.1214 0.1642      5.1318      5.3631|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.1105 0.1712      5.0412      5.3451|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.1113 0.1618      4.9942      5.2118|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.1087 0.1763      4.9477      5.2327|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.1106 0.1653      4.9069      5.1887|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.1077 0.1619      4.8561      5.1935|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.1044 0.1622       4.758      5.0414|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.1010 0.1709      4.6318      4.9212|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7727  1370   153  0.94   9.40   0.98     0.95       7353.28|
|  2:  4.7727 -  3.8087  1303   145  0.95   8.01   1.01     0.99       9166.24|
|  3:  3.8087 -  3.3333  1280   142  0.94  10.88   1.01     1.00      10220.68|
|  4:  3.3333 -  3.0313  1281   140  0.92  13.00   1.00     0.98       9842.74|
|  5:  3.0313 -  2.8155  1257   142  0.91  15.14   0.98     0.95       7861.93|
|  6:  2.8155 -  2.6505  1273   140  0.91  15.06   0.98     0.95       6596.39|
|  7:  2.6505 -  2.5184  1251   139  0.91  14.89   0.98     0.96       5717.28|
|  8:  2.5184 -  2.4092  1254   140  0.92  13.82   0.99     0.97       4918.84|
|  9:  2.4092 -  2.3168  1240   140  0.92  14.59   1.00     0.96       4616.13|
| 10:  2.3168 -  2.2372  1236   137  0.91  14.82   0.99     0.95       4162.15|
| 11:  2.2372 -  2.1674  1254   137  0.91  15.28   0.99     0.96       4059.53|
| 12:  2.1674 -  2.1056  1236   138  0.92  14.43   1.00     0.98       3708.88|
| 13:  2.1056 -  2.0503  1229   134  0.92  14.57   0.99     0.99       3126.50|
| 14:  2.0503 -  2.0004  1166   132  0.92  13.79   0.97     0.93       2329.11|
|alpha:            min =        0.93 max =            1.00 mean =         0.97|
|beta:             min =     2329.11 max =        10220.68 mean =      6035.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.35|
|phase err.(test): min =        0.00 max =           89.48 mean =        12.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1534   ksol= 0.33   Bsol= 50.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.64,-0.70,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1534   ksol= 0.33   Bsol= 50.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-1.64,-0.70,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116656                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7727 0.99   1370  153 0.1021 0.1281      5.4046      5.5136|
|  2:  4.7727 -  3.8087 0.99   1303  145 0.0878 0.1133      5.4549      5.6491|
|  3:  3.8087 -  3.3333 0.99   1280  142 0.1041 0.1489      5.4709      5.8593|
|  4:  3.3333 -  3.0313 0.99   1281  140 0.1184 0.1467      5.4358      5.5654|
|  5:  3.0313 -  2.8155 0.99   1257  142 0.1284 0.1724      5.3102       5.522|
|  6:  2.8155 -  2.6505 0.99   1273  140 0.1163 0.1720      5.1851      5.4134|
|  7:  2.6505 -  2.5184 0.99   1251  139 0.1214 0.1642      5.1318      5.3632|
|  8:  2.5184 -  2.4092 0.98   1254  140 0.1105 0.1712      5.0412       5.345|
|  9:  2.4092 -  2.3168 0.98   1240  140 0.1113 0.1618      4.9942      5.2117|
| 10:  2.3168 -  2.2372 0.99   1236  137 0.1087 0.1764      4.9478      5.2329|
| 11:  2.2372 -  2.1674 0.98   1254  137 0.1106 0.1653      4.9069      5.1886|
| 12:  2.1674 -  2.1056 0.97   1236  138 0.1076 0.1619       4.856      5.1935|
| 13:  2.1056 -  2.0503 1.00   1229  134 0.1044 0.1622      4.7579      5.0414|
| 14:  2.0503 -  2.0004 0.91   1166  132 0.1010 0.1708      4.6317      4.9209|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7727  1370   153  0.94   9.41   0.98     0.95       7362.89|
|  2:  4.7727 -  3.8087  1303   145  0.95   8.01   1.01     1.00       9172.63|
|  3:  3.8087 -  3.3333  1280   142  0.94  10.88   1.01     1.00      10221.92|
|  4:  3.3333 -  3.0313  1281   140  0.92  13.00   1.00     0.98       9841.65|
|  5:  3.0313 -  2.8155  1257   142  0.91  15.13   0.99     0.96       7859.40|
|  6:  2.8155 -  2.6505  1273   140  0.91  15.06   0.98     0.96       6594.71|
|  7:  2.6505 -  2.5184  1251   139  0.91  14.89   0.98     0.96       5716.78|
|  8:  2.5184 -  2.4092  1254   140  0.92  13.82   0.99     0.97       4918.32|
|  9:  2.4092 -  2.3168  1240   140  0.92  14.59   1.00     0.97       4616.84|
| 10:  2.3168 -  2.2372  1236   137  0.91  14.82   1.00     0.96       4162.14|
| 11:  2.2372 -  2.1674  1254   137  0.91  15.28   0.99     0.96       4059.89|
| 12:  2.1674 -  2.1056  1236   138  0.92  14.43   1.00     0.99       3708.34|
| 13:  2.1056 -  2.0503  1229   134  0.92  14.56   1.00     1.00       3125.50|
| 14:  2.0503 -  2.0004  1166   132  0.92  13.78   0.97     0.94       2328.03|
|alpha:            min =        0.94 max =            1.00 mean =         0.97|
|beta:             min =     2328.03 max =        10221.92 mean =      6036.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.36|
|phase err.(test): min =        0.00 max =           89.48 mean =        12.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    77.01   15.76    None  None   None       |
|    all(noH): 2823   0      1.27    77.01   15.76    None  None   None       |
|    Sol.    : 438    0      5.71    64.05   35.50    None  None   None       |
|    Mac.    : 2385   0      1.27    77.01   12.14    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:     1.273 -   8.847:  848   |   5:    39.142 -  46.716:  116        |
|      1:     8.847 -  16.421: 1196   |   6:    46.716 -  54.289:   73        |
|      2:    16.421 -  23.994:  291   |   7:    54.289 -  61.863:   22        |
|      3:    23.994 -  31.568:  135   |   8:    61.863 -  69.437:    6        |
|      4:    31.568 -  39.142:  133   |   9:    69.437 -  77.011:    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)= 290         
Filter by distance & map next to the model:
   mapped sites are within: 0.432 - 4.797
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 283 from: 290
   mapped sites are within: 0.706 - 4.797

peak=    6.069 closest distance to " NH2 ARG A  56 " =    2.296
peak=    5.386 closest distance to " CB  GLN A 223 " =    1.397
peak=    5.345 closest distance to " CB  ARG A 275 " =    0.940
peak=    5.210 closest distance to " O   HOH Z 126 " =    1.832
peak=    5.055 closest distance to " O   HOH Z 232 " =    2.355
peak=    5.016 closest distance to " CB  SER A  63 " =    1.177
peak=    4.888 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.667 closest distance to " C   PRO A 198 " =    1.465
peak=    4.647 closest distance to " CB  GLN A 183 " =    1.197
peak=    4.591 closest distance to " O   HOH Z 236 " =    1.895
peak=    4.527 closest distance to " CB  ASN A 148 " =    1.580
peak=    4.442 closest distance to " CB  TYR A 169 " =    0.706
peak=    4.427 closest distance to " O   HOH Z 142 " =    1.616
peak=    4.403 closest distance to " ND2 ASN A 187 " =    1.501
peak=    4.398 closest distance to " O   HOH Z  40 " =    1.704
peak=    4.388 closest distance to " CA  TYR A  30 " =    0.926
peak=    4.383 closest distance to " CG  PRO A  90 " =    1.164
peak=    4.374 closest distance to " O   HOH Z 298 " =    1.880
peak=    4.317 closest distance to " O   HOH Z 234 " =    3.746
peak=    4.299 closest distance to " CB  ARG A  79 " =    1.326
peak=    4.296 closest distance to " O   HOH Z 369 " =    2.151
peak=    4.277 closest distance to " O   HOH Z 303 " =    2.070
peak=    4.272 closest distance to " O   HOH Z  78 " =    1.689
peak=    4.256 closest distance to " O   HOH Z 250 " =    1.494
peak=    4.233 closest distance to " CB  ARG A 190 " =    1.677
peak=    4.161 closest distance to " CG  PRO A 198 " =    1.344
peak=    4.161 closest distance to " CZ  PHE A 218 " =    1.063
peak=    4.158 closest distance to " CB  LEU A 228 " =    1.055
peak=    4.127 closest distance to " O   HOH Z 427 " =    2.992
peak=    4.123 closest distance to " O   HOH Z 158 " =    3.095
peak=    4.118 closest distance to " CG  PRO A 243 " =    1.035
peak=    4.114 closest distance to " OD1 ASN A  69 " =    2.594
peak=    4.091 closest distance to " O   HOH Z  15 " =    2.129
peak=    4.081 closest distance to " O   HOH Z  61 " =    1.611
peak=    4.059 closest distance to " CB  TRP A 266 " =    0.927
peak=    4.059 closest distance to " O   HOH Z 261 " =    2.246
peak=    4.047 closest distance to " NE2 GLN A  11 " =    1.056
peak=    4.031 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.020 closest distance to " O   HOH Z 189 " =    2.336
peak=    4.018 closest distance to " CA  ASN A 215 " =    1.157
peak=    4.005 closest distance to " CG2 VAL A 257 " =    0.933
peak=    4.001 closest distance to " CB  GLU A 128 " =    1.022
peak=    3.998 closest distance to " O   HOH Z 193 " =    1.884
peak=    3.996 closest distance to " O   HOH Z 203 " =    1.739
peak=    3.985 closest distance to " O   HOH Z 346 " =    1.650
peak=    3.983 closest distance to " O   HOH Z  19 " =    2.410
peak=    3.982 closest distance to " O   HOH Z 402 " =    1.449
peak=    3.969 closest distance to " CB  SER A   3 " =    1.303
peak=    3.964 closest distance to " O   SER A  87 " =    2.188
peak=    3.964 closest distance to " O   HOH Z  66 " =    2.139
peak=    3.959 closest distance to " O   HOH Z 197 " =    3.071
peak=    3.951 closest distance to " O   HOH Z 403 " =    1.594
peak=    3.944 closest distance to " O   HOH Z 272 " =    1.871
peak=    3.925 closest distance to " O   HOH Z 368 " =    1.980
peak=    3.923 closest distance to " O   HOH Z 209 " =    2.323
peak=    3.918 closest distance to " CB  TYR A 169 " =    0.740
peak=    3.905 closest distance to " CB  ILE A 120 " =    1.216
peak=    3.890 closest distance to " O   HOH Z 423 " =    1.943
peak=    3.883 closest distance to " O   HOH Z 147 " =    1.809
peak=    3.874 closest distance to " CB  ALA A 291 " =    1.293
peak=    3.865 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.832 closest distance to " CE  LYS A  76 " =    0.900
peak=    3.827 closest distance to " CB  GLU A 277 " =    3.570
peak=    3.824 closest distance to " OG ASER A 258 " =    3.134
peak=    3.823 closest distance to " CB  ASP A 140 " =    0.821
peak=    3.817 closest distance to " O   HOH Z  43 " =    1.969
peak=    3.816 closest distance to " O   HOH Z  10 " =    1.791
peak=    3.804 closest distance to " N   ARG A 156 " =    1.367
peak=    3.781 closest distance to " CB  VAL A 202 " =    1.498
peak=    3.776 closest distance to " O   HOH Z 389 " =    1.880
peak=    3.763 closest distance to " CG1BVAL A  72 " =    1.663
peak=    3.755 closest distance to " CD  ARG A 159 " =    0.727
peak=    3.754 closest distance to " O   HOH Z 344 " =    3.163
peak=    3.750 closest distance to " CA  ARG A  36 " =    1.056
peak=    3.750 closest distance to " NH1AARG A 145 " =    1.222
peak=    3.739 closest distance to " O   TRP A 274 " =    1.897
peak=    3.734 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.732 closest distance to " O   HOH Z   1 " =    2.001
peak=    3.731 closest distance to " NH2 ARG A 156 " =    1.148
peak=    3.727 closest distance to " O   HOH Z  21 " =    1.802
peak=    3.726 closest distance to " NH2BARG A 145 " =    2.008
peak=    3.725 closest distance to " O   HOH Z  97 " =    1.945
peak=    3.714 closest distance to " CG2 ILE A 120 " =    1.124
peak=    3.684 closest distance to " O   HOH Z  97 " =    2.517
peak=    3.684 closest distance to " CB  GLU A  46 " =    0.968
peak=    3.679 closest distance to " O   HOH Z 248 " =    1.669
peak=    3.678 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.642 closest distance to " O   HOH Z 128 " =    2.054
peak=    3.638 closest distance to " O   HOH Z 305 " =    3.643
peak=    3.624 closest distance to " CA  SER A  87 " =    1.013
peak=    3.619 closest distance to " CD1 ILE A 106 " =    0.870
peak=    3.610 closest distance to " CB  ALA A 114 " =    1.179
peak=    3.608 closest distance to " O   HOH Z 148 " =    3.306
peak=    3.605 closest distance to " CB  TRP A 179 " =    1.362
peak=    3.601 closest distance to " O   HOH Z 214 " =    2.103
peak=    3.594 closest distance to " CG1 ILE A  33 " =    1.272
peak=    3.590 closest distance to " CG  ARG A  66 " =    2.666
peak=    3.587 closest distance to " O   HOH Z 425 " =    2.001
peak=    3.575 closest distance to " O   HOH Z 371 " =    3.168
peak=    3.572 closest distance to " CA  THR A 221 " =    0.975
peak=    3.571 closest distance to " CB  ARG A 139 " =    0.932
peak=    3.570 closest distance to " CZ2 TRP A 179 " =    1.794
peak=    3.566 closest distance to " O   HOH Z  44 " =    1.835
peak=    3.558 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.557 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.553 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.549 closest distance to " CA  ALA A  21 " =    1.162
peak=    3.546 closest distance to " O   HOH Z 187 " =    2.297
peak=    3.540 closest distance to " CB  MET A  40 " =    0.842
peak=    3.538 closest distance to " OD2 ASP A 286 " =    2.858
peak=    3.535 closest distance to " NZ  LYS A 117 " =    3.263
peak=    3.531 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.530 closest distance to " CB  SER A  26 " =    1.643
peak=    3.529 closest distance to " O   HOH Z  54 " =    1.673
peak=    3.526 closest distance to " CA  ASP A 162 " =    1.046
peak=    3.518 closest distance to " CA  ARG A 195 " =    1.160
peak=    3.510 closest distance to " O   HOH Z 193 " =    1.641
peak=    3.495 closest distance to " NE2 GLN A  77 " =    3.253
peak=    3.490 closest distance to " CG2 ILE A  20 " =    1.417
peak=    3.485 closest distance to " O   MET A 105 " =    1.842
peak=    3.480 closest distance to " CB  ASN A 142 " =    1.092
peak=    3.478 closest distance to " O   HOH Z 172 " =    3.663
peak=    3.475 closest distance to " O   HOH Z 417 " =    3.161
peak=    3.470 closest distance to " CA  ALA A  51 " =    0.872
peak=    3.465 closest distance to " CG  GLN A  77 " =    1.948
peak=    3.465 closest distance to " O   HOH Z  66 " =    2.184
peak=    3.463 closest distance to " CA  THR A 264 " =    0.913
peak=    3.460 closest distance to " O   HOH Z 132 " =    2.636
peak=    3.459 closest distance to " O   HOH Z 383 " =    1.771
peak=    3.458 closest distance to " O   HOH Z 426 " =    1.530
peak=    3.457 closest distance to " CD  LYS A 166 " =    1.211
peak=    3.454 closest distance to " O   HOH Z 234 " =    1.855
peak=    3.448 closest distance to " O   HOH Z  50 " =    2.137
peak=    3.441 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.441 closest distance to " O   HOH Z 173 " =    1.984
peak=    3.439 closest distance to " OG1 THR A 294 " =    2.435
peak=    3.439 closest distance to " CB  MET A  47 " =    1.041
peak=    3.438 closest distance to " O   HOH Z 265 " =    2.349
peak=    3.438 closest distance to " O   HOH Z 313 " =    1.862
peak=    3.427 closest distance to " O   HOH Z 213 " =    1.741
peak=    3.426 closest distance to " O   HOH Z 403 " =    1.411
peak=    3.423 closest distance to " CG  LYS A  76 " =    0.969
peak=    3.421 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.419 closest distance to " O   ALA A 165 " =    1.499
peak=    3.419 closest distance to " O   HOH Z 368 " =    3.583
peak=    3.412 closest distance to " CA  ILE A  33 " =    1.448
peak=    3.409 closest distance to " ND2 ASN A 110 " =    1.643
peak=    3.406 closest distance to " O   HOH Z 421 " =    1.768
peak=    3.401 closest distance to " CD2 LEU A 297 " =    0.844
peak=    3.399 closest distance to " CB  SER A 212 " =    1.173
peak=    3.397 closest distance to " CG2 THR A 221 " =    1.138
peak=    3.395 closest distance to " CA  ALA A  84 " =    1.205
peak=    3.392 closest distance to " O   HOH Z 406 " =    1.573
peak=    3.391 closest distance to " O   HOH Z 250 " =    2.083
peak=    3.387 closest distance to " CB  GLN A 278 " =    0.855
peak=    3.376 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.368 closest distance to " O   HOH Z 185 " =    1.757
peak=    3.368 closest distance to " N   ASN A  39 " =    1.232
peak=    3.365 closest distance to " CE1 TYR A 186 " =    1.382
peak=    3.364 closest distance to " O   HOH Z 435 " =    1.919
peak=    3.358 closest distance to " CG2 THR A 220 " =    0.766
peak=    3.356 closest distance to " CB  THR A  31 " =    1.650
peak=    3.356 closest distance to " O   HOH Z 166 " =    3.903
peak=    3.355 closest distance to " CD BLYS A 290 " =    1.102
peak=    3.345 closest distance to " O   HOH Z  88 " =    3.096
peak=    3.345 closest distance to " O   HOH Z 433 " =    1.815
peak=    3.344 closest distance to " O   HOH Z 193 " =    2.048
peak=    3.340 closest distance to " CA  ASP A 191 " =    0.726
peak=    3.339 closest distance to " CA  ALA A 233 " =    1.408
peak=    3.338 closest distance to " CB  ALA A 242 " =    0.902
peak=    3.337 closest distance to " O   HOH Z  61 " =    1.479
peak=    3.332 closest distance to " O   HOH Z 407 " =    2.524
peak=    3.331 closest distance to " CB  HIS A 108 " =    0.817
peak=    3.330 closest distance to " CA  ALA A  43 " =    1.199
peak=    3.330 closest distance to " CB  SER A 141 " =    0.991
peak=    3.328 closest distance to " O  BHOH Z 338 " =    2.323
peak=    3.327 closest distance to " CB  PRO A 198 " =    1.033
peak=    3.324 closest distance to " CB  ASN A 224 " =    1.101
peak=    3.323 closest distance to " O   HOH Z  85 " =    2.281
peak=    3.311 closest distance to " O   HOH Z 219 " =    1.943
peak=    3.305 closest distance to " O   HOH Z 133 " =    2.539
peak=    3.298 closest distance to " CB  ASN A 110 " =    1.098
peak=    3.295 closest distance to " CB  ALA A   1 " =    4.797
peak=    3.290 closest distance to " O   HOH Z  88 " =    1.854
peak=    3.284 closest distance to " O   HOH Z 327 " =    1.687
peak=    3.281 closest distance to " O   HOH Z 273 " =    2.744
peak=    3.280 closest distance to " CA  ASN A 217 " =    1.251
peak=    3.277 closest distance to " CG  MET A 185 " =    1.059
peak=    3.277 closest distance to " CD  ARG A  36 " =    1.007
peak=    3.277 closest distance to " N   SER A 135 " =    1.280
peak=    3.273 closest distance to " O   THR A 251 " =    1.162
peak=    3.272 closest distance to " CA  MET A  40 " =    1.110
peak=    3.269 closest distance to " CB  SER A 216 " =    0.753
peak=    3.266 closest distance to " OD1 ASN A 217 " =    1.743
peak=    3.263 closest distance to " O   HOH Z 285 " =    2.962
peak=    3.262 closest distance to " OE1 GLU A 277 " =    2.036
peak=    3.261 closest distance to " O   HOH Z 180 " =    2.164
peak=    3.257 closest distance to " O   HOH Z 209 " =    2.451
peak=    3.249 closest distance to " O   HOH Z 171 " =    2.286
peak=    3.246 closest distance to " O   HOH Z 188 " =    2.124
peak=    3.244 closest distance to " CB  ALA A   9 " =    1.527
peak=    3.242 closest distance to " O   HOH Z 294 " =    1.484
peak=    3.241 closest distance to " CA  ASP A 140 " =    1.159
peak=    3.235 closest distance to " CA  TYR A 116 " =    1.385
peak=    3.234 closest distance to " O   HOH Z 365 " =    3.003
peak=    3.233 closest distance to " O   HOH Z  59 " =    2.145
peak=    3.230 closest distance to " O   HOH Z 295 " =    1.508
peak=    3.227 closest distance to " O   HOH Z 126 " =    1.745
peak=    3.222 closest distance to " N   VAL A 126 " =    1.407
peak=    3.222 closest distance to " N   ASN A 127 " =    1.252
peak=    3.221 closest distance to " CB  ALA A 248 " =    1.378
peak=    3.218 closest distance to " OG BSER A 164 " =    2.358
peak=    3.217 closest distance to " CG1 ILE A 120 " =    1.088
peak=    3.216 closest distance to " OE1 GLU A   2 " =    2.252
peak=    3.211 closest distance to " CB  GLN A 103 " =    0.784
peak=    3.210 closest distance to " CD  LYS A 119 " =    1.471
peak=    3.205 closest distance to " CG BARG A 275 " =    1.451
peak=    3.205 closest distance to " CA  ILE A 234 " =    0.866
peak=    3.201 closest distance to " O   HOH Z  62 " =    2.168
peak=    3.201 closest distance to " CA  MET A 105 " =    0.979
peak=    3.201 closest distance to " O   HOH Z  30 " =    2.261
peak=    3.199 closest distance to " CB  ALA A 291 " =    0.801
peak=    3.193 closest distance to " O   HOH Z 201 " =    3.203
peak=    3.193 closest distance to " CB  TYR A 116 " =    0.788
peak=    3.193 closest distance to " O   HOH Z  44 " =    3.289
peak=    3.191 closest distance to " CD  ARG A 219 " =    1.130
peak=    3.191 closest distance to " O   HOH Z 380 " =    1.882
peak=    3.189 closest distance to " CD1AILE A 234 " =    0.953
peak=    3.187 closest distance to " CA  ALA A 248 " =    1.213
peak=    3.186 closest distance to " O   HOH Z 281 " =    4.058
peak=    3.183 closest distance to " O   HOH Z 258 " =    1.912
peak=    3.183 closest distance to " O   HOH Z 250 " =    1.462
peak=    3.176 closest distance to " O   HOH Z 345 " =    3.249
peak=    3.174 closest distance to " NH2AARG A 190 " =    1.200
peak=    3.172 closest distance to " CG2 VAL A 197 " =    1.061
peak=    3.169 closest distance to " CA  THR A 221 " =    1.446
peak=    3.166 closest distance to " O   HOH Z 337 " =    3.618
peak=    3.165 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.164 closest distance to " OG  SER A 206 " =    1.322
peak=    3.162 closest distance to " O   HOH Z 359 " =    1.513
peak=    3.159 closest distance to " O   HOH Z 163 " =    1.770
peak=    3.159 closest distance to " CE BLYS A 290 " =    1.102
peak=    3.155 closest distance to " O   THR A 220 " =    1.265
peak=    3.151 closest distance to " O   HOH Z 411 " =    1.738
peak=    3.150 closest distance to " O   HOH Z 437 " =    1.490
peak=    3.149 closest distance to " ND1 HIS A  81 " =    1.676
peak=    3.144 closest distance to " O   HOH Z 263 " =    1.719
peak=    3.142 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.138 closest distance to " CG  GLN A  11 " =    1.473
peak=    3.137 closest distance to " CA  ASN A 176 " =    1.228
peak=    3.134 closest distance to " NH1 ARG A 138 " =    1.162
peak=    3.133 closest distance to " NZ  LYS A  76 " =    1.379
peak=    3.132 closest distance to " O   HOH Z 108 " =    2.615
peak=    3.132 closest distance to " N   PHE A 130 " =    1.314
peak=    3.130 closest distance to " N   GLY A  98 " =    1.070
peak=    3.129 closest distance to " CD  ARG A  66 " =    2.455
peak=    3.129 closest distance to " OG BSER A 134 " =    2.917
peak=    3.128 closest distance to " O   HOH Z 357 " =    1.889
peak=    3.125 closest distance to " OG1 THR A 294 " =    1.635
peak=    3.121 closest distance to " CB  SER A  62 " =    1.247
peak=    3.121 closest distance to " CD  ARG A 156 " =    1.452
peak=    3.120 closest distance to " C   TYR A 214 " =    1.409
peak=    3.118 closest distance to " O   HOH Z 411 " =    3.834
peak=    3.117 closest distance to " O   HOH Z  48 " =    1.739
peak=    3.116 closest distance to " CG  MET A 185 " =    1.002
peak=    3.111 closest distance to " CG1 ILE A 151 " =    1.003
peak=    3.109 closest distance to " CG  GLU A 277 " =    2.253
peak=    3.108 closest distance to " O   HOH Z 374 " =    2.649
peak=    3.103 closest distance to " O   HOH Z 329 " =    3.803
peak=    3.101 closest distance to " CA  ASN A 252 " =    1.930
peak=    3.099 closest distance to " O   ALA A   1 " =    1.663
peak=    3.094 closest distance to " CD1 ILE A 263 " =    1.266
peak=    3.090 closest distance to " CB  ASN A 215 " =    1.177
peak=    3.084 closest distance to " O   HOH Z 261 " =    1.538
peak=    3.083 closest distance to " CA  ALA A 158 " =    1.234
peak=    3.077 closest distance to " O   SER A 164 " =    1.162
peak=    3.073 closest distance to " O   HOH Z  49 " =    2.851
peak=    3.071 closest distance to " CG1 ILE A  49 " =    1.452
peak=    3.069 closest distance to " O   HOH Z  49 " =    2.273
peak=    3.060 closest distance to " O   HOH Z 391 " =    2.915
peak=    3.046 closest distance to " CB  ALA A 100 " =    1.132
peak=    3.026 closest distance to " O   HOH Z 417 " =    2.466
peak=    2.997 closest distance to " O   HOH Z   9 " =    2.167

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.505 - 5.267
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 188
   mapped sites are within: 0.785 - 5.267

peak=   -4.650 closest distance to " O   HOH Z 290 " =    1.036
peak=   -4.611 closest distance to " O   HOH Z 266 " =    5.022
peak=   -4.602 closest distance to " CD  GLN A  58 " =    0.926
peak=   -4.520 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.480 closest distance to " CB  PRO A 243 " =    2.651
peak=   -4.366 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.349 closest distance to " C   HIS A 108 " =    1.120
peak=   -4.239 closest distance to " SG  CYS A 254 " =    3.558
peak=   -4.178 closest distance to " CB  ALA A 161 " =    2.614
peak=   -4.125 closest distance to " CG  GLN A 223 " =    1.748
peak=   -4.061 closest distance to " CZ3 TRP A 179 " =    1.194
peak=   -4.043 closest distance to " OG  SER A  97 " =    2.247
peak=   -4.019 closest distance to " ND2 ASN A  45 " =    1.677
peak=   -3.977 closest distance to " O   VAL A  67 " =    2.827
peak=   -3.954 closest distance to " O   HOH Z  10 " =    1.526
peak=   -3.936 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.921 closest distance to " O   HOH Z 114 " =    3.179
peak=   -3.914 closest distance to " CD2 PHE A 192 " =    2.069
peak=   -3.905 closest distance to " O   HOH Z 372 " =    2.302
peak=   -3.900 closest distance to " O   HOH Z 389 " =    1.840
peak=   -3.889 closest distance to " OG BSER A 134 " =    1.196
peak=   -3.856 closest distance to " CG1 VAL A 112 " =    2.769
peak=   -3.856 closest distance to " O   HOH Z 211 " =    1.710
peak=   -3.854 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.845 closest distance to " O   HOH Z 231 " =    2.257
peak=   -3.829 closest distance to " CE2 TYR A  30 " =    2.734
peak=   -3.814 closest distance to " O   HOH Z 196 " =    1.969
peak=   -3.808 closest distance to " CG2 ILE A 263 " =    2.306
peak=   -3.780 closest distance to " O   HOH Z 185 " =    2.365
peak=   -3.772 closest distance to " CD  GLN A 223 " =    1.091
peak=   -3.742 closest distance to " CG  ASP A 132 " =    2.290
peak=   -3.736 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -3.726 closest distance to " OD1 ASP A 171 " =    1.641
peak=   -3.725 closest distance to " O   HOH Z 377 " =    2.124
peak=   -3.713 closest distance to " O   HOH Z 353 " =    2.097
peak=   -3.710 closest distance to " O   HOH Z 126 " =    1.954
peak=   -3.700 closest distance to " NH2 ARG A  79 " =    1.603
peak=   -3.680 closest distance to " CB  ASN A  39 " =    2.327
peak=   -3.666 closest distance to " CD1 LEU A 101 " =    2.394
peak=   -3.650 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.648 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.630 closest distance to " O   PRO A 163 " =    2.063
peak=   -3.628 closest distance to " CZ  TYR A 169 " =    1.736
peak=   -3.617 closest distance to " O   HOH Z 407 " =    3.123
peak=   -3.615 closest distance to " N   ALA A  43 " =    2.543
peak=   -3.611 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -3.611 closest distance to " OXT GLY A 302 " =    2.838
peak=   -3.610 closest distance to " O   HOH Z 311 " =    3.652
peak=   -3.603 closest distance to " CB  ALA A  43 " =    2.472
peak=   -3.601 closest distance to " N   SER A 212 " =    1.938
peak=   -3.600 closest distance to " NH2AARG A 275 " =    5.267
peak=   -3.572 closest distance to " CD2 PHE A  61 " =    2.490
peak=   -3.566 closest distance to " CB  ALA A 248 " =    2.361
peak=   -3.558 closest distance to " CZ3 TRP A 274 " =    1.028
peak=   -3.557 closest distance to " O   HOH Z 198 " =    2.014
peak=   -3.543 closest distance to " ND2 ASN A  45 " =    1.114
peak=   -3.533 closest distance to " CD  ARG A 139 " =    1.529
peak=   -3.532 closest distance to " CA  GLY A 241 " =    3.078
peak=   -3.532 closest distance to " O   HOH Z 435 " =    2.816
peak=   -3.518 closest distance to " CG  ARG A  66 " =    2.447
peak=   -3.507 closest distance to " C   ALA A 158 " =    1.289
peak=   -3.507 closest distance to " CG  ARG A 269 " =    2.345
peak=   -3.503 closest distance to " O   HOH Z 313 " =    1.951
peak=   -3.503 closest distance to " CE  MET A 105 " =    2.304
peak=   -3.498 closest distance to " CG  PHE A 283 " =    2.619
peak=   -3.498 closest distance to " CD  ARG A 195 " =    5.165
peak=   -3.497 closest distance to " O   HOH Z  73 " =    2.288
peak=   -3.485 closest distance to " CG  GLU A 277 " =    1.158
peak=   -3.481 closest distance to " OD1 ASN A 148 " =    1.513
peak=   -3.477 closest distance to " CB  ALA A 291 " =    2.346
peak=   -3.476 closest distance to " CD1 LEU A 297 " =    2.333
peak=   -3.472 closest distance to " CD1 LEU A 101 " =    2.971
peak=   -3.468 closest distance to " C   ASP A 231 " =    2.646
peak=   -3.468 closest distance to " CG  GLU A 152 " =    0.791
peak=   -3.455 closest distance to " SG ACYS A 201 " =    1.945
peak=   -3.453 closest distance to " O   HOH Z  43 " =    1.636
peak=   -3.451 closest distance to " C   MET A 188 " =    1.370
peak=   -3.449 closest distance to " NE2 GLN A 194 " =    1.776
peak=   -3.445 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.437 closest distance to " CB  ASP A 286 " =    2.074
peak=   -3.431 closest distance to " NE2 GLN A 278 " =    1.790
peak=   -3.428 closest distance to " O   HOH Z 394 " =    1.468
peak=   -3.425 closest distance to " O   HOH Z  52 " =    1.351
peak=   -3.425 closest distance to " O   HOH Z 198 " =    1.228
peak=   -3.425 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.422 closest distance to " CG1 VAL A 250 " =    2.719
peak=   -3.421 closest distance to " CB  ALA A 248 " =    2.196
peak=   -3.420 closest distance to " NH1 ARG A 195 " =    2.525
peak=   -3.419 closest distance to " O   HOH Z 377 " =    1.674
peak=   -3.406 closest distance to " N   ALA A 226 " =    2.063
peak=   -3.399 closest distance to " OD2 ASP A  50 " =    2.238
peak=   -3.398 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.384 closest distance to " CE2 PHE A 218 " =    2.458
peak=   -3.380 closest distance to " CZ  PHE A  59 " =    1.575
peak=   -3.377 closest distance to " CZ  PHE A 155 " =    1.192
peak=   -3.357 closest distance to " C   LEU A 143 " =    1.036
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    2.372
peak=   -3.345 closest distance to " CA  ASP A 298 " =    1.106
peak=   -3.343 closest distance to " CD1 LEU A 228 " =    2.274
peak=   -3.343 closest distance to " O   HOH Z 166 " =    1.918
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.584
peak=   -3.338 closest distance to " O   HOH Z  76 " =    1.944
peak=   -3.336 closest distance to " O   HOH Z  11 " =    1.744
peak=   -3.330 closest distance to " O   HOH Z  44 " =    2.206
peak=   -3.328 closest distance to " C   ASN A 285 " =    2.409
peak=   -3.325 closest distance to " O   HOH Z 292 " =    4.559
peak=   -3.323 closest distance to " O   HOH Z 174 " =    4.308
peak=   -3.318 closest distance to " CD1 ILE A 239 " =    2.112
peak=   -3.317 closest distance to " OG BSER A 134 " =    1.852
peak=   -3.316 closest distance to " CG1 VAL A  67 " =    3.210
peak=   -3.315 closest distance to " O   HOH Z  60 " =    2.276
peak=   -3.310 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.308 closest distance to " O   HOH Z  38 " =    1.525
peak=   -3.305 closest distance to " O   HOH Z 322 " =    1.600
peak=   -3.304 closest distance to " N   ALA A 248 " =    1.720
peak=   -3.296 closest distance to " O   ALA A 161 " =    1.640
peak=   -3.294 closest distance to " OG  SER A  62 " =    1.555
peak=   -3.292 closest distance to " ND2 ASN A 187 " =    1.285
peak=   -3.292 closest distance to " O   GLN A 240 " =    2.080
peak=   -3.288 closest distance to " O   HOH Z 193 " =    2.012
peak=   -3.276 closest distance to " O   HOH Z 298 " =    1.286
peak=   -3.262 closest distance to " CG1 VAL A 197 " =    2.275
peak=   -3.260 closest distance to " CA  GLY A 203 " =    2.312
peak=   -3.257 closest distance to " O   HOH Z 253 " =    3.902
peak=   -3.256 closest distance to " OD1 ASN A 187 " =    1.660
peak=   -3.254 closest distance to " O   ALA A  10 " =    1.700
peak=   -3.253 closest distance to " O   HOH Z 351 " =    1.411
peak=   -3.250 closest distance to " O   HOH Z  13 " =    1.481
peak=   -3.247 closest distance to " OG BSER A 210 " =    2.305
peak=   -3.241 closest distance to " ND2 ASN A 249 " =    2.326
peak=   -3.232 closest distance to " O   ARG A 145 " =    1.628
peak=   -3.231 closest distance to " CB  LEU A  83 " =    2.382
peak=   -3.227 closest distance to " O   HOH Z   6 " =    1.417
peak=   -3.227 closest distance to " O   HOH Z 165 " =    1.894
peak=   -3.226 closest distance to " O   HOH Z 317 " =    1.534
peak=   -3.225 closest distance to " CG2 THR A 221 " =    2.196
peak=   -3.224 closest distance to " CG  TRP A 266 " =    1.964
peak=   -3.214 closest distance to " O   HOH Z 134 " =    2.894
peak=   -3.212 closest distance to " O   GLY A 211 " =    1.382
peak=   -3.209 closest distance to " O   HOH Z 244 " =    2.030
peak=   -3.209 closest distance to " O   HOH Z 262 " =    2.911
peak=   -3.209 closest distance to " OD2 ASP A 191 " =    1.479
peak=   -3.203 closest distance to " O   SER A  95 " =    1.591
peak=   -3.198 closest distance to " O   LYS A 117 " =    1.714
peak=   -3.194 closest distance to " CE1 TYR A 247 " =    2.747
peak=   -3.193 closest distance to " CD  GLN A  88 " =    0.985
peak=   -3.187 closest distance to " N   ALA A 100 " =    2.149
peak=   -3.187 closest distance to " CG1AVAL A  41 " =    2.919
peak=   -3.185 closest distance to " OG  SER A 206 " =    1.737
peak=   -3.183 closest distance to " CG  PRO A 163 " =    2.597
peak=   -3.183 closest distance to " O   HOH Z  51 " =    1.368
peak=   -3.179 closest distance to " N   PHE A  59 " =    2.123
peak=   -3.178 closest distance to " CD2 LEU A 300 " =    2.914
peak=   -3.176 closest distance to " O   HOH Z 426 " =    1.573
peak=   -3.162 closest distance to " O   LEU A 167 " =    1.449
peak=   -3.156 closest distance to " CA  GLY A 241 " =    2.795
peak=   -3.154 closest distance to " CG  GLN A  11 " =    1.457
peak=   -3.153 closest distance to " NE2 GLN A  88 " =    1.830
peak=   -3.149 closest distance to " CD2 LEU A 237 " =    2.746
peak=   -3.149 closest distance to " O   HOH Z 417 " =    2.546
peak=   -3.147 closest distance to " O   HOH Z 123 " =    2.350
peak=   -3.138 closest distance to " OE2 GLU A   2 " =    1.653
peak=   -3.136 closest distance to " O   HOH Z  37 " =    1.793
peak=   -3.136 closest distance to " O   HOH Z 166 " =    1.587
peak=   -3.135 closest distance to " CE  LYS A  76 " =    2.760
peak=   -3.129 closest distance to " O   HOH Z 317 " =    2.395
peak=   -3.122 closest distance to " O   HOH Z  41 " =    2.468
peak=   -3.115 closest distance to " O   HOH Z 421 " =    3.121
peak=   -3.113 closest distance to " CE3 TRP A 150 " =    2.235
peak=   -3.112 closest distance to " N   GLY A  23 " =    2.216
peak=   -3.105 closest distance to " O   HOH Z 414 " =    1.561
peak=   -3.102 closest distance to " CG1 VAL A 125 " =    1.988
peak=   -3.097 closest distance to " O   HOH Z  77 " =    2.076
peak=   -3.096 closest distance to " O   PHE A 218 " =    1.612
peak=   -3.094 closest distance to " CG  LEU A  83 " =    1.846
peak=   -3.090 closest distance to " O   PRO A 198 " =    1.941
peak=   -3.084 closest distance to " O   HOH Z 298 " =    2.494
peak=   -3.078 closest distance to " CB  TYR A  15 " =    2.188
peak=   -3.075 closest distance to " O   LYS A 289 " =    2.856
peak=   -3.067 closest distance to " CB  PHE A 208 " =    2.275
peak=   -3.060 closest distance to " O   HOH Z 323 " =    1.361
peak=   -3.057 closest distance to " O   HOH Z 234 " =    4.127
peak=   -3.053 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.052 closest distance to " N   ASP A 171 " =    2.352
peak=   -3.039 closest distance to " O   HOH Z 407 " =    3.247

================= 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    :  0.1953 0.1852   5.566820e+00   5.513562e+00
   1_bss:  0.1750 0.1633   5.517618e+00   5.455580e+00
   1_xyz:  0.1264 0.1467   5.184800e+00   5.311090e+00
   1_adp:  0.1197 0.1457   5.141022e+00   5.304741e+00
   1_occ:  0.1192 0.1450   5.138287e+00   5.302913e+00
   2_bss:  0.1193 0.1449   5.138310e+00   5.302590e+00
   2_xyz:  0.1191 0.1463   5.142498e+00   5.312406e+00
   2_adp:  0.1125 0.1495   5.122131e+00   5.338983e+00
   2_occ:  0.1124 0.1496   5.122110e+00   5.339326e+00
   3_bss:  0.1122 0.1494   5.121751e+00   5.339019e+00
   3_xyz:  0.1079 0.1517   5.105831e+00   5.349533e+00
   3_adp:  0.1073 0.1529   5.106315e+00   5.355727e+00
   3_occ:  0.1073 0.1529   5.106503e+00   5.356284e+00
   4_bss:  0.1071 0.1529   5.106577e+00   5.356326e+00
   4_xyz:  0.1081 0.1552   5.118234e+00   5.370855e+00
   4_adp:  0.1112 0.1534   5.126001e+00   5.363545e+00
   4_occ:  0.1111 0.1534   5.126186e+00   5.364197e+00
   5_bss:  0.1111 0.1535   5.126350e+00   5.364420e+00
   5_xyz:  0.1096 0.1533   5.119245e+00   5.363524e+00
   5_adp:  0.1089 0.1534   5.116646e+00   5.364399e+00
   5_occ:  0.1089 0.1534   5.116624e+00   5.364381e+00
   5_bss:  0.1089 0.1534   5.116656e+00   5.364402e+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:  0.322  50.481  -3.203  -1.562  -1.656  -0.000  -0.000  -0.000
   1_xyz:  0.322  50.481  -3.203  -1.562  -1.656  -0.000  -0.000  -0.000
   1_adp:  0.322  50.481  -3.203  -1.562  -1.656  -0.000  -0.000  -0.000
   1_occ:  0.322  50.481  -3.203  -1.562  -1.656  -0.000  -0.000  -0.000
   2_bss:  0.327  50.481  -3.095  -2.275  -1.554  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.481  -3.095  -2.275  -1.554  -0.000  -0.000  -0.000
   2_adp:  0.327  50.481  -3.095  -2.275  -1.554  -0.000  -0.000  -0.000
   2_occ:  0.327  50.481  -3.095  -2.275  -1.554  -0.000  -0.000  -0.000
   3_bss:  0.322  50.562  -2.703  -2.088  -1.283  -0.000  -0.000  -0.000
   3_xyz:  0.322  50.562  -2.703  -2.088  -1.283  -0.000  -0.000  -0.000
   3_adp:  0.322  50.562  -2.703  -2.088  -1.283  -0.000  -0.000  -0.000
   3_occ:  0.322  50.562  -2.703  -2.088  -1.283  -0.000  -0.000  -0.000
   4_bss:  0.323  50.916  -2.335  -1.803  -0.952  -0.000  -0.000  -0.000
   4_xyz:  0.323  50.916  -2.335  -1.803  -0.952  -0.000  -0.000  -0.000
   4_adp:  0.323  50.916  -2.335  -1.803  -0.952  -0.000  -0.000  -0.000
   4_occ:  0.323  50.916  -2.335  -1.803  -0.952  -0.000  -0.000  -0.000
   5_bss:  0.328  50.916  -2.305  -1.797  -0.879  -0.000  -0.000  -0.000
   5_xyz:  0.328  50.916  -2.305  -1.797  -0.879  -0.000  -0.000  -0.000
   5_adp:  0.328  50.916  -2.305  -1.797  -0.879  -0.000  -0.000  -0.000
   5_occ:  0.328  50.916  -2.305  -1.797  -0.879  -0.000  -0.000  -0.000
   5_bss:  0.328  50.869  -2.120  -1.639  -0.698  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  16.337 0.8982  1.0341     9963.101
   1_bss:  14.863 0.9101  0.9688     7124.291
   1_xyz:  12.346 0.9285  0.9805     5462.457
   1_adp:  12.280 0.9287  0.9759     5393.663
   1_occ:  12.250 0.9289  0.9757     5360.675
   2_bss:  12.226 0.9290  0.9703     5364.654
   2_xyz:  12.338 0.9285  0.9684     5491.115
   2_adp:  12.898 0.9241  0.9617     5669.266
   2_occ:  12.903 0.9240  0.9616     5672.489
   3_bss:  12.894 0.9241  0.9717     5667.677
   3_xyz:  13.083 0.9225  0.9715     5834.892
   3_adp:  13.225 0.9214  0.9634     5885.181
   3_occ:  13.232 0.9213  0.9633     5891.696
   4_bss:  13.233 0.9213  0.9750     5893.803
   4_xyz:  13.485 0.9195  0.9739     6072.594
   4_adp:  13.287 0.9211  0.9697     6023.141
   4_occ:  13.298 0.9210  0.9696     6030.863
   5_bss:  13.303 0.9209  0.9710     6035.858
   5_xyz:  13.284 0.9210  0.9714     6032.299
   5_adp:  13.310 0.9208  0.9664     6035.588
   5_occ:  13.313 0.9208  0.9663     6035.418
   5_bss:  13.313 0.9208  0.9709     6036.171
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.5965e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.5965e-01
   1_xyz:   1.056  0.009  0.078 15.406  0.004  4.117   6.9045e-02
   1_adp:   1.056  0.009  0.078 15.406  0.004  4.117   6.9045e-02
   1_occ:   1.056  0.009  0.078 15.406  0.004  4.117   6.9045e-02
   2_bss:   1.056  0.009  0.078 15.406  0.004  4.117   6.9045e-02
   2_xyz:   0.911  0.006  0.072 15.052  0.004  4.118   5.3406e-02
   2_adp:   0.911  0.006  0.072 15.052  0.004  4.118   5.3406e-02
   2_occ:   0.911  0.006  0.072 15.052  0.004  4.118   5.3406e-02
   3_bss:   0.911  0.006  0.072 15.052  0.004  4.118   5.3406e-02
   3_xyz:   1.001  0.008  0.078 15.216  0.004  4.119   6.2450e-02
   3_adp:   1.001  0.008  0.078 15.216  0.004  4.119   6.2450e-02
   3_occ:   1.001  0.008  0.078 15.216  0.004  4.119   6.2450e-02
   4_bss:   1.001  0.008  0.078 15.216  0.004  4.119   6.2450e-02
   4_xyz:   0.941  0.007  0.074 15.051  0.004  4.120   5.6496e-02
   4_adp:   0.941  0.007  0.074 15.051  0.004  4.120   5.6496e-02
   4_occ:   0.941  0.007  0.074 15.051  0.004  4.120   5.6496e-02
   5_bss:   0.941  0.007  0.074 15.051  0.004  4.120   5.6496e-02
   5_xyz:   0.976  0.007  0.077 15.088  0.004  4.121   5.9849e-02
   5_adp:   0.976  0.007  0.077 15.088  0.004  4.121   5.9849e-02
   5_occ:   0.976  0.007  0.077 15.088  0.004  4.121   5.9849e-02
   5_bss:   0.976  0.007  0.077 15.088  0.004  4.121   5.9849e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4144e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4144e-01
   1_xyz:   7.482  0.047  0.240 83.746  0.041  2.317   5.6007e-02
   1_adp:   7.482  0.047  0.240 83.746  0.041  2.317   5.6007e-02
   1_occ:   7.482  0.047  0.240 83.746  0.041  2.317   5.6007e-02
   2_bss:   7.482  0.047  0.240 83.746  0.041  2.317   5.6007e-02
   2_xyz:   6.642  0.037  0.211 84.577  0.037  2.401   3.9249e-02
   2_adp:   6.642  0.037  0.211 84.577  0.037  2.401   3.9249e-02
   2_occ:   6.642  0.037  0.211 84.577  0.037  2.401   3.9249e-02
   3_bss:   6.642  0.037  0.211 84.577  0.037  2.401   3.9249e-02
   3_xyz:   7.020  0.042  0.251 83.295  0.037  2.342   4.3407e-02
   3_adp:   7.020  0.042  0.251 83.295  0.037  2.342   4.3407e-02
   3_occ:   7.020  0.042  0.251 83.295  0.037  2.342   4.3407e-02
   4_bss:   7.020  0.042  0.251 83.295  0.037  2.342   4.3407e-02
   4_xyz:   6.640  0.043  0.233 82.666  0.035  2.389   3.6859e-02
   4_adp:   6.640  0.043  0.233 82.666  0.035  2.389   3.6859e-02
   4_occ:   6.640  0.043  0.233 82.666  0.035  2.389   3.6859e-02
   5_bss:   6.640  0.043  0.233 82.666  0.035  2.389   3.6859e-02
   5_xyz:   6.963  0.042  0.242 83.490  0.035  2.327   3.8859e-02
   5_adp:   6.963  0.042  0.242 83.490  0.035  2.327   3.8859e-02
   5_occ:   6.963  0.042  0.242 83.490  0.035  2.327   3.8859e-02
   5_bss:   6.963  0.042  0.242 83.490  0.035  2.327   3.8859e-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:  76.29   0.00  16.09  76.29   0.00  12.28  62.44   4.81  36.83
   1_occ:  76.29   0.00  16.09  76.29   0.00  12.28  62.44   4.81  36.83
   2_bss:  76.29   0.00  16.09  76.29   0.00  12.28  62.44   4.81  36.83
   2_xyz:  76.29   0.00  16.09  76.29   0.00  12.28  62.44   4.81  36.83
   2_adp:  76.31   0.87  16.96  76.31   0.87  12.87  70.36   6.10  39.20
   2_occ:  76.31   0.87  16.96  76.31   0.87  12.87  70.36   6.10  39.20
   3_bss:  76.31   0.87  16.96  76.31   0.87  12.87  70.36   6.10  39.20
   3_xyz:  76.31   0.87  16.96  76.31   0.87  12.87  70.36   6.10  39.20
   3_adp:  90.72   0.00  16.97  90.72   0.00  12.79  80.75   6.14  39.72
   3_occ:  90.72   0.00  16.97  90.72   0.00  12.79  80.75   6.14  39.72
   4_bss:  90.72   0.00  16.97  90.72   0.00  12.79  80.75   6.14  39.72
   4_xyz:  90.72   0.00  16.97  90.72   0.00  12.79  80.75   6.14  39.72
   4_adp:  78.07   1.86  15.84  78.07   1.86  12.30  65.43   5.79  35.08
   4_occ:  78.07   1.86  15.84  78.07   1.86  12.30  65.43   5.79  35.08
   5_bss:  78.07   1.86  15.84  78.07   1.86  12.30  65.43   5.79  35.08
   5_xyz:  78.07   1.86  15.84  78.07   1.86  12.30  65.43   5.79  35.08
   5_adp:  77.06   1.32  15.81  77.06   1.32  12.18  64.10   5.76  35.55
   5_occ:  77.06   1.32  15.81  77.06   1.32  12.18  64.10   5.76  35.55
   5_bss:  77.01   1.27  15.76  77.01   1.27  12.14  64.05   5.71  35.50
------------------------------------------------------------------------
 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:    0.469    0.009    0.152
   1_adp:    0.469    0.009    0.152
   1_occ:    0.469    0.009    0.152
   2_bss:    0.469    0.009    0.152
   2_xyz:    0.663    0.008    0.159
   2_adp:    0.663    0.008    0.159
   2_occ:    0.663    0.008    0.159
   3_bss:    0.663    0.008    0.159
   3_xyz:    0.760    0.013    0.171
   3_adp:    0.760    0.013    0.171
   3_occ:    0.760    0.013    0.171
   4_bss:    0.760    0.013    0.171
   4_xyz:    0.845    0.013    0.177
   4_adp:    0.845    0.013    0.177
   4_occ:    0.845    0.013    0.177
   5_bss:    0.845    0.013    0.177
   5_xyz:    0.900    0.016    0.179
   5_adp:    0.900    0.016    0.179
   5_occ:    0.900    0.016    0.179
   5_bss:    0.900    0.016    0.179
------------------------------------------------------------------------

CPU time actual refinement: 320.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/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_676/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_676/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.30 
  Macro-tasks:
    bulk solvent and scale       = 36.93  
    individual site refinement   = 129.95 
    weights calculation          = 29.74  
    collect and process          = 6.54   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 203.27 
  Micro-tasks:
    mask                            = 0.59   
    f_calc                          = 102.60 
    alpha_beta                      = 7.95   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.62 
    fmodel                         = 6.49   
    r_factors                      = 0.21   
    phase_errors                   = 11.19  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 241.10 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.592 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    631 calls, 102.21 s
gradients_fft:          576 calls,  97.50 s

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

# Date 2008-01-16 Time 05:23:49 PST -0800 (1200489829.93 s)
Start R-work = 0.1953, R-free = 0.1852 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1720 (no bulk solvent and anisotropic scale)

Start R-work = 0.1750, R-free = 0.1633
Final R-work = 0.1089, R-free = 0.1534