# Date 2008-01-16 Time 05:12:38 PST -0800 (1200489158.40 s)
#phil __OFF__

Command line arguments: "../635.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16616
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 635

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.2261, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.97282
Completeness in resolution range: 0.946603
Completeness with d_max=infinity: 0.943775

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9728

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.97282
Completeness in resolution range: 0.946603
Completeness with d_max=infinity: 0.943775

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2220 [2172/2197]  1952   220  10.1%
  bin  2:  4.2220 -  3.3634 [2086/2106]  1881   205   9.8%
  bin  3:  3.3634 -  2.9419 [2077/2096]  1869   208  10.0%
  bin  4:  2.9419 -  2.6745 [2026/2056]  1820   206  10.2%
  bin  5:  2.6745 -  2.4837 [2032/2051]  1833   199   9.8%
  bin  6:  2.4837 -  2.3379 [2013/2038]  1810   203  10.1%
  bin  7:  2.3379 -  2.2212 [2025/2053]  1820   205  10.1%
  bin  8:  2.2212 -  2.1248 [1988/2024]  1790   198  10.0%
  bin  9:  2.1248 -  2.0432 [2001/2043]  1806   195   9.7%
  bin 10:  2.0432 -  1.9728 [1169/2030]  1049   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 34
        2.42 -     3.04: 2184
        3.04 -     3.66: 4708
        3.66 -     4.28: 9035
        4.28 -     4.90: 12351
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.818 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.921 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.978 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.070 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28307 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_635/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/model_refine_001.geo

CPU time processing inputs: 8.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.22605 87.68585 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: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3923   r_free= 0.3903   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.190109                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7093 0.99   1413  156 0.3193 0.2963      6.4638      6.3701|
|  2:  4.7093 -  3.7570 0.99   1364  153 0.3135 0.3194      6.6204      6.5683|
|  3:  3.7570 -  3.2878 0.99   1323  143 0.3411 0.3200      6.5221       6.531|
|  4:  3.2878 -  2.9897 0.99   1334  152 0.3760 0.4190      6.4067      6.4837|
|  5:  2.9897 -  2.7769 0.99   1310  147 0.4167 0.3383      6.2612      6.1699|
|  6:  2.7769 -  2.6140 0.99   1310  143 0.4073 0.4415      6.1579      6.1167|
|  7:  2.6140 -  2.4837 0.99   1301  144 0.4168 0.3954      6.1455      6.0885|
|  8:  2.4837 -  2.3760 0.98   1295  147 0.4439 0.4737      6.1176      6.1517|
|  9:  2.3760 -  2.2849 0.98   1293  137 0.4442 0.4477      6.0592       6.074|
| 10:  2.2849 -  2.2063 1.00   1271  150 0.4553 0.4305      6.0423      5.9916|
| 11:  2.2063 -  2.1375 0.98   1311  142 0.4555 0.4838      5.9867      6.0375|
| 12:  2.1375 -  2.0766 0.98   1268  144 0.4612 0.4370      5.9292      5.9269|
| 13:  2.0766 -  2.0220 0.99   1279  140 0.4505 0.4484      5.8227       5.763|
| 14:  2.0220 -  1.9728 0.42    558   61 0.4848 0.5014      5.8737      5.8205|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7093  1413   156  0.80  25.63   0.85     0.83      43362.06|
|  2:  4.7093 -  3.7570  1364   153  0.80  25.93   0.94     0.90      63310.90|
|  3:  3.7570 -  3.2878  1323   143  0.74  32.32   0.97     0.90      68217.50|
|  4:  3.2878 -  2.9897  1334   152  0.68  37.42   0.95     0.86      62369.94|
|  5:  2.9897 -  2.7769  1310   147  0.62  42.22   0.94     0.81      48441.79|
|  6:  2.7769 -  2.6140  1310   143  0.60  43.97   0.95     0.77      43689.98|
|  7:  2.6140 -  2.4837  1301   144  0.57  46.48   0.96     0.74      42930.07|
|  8:  2.4837 -  2.3760  1295   147  0.54  49.04   0.95     0.72      41781.31|
|  9:  2.3760 -  2.2849  1293   137  0.53  49.75   0.97     0.73      38892.54|
| 10:  2.2849 -  2.2063  1271   150  0.53  49.73   0.98     0.74      35398.34|
| 11:  2.2063 -  2.1375  1311   142  0.51  51.31   0.97     0.76      36013.65|
| 12:  2.1375 -  2.0766  1268   144  0.48  53.46   0.98     0.73      33944.50|
| 13:  2.0766 -  2.0220  1279   140  0.45  55.97   0.97     0.70      30457.55|
| 14:  2.0220 -  1.9728   558    61  0.48  53.69   1.01     0.67      24606.82|
|alpha:            min =        0.67 max =            0.90 mean =         0.78|
|beta:             min =    24606.82 max =        68217.50 mean =     44807.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.41|
|phase err.(test): min =        0.00 max =           89.64 mean =        43.70|
|-----------------------------------------------------------------------------|

============================== 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 = 8.674742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.067   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.244663              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.724   (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:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       28 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1989 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1870 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2838 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4629 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4406 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5640 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6711 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.254 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    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: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3923   r_free= 0.3903   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.190109                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3786   r_free= 0.3812   ksol= 0.33   Bsol= 44.41   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,1.72,1.95,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.177266                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.197579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.065   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.629175              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.556   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3786      final r-factor (work) = 0.2244          |
| start r-factor (free) = 0.3812      final r-factor (free) = 0.2546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3714 = 7.20 * 0.50 * 6.1698 + 1.00 * 0.1676                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4312 = 7.20 * 0.50 * 5.9282 + 1.00 * 0.0970                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2244      final r-factor (work) = 0.2031          |
| start r-factor (free) = 0.2546      final r-factor (free) = 0.2634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7359 = 0.63 * 1.00 * 5.9282 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5681 = 0.63 * 1.00 * 5.6514 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.18   17.63    None  None   None       |
|    all(noH): 2823   0      0.00    86.18   17.63    None  None   None       |
|    Sol.    : 438    0      3.61    86.18   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    73.39   13.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.618:  731   |   5:    43.088 -  51.705:  104        |
|      1:     8.618 -  17.235: 1201   |   6:    51.705 -  60.323:   88        |
|      2:    17.235 -  25.853:  359   |   7:    60.323 -  68.940:   41        |
|      3:    25.853 -  34.470:  162   |   8:    68.940 -  77.558:   11        |
|      4:    34.470 -  43.088:  123   |   9:    77.558 -  86.176:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2031 r_free = 0.2634             target_work(ml) = 5.665         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2030 r_free = 0.2630             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2030   r_free= 0.2630   ksol= 0.33   Bsol= 44.41   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,1.72,1.95,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.663680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2001   r_free= 0.2595   ksol= 0.33   Bsol= 62.84   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.19,-0.03,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.656193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.527679              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.265   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.176887              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.202  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2001      final r-factor (work) = 0.1481          |
| start r-factor (free) = 0.2595      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0778 = 3.53 * 0.50 * 5.6585 + 1.00 * 0.0970                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8190 = 3.53 * 0.50 * 5.5319 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1481      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.1980      final r-factor (free) = 0.1849          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9908 = 0.18 * 1.00 * 5.5319 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9555 = 0.18 * 1.00 * 5.3579 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.27   16.91    None  None   None       |
|    all(noH): 2823   0      0.00    80.27   16.91    None  None   None       |
|    Sol.    : 438    0      6.16    80.27   39.31    None  None   None       |
|    Mac.    : 2385   0      0.00    71.48   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.027:  546   |   5:    40.136 -  48.163:  110        |
|      1:     8.027 -  16.055: 1398   |   6:    48.163 -  56.191:   99        |
|      2:    16.055 -  24.082:  367   |   7:    56.191 -  64.218:   37        |
|      3:    24.082 -  32.109:  137   |   8:    64.218 -  72.245:   17        |
|      4:    32.109 -  40.136:  109   |   9:    72.245 -  80.272:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1385 r_free = 0.1849             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1383 r_free = 0.1848             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1848   ksol= 0.33   Bsol= 62.84   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.19,-0.03,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.319760                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1839   ksol= 0.33   Bsol= 62.84   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.15,-0.51,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.315292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.317183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.071  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265909              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.294  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1839      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2682 = 2.32 * 0.50 * 5.3570 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1488 = 2.32 * 0.50 * 5.2571 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4056 = 0.27 * 1.00 * 5.2571 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3868 = 0.27 * 1.00 * 5.1847 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    79.41   16.83    None  None   None       |
|    all(noH): 2823   0      0.88    79.41   16.83    None  None   None       |
|    Sol.    : 438    0      2.83    79.41   39.46    None  None   None       |
|    Mac.    : 2385   0      0.88    75.05   12.67    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:     0.885 -   8.738:  735   |   5:    40.149 -  48.002:  102        |
|      1:     8.738 -  16.591: 1273   |   6:    48.002 -  55.855:   94        |
|      2:    16.591 -  24.443:  312   |   7:    55.855 -  63.708:   44        |
|      3:    24.443 -  32.296:  126   |   8:    63.708 -  71.561:   23        |
|      4:    32.296 -  40.149:  108   |   9:    71.561 -  79.414:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1608             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1609             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1609   ksol= 0.33   Bsol= 62.84   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.15,-0.51,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1608   ksol= 0.32   Bsol= 55.49   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.37,-0.58,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175596                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.166161              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.349  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.838849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6725 = 2.17 * 0.50 * 5.1840 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6470 = 2.17 * 0.50 * 5.1585 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6523 = 2.84 * 1.00 * 5.1585 + 1.00 * 0.0080                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6097 = 2.84 * 1.00 * 5.1427 + 1.00 * 0.0103                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.98   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    90.98   17.20    None  None   None       |
|    Sol.    : 438    0      2.94    83.19   41.41    None  None   None       |
|    Mac.    : 2385   0      0.00    90.98   12.75    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 -   9.098:  895   |   5:    45.488 -  54.585:   95        |
|      1:     9.098 -  18.195: 1214   |   6:    54.585 -  63.683:   81        |
|      2:    18.195 -  27.293:  246   |   7:    63.683 -  72.780:   34        |
|      3:    27.293 -  36.390:  138   |   8:    72.780 -  81.878:   19        |
|      4:    36.390 -  45.488:   98   |   9:    81.878 -  90.975:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1588             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1589             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1589   ksol= 0.32   Bsol= 55.49   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.37,-0.58,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147855                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1583   ksol= 0.32   Bsol= 57.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.28,-0.45,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.237123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.036  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707188              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.636  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8128 = 2.24 * 0.50 * 5.1432 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8087 = 2.24 * 0.50 * 5.1400 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6452 = 0.71 * 1.00 * 5.1400 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6437 = 0.71 * 1.00 * 5.1384 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.07   16.90    None  None   None       |
|    all(noH): 2823   0      0.00    93.07   16.90    None  None   None       |
|    Sol.    : 438    0      4.23    82.89   40.58    None  None   None       |
|    Mac.    : 2385   0      0.00    93.07   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.307:  977   |   5:    46.536 -  55.843:   87        |
|      1:     9.307 -  18.615: 1162   |   6:    55.843 -  65.151:   73        |
|      2:    18.615 -  27.922:  236   |   7:    65.151 -  74.458:   27        |
|      3:    27.922 -  37.229:  139   |   8:    74.458 -  83.765:   17        |
|      4:    37.229 -  46.536:  104   |   9:    83.765 -  93.072:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1572             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1572             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1572   ksol= 0.32   Bsol= 57.64   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.28,-0.45,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136747                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7093 0.99   1413  156 0.0940 0.1226      5.3481      5.5268|
|  2:  4.7093 -  3.7570 0.99   1364  153 0.0827 0.1112      5.4091      5.6001|
|  3:  3.7570 -  3.2878 0.99   1323  143 0.1045 0.1508      5.4626      5.8463|
|  4:  3.2878 -  2.9897 0.99   1334  152 0.1194 0.1677      5.4389      5.6088|
|  5:  2.9897 -  2.7769 0.99   1310  147 0.1293 0.1694      5.3151      5.5625|
|  6:  2.7769 -  2.6140 0.99   1310  143 0.1186 0.1937      5.1926      5.4905|
|  7:  2.6140 -  2.4837 0.99   1301  144 0.1276 0.1548      5.1726      5.2938|
|  8:  2.4837 -  2.3760 0.98   1295  147 0.1124 0.1553      5.0439      5.2925|
|  9:  2.3760 -  2.2849 0.98   1293  137 0.1163 0.1849      5.0242      5.3324|
| 10:  2.2849 -  2.2063 1.00   1271  150 0.1103 0.1688      4.9313      5.1952|
| 11:  2.2063 -  2.1375 0.98   1311  142 0.1088 0.1748      4.9277      5.2829|
| 12:  2.1375 -  2.0766 0.98   1268  144 0.1139 0.1694      4.8825      5.1748|
| 13:  2.0766 -  2.0220 0.99   1279  140 0.1094 0.1830      4.7796      5.0572|
| 14:  2.0220 -  1.9728 0.42    558   61 0.0946 0.1492      4.6388      4.8529|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7093  1413   156  0.94   8.60   0.97     0.94       6561.36|
|  2:  4.7093 -  3.7570  1364   153  0.96   7.63   1.01     1.00       8644.93|
|  3:  3.7570 -  3.2878  1323   143  0.93  11.21   1.02     1.02      10162.87|
|  4:  3.2878 -  2.9897  1334   152  0.92  13.96   1.01     0.98      10243.74|
|  5:  2.9897 -  2.7769  1310   147  0.90  15.67   1.00     0.98       8305.62|
|  6:  2.7769 -  2.6140  1310   143  0.90  16.14   0.98     0.95       6951.98|
|  7:  2.6140 -  2.4837  1301   144  0.91  15.55   0.99     0.95       6253.97|
|  8:  2.4837 -  2.3760  1295   147  0.91  15.12   0.99     0.96       5163.03|
|  9:  2.3760 -  2.2849  1293   137  0.91  15.37   0.99     0.96       4939.22|
| 10:  2.2849 -  2.2063  1271   150  0.91  15.22   0.99     0.96       4197.75|
| 11:  2.2063 -  2.1375  1311   142  0.90  16.00   0.97     0.93       4251.27|
| 12:  2.1375 -  2.0766  1268   144  0.90  15.97   1.00     1.00       4047.92|
| 13:  2.0766 -  2.0220  1279   140  0.90  16.46   0.98     0.97       3414.89|
| 14:  2.0220 -  1.9728   558    61  0.93  13.39   0.97     0.94       2505.54|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2505.54 max =        10243.74 mean =      6306.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.98|
|phase err.(test): min =        0.00 max =           89.42 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1571   ksol= 0.32   Bsol= 57.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.12,-0.26,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136852                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1571   ksol= 0.32   Bsol= 57.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.12,-0.26,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136852                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7093 0.99   1413  156 0.0941 0.1228      5.3492      5.5286|
|  2:  4.7093 -  3.7570 0.99   1364  153 0.0827 0.1112      5.4097         5.6|
|  3:  3.7570 -  3.2878 0.99   1323  143 0.1045 0.1508      5.4627      5.8467|
|  4:  3.2878 -  2.9897 0.99   1334  152 0.1194 0.1677       5.439      5.6088|
|  5:  2.9897 -  2.7769 0.99   1310  147 0.1293 0.1693      5.3149      5.5619|
|  6:  2.7769 -  2.6140 0.99   1310  143 0.1186 0.1936      5.1925      5.4905|
|  7:  2.6140 -  2.4837 0.99   1301  144 0.1276 0.1549      5.1727      5.2942|
|  8:  2.4837 -  2.3760 0.98   1295  147 0.1125 0.1552       5.044       5.292|
|  9:  2.3760 -  2.2849 0.98   1293  137 0.1163 0.1848      5.0241      5.3324|
| 10:  2.2849 -  2.2063 1.00   1271  150 0.1103 0.1688      4.9315      5.1954|
| 11:  2.2063 -  2.1375 0.98   1311  142 0.1088 0.1748      4.9279       5.283|
| 12:  2.1375 -  2.0766 0.98   1268  144 0.1139 0.1693      4.8824      5.1745|
| 13:  2.0766 -  2.0220 0.99   1279  140 0.1093 0.1829      4.7792      5.0562|
| 14:  2.0220 -  1.9728 0.42    558   61 0.0946 0.1491      4.6385      4.8526|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7093  1413   156  0.94   8.61   0.97     0.94       6579.43|
|  2:  4.7093 -  3.7570  1364   153  0.96   7.64   1.02     1.00       8658.47|
|  3:  3.7570 -  3.2878  1323   143  0.93  11.21   1.03     1.02      10166.10|
|  4:  3.2878 -  2.9897  1334   152  0.92  13.96   1.01     0.99      10243.86|
|  5:  2.9897 -  2.7769  1310   147  0.90  15.67   1.00     0.99       8302.86|
|  6:  2.7769 -  2.6140  1310   143  0.90  16.14   0.99     0.96       6949.68|
|  7:  2.6140 -  2.4837  1301   144  0.91  15.55   0.99     0.96       6254.20|
|  8:  2.4837 -  2.3760  1295   147  0.91  15.13   1.00     0.97       5161.86|
|  9:  2.3760 -  2.2849  1293   137  0.91  15.37   1.00     0.97       4939.75|
| 10:  2.2849 -  2.2063  1271   150  0.91  15.23   1.00     0.97       4198.85|
| 11:  2.2063 -  2.1375  1311   142  0.90  16.00   0.98     0.94       4252.77|
| 12:  2.1375 -  2.0766  1268   144  0.90  15.98   1.01     1.01       4047.96|
| 13:  2.0766 -  2.0220  1279   140  0.90  16.46   1.00     0.98       3411.73|
| 14:  2.0220 -  1.9728   558    61  0.93  13.38   0.98     0.95       2501.93|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2501.93 max =        10243.86 mean =      6308.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.98|
|phase err.(test): min =        0.00 max =           89.42 mean =        13.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.855)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.08   16.90    None  None   None       |
|    all(noH): 2823   0      0.00    93.08   16.90    None  None   None       |
|    Sol.    : 438    0      4.23    82.89   40.58    None  None   None       |
|    Mac.    : 2385   0      0.00    93.08   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.310:  977   |   5:    46.539 -  55.846:   87        |
|      1:     9.310 -  18.618: 1162   |   6:    55.846 -  65.154:   73        |
|      2:    18.618 -  27.925:  236   |   7:    65.154 -  74.461:   27        |
|      3:    27.925 -  37.232:  139   |   8:    74.461 -  83.768:   17        |
|      4:    37.232 -  46.539:  104   |   9:    83.768 -  93.075:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.573 - 4.733
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 302
   mapped sites are within: 0.700 - 4.733

peak=    6.061 closest distance to " NE2 GLN A  11 " =    1.205
peak=    5.693 closest distance to " CG  PRO A  54 " =    1.307
peak=    5.519 closest distance to " NH2 ARG A  56 " =    2.145
peak=    5.499 closest distance to " O   HOH Z 144 " =    1.860
peak=    4.972 closest distance to " O   HOH Z 126 " =    1.941
peak=    4.957 closest distance to " CG  PRO A 213 " =    1.246
peak=    4.939 closest distance to " CB  PRO A  54 " =    1.011
peak=    4.832 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.755 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.705 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.658 closest distance to " CB  GLN A 223 " =    1.474
peak=    4.554 closest distance to " O   HOH Z 423 " =    1.520
peak=    4.548 closest distance to " O   HOH Z   9 " =    1.443
peak=    4.543 closest distance to " O   HOH Z 427 " =    2.854
peak=    4.525 closest distance to " CB  ARG A 190 " =    1.673
peak=    4.483 closest distance to " CB  SER A  63 " =    1.215
peak=    4.457 closest distance to " CG  PRO A 280 " =    0.837
peak=    4.450 closest distance to " CB  ARG A  79 " =    1.463
peak=    4.424 closest distance to " ND2 ASN A 187 " =    1.554
peak=    4.421 closest distance to " O   HOH Z  78 " =    1.821
peak=    4.413 closest distance to " CB  GLN A 183 " =    1.218
peak=    4.409 closest distance to " O   HOH Z 287 " =    2.086
peak=    4.405 closest distance to " O   HOH Z 298 " =    1.910
peak=    4.387 closest distance to " CG  PRO A 198 " =    1.281
peak=    4.382 closest distance to " CB  ASN A 148 " =    1.391
peak=    4.374 closest distance to " O   HOH Z 417 " =    1.291
peak=    4.342 closest distance to " O   HOH Z  63 " =    1.457
peak=    4.336 closest distance to " C   PRO A 198 " =    1.494
peak=    4.257 closest distance to " CG  TRP A 179 " =    2.172
peak=    4.209 closest distance to " CZ  PHE A 218 " =    1.027
peak=    4.195 closest distance to " CA  TYR A  30 " =    0.931
peak=    4.189 closest distance to " CG2 VAL A 257 " =    0.840
peak=    4.181 closest distance to " O   HOH Z 133 " =    2.578
peak=    4.128 closest distance to " O   HOH Z 362 " =    2.584
peak=    4.111 closest distance to " O   HOH Z 189 " =    2.734
peak=    4.109 closest distance to " O   HOH Z 419 " =    2.275
peak=    4.097 closest distance to " OD1 ASN A  69 " =    2.604
peak=    4.095 closest distance to " CD  ARG A 159 " =    0.756
peak=    4.034 closest distance to " CD  ARG A  66 " =    2.326
peak=    4.021 closest distance to " O   HOH Z 406 " =    1.651
peak=    4.020 closest distance to " O   HOH Z 371 " =    2.017
peak=    4.018 closest distance to " O   HOH Z 158 " =    3.128
peak=    4.018 closest distance to " CD2 TRP A 179 " =    1.290
peak=    4.013 closest distance to " O   HOH Z  61 " =    1.642
peak=    4.002 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.996 closest distance to " CB  VAL A 265 " =    1.350
peak=    3.991 closest distance to " CG  PRO A 243 " =    1.068
peak=    3.982 closest distance to " O   HOH Z 261 " =    2.067
peak=    3.975 closest distance to " CB  LEU A 228 " =    1.094
peak=    3.961 closest distance to " O   HOH Z 203 " =    1.835
peak=    3.955 closest distance to " O   HOH Z   1 " =    1.923
peak=    3.950 closest distance to " O   HOH Z 380 " =    1.668
peak=    3.946 closest distance to " O   SER A  87 " =    2.131
peak=    3.931 closest distance to " CB  TRP A 266 " =    1.094
peak=    3.922 closest distance to " CE  LYS A  76 " =    0.889
peak=    3.920 closest distance to " OG BSER A 164 " =    2.300
peak=    3.912 closest distance to " OG ASER A 258 " =    3.115
peak=    3.909 closest distance to " CB  SER A 212 " =    1.175
peak=    3.898 closest distance to " NZ  LYS A 117 " =    3.168
peak=    3.879 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.876 closest distance to " CB  GLU A 128 " =    0.967
peak=    3.872 closest distance to " NH2AARG A 190 " =    2.018
peak=    3.850 closest distance to " O   HOH Z 327 " =    1.579
peak=    3.847 closest distance to " CB  VAL A 202 " =    1.640
peak=    3.834 closest distance to " O   HOH Z 272 " =    1.760
peak=    3.834 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.821 closest distance to " CG  LEU A 167 " =    1.239
peak=    3.821 closest distance to " CB  ASN A  39 " =    0.923
peak=    3.818 closest distance to " O   HOH Z 250 " =    1.491
peak=    3.813 closest distance to " O   HOH Z 405 " =    1.291
peak=    3.811 closest distance to " NH1AARG A 145 " =    1.230
peak=    3.807 closest distance to " CZ3 TRP A 266 " =    1.135
peak=    3.804 closest distance to " O   HOH Z 437 " =    1.435
peak=    3.802 closest distance to " O   HOH Z 209 " =    2.270
peak=    3.775 closest distance to " CB  GLU A 152 " =    1.302
peak=    3.765 closest distance to " CB  GLU A 277 " =    3.652
peak=    3.763 closest distance to " CA  ASN A 215 " =    1.120
peak=    3.763 closest distance to " CB  GLU A  46 " =    1.036
peak=    3.761 closest distance to " CA  ALA A 233 " =    1.053
peak=    3.749 closest distance to " O   HOH Z 234 " =    3.667
peak=    3.744 closest distance to " CA  ARG A 195 " =    1.207
peak=    3.741 closest distance to " CB  SER A   3 " =    1.335
peak=    3.739 closest distance to " O   HOH Z 172 " =    2.749
peak=    3.726 closest distance to " CB  ASN A 142 " =    0.985
peak=    3.723 closest distance to " O   HOH Z   1 " =    1.736
peak=    3.718 closest distance to " O   HOH Z  10 " =    1.756
peak=    3.717 closest distance to " O   HOH Z 346 " =    1.644
peak=    3.714 closest distance to " O   HOH Z 214 " =    2.213
peak=    3.703 closest distance to " O   HOH Z 128 " =    2.207
peak=    3.703 closest distance to " O   HOH Z 265 " =    2.131
peak=    3.689 closest distance to " O   HOH Z  68 " =    2.176
peak=    3.689 closest distance to " CB  SER A 216 " =    0.898
peak=    3.680 closest distance to " CA  SER A  87 " =    0.993
peak=    3.677 closest distance to " O   HOH Z 359 " =    1.505
peak=    3.670 closest distance to " O   HOH Z 371 " =    3.014
peak=    3.660 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.658 closest distance to " O   HOH Z   9 " =    1.873
peak=    3.649 closest distance to " CB  TYR A 169 " =    0.749
peak=    3.646 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.641 closest distance to " N   PHE A 130 " =    1.257
peak=    3.615 closest distance to " NE2 HIS A 207 " =    1.253
peak=    3.605 closest distance to " O   HOH Z 132 " =    2.544
peak=    3.602 closest distance to " CB  LYS A 117 " =    1.247
peak=    3.602 closest distance to " O   HOH Z 391 " =    2.861
peak=    3.600 closest distance to " CB  TYR A 116 " =    0.884
peak=    3.594 closest distance to " CD BLYS A 290 " =    1.138
peak=    3.587 closest distance to " O   HOH Z 126 " =    1.513
peak=    3.582 closest distance to " O   HOH Z 425 " =    2.034
peak=    3.567 closest distance to " O   HOH Z 325 " =    3.993
peak=    3.563 closest distance to " ND1 HIS A  86 " =    1.723
peak=    3.562 closest distance to " O   HOH Z 402 " =    1.418
peak=    3.560 closest distance to " CB  ASP A 124 " =    0.773
peak=    3.560 closest distance to " O   HOH Z 389 " =    1.858
peak=    3.552 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.542 closest distance to " O   HOH Z 285 " =    2.285
peak=    3.541 closest distance to " O   HOH Z  21 " =    1.780
peak=    3.539 closest distance to " O   HOH Z  44 " =    2.846
peak=    3.536 closest distance to " O   HOH Z 421 " =    2.131
peak=    3.534 closest distance to " N   GLN A 278 " =    1.307
peak=    3.531 closest distance to " O   HOH Z 426 " =    1.971
peak=    3.530 closest distance to " CB  ASN A 187 " =    1.241
peak=    3.526 closest distance to " CB  TYR A 169 " =    0.788
peak=    3.524 closest distance to " OD1BASN A 224 " =    2.333
peak=    3.511 closest distance to " CA  TYR A 116 " =    1.342
peak=    3.510 closest distance to " O   HOH Z 365 " =    2.780
peak=    3.509 closest distance to " O   HOH Z 258 " =    2.099
peak=    3.505 closest distance to " CB  ARG A 139 " =    1.050
peak=    3.502 closest distance to " O   HOH Z 116 " =    3.049
peak=    3.498 closest distance to " O   HOH Z 386 " =    3.051
peak=    3.489 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.487 closest distance to " O   HOH Z 193 " =    1.641
peak=    3.485 closest distance to " CA  GLU A  46 " =    0.922
peak=    3.476 closest distance to " CB  ASN A 110 " =    1.061
peak=    3.474 closest distance to " OE1 GLN A  11 " =    2.151
peak=    3.471 closest distance to " O   HOH Z  88 " =    3.918
peak=    3.468 closest distance to " NH2BARG A 145 " =    1.994
peak=    3.463 closest distance to " CA  ALA A 158 " =    1.182
peak=    3.459 closest distance to " CG  GLN A  11 " =    2.019
peak=    3.458 closest distance to " CD2 LEU A 297 " =    0.928
peak=    3.455 closest distance to " O   HOH Z  40 " =    2.066
peak=    3.455 closest distance to " CD1 LEU A 300 " =    1.100
peak=    3.453 closest distance to " O   HOH Z 193 " =    2.053
peak=    3.451 closest distance to " O   HOH Z 422 " =    2.689
peak=    3.442 closest distance to " CA  ASP A 124 " =    0.700
peak=    3.439 closest distance to " N   TYR A 116 " =    1.514
peak=    3.439 closest distance to " N   CYS A 260 " =    0.842
peak=    3.439 closest distance to " CA  ARG A 102 " =    1.133
peak=    3.436 closest distance to " O   HOH Z 326 " =    2.447
peak=    3.435 closest distance to " O   HOH Z 425 " =    1.289
peak=    3.434 closest distance to " O   ASN A  74 " =    1.446
peak=    3.433 closest distance to " O   HOH Z 290 " =    0.935
peak=    3.433 closest distance to " NH2AARG A 275 " =    3.614
peak=    3.432 closest distance to " CB  THR A  31 " =    1.705
peak=    3.428 closest distance to " O  BHOH Z 338 " =    2.373
peak=    3.423 closest distance to " CB  MET A  47 " =    1.170
peak=    3.422 closest distance to " N   ASN A  39 " =    1.240
peak=    3.414 closest distance to " O   HOH Z 345 " =    1.722
peak=    3.414 closest distance to " O   HOH Z 344 " =    3.120
peak=    3.411 closest distance to " NE2 GLN A  73 " =    3.804
peak=    3.410 closest distance to " CB  PRO A  90 " =    1.175
peak=    3.405 closest distance to " CA  ARG A  36 " =    1.012
peak=    3.401 closest distance to " O   HOH Z 261 " =    2.496
peak=    3.394 closest distance to " CG1 ILE A  33 " =    1.256
peak=    3.393 closest distance to " O   HOH Z 373 " =    1.475
peak=    3.393 closest distance to " CD  LYS A 166 " =    1.259
peak=    3.388 closest distance to " O   HOH Z 411 " =    3.799
peak=    3.387 closest distance to " O   TYR A 116 " =    1.335
peak=    3.387 closest distance to " O   HOH Z 305 " =    3.570
peak=    3.385 closest distance to " OG BSER A 134 " =    3.042
peak=    3.382 closest distance to " O   HOH Z  53 " =    2.527
peak=    3.380 closest distance to " O   HOH Z 368 " =    2.059
peak=    3.378 closest distance to " CB  TRP A 179 " =    1.433
peak=    3.377 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.375 closest distance to " CA  THR A 264 " =    0.879
peak=    3.374 closest distance to " O   HOH Z 116 " =    1.751
peak=    3.369 closest distance to " CG2 ILE A 120 " =    1.351
peak=    3.365 closest distance to " CD1 ILE A 263 " =    1.331
peak=    3.360 closest distance to " OG  SER A  62 " =    2.908
peak=    3.360 closest distance to " CB  MET A  40 " =    0.814
peak=    3.357 closest distance to " O   HOH Z 345 " =    3.296
peak=    3.356 closest distance to " CE1 TYR A 186 " =    1.368
peak=    3.354 closest distance to " O   HOH Z 128 " =    2.054
peak=    3.351 closest distance to " O   HOH Z 286 " =    2.275
peak=    3.346 closest distance to " NH1 ARG A 138 " =    1.116
peak=    3.345 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.340 closest distance to " CG2 ILE A  20 " =    1.543
peak=    3.337 closest distance to " O   HOH Z  59 " =    1.586
peak=    3.335 closest distance to " O   HOH Z  44 " =    1.668
peak=    3.333 closest distance to " CB  THR A 157 " =    1.128
peak=    3.330 closest distance to " CA  PHE A 283 " =    1.258
peak=    3.327 closest distance to " CA  THR A 221 " =    1.026
peak=    3.326 closest distance to " CB  ILE A 120 " =    1.391
peak=    3.324 closest distance to " O   HOH Z 109 " =    2.600
peak=    3.323 closest distance to " O   HOH Z 294 " =    1.507
peak=    3.323 closest distance to " CB  VAL A 265 " =    1.939
peak=    3.321 closest distance to " CA  ASN A 127 " =    1.097
peak=    3.316 closest distance to " CB  GLN A  88 " =    1.242
peak=    3.315 closest distance to " O   HOH Z 409 " =    2.435
peak=    3.310 closest distance to " O   HOH Z 368 " =    4.178
peak=    3.309 closest distance to " O   HOH Z  88 " =    2.855
peak=    3.305 closest distance to " O   HOH Z  28 " =    1.775
peak=    3.305 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.304 closest distance to " CA  VAL A 125 " =    1.141
peak=    3.303 closest distance to " CB  SER A 210 " =    0.727
peak=    3.299 closest distance to " O   HOH Z   2 " =    1.287
peak=    3.297 closest distance to " O   THR A 220 " =    1.283
peak=    3.295 closest distance to " O   HOH Z 369 " =    1.717
peak=    3.292 closest distance to " O   HOH Z 132 " =    3.520
peak=    3.291 closest distance to " CB  SER A  62 " =    1.098
peak=    3.291 closest distance to " O   HOH Z 340 " =    2.104
peak=    3.291 closest distance to " CB  SER A 273 " =    0.867
peak=    3.287 closest distance to " CB  ALA A   1 " =    4.733
peak=    3.287 closest distance to " O   HOH Z 188 " =    1.983
peak=    3.285 closest distance to " O   HOH Z 175 " =    2.174
peak=    3.285 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.284 closest distance to " O   HOH Z  43 " =    1.714
peak=    3.283 closest distance to " CB  ALA A 114 " =    1.432
peak=    3.273 closest distance to " CD  PRO A 243 " =    1.568
peak=    3.271 closest distance to " O   HOH Z 227 " =    1.773
peak=    3.269 closest distance to " CA  ALA A 299 " =    0.885
peak=    3.268 closest distance to " OG  SER A  22 " =    2.784
peak=    3.268 closest distance to " CA  LYS A 290 " =    1.302
peak=    3.268 closest distance to " O   HOH Z 291 " =    1.528
peak=    3.265 closest distance to " CB  ALA A  34 " =    1.064
peak=    3.261 closest distance to " O   HOH Z 336 " =    1.861
peak=    3.259 closest distance to " O   HOH Z 403 " =    1.460
peak=    3.254 closest distance to " CA  ALA A  84 " =    1.332
peak=    3.252 closest distance to " CB  GLN A  89 " =    1.423
peak=    3.250 closest distance to " CA  ILE A 234 " =    1.004
peak=    3.249 closest distance to " CA  PRO A 280 " =    1.254
peak=    3.240 closest distance to " CG1 VAL A 189 " =    2.013
peak=    3.240 closest distance to " O   HOH Z 213 " =    2.732
peak=    3.233 closest distance to " CA  MET A 105 " =    0.956
peak=    3.232 closest distance to " CB  ARG A 138 " =    0.956
peak=    3.231 closest distance to " O   HOH Z 329 " =    3.969
peak=    3.229 closest distance to " CB  ASN A 215 " =    1.087
peak=    3.225 closest distance to " CG1 ILE A 151 " =    1.044
peak=    3.224 closest distance to " CG1 VAL A 153 " =    0.979
peak=    3.224 closest distance to " O   HOH Z 423 " =    2.343
peak=    3.222 closest distance to " O   HOH Z   9 " =    3.016
peak=    3.217 closest distance to " CZ  PHE A  38 " =    1.197
peak=    3.215 closest distance to " O   ARG A 145 " =    1.694
peak=    3.212 closest distance to " CB  ALA A 114 " =    0.865
peak=    3.207 closest distance to " CB  ALA A 248 " =    0.921
peak=    3.204 closest distance to " O   HOH Z  97 " =    2.249
peak=    3.202 closest distance to " CD1AILE A 234 " =    0.882
peak=    3.202 closest distance to " CG2AVAL A  72 " =    1.541
peak=    3.197 closest distance to " O   HOH Z 271 " =    2.401
peak=    3.197 closest distance to " CA  ALA A 100 " =    0.982
peak=    3.195 closest distance to " CG  LYS A 119 " =    1.128
peak=    3.195 closest distance to " CG  LYS A  76 " =    1.787
peak=    3.192 closest distance to " CB  PHE A 204 " =    0.775
peak=    3.191 closest distance to " O   HOH Z 188 " =    1.414
peak=    3.188 closest distance to " CA  SER A  95 " =    0.992
peak=    3.180 closest distance to " N   ASN A 127 " =    1.334
peak=    3.180 closest distance to " CG  GLN A  89 " =    1.536
peak=    3.180 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.179 closest distance to " CA  GLY A 267 " =    1.195
peak=    3.179 closest distance to " O   HOH Z 213 " =    1.872
peak=    3.178 closest distance to " CB  TRP A 179 " =    1.691
peak=    3.174 closest distance to " CG  GLN A 278 " =    1.320
peak=    3.171 closest distance to " OD2 ASP A 286 " =    3.267
peak=    3.170 closest distance to " CA  ASP A 162 " =    1.045
peak=    3.169 closest distance to " O   HOH Z 245 " =    1.267
peak=    3.166 closest distance to " O   ASN A 209 " =    1.289
peak=    3.165 closest distance to " OG BSER A  99 " =    2.271
peak=    3.162 closest distance to " NH1BARG A 145 " =    1.178
peak=    3.160 closest distance to " CG AARG A 275 " =    1.139
peak=    3.159 closest distance to " O   SER A 164 " =    1.296
peak=    3.155 closest distance to " O   HOH Z 218 " =    4.478
peak=    3.152 closest distance to " O   HOH Z 359 " =    4.376
peak=    3.152 closest distance to " CA  ARG A 159 " =    1.274
peak=    3.151 closest distance to " CB  ALA A 291 " =    1.322
peak=    3.149 closest distance to " O   MET A 105 " =    1.834
peak=    3.148 closest distance to " CD  ARG A 138 " =    0.801
peak=    3.142 closest distance to " CA  ASN A 217 " =    1.196
peak=    3.136 closest distance to " O   HOH Z 357 " =    1.985
peak=    3.134 closest distance to " CD1 ILE A 106 " =    0.873
peak=    3.132 closest distance to " O   HOH Z 236 " =    1.486
peak=    3.124 closest distance to " O   HOH Z 287 " =    2.176
peak=    3.124 closest distance to " CG BARG A 190 " =    1.204
peak=    3.119 closest distance to " CB  LEU A 300 " =    0.896
peak=    3.117 closest distance to " O   HOH Z  64 " =    2.088
peak=    3.113 closest distance to " O   HOH Z 233 " =    1.698
peak=    3.109 closest distance to " O   HOH Z 298 " =    2.505
peak=    3.105 closest distance to " CB  LEU A  83 " =    0.740
peak=    3.104 closest distance to " CG  MET A 113 " =    1.250
peak=    3.103 closest distance to " CA  LYS A 117 " =    1.168
peak=    3.101 closest distance to " OE2 GLU A  53 " =    1.985
peak=    3.092 closest distance to " O   HOH Z  47 " =    1.857
peak=    3.086 closest distance to " O   HOH Z  30 " =    1.647
peak=    3.083 closest distance to " O   HOH Z 272 " =    2.223
peak=    3.069 closest distance to " O   HOH Z  89 " =    2.051
peak=    3.069 closest distance to " O  BHOH Z  74 " =    1.340
peak=    3.065 closest distance to " O   HOH Z 181 " =    2.116
peak=    3.062 closest distance to " O   HOH Z 302 " =    1.816
peak=    3.038 closest distance to " O   HOH Z 219 " =    1.736
peak=    3.037 closest distance to " O   HOH Z 153 " =    1.610
peak=    3.028 closest distance to " O   HOH Z 407 " =    2.283

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.723 - 5.977
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.723 - 5.977

peak=   -4.786 closest distance to " O   HOH Z 377 " =    1.993
peak=   -4.563 closest distance to " CB  PRO A 243 " =    2.660
peak=   -4.407 closest distance to " CD  ARG A  14 " =    3.435
peak=   -4.349 closest distance to " CD  ARG A 156 " =    2.107
peak=   -4.286 closest distance to " OG BSER A 134 " =    1.293
peak=   -4.234 closest distance to " O   HOH Z 266 " =    5.159
peak=   -4.214 closest distance to " O   HOH Z 231 " =    2.233
peak=   -4.142 closest distance to " C   HIS A 108 " =    1.171
peak=   -4.121 closest distance to " O   VAL A  67 " =    2.673
peak=   -4.095 closest distance to " O   PRO A 198 " =    1.225
peak=   -4.055 closest distance to " CB  ALA A  43 " =    2.549
peak=   -4.011 closest distance to " O   HOH Z 372 " =    2.518
peak=   -3.997 closest distance to " CB  ALA A 291 " =    2.248
peak=   -3.986 closest distance to " CG  GLN A 223 " =    2.060
peak=   -3.938 closest distance to " CD2 PHE A 192 " =    2.048
peak=   -3.935 closest distance to " CZ3 TRP A 179 " =    1.250
peak=   -3.927 closest distance to " O   HOH Z 351 " =    1.529
peak=   -3.918 closest distance to " CD  GLN A  58 " =    1.080
peak=   -3.906 closest distance to " CG1 VAL A 112 " =    3.018
peak=   -3.897 closest distance to " O   HOH Z 198 " =    1.904
peak=   -3.878 closest distance to " CE  MET A 105 " =    2.523
peak=   -3.848 closest distance to " ND2 ASN A 249 " =    2.343
peak=   -3.831 closest distance to " O   HOH Z 389 " =    1.995
peak=   -3.791 closest distance to " ND2 ASN A 187 " =    1.458
peak=   -3.782 closest distance to " O   HOH Z 185 " =    2.277
peak=   -3.758 closest distance to " N   THR A 157 " =    1.521
peak=   -3.740 closest distance to " O   HOH Z 131 " =    4.105
peak=   -3.740 closest distance to " CB  TRP A  85 " =    2.450
peak=   -3.739 closest distance to " O   HOH Z 407 " =    3.135
peak=   -3.738 closest distance to " OD1 ASP A 171 " =    1.604
peak=   -3.734 closest distance to " N   ALA A  43 " =    2.557
peak=   -3.723 closest distance to " CB  ASN A  39 " =    2.288
peak=   -3.713 closest distance to " CB  ALA A 291 " =    2.026
peak=   -3.688 closest distance to " O   HOH Z  38 " =    1.655
peak=   -3.685 closest distance to " ND2 ASN A  45 " =    1.963
peak=   -3.684 closest distance to " O   HOH Z  60 " =    2.354
peak=   -3.670 closest distance to " O   HOH Z 290 " =    1.193
peak=   -3.657 closest distance to " CE BMET A  47 " =    1.300
peak=   -3.652 closest distance to " O   HOH Z   9 " =    1.601
peak=   -3.650 closest distance to " O   TYR A 247 " =    2.842
peak=   -3.642 closest distance to " O   ALA A  10 " =    1.650
peak=   -3.631 closest distance to " CD1 LEU A 255 " =    2.879
peak=   -3.630 closest distance to " O   HOH Z  52 " =    1.230
peak=   -3.628 closest distance to " CG2 ILE A 263 " =    2.266
peak=   -3.611 closest distance to " CD2 TYR A 293 " =    1.925
peak=   -3.609 closest distance to " ND2 ASN A  45 " =    1.173
peak=   -3.607 closest distance to " O   PRO A 163 " =    2.019
peak=   -3.599 closest distance to " CE2 TYR A  30 " =    2.601
peak=   -3.596 closest distance to " O   GLU A 152 " =    1.395
peak=   -3.594 closest distance to " O   HOH Z 313 " =    1.894
peak=   -3.593 closest distance to " O   HOH Z 316 " =    1.768
peak=   -3.592 closest distance to " CA  GLY A  98 " =    1.862
peak=   -3.590 closest distance to " O   HOH Z 348 " =    2.290
peak=   -3.581 closest distance to " O   HOH Z 166 " =    2.196
peak=   -3.578 closest distance to " CD1 PHE A  59 " =    2.042
peak=   -3.569 closest distance to " CB  ALA A 248 " =    2.153
peak=   -3.562 closest distance to " O   HOH Z  73 " =    2.164
peak=   -3.559 closest distance to " O   PRO A 198 " =    1.326
peak=   -3.559 closest distance to " O   HOH Z 395 " =    5.101
peak=   -3.552 closest distance to " OXT GLY A 302 " =    3.028
peak=   -3.548 closest distance to " O   PHE A 218 " =    1.541
peak=   -3.543 closest distance to " O   SER A 135 " =    1.465
peak=   -3.532 closest distance to " CB  TYR A  15 " =    2.236
peak=   -3.532 closest distance to " O   ARG A 145 " =    1.495
peak=   -3.530 closest distance to " CG2 ILE A  49 " =    2.705
peak=   -3.523 closest distance to " CA  GLY A 241 " =    2.257
peak=   -3.513 closest distance to " CB  ALA A 161 " =    2.491
peak=   -3.507 closest distance to " CE2 PHE A 218 " =    2.411
peak=   -3.506 closest distance to " CG1 VAL A  67 " =    2.977
peak=   -3.502 closest distance to " O   HOH Z  22 " =    2.530
peak=   -3.498 closest distance to " CG2 THR A 178 " =    2.249
peak=   -3.489 closest distance to " CB  ALA A 248 " =    2.334
peak=   -3.488 closest distance to " O   HOH Z 191 " =    5.613
peak=   -3.486 closest distance to " CG1 VAL A 112 " =    2.598
peak=   -3.467 closest distance to " N   SER A 212 " =    1.977
peak=   -3.463 closest distance to " CD1 LEU A 101 " =    2.240
peak=   -3.459 closest distance to " CA  ASP A  27 " =    2.459
peak=   -3.454 closest distance to " OG  SER A  97 " =    2.167
peak=   -3.450 closest distance to " CD2 PHE A  61 " =    2.008
peak=   -3.448 closest distance to " OD1 ASN A 148 " =    1.535
peak=   -3.447 closest distance to " O   PRO A 243 " =    2.522
peak=   -3.446 closest distance to " CB  ASP A 132 " =    2.397
peak=   -3.445 closest distance to " O   VAL A 189 " =    1.679
peak=   -3.442 closest distance to " CG2 THR A  18 " =    2.820
peak=   -3.439 closest distance to " CA  GLY A 203 " =    2.385
peak=   -3.438 closest distance to " O   ALA A 161 " =    1.658
peak=   -3.438 closest distance to " OH  TYR A 172 " =    1.774
peak=   -3.433 closest distance to " O   HOH Z 111 " =    1.881
peak=   -3.432 closest distance to " NH2AARG A 275 " =    5.315
peak=   -3.432 closest distance to " O   HOH Z  11 " =    1.846
peak=   -3.429 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.428 closest distance to " O   HOH Z 174 " =    2.661
peak=   -3.426 closest distance to " CG  PHE A 283 " =    2.628
peak=   -3.424 closest distance to " O   VAL A 189 " =    2.559
peak=   -3.421 closest distance to " OG  SER A  87 " =    1.319
peak=   -3.411 closest distance to " O   HOH Z 394 " =    1.440
peak=   -3.409 closest distance to " O   HOH Z 412 " =    4.249
peak=   -3.404 closest distance to " NH2BARG A 275 " =    1.762
peak=   -3.402 closest distance to " O   HOH Z 211 " =    1.613
peak=   -3.401 closest distance to " C   ALA A 114 " =    2.157
peak=   -3.397 closest distance to " CA  GLY A 133 " =    2.017
peak=   -3.396 closest distance to " O   HOH Z 102 " =    1.563
peak=   -3.385 closest distance to " CG  MET A 105 " =    1.008
peak=   -3.384 closest distance to " O   HOH Z 359 " =    3.250
peak=   -3.383 closest distance to " OG BSER A 134 " =    1.774
peak=   -3.377 closest distance to " CG  TRP A 266 " =    1.834
peak=   -3.376 closest distance to " O   HOH Z 298 " =    1.292
peak=   -3.376 closest distance to " ND2 ASN A  60 " =    4.117
peak=   -3.375 closest distance to " OE1 GLN A  88 " =    1.139
peak=   -3.372 closest distance to " O   HOH Z 298 " =    2.497
peak=   -3.367 closest distance to " CA  GLY A 241 " =    3.131
peak=   -3.364 closest distance to " O   HOH Z 253 " =    3.861
peak=   -3.350 closest distance to " OD2 ASP A 191 " =    1.399
peak=   -3.346 closest distance to " CB  ALA A 114 " =    2.511
peak=   -3.343 closest distance to " O   SER A  95 " =    1.495
peak=   -3.341 closest distance to " O   HOH Z 281 " =    2.664
peak=   -3.336 closest distance to " CE3 TRP A 274 " =    2.276
peak=   -3.335 closest distance to " O   HOH Z 384 " =    2.780
peak=   -3.334 closest distance to " CZ  PHE A  59 " =    1.600
peak=   -3.331 closest distance to " CZ  TYR A 169 " =    1.721
peak=   -3.331 closest distance to " CB  ASP A 286 " =    2.211
peak=   -3.329 closest distance to " O   HOH Z 385 " =    1.884
peak=   -3.329 closest distance to " NE2 GLN A 278 " =    1.641
peak=   -3.327 closest distance to " O   HOH Z 140 " =    1.548
peak=   -3.326 closest distance to " NH1AARG A 275 " =    1.881
peak=   -3.322 closest distance to " NE  ARG A  36 " =    1.990
peak=   -3.313 closest distance to " O   HOH Z 409 " =    5.977
peak=   -3.308 closest distance to " O   HOH Z 286 " =    1.919
peak=   -3.308 closest distance to " C   ALA A 158 " =    1.698
peak=   -3.304 closest distance to " CG1 VAL A 250 " =    2.658
peak=   -3.304 closest distance to " CB  ALA A   7 " =    2.133
peak=   -3.302 closest distance to " O   HOH Z 318 " =    1.886
peak=   -3.301 closest distance to " O   ALA A 292 " =    2.114
peak=   -3.301 closest distance to " CB  PRO A  54 " =    2.464
peak=   -3.298 closest distance to " CD  ARG A 139 " =    1.587
peak=   -3.295 closest distance to " CE2 PHE A  61 " =    2.626
peak=   -3.294 closest distance to " O   ALA A  51 " =    1.288
peak=   -3.287 closest distance to " O   HOH Z  65 " =    1.294
peak=   -3.286 closest distance to " O   ALA A  34 " =    2.441
peak=   -3.282 closest distance to " O   SER A  22 " =    2.534
peak=   -3.282 closest distance to " OD1 ASN A 187 " =    1.606
peak=   -3.281 closest distance to " CD2 PHE A 225 " =    1.165
peak=   -3.279 closest distance to " O   HOH Z 421 " =    2.886
peak=   -3.275 closest distance to " CG2 VAL A 189 " =    1.903
peak=   -3.274 closest distance to " O   HOH Z 357 " =    2.037
peak=   -3.273 closest distance to " CD2 HIS A 207 " =    2.266
peak=   -3.268 closest distance to " O   HOH Z 189 " =    1.929
peak=   -3.263 closest distance to " OG  SER A  63 " =    1.231
peak=   -3.263 closest distance to " O   HOH Z 292 " =    1.706
peak=   -3.262 closest distance to " CB  ALA A 100 " =    2.237
peak=   -3.262 closest distance to " CB  ALA A  10 " =    2.282
peak=   -3.260 closest distance to " CB  GLN A  11 " =    1.802
peak=   -3.258 closest distance to " O   HOH Z 147 " =    1.909
peak=   -3.258 closest distance to " O   VAL A 174 " =    2.263
peak=   -3.253 closest distance to " O   HOH Z  10 " =    1.433
peak=   -3.253 closest distance to " O   HOH Z  63 " =    2.042
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    2.156
peak=   -3.252 closest distance to " CA  GLY A  57 " =    2.216
peak=   -3.247 closest distance to " OE1 GLN A 183 " =    1.648
peak=   -3.246 closest distance to " OD1AASN A 224 " =    1.827
peak=   -3.245 closest distance to " N   ASP A 171 " =    2.352
peak=   -3.245 closest distance to " O   GLY A 229 " =    1.924
peak=   -3.225 closest distance to " CG  LEU A  83 " =    1.978
peak=   -3.222 closest distance to " CB  PRO A 163 " =    2.490
peak=   -3.219 closest distance to " N   SER A 276 " =    1.304
peak=   -3.218 closest distance to " O   ILE A 106 " =    2.052
peak=   -3.215 closest distance to " N   ALA A 248 " =    1.540
peak=   -3.215 closest distance to " CG  GLU A 277 " =    1.296
peak=   -3.214 closest distance to " CB  ALA A 131 " =    2.050
peak=   -3.211 closest distance to " C   PHE A  59 " =    1.287
peak=   -3.208 closest distance to " CE3 TRP A 150 " =    2.205
peak=   -3.204 closest distance to " O   HOH Z 266 " =    4.961
peak=   -3.201 closest distance to " O   HOH Z 165 " =    2.188
peak=   -3.199 closest distance to " O   TRP A  70 " =    1.422
peak=   -3.196 closest distance to " O   ALA A 180 " =    1.248
peak=   -3.194 closest distance to " O   HOH Z 414 " =    2.504
peak=   -3.189 closest distance to " SG BCYS A 201 " =    1.937
peak=   -3.183 closest distance to " O   HOH Z 114 " =    2.909
peak=   -3.182 closest distance to " C   LEU A 222 " =    0.723
peak=   -3.181 closest distance to " O   HOH Z 166 " =    1.307
peak=   -3.177 closest distance to " OD2 ASP A 171 " =    2.155
peak=   -3.169 closest distance to " O   HOH Z 350 " =    1.845
peak=   -3.169 closest distance to " O   HOH Z 198 " =    1.776
peak=   -3.167 closest distance to " O   HOH Z 317 " =    1.502
peak=   -3.165 closest distance to " CG  ASP A 231 " =    0.730
peak=   -3.163 closest distance to " CD1 LEU A 297 " =    2.577
peak=   -3.163 closest distance to " CB  ALA A 244 " =    2.057
peak=   -3.162 closest distance to " O   HOH Z 174 " =    4.023
peak=   -3.156 closest distance to " CG  ARG A 269 " =    2.540
peak=   -3.153 closest distance to " N   MET A 188 " =    1.877
peak=   -3.149 closest distance to " O   GLN A 240 " =    2.401
peak=   -3.144 closest distance to " O   HOH Z 353 " =    2.305
peak=   -3.142 closest distance to " CE  LYS A  76 " =    2.699
peak=   -3.133 closest distance to " CG2 ILE A 151 " =    2.567
peak=   -3.126 closest distance to " CA  GLY A 133 " =    2.270
peak=   -3.122 closest distance to " CD1 LEU A   5 " =    2.415
peak=   -3.120 closest distance to " NH2 ARG A  79 " =    1.577
peak=   -3.120 closest distance to " O   SER A 276 " =    1.726
peak=   -3.110 closest distance to " O   HOH Z 219 " =    4.635
peak=   -3.106 closest distance to " O   HOH Z 218 " =    3.854
peak=   -3.098 closest distance to " CA  GLY A 241 " =    2.864
peak=   -3.096 closest distance to " NH1 ARG A 195 " =    2.694
peak=   -3.085 closest distance to " CG  PRO A 163 " =    2.678
peak=   -3.085 closest distance to " O   HOH Z 184 " =    1.652
peak=   -3.072 closest distance to " O   HOH Z 352 " =    2.211
peak=   -3.071 closest distance to " CD  GLN A  77 " =    1.517
peak=   -3.069 closest distance to " O   GLN A 240 " =    1.882
peak=   -3.063 closest distance to " O   HOH Z 250 " =    1.289
peak=   -3.054 closest distance to " CE1 TYR A 247 " =    2.833
peak=   -3.050 closest distance to " CD1 ILE A 199 " =    2.489

================= 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    :  0.3923 0.3903   6.190109e+00   6.168651e+00
   1_bss:  0.3786 0.3812   6.177266e+00   6.151447e+00
   1_xyz:  0.2244 0.2546   5.720494e+00   5.808935e+00
   1_adp:  0.2031 0.2634   5.664644e+00   5.844323e+00
   1_occ:  0.2030 0.2630   5.663680e+00   5.843584e+00
   2_bss:  0.2001 0.2595   5.656193e+00   5.834570e+00
   2_xyz:  0.1481 0.1980   5.383777e+00   5.598553e+00
   2_adp:  0.1385 0.1849   5.320456e+00   5.528007e+00
   2_occ:  0.1383 0.1848   5.319760e+00   5.527676e+00
   3_bss:  0.1381 0.1839   5.315292e+00   5.523381e+00
   3_xyz:  0.1209 0.1640   5.198792e+00   5.421706e+00
   3_adp:  0.1173 0.1608   5.176355e+00   5.404824e+00
   3_occ:  0.1173 0.1609   5.176336e+00   5.405022e+00
   4_bss:  0.1172 0.1608   5.175596e+00   5.404621e+00
   4_xyz:  0.1129 0.1577   5.150327e+00   5.390867e+00
   4_adp:  0.1112 0.1588   5.147671e+00   5.397109e+00
   4_occ:  0.1112 0.1589   5.147855e+00   5.397515e+00
   5_bss:  0.1113 0.1583   5.146077e+00   5.393655e+00
   5_xyz:  0.1097 0.1578   5.139906e+00   5.393634e+00
   5_adp:  0.1095 0.1572   5.136657e+00   5.390244e+00
   5_occ:  0.1095 0.1572   5.136747e+00   5.390437e+00
   5_bss:  0.1094 0.1571   5.136852e+00   5.390481e+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:  0.332  44.412  -3.326   1.720   1.948   0.000   0.000   0.000
   1_xyz:  0.332  44.412  -3.326   1.720   1.948   0.000   0.000   0.000
   1_adp:  0.332  44.412  -3.326   1.720   1.948   0.000   0.000   0.000
   1_occ:  0.332  44.412  -3.326   1.720   1.948   0.000   0.000   0.000
   2_bss:  0.334  62.844  -2.907  -1.190  -0.031  -0.000  -0.000  -0.000
   2_xyz:  0.334  62.844  -2.907  -1.190  -0.031  -0.000  -0.000  -0.000
   2_adp:  0.334  62.844  -2.907  -1.190  -0.031  -0.000  -0.000  -0.000
   2_occ:  0.334  62.844  -2.907  -1.190  -0.031  -0.000  -0.000  -0.000
   3_bss:  0.334  62.844  -2.727  -2.148  -0.514  -0.000  -0.000  -0.000
   3_xyz:  0.334  62.844  -2.727  -2.148  -0.514  -0.000  -0.000  -0.000
   3_adp:  0.334  62.844  -2.727  -2.148  -0.514  -0.000  -0.000  -0.000
   3_occ:  0.334  62.844  -2.727  -2.148  -0.514  -0.000  -0.000  -0.000
   4_bss:  0.324  55.491  -2.581  -2.368  -0.583  -0.000  -0.000  -0.000
   4_xyz:  0.324  55.491  -2.581  -2.368  -0.583  -0.000  -0.000  -0.000
   4_adp:  0.324  55.491  -2.581  -2.368  -0.583  -0.000  -0.000  -0.000
   4_occ:  0.324  55.491  -2.581  -2.368  -0.583  -0.000  -0.000  -0.000
   5_bss:  0.323  57.636  -2.347  -2.284  -0.451  -0.000  -0.000  -0.000
   5_xyz:  0.323  57.636  -2.347  -2.284  -0.451  -0.000  -0.000  -0.000
   5_adp:  0.323  57.636  -2.347  -2.284  -0.451  -0.000  -0.000  -0.000
   5_occ:  0.323  57.636  -2.347  -2.284  -0.451  -0.000  -0.000  -0.000
   5_bss:  0.323  57.639  -2.128  -2.124  -0.262  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.438 0.6026  0.7818    44807.589
   1_bss:  42.454 0.6126  0.7998    42108.703
   1_xyz:  24.539 0.8174  0.9951    16112.706
   1_adp:  25.773 0.8034  0.9822    17272.946
   1_occ:  25.768 0.8034  0.9816    17214.126
   2_bss:  25.305 0.8085  0.9388    16826.718
   2_xyz:  18.892 0.8714  0.9827     9792.053
   2_adp:  17.080 0.8889  0.9858     8596.986
   2_occ:  17.077 0.8890  0.9857     8585.497
   3_bss:  16.953 0.8899  0.9720     8477.647
   3_xyz:  14.721 0.9088  0.9806     6776.237
   3_adp:  14.306 0.9125  0.9763     6577.086
   3_occ:  14.313 0.9125  0.9761     6579.040
   4_bss:  14.304 0.9125  0.9745     6572.531
   4_xyz:  13.961 0.9155  0.9764     6386.901
   4_adp:  14.062 0.9148  0.9696     6415.188
   4_occ:  14.071 0.9147  0.9695     6421.852
   5_bss:  14.002 0.9152  0.9750     6338.036
   5_xyz:  14.005 0.9151  0.9750     6359.452
   5_adp:  13.933 0.9157  0.9689     6305.091
   5_occ:  13.938 0.9156  0.9688     6306.202
   5_bss:  13.941 0.9156  0.9755     6308.393
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6757e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6757e-01
   1_xyz:   1.358  0.010  0.088 15.835  0.006  4.112   9.7042e-02
   1_adp:   1.358  0.010  0.088 15.835  0.006  4.112   9.7042e-02
   1_occ:   1.358  0.010  0.088 15.835  0.006  4.112   9.7042e-02
   2_bss:   1.358  0.010  0.088 15.835  0.006  4.112   9.7042e-02
   2_xyz:   1.047  0.007  0.076 14.916  0.004  4.121   6.1557e-02
   2_adp:   1.047  0.007  0.076 14.916  0.004  4.121   6.1557e-02
   2_occ:   1.047  0.007  0.076 14.916  0.004  4.121   6.1557e-02
   3_bss:   1.047  0.007  0.076 14.916  0.004  4.121   6.1557e-02
   3_xyz:   0.968  0.007  0.073 14.832  0.003  4.110   5.7890e-02
   3_adp:   0.968  0.007  0.073 14.832  0.003  4.110   5.7890e-02
   3_occ:   0.968  0.007  0.073 14.832  0.003  4.110   5.7890e-02
   4_bss:   0.968  0.007  0.073 14.832  0.003  4.110   5.7890e-02
   4_xyz:   0.999  0.007  0.076 14.757  0.004  4.114   5.9861e-02
   4_adp:   0.999  0.007  0.076 14.757  0.004  4.114   5.9861e-02
   4_occ:   0.999  0.007  0.076 14.757  0.004  4.114   5.9861e-02
   5_bss:   0.999  0.007  0.076 14.757  0.004  4.114   5.9861e-02
   5_xyz:   0.980  0.007  0.075 14.692  0.004  4.115   5.9272e-02
   5_adp:   0.980  0.007  0.075 14.692  0.004  4.115   5.9272e-02
   5_occ:   0.980  0.007  0.075 14.692  0.004  4.115   5.9272e-02
   5_bss:   0.980  0.007  0.075 14.692  0.004  4.115   5.9272e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4091e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4091e-01
   1_xyz:  13.790  0.072  0.263 84.026  0.052  2.108   9.0057e-02
   1_adp:  13.790  0.072  0.263 84.026  0.052  2.108   9.0057e-02
   1_occ:  13.790  0.072  0.263 84.026  0.052  2.108   9.0057e-02
   2_bss:  13.790  0.072  0.263 84.026  0.052  2.108   9.0057e-02
   2_xyz:   6.695  0.061  0.290 82.440  0.025  2.379   5.4681e-02
   2_adp:   6.695  0.061  0.290 82.440  0.025  2.379   5.4681e-02
   2_occ:   6.695  0.061  0.290 82.440  0.025  2.379   5.4681e-02
   3_bss:   6.695  0.061  0.290 82.440  0.025  2.379   5.4681e-02
   3_xyz:   6.903  0.044  0.240 84.350  0.025  2.356   5.0229e-02
   3_adp:   6.903  0.044  0.240 84.350  0.025  2.356   5.0229e-02
   3_occ:   6.903  0.044  0.240 84.350  0.025  2.356   5.0229e-02
   4_bss:   6.903  0.044  0.240 84.350  0.025  2.356   5.0229e-02
   4_xyz:   6.728  0.046  0.244 83.392  0.029  2.327   4.1437e-02
   4_adp:   6.728  0.046  0.244 83.392  0.029  2.327   4.1437e-02
   4_occ:   6.728  0.046  0.244 83.392  0.029  2.327   4.1437e-02
   5_bss:   6.728  0.046  0.244 83.392  0.029  2.327   4.1437e-02
   5_xyz:   6.736  0.042  0.247 84.190  0.028  2.356   4.2615e-02
   5_adp:   6.736  0.042  0.247 84.190  0.028  2.356   4.2615e-02
   5_occ:   6.736  0.042  0.247 84.190  0.028  2.356   4.2615e-02
   5_bss:   6.736  0.042  0.247 84.190  0.028  2.356   4.2615e-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:  86.18   0.00  17.63  73.39   0.00  13.26  86.18   3.61  41.46
   1_occ:  86.18   0.00  17.63  73.39   0.00  13.26  86.18   3.61  41.46
   2_bss:  86.18   0.00  17.63  73.39   0.00  13.26  86.18   3.61  41.46
   2_xyz:  86.18   0.00  17.63  73.39   0.00  13.26  86.18   3.61  41.46
   2_adp:  80.27   0.00  16.91  71.48   0.00  12.80  80.27   6.16  39.31
   2_occ:  80.27   0.00  16.91  71.48   0.00  12.80  80.27   6.16  39.31
   3_bss:  80.27   0.00  16.91  71.48   0.00  12.80  80.27   6.16  39.31
   3_xyz:  80.27   0.00  16.91  71.48   0.00  12.80  80.27   6.16  39.31
   3_adp:  79.41   0.88  16.83  75.05   0.88  12.67  79.41   2.83  39.46
   3_occ:  79.41   0.88  16.83  75.05   0.88  12.67  79.41   2.83  39.46
   4_bss:  79.41   0.88  16.83  75.05   0.88  12.67  79.41   2.83  39.46
   4_xyz:  79.41   0.88  16.83  75.05   0.88  12.67  79.41   2.83  39.46
   4_adp:  90.98   0.00  17.20  90.98   0.00  12.75  83.19   2.94  41.41
   4_occ:  90.98   0.00  17.20  90.98   0.00  12.75  83.19   2.94  41.41
   5_bss:  90.98   0.00  17.20  90.98   0.00  12.75  83.19   2.94  41.41
   5_xyz:  90.98   0.00  17.20  90.98   0.00  12.75  83.19   2.94  41.41
   5_adp:  93.07   0.00  16.90  93.07   0.00  12.55  82.89   4.23  40.58
   5_occ:  93.07   0.00  16.90  93.07   0.00  12.55  82.89   4.23  40.58
   5_bss:  93.08   0.00  16.90  93.08   0.00  12.56  82.89   4.23  40.58
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.342    0.034    0.421
   1_adp:    1.342    0.034    0.421
   1_occ:    1.342    0.034    0.421
   2_bss:    1.342    0.034    0.421
   2_xyz:    1.120    0.025    0.493
   2_adp:    1.120    0.025    0.493
   2_occ:    1.120    0.025    0.493
   3_bss:    1.120    0.025    0.493
   3_xyz:    1.231    0.071    0.544
   3_adp:    1.231    0.071    0.544
   3_occ:    1.231    0.071    0.544
   4_bss:    1.231    0.071    0.544
   4_xyz:    1.397    0.059    0.560
   4_adp:    1.397    0.059    0.560
   4_occ:    1.397    0.059    0.560
   5_bss:    1.397    0.059    0.560
   5_xyz:    1.420    0.080    0.571
   5_adp:    1.420    0.080    0.571
   5_occ:    1.420    0.080    0.571
   5_bss:    1.420    0.080    0.571
------------------------------------------------------------------------

CPU time actual refinement: 283.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/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_635/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_635/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 282.90 
  Macro-tasks:
    bulk solvent and scale       = 32.34  
    individual site refinement   = 123.59 
    weights calculation          = 24.29  
    collect and process          = 5.49   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 185.80 
  Micro-tasks:
    mask                            = 1.45   
    f_calc                          = 90.16  
    alpha_beta                      = 7.09   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 99.68  
    fmodel                         = 5.48   
    r_factors                      = 0.19   
    phase_errors                   = 9.03   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 214.19 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.904 micro seconds
Total CPU time: 4.91 minutes
from_scatterers_fft:    668 calls, 89.85 s
gradients_fft:          613 calls, 87.11 s

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

# Date 2008-01-16 Time 05:17:32 PST -0800 (1200489452.27 s)
Start R-work = 0.3923, R-free = 0.3903 (no bulk solvent and anisotropic scale)
Final R-work = 0.1317, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.3786, R-free = 0.3812
Final R-work = 0.1094, R-free = 0.1571